migrate to standard svn repo layout
This commit is contained in:
Markus Rosenstihl
commit
0a393b0748
7
MANIFEST.in
Normal file
7
MANIFEST.in
Normal file
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|||||||
|
include src/gui/DAMARIS.png
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include src/gui/DAMARIS.ico
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include src/gui/damaris.glade
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||||||
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include src/gui/damaris.gladep
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||||||
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include doc/index.html
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||||||
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recursive-include doc/reference-html *.html *.gif *.png *.css
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recursive-include doc/tutorial-html *.html *.gif *.png *.css *.tar.gz *.sh
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17
README
Normal file
17
README
Normal file
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|||||||
|
|
||||||
|
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||||||
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||||||
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Installing into private directory
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|
=================================
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||||||
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||||||
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For whatever reason, it might be useful to install the
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||||||
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python frontend into a private directory.
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||||||
|
Here are some examples on how to do it:
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||||||
|
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||||||
|
python setup.py install --home=/opt/damaris-private
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or
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python setup.py install --home=$HOME/devel/damaris-installed
|
||||||
|
|
||||||
|
To start Damaris use for example:
|
||||||
|
|
||||||
|
/opt/damaris-private/bin/DAMARIS
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||||||
68
debian/changelog
vendored
Normal file
68
debian/changelog
vendored
Normal file
@ -0,0 +1,68 @@
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python-damaris (0.14-svn) experimental; urgency=low
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||||||
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* MeasurementResults (MR) can be lineplots (Oleg Petrov)
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* Default symbol for MR changed to "*"
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* Several more improvements to GUI code
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* Fixed some errors in FFT module (oelg Petrov)
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||||||
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* Config now according to XDG standard
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|
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|
-- Markus Rosenstihl <Markus.Rosenstihl@physik.tu-darmstadt.de> Wed, 07 Nov 2012 12:36:40 +0000
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||||||
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python-damaris (0.13-0) experimental; urgency=low
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* using cElementTree if available, giving the ResultReader almost 20x speed up
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|
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-- Markus Rosenstihl <Markus Rosenstihl <markus.rosenstihl@physik.tu-darmstadt.de> Wed, 03 Nov 2010 18:49:46 +0000
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|
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|
python-damaris (0.12-0.0) experimental; urgency=low
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|
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|
* new development version
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||||||
|
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||||||
|
-- Achim Gaedke <Achim.Gaedke@physik.tu-darmstadt.de> Sat, 24 May 2008 17:49:25 +0200
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|
|
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|
python-damaris (0.11-0.1) experimental; urgency=low
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|
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|
* updated debian python policy
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* job descriptions: types are saved and recovered
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|
* support for system wide defaults file thanks to Christian
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|
* new interleaved range by Markus Rosenstihl
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|
* revised display source change event handling, found some severe errors
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|
* cursor movement and selection problems solved
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* log window information are saved in hdf files
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|
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||||||
|
-- Achim Gaedke <Achim.Gaedke@physik.tu-darmstadt.de> Thu, 17 Mar 2008 17:28:13 +0100
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|
python-damaris (0.11-0.0) experimental; urgency=low
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|
|
||||||
|
* rename to python-damaris
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|
* x axis log plot
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|
* %()s functions for hdf file naming
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|
* line number widgets for scripts
|
||||||
|
* Persistance class added (scope like fade away of signal changes)
|
||||||
|
|
||||||
|
-- Achim Gaedke <Achim.Gaedke@physik.tu-darmstadt.de> Thu, 07 Feb 2008 02:21:45 +0100
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||||||
|
|
||||||
|
greendamaris (0.10-0.2) experimental; urgency=medium
|
||||||
|
|
||||||
|
* increased compatibility with pytables version 1 and 2
|
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|
* sending signals to backend, when it fails to quit properly
|
||||||
|
* correcting quit event return value
|
||||||
|
|
||||||
|
-- Achim Gaedke <Achim.Gaedke@physik.tu-darmstadt.de> Fri, 12 Oct 2007 13:34:33 +0200
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|
|
||||||
|
greendamaris (0.10-0.1) experimental; urgency=low
|
||||||
|
|
||||||
|
* added docs and browser button for docs
|
||||||
|
* limited number of points to display for GTKCairo backend
|
||||||
|
* numarray replaced by numpy
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|
* adapted width of window to fit even gnome icon size
|
||||||
|
|
||||||
|
-- Achim Gaedke <Achim.Gaedke@physik.tu-darmstadt.de> Tue, 02 Oct 2007 19:11:33 +0200
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|
|
||||||
|
greendamaris (0.10-0.0) experimental; urgency=medium
|
||||||
|
|
||||||
|
* started separate source package of pyhton-damaris
|
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|
* pycentral used to support both python 2.4 and 2.5
|
||||||
|
|
||||||
|
-- Achim Gaedke <Achim.Gaedke@physik.tu-darmstadt.de> Sat, 08 Sep 2007 12:56:06 +0200
|
||||||
|
|
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1
debian/compat
vendored
Normal file
1
debian/compat
vendored
Normal file
@ -0,0 +1 @@
|
|||||||
|
5
|
||||||
16
debian/control
vendored
Normal file
16
debian/control
vendored
Normal file
@ -0,0 +1,16 @@
|
|||||||
|
Source: python-damaris
|
||||||
|
Section: science
|
||||||
|
Priority: optional
|
||||||
|
Maintainer: Achim Gaedke <Achim.Gaedke@physik.tu-darmstadt.de>
|
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|
Build-Depends: debhelper, python-dev, python-central, dpkg-dev
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|
Standards-Version: 3.7.3
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|
XS-Python-Version: current
|
||||||
|
|
||||||
|
Package: python-damaris
|
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|
Architecture: all
|
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|
XB-Python-Version: ${python:Versions}
|
||||||
|
Provides: ${python:Provides}, damaris-frontend
|
||||||
|
Depends: ${python:Depends}, python-numpy (>=1.0), python-scipy, python-gtk2 (>=2.8.0), python-glade2, python-matplotlib (>=0.90), python-tables (>=1.3.2), lzop
|
||||||
|
Recommends: damaris-backends, python-numpy-ext
|
||||||
|
Suggests: python-doc, python-tables-doc, python-numpy-doc
|
||||||
|
Description: python frontend for DAMARIS project
|
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10
debian/damaris.desktop
vendored
Normal file
10
debian/damaris.desktop
vendored
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
[Desktop Entry]
|
||||||
|
Name=DAMARIS
|
||||||
|
Comment=DArmstadt MAgnetic Resonance Instrument Software
|
||||||
|
Exec=/usr/bin/DAMARIS %F
|
||||||
|
X-MultipleArgs=true
|
||||||
|
Terminal=false
|
||||||
|
MimeType=text/x-python;text/plain;
|
||||||
|
Type=Application
|
||||||
|
Categories=Science;Education;Physics;Chemistry;
|
||||||
|
Icon=DAMARIS
|
||||||
1
debian/pycompat
vendored
Normal file
1
debian/pycompat
vendored
Normal file
@ -0,0 +1 @@
|
|||||||
|
2
|
||||||
1
debian/python-damaris.menu
vendored
Normal file
1
debian/python-damaris.menu
vendored
Normal file
@ -0,0 +1 @@
|
|||||||
|
?package(python-damaris): needs="X11" section="Apps/Science" title="DAMARIS" longtitle="DArmstadt Magnetic Resonance Instrument Software" command="DAMARIS -dGTKAgg" icon="/usr/share/python-damaris/images/DAMARIS.png"
|
||||||
65
debian/rules
vendored
Executable file
65
debian/rules
vendored
Executable file
@ -0,0 +1,65 @@
|
|||||||
|
#!/usr/bin/make -f
|
||||||
|
|
||||||
|
# Achim Gaedke
|
||||||
|
# May 2007
|
||||||
|
|
||||||
|
# Uncomment this to turn on verbose mode.
|
||||||
|
export DH_VERBOSE=1
|
||||||
|
PYVERS=$(shell pyversions -vr)
|
||||||
|
PACKAGE_NAME=python-damaris
|
||||||
|
MODULE_NAME=damaris
|
||||||
|
PYBASE=$(CURDIR)/debian/${PACKAGE_NAME}
|
||||||
|
DH_ALWAYS_EXCLUDE=CVS:.svn
|
||||||
|
|
||||||
|
clean:
|
||||||
|
dh_testdir
|
||||||
|
dh_testroot
|
||||||
|
dh_installdirs
|
||||||
|
# Add here commands to clean up after the build process.
|
||||||
|
rm -f *-stamp
|
||||||
|
rm -rf dist build $(PYVERS:%=build-ext-%)
|
||||||
|
find . -name *\.py[co] -exec rm {} \;
|
||||||
|
dh_clean
|
||||||
|
|
||||||
|
build: build-stamp
|
||||||
|
build-stamp: $(PYVERS:%=build-ext-%)
|
||||||
|
touch $@
|
||||||
|
build-ext-%:
|
||||||
|
dh_testdir
|
||||||
|
python$* setup.py build
|
||||||
|
touch $@
|
||||||
|
|
||||||
|
install: install-stamp
|
||||||
|
# install menu related things
|
||||||
|
dh_install debian/damaris.desktop /usr/share/applications/
|
||||||
|
|
||||||
|
install-stamp: build-stamp $(PYVERS:%=install-ext-%)
|
||||||
|
install-ext-%:
|
||||||
|
python$* setup.py install --root $(PYBASE) --install-layout=deb
|
||||||
|
echo "DAMARIS script: removing path to local installation"
|
||||||
|
-sed 's/^sys.path.insert(0,.*).*/# damaris package is found on default path/' <$(PYBASE)/usr/bin/DAMARIS >$(PYBASE)/usr/bin/DAMARIS.new
|
||||||
|
-mv $(PYBASE)/usr/bin/DAMARIS.new $(PYBASE)/usr/bin/DAMARIS
|
||||||
|
|
||||||
|
binary-indep: build install
|
||||||
|
dh_link usr/share/python-damaris/doc usr/share/doc/python-damaris/html
|
||||||
|
dh_link usr/share/python-damaris/images usr/share/doc/python-damaris/images
|
||||||
|
dh_link usr/share/python-damaris/images/DAMARIS.png usr/share/icons/DAMARIS.png
|
||||||
|
dh_testdir -i
|
||||||
|
dh_testroot -i
|
||||||
|
dh_installchangelogs -i
|
||||||
|
dh_installdocs -i
|
||||||
|
dh_pysupport
|
||||||
|
dh_installmenu -i
|
||||||
|
dh_desktop -i
|
||||||
|
dh_compress -i -X.py
|
||||||
|
dh_fixperms -i
|
||||||
|
dh_installdeb -i
|
||||||
|
dh_gencontrol -i
|
||||||
|
dh_md5sums -i
|
||||||
|
dh_builddeb -i
|
||||||
|
|
||||||
|
binary-arch: build install
|
||||||
|
|
||||||
|
binary: binary-indep binary-arch
|
||||||
|
|
||||||
|
.PHONY: build clean binary-indep binary-arch binary install configure
|
||||||
242
doc/Doxyfile
Normal file
242
doc/Doxyfile
Normal file
@ -0,0 +1,242 @@
|
|||||||
|
# Doxyfile 1.5.3
|
||||||
|
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Project related configuration options
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
DOXYFILE_ENCODING = UTF-8
|
||||||
|
PROJECT_NAME = "python DAMARIS"
|
||||||
|
PROJECT_NUMBER = 0.13-svn
|
||||||
|
OUTPUT_DIRECTORY = .
|
||||||
|
CREATE_SUBDIRS = NO
|
||||||
|
OUTPUT_LANGUAGE = English
|
||||||
|
BRIEF_MEMBER_DESC = YES
|
||||||
|
REPEAT_BRIEF = YES
|
||||||
|
ABBREVIATE_BRIEF = "The $name class " \
|
||||||
|
"The $name widget " \
|
||||||
|
"The $name file " \
|
||||||
|
is \
|
||||||
|
provides \
|
||||||
|
specifies \
|
||||||
|
contains \
|
||||||
|
represents \
|
||||||
|
a \
|
||||||
|
an \
|
||||||
|
the
|
||||||
|
ALWAYS_DETAILED_SEC = NO
|
||||||
|
INLINE_INHERITED_MEMB = NO
|
||||||
|
FULL_PATH_NAMES = NO
|
||||||
|
STRIP_FROM_PATH =
|
||||||
|
STRIP_FROM_INC_PATH =
|
||||||
|
SHORT_NAMES = NO
|
||||||
|
JAVADOC_AUTOBRIEF = NO
|
||||||
|
QT_AUTOBRIEF = NO
|
||||||
|
MULTILINE_CPP_IS_BRIEF = NO
|
||||||
|
DETAILS_AT_TOP = NO
|
||||||
|
INHERIT_DOCS = YES
|
||||||
|
SEPARATE_MEMBER_PAGES = NO
|
||||||
|
TAB_SIZE = 8
|
||||||
|
ALIASES =
|
||||||
|
OPTIMIZE_OUTPUT_FOR_C = NO
|
||||||
|
OPTIMIZE_OUTPUT_JAVA = NO
|
||||||
|
BUILTIN_STL_SUPPORT = NO
|
||||||
|
CPP_CLI_SUPPORT = NO
|
||||||
|
DISTRIBUTE_GROUP_DOC = NO
|
||||||
|
SUBGROUPING = YES
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Build related configuration options
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
EXTRACT_ALL = YES
|
||||||
|
EXTRACT_PRIVATE = YES
|
||||||
|
EXTRACT_STATIC = YES
|
||||||
|
EXTRACT_LOCAL_CLASSES = YES
|
||||||
|
EXTRACT_LOCAL_METHODS = NO
|
||||||
|
EXTRACT_ANON_NSPACES = NO
|
||||||
|
HIDE_UNDOC_MEMBERS = NO
|
||||||
|
HIDE_UNDOC_CLASSES = NO
|
||||||
|
HIDE_FRIEND_COMPOUNDS = NO
|
||||||
|
HIDE_IN_BODY_DOCS = NO
|
||||||
|
INTERNAL_DOCS = NO
|
||||||
|
CASE_SENSE_NAMES = YES
|
||||||
|
HIDE_SCOPE_NAMES = NO
|
||||||
|
SHOW_INCLUDE_FILES = YES
|
||||||
|
INLINE_INFO = YES
|
||||||
|
SORT_MEMBER_DOCS = YES
|
||||||
|
SORT_BRIEF_DOCS = NO
|
||||||
|
SORT_BY_SCOPE_NAME = NO
|
||||||
|
GENERATE_TODOLIST = YES
|
||||||
|
GENERATE_TESTLIST = YES
|
||||||
|
GENERATE_BUGLIST = YES
|
||||||
|
GENERATE_DEPRECATEDLIST= YES
|
||||||
|
ENABLED_SECTIONS =
|
||||||
|
MAX_INITIALIZER_LINES = 30
|
||||||
|
SHOW_USED_FILES = YES
|
||||||
|
SHOW_DIRECTORIES = NO
|
||||||
|
FILE_VERSION_FILTER =
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to warning and progress messages
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
QUIET = NO
|
||||||
|
WARNINGS = YES
|
||||||
|
WARN_IF_UNDOCUMENTED = YES
|
||||||
|
WARN_IF_DOC_ERROR = YES
|
||||||
|
WARN_NO_PARAMDOC = NO
|
||||||
|
WARN_FORMAT = "$file:$line: $text "
|
||||||
|
WARN_LOGFILE =
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the input files
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
INPUT = damaris
|
||||||
|
INPUT_ENCODING = ISO-8859-15
|
||||||
|
FILE_PATTERNS = *.py \
|
||||||
|
*.PY
|
||||||
|
RECURSIVE = YES
|
||||||
|
EXCLUDE =
|
||||||
|
EXCLUDE_SYMLINKS = NO
|
||||||
|
EXCLUDE_PATTERNS =
|
||||||
|
EXCLUDE_SYMBOLS =
|
||||||
|
EXAMPLE_PATH =
|
||||||
|
EXAMPLE_PATTERNS = *
|
||||||
|
EXAMPLE_RECURSIVE = YES
|
||||||
|
IMAGE_PATH =
|
||||||
|
INPUT_FILTER =
|
||||||
|
FILTER_PATTERNS =
|
||||||
|
FILTER_SOURCE_FILES = NO
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to source browsing
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
SOURCE_BROWSER = YES
|
||||||
|
INLINE_SOURCES = NO
|
||||||
|
STRIP_CODE_COMMENTS = YES
|
||||||
|
REFERENCED_BY_RELATION = NO
|
||||||
|
REFERENCES_RELATION = NO
|
||||||
|
REFERENCES_LINK_SOURCE = YES
|
||||||
|
USE_HTAGS = NO
|
||||||
|
VERBATIM_HEADERS = NO
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the alphabetical class index
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
ALPHABETICAL_INDEX = NO
|
||||||
|
COLS_IN_ALPHA_INDEX = 5
|
||||||
|
IGNORE_PREFIX =
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the HTML output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
GENERATE_HTML = YES
|
||||||
|
HTML_OUTPUT = reference-html
|
||||||
|
HTML_FILE_EXTENSION = .html
|
||||||
|
HTML_HEADER =
|
||||||
|
HTML_FOOTER =
|
||||||
|
HTML_STYLESHEET =
|
||||||
|
HTML_ALIGN_MEMBERS = YES
|
||||||
|
GENERATE_HTMLHELP = NO
|
||||||
|
HTML_DYNAMIC_SECTIONS = NO
|
||||||
|
CHM_FILE =
|
||||||
|
HHC_LOCATION =
|
||||||
|
GENERATE_CHI = NO
|
||||||
|
BINARY_TOC = NO
|
||||||
|
TOC_EXPAND = NO
|
||||||
|
DISABLE_INDEX = NO
|
||||||
|
ENUM_VALUES_PER_LINE = 4
|
||||||
|
GENERATE_TREEVIEW = NO
|
||||||
|
TREEVIEW_WIDTH = 250
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the LaTeX output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
GENERATE_LATEX = NO
|
||||||
|
LATEX_OUTPUT = latex
|
||||||
|
LATEX_CMD_NAME = latex
|
||||||
|
MAKEINDEX_CMD_NAME = makeindex
|
||||||
|
COMPACT_LATEX = NO
|
||||||
|
PAPER_TYPE = a4wide
|
||||||
|
EXTRA_PACKAGES =
|
||||||
|
LATEX_HEADER =
|
||||||
|
PDF_HYPERLINKS = NO
|
||||||
|
USE_PDFLATEX = NO
|
||||||
|
LATEX_BATCHMODE = NO
|
||||||
|
LATEX_HIDE_INDICES = NO
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the RTF output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
GENERATE_RTF = NO
|
||||||
|
RTF_OUTPUT = rtf
|
||||||
|
COMPACT_RTF = NO
|
||||||
|
RTF_HYPERLINKS = NO
|
||||||
|
RTF_STYLESHEET_FILE =
|
||||||
|
RTF_EXTENSIONS_FILE =
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the man page output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
GENERATE_MAN = NO
|
||||||
|
MAN_OUTPUT = man
|
||||||
|
MAN_EXTENSION = .3
|
||||||
|
MAN_LINKS = NO
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the XML output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
GENERATE_XML = NO
|
||||||
|
XML_OUTPUT = xml
|
||||||
|
XML_SCHEMA =
|
||||||
|
XML_DTD =
|
||||||
|
XML_PROGRAMLISTING = YES
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options for the AutoGen Definitions output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
GENERATE_AUTOGEN_DEF = NO
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# configuration options related to the Perl module output
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
GENERATE_PERLMOD = NO
|
||||||
|
PERLMOD_LATEX = NO
|
||||||
|
PERLMOD_PRETTY = YES
|
||||||
|
PERLMOD_MAKEVAR_PREFIX =
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration options related to the preprocessor
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
ENABLE_PREPROCESSING = NO
|
||||||
|
MACRO_EXPANSION = NO
|
||||||
|
EXPAND_ONLY_PREDEF = NO
|
||||||
|
SEARCH_INCLUDES = YES
|
||||||
|
INCLUDE_PATH =
|
||||||
|
INCLUDE_FILE_PATTERNS =
|
||||||
|
PREDEFINED =
|
||||||
|
EXPAND_AS_DEFINED =
|
||||||
|
SKIP_FUNCTION_MACROS = YES
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration::additions related to external references
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
TAGFILES =
|
||||||
|
GENERATE_TAGFILE =
|
||||||
|
ALLEXTERNALS = NO
|
||||||
|
EXTERNAL_GROUPS = YES
|
||||||
|
PERL_PATH = /usr/bin/perl
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration options related to the dot tool
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
CLASS_DIAGRAMS = YES
|
||||||
|
MSCGEN_PATH =
|
||||||
|
HIDE_UNDOC_RELATIONS = YES
|
||||||
|
HAVE_DOT = YES
|
||||||
|
CLASS_GRAPH = YES
|
||||||
|
COLLABORATION_GRAPH = YES
|
||||||
|
GROUP_GRAPHS = YES
|
||||||
|
UML_LOOK = NO
|
||||||
|
TEMPLATE_RELATIONS = NO
|
||||||
|
INCLUDE_GRAPH = YES
|
||||||
|
INCLUDED_BY_GRAPH = YES
|
||||||
|
CALL_GRAPH = NO
|
||||||
|
CALLER_GRAPH = NO
|
||||||
|
GRAPHICAL_HIERARCHY = YES
|
||||||
|
DIRECTORY_GRAPH = YES
|
||||||
|
DOT_IMAGE_FORMAT = png
|
||||||
|
DOT_PATH = /usr/bin/
|
||||||
|
DOTFILE_DIRS =
|
||||||
|
DOT_GRAPH_MAX_NODES = 50
|
||||||
|
MAX_DOT_GRAPH_DEPTH = 1000
|
||||||
|
DOT_TRANSPARENT = NO
|
||||||
|
DOT_MULTI_TARGETS = NO
|
||||||
|
GENERATE_LEGEND = YES
|
||||||
|
DOT_CLEANUP = YES
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
# Configuration::additions related to the search engine
|
||||||
|
#---------------------------------------------------------------------------
|
||||||
|
SEARCHENGINE = NO
|
||||||
24
doc/README.txt
Normal file
24
doc/README.txt
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
by now the documentation creation is not automatized...
|
||||||
|
|
||||||
|
# html reference
|
||||||
|
# requires dot and doxygen
|
||||||
|
|
||||||
|
cd doc
|
||||||
|
ln -s ../src damaris
|
||||||
|
doxygen Doxyfile
|
||||||
|
rm damaris
|
||||||
|
|
||||||
|
# todo: copy damaris logo
|
||||||
|
|
||||||
|
# html wiki export
|
||||||
|
# requires moinmoin and damaris/data as wikidata
|
||||||
|
|
||||||
|
cd doc
|
||||||
|
# underlay must be writable, so we have to copy it...
|
||||||
|
cp -r /usr/share/moin/underlay wikiunderlay
|
||||||
|
python dump_wiki.py
|
||||||
|
cp -r /usr/share/moin/htdocs/modern tutorial-html
|
||||||
|
rm -r wikiunderlay wikiconfig.py
|
||||||
|
|
||||||
|
# get useful numpy doc
|
||||||
|
wget http://www.scipy.org/Numpy_Example_List_With_Doc?action=print
|
||||||
177
doc/dump_wiki.py
Normal file
177
doc/dump_wiki.py
Normal file
@ -0,0 +1,177 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
"""
|
||||||
|
MoinMoin - Dump a MoinMoin wiki to static pages
|
||||||
|
|
||||||
|
based on "moin.py export dump" command
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
import sys, os, time, StringIO, codecs, shutil, re, errno
|
||||||
|
|
||||||
|
from MoinMoin import config, wikiutil, Page
|
||||||
|
from MoinMoin.request import RequestCLI
|
||||||
|
from MoinMoin.action import AttachFile
|
||||||
|
|
||||||
|
HTML_SUFFIX = ".html"
|
||||||
|
|
||||||
|
page_template = u'''<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
|
||||||
|
<html>
|
||||||
|
<head>
|
||||||
|
<meta http-equiv="content-type" content="text/html; charset=%(charset)s">
|
||||||
|
<title>%(pagename)s</title>
|
||||||
|
<link rel="stylesheet" type="text/css" media="all" charset="utf-8" href="%(theme)s/css/common.css">
|
||||||
|
<link rel="stylesheet" type="text/css" media="screen" charset="utf-8" href="%(theme)s/css/screen.css">
|
||||||
|
<link rel="stylesheet" type="text/css" media="print" charset="utf-8" href="%(theme)s/css/print.css">
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<div id="page">
|
||||||
|
<h1 id="title">%(pagename)s</h1>
|
||||||
|
%(pagehtml)s
|
||||||
|
</div>
|
||||||
|
<hr>
|
||||||
|
%(timestamp)s
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
|
'''
|
||||||
|
|
||||||
|
def _attachment(request, pagename, filename, outputdir):
|
||||||
|
filename = filename.encode(config.charset)
|
||||||
|
source_dir = AttachFile.getAttachDir(request, pagename)
|
||||||
|
source_file = os.path.join(source_dir, filename)
|
||||||
|
dest_dir = os.path.join(outputdir, "attachments", wikiutil.quoteWikinameFS(pagename))
|
||||||
|
dest_file = os.path.join(dest_dir, filename)
|
||||||
|
dest_url = "attachments/%s/%s" % (wikiutil.quoteWikinameFS(pagename), wikiutil.url_quote(filename))
|
||||||
|
if os.access(source_file, os.R_OK):
|
||||||
|
if not os.access(dest_dir, os.F_OK):
|
||||||
|
try:
|
||||||
|
os.makedirs(dest_dir)
|
||||||
|
except:
|
||||||
|
print ("Cannot create attachment directory '%s'" % dest_dir)
|
||||||
|
raise
|
||||||
|
elif not os.path.isdir(dest_dir):
|
||||||
|
print ("'%s' is not a directory" % dest_dir)
|
||||||
|
|
||||||
|
shutil.copyfile(source_file, dest_file)
|
||||||
|
print ('Writing "%s"...' % dest_url)
|
||||||
|
return dest_url
|
||||||
|
else:
|
||||||
|
return ""
|
||||||
|
|
||||||
|
|
||||||
|
class PluginScript: #(MoinScript):
|
||||||
|
""" Dump script class """
|
||||||
|
|
||||||
|
def __init__(self):
|
||||||
|
pass
|
||||||
|
|
||||||
|
def mainloop(self):
|
||||||
|
""" moin-dump's main code. """
|
||||||
|
|
||||||
|
# Prepare output directory
|
||||||
|
outputdir=os.path.join(os.curdir,"tutorial-html")
|
||||||
|
try:
|
||||||
|
os.mkdir(outputdir)
|
||||||
|
print "Created output directory '%s'!" % outputdir
|
||||||
|
except OSError, err:
|
||||||
|
if err.errno != errno.EEXIST:
|
||||||
|
print "Cannot create output directory '%s'!" % outputdir
|
||||||
|
raise
|
||||||
|
|
||||||
|
sys.path.insert(0, os.path.abspath(os.curdir))
|
||||||
|
|
||||||
|
wikiconfig_template="""
|
||||||
|
from MoinMoin.multiconfig import DefaultConfig
|
||||||
|
class Config(DefaultConfig):
|
||||||
|
sitename = u'DAMARIS Homepage and Usergroup'
|
||||||
|
logo_string = u'<img src="/damaris/wiki/damaris/DAMARIS.png" alt="DAMARIS Logo">'
|
||||||
|
page_front_page = u"Welcome"
|
||||||
|
interwikiname = 'damaris'
|
||||||
|
data_dir = '%(pwd)s/wikidata/'
|
||||||
|
data_underlay_dir = '%(pwd)s/wikiunderlay'
|
||||||
|
url_prefix = '/damaris/wiki'
|
||||||
|
theme_default = 'modern'
|
||||||
|
"""%{"pwd": os.curdir, "underlay": "/home/achim/underlay" }
|
||||||
|
|
||||||
|
config_file = open("wikiconfig.py","w")
|
||||||
|
print >>config_file, wikiconfig_template
|
||||||
|
config_file.close()
|
||||||
|
|
||||||
|
# start with wiki entry page
|
||||||
|
request = RequestCLI(pagename="Welcome")
|
||||||
|
|
||||||
|
# fix url_prefix so we get relative paths in output html
|
||||||
|
url_prefix = "."
|
||||||
|
request.cfg.url_prefix = url_prefix
|
||||||
|
|
||||||
|
pages = request.rootpage.getPageList(user='') # get list of all pages in wiki
|
||||||
|
pages.sort()
|
||||||
|
|
||||||
|
# extract a list of pages to be extracted
|
||||||
|
# trial session to fat!!!
|
||||||
|
try:
|
||||||
|
pages_match = re.compile("^(Tutorial|auxiliary tools|overview|installation|code snippets)")
|
||||||
|
pages = [page for page in pages if pages_match.match(page)]
|
||||||
|
except:
|
||||||
|
print "did not find suitable pages"
|
||||||
|
raise
|
||||||
|
|
||||||
|
wikiutil.quoteWikinameURL = lambda pagename, qfn=wikiutil.quoteWikinameFS: (qfn(pagename) + HTML_SUFFIX)
|
||||||
|
|
||||||
|
AttachFile.getAttachUrl = lambda pagename, filename, request, addts=0, escaped=0: (_attachment(request, pagename, filename, outputdir))
|
||||||
|
|
||||||
|
errfile = os.path.join(outputdir, 'error.log')
|
||||||
|
errlog = open(errfile, 'w')
|
||||||
|
errcnt = 0
|
||||||
|
|
||||||
|
page_front_page = wikiutil.getSysPage(request, request.cfg.page_front_page).page_name
|
||||||
|
page_title_index = wikiutil.getSysPage(request, 'TitleIndex').page_name
|
||||||
|
page_word_index = wikiutil.getSysPage(request, 'WordIndex').page_name
|
||||||
|
|
||||||
|
navibar_html = ''
|
||||||
|
for p in [page_front_page, page_title_index, page_word_index]:
|
||||||
|
navibar_html += ' [<a href="%s">%s</a>]' % (wikiutil.quoteWikinameURL(p), wikiutil.escape(p))
|
||||||
|
|
||||||
|
urlbase = request.url # save wiki base url
|
||||||
|
for pagename in pages:
|
||||||
|
# we have the same name in URL and FS
|
||||||
|
file = wikiutil.quoteWikinameURL(pagename)
|
||||||
|
print ('Writing "%s"...' % file)
|
||||||
|
try:
|
||||||
|
pagehtml = ''
|
||||||
|
request.url = urlbase + pagename # add current pagename to url base
|
||||||
|
page = Page.Page(request, pagename)
|
||||||
|
request.page = page
|
||||||
|
try:
|
||||||
|
request.reset()
|
||||||
|
pagehtml = request.redirectedOutput(page.send_page, request, count_hit=0, content_only=1)
|
||||||
|
except:
|
||||||
|
errcnt = errcnt + 1
|
||||||
|
print >>sys.stderr, "*** Caught exception while writing page!"
|
||||||
|
print >>errlog, "~" * 78
|
||||||
|
print >>errlog, file # page filename
|
||||||
|
import traceback
|
||||||
|
traceback.print_exc(None, errlog)
|
||||||
|
finally:
|
||||||
|
timestamp = time.strftime("%Y-%m-%d %H:%M")
|
||||||
|
filepath = os.path.join(outputdir, file)
|
||||||
|
fileout = codecs.open(filepath, 'w', config.charset)
|
||||||
|
logo_html = '<img src="logo.png">'
|
||||||
|
fileout.write(page_template % {
|
||||||
|
'charset': config.charset,
|
||||||
|
'pagename': pagename,
|
||||||
|
'pagehtml': pagehtml,
|
||||||
|
'logo_html': logo_html,
|
||||||
|
'navibar_html': navibar_html,
|
||||||
|
'timestamp': timestamp,
|
||||||
|
'theme': request.cfg.theme_default,
|
||||||
|
})
|
||||||
|
fileout.close()
|
||||||
|
|
||||||
|
# ToDo: insert style sheets and logo
|
||||||
|
|
||||||
|
errlog.close()
|
||||||
|
if errcnt:
|
||||||
|
print >>sys.stderr, "*** %d error(s) occurred, see '%s'!" % (errcnt, errfile)
|
||||||
|
|
||||||
|
if __name__=="__main__":
|
||||||
|
PluginScript().mainloop()
|
||||||
84
doc/index.html
Normal file
84
doc/index.html
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
|
||||||
|
<html>
|
||||||
|
<head>
|
||||||
|
<meta content="text/html; charset=ISO-8859-1"
|
||||||
|
http-equiv="content-type">
|
||||||
|
<title>python-damaris documentation index</title>
|
||||||
|
</head>
|
||||||
|
<body>
|
||||||
|
<h1><img alt="DAMARIS" src="../images/DAMARIS.png" align="middle">DAMARIS
|
||||||
|
Documentation Index<br>
|
||||||
|
</h1>
|
||||||
|
<h2>Local Resources:</h2>
|
||||||
|
<br>
|
||||||
|
Documentation from DAMARIS wiki:<br>
|
||||||
|
<ul>
|
||||||
|
<li><a href="tutorial-html/Tutorial.html">Tutorial</a></li>
|
||||||
|
<li><a href="tutorial-html/Tutorial%282f%29List_of_Commands.html">Command
|
||||||
|
Reference</a></li>
|
||||||
|
</ul>
|
||||||
|
python-damaris source code reference (generated by <a
|
||||||
|
href="http://www.doxygen.org/">doxygen</a>)<br>
|
||||||
|
<ul>
|
||||||
|
<li><a href="reference-html/index.html">index</a></li>
|
||||||
|
<li><a href="reference-html/namespacedamaris_1_1data.html">result
|
||||||
|
reference</a><br>
|
||||||
|
</li>
|
||||||
|
<li><a
|
||||||
|
href="reference-html/namespacedamaris_1_1experiments_1_1Experiment.html">experiment
|
||||||
|
reference</a></li>
|
||||||
|
</ul>
|
||||||
|
<h2>Internet Resources:</h2>
|
||||||
|
<ul>
|
||||||
|
<li><a href="http://damaris.berlios.de/">DAMARIS
|
||||||
|
Homepage</a></li>
|
||||||
|
<li>Software Related</li>
|
||||||
|
<ul>
|
||||||
|
<li><a href="http://www.python.org/">Python Homepage</a></li>
|
||||||
|
<li><a href="http://www.numpy.org/">Numeric Python (numpy)</a></li>
|
||||||
|
<li><a href="http://www.pytables.org/">HDF Support (pytables)</a><br>
|
||||||
|
</li>
|
||||||
|
<li><a href="http://www.scipy.org/">Scientific Python (scipy)</a></li>
|
||||||
|
<li><a href="http://www.pygtk.org/">PyGTK Homepage (Graphics)<br>
|
||||||
|
</a></li>
|
||||||
|
<li><a href="matplotlib.sourceforge.net">2D Graph drawing
|
||||||
|
(Matplotlib)</a></li>
|
||||||
|
<li><a href="http://ipython.scipy.org/">Interactive Python
|
||||||
|
Interpreter (iPython)</a><br>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<li>More Documentation:</li>
|
||||||
|
<ul>
|
||||||
|
<li>Official Python <a href="http://www.python.org/doc/">Documentation</a>
|
||||||
|
/ <a href="http://docs.python.org/tut/tut.html">Tutorial</a></li>
|
||||||
|
<li>More Python <a
|
||||||
|
href="http://www.awaretek.com/tutorials.html#begin">Tutorials</a><br>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<ul>
|
||||||
|
<li><a href="http://www.scipy.org/Numpy_Example_List_With_Doc">Numpy
|
||||||
|
Example List</a></li>
|
||||||
|
<li><a href="http://www.tramy.us/numpybook.pdf">Numpy Book (pdf)</a>
|
||||||
|
von Travis E. Oliphant</li>
|
||||||
|
<li>A <a href="http://www.scipy.org/Cookbook">Cookbook</a> for
|
||||||
|
many advanced data processing tasks<br>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<li>NMR Links</li>
|
||||||
|
<ul>
|
||||||
|
<li><a href="http://www.nmrwiki.org/">NMR wiki</a><br>
|
||||||
|
</li>
|
||||||
|
<li><a href="http://www.spincore.com/nmrinfo/">NMR Info</a><br>
|
||||||
|
</li>
|
||||||
|
<li><a href="http://www.diffusion-fundamentals.org/">Diffusion
|
||||||
|
Fundamentals</a><br>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
<ul>
|
||||||
|
<li><a href="http://www.fkp.tu-darmstadt.de/groups/ag_fujara/fup/index.de.jsp">AG Fujara</a></li>
|
||||||
|
<li><a href="http://www.fkp.tu-darmstadt.de/groups/ag_vogel/index.de.jsp">AG Vogel</a><br>
|
||||||
|
</li>
|
||||||
|
</ul>
|
||||||
|
</ul>
|
||||||
|
</body>
|
||||||
|
</html>
|
||||||
1864
doxygen.conf
Normal file
1864
doxygen.conf
Normal file
File diff suppressed because it is too large
Load Diff
51
scripts/DAMARIS
Executable file
51
scripts/DAMARIS
Executable file
@ -0,0 +1,51 @@
|
|||||||
|
#!/usr/bin/python
|
||||||
|
|
||||||
|
# setup script will insert local DAMARIS installation path behind import sys statement
|
||||||
|
# this must happen before any damaris stuff is called!
|
||||||
|
import sys
|
||||||
|
|
||||||
|
import os
|
||||||
|
# for numpy-1.1 and later: check the environment for LANG and LC_NUMERIC
|
||||||
|
# see: http://projects.scipy.org/scipy/numpy/ticket/902
|
||||||
|
if os.environ.get("LANG","").startswith("de") or os.environ.get("LC_NUMERIC", "").startswith("de"):
|
||||||
|
os.environ["LC_NUMERIC"]="C"
|
||||||
|
|
||||||
|
import damaris.gui.DamarisGUI
|
||||||
|
import matplotlib
|
||||||
|
|
||||||
|
import os.path
|
||||||
|
# argv is already parsed by gtk initialisation
|
||||||
|
myargs=sys.argv[1:]
|
||||||
|
myname=os.path.basename(sys.argv[0])
|
||||||
|
|
||||||
|
# find debug flag:
|
||||||
|
if "--debug" in myargs:
|
||||||
|
damaris.gui.DamarisGUI.debug = True
|
||||||
|
print "debug flag set"
|
||||||
|
try:
|
||||||
|
import resource
|
||||||
|
resource.setrlimit(resource.RLIMIT_CORE, (-1,-1))
|
||||||
|
except ImportError:
|
||||||
|
pass
|
||||||
|
matplotlib.rcParams["verbose.level"]="debug"
|
||||||
|
myargs.remove("--debug")
|
||||||
|
|
||||||
|
# remove matplotlib flags
|
||||||
|
if "-d"+matplotlib.rcParams["backend"] in myargs:
|
||||||
|
myargs.remove("-d"+matplotlib.rcParams["backend"])
|
||||||
|
|
||||||
|
# find scripts to load in parameter list
|
||||||
|
exp_script = None
|
||||||
|
res_script = None
|
||||||
|
if len(myargs)<=2:
|
||||||
|
if len(myargs)>=1:
|
||||||
|
exp_script=myargs[0]
|
||||||
|
if len(myargs)==2:
|
||||||
|
res_script=myargs[1]
|
||||||
|
else:
|
||||||
|
print """too many arguments.\n%s [--debug] [-dGTK(Agg|Cairo|)] (Experiment File|"") (Result File|"")"""%(myname)
|
||||||
|
|
||||||
|
d=damaris.gui.DamarisGUI.DamarisGUI(exp_script, res_script)
|
||||||
|
d.run()
|
||||||
|
sys.stdout=sys.__stdout__
|
||||||
|
sys.stderr=sys.__stderr__
|
||||||
121
setup.py
Normal file
121
setup.py
Normal file
@ -0,0 +1,121 @@
|
|||||||
|
#!/usr/bin/env python
|
||||||
|
|
||||||
|
import shutil
|
||||||
|
import os
|
||||||
|
import os.path
|
||||||
|
import sys
|
||||||
|
from distutils.core import setup
|
||||||
|
from distutils.command.build_scripts import build_scripts as _build_scripts
|
||||||
|
from distutils import log
|
||||||
|
from distutils.util import convert_path
|
||||||
|
from distutils.dep_util import newer
|
||||||
|
|
||||||
|
#if sys.version_info < (2, 5, 3):
|
||||||
|
# log.error("**** ERROR: Install manually: python setup.py install ****")
|
||||||
|
# raise ValueError
|
||||||
|
|
||||||
|
class build_damaris_scripts(_build_scripts):
|
||||||
|
|
||||||
|
#user_options=_build_scripts.user_options[:]
|
||||||
|
#user_options.append(('install-dir=', 'd', "directory to install scripts to"))
|
||||||
|
|
||||||
|
def initialize_options (self):
|
||||||
|
_build_scripts.initialize_options(self)
|
||||||
|
self.damaris_dir = None
|
||||||
|
|
||||||
|
def finalize_options (self):
|
||||||
|
_build_scripts.finalize_options(self)
|
||||||
|
self.set_undefined_options('install',
|
||||||
|
('install_lib', 'damaris_dir'))
|
||||||
|
|
||||||
|
def run (self):
|
||||||
|
"change PYTHON_PATH for DAMARIS executable"
|
||||||
|
_build_scripts.run(self)
|
||||||
|
script="scripts/DAMARIS"
|
||||||
|
script = convert_path(script)
|
||||||
|
outfile = os.path.join(self.build_dir, os.path.basename(script))
|
||||||
|
self.damaris_dir=os.path.normpath(self.damaris_dir)
|
||||||
|
if self.damaris_dir in sys.path:
|
||||||
|
log.debug("not changing %s (this path is on standard path)", script)
|
||||||
|
# nothing to do for us
|
||||||
|
return
|
||||||
|
|
||||||
|
# now change PATH in DAMARIS script
|
||||||
|
# copy backup
|
||||||
|
log.info("adapting DAMARIS script to use local installation")
|
||||||
|
shutil.copyfile(outfile, outfile+".bak")
|
||||||
|
# the file should keep all its attributes (executable...)
|
||||||
|
inf=file(outfile+".bak","r")
|
||||||
|
outf=file(outfile,"w")
|
||||||
|
l=inf.readline()
|
||||||
|
while not l.startswith("import sys") and l!="":
|
||||||
|
outf.write(l)
|
||||||
|
l=inf.readline()
|
||||||
|
|
||||||
|
if l!="":
|
||||||
|
outf.write(l)
|
||||||
|
l=inf.readline()
|
||||||
|
while l.endswith("# inserted by setup.py\n"):
|
||||||
|
l=inf.readline()
|
||||||
|
outf.write("sys.path.insert(0,\"%s\") # inserted by setup.py\n"%self.damaris_dir)
|
||||||
|
outf.write(l)
|
||||||
|
|
||||||
|
outf.writelines(inf.readlines())
|
||||||
|
inf.close()
|
||||||
|
outf.close()
|
||||||
|
os.remove(outfile+".bak")
|
||||||
|
|
||||||
|
# create doc data file information
|
||||||
|
distribution_doc_prefix=os.path.join("share","python-damaris","doc")
|
||||||
|
distribution_data_files = [[ "share", []],
|
||||||
|
[os.path.join("share", "python-damaris", "images"),
|
||||||
|
["src/gui/DAMARIS.png", "src/gui/DAMARIS.ico"]],
|
||||||
|
[os.path.join("share", "python-damaris"), []],
|
||||||
|
[distribution_doc_prefix, ['doc/index.html']]]
|
||||||
|
|
||||||
|
if os.path.isdir(os.path.join("doc","reference-html")):
|
||||||
|
# no subdirs, work can be done in simple way
|
||||||
|
distribution_data_files.append([os.path.join(distribution_doc_prefix, 'reference-html'),
|
||||||
|
[os.path.join('doc', 'reference-html', f)
|
||||||
|
for f in os.listdir(os.path.join('doc', 'reference-html'))]])
|
||||||
|
|
||||||
|
if os.path.isdir(os.path.join("doc","tutorial-html")):
|
||||||
|
# here, modern style file and attachment directories should be handled
|
||||||
|
for d in os.walk(os.path.join("doc","tutorial-html")):
|
||||||
|
distribution_data_files.append([os.path.join(os.path.dirname(distribution_doc_prefix),d[0]),
|
||||||
|
[os.path.join(d[0], f) for f in d[2]]])
|
||||||
|
|
||||||
|
LONG_DESCRIPTION="""
|
||||||
|
DArmstadt MAgnetic Resonance Instrument Software
|
||||||
|
"""
|
||||||
|
|
||||||
|
GPL_LICENCE = "feed licence here"
|
||||||
|
|
||||||
|
setup (
|
||||||
|
name = 'python-damaris',
|
||||||
|
version = "0.14-svn",
|
||||||
|
description = 'python frontend for DAMARIS (DArmstadt MAgnetic Resonance Instrument Software)',
|
||||||
|
long_description = LONG_DESCRIPTION,
|
||||||
|
author = 'Achim Gaedke',
|
||||||
|
author_email = 'Achim.Gaedke@physik.tu-darmstadt.de',
|
||||||
|
maintainer = 'Achim Gaedke',
|
||||||
|
maintainer_email = 'Achim.Gaedke@physik.tu-darmstadt.de',
|
||||||
|
url = 'http://www.fkp.physik.tu-darmstadt.de/damaris/',
|
||||||
|
license = GPL_LICENCE,
|
||||||
|
platforms = ('Any',),
|
||||||
|
keywords = ('NMR', 'data-processing'),
|
||||||
|
packages = [ 'damaris',
|
||||||
|
'damaris.data',
|
||||||
|
'damaris.experiments',
|
||||||
|
'damaris.gui',
|
||||||
|
'damaris.tools' ],
|
||||||
|
package_dir = { 'damaris': 'src',
|
||||||
|
'damaris.data': 'src/data',
|
||||||
|
'damaris.experiments': 'src/experiments',
|
||||||
|
'damaris.gui': 'src/gui',
|
||||||
|
'damaris.tools': 'src/tools' },
|
||||||
|
package_data = { 'damaris.gui': ['DAMARIS.png', 'DAMARIS.ico', 'damaris.glade', 'damaris.gladep', 'python.xml']},
|
||||||
|
scripts = ['scripts/DAMARIS'],
|
||||||
|
cmdclass={"build_scripts": build_damaris_scripts},
|
||||||
|
data_files = distribution_data_files
|
||||||
|
)
|
||||||
18
src/__init__.py
Normal file
18
src/__init__.py
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
##\mainpage DArmstadt MAgnetic Resonance Instrument Software
|
||||||
|
#
|
||||||
|
#Python Frontend based on
|
||||||
|
# - Python/GTK
|
||||||
|
# - Matplotlib
|
||||||
|
# - Numpy
|
||||||
|
# - PyTables
|
||||||
|
#
|
||||||
|
#Written by
|
||||||
|
# - Achim Gaedke
|
||||||
|
# - Christopher Schmitt
|
||||||
|
# - Markus Rosenstihl
|
||||||
|
# - Holger Stork
|
||||||
|
# - Christian Tacke
|
||||||
|
|
||||||
|
## module contents
|
||||||
|
#
|
||||||
|
__all__=["experiments", "data", "gui"]
|
||||||
523
src/data/ADC_Result.py
Normal file
523
src/data/ADC_Result.py
Normal file
@ -0,0 +1,523 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
from Resultable import Resultable
|
||||||
|
from Drawable import Drawable
|
||||||
|
from Signalpath import Signalpath
|
||||||
|
from DamarisFFT import DamarisFFT
|
||||||
|
import threading
|
||||||
|
import numpy
|
||||||
|
import sys
|
||||||
|
import types
|
||||||
|
import datetime
|
||||||
|
import tables
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class ADC_Result #
|
||||||
|
# #
|
||||||
|
# Purpose: Specialised class of Resultable and Drawable #
|
||||||
|
# Contains recorded ADC Data #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
class ADC_Result(Resultable, Drawable, DamarisFFT, Signalpath):
|
||||||
|
def __init__(self, x = None, y = None, index = None, sampl_freq = None, desc = None, job_id = None, job_date = None):
|
||||||
|
Resultable.__init__(self)
|
||||||
|
Drawable.__init__(self)
|
||||||
|
|
||||||
|
# Title of this accumulation: set Values: Job-ID and Description (plotted in GUI -> look Drawable)
|
||||||
|
# Is set in ResultReader.py (or in copy-construktor)
|
||||||
|
self.__title_pattern = "ADC-Result: job_id = %s, desc = %s"
|
||||||
|
|
||||||
|
# Axis-Labels (inherited from Drawable)
|
||||||
|
self.xlabel = "Time (s)"
|
||||||
|
self.ylabel = "Samples [Digits]"
|
||||||
|
self.lock=threading.RLock()
|
||||||
|
self.nChannels = 0
|
||||||
|
|
||||||
|
if (x is None) and (y is None) and (index is None) and (sampl_freq is None) and (desc is None) and (job_id is None) and (job_date is None):
|
||||||
|
self.cont_data = False
|
||||||
|
self.sampling_rate = 0
|
||||||
|
self.index = []
|
||||||
|
self.x = []
|
||||||
|
self.y = []
|
||||||
|
|
||||||
|
elif (x is not None) and (y is not None) and (index is not None) and (sampl_freq is not None) and (desc is not None) and (job_id is not None) and (job_date is not None):
|
||||||
|
self.x = x
|
||||||
|
self.y = y
|
||||||
|
self.index = index
|
||||||
|
self.sampling_rate = sampl_freq
|
||||||
|
self.cont_data = True
|
||||||
|
self.description = desc
|
||||||
|
self.job_id = job_id
|
||||||
|
self.job_date = job_date
|
||||||
|
title="ADC-Result: job-id=%d"%int(self.job_id)
|
||||||
|
if len(self.description)>0:
|
||||||
|
for k,v in self.description.iteritems():
|
||||||
|
# string keys can be made invisible by adding two underscores in front of them
|
||||||
|
if not (type(k) in types.StringTypes and k[0] == '_' and k[1] == '_'):
|
||||||
|
title+=", %s=%s"%(k,v)
|
||||||
|
self.set_title(title)
|
||||||
|
|
||||||
|
else:
|
||||||
|
raise ValueError("Wrong usage of __init__!")
|
||||||
|
|
||||||
|
|
||||||
|
def create_data_space(self, channels, samples):
|
||||||
|
"Initialises the internal data-structures"
|
||||||
|
|
||||||
|
if self.contains_data():
|
||||||
|
print "Warning ADC-Result: Tried to run \"create_data_space()\" more than once."
|
||||||
|
return
|
||||||
|
|
||||||
|
if channels <= 0: raise ValueError("ValueError: You cant create an ADC-Result with less than 1 channel!")
|
||||||
|
if samples <= 0: raise ValueError("ValueError: You cant create an ADC-Result with less than 1 sample!")
|
||||||
|
|
||||||
|
for i in range(channels):
|
||||||
|
self.y.append(numpy.zeros((samples,), dtype="Int16"))
|
||||||
|
|
||||||
|
self.x = numpy.zeros((samples,), dtype="Float64")
|
||||||
|
|
||||||
|
self.index.append((0, samples-1))
|
||||||
|
self.cont_data = True
|
||||||
|
|
||||||
|
|
||||||
|
def contains_data(self):
|
||||||
|
"Returns true if ADC_Result contains data. (-> create_data_space() was called)"
|
||||||
|
return self.cont_data
|
||||||
|
|
||||||
|
|
||||||
|
def add_sample_space(self, samples):
|
||||||
|
"Adds space for n samples, where n can also be negative (deletes space). New space is filled up with \"0\""
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
|
||||||
|
if not self.cont_data:
|
||||||
|
print "Warning ADC-Result: Tried to resize empty array!"
|
||||||
|
return
|
||||||
|
|
||||||
|
length = len(self.y[0])
|
||||||
|
|
||||||
|
self.x = numpy.resize(self.x, (length+samples))
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
self.y[i] = numpy.resize(self.y[i], (length+samples))
|
||||||
|
|
||||||
|
self.index.append((length, len(self.y[0])-1))
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
|
||||||
|
def get_result_by_index(self, index):
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
start = self.index[index][0]
|
||||||
|
end = self.index[index][1]
|
||||||
|
except:
|
||||||
|
self.lock.release()
|
||||||
|
raise
|
||||||
|
|
||||||
|
tmp_x = self.x[start:end+1].copy()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(self.y[i][start:end+1].copy())
|
||||||
|
|
||||||
|
r = ADC_Result(x = tmp_x, y = tmp_y, index = [(0,len(tmp_y[0])-1)], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
|
||||||
|
def get_sampling_rate(self):
|
||||||
|
"Returns the samplingfrequency"
|
||||||
|
return self.sampling_rate + 0
|
||||||
|
|
||||||
|
|
||||||
|
def set_sampling_rate(self, hz):
|
||||||
|
"Sets the samplingfrequency in hz"
|
||||||
|
self.sampling_rate = float(hz)
|
||||||
|
|
||||||
|
|
||||||
|
def get_nChannels(self):
|
||||||
|
"Gets the number of channels"
|
||||||
|
return self.nChannels + 0
|
||||||
|
|
||||||
|
def set_nChannels(self, channels):
|
||||||
|
"Sets the number of channels"
|
||||||
|
self.nChannels = int(channels)
|
||||||
|
|
||||||
|
|
||||||
|
def get_index_bounds(self, index):
|
||||||
|
"Returns a tuple with (start, end) of the wanted result"
|
||||||
|
return self.index[index]
|
||||||
|
|
||||||
|
def uses_statistics(self):
|
||||||
|
return False
|
||||||
|
|
||||||
|
def write_to_csv(self, destination=sys.stdout, delimiter=" "):
|
||||||
|
"""
|
||||||
|
writes the data to a file or to sys.stdout
|
||||||
|
destination can be a file or a filename
|
||||||
|
suitable for further processing
|
||||||
|
"""
|
||||||
|
# write sorted
|
||||||
|
the_destination=destination
|
||||||
|
if type(destination) in types.StringTypes:
|
||||||
|
the_destination=file(destination, "w")
|
||||||
|
|
||||||
|
the_destination.write("# adc_result\n")
|
||||||
|
the_destination.write("# t y0 y1 ...\n")
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
xdata=self.get_xdata()
|
||||||
|
ch_no=self.get_number_of_channels()
|
||||||
|
ydata=map(self.get_ydata, xrange(ch_no))
|
||||||
|
#yerr=map(self.get_yerr, xrange(ch_no))
|
||||||
|
for i in xrange(len(xdata)):
|
||||||
|
the_destination.write("%e"%xdata[i])
|
||||||
|
for j in xrange(ch_no):
|
||||||
|
the_destination.write("%s%e"%(delimiter, ydata[j][i]))
|
||||||
|
the_destination.write("\n")
|
||||||
|
the_destination=None
|
||||||
|
xdata=ydata=None
|
||||||
|
finally:
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
def write_to_simpson(self, destination=sys.stdout, delimiter=" "):
|
||||||
|
"""
|
||||||
|
writes the data to a text file or sys.stdout in Simpson format,
|
||||||
|
for further processing with the NMRnotebook software;
|
||||||
|
destination can be a file or a filename
|
||||||
|
"""
|
||||||
|
# write sorted
|
||||||
|
the_destination=destination
|
||||||
|
if type(destination) in types.StringTypes:
|
||||||
|
the_destination=file(destination, "w")
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
xdata=self.get_xdata()
|
||||||
|
the_destination.write("SIMP\n")
|
||||||
|
the_destination.write("%s%i%s"%("NP=", len(xdata), "\n"))
|
||||||
|
the_destination.write("%s%i%s"%("SW=", self.get_sampling_rate(), "\n"))
|
||||||
|
the_destination.write("TYPE=FID\n")
|
||||||
|
the_destination.write("DATA\n")
|
||||||
|
ch_no=self.get_number_of_channels()
|
||||||
|
ydata=map(self.get_ydata, xrange(ch_no))
|
||||||
|
for i in xrange(len(xdata)):
|
||||||
|
for j in xrange(ch_no):
|
||||||
|
the_destination.write("%g%s"%(ydata[j][i], delimiter))
|
||||||
|
the_destination.write("\n")
|
||||||
|
the_destination.write("END\n")
|
||||||
|
the_destination=None
|
||||||
|
xdata=ydata=None
|
||||||
|
finally:
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
def write_to_hdf(self, hdffile, where, name, title, complib=None, complevel=None):
|
||||||
|
accu_group=hdffile.createGroup(where=where,name=name,title=title)
|
||||||
|
accu_group._v_attrs.damaris_type="ADC_Result"
|
||||||
|
if self.contains_data():
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
# save time stamps
|
||||||
|
if "job_date" in dir(self) and self.job_date is not None:
|
||||||
|
accu_group._v_attrs.time="%04d%02d%02d %02d:%02d:%02d.%03d"%(self.job_date.year,
|
||||||
|
self.job_date.month,
|
||||||
|
self.job_date.day,
|
||||||
|
self.job_date.hour,
|
||||||
|
self.job_date.minute,
|
||||||
|
self.job_date.second,
|
||||||
|
self.job_date.microsecond/1000)
|
||||||
|
|
||||||
|
if self.description is not None:
|
||||||
|
for (key,value) in self.description.iteritems():
|
||||||
|
accu_group._v_attrs.__setattr__("description_"+key,str(value))
|
||||||
|
|
||||||
|
# save interval information
|
||||||
|
filter=None
|
||||||
|
if complib is not None:
|
||||||
|
if complevel is None:
|
||||||
|
complevel=9
|
||||||
|
filter=tables.Filters(complevel=complevel,complib=complib,shuffle=1)
|
||||||
|
|
||||||
|
index_table=hdffile.createTable(where=accu_group,
|
||||||
|
name="indices",
|
||||||
|
description={"start": tables.UInt64Col(),
|
||||||
|
"length": tables.UInt64Col(),
|
||||||
|
"start_time": tables.Float64Col(),
|
||||||
|
"dwelltime": tables.Float64Col()},
|
||||||
|
title="indices of adc data intervals",
|
||||||
|
filters=filter,
|
||||||
|
expectedrows=len(self.index))
|
||||||
|
index_table.flavor="numpy"
|
||||||
|
# save channel data
|
||||||
|
new_row=index_table.row
|
||||||
|
for i in xrange(len(self.index)):
|
||||||
|
new_row["start"]=self.index[i][0]
|
||||||
|
new_row["dwelltime"]=1.0/self.sampling_rate
|
||||||
|
new_row["start_time"]=1.0/self.sampling_rate*self.index[i][0]
|
||||||
|
new_row["length"]=self.index[i][1]-self.index[i][0]+1
|
||||||
|
new_row.append()
|
||||||
|
|
||||||
|
index_table.flush()
|
||||||
|
new_row=None
|
||||||
|
index_table=None
|
||||||
|
|
||||||
|
# prepare saving data
|
||||||
|
channel_no=len(self.y)
|
||||||
|
timedata=numpy.empty((len(self.y[0]),channel_no),
|
||||||
|
dtype = "Int32")
|
||||||
|
for ch in xrange(channel_no):
|
||||||
|
timedata[:,ch]=self.get_ydata(ch)
|
||||||
|
|
||||||
|
# save data
|
||||||
|
time_slice_data=None
|
||||||
|
if filter is not None:
|
||||||
|
chunkshape = numpy.shape(timedata)
|
||||||
|
if len(chunkshape) <= 1:
|
||||||
|
chunkshape = (min(chunkshape[0],1024*8),)
|
||||||
|
else:
|
||||||
|
chunkshape = (min(chunkshape[0],1024*8), chunkshape[1])
|
||||||
|
if tables.__version__[0]=="1":
|
||||||
|
time_slice_data=hdffile.createCArray(accu_group,
|
||||||
|
name="adc_data",
|
||||||
|
shape=timedata.shape,
|
||||||
|
atom=tables.Int32Atom(shape=chunkshape,
|
||||||
|
flavor="numpy"),
|
||||||
|
filters=filter,
|
||||||
|
title="adc data")
|
||||||
|
else:
|
||||||
|
time_slice_data=hdffile.createCArray(accu_group,
|
||||||
|
name="adc_data",
|
||||||
|
shape=timedata.shape,
|
||||||
|
chunkshape=chunkshape,
|
||||||
|
atom=tables.Int32Atom(),
|
||||||
|
filters=filter,
|
||||||
|
title="adc data")
|
||||||
|
time_slice_data[:]=timedata
|
||||||
|
else:
|
||||||
|
time_slice_data=hdffile.createArray(accu_group,
|
||||||
|
name="adc_data",
|
||||||
|
object=timedata,
|
||||||
|
title="adc data")
|
||||||
|
|
||||||
|
finally:
|
||||||
|
timedata=None
|
||||||
|
time_slice_data=None
|
||||||
|
accu_group=None
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
# <20>berladen von Operatoren und Built-Ins -------------------------------------------------------
|
||||||
|
|
||||||
|
def __len__(self):
|
||||||
|
"Redefining len(ADC_Result obj), returns the number of samples in one channel and 0 without data"
|
||||||
|
if len(self.y)>0:
|
||||||
|
return len(self.y[0])
|
||||||
|
return 0
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"""
|
||||||
|
writes job meta data and data to string returned
|
||||||
|
"""
|
||||||
|
tmp_string = "Job ID: " + str(self.job_id) + "\n"
|
||||||
|
tmp_string += "Job Date: " + str(self.job_date) + "\n"
|
||||||
|
tmp_string += "Description: " + str(self.description) + "\n"
|
||||||
|
if len(self.y)>0:
|
||||||
|
tmp_string += "Indexes: " + str(self.index) + "\n"
|
||||||
|
tmp_string += "Samples per Channel: " + str(len(self.y[0])) + "\n"
|
||||||
|
tmp_string += "Samplingfrequency: " + str(self.sampling_rate) + "\n"
|
||||||
|
tmp_string += "X: " + repr(self.x) + "\n"
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_string += ("Y(%d): " % i) + repr(self.y[i]) + "\n"
|
||||||
|
|
||||||
|
return tmp_string
|
||||||
|
|
||||||
|
def __add__(self, other):
|
||||||
|
"Redefining self + other (scalar)"
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(self.y[i], dtype="Float64") + other)
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
else:
|
||||||
|
raise ValueError("ValueError: Cannot add \"%s\" to ADC-Result!" % str(other.__class__))
|
||||||
|
|
||||||
|
|
||||||
|
def __radd__(self, other):
|
||||||
|
"Redefining other (scalar) + self"
|
||||||
|
return self.__add__(other)
|
||||||
|
|
||||||
|
|
||||||
|
def __sub__(self, other):
|
||||||
|
"Redefining self - other (scalar)"
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(self.y[i], dtype="Float64") - other)
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
else:
|
||||||
|
raise ValueError("ValueError: Cannot subtract \"%s\" to ADC-Result!") % str(other.__class__)
|
||||||
|
|
||||||
|
|
||||||
|
def __rsub__(self, other):
|
||||||
|
"Redefining other (scalar) - self"
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(other - numpy.array(self.y[i], dtype="Float64"))
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
else:
|
||||||
|
raise ValueError("ValueError: Cannot subtract \"%s\" to ADC-Result!") % str(other.__class__)
|
||||||
|
|
||||||
|
|
||||||
|
def __mul__(self, other):
|
||||||
|
"Redefining self * other (scalar)"
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(self.y[i], dtype="Float64") * other)
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
else:
|
||||||
|
raise ValueError("ValueError: Cannot multiply \"%s\" to ADC-Result!") % str(other.__class__)
|
||||||
|
|
||||||
|
|
||||||
|
def __rmul__(self, other):
|
||||||
|
"Redefining other (scalar) * self"
|
||||||
|
return self.__mul__(other)
|
||||||
|
|
||||||
|
|
||||||
|
def __pow__(self, other):
|
||||||
|
"Redefining self ** other (scalar)"
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(self.y[i], dtype="Float64") ** other)
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
else:
|
||||||
|
raise ValueError("ValueError: Cannot multiply \"%s\" to ADC-Result!") % str(other.__class__)
|
||||||
|
|
||||||
|
|
||||||
|
def __div__(self, other):
|
||||||
|
"Redefining self / other (scalar)"
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(self.y[i], dtype="Float64") / other)
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
else:
|
||||||
|
raise ValueError("ValueError: Cannot multiply \"%s\" to ADC-Result!") % str(other.__class__)
|
||||||
|
|
||||||
|
|
||||||
|
def __rdiv__(self, other):
|
||||||
|
"Redefining other (scalar) / self"
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(other / numpy.array(self.y[i], dtype="Float64"))
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
else:
|
||||||
|
raise ValueError("ValueError: Cannot multiply \"%s\" to ADC-Result!") % str(other.__class__)
|
||||||
|
|
||||||
|
|
||||||
|
def __neg__(self):
|
||||||
|
"Redefining -self"
|
||||||
|
self.lock.acquire()
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(-self.y[i]))
|
||||||
|
|
||||||
|
r = ADC_Result(x = self.x[:], y = tmp_y, index = self.index[:], sampl_freq = self.sampling_rate, desc = self.description, job_id = self.job_id, job_date = self.job_date)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
|
||||||
|
def read_from_hdf(hdf_node):
|
||||||
|
"""
|
||||||
|
read accumulation data from HDF node and return it.
|
||||||
|
"""
|
||||||
|
|
||||||
|
# formal checks first
|
||||||
|
if not isinstance(hdf_node, tables.Group):
|
||||||
|
return None
|
||||||
|
|
||||||
|
if hdf_node._v_attrs.damaris_type!="ADC_Result":
|
||||||
|
return None
|
||||||
|
|
||||||
|
if not (hdf_node.__contains__("indices") and hdf_node.__contains__("adc_data")):
|
||||||
|
return None
|
||||||
|
|
||||||
|
# job id and x,y titles are missing
|
||||||
|
adc=ADC_Result()
|
||||||
|
# populate description dictionary
|
||||||
|
adc.description={}
|
||||||
|
for attrname in hdf_node._v_attrs._v_attrnamesuser:
|
||||||
|
if attrname.startswith("description_"):
|
||||||
|
adc.description[attrname[12:]]=hdf_node._v_attrs.__getattr__(attrname)
|
||||||
|
|
||||||
|
if "time" in dir(hdf_node._v_attrs):
|
||||||
|
timestring=hdf_node._v_attrs.__getattr__("time")
|
||||||
|
adc.job_date=datetime.datetime(int(timestring[:4]), # year
|
||||||
|
int(timestring[4:6]), # month
|
||||||
|
int(timestring[6:8]), # day
|
||||||
|
int(timestring[9:11]), # hour
|
||||||
|
int(timestring[12:14]), # minute
|
||||||
|
int(timestring[15:17]), # second
|
||||||
|
int(timestring[18:21])*1000 # microsecond
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
# start with indices
|
||||||
|
for r in hdf_node.indices.iterrows():
|
||||||
|
adc.index.append((r["start"],r["start"]+r["length"]-1))
|
||||||
|
adc.sampling_rate=1.0/r["dwelltime"]
|
||||||
|
|
||||||
|
# now really belief there are no data
|
||||||
|
if len(adc.index)==0:
|
||||||
|
adc.cont_data=False
|
||||||
|
return adc
|
||||||
|
|
||||||
|
adc.cont_data=True
|
||||||
|
# now do the real data
|
||||||
|
adc_data=hdf_node.adc_data.read()
|
||||||
|
|
||||||
|
adc.x=numpy.arange(adc_data.shape[0], dtype="Float64")/adc.sampling_rate
|
||||||
|
|
||||||
|
for ch in xrange(adc_data.shape[1]):
|
||||||
|
adc.y.append(adc_data[:,ch])
|
||||||
|
|
||||||
|
return adc
|
||||||
824
src/data/Accumulation.py
Normal file
824
src/data/Accumulation.py
Normal file
@ -0,0 +1,824 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class Accumulation #
|
||||||
|
# #
|
||||||
|
# Purpose: Specialised class of Errorable and Drawable #
|
||||||
|
# Contains accumulated ADC-Data #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
from Errorable import Errorable
|
||||||
|
from Drawable import Drawable
|
||||||
|
from DamarisFFT import DamarisFFT
|
||||||
|
from Signalpath import Signalpath
|
||||||
|
import sys
|
||||||
|
import threading
|
||||||
|
import types
|
||||||
|
import tables
|
||||||
|
import numpy
|
||||||
|
import datetime
|
||||||
|
|
||||||
|
class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath):
|
||||||
|
def __init__(self, x = None, y = None, y_2 = None, n = None, index = None, sampl_freq = None, error = False):
|
||||||
|
Errorable.__init__(self)
|
||||||
|
Drawable.__init__(self)
|
||||||
|
|
||||||
|
# Title of this accumulation (plotted in GUI -> look Drawable)
|
||||||
|
self.__title_pattern = "Accumulation: n = %d"
|
||||||
|
|
||||||
|
# Axis-Labels (inherited from Drawable)
|
||||||
|
self.xlabel = "Time (s)"
|
||||||
|
self.ylabel = "Avg. Samples [Digits]"
|
||||||
|
self.lock=threading.RLock()
|
||||||
|
|
||||||
|
self.common_descriptions=None
|
||||||
|
self.time_period=[]
|
||||||
|
|
||||||
|
self.use_error = error
|
||||||
|
|
||||||
|
if self.uses_statistics():
|
||||||
|
if (y_2 is not None):
|
||||||
|
self.y_square = y_2
|
||||||
|
elif (y_2 is None) :
|
||||||
|
self.y_square = []
|
||||||
|
else:
|
||||||
|
raise ValueError("Wrong usage of __init__!")
|
||||||
|
|
||||||
|
|
||||||
|
if (x is None) and (y is None) and (index is None) and (sampl_freq is None) and (n is None):
|
||||||
|
self.sampling_rate = 0
|
||||||
|
|
||||||
|
self.n = 0
|
||||||
|
self.set_title(self.__title_pattern % self.n)
|
||||||
|
|
||||||
|
self.cont_data = False
|
||||||
|
self.index = []
|
||||||
|
self.x = []
|
||||||
|
self.y = []
|
||||||
|
|
||||||
|
elif (x is not None) and (y is not None) and (index is not None) and (sampl_freq is not None) and (n is not None):
|
||||||
|
self.x = x
|
||||||
|
self.y = y
|
||||||
|
self.sampling_rate = sampl_freq
|
||||||
|
|
||||||
|
self.n = n
|
||||||
|
self.set_title(self.__title_pattern % self.n)
|
||||||
|
|
||||||
|
self.index = index
|
||||||
|
self.cont_data = True
|
||||||
|
|
||||||
|
else:
|
||||||
|
raise ValueError("Wrong usage of __init__!")
|
||||||
|
|
||||||
|
|
||||||
|
def get_accu_by_index(self, index):
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
start = self.index[index][0]
|
||||||
|
end = self.index[index][1]
|
||||||
|
except:
|
||||||
|
self.lock.release()
|
||||||
|
raise
|
||||||
|
|
||||||
|
tmp_x = self.x[start:end+1]
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(self.y[i][start:end+1])
|
||||||
|
|
||||||
|
r = Accumulation(x = tmp_x, y = tmp_y, n = self.n, index = [(0,len(tmp_y[0])-1)], sampl_freq = self.sampling_rate, error = self.use_error)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
def get_ysquare(self, channel):
|
||||||
|
if self.uses_statistics():
|
||||||
|
try:
|
||||||
|
return self.y_square[channel]
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
else: return None
|
||||||
|
|
||||||
|
def contains_data(self):
|
||||||
|
return self.cont_data
|
||||||
|
|
||||||
|
|
||||||
|
def get_sampling_rate(self):
|
||||||
|
"Returns the samplingfrequency"
|
||||||
|
return self.sampling_rate + 0
|
||||||
|
|
||||||
|
|
||||||
|
def get_index_bounds(self, index):
|
||||||
|
"Returns a tuple with (start, end) of the wanted result"
|
||||||
|
return self.index[index]
|
||||||
|
|
||||||
|
|
||||||
|
def uses_statistics(self):
|
||||||
|
return self.use_error
|
||||||
|
|
||||||
|
# Schnittstellen nach Außen --------------------------------------------------------------------
|
||||||
|
|
||||||
|
def get_yerr(self, channel):
|
||||||
|
"""
|
||||||
|
return error (std.dev/sqrt(n)) of mean
|
||||||
|
"""
|
||||||
|
|
||||||
|
if not self.uses_statistics(): return numpy.zeros((len(self.y[0]),),dtype="Float64")
|
||||||
|
if not self.contains_data(): return []
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
if self.n < 2:
|
||||||
|
retval=numpy.zeros((len(self.y[0]),),dtype="Float64")
|
||||||
|
self.lock.release()
|
||||||
|
return retval
|
||||||
|
try:
|
||||||
|
variance_over_n = (self.y_square[channel] - (self.y[channel]**2 / float(self.n)))/float((self.n-1)*self.n)
|
||||||
|
except IndexError:
|
||||||
|
print "Warning Accumulation.get_ydata(channel): Channel index does not exist."
|
||||||
|
variance_over_n = numpy.zeros((len(self.y[0]),), dtype="Float64")
|
||||||
|
self.lock.release()
|
||||||
|
# sample standard deviation / sqrt(n)
|
||||||
|
return numpy.nan_to_num(numpy.sqrt(variance_over_n))
|
||||||
|
|
||||||
|
def get_ydata(self, channel):
|
||||||
|
"""
|
||||||
|
return mean data
|
||||||
|
"""
|
||||||
|
|
||||||
|
if not self.contains_data(): return []
|
||||||
|
self.lock.acquire()
|
||||||
|
|
||||||
|
try:
|
||||||
|
tmp_y = self.y[channel] / self.n
|
||||||
|
except IndexError:
|
||||||
|
print "Warning Accumulation.get_ydata(channel): Channel index does not exist."
|
||||||
|
tmp_y = numpy.zeros((len(self.y[0]),), dtype="Float64")
|
||||||
|
|
||||||
|
self.lock.release()
|
||||||
|
return tmp_y
|
||||||
|
|
||||||
|
|
||||||
|
def get_ymin(self):
|
||||||
|
|
||||||
|
if not self.contains_data(): return 0
|
||||||
|
|
||||||
|
tmp_min = []
|
||||||
|
self.lock.acquire()
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_min.append(self.get_ydata(i).min())
|
||||||
|
|
||||||
|
if self.uses_statistics() and self.ready_for_drawing_error():
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_min.append((self.get_ydata(i) - self.get_yerr(i)).min())
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
return min(tmp_min)
|
||||||
|
|
||||||
|
|
||||||
|
def get_ymax(self):
|
||||||
|
|
||||||
|
if not self.contains_data(): return 0
|
||||||
|
|
||||||
|
tmp_max = []
|
||||||
|
self.lock.acquire()
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_max.append(self.get_ydata(i).max())
|
||||||
|
|
||||||
|
if self.uses_statistics() and self.ready_for_drawing_error():
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_max.append((self.get_ydata(i) + self.get_yerr(i)).max())
|
||||||
|
self.lock.release()
|
||||||
|
return max(tmp_max)
|
||||||
|
|
||||||
|
def get_job_id(self):
|
||||||
|
return None
|
||||||
|
|
||||||
|
def write_to_csv(self, destination=sys.stdout, delimiter=" "):
|
||||||
|
"""
|
||||||
|
writes the data to a file or to sys.stdout
|
||||||
|
destination can be a file or a filename
|
||||||
|
suitable for further processing
|
||||||
|
"""
|
||||||
|
|
||||||
|
the_destination=destination
|
||||||
|
if type(destination) in types.StringTypes:
|
||||||
|
the_destination=file(destination, "w")
|
||||||
|
|
||||||
|
the_destination.write("# accumulation %d\n"%self.n)
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
if self.common_descriptions is not None:
|
||||||
|
for (key,value) in self.common_descriptions.iteritems():
|
||||||
|
the_destination.write("# %s : %s\n"%(key, str(value)))
|
||||||
|
the_destination.write("# t")
|
||||||
|
ch_no=self.get_number_of_channels()
|
||||||
|
if self.use_error:
|
||||||
|
for i in xrange(ch_no): the_destination.write(" ch%d_mean ch%d_err"%(i,i))
|
||||||
|
else:
|
||||||
|
for i in xrange(ch_no): the_destination.write(" ch%d_mean"%i)
|
||||||
|
the_destination.write("\n")
|
||||||
|
xdata=self.get_xdata()
|
||||||
|
ydata=map(self.get_ydata, xrange(ch_no))
|
||||||
|
yerr=None
|
||||||
|
if self.use_error:
|
||||||
|
yerr=map(self.get_yerr, xrange(ch_no))
|
||||||
|
for i in xrange(len(xdata)):
|
||||||
|
the_destination.write("%e"%xdata[i])
|
||||||
|
for j in xrange(ch_no):
|
||||||
|
if self.use_error:
|
||||||
|
the_destination.write("%s%e%s%e"%(delimiter, ydata[j][i], delimiter, yerr[j][i]))
|
||||||
|
else:
|
||||||
|
the_destination.write("%s%e"%(delimiter,ydata[j][i]))
|
||||||
|
the_destination.write("\n")
|
||||||
|
the_destination=None
|
||||||
|
xdata=yerr=ydata=None
|
||||||
|
finally:
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
def write_to_simpson(self, destination=sys.stdout, delimiter=" "):
|
||||||
|
"""
|
||||||
|
writes the data to a text file or sys.stdout in Simpson format,
|
||||||
|
for further processing with the NMRnotebook software;
|
||||||
|
destination can be a file or a filename
|
||||||
|
"""
|
||||||
|
# write sorted
|
||||||
|
the_destination=destination
|
||||||
|
if type(destination) in types.StringTypes:
|
||||||
|
the_destination=file(destination, "w")
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
xdata=self.get_xdata()
|
||||||
|
the_destination.write("SIMP\n")
|
||||||
|
the_destination.write("%s%i%s"%("NP=", len(xdata), "\n"))
|
||||||
|
the_destination.write("%s%i%s"%("SW=", self.get_sampling_rate(), "\n"))
|
||||||
|
the_destination.write("TYPE=FID\n")
|
||||||
|
the_destination.write("DATA\n")
|
||||||
|
ch_no=self.get_number_of_channels()
|
||||||
|
ydata=map(self.get_ydata, xrange(ch_no))
|
||||||
|
for i in xrange(len(xdata)):
|
||||||
|
for j in xrange(ch_no):
|
||||||
|
the_destination.write("%g%s"%(ydata[j][i], delimiter))
|
||||||
|
the_destination.write("\n")
|
||||||
|
the_destination.write("END\n")
|
||||||
|
the_destination=None
|
||||||
|
xdata=ydata=None
|
||||||
|
finally:
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
def write_to_hdf(self, hdffile, where, name, title, complib=None, complevel=None):
|
||||||
|
accu_group=hdffile.createGroup(where=where,name=name,title=title)
|
||||||
|
accu_group._v_attrs.damaris_type="Accumulation"
|
||||||
|
if self.contains_data():
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
# save time stamps
|
||||||
|
if self.time_period is not None and len(self.time_period)>0:
|
||||||
|
accu_group._v_attrs.earliest_time="%04d%02d%02d %02d:%02d:%02d.%03d"%(self.time_period[0].year,
|
||||||
|
self.time_period[0].month,
|
||||||
|
self.time_period[0].day,
|
||||||
|
self.time_period[0].hour,
|
||||||
|
self.time_period[0].minute,
|
||||||
|
self.time_period[0].second,
|
||||||
|
self.time_period[0].microsecond/1000)
|
||||||
|
accu_group._v_attrs.oldest_time="%04d%02d%02d %02d:%02d:%02d.%03d"%(self.time_period[1].year,
|
||||||
|
self.time_period[1].month,
|
||||||
|
self.time_period[1].day,
|
||||||
|
self.time_period[1].hour,
|
||||||
|
self.time_period[1].minute,
|
||||||
|
self.time_period[1].second,
|
||||||
|
self.time_period[1].microsecond/1000)
|
||||||
|
if self.common_descriptions is not None:
|
||||||
|
for (key,value) in self.common_descriptions.iteritems():
|
||||||
|
accu_group._v_attrs.__setattr__("description_"+key,str(value))
|
||||||
|
|
||||||
|
# save interval information
|
||||||
|
filter=None
|
||||||
|
if complib is not None:
|
||||||
|
if complevel is None:
|
||||||
|
complevel=9
|
||||||
|
filter=tables.Filters(complevel=complevel,complib=complib,shuffle=1)
|
||||||
|
|
||||||
|
# tried compression filter, but no effect...
|
||||||
|
index_table=hdffile.createTable(where=accu_group,
|
||||||
|
name="indices",
|
||||||
|
description={"start": tables.UInt64Col(),
|
||||||
|
"length": tables.UInt64Col(),
|
||||||
|
"start_time": tables.Float64Col(),
|
||||||
|
"dwelltime": tables.Float64Col(),
|
||||||
|
"number": tables.UInt64Col()},
|
||||||
|
title="indices of adc data intervals",
|
||||||
|
filters=filter,
|
||||||
|
expectedrows=len(self.index))
|
||||||
|
index_table.flavor="numpy"
|
||||||
|
# save interval data
|
||||||
|
new_row=index_table.row
|
||||||
|
for i in xrange(len(self.index)):
|
||||||
|
new_row["start"]=self.index[i][0]
|
||||||
|
new_row["dwelltime"]=1.0/self.sampling_rate
|
||||||
|
new_row["start_time"]=1.0/self.sampling_rate*self.index[i][0]
|
||||||
|
new_row["length"]=self.index[i][1]-self.index[i][0]+1
|
||||||
|
new_row["number"]=self.n
|
||||||
|
new_row.append()
|
||||||
|
|
||||||
|
index_table.flush()
|
||||||
|
new_row=None
|
||||||
|
index_table=None
|
||||||
|
|
||||||
|
# prepare saving data
|
||||||
|
channel_no=len(self.y)
|
||||||
|
timedata=numpy.empty((len(self.y[0]),channel_no*2), dtype = "Float64")
|
||||||
|
for ch in xrange(channel_no):
|
||||||
|
timedata[:,ch*2]=self.get_ydata(ch)
|
||||||
|
if self.uses_statistics():
|
||||||
|
timedata[:,ch*2+1]=self.get_yerr(ch)
|
||||||
|
else:
|
||||||
|
timedata[:,ch*2+1]=numpy.zeros((len(self.y[0]),),dtype = "Float64")
|
||||||
|
|
||||||
|
# save data
|
||||||
|
time_slice_data=None
|
||||||
|
if filter is not None:
|
||||||
|
chunkshape=timedata.shape
|
||||||
|
if len(chunkshape) <= 1:
|
||||||
|
chunkshape = (min(chunkshape[0],1024*8),)
|
||||||
|
else:
|
||||||
|
chunkshape = (min(chunkshape[0],1024*8), chunkshape[1])
|
||||||
|
if tables.__version__[0]=="1":
|
||||||
|
time_slice_data=hdffile.createCArray(accu_group,
|
||||||
|
name="accu_data",
|
||||||
|
shape=timedata.shape,
|
||||||
|
atom=tables.Float64Atom(shape=chunkshape,
|
||||||
|
flavor="numpy"),
|
||||||
|
filters=filter,
|
||||||
|
title="accu data")
|
||||||
|
else:
|
||||||
|
time_slice_data=hdffile.createCArray(accu_group,
|
||||||
|
name="accu_data",
|
||||||
|
shape=timedata.shape,
|
||||||
|
chunkshape=chunkshape,
|
||||||
|
atom=tables.Float64Atom(),
|
||||||
|
filters=filter,
|
||||||
|
title="accu data")
|
||||||
|
|
||||||
|
time_slice_data[:]=timedata
|
||||||
|
else:
|
||||||
|
time_slice_data=hdffile.createArray(accu_group,
|
||||||
|
name="accu_data",
|
||||||
|
object=timedata,
|
||||||
|
title="accu data")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
finally:
|
||||||
|
time_slice_data=None
|
||||||
|
accu_group=None
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
# / Schnittstellen nach Außen ------------------------------------------------------------------
|
||||||
|
|
||||||
|
# Überladen von Operatoren ---------------------------------------------------------------------
|
||||||
|
|
||||||
|
def __len__(self):
|
||||||
|
"""
|
||||||
|
return number of samples per channel, 0 if empty
|
||||||
|
"""
|
||||||
|
if len(self.y)>0:
|
||||||
|
return len(self.y[0])
|
||||||
|
return 0
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
"Redefining repr(Accumulation)"
|
||||||
|
|
||||||
|
if not self.contains_data(): return "Empty"
|
||||||
|
|
||||||
|
tmp_string = "X: " + repr(self.x) + "\n"
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_string += ("Y(%d): " % i) + repr(self.y[i]) + "\n"
|
||||||
|
if self.uses_statistics(): tmp_string += "y_square(%d): " % i + str(self.y_square[i]) + "\n"
|
||||||
|
|
||||||
|
tmp_string += "Indexes: " + str(self.index) + "\n"
|
||||||
|
|
||||||
|
tmp_string += "Samples per Channel: " + str(len(self.y[0])) + "\n"
|
||||||
|
tmp_string += "Samplingfrequency: " + str(self.sampling_rate) + "\n"
|
||||||
|
|
||||||
|
tmp_string += "n: " + str(self.n)
|
||||||
|
|
||||||
|
return tmp_string
|
||||||
|
|
||||||
|
|
||||||
|
def __add__(self, other):
|
||||||
|
"Redefining self + other"
|
||||||
|
# Float or int
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
if not self.contains_data(): raise ValueError("Accumulation: You cant add integers/floats to an empty accumulation")
|
||||||
|
else:
|
||||||
|
|
||||||
|
tmp_y = []
|
||||||
|
tmp_ysquare = []
|
||||||
|
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
# Dont change errors and mean value
|
||||||
|
if self.uses_statistics(): tmp_ysquare.append(self.y_square[i] + ( (2*self.y[i]*other) + ((other**2)*self.n) ))
|
||||||
|
tmp_y.append(self.y[i] + (other*self.n))
|
||||||
|
|
||||||
|
if self.uses_statistics():
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, y_2 = tmp_ysquare, n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = self.use_error)
|
||||||
|
else:
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = self.use_error)
|
||||||
|
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
# ADC_Result
|
||||||
|
elif str(other.__class__) == "damaris.data.ADC_Result.ADC_Result":
|
||||||
|
|
||||||
|
# Other empty (return)
|
||||||
|
# todo: this is seems to be bugy!!!! (Achim)
|
||||||
|
if not other.contains_data(): return
|
||||||
|
|
||||||
|
# Self empty (copy)
|
||||||
|
if not self.contains_data():
|
||||||
|
|
||||||
|
tmp_y = []
|
||||||
|
tmp_ysquare = []
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
|
||||||
|
for i in range(other.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(other.y[i], dtype="Float64"))
|
||||||
|
if self.uses_statistics(): tmp_ysquare.append(tmp_y[i] ** 2)
|
||||||
|
|
||||||
|
|
||||||
|
if self.uses_statistics():
|
||||||
|
r = Accumulation(x = numpy.array(other.x, dtype="Float64"), y = tmp_y, y_2 = tmp_ysquare, n = 1, index = other.index, sampl_freq = other.sampling_rate, error = True)
|
||||||
|
else:
|
||||||
|
r = Accumulation(x = numpy.array(other.x, dtype="Float64"), y = tmp_y, index = other.index, sampl_freq = other.sampling_rate, n = 1, error = False)
|
||||||
|
r.time_period=[other.job_date,other.job_date]
|
||||||
|
r.common_descriptions=other.description.copy()
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
# Other and self not empty (self + other)
|
||||||
|
else:
|
||||||
|
self.lock.acquire()
|
||||||
|
|
||||||
|
if self.sampling_rate != other.get_sampling_rate(): raise ValueError("Accumulation: You cant add ADC-Results with diffrent sampling-rates")
|
||||||
|
if len(self.y[0]) != len(other): raise ValueError("Accumulation: You cant add ADC-Results with diffrent number of samples")
|
||||||
|
if len(self.y) != other.get_number_of_channels(): raise ValueError("Accumulation: You cant add ADC-Results with diffrent number of channels")
|
||||||
|
for i in range(len(self.index)):
|
||||||
|
if self.index[i] != other.get_index_bounds(i): raise ValueError("Accumulation: You cant add ADC-Results with diffrent indexing")
|
||||||
|
|
||||||
|
tmp_y = []
|
||||||
|
tmp_ysquare = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(self.y[i] + other.y[i])
|
||||||
|
if self.uses_statistics(): tmp_ysquare.append(self.y_square[i] + (numpy.array(other.y[i], dtype="Float64") ** 2))
|
||||||
|
|
||||||
|
if self.uses_statistics():
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, y_2 = tmp_ysquare, n = self.n + 1, index = self.index, sampl_freq = self.sampling_rate, error = True)
|
||||||
|
else:
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, n = self.n + 1, index = self.index, sampl_freq = self.sampling_rate, error = False)
|
||||||
|
r.time_period=[min(self.time_period[0],other.job_date),
|
||||||
|
max(self.time_period[1],other.job_date)]
|
||||||
|
if self.common_descriptions is not None:
|
||||||
|
r.common_descriptions={}
|
||||||
|
for key in self.common_descriptions.keys():
|
||||||
|
if (key in other.description and self.common_descriptions[key]==other.description[key]):
|
||||||
|
r.common_descriptions[key]=value
|
||||||
|
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
# Accumulation
|
||||||
|
elif str(other.__class__) == "damaris.data.Accumulation.Accumulation":
|
||||||
|
|
||||||
|
# Other empty (return)
|
||||||
|
if not other.contains_data(): return
|
||||||
|
|
||||||
|
# Self empty (copy)
|
||||||
|
if not self.contains_data():
|
||||||
|
|
||||||
|
tmp_y = []
|
||||||
|
tmp_ysquare = []
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
|
||||||
|
if self.uses_statistics():
|
||||||
|
r = Accumulation(x = numpy.array(other.x, dtype="Float64"), y = tmp_y, y_2 = tmp_ysquare, n = other.n, index = other.index, sampl_freq = other.sampling_rate, error = True)
|
||||||
|
else:
|
||||||
|
r = Accumulation(x = numpy.array(other.x, dtype="Float64"), y = tmp_y, n = other.n, index = other.index, sampl_freq = other.sampling_rate, error = False)
|
||||||
|
for i in range(other.get_number_of_channels()):
|
||||||
|
tmp_y.append(other.y[i])
|
||||||
|
tmp_ysquare.append(other.y_square[i])
|
||||||
|
r.time_period=other.time_period[:]
|
||||||
|
if other.common_descriptions is not None:
|
||||||
|
r.common_descriptions=othter.common_descriptions.copy()
|
||||||
|
else:
|
||||||
|
r.common_descriptions=None
|
||||||
|
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
# Other and self not empty (self + other)
|
||||||
|
else:
|
||||||
|
self.lock.acquire()
|
||||||
|
|
||||||
|
if self.sampling_rate != other.get_sampling_rate(): raise ValueError("Accumulation: You cant add accumulations with diffrent sampling-rates")
|
||||||
|
if len(self.y[0]) != len(other): raise ValueError("Accumulation: You cant add accumulations with diffrent number of samples")
|
||||||
|
if len(self.y) != other.get_number_of_channels(): raise ValueError("Accumulation: You cant add accumulations with diffrent number of channels")
|
||||||
|
for i in range(len(self.index)):
|
||||||
|
if self.index[i] != other.get_index_bounds(i): raise ValueError("Accumulation: You cant add accumulations with diffrent indexing")
|
||||||
|
if self.uses_statistics() and not other.uses_statistics(): raise ValueError("Accumulation: You cant add non-error accumulations to accumulations with error")
|
||||||
|
|
||||||
|
tmp_y = []
|
||||||
|
tmp_ysquare = []
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(self.y[i] + other.y[i])
|
||||||
|
tmp_ysquare.append(self.y_square[i] + other.y_square[i])
|
||||||
|
|
||||||
|
if self.uses_statistics():
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, y_2 = tmp_ysquare, n = other.n + self.n, index = self.index, sampl_freq = self.sampling_rate, error = True)
|
||||||
|
else:
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, n = other.n + self.n, index = self.index, sampl_freq = self.sampling_rate, error = False)
|
||||||
|
|
||||||
|
r.time_period=[min(self.time_period[0],other.time_period[0]),
|
||||||
|
max(self.time_period[1],other.time_period[1])]
|
||||||
|
r.common_descriptions={}
|
||||||
|
if self.common_descriptions is not None and other.common_descriptions is not None:
|
||||||
|
for key in self.common_descriptions.keys():
|
||||||
|
if (key in other.common_descriptions and
|
||||||
|
self.common_descriptions[key]==other.common_descriptions[key]):
|
||||||
|
r.common_descriptions[key]=value
|
||||||
|
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
|
||||||
|
def __radd__(self, other):
|
||||||
|
"Redefining other + self"
|
||||||
|
return self.__add__(other)
|
||||||
|
|
||||||
|
|
||||||
|
def __sub__(self, other):
|
||||||
|
"Redefining self - other"
|
||||||
|
return self.__add__(-other)
|
||||||
|
|
||||||
|
|
||||||
|
def __rsub__(self, other):
|
||||||
|
"Redefining other - self"
|
||||||
|
return self.__neg__(self.__add__(-other))
|
||||||
|
|
||||||
|
|
||||||
|
def __iadd__(self, other):
|
||||||
|
"Redefining self += other"
|
||||||
|
# Float or int
|
||||||
|
if isinstance(other, types.IntType) or isinstance(other, types.FloatType):
|
||||||
|
if not self.contains_data(): raise ValueError("Accumulation: You cant add integers/floats to an empty accumulation")
|
||||||
|
else:
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
#Dont change errors and mean value
|
||||||
|
if self.uses_statistics(): self.y_square[i] += (2*self.y[i]*other) + ((other**2)*self.n)
|
||||||
|
self.y[i] += other*self.n
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
return self
|
||||||
|
|
||||||
|
# ADC_Result
|
||||||
|
elif str(other.__class__) == "damaris.data.ADC_Result.ADC_Result":
|
||||||
|
|
||||||
|
# Other empty (return)
|
||||||
|
if not other.contains_data(): return self
|
||||||
|
|
||||||
|
# Self empty (copy)
|
||||||
|
if not self.contains_data():
|
||||||
|
self.lock.acquire()
|
||||||
|
self.n += 1
|
||||||
|
self.index = other.index[0:]
|
||||||
|
self.sampling_rate = other.sampling_rate
|
||||||
|
self.x = numpy.array(other.x, dtype="Float64")
|
||||||
|
self.cont_data = True
|
||||||
|
|
||||||
|
for i in range(other.get_number_of_channels()):
|
||||||
|
self.y.append(numpy.array(other.y[i], dtype="Float64"))
|
||||||
|
if self.uses_statistics(): self.y_square.append(self.y[i] ** 2)
|
||||||
|
|
||||||
|
self.set_title(self.__title_pattern % self.n)
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
self.time_period=[other.job_date,other.job_date]
|
||||||
|
self.common_descriptions=other.description.copy()
|
||||||
|
|
||||||
|
return self
|
||||||
|
|
||||||
|
|
||||||
|
# Other and self not empty (self + other)
|
||||||
|
else:
|
||||||
|
self.lock.acquire()
|
||||||
|
|
||||||
|
if self.sampling_rate != other.get_sampling_rate(): raise ValueError("Accumulation: You cant add ADC-Results with diffrent sampling-rates")
|
||||||
|
if len(self.y[0]) != len(other): raise ValueError("Accumulation: You cant add ADC-Results with diffrent number of samples")
|
||||||
|
if len(self.y) != other.get_number_of_channels(): raise ValueError("Accumulation: You cant add ADC-Results with diffrent number of channels")
|
||||||
|
for i in range(len(self.index)):
|
||||||
|
if self.index[i] != other.get_index_bounds(i): raise ValueError("Accumulation: You cant add ADC-Results with diffrent indexing")
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
self.y[i] += other.y[i]
|
||||||
|
if self.uses_statistics(): self.y_square[i] += numpy.array(other.y[i], dtype="Float64") ** 2
|
||||||
|
|
||||||
|
self.n += 1
|
||||||
|
self.time_period=[min(self.time_period[0],other.job_date),
|
||||||
|
max(self.time_period[1],other.job_date)]
|
||||||
|
if self.common_descriptions is not None:
|
||||||
|
for key in self.common_descriptions.keys():
|
||||||
|
if not (key in other.description and self.common_descriptions[key]==other.description[key]):
|
||||||
|
del self.common_descriptions[key]
|
||||||
|
|
||||||
|
self.set_title(self.__title_pattern % self.n)
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
return self
|
||||||
|
|
||||||
|
# Accumulation
|
||||||
|
elif str(other.__class__) == "damaris.data.Accumulation.Accumulation":
|
||||||
|
|
||||||
|
# Other empty (return)
|
||||||
|
if not other.contains_data(): return
|
||||||
|
|
||||||
|
# Self empty (copy)
|
||||||
|
if not self.contains_data():
|
||||||
|
if self.uses_statistics() and not other.uses_statistics(): raise ValueError("Accumulation: You cant add non-error accumulations to accumulations with error")
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
self.n += other.n
|
||||||
|
self.index = other.index[0:]
|
||||||
|
self.sampling_rate = other.sampling_rate
|
||||||
|
self.x = numpy.array(other.x, dtype="Float64")
|
||||||
|
self.cont_data = True
|
||||||
|
|
||||||
|
for i in range(other.get_number_of_channels()):
|
||||||
|
self.y.append(numpy.array(other.y[i], dtype="Float64"))
|
||||||
|
if self.uses_statistics(): self.y_square.append(self.y[i] ** 2)
|
||||||
|
|
||||||
|
self.set_title(self.__title_pattern % self.n)
|
||||||
|
self.common_descriptions=other.common_desriptions.copy()
|
||||||
|
self.time_period=other.time_period[:]
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
return self
|
||||||
|
|
||||||
|
# Other and self not empty (self + other)
|
||||||
|
else:
|
||||||
|
self.lock.acquire()
|
||||||
|
if self.sampling_rate != other.get_sampling_rate(): raise ValueError("Accumulation: You cant add accumulations with diffrent sampling-rates")
|
||||||
|
if len(self.y[0]) != len(other): raise ValueError("Accumulation: You cant add accumulations with diffrent number of samples")
|
||||||
|
if len(self.y) != other.get_number_of_channels(): raise ValueError("Accumulation: You cant add accumulations with diffrent number of channels")
|
||||||
|
for i in range(len(self.index)):
|
||||||
|
if self.index[i] != other.get_index_bounds(i): raise ValueError("Accumulation: You cant add accumulations with diffrent indexing")
|
||||||
|
if self.uses_statistics() and not other.uses_statistics(): raise ValueError("Accumulation: You cant add non-error accumulations to accumulations with error")
|
||||||
|
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
self.y[i] += other.y[i]
|
||||||
|
if self.uses_statistics(): self.y_square[i] += other.y_square[i]
|
||||||
|
|
||||||
|
self.n += other.n
|
||||||
|
self.time_period=[min(self.time_period[0],other.time_period[0]),
|
||||||
|
max(self.time_period[1],other.time_period[1])]
|
||||||
|
if self.common_descriptions is not None and other.common_descriptions is not None:
|
||||||
|
for key in self.common_descriptions.keys():
|
||||||
|
if not (key in other.description and
|
||||||
|
self.common_descriptions[key]==other.common_descriptions[key]):
|
||||||
|
del self.common_descriptions[key]
|
||||||
|
|
||||||
|
self.set_title(self.__title_pattern % self.n)
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
return self
|
||||||
|
|
||||||
|
elif other is None:
|
||||||
|
# Convenience: ignore add of None
|
||||||
|
return self
|
||||||
|
else:
|
||||||
|
raise ValueError("can not add "+repr(type(other))+" to Accumulation")
|
||||||
|
|
||||||
|
|
||||||
|
def __isub__(self, other):
|
||||||
|
"Redefining self -= other"
|
||||||
|
return self.__iadd__(-other)
|
||||||
|
|
||||||
|
|
||||||
|
def __neg__(self):
|
||||||
|
"Redefining -self"
|
||||||
|
|
||||||
|
if not self.contains_data(): return
|
||||||
|
|
||||||
|
tmp_y = []
|
||||||
|
|
||||||
|
self.lock.acquire()
|
||||||
|
for i in range(self.get_number_of_channels()):
|
||||||
|
tmp_y.append(numpy.array(-self.y[i], dtype="Float64"))
|
||||||
|
|
||||||
|
if self.uses_statistics():
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, y_2 = numpy.array(self.y_square), n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = True)
|
||||||
|
else:
|
||||||
|
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = False)
|
||||||
|
self.lock.release()
|
||||||
|
return r
|
||||||
|
|
||||||
|
|
||||||
|
def read_from_hdf(hdf_node):
|
||||||
|
"""
|
||||||
|
read accumulation data from HDF node and return it.
|
||||||
|
"""
|
||||||
|
|
||||||
|
# formal checks first
|
||||||
|
if not isinstance(hdf_node, tables.Group):
|
||||||
|
return None
|
||||||
|
|
||||||
|
if hdf_node._v_attrs.damaris_type!="Accumulation":
|
||||||
|
return None
|
||||||
|
|
||||||
|
if not (hdf_node.__contains__("indices") and hdf_node.__contains__("accu_data")):
|
||||||
|
print "no accu data"
|
||||||
|
return None
|
||||||
|
|
||||||
|
accu=Accumulation()
|
||||||
|
|
||||||
|
# populate description dictionary
|
||||||
|
accu.common_descriptions={}
|
||||||
|
for attrname in hdf_node._v_attrs._v_attrnamesuser:
|
||||||
|
if attrname.startswith("description_"):
|
||||||
|
accu.common_descriptions[attrname[12:]]=hdf_node._v_attrs.__getattr__(attrname)
|
||||||
|
|
||||||
|
eariliest_time=None
|
||||||
|
if "earliest_time" in dir(hdf_node._v_attrs):
|
||||||
|
timestring=hdf_node._v_attrs.__getattr__("earliest_time")
|
||||||
|
earliest_time=datetime.datetime(int(timestring[:4]), # year
|
||||||
|
int(timestring[4:6]), # month
|
||||||
|
int(timestring[6:8]), # day
|
||||||
|
int(timestring[9:11]), # hour
|
||||||
|
int(timestring[12:14]), # minute
|
||||||
|
int(timestring[15:17]), # second
|
||||||
|
int(timestring[18:21])*1000 # microsecond
|
||||||
|
)
|
||||||
|
|
||||||
|
oldest_time=None
|
||||||
|
if "oldest_time" in dir(hdf_node._v_attrs):
|
||||||
|
timestring=hdf_node._v_attrs.__getattr__("oldest_time")
|
||||||
|
oldest_time=datetime.datetime(int(timestring[:4]), # year
|
||||||
|
int(timestring[4:6]), # month
|
||||||
|
int(timestring[6:8]), # day
|
||||||
|
int(timestring[9:11]), # hour
|
||||||
|
int(timestring[12:14]), # minute
|
||||||
|
int(timestring[15:17]), # second
|
||||||
|
int(timestring[18:21])*1000 # microsecond
|
||||||
|
)
|
||||||
|
|
||||||
|
if oldest_time is None or earliest_time is None:
|
||||||
|
accu.time_period=None
|
||||||
|
if len(accu.common_descriptions)==0:
|
||||||
|
# no accus inside, so no common description expected
|
||||||
|
accu.common_descriptions=None
|
||||||
|
accu.cont_data=False
|
||||||
|
else:
|
||||||
|
accu.time_period=[oldest_time, earliest_time]
|
||||||
|
accu.cont_data=True
|
||||||
|
|
||||||
|
# start with indices
|
||||||
|
for r in hdf_node.indices.iterrows():
|
||||||
|
accu.index.append((r["start"],r["start"]+r["length"]-1))
|
||||||
|
accu.n=r["number"]
|
||||||
|
accu.sampling_rate=1.0/r["dwelltime"]
|
||||||
|
|
||||||
|
# now really belief there are no data
|
||||||
|
if len(accu.index)==0 or accu.n==0:
|
||||||
|
accu.cont_data=False
|
||||||
|
return accu
|
||||||
|
|
||||||
|
# now do the real data
|
||||||
|
accu_data=hdf_node.accu_data.read()
|
||||||
|
|
||||||
|
accu.x=numpy.arange(accu_data.shape[0], dtype="Float64")/accu.sampling_rate
|
||||||
|
# assume error information, todo: save this information explicitly
|
||||||
|
accu.y_square=[]
|
||||||
|
accu.use_error=False
|
||||||
|
|
||||||
|
for ch in xrange(accu_data.shape[1]/2):
|
||||||
|
accu.y.append(accu_data[:,ch*2]*accu.n)
|
||||||
|
if accu.n<2 or numpy.all(accu_data[:,ch*2+1]==0.0):
|
||||||
|
accu.y_square.append(numpy.zeros((accu_data.shape[0]) ,dtype="Float64"))
|
||||||
|
else:
|
||||||
|
accu.use_error=True
|
||||||
|
accu.y_square.append((accu_data[:,ch*2+1]**2)*float((accu.n-1.0)*accu.n)+(accu_data[:,ch*2]**2)*accu.n)
|
||||||
|
|
||||||
|
if not accu.use_error:
|
||||||
|
del accu.y_square
|
||||||
|
|
||||||
|
return accu
|
||||||
54
src/data/Config_Result.py
Normal file
54
src/data/Config_Result.py
Normal file
@ -0,0 +1,54 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
from Resultable import Resultable
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class Error_Result #
|
||||||
|
# #
|
||||||
|
# Purpose: Specialised class of Resultable #
|
||||||
|
# Contains occured error-messages from the core #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
class Config_Result(Resultable):
|
||||||
|
def __init__(self, config = None, desc = None, job_id = None, job_date = None):
|
||||||
|
Resultable.__init__(self)
|
||||||
|
|
||||||
|
if config is None: self.config = { }
|
||||||
|
if desc is None: self.description = { }
|
||||||
|
self.job_id = job_id
|
||||||
|
self.job_date = job_date
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def get_config_dictionary(self):
|
||||||
|
return self.config
|
||||||
|
|
||||||
|
|
||||||
|
def set_config_dictionary(self, config):
|
||||||
|
self.config = config
|
||||||
|
|
||||||
|
|
||||||
|
def get_config(self, key):
|
||||||
|
if self.config.has_key(key): return self.config[key]
|
||||||
|
else: return None
|
||||||
|
|
||||||
|
|
||||||
|
def set_config(self, key, value):
|
||||||
|
if self.config.has_key(key):
|
||||||
|
print "Warning Config_Result: Key \"%s\" will be overwritten with \"%s\"" % (key, value)
|
||||||
|
|
||||||
|
self.config[key] = value
|
||||||
|
|
||||||
|
|
||||||
|
# Überladen von Operatoren und Built-Ins -------------------------------------------------------
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
return str(self.config)
|
||||||
|
|
||||||
|
|
||||||
|
def __str__(self):
|
||||||
|
return str(self.config)
|
||||||
|
|
||||||
|
|
||||||
211
src/data/DaFFT.py
Normal file
211
src/data/DaFFT.py
Normal file
@ -0,0 +1,211 @@
|
|||||||
|
import warnings
|
||||||
|
# enable warnings in Python 2.7
|
||||||
|
warnings.simplefilter('default')
|
||||||
|
warnings.warn("use of DaFFT is deprecated, please use the methods of Accumulation and ADC_data classes provided by DamarisFFT.", DeprecationWarning)
|
||||||
|
import numpy as N
|
||||||
|
import numpy.fft as F
|
||||||
|
|
||||||
|
class FFT:
|
||||||
|
def __init__(self, one_result):
|
||||||
|
# create copy of one_result and work only on the copy
|
||||||
|
# also extract some informations
|
||||||
|
self.the_result = one_result + 0
|
||||||
|
self.timepoints = N.array(one_result.x)
|
||||||
|
self.sampling_rate = one_result.get_sampling_rate()
|
||||||
|
self.data_points = one_result.get_ydata(0).size
|
||||||
|
self.aquisition_time = self.data_points / float(self.sampling_rate)
|
||||||
|
self.the_result.set_xlabel('Frequency [Hz]')
|
||||||
|
|
||||||
|
def write_n(self, afile):
|
||||||
|
filename = open(afile,'w')
|
||||||
|
filename = open(afile,'a')
|
||||||
|
#print self.the_result.get_description_dictionary()
|
||||||
|
#filename.write('%s'%self.get_description_dictionary())
|
||||||
|
for i in range(self.data_points):
|
||||||
|
filename.write('%e\t%e\t%e\n'%(self.the_result.x[i], self.the_result.y[0][i], self.the_result.y[1][i]))
|
||||||
|
filename.close()
|
||||||
|
return self
|
||||||
|
|
||||||
|
def base_corr(self, cutoff=0.3, show=0):
|
||||||
|
"""
|
||||||
|
Subtracts the mean of the last cutoff % of the timsignal
|
||||||
|
to get rid of the DC part in the FFT and returns the
|
||||||
|
new data.
|
||||||
|
If cutoff is not given, the mean of the last 30% will be
|
||||||
|
subtracted.
|
||||||
|
If show=1 the result is return and not the instance. This allows to plot the baseline corrected signal
|
||||||
|
Example:
|
||||||
|
base_corr(cutoff=0.2, show=1)
|
||||||
|
"""
|
||||||
|
last_points = int(cutoff*self.data_points)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i] - self.the_result.y[i][-last_points:].mean()
|
||||||
|
if show == 1 :
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def abs_fft(self, points=None, zoom=None,write = 'off'):
|
||||||
|
"""
|
||||||
|
Fourier transforms the timesignal;
|
||||||
|
points is the number of points to transform, if more points given than data points
|
||||||
|
the rest is zero padded
|
||||||
|
|
||||||
|
absfft(points=4096)
|
||||||
|
"""
|
||||||
|
realdata = N.array(self.the_result.y[0])
|
||||||
|
imdata = N.array(self.the_result.y[1])
|
||||||
|
data = realdata + 1j*imdata
|
||||||
|
fftdata = F.fftshift(F.fft(data, points))
|
||||||
|
absfft = N.sqrt(fftdata.real**2 + fftdata.imag**2)
|
||||||
|
# create our x axis
|
||||||
|
n = fftdata.size
|
||||||
|
self.the_result.x = F.fftshift(F.fftfreq(n, 1.0/self.sampling_rate))
|
||||||
|
self.the_result.y[0] = absfft
|
||||||
|
self.the_result.y[1] = N.zeros(n)
|
||||||
|
if write == 'on':
|
||||||
|
return self
|
||||||
|
else:
|
||||||
|
if zoom is None:
|
||||||
|
return self.the_result
|
||||||
|
else:
|
||||||
|
center, width = zoom
|
||||||
|
return self.zoom(self.the_result, center, width)
|
||||||
|
|
||||||
|
|
||||||
|
def fft(self, points=None, zoom=None, write='off'):
|
||||||
|
realdata = N.array(self.the_result.y[0])
|
||||||
|
imdata = N.array(self.the_result.y[1])
|
||||||
|
data = realdata + 1j*imdata
|
||||||
|
fftdata = F.fftshift(F.fft(data, points))
|
||||||
|
# create our x axis
|
||||||
|
n = fftdata.size
|
||||||
|
self.the_result.x = F.fftshift(F.fftfreq(n, 1.0/self.sampling_rate))
|
||||||
|
self.the_result.y[0] = fftdata.real
|
||||||
|
self.the_result.y[1] = fftdata.imag
|
||||||
|
if write == 'on':
|
||||||
|
return self
|
||||||
|
else:
|
||||||
|
if zoom is None:
|
||||||
|
return self.the_result
|
||||||
|
else:
|
||||||
|
center, width = zoom
|
||||||
|
return self.zoom(self.the_result, center, width)
|
||||||
|
|
||||||
|
def zoom(self,some_result, center="auto", width=1000):
|
||||||
|
if center == "auto":
|
||||||
|
i_center = int(self.the_result.y[0].argmax())
|
||||||
|
maximum = self.the_result.y[0][i_center]
|
||||||
|
print "Maximum at Frequency:", self.the_result.x[i_center]
|
||||||
|
else:
|
||||||
|
i_center = int(self.data_points/2.0+self.data_points*center/self.sampling_rate)
|
||||||
|
#print "TODO: set width automagically"
|
||||||
|
#if width == "auto":
|
||||||
|
# i_width = int(self.data_points*width)
|
||||||
|
i_width = int(self.data_points*width/self.sampling_rate)
|
||||||
|
some_result.x=some_result.x[i_center-i_width/2:i_center+i_width/2]
|
||||||
|
some_result.y[0]=some_result.y[0][i_center-i_width/2:i_center+i_width/2]
|
||||||
|
some_result.y[1]=some_result.y[1][i_center-i_width/2:i_center+i_width/2]
|
||||||
|
return some_result
|
||||||
|
|
||||||
|
"""
|
||||||
|
Apodization functions:
|
||||||
|
* exp_window and gauss_window are S/N enhancing,
|
||||||
|
* dexp_window and traf_window are resolution enhancing
|
||||||
|
* standard windows [hamming, hanning, bartlett, blackman, kaiser-bessel] are also available
|
||||||
|
self.timepoints = time points
|
||||||
|
self.aquisition_time = aquisition time (no. samples / sampling_rate)
|
||||||
|
line_broadening = line broadening factor (standard = 10 Hz)
|
||||||
|
gaussian_multiplicator = Gaussian Multiplication Factor for
|
||||||
|
the double exponential apodization
|
||||||
|
function (standard = 0.3)
|
||||||
|
"""
|
||||||
|
def exp_window(self, line_broadening=10, show=0):
|
||||||
|
apod = N.exp(-self.timepoints*line_broadening)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1 :
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def gauss_window(self, line_broadening=10, show=0):
|
||||||
|
apod = N.exp(-(self.timepoints*line_broadening)**2)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1 :
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def dexp_window(self, line_broadening=10, gaussian_multiplicator=0.3, show=0):
|
||||||
|
apod = N.exp(-(self.timepoints*line_broadening - gaussian_multiplicator*self.aquisition_time)**2)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1:
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def traf_window(self, line_broadening=10, show=0):
|
||||||
|
apod = (N.exp(-self.timepoints*line_broadening))**2 / ( (N.exp(-self.timepoints*line_broadening))**3
|
||||||
|
+ (N.exp(-self.aquisition_time*line_broadening))**3 )
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1:
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def hanning_window(self, show=0):
|
||||||
|
apod = N.hanning(self.data_points)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1:
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def hamming_window(self, show=0):
|
||||||
|
apod = N.hamming(self.data_points)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1:
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def blackman_window(self, show=0):
|
||||||
|
apod = N.blackman(self.data_points)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1:
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def bartlett_window(self, show=0):
|
||||||
|
apod = N.bartlett(self.data_points)
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1:
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
|
def kaiser_window(self, beta=4, show=0, use_scipy=None):
|
||||||
|
if use_scipy == None:
|
||||||
|
# modified Bessel function of zero kind order from somewhere
|
||||||
|
def I_0(x):
|
||||||
|
i0=0
|
||||||
|
fac = lambda n:reduce(lambda a,b:a*(b+1),range(n),1)
|
||||||
|
for n in range(20):
|
||||||
|
i0 += ((x/2.0)**n/(fac(n)))**2
|
||||||
|
return i0
|
||||||
|
|
||||||
|
t = N.arange(self.data_points, type=N.Float) - self.data_points/2.0
|
||||||
|
T = self.data_points
|
||||||
|
# this is the window function array
|
||||||
|
apod = I_0(beta*N.sqrt(1-(2*t/T)**2))/I_0(beta)
|
||||||
|
else:
|
||||||
|
# alternative method using scipy
|
||||||
|
import scipy
|
||||||
|
apod=scipy.kaiser(self.data_points, beta)
|
||||||
|
|
||||||
|
for i in range(2):
|
||||||
|
self.the_result.y[i] = self.the_result.y[i]*apod
|
||||||
|
if show == 1:
|
||||||
|
return self.the_result
|
||||||
|
return self
|
||||||
|
|
||||||
196
src/data/DamarisFFT.py
Normal file
196
src/data/DamarisFFT.py
Normal file
@ -0,0 +1,196 @@
|
|||||||
|
import numpy
|
||||||
|
import sys
|
||||||
|
import autophase
|
||||||
|
|
||||||
|
class DamarisFFT:
|
||||||
|
def clip(self, start=None, stop=None):
|
||||||
|
"""
|
||||||
|
Method for clipping data, only the timesignal between start and stop
|
||||||
|
is returned.
|
||||||
|
start and stop can be either time or frequency. The unit is automatically determined
|
||||||
|
"""
|
||||||
|
# check if start/stop order is properly
|
||||||
|
if start > stop:
|
||||||
|
# I could swap start/stop actually
|
||||||
|
# TODO swap values?
|
||||||
|
raise
|
||||||
|
# if one uses clip as a "placeholder"
|
||||||
|
if start==None and stop==None:
|
||||||
|
return self
|
||||||
|
|
||||||
|
if start==None:
|
||||||
|
start = 0
|
||||||
|
if stop==None:
|
||||||
|
stop = -1
|
||||||
|
# check if data is fft which changes the start/stop units
|
||||||
|
# TODO should get nicer(failsafe), i.e. flags in the object?
|
||||||
|
if self.xlabel == "Frequency / Hz":
|
||||||
|
isfft = True
|
||||||
|
start = self.x.size*(0.5 + start/self.sampling_rate)
|
||||||
|
stop = self.x.size*(0.5 + stop/self.sampling_rate)
|
||||||
|
else:
|
||||||
|
isfft = False
|
||||||
|
# get the corresponding indices
|
||||||
|
start *= self.sampling_rate
|
||||||
|
stop *= self.sampling_rate
|
||||||
|
# check if boundaries make sense, raise exception otherwise
|
||||||
|
if numpy.abs(int(start)-int(stop))<=0:
|
||||||
|
raise ValueError("start stop too close: There are no values in the given boundaries!")
|
||||||
|
for ch in xrange(len(self.y)):
|
||||||
|
# clip the data for each channel
|
||||||
|
# TODO multi records
|
||||||
|
self.y[ch] = self.y[ch][int(start):int(stop)]
|
||||||
|
# TODO what to do with x? Should it start from 0 or from start?
|
||||||
|
# self.x = self.x[:int(stop)-int(start)]
|
||||||
|
self.x = self.x[int(start):int(stop)]
|
||||||
|
return self
|
||||||
|
|
||||||
|
def baseline(self, last_part=0.1):
|
||||||
|
"""
|
||||||
|
Correct the baseline of your data by subtracting the mean of the
|
||||||
|
last_part fraction of your data.
|
||||||
|
|
||||||
|
last_part defaults to 0.1, i.e. last 10% of your data
|
||||||
|
"""
|
||||||
|
# TODO baselinecorrection for spectra after:
|
||||||
|
# Heuer, A; Haeberlen, U.: J. Mag. Res.(1989) 85, Is 1, 79-94
|
||||||
|
# Should I create an empty object?
|
||||||
|
# I deided to do NOT a copy, but
|
||||||
|
# rather modify the object
|
||||||
|
n = int(self.x.size*last_part)
|
||||||
|
for ch in xrange(len(self.y)):
|
||||||
|
self.y[ch] -= self.y[ch][-n:].mean()
|
||||||
|
# Skip the following due to design reasons
|
||||||
|
# new_object.was_copied = True
|
||||||
|
return self
|
||||||
|
|
||||||
|
|
||||||
|
"""
|
||||||
|
Apodization functions:
|
||||||
|
* exp_window and gauss_window are S/N enhancing,
|
||||||
|
* dexp_window and traf_window are resolution enhancing
|
||||||
|
* standard windows [hamming, hanning, bartlett, blackman, kaiser-bessel]
|
||||||
|
are also available
|
||||||
|
self.x = time points
|
||||||
|
elf.aquisition_time = aquisition time (no. samples / sampling_rate)
|
||||||
|
line_broadening = line broadening factor (standard = 10 Hz)
|
||||||
|
gaussian_multiplicator = Gaussian Multiplication Factor for
|
||||||
|
the double exponential apodization
|
||||||
|
function (standard = 0.3)
|
||||||
|
"""
|
||||||
|
def exp_window(self, line_broadening=10):
|
||||||
|
"""
|
||||||
|
exponential window
|
||||||
|
"""
|
||||||
|
apod = numpy.exp(-self.x*numpy.pi*line_broadening)
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def gauss_window(self, line_broadening=10):
|
||||||
|
apod = numpy.exp(-(self.x*line_broadening)**2)
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def dexp_window(self, line_broadening=-10, gaussian_multiplicator=0.3):
|
||||||
|
apod = numpy.exp(-(self.x*line_broadening - gaussian_multiplicator*self.x.max())**2)
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def traf_window(self, line_broadening=10):
|
||||||
|
apod = (numpy.exp(-self.x*line_broadening))**2 / ( (numpy.exp(-self.x*line_broadening))**3
|
||||||
|
+ (numpy.exp(-self.x.max()*line_broadening))**3 )
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def hanning_window(self):
|
||||||
|
apod = numpy.hanning(self.x.size)
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def hamming_window(self):
|
||||||
|
apod = numpy.hamming(self.x.size)
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def blackman_window(self):
|
||||||
|
apod = numpy.blackman(self.x.size)
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def bartlett_window(self):
|
||||||
|
apod = numpy.bartlett(self.x.size)
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def kaiser_window(self, beta=4, use_scipy=None):
|
||||||
|
if use_scipy == None:
|
||||||
|
# modified Bessel function of zero kind order from somewhere
|
||||||
|
def I_0(x):
|
||||||
|
i0=0
|
||||||
|
fac = lambda n:reduce(lambda a,b:a*(b+1),range(n),1)
|
||||||
|
for n in xrange(20):
|
||||||
|
i0 += ((x/2.0)**n/(fac(n)))**2
|
||||||
|
return i0
|
||||||
|
|
||||||
|
t = numpy.arange(self.x.size, type=numpy.Float) - self.x.size/2.0
|
||||||
|
T = self.x.size
|
||||||
|
# this is the window function array
|
||||||
|
apod = I_0(beta*numpy.sqrt(1-(2*t/T)**2))/I_0(beta)
|
||||||
|
else:
|
||||||
|
# alternative method using scipy
|
||||||
|
import scipy
|
||||||
|
apod=scipy.kaiser(self.x.size, beta)
|
||||||
|
|
||||||
|
for i in range(2):
|
||||||
|
self.y[i] = self.y[i]*apod
|
||||||
|
return self
|
||||||
|
|
||||||
|
def autophase(self):
|
||||||
|
"""
|
||||||
|
works nice with a SNR above 20 dB
|
||||||
|
10 V signal height to 1V noise width
|
||||||
|
"""
|
||||||
|
autophase.get_phase(self)
|
||||||
|
return self
|
||||||
|
|
||||||
|
def fft(self, samples=None):
|
||||||
|
"""
|
||||||
|
Fouriertransform the timesignal inplace.
|
||||||
|
For "zerofilling" set "samples" to a value higher than your data length.
|
||||||
|
Shorten "samples" to truncate your data.
|
||||||
|
samples takes only integer values
|
||||||
|
|
||||||
|
"""
|
||||||
|
# Is this smart performance wise? Should I create an empty object?
|
||||||
|
# Tests showed that this try except block performed 3.78ms
|
||||||
|
# timesignal.baseline().fft()
|
||||||
|
# with out this it needed 4.41 ms, thus this is justified :-)
|
||||||
|
#try:
|
||||||
|
# if self.was_copied:
|
||||||
|
# new_object = self
|
||||||
|
#except:
|
||||||
|
# new_object = self+0
|
||||||
|
fft_of_signal = numpy.fft.fft(self.y[0] + 1j*self.y[1], n=samples)
|
||||||
|
fft_of_signal = numpy.fft.fftshift(fft_of_signal)
|
||||||
|
dwell = 1.0/self.sampling_rate
|
||||||
|
n = fft_of_signal.size
|
||||||
|
fft_frequencies = numpy.fft.fftfreq(n, dwell)
|
||||||
|
self.x = numpy.fft.fftshift(fft_frequencies)
|
||||||
|
self.y[0] = fft_of_signal.real
|
||||||
|
self.y[1] = fft_of_signal.imag
|
||||||
|
self.set_xlabel("Frequency / Hz")
|
||||||
|
return self
|
||||||
|
|
||||||
|
def magnitude(self):
|
||||||
|
# this should calculate the absolute value, and set the imag channel to zero
|
||||||
|
self.y[0] = numpy.sqrt(self.y [0]**2+self.y [1]**2)
|
||||||
|
self.y[1] *= 0 #self.y[0].copy()
|
||||||
|
return self
|
||||||
177
src/data/DataPool.py
Normal file
177
src/data/DataPool.py
Normal file
@ -0,0 +1,177 @@
|
|||||||
|
# data pool collects data from data handling script
|
||||||
|
# provides data to experiment script and display
|
||||||
|
|
||||||
|
import sys
|
||||||
|
import types
|
||||||
|
import tables
|
||||||
|
import UserDict
|
||||||
|
import threading
|
||||||
|
import traceback
|
||||||
|
import StringIO
|
||||||
|
import ADC_Result
|
||||||
|
import Accumulation
|
||||||
|
import MeasurementResult
|
||||||
|
|
||||||
|
class DataPool(UserDict.DictMixin):
|
||||||
|
"""
|
||||||
|
dictionary with sending change events
|
||||||
|
"""
|
||||||
|
|
||||||
|
# supports tranlation from dictionary keys to pytables hdf node names
|
||||||
|
# taken from: Python Ref Manual Section 2.3: Identifiers and keywords
|
||||||
|
# things are always prefixed by "dir_" or "dict_"
|
||||||
|
translation_table=""
|
||||||
|
for i in xrange(256):
|
||||||
|
c=chr(i)
|
||||||
|
if (c>="a" and c<="z") or \
|
||||||
|
(c>="A" and c<="Z") or \
|
||||||
|
(c>="0" and c<="9"):
|
||||||
|
translation_table+=c
|
||||||
|
else:
|
||||||
|
translation_table+="_"
|
||||||
|
|
||||||
|
class Event:
|
||||||
|
access=0
|
||||||
|
updated_value=1
|
||||||
|
new_key=2
|
||||||
|
deleted_key=3
|
||||||
|
destroy=4
|
||||||
|
|
||||||
|
def __init__(self, what, subject="", origin=None):
|
||||||
|
self.what=what
|
||||||
|
self.subject=subject
|
||||||
|
self.origin=origin
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
return "<DataPool.Event origin=%s what=%d subject='%s'>"%(self.origin, self.what,self.subject)
|
||||||
|
|
||||||
|
def copy(self):
|
||||||
|
return DataPool.Event(self.what+0, self.subject+"", self.origin)
|
||||||
|
|
||||||
|
def __init__(self):
|
||||||
|
self.__mydict={}
|
||||||
|
self.__dictlock=threading.Lock()
|
||||||
|
self.__registered_listeners=[]
|
||||||
|
|
||||||
|
def __getitem__(self, name):
|
||||||
|
try:
|
||||||
|
self.__dictlock.acquire()
|
||||||
|
return self.__mydict[name]
|
||||||
|
finally:
|
||||||
|
self.__dictlock.release()
|
||||||
|
|
||||||
|
def __setitem__(self, name, value):
|
||||||
|
try:
|
||||||
|
self.__dictlock.acquire()
|
||||||
|
if name in self.__mydict:
|
||||||
|
e=DataPool.Event(DataPool.Event.updated_value,name,self)
|
||||||
|
else:
|
||||||
|
e=DataPool.Event(DataPool.Event.new_key, name,self)
|
||||||
|
self.__mydict[name]=value
|
||||||
|
finally:
|
||||||
|
self.__dictlock.release()
|
||||||
|
self.__send_event(e)
|
||||||
|
|
||||||
|
|
||||||
|
def __delitem__(self, name):
|
||||||
|
try:
|
||||||
|
self.__dictlock.acquire()
|
||||||
|
del self.__mydict[name]
|
||||||
|
finally:
|
||||||
|
self.__dictlock.release()
|
||||||
|
self.__send_event(DataPool.Event(DataPool.Event.deleted_key,name,self))
|
||||||
|
|
||||||
|
def keys(self):
|
||||||
|
try:
|
||||||
|
self.__dictlock.acquire()
|
||||||
|
return self.__mydict.keys()
|
||||||
|
finally:
|
||||||
|
self.__dictlock.release()
|
||||||
|
|
||||||
|
def __send_event(self, _event):
|
||||||
|
for l in self.__registered_listeners:
|
||||||
|
l(_event.copy())
|
||||||
|
|
||||||
|
def __del__(self):
|
||||||
|
self.__send_event(DataPool.Event(DataPool.Event.destroy))
|
||||||
|
self.__registered_listeners=None
|
||||||
|
|
||||||
|
def write_hdf5(self,hdffile,where="/",name="data_pool", complib=None, complevel=None):
|
||||||
|
if type(hdffile) is types.StringType:
|
||||||
|
dump_file=tables.openFile(hdffile, mode="a")
|
||||||
|
elif isinstance(hdffile,tables.File):
|
||||||
|
dump_file=hdffile
|
||||||
|
else:
|
||||||
|
raise Exception("expecting hdffile or string")
|
||||||
|
|
||||||
|
dump_group=dump_file.createGroup(where, name, "DAMARIS data pool")
|
||||||
|
self.__dictlock.acquire()
|
||||||
|
dict_keys=self.__mydict.keys()
|
||||||
|
self.__dictlock.release()
|
||||||
|
try:
|
||||||
|
for key in dict_keys:
|
||||||
|
if key[:2]=="__": continue
|
||||||
|
dump_dir=dump_group
|
||||||
|
# walk along the given path and create groups if necessary
|
||||||
|
namelist = key.split("/")
|
||||||
|
for part in namelist[:-1]:
|
||||||
|
dir_part="dir_"+str(part).translate(DataPool.translation_table)
|
||||||
|
if not dir_part in dump_dir:
|
||||||
|
dump_dir=dump_file.createGroup(dump_dir,name=dir_part,title=part)
|
||||||
|
else:
|
||||||
|
if dump_dir._v_children[dir_part]._v_title==part:
|
||||||
|
dump_dir=dump_dir._v_children[dir_part]
|
||||||
|
else:
|
||||||
|
extension_count=0
|
||||||
|
while dir_part+"_%03d"%extension_count in dump_dir:
|
||||||
|
extension_count+=1
|
||||||
|
dump_dir=dump_file.createGroup(dump_dir,
|
||||||
|
name=dir_part+"_%03d"%extension_count,
|
||||||
|
title=part)
|
||||||
|
|
||||||
|
# convert last part of key to a valid name
|
||||||
|
group_keyname="dict_"+str(namelist[-1]).translate(DataPool.translation_table)
|
||||||
|
# avoid double names by adding number extension
|
||||||
|
if group_keyname in dump_dir:
|
||||||
|
extension_count=0
|
||||||
|
while group_keyname+"_%03d"%extension_count in dump_dir:
|
||||||
|
extension_count+=1
|
||||||
|
group_keyname+="_%03d"%extension_count
|
||||||
|
self.__dictlock.acquire()
|
||||||
|
if key not in self.__mydict:
|
||||||
|
# outdated ...
|
||||||
|
self.__dictlock.release()
|
||||||
|
continue
|
||||||
|
value=self.__mydict[key]
|
||||||
|
self.__dictlock.release()
|
||||||
|
# now write data, assuming, the object is constant during write operation
|
||||||
|
if "write_to_hdf" in dir(value):
|
||||||
|
try:
|
||||||
|
value.write_to_hdf(hdffile=dump_file,
|
||||||
|
where=dump_dir,
|
||||||
|
name=group_keyname,
|
||||||
|
title=key,
|
||||||
|
complib=complib,
|
||||||
|
complevel=complevel)
|
||||||
|
except Exception,e:
|
||||||
|
print "failed to write data_pool[\"%s\"]: %s"%(key,str(e))
|
||||||
|
traceback_file=StringIO.StringIO()
|
||||||
|
traceback.print_tb(sys.exc_info()[2], None, traceback_file)
|
||||||
|
print "detailed traceback: %s\n"%str(e)+traceback_file.getvalue()
|
||||||
|
traceback_file=None
|
||||||
|
else:
|
||||||
|
print "don't know how to store data_pool[\"%s\"]"%key
|
||||||
|
value=None
|
||||||
|
|
||||||
|
finally:
|
||||||
|
dump_group=None
|
||||||
|
if type(hdffile) is types.StringType:
|
||||||
|
dump_file.close()
|
||||||
|
dump_file=None
|
||||||
|
|
||||||
|
def register_listener(self, listening_function):
|
||||||
|
self.__registered_listeners.append(listening_function)
|
||||||
|
|
||||||
|
def unregister_listener(self, listening_function):
|
||||||
|
if listening_function in self.__registered_listeners:
|
||||||
|
self.__registered_listeners.remove(listening_function)
|
||||||
192
src/data/Drawable.py
Normal file
192
src/data/Drawable.py
Normal file
@ -0,0 +1,192 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
import threading
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class Drawable #
|
||||||
|
# #
|
||||||
|
# Purpose: Base class of everything plottable #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
class Drawable:
|
||||||
|
def __init__(self):
|
||||||
|
|
||||||
|
# Will be set correctly in one of the subclasses
|
||||||
|
self.x = []
|
||||||
|
self.y = []
|
||||||
|
|
||||||
|
self.styles = { }
|
||||||
|
|
||||||
|
self.xlabel = None
|
||||||
|
self.ylabel = None
|
||||||
|
|
||||||
|
self.title = None
|
||||||
|
|
||||||
|
self.legend = { }
|
||||||
|
|
||||||
|
self.text = {}
|
||||||
|
|
||||||
|
self.xmin = 0
|
||||||
|
self.xmax = 0
|
||||||
|
self.ymin = 0
|
||||||
|
self.ymax = 0
|
||||||
|
|
||||||
|
|
||||||
|
def get_xdata(self):
|
||||||
|
"Returns a reference to the x-Plotdata (array)"
|
||||||
|
return self.x
|
||||||
|
|
||||||
|
|
||||||
|
def set_xdata(self, pos, value):
|
||||||
|
"Sets a point in x"
|
||||||
|
try:
|
||||||
|
self.x[pos] = value
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
|
||||||
|
|
||||||
|
def get_ydata(self, channel):
|
||||||
|
"Returns the y-Plotdata of channel n (array)"
|
||||||
|
try:
|
||||||
|
return self.y[channel]
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
|
||||||
|
|
||||||
|
def set_ydata(self, channel, pos, value):
|
||||||
|
"Sets a point in y"
|
||||||
|
try:
|
||||||
|
self.y[channel][pos] = value
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
|
||||||
|
|
||||||
|
def get_number_of_channels(self):
|
||||||
|
"Returns the number of channels in y"
|
||||||
|
return len(self.y)
|
||||||
|
|
||||||
|
|
||||||
|
def get_style(self):
|
||||||
|
"Returns a reference to plot-styles (dictionary)"
|
||||||
|
return self.styles
|
||||||
|
|
||||||
|
|
||||||
|
def set_style(self, channel, value):
|
||||||
|
"Sets a channel to a certain plot-style"
|
||||||
|
if self.styles.has_key(channel):
|
||||||
|
print "Drawable Warning: Style key \"%s\" will be overwritten with \"%s\"" % (str(channel), str(value))
|
||||||
|
|
||||||
|
self.styles[channel] = str(value)
|
||||||
|
|
||||||
|
|
||||||
|
def get_xlabel(self):
|
||||||
|
"Returns the label for the x-axis"
|
||||||
|
return self.xlabel
|
||||||
|
|
||||||
|
|
||||||
|
def set_xlabel(self, label):
|
||||||
|
"Sets the label for the x-axis"
|
||||||
|
self.xlabel = str(label)
|
||||||
|
|
||||||
|
|
||||||
|
def get_ylabel(self):
|
||||||
|
"Gets the label for the y-axis"
|
||||||
|
return self.ylabel
|
||||||
|
|
||||||
|
|
||||||
|
def set_ylabel(self, label):
|
||||||
|
"Sets the label for the y-axis"
|
||||||
|
self.ylabel = str(label)
|
||||||
|
|
||||||
|
|
||||||
|
def get_text(self, index):
|
||||||
|
"Returns labels to be plotted (List)"
|
||||||
|
if self.text.has_key(index):
|
||||||
|
return self.text[index]
|
||||||
|
else: return None
|
||||||
|
|
||||||
|
|
||||||
|
def set_text(self, index, text):
|
||||||
|
"Sets labels to be plotted "
|
||||||
|
self.text[index] = str(text)
|
||||||
|
|
||||||
|
|
||||||
|
def get_title(self):
|
||||||
|
"Returns the title of the plot"
|
||||||
|
return self.title
|
||||||
|
|
||||||
|
|
||||||
|
def set_title(self, title):
|
||||||
|
"Sets the title of the plot"
|
||||||
|
self.title = str(title)
|
||||||
|
|
||||||
|
|
||||||
|
def get_legend(self):
|
||||||
|
"Returns the legend of the plot (Dictionary)"
|
||||||
|
return self.legend
|
||||||
|
|
||||||
|
|
||||||
|
def set_legend(self, channel, value):
|
||||||
|
"Sets the legend of the plot"
|
||||||
|
if self.legend.has_key(key):
|
||||||
|
print "Drawable Warning: Legend key \"%s\" will be overwritten with \"%s\"" % (str(channel), str(value))
|
||||||
|
|
||||||
|
self.legend[channel] = str(value)
|
||||||
|
|
||||||
|
|
||||||
|
def get_xmin(self):
|
||||||
|
"Returns minimun of x"
|
||||||
|
return self.x.min()
|
||||||
|
|
||||||
|
def set_xmin(self, xmin):
|
||||||
|
"Sets minimum of x"
|
||||||
|
self.xmin = xmin
|
||||||
|
|
||||||
|
|
||||||
|
def get_xmax(self):
|
||||||
|
"Returns maximum of x"
|
||||||
|
return self.x.max()
|
||||||
|
|
||||||
|
|
||||||
|
def set_xmax(self, xmax):
|
||||||
|
"Sets maximum of x"
|
||||||
|
self.xmax = xmax
|
||||||
|
|
||||||
|
|
||||||
|
def get_ymin(self):
|
||||||
|
"Returns minimum of y"
|
||||||
|
if type(self.y)==type([]):
|
||||||
|
return min(map(lambda l:l.min(),self.y))
|
||||||
|
else:
|
||||||
|
return self.y.min()
|
||||||
|
|
||||||
|
|
||||||
|
def set_ymin(self, ymin):
|
||||||
|
"Sets minimum of y"
|
||||||
|
self.ymin = ymin
|
||||||
|
|
||||||
|
|
||||||
|
def get_ymax(self):
|
||||||
|
"Returns maximimum of y"
|
||||||
|
if type(self.y)==type([]):
|
||||||
|
return max(map(lambda l:l.max(),self.y))
|
||||||
|
else:
|
||||||
|
return self.y.max()
|
||||||
|
|
||||||
|
|
||||||
|
def set_ymax(self, ymax):
|
||||||
|
"Sets maximum of y"
|
||||||
|
self.ymax = ymax
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
71
src/data/Error_Result.py
Normal file
71
src/data/Error_Result.py
Normal file
@ -0,0 +1,71 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
from Resultable import Resultable
|
||||||
|
from Drawable import Drawable
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class Error_Result #
|
||||||
|
# #
|
||||||
|
# Purpose: Specialised class of Resultable #
|
||||||
|
# Contains occured error-messages from the core #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
class Error_Result(Resultable, Drawable):
|
||||||
|
def __init__(self, error_msg = None, desc = {}, job_id = None, job_date = None):
|
||||||
|
Resultable.__init__(self)
|
||||||
|
Drawable.__init__(self)
|
||||||
|
|
||||||
|
if error_msg is not None:
|
||||||
|
self.error_message = error_msg
|
||||||
|
self.set_title("Error-Result: %s" % error_msg)
|
||||||
|
else:
|
||||||
|
self.error_message = error_msg
|
||||||
|
self.description = desc
|
||||||
|
self.job_id = job_id
|
||||||
|
self.job_date = job_date
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def get_error_message(self):
|
||||||
|
return self.error_message
|
||||||
|
|
||||||
|
|
||||||
|
def set_error_message(self, error_msg):
|
||||||
|
self.set_title("Error-Result: %s" % error_msg)
|
||||||
|
self.error_message = error_msg
|
||||||
|
|
||||||
|
|
||||||
|
# No statistics
|
||||||
|
def uses_statistics(self):
|
||||||
|
return False
|
||||||
|
|
||||||
|
# Nothing to plot
|
||||||
|
def get_ydata(self):
|
||||||
|
return [0.0]
|
||||||
|
|
||||||
|
# Nothing to plot
|
||||||
|
def get_xdata(self):
|
||||||
|
return [0.0]
|
||||||
|
|
||||||
|
# Überladen von Operatoren und Built-Ins -------------------------------------------------------
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
tmp_string = "Core error-message: %s" % self.error_message
|
||||||
|
|
||||||
|
return tmp_string
|
||||||
|
|
||||||
|
def __len__(self):
|
||||||
|
return len(self.error_message)
|
||||||
|
|
||||||
|
|
||||||
|
def __str__(self):
|
||||||
|
return self.error_message
|
||||||
|
|
||||||
|
|
||||||
|
# Preventing an error when adding something to an error-result (needed for plotting error-results)
|
||||||
|
def __add__(self, other):
|
||||||
|
return self
|
||||||
|
|
||||||
|
|
||||||
76
src/data/Errorable.py
Normal file
76
src/data/Errorable.py
Normal file
@ -0,0 +1,76 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class Errorable #
|
||||||
|
# #
|
||||||
|
# Purpose: Base class of everything what could contain a statistic error #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
class Errorable:
|
||||||
|
def __init__(self):
|
||||||
|
|
||||||
|
# Will be determined in one of the subclasses
|
||||||
|
self.xerr = []
|
||||||
|
self.yerr = []
|
||||||
|
|
||||||
|
self.error_color = ""
|
||||||
|
self.bars_above = False
|
||||||
|
|
||||||
|
self.n = 0
|
||||||
|
|
||||||
|
|
||||||
|
def get_xerr(self):
|
||||||
|
"Returns a reference to x-Error (array)"
|
||||||
|
return self.xerr
|
||||||
|
|
||||||
|
|
||||||
|
def set_xerr(self, pos, value):
|
||||||
|
"Sets a point in x-Error"
|
||||||
|
try:
|
||||||
|
self.xerr[pos] = value
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
|
||||||
|
|
||||||
|
def get_yerr(self, channel):
|
||||||
|
"Returns a list of y-Errors (list of arrays, corresponding channels)"
|
||||||
|
try:
|
||||||
|
return self.yerr[channel]
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
|
||||||
|
|
||||||
|
def set_yerr(self, channel, pos, value):
|
||||||
|
"Sets a point in y-Error"
|
||||||
|
try:
|
||||||
|
self.yerr[channel][pos] = value
|
||||||
|
except:
|
||||||
|
raise
|
||||||
|
|
||||||
|
|
||||||
|
def get_error_color(self):
|
||||||
|
"Returns the error-bar color"
|
||||||
|
return self.error_color
|
||||||
|
|
||||||
|
|
||||||
|
def set_error_color(self, color):
|
||||||
|
"Sets the error-bar color"
|
||||||
|
self.error_color = color
|
||||||
|
|
||||||
|
|
||||||
|
def get_bars_above(self):
|
||||||
|
"Gets bars-above property of errorplot"
|
||||||
|
return self.bars_above
|
||||||
|
|
||||||
|
|
||||||
|
def set_bars_above(self, bars_above):
|
||||||
|
"Sets bars-above property of errorplot"
|
||||||
|
self.bars_above = bool(bars_above)
|
||||||
|
|
||||||
|
|
||||||
|
def ready_for_drawing_error(self):
|
||||||
|
"Returns true if more than one result have been accumulated"
|
||||||
|
if self.n >= 2: return True
|
||||||
|
else: return False
|
||||||
291
src/data/MeasurementResult.py
Normal file
291
src/data/MeasurementResult.py
Normal file
@ -0,0 +1,291 @@
|
|||||||
|
import threading
|
||||||
|
import math
|
||||||
|
import types
|
||||||
|
import sys
|
||||||
|
import tables
|
||||||
|
import numpy
|
||||||
|
import exceptions
|
||||||
|
import UserDict
|
||||||
|
import Drawable
|
||||||
|
|
||||||
|
## provide gaussian statistics for a series of measured data points
|
||||||
|
#
|
||||||
|
# AccumulatedValue provides mean and error of mean after being fed with measured data
|
||||||
|
# internaly it keeps the sum, the sum of squares and the number of data points
|
||||||
|
class AccumulatedValue:
|
||||||
|
|
||||||
|
def __init__(self, mean=None, mean_err=None, n=None):
|
||||||
|
"""
|
||||||
|
one value with std. deviation
|
||||||
|
can be initialized by:
|
||||||
|
No argument: no entries
|
||||||
|
one argument: first entry
|
||||||
|
two arguments: mean and its error, n is set 2
|
||||||
|
three arguments: already existing statistics defined by mean, mean's error, n
|
||||||
|
"""
|
||||||
|
if mean is None:
|
||||||
|
self.y=0.0
|
||||||
|
self.y2=0.0
|
||||||
|
self.n=0
|
||||||
|
elif mean_err is None and n is None:
|
||||||
|
self.y=float(mean)
|
||||||
|
self.y2=self.y**2
|
||||||
|
self.n=1
|
||||||
|
elif mean_err is None:
|
||||||
|
self.n=max(1, int(n))
|
||||||
|
self.y=float(mean)*self.n
|
||||||
|
self.y2=(float(mean)**2)*self.n
|
||||||
|
elif n is None:
|
||||||
|
self.n=2
|
||||||
|
self.y=float(mean)*2
|
||||||
|
self.y2=(float(mean_err)**2+float(mean)**2)*2
|
||||||
|
else:
|
||||||
|
self.n=int(n)
|
||||||
|
self.y=float(mean)*self.n
|
||||||
|
self.y2=float(mean_err)**2*n*(n-1.0)+float(mean)**2*n
|
||||||
|
|
||||||
|
def __add__(self,y):
|
||||||
|
new_one=AccumulatedValue()
|
||||||
|
if (type(y) is types.InstanceType and isinstance(y, AccumulatedValue)):
|
||||||
|
new_one.y=self.y+y.y
|
||||||
|
new_one.y2=self.y2+y.y2
|
||||||
|
new_one.n=self.n+y.n
|
||||||
|
else:
|
||||||
|
new_one.y=self.y+float(y)
|
||||||
|
new_one.y2=self.y2+float(y)**2
|
||||||
|
new_one.n=self.n+1
|
||||||
|
return new_one
|
||||||
|
|
||||||
|
def __iadd__(self,y):
|
||||||
|
if (type(y) is types.InstanceType and isinstance(y, AccumulatedValue)):
|
||||||
|
self.y+=y.y
|
||||||
|
self.y2+=y.y2
|
||||||
|
self.n+=y.n
|
||||||
|
else:
|
||||||
|
self.y+=float(y)
|
||||||
|
self.y2+=float(y)**2
|
||||||
|
self.n+=1
|
||||||
|
return self
|
||||||
|
|
||||||
|
def copy(self):
|
||||||
|
a=AccumulatedValue()
|
||||||
|
a.y=self.y
|
||||||
|
a.y2=self.y2
|
||||||
|
a.n=self.n
|
||||||
|
return a
|
||||||
|
|
||||||
|
def mean(self):
|
||||||
|
"""
|
||||||
|
returns the mean of all added/accumulated values
|
||||||
|
"""
|
||||||
|
if self.n is None or self.n==0:
|
||||||
|
return None
|
||||||
|
else:
|
||||||
|
return self.y/self.n
|
||||||
|
|
||||||
|
def sigma(self):
|
||||||
|
"""
|
||||||
|
returns the standard deviation added/accumulated values
|
||||||
|
"""
|
||||||
|
if self.n>1:
|
||||||
|
variance=(self.y2-(self.y**2)/float(self.n))/(self.n-1.0)
|
||||||
|
if variance<0:
|
||||||
|
if variance<-1e-20:
|
||||||
|
print "variance=%g<0! assuming 0"%variance
|
||||||
|
return 0.0
|
||||||
|
return math.sqrt(variance)
|
||||||
|
elif self.n==1:
|
||||||
|
return 0.0
|
||||||
|
else:
|
||||||
|
return None
|
||||||
|
|
||||||
|
def mean_error(self):
|
||||||
|
"""
|
||||||
|
returns the mean's error (=std.dev/sqrt(n)) of all added/accumulated values
|
||||||
|
"""
|
||||||
|
if self.n>1:
|
||||||
|
variance=(self.y2-(self.y**2)/float(self.n))/(self.n-1.0)
|
||||||
|
if variance<0:
|
||||||
|
if variance<-1e-20:
|
||||||
|
print "variance=%g<0! assuming 0"%variance
|
||||||
|
return 0.0
|
||||||
|
return math.sqrt(variance/self.n)
|
||||||
|
elif self.n==1:
|
||||||
|
return 0.0
|
||||||
|
else:
|
||||||
|
return None
|
||||||
|
|
||||||
|
def __str__(self):
|
||||||
|
if self.n==0:
|
||||||
|
return "no value"
|
||||||
|
elif self.n==1:
|
||||||
|
return str(self.y)
|
||||||
|
else:
|
||||||
|
return "%g +/- %g (%d accumulations)"%(self.mean(),self.mean_error(),self.n)
|
||||||
|
|
||||||
|
def __repr__(self):
|
||||||
|
return str(self)
|
||||||
|
|
||||||
|
class MeasurementResult(Drawable.Drawable, UserDict.UserDict):
|
||||||
|
|
||||||
|
def __init__(self, quantity_name):
|
||||||
|
"""
|
||||||
|
convenient accumulation and interface to plot functions
|
||||||
|
|
||||||
|
dictionary must not contain anything but AccumulatedValue instances
|
||||||
|
"""
|
||||||
|
Drawable.Drawable.__init__(self)
|
||||||
|
UserDict.UserDict.__init__(self)
|
||||||
|
self.quantity_name=quantity_name
|
||||||
|
self.lock=threading.RLock()
|
||||||
|
|
||||||
|
# get the selected item, if it does not exist, create an empty one
|
||||||
|
def __getitem__(self, key):
|
||||||
|
if key not in self:
|
||||||
|
a=AccumulatedValue()
|
||||||
|
self.data[float(key)]=a
|
||||||
|
return a
|
||||||
|
else:
|
||||||
|
return self.data[float(key)]
|
||||||
|
|
||||||
|
def __setitem__(self,key,value):
|
||||||
|
if not (type(value) is types.InstanceType and isinstance(value, AccumulatedValue)):
|
||||||
|
value=AccumulatedValue(float(value))
|
||||||
|
return UserDict.UserDict.__setitem__(self,
|
||||||
|
float(key),
|
||||||
|
value)
|
||||||
|
|
||||||
|
def __add__(self, right_value):
|
||||||
|
if right_value==0:
|
||||||
|
return self.copy()
|
||||||
|
else:
|
||||||
|
raise Exception("not implemented")
|
||||||
|
|
||||||
|
def get_title(self):
|
||||||
|
return self.quantity_name
|
||||||
|
|
||||||
|
def get_xdata(self):
|
||||||
|
"""
|
||||||
|
sorted array of all dictionary entries without Accumulated Value objects with n==0
|
||||||
|
"""
|
||||||
|
keys=numpy.array(filter(lambda k: not (isinstance(self.data[k], AccumulatedValue) and self.data[k].n==0), self.data.keys()),
|
||||||
|
dtype="Float64")
|
||||||
|
keys.sort()
|
||||||
|
return keys
|
||||||
|
|
||||||
|
def get_ydata(self):
|
||||||
|
return self.get_xydata()[1]
|
||||||
|
|
||||||
|
def get_xydata(self):
|
||||||
|
k=self.get_xdata()
|
||||||
|
v=numpy.array(map(lambda key: self.data[key].mean(), k), dtype="Float64")
|
||||||
|
return [k,v]
|
||||||
|
|
||||||
|
def get_errorplotdata(self):
|
||||||
|
k=self.get_xdata()
|
||||||
|
v=numpy.array(map(lambda key: self.data[key].mean(), k), dtype="Float64")
|
||||||
|
e=numpy.array(map(lambda key: self.data[key].mean_error(), k), dtype="Float64")
|
||||||
|
return [k,v,e]
|
||||||
|
|
||||||
|
def get_lineplotdata(self):
|
||||||
|
k=self.get_xdata()
|
||||||
|
v=numpy.array(self.y, dtype="Float64")
|
||||||
|
return [k, v]
|
||||||
|
|
||||||
|
def uses_statistics(self):
|
||||||
|
"""
|
||||||
|
drawable interface method, returns True
|
||||||
|
"""
|
||||||
|
return True
|
||||||
|
|
||||||
|
def write_to_csv(self,destination=sys.stdout, delimiter=" "):
|
||||||
|
"""
|
||||||
|
writes the data to a file or to sys.stdout
|
||||||
|
destination can be a file or a filename
|
||||||
|
suitable for further processing
|
||||||
|
"""
|
||||||
|
# write sorted
|
||||||
|
the_destination=destination
|
||||||
|
if type(destination) in types.StringTypes:
|
||||||
|
the_destination=file(destination, "w")
|
||||||
|
|
||||||
|
the_destination.write("# quantity:"+str(self.quantity_name)+"\n")
|
||||||
|
the_destination.write("# x y ysigma n\n")
|
||||||
|
for x in self.get_xdata():
|
||||||
|
y=self.data[x]
|
||||||
|
if type(y) in [types.FloatType, types.IntType, types.LongType]:
|
||||||
|
the_destination.write("%e%s%e%s0%s1\n"%(x, delimiter, y, delimiter, delimiter))
|
||||||
|
else:
|
||||||
|
the_destination.write("%e%s%e%s%e%s%d\n"%(x,
|
||||||
|
delimiter,
|
||||||
|
y.mean(),
|
||||||
|
delimiter,
|
||||||
|
y.mean_error(),
|
||||||
|
delimiter,
|
||||||
|
y.n))
|
||||||
|
the_destination=None
|
||||||
|
|
||||||
|
|
||||||
|
def write_to_hdf(self, hdffile, where, name, title, complib=None, complevel=None):
|
||||||
|
|
||||||
|
h5_table_format= {
|
||||||
|
"x" : tables.Float64Col(),
|
||||||
|
"y" : tables.Float64Col(),
|
||||||
|
"y_err" : tables.Float64Col(),
|
||||||
|
"n" : tables.Int64Col()
|
||||||
|
}
|
||||||
|
filter=None
|
||||||
|
if complib is not None:
|
||||||
|
if complevel is None:
|
||||||
|
complevel=9
|
||||||
|
filter=tables.Filters(complevel=complevel,complib=complib,shuffle=1)
|
||||||
|
|
||||||
|
mr_table=hdffile.createTable(where=where,name=name,
|
||||||
|
description=h5_table_format,
|
||||||
|
title=title,
|
||||||
|
filters=filter,
|
||||||
|
expectedrows=len(self))
|
||||||
|
mr_table.flavor="numpy"
|
||||||
|
mr_table.attrs.damaris_type="MeasurementResult"
|
||||||
|
self.lock.acquire()
|
||||||
|
try:
|
||||||
|
mr_table.attrs.quantity_name=self.quantity_name
|
||||||
|
|
||||||
|
row=mr_table.row
|
||||||
|
xdata=self.get_xdata()
|
||||||
|
if xdata.shape[0]!=0:
|
||||||
|
for x in self.get_xdata():
|
||||||
|
y=self.data[x]
|
||||||
|
row["x"]=x
|
||||||
|
if type(y) in [types.FloatType, types.IntType, types.LongType]:
|
||||||
|
row["y"]=y
|
||||||
|
row["y_err"]=0.0
|
||||||
|
row["n"]=1
|
||||||
|
else:
|
||||||
|
row["y"]=y.mean()
|
||||||
|
row["y_err"]=y.mean_error()
|
||||||
|
row["n"]=y.n
|
||||||
|
row.append()
|
||||||
|
|
||||||
|
finally:
|
||||||
|
mr_table.flush()
|
||||||
|
self.lock.release()
|
||||||
|
|
||||||
|
def read_from_hdf(hdf_node):
|
||||||
|
"""
|
||||||
|
reads a MeasurementResult object from the hdf_node
|
||||||
|
or None if the node is not suitable
|
||||||
|
"""
|
||||||
|
|
||||||
|
if not isinstance(hdf_node, tables.Table):
|
||||||
|
return None
|
||||||
|
|
||||||
|
if hdf_node._v_attrs.damaris_type!="MeasurementResult":
|
||||||
|
return None
|
||||||
|
|
||||||
|
mr=MeasurementResult(hdf_node._v_attrs.quantity_name)
|
||||||
|
|
||||||
|
for r in hdf_node.iterrows():
|
||||||
|
mr[r["x"]]=AccumulatedValue(r["y"],r["y_err"],r["n"])
|
||||||
|
|
||||||
|
return mr
|
||||||
29
src/data/Persistance.py
Normal file
29
src/data/Persistance.py
Normal file
@ -0,0 +1,29 @@
|
|||||||
|
class Persistance :
|
||||||
|
def __init__(self, shots):
|
||||||
|
self.shots = shots
|
||||||
|
self.accu = 0
|
||||||
|
self.counter = 0
|
||||||
|
self.result_list = []
|
||||||
|
|
||||||
|
def fade(self, res):
|
||||||
|
self.counter += 1
|
||||||
|
if self.accu == 0:
|
||||||
|
self.accu=res+0
|
||||||
|
self.result_list.append(res)
|
||||||
|
if self.counter < 1:
|
||||||
|
for i,ch in enumerate(self.accu.y):
|
||||||
|
ch += res.y[i]
|
||||||
|
|
||||||
|
elif len(self.result_list) == self.shots:
|
||||||
|
self.counter = len(self.result_list)
|
||||||
|
old_result = self.result_list.pop(0)
|
||||||
|
for i,ch in enumerate(self.accu.y):
|
||||||
|
ch *= self.shots
|
||||||
|
ch -= old_result.y[i]
|
||||||
|
ch += res.y[i]
|
||||||
|
else:
|
||||||
|
for i,ch in enumerate(self.accu.y):
|
||||||
|
ch *= self.counter-1
|
||||||
|
ch += res.y[i]
|
||||||
|
self.accu /= self.counter
|
||||||
|
return self.accu
|
||||||
65
src/data/Resultable.py
Normal file
65
src/data/Resultable.py
Normal file
@ -0,0 +1,65 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class Resultable #
|
||||||
|
# #
|
||||||
|
# Purpose: Base class of everything what could be a core-result #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
class Resultable:
|
||||||
|
def __init__(self):
|
||||||
|
|
||||||
|
self.job_id = None
|
||||||
|
self.job_date = None
|
||||||
|
|
||||||
|
self.description = { }
|
||||||
|
|
||||||
|
|
||||||
|
def get_job_id(self):
|
||||||
|
"Returns the job-id of this result"
|
||||||
|
return self.job_id
|
||||||
|
|
||||||
|
|
||||||
|
def set_job_id(self, _id):
|
||||||
|
"Sets the job-id of this result"
|
||||||
|
self.job_id = _id
|
||||||
|
|
||||||
|
|
||||||
|
def get_job_date(self):
|
||||||
|
"Gets the date of this result"
|
||||||
|
return self.job_date
|
||||||
|
|
||||||
|
|
||||||
|
def set_job_date(self, date):
|
||||||
|
"Sets the date of this result"
|
||||||
|
self.job_date = date
|
||||||
|
|
||||||
|
|
||||||
|
def get_description_dictionary(self):
|
||||||
|
"Returns a reference to the description (Dictionary)"
|
||||||
|
return self.description
|
||||||
|
|
||||||
|
|
||||||
|
def set_description_dictionary(self, dictionary):
|
||||||
|
"Sets the entire description"
|
||||||
|
self.description = dictionary
|
||||||
|
|
||||||
|
|
||||||
|
def get_description(self, key):
|
||||||
|
"Returns the description value for a given key"
|
||||||
|
if self.description.has_key(key):
|
||||||
|
return self.description[key]
|
||||||
|
|
||||||
|
else:
|
||||||
|
print "Warning Resultable: No value for key \"%s\". Returned None" % str(key)
|
||||||
|
return None
|
||||||
|
|
||||||
|
|
||||||
|
def set_description(self, key, value):
|
||||||
|
"Adds a attribute to the description"
|
||||||
|
if self.description.has_key(key):
|
||||||
|
print "Warning: Result key \"%s\" will be overwritten with \"%s\"." % (str(key), str(value))
|
||||||
|
|
||||||
|
self.description[key] = value
|
||||||
9
src/data/Signalpath.py
Normal file
9
src/data/Signalpath.py
Normal file
@ -0,0 +1,9 @@
|
|||||||
|
import numpy as N
|
||||||
|
class Signalpath:
|
||||||
|
def phase(self, degrees):
|
||||||
|
tmp = self.y[0] + 1j*self.y[1]
|
||||||
|
tmp *= N.exp(1j*degrees*N.pi/180)
|
||||||
|
self.y[0] = tmp.real
|
||||||
|
self.y[1] = tmp.imag
|
||||||
|
del tmp
|
||||||
|
return self
|
||||||
35
src/data/Temp_Result.py
Normal file
35
src/data/Temp_Result.py
Normal file
@ -0,0 +1,35 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
from Resultable import Resultable
|
||||||
|
from Drawable import Drawable
|
||||||
|
|
||||||
|
from types import *
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class Temp_Result #
|
||||||
|
# #
|
||||||
|
# Purpose: Specialised class of Resultable and Drawable #
|
||||||
|
# Contains recorded temperature data #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
class Temp_Result(Resultable, Drawable):
|
||||||
|
def __init__(self, x = None, y = None, desc = None, job_id = None, job_date = None):
|
||||||
|
Resultable.__init__(self)
|
||||||
|
Drawable.__init__(self)
|
||||||
|
|
||||||
|
|
||||||
|
if (x is None) and (y is None) and (desc is None) and (job_id is None) and (job_date is None):
|
||||||
|
pass
|
||||||
|
|
||||||
|
elif (x is not None) and (y is not None) and (desc is not None) and (job_id is not None) and (job_date is not None):
|
||||||
|
pass
|
||||||
|
|
||||||
|
else:
|
||||||
|
raise ValueError("Wrong usage of __init__!")
|
||||||
|
|
||||||
|
|
||||||
|
# Überladen von Operatoren und Built-Ins -------------------------------------------------------
|
||||||
|
|
||||||
|
# / Überladen von Operatoren und Built-Ins -----------------------------------------------------
|
||||||
9
src/data/__init__.py
Normal file
9
src/data/__init__.py
Normal file
@ -0,0 +1,9 @@
|
|||||||
|
from damaris.data.ADC_Result import ADC_Result
|
||||||
|
from damaris.data.Accumulation import Accumulation
|
||||||
|
from damaris.data.MeasurementResult import MeasurementResult, AccumulatedValue
|
||||||
|
from damaris.data.DataPool import DataPool
|
||||||
|
from damaris.data.Error_Result import Error_Result
|
||||||
|
from damaris.data.Config_Result import Config_Result
|
||||||
|
|
||||||
|
__all__=["ADC_Result", "Accumulation", "MeasurementResult", "AccumulatedValue", "DataPool", "FFT", "Error_Result", "Config_Result" ]
|
||||||
|
|
||||||
63
src/data/autophase.py
Normal file
63
src/data/autophase.py
Normal file
@ -0,0 +1,63 @@
|
|||||||
|
from scipy.optimize import fmin_powell, bisect, ridder, brentq
|
||||||
|
import numpy as N
|
||||||
|
|
||||||
|
def calculate_entropy(phi, real, imag, gamma, dwell):
|
||||||
|
"""
|
||||||
|
Calculates the entropy of the spectrum (real part).
|
||||||
|
p = phase
|
||||||
|
gamma should be adjusted such that the penalty and entropy are in the same magnitude
|
||||||
|
"""
|
||||||
|
# This is first order phasecorrection
|
||||||
|
# corr_phase = phi[0]+phi[1]*arange(0,len(signal),1.0)/len(signal) # For 0th and 1st correction
|
||||||
|
|
||||||
|
# Zero order phase correction
|
||||||
|
real_part = real*N.cos(phi)-imag*N.sin(phi)
|
||||||
|
|
||||||
|
# Either this for calculating derivatives:
|
||||||
|
# Zwei-Punkt-Formel
|
||||||
|
# real_diff = (Re[1:]-Re[:-1])/dwell
|
||||||
|
# Better this:
|
||||||
|
# Drei-Punkte-Mittelpunkt-Formel (Ränder werden nicht beachtet)
|
||||||
|
# real_diff = abs((Re[2:]-Re[:-2])/(dwell*2))
|
||||||
|
# Even better:
|
||||||
|
# Fünf-Punkte-Mittelpunkt-Formel (ohne Ränder)
|
||||||
|
real_diff = N.abs((real_part[:-4]-8*real_part[1:-3]
|
||||||
|
+8*real_part[3:-1]-2*real_part[4:])/(12*dwell))
|
||||||
|
|
||||||
|
# TODO Ränder, sind wahrscheinlich nicht kritisch
|
||||||
|
|
||||||
|
# Calculate the entropy
|
||||||
|
h = real_diff/real_diff.sum()
|
||||||
|
# Set all h with 0 to 1 (log would complain)
|
||||||
|
h[h==0]=1
|
||||||
|
entropy = N.sum(-h*N.log(h))
|
||||||
|
|
||||||
|
# My version, according the paper
|
||||||
|
#penalty = gamma*sum([val**2 for val in Re if val < 0])
|
||||||
|
# calculate penalty value: a real spectrum should have positive values
|
||||||
|
if real_part.sum() < 0:
|
||||||
|
tmp = real_part[real_part<0]
|
||||||
|
penalty = N.dot(tmp,tmp)
|
||||||
|
if gamma == 0:
|
||||||
|
gamma = entropy/penalty
|
||||||
|
penalty = N.dot(tmp,tmp)*gamma
|
||||||
|
else:
|
||||||
|
penalty = 0
|
||||||
|
#print "Entropy:",entrop,"Penalty:",penalty # Debugging
|
||||||
|
shannon = entropy+penalty
|
||||||
|
return shannon
|
||||||
|
|
||||||
|
def get_phase(result_object):
|
||||||
|
global gamma
|
||||||
|
gamma=0
|
||||||
|
real = result_object.y[0].copy()
|
||||||
|
imag = result_object.y[1].copy()
|
||||||
|
dwell = 1.0/result_object.sampling_rate
|
||||||
|
# fmin also possible
|
||||||
|
xopt = fmin_powell( func=calculate_entropy,
|
||||||
|
x0=N.array([0.0]),
|
||||||
|
args=(real, imag, gamma, dwell),
|
||||||
|
disp=0)
|
||||||
|
result_object.y[0] = real*N.cos(xopt) - imag*N.sin(xopt)
|
||||||
|
result_object.y[1] = real*N.sin(xopt) + imag*N.cos(xopt)
|
||||||
|
return result_object
|
||||||
491
src/experiments/Experiment.py
Normal file
491
src/experiments/Experiment.py
Normal file
@ -0,0 +1,491 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
import types
|
||||||
|
import numpy
|
||||||
|
|
||||||
|
class StateBase(object):
|
||||||
|
def __init__(self):
|
||||||
|
pass
|
||||||
|
def to_xml(self, indent = ""):
|
||||||
|
return indent + "<!-- " + repr(self) + " -->"
|
||||||
|
|
||||||
|
class StateSimple(StateBase):
|
||||||
|
def __init__(self, time, content=None):
|
||||||
|
super(StateSimple, self).__init__()
|
||||||
|
if time < 0:
|
||||||
|
raise AssertionError("time for state is negative!")
|
||||||
|
self.time = time
|
||||||
|
self.content = content
|
||||||
|
|
||||||
|
def to_xml(self, indent = ""):
|
||||||
|
s = indent + '<state time="%s"' % repr(self.time)
|
||||||
|
if self.content is None:
|
||||||
|
return s + '/>\n'
|
||||||
|
s += '>\n'
|
||||||
|
s += indent + ' ' + str(self.content) + '\n'
|
||||||
|
s += indent + '</state>\n'
|
||||||
|
return s
|
||||||
|
def __repr__(self):
|
||||||
|
return 'StateSimple(%s, %s)' % (self.time, repr(self.content))
|
||||||
|
|
||||||
|
class StateList(StateBase):
|
||||||
|
def __init__(self):
|
||||||
|
super(StateList, self).__init__()
|
||||||
|
self.list = []
|
||||||
|
def to_xml(self, indent = " "):
|
||||||
|
s = ""
|
||||||
|
for k in self.list:
|
||||||
|
if hasattr(k, "to_xml"):
|
||||||
|
s += k.to_xml(indent)
|
||||||
|
else:
|
||||||
|
s += indent + str(k)
|
||||||
|
return s
|
||||||
|
def append(self, val):
|
||||||
|
self.list.append(val)
|
||||||
|
|
||||||
|
|
||||||
|
class StateLoop(StateList):
|
||||||
|
"""Represents a loop in the state tree"""
|
||||||
|
def __init__(self, repeat):
|
||||||
|
super(StateLoop, self).__init__()
|
||||||
|
self.repeat = repeat
|
||||||
|
def to_xml(self, indent = ""):
|
||||||
|
s = indent + ('<sequent repeat="%d">\n' % self.repeat)
|
||||||
|
s += super(StateLoop, self).to_xml(indent + " ")
|
||||||
|
s += indent + '</sequent>\n'
|
||||||
|
return s
|
||||||
|
def __repr__(self):
|
||||||
|
return 'StateLoop(repeat=%d, %s)' \
|
||||||
|
% (self.repeat, repr(self.list))
|
||||||
|
|
||||||
|
|
||||||
|
#############################################################
|
||||||
|
# #
|
||||||
|
# Class: Experiment #
|
||||||
|
# #
|
||||||
|
# Purpose: Represents one full experiment (one program on #
|
||||||
|
# the pulse-card; one file) #
|
||||||
|
# #
|
||||||
|
#############################################################
|
||||||
|
import dac
|
||||||
|
|
||||||
|
class Experiment:
|
||||||
|
## Experiment class holding the state tree
|
||||||
|
|
||||||
|
job_id = 0
|
||||||
|
|
||||||
|
def __init__(self):
|
||||||
|
self.job_id = Experiment.job_id
|
||||||
|
Experiment.job_id += 1
|
||||||
|
|
||||||
|
self.state_list = StateList()
|
||||||
|
self.list_stack = []
|
||||||
|
self.description = { }
|
||||||
|
|
||||||
|
|
||||||
|
# Commands -------------------------------------------------------------------------------------
|
||||||
|
## Deprecated
|
||||||
|
def rf_pulse(self, value, length = None):
|
||||||
|
"""
|
||||||
|
deprecated: use ttl_pulse
|
||||||
|
"""
|
||||||
|
s_content = '<ttlout value="0x%06x"/>' % value
|
||||||
|
|
||||||
|
if length is None:
|
||||||
|
self.state_list.append(s_content)
|
||||||
|
else:
|
||||||
|
self.state_list.append(StateSimple(length, s_content))
|
||||||
|
|
||||||
|
## Creates a state with ttl signals of duration *length*.
|
||||||
|
#
|
||||||
|
# **Example:**
|
||||||
|
# ttl_pulse(length=1e-6,value=3)
|
||||||
|
# will create a ttl pulse on channels 0 and 1 (2**0 + 2**1) of duration 1us
|
||||||
|
# @param length time length if this state
|
||||||
|
# @param channel select a single channel (1...24)
|
||||||
|
# @param value select the channels via decimal representation (2**0 + 2**1 ...)
|
||||||
|
def ttl_pulse(self, length, channel = None, value = None):
|
||||||
|
"""
|
||||||
|
Creates a state with length *length* and switches
|
||||||
|
some bits of the pulse programmer to HIGH:
|
||||||
|
* channel: this selects a single channel (No. 1 - 24)
|
||||||
|
* value: this is the integer representation of the 24bit word,
|
||||||
|
as an example value=3 selects channels 1 and 2 (2**1 + 2**2)
|
||||||
|
"""
|
||||||
|
the_value=0
|
||||||
|
if value is not None:
|
||||||
|
the_value=int(value)
|
||||||
|
elif channel is not None:
|
||||||
|
the_value=1<<channel
|
||||||
|
self.state_list.append(StateSimple(length, \
|
||||||
|
'<ttlout value="0x%06x"/>' % the_value))
|
||||||
|
|
||||||
|
## Same as ttl_pulse, but no *channel* keyword
|
||||||
|
def ttls(self, length = None, value = None):
|
||||||
|
"""
|
||||||
|
same as ttl_pulse, but no *channel* keyword
|
||||||
|
"""
|
||||||
|
the_value=int(value)
|
||||||
|
s_content = '<ttlout value="0x%06x"/>' % the_value
|
||||||
|
if length is not None:
|
||||||
|
self.state_list.append(StateSimple(length, s_content))
|
||||||
|
else:
|
||||||
|
self.state_list.append(s_content)
|
||||||
|
## Beginning of a new state
|
||||||
|
def state_start(self, time):
|
||||||
|
"""
|
||||||
|
starts a state in the pulse programs with duration *time*.
|
||||||
|
This must be closed with state_end
|
||||||
|
"""
|
||||||
|
self.state_list.append('<state time="%s">\n' % repr(time))
|
||||||
|
|
||||||
|
## End of *state_start*
|
||||||
|
def state_end(self):
|
||||||
|
"""
|
||||||
|
closes a state after start_state
|
||||||
|
"""
|
||||||
|
self.state_list.append('</state>\n')
|
||||||
|
|
||||||
|
## An empty state doing nothing
|
||||||
|
# @param time Duration of this state
|
||||||
|
# @param ttls Additinional ttl channels
|
||||||
|
def wait(self, time, ttls=None):
|
||||||
|
if ttls is not None:
|
||||||
|
s_content = '<ttlout value="0x%06x"/>' % ttls
|
||||||
|
self.state_list.append(StateSimple(time,s_content))
|
||||||
|
else:
|
||||||
|
self.state_list.append(StateSimple(time))
|
||||||
|
|
||||||
|
## Records data with given number of samples, sampling-frequency frequency and sensitivity
|
||||||
|
# @param samples Number of samples to record
|
||||||
|
# @param frequency Sampling frequency
|
||||||
|
# @param timelength Length of this state, per default calculated automatically
|
||||||
|
# @param sensitivity Sensitivity in Umax/V
|
||||||
|
# @param ttls Additional ttl channels
|
||||||
|
def record(self, samples, frequency, timelength=None, sensitivity = None, ttls=None, channels = 3, offset = None, impedance = None):
|
||||||
|
attributes='s="%d" f="%d"'%(samples,frequency)#%g
|
||||||
|
if channels != 1 and channels != 3 and channels != 5 and channels != 15:
|
||||||
|
raise ValueError, "Channel definition is illegal"
|
||||||
|
attributes += ' channels="%i"'%(channels)
|
||||||
|
|
||||||
|
nchannels = 0
|
||||||
|
if channels == 1:
|
||||||
|
nchannels = 1
|
||||||
|
elif channels == 3 or channels == 5:
|
||||||
|
nchannels = 2
|
||||||
|
elif channels == 15:
|
||||||
|
nchannels = 4
|
||||||
|
if sensitivity is not None:
|
||||||
|
# float values are allowed and applied to all channels
|
||||||
|
if isinstance(sensitivity, float) or isinstance(sensitivity, int):
|
||||||
|
for i in range(nchannels):
|
||||||
|
attributes +=' sensitivity%i="%f"'%(i, float(sensitivity))
|
||||||
|
else:
|
||||||
|
for i in range(nchannels):
|
||||||
|
attributes +=' sensitivity%i="%f"'%(i, sensitivity[i])
|
||||||
|
if offset is not None:
|
||||||
|
# int values are allowed and applied to all channels
|
||||||
|
if isinstance(offset, int):
|
||||||
|
for i in range(nchannels):
|
||||||
|
attributes +=' offset%i="%f"'%(i, offset)
|
||||||
|
else:
|
||||||
|
for i in range(nchannels):
|
||||||
|
attributes +=' offset%i="%f"'%(i, offset[i])
|
||||||
|
if impedance is not None:
|
||||||
|
# float values are allowed and applied to all channels
|
||||||
|
if isinstance(impedance, float):
|
||||||
|
for i in range(nchannels):
|
||||||
|
attributes += ' impedance%i="%i"'%(i, impedance)
|
||||||
|
else:
|
||||||
|
for i in range(nchannels):
|
||||||
|
attributes += ' impedance%i="%i"'%(i, impedance[i])
|
||||||
|
|
||||||
|
s_content = '<analogin %s/>' % attributes
|
||||||
|
if ttls is not None:
|
||||||
|
s_content+='<ttlout value="0x%06x"/>' % ttls
|
||||||
|
if timelength is None:
|
||||||
|
timelength = samples / float(frequency)#*1.01
|
||||||
|
self.state_list.append(StateSimple(timelength, s_content))
|
||||||
|
|
||||||
|
## Create a loop on the pulse programmer. Loop contents can not change inside the loop.
|
||||||
|
# @params iterations Number of loop iterations
|
||||||
|
def loop_start(self, iterations):
|
||||||
|
"""creates a loop of given number of iterations and has to be closed by loop_end().
|
||||||
|
Commands inside the loop can not change, i.e. the parameters are the same for each loop run.
|
||||||
|
This loop is created on the pulse programmer, thus saving commands.
|
||||||
|
One must close the loop with loop_end (see below)"""
|
||||||
|
l = StateLoop(iterations)
|
||||||
|
self.state_list.append(l)
|
||||||
|
# (These two lines could probably be guarded by a mutex)
|
||||||
|
self.list_stack.append(self.state_list)
|
||||||
|
self.state_list = l
|
||||||
|
|
||||||
|
## End loop state
|
||||||
|
def loop_end(self):
|
||||||
|
# (This line could probably be guarded by a mutex)
|
||||||
|
self.state_list = self.list_stack.pop(-1)
|
||||||
|
|
||||||
|
## Set the frequency and phase of the frequency source.
|
||||||
|
## This state needs 2us.
|
||||||
|
# @param frequency New frequency in Hz
|
||||||
|
# @param phase New phase in degrees
|
||||||
|
# @param ttls Additional ttl channels
|
||||||
|
def set_frequency(self, frequency, phase, ttls=0):
|
||||||
|
"""
|
||||||
|
Sets the frequency and phase of the frequency source and optionally further channels.
|
||||||
|
The time needed to set the frequency is 2 us.
|
||||||
|
Switch pulse programmer line with *ttls* .
|
||||||
|
|
||||||
|
"""
|
||||||
|
"Sets the frequency generator to a desired frequency (Hz)"
|
||||||
|
s_content = '<analogout id="0" f="%f" phase="%f"/>' % (frequency, phase)
|
||||||
|
if ttls != 0:
|
||||||
|
s_content += '<ttlout value="0x%06x"/>' % ttls
|
||||||
|
self.state_list.append(StateSimple(2e-6, s_content))
|
||||||
|
## Creates a, possibly shaped, pulsed gradient.
|
||||||
|
# @param dac_value DAC value to set
|
||||||
|
# @param length Duration of the state, minimum length is 42*90ns=3.78us (default)
|
||||||
|
# @param shape Tuple of (shape, resolution/seconds), shape can be one of: rec (default), sin2, sin
|
||||||
|
# @param is_seq If set to *True*, do NOT set DAC to zero after this state
|
||||||
|
# @param trigger Additional ttl channels
|
||||||
|
def set_pfg(self, dac_value=None, length=None, shape=('rec',0), trigger=4, is_seq=False):
|
||||||
|
"""
|
||||||
|
This sets the value for the PFG, it also sets it back automatically.
|
||||||
|
If you don't whish to do so (i.e. line shapes) set is_seq=1
|
||||||
|
If you wnat to set a trigger, set trigger (default=4, i.e. channel 2)
|
||||||
|
If you want shaped gradients: shape=(ashape, resolution), ashape can be rec, sin2, sin
|
||||||
|
|
||||||
|
"""
|
||||||
|
try:
|
||||||
|
form, resolution = shape
|
||||||
|
except:
|
||||||
|
raise SyntaxError, "shape argument needs to be a tuple, i.e. ('shape',resolution), shape can be sin, sin2, rec"
|
||||||
|
|
||||||
|
if length == None:
|
||||||
|
# mimimum length
|
||||||
|
length=42*9e-8
|
||||||
|
if resolution >= length:
|
||||||
|
raise ValueError, "Resolution %.3e of shaped gradients can not be longer than total length %.3e"%(resolution, length)
|
||||||
|
|
||||||
|
if resolution < 42*9e-8:
|
||||||
|
raise ValueError, "Resulution %.3e can not be smaller than %.3e"%(resolution, 42*9e-8)
|
||||||
|
|
||||||
|
t_steps = numpy.arange(0,length,resolution)
|
||||||
|
|
||||||
|
if form == 'rec': # shape==None --> rectangular gradients
|
||||||
|
s_content = '<ttlout value="%s"/><analogout id="1" dac_value="%i"/>' % (trigger, dac_value)
|
||||||
|
self.state_list.append(StateSimple(length, s_content))
|
||||||
|
|
||||||
|
if not is_seq and shape == None:
|
||||||
|
s_content = '<analogout id="1" dac_value="0"/>'
|
||||||
|
self.state_list.append(StateSimple(42*9e-8, s_content))
|
||||||
|
|
||||||
|
elif form == 'sin2':
|
||||||
|
# sin**2 shape
|
||||||
|
for t in t_steps:
|
||||||
|
dac = int (dac_value*numpy.sin(numpy.pi/length*t)**2)
|
||||||
|
s_content = '<ttlout value="%s"/><analogout id="1" dac_value="%i"/>' % (trigger, dac)
|
||||||
|
self.state_list.append(StateSimple(resolution, s_content))
|
||||||
|
# set it back to zero
|
||||||
|
s_content = '<ttlout value="%s"/><analogout id="1" dac_value="0"/>' % (trigger)
|
||||||
|
self.state_list.append(StateSimple(resolution, s_content))
|
||||||
|
|
||||||
|
elif form == 'sin':
|
||||||
|
# sin shape
|
||||||
|
for t in t_steps:
|
||||||
|
dac = int (dac_value*numpy.sin(numpy.pi/length*t))
|
||||||
|
s_content = '<ttlout value="%s"/><analogout id="1" dac_value="%i"/>' % (trigger, dac)
|
||||||
|
self.state_list.append(StateSimple(resolution, s_content))
|
||||||
|
# set it back to zero
|
||||||
|
s_content = '<ttlout value="%s"/><analogout id="1" dac_value="0"/>' % (trigger)
|
||||||
|
self.state_list.append(StateSimple(resolution, s_content))
|
||||||
|
|
||||||
|
else: # don't know what to do
|
||||||
|
raise SyntaxError , "form is unknown: %s"%form
|
||||||
|
|
||||||
|
## Deprecated, use set_pfg instead
|
||||||
|
def set_pfg_wt(self, I_out=None, dac_value=None, length=None, is_seq=0, trigger=4):
|
||||||
|
"""
|
||||||
|
This sets the value for the PFG (plus trigger, default=2**2), it also sets it back automatically.
|
||||||
|
If you don't whish to do so (i.e. line shapes) set is_seq=1
|
||||||
|
"""
|
||||||
|
# raise DeprecationWarning, "to be removed in future, use set_pfg instead"
|
||||||
|
if I_out == None and dac_value == None:
|
||||||
|
dac_value=0
|
||||||
|
if I_out != None and dac_value == None:
|
||||||
|
dac_value=dac.conv(I_out)
|
||||||
|
if I_out == None and dac_value != None:
|
||||||
|
dac_value=dac_value
|
||||||
|
if I_out !=None and dac_value != None:
|
||||||
|
dac_value = 0
|
||||||
|
print "WARNING: You can't set both, I_out and dac_value! dac_value set to 0"
|
||||||
|
if length==None:
|
||||||
|
length=42*9e-8
|
||||||
|
s_content = '<analogout id="1" dac_value="%i"/><ttlout value="%s"/>' \
|
||||||
|
% (dac_value, trigger)
|
||||||
|
self.state_list.append(StateSimple(length, s_content))
|
||||||
|
if is_seq == 0:
|
||||||
|
s_content = '<analogout id="1" dac_value="0"/><ttlout value="%s"/>' \
|
||||||
|
% trigger
|
||||||
|
self.state_list.append(StateSimple(42*9e-8, s_content))
|
||||||
|
|
||||||
|
## sets the value of a DAC
|
||||||
|
# @param dac_value DAC value to set
|
||||||
|
# @param dac_id ID of the dac in case of multiple DAC(default=1)
|
||||||
|
# @param length Duration of the state
|
||||||
|
# @param is_seq If set to *True*, do NOT set DAC to zero after this state
|
||||||
|
# @param ttls Additional ttl channels
|
||||||
|
def set_dac(self, dac_value, dac_id=1, length=None, is_seq=False, ttls=0):
|
||||||
|
"""
|
||||||
|
This sets the value for the DAC and possibly some TTLs.
|
||||||
|
It also sets it back automatically.
|
||||||
|
If you don't whish to do so (i.e. line shapes) set is_seq=True
|
||||||
|
"""
|
||||||
|
if length==None:
|
||||||
|
length=42*9e-8
|
||||||
|
s_content = '<analogout id="%d" dac_value="%i"/><ttlout value="0x%06x"/>' \
|
||||||
|
% (dac_id, dac_value, ttls)
|
||||||
|
self.state_list.append(StateSimple(length, s_content))
|
||||||
|
if not is_seq:
|
||||||
|
s_content = '<analogout id="%d" dac_value="0"/><ttlout value="0x%06x"/>' \
|
||||||
|
% (dac_id, ttls)
|
||||||
|
self.state_list.append(StateSimple(42*9e-8, s_content))
|
||||||
|
|
||||||
|
## sets the phase of the frequency source.
|
||||||
|
## This state needs 0.5us, though the phase switching time is dependent on the frequency source
|
||||||
|
# @param phase New phase to set
|
||||||
|
# @param ttls Additional ttl channels
|
||||||
|
def set_phase(self, phase, ttls=0):
|
||||||
|
s_content = '<analogout phase="%f" />' % (phase)
|
||||||
|
if ttls!=0:
|
||||||
|
s_content += '<ttlout value="%d"/>' % ttls
|
||||||
|
self.state_list.append(StateSimple(0.5e-6, s_content))
|
||||||
|
|
||||||
|
## sets a description which is carried via the back end result
|
||||||
|
## file to the result script in the front end. In the result script
|
||||||
|
## you can extract the description with get_description(key)
|
||||||
|
# @param key Name of description
|
||||||
|
# @param value Value of description
|
||||||
|
def set_description(self, key, value):
|
||||||
|
"""Sets a description which is carried via the back end result
|
||||||
|
file to the result script in the front end. In the result script
|
||||||
|
you can extract the description with get_description"""
|
||||||
|
if key in self.description.keys():
|
||||||
|
print 'Warning: Overwriting existing description "%s" = "%s" with "%s"' % (key, self.description[key], value)
|
||||||
|
|
||||||
|
self.description[key] = value
|
||||||
|
|
||||||
|
## set the PTS310/PTS500 frequency source to local mode
|
||||||
|
def set_pts_local(self):
|
||||||
|
"""
|
||||||
|
this will set the PTS310/PTS500 frequency source to local mode
|
||||||
|
"""
|
||||||
|
self.state_list.append(StateSimple(1e-6, '<ttlout value="0xf000"/>'))
|
||||||
|
self.state_list.append(StateSimple(1e-6, '<ttlout value="0x8000"/>'))
|
||||||
|
|
||||||
|
# / Commands -----------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
|
||||||
|
# Public Methods -------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
def get_job_id(self):
|
||||||
|
"Returns the current job-id the experiment got"
|
||||||
|
return self.job_id
|
||||||
|
|
||||||
|
|
||||||
|
def write_xml_string(self):
|
||||||
|
"Returns the current program as a string"
|
||||||
|
|
||||||
|
# Standart XML-Kopf
|
||||||
|
xml_string = '<?xml version="1.0" encoding="ISO-8859-1"?>\n'
|
||||||
|
|
||||||
|
# Experiment-Start-Tag einfügen
|
||||||
|
xml_string += '<experiment no="%d">\n' % self.job_id
|
||||||
|
|
||||||
|
# Descriptions einfügen
|
||||||
|
if len(self.description)==0:
|
||||||
|
xml_string += ' <description/>\n'
|
||||||
|
else:
|
||||||
|
xml_string += ' <description>\n'
|
||||||
|
for key,value in self.description.iteritems():
|
||||||
|
type_string="repr"
|
||||||
|
if value is None:
|
||||||
|
type_string="None"
|
||||||
|
value=""
|
||||||
|
elif type(value) is types.FloatType or isinstance(value, numpy.floating):
|
||||||
|
type_string="Float"
|
||||||
|
value=repr(value)
|
||||||
|
elif type(value) is types.IntType or isinstance(value, numpy.integer):
|
||||||
|
type_string="Int"
|
||||||
|
value=repr(value)
|
||||||
|
elif type(value) is types.LongType:
|
||||||
|
type_string="Long"
|
||||||
|
value=repr(value)
|
||||||
|
elif type(value) is types.ComplexType or isinstance(value, numpy.complexfloating):
|
||||||
|
type_string="Complex"
|
||||||
|
value=repr(value)
|
||||||
|
elif type(value) is types.BooleanType or isinstance(value, numpy.bool_):
|
||||||
|
type_string="Boolean"
|
||||||
|
value=repr(value)
|
||||||
|
elif type(value) in types.StringTypes:
|
||||||
|
type_string="String"
|
||||||
|
else:
|
||||||
|
value=repr(value)
|
||||||
|
xml_string += ' <item key="%s" type="%s">%s</item>\n'%(key, type_string ,value)
|
||||||
|
xml_string += " </description>\n"
|
||||||
|
|
||||||
|
# Experiment-Inhalt einfügen
|
||||||
|
xml_string += self.state_list.to_xml(indent = " ")
|
||||||
|
|
||||||
|
# Experiment-End-Tag
|
||||||
|
xml_string += '</experiment>\n'
|
||||||
|
|
||||||
|
return xml_string
|
||||||
|
|
||||||
|
def write_quit_job(self):
|
||||||
|
"Returns a xml quit-job"
|
||||||
|
return '<?xml version="1.0" encoding="ISO-8859-1"?>\n<quit/>'
|
||||||
|
|
||||||
|
|
||||||
|
class Quit(Experiment):
|
||||||
|
def write_xml_string(self):
|
||||||
|
return '<?xml version="1.0" encoding="ISO-8859-1"?>\n<quit no="%d"/>'%self.job_id
|
||||||
|
|
||||||
|
|
||||||
|
# /Public Methods ------------------------------------------------------------------------------
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def self_test():
|
||||||
|
e = Experiment()
|
||||||
|
e.set_description("key", "value")
|
||||||
|
e.set_frequency(85e6, 90, ttls=16)
|
||||||
|
e.wait(1e-6)
|
||||||
|
e.rf_pulse(1, 1e-6/3) # val = 1
|
||||||
|
e.ttl_pulse(1e-6/3, 1) # val = 2
|
||||||
|
e.ttl_pulse(1e-6/3, None, 7) # val = 7
|
||||||
|
if True:
|
||||||
|
e.loop_start(30)
|
||||||
|
e.set_pfg(dac_value=1024, is_seq = True)
|
||||||
|
e.set_pfg_wt(dac_value=2048)
|
||||||
|
e.loop_start(400)
|
||||||
|
e.set_phase(270, ttls = 32)
|
||||||
|
e.loop_end()
|
||||||
|
e.ttl_pulse(5e-6, channel = 6)
|
||||||
|
e.loop_end()
|
||||||
|
else:
|
||||||
|
l = StateLoop(3)
|
||||||
|
l.append(StateSimple(5e-6, '<ttlout value="1"/>'))
|
||||||
|
e.state_list.append(l)
|
||||||
|
e.set_dac(12345, dac_id=2, is_seq = True, ttls=16)
|
||||||
|
e.record(1024, 20e6)
|
||||||
|
try:
|
||||||
|
e.wait(-1)
|
||||||
|
except AssertionError:
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
raise AssertionError("An exception should happen")
|
||||||
|
e.set_pts_local()
|
||||||
|
print e.write_xml_string()
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
self_test()
|
||||||
3
src/experiments/__init__.py
Normal file
3
src/experiments/__init__.py
Normal file
@ -0,0 +1,3 @@
|
|||||||
|
from Experiment import Experiment
|
||||||
|
from damaris.tools.ranges import *
|
||||||
|
#__all__=["Experiment"]
|
||||||
12
src/experiments/dac.py
Normal file
12
src/experiments/dac.py
Normal file
@ -0,0 +1,12 @@
|
|||||||
|
#import math
|
||||||
|
"""
|
||||||
|
This module holds everything connected with the DAC and PFG
|
||||||
|
"""
|
||||||
|
def conv(I_out=0):
|
||||||
|
"""
|
||||||
|
converts the demanded Output current in Integer
|
||||||
|
"""
|
||||||
|
V_dac=I_out/50.0
|
||||||
|
dac_value=-(V_dac-0.00983)/1.81413e-5
|
||||||
|
return int(dac_value)
|
||||||
|
|
||||||
294
src/gui/BackendDriver.py
Normal file
294
src/gui/BackendDriver.py
Normal file
@ -0,0 +1,294 @@
|
|||||||
|
import os
|
||||||
|
import os.path
|
||||||
|
import subprocess
|
||||||
|
import sys
|
||||||
|
import time
|
||||||
|
import re
|
||||||
|
import glob
|
||||||
|
import ExperimentWriter
|
||||||
|
import ResultReader
|
||||||
|
import threading
|
||||||
|
import types
|
||||||
|
import signal
|
||||||
|
|
||||||
|
if sys.platform=="win32":
|
||||||
|
import _winreg
|
||||||
|
|
||||||
|
__doc__ = """
|
||||||
|
This class handles the backend driver
|
||||||
|
"""
|
||||||
|
|
||||||
|
class BackendDriver(threading.Thread):
|
||||||
|
|
||||||
|
def __init__(self, executable, spool, clear_jobs=False, clear_results=False):
|
||||||
|
threading.Thread.__init__(self, name="Backend Driver")
|
||||||
|
self.core_pid = None
|
||||||
|
self.core_input = None
|
||||||
|
self.core_output = None
|
||||||
|
self.statefilename = None
|
||||||
|
|
||||||
|
self.executable=str(executable)
|
||||||
|
self.spool_dir=spool
|
||||||
|
self.experiment_pattern="job.%09d"
|
||||||
|
self.result_pattern=self.experiment_pattern+".result"
|
||||||
|
|
||||||
|
if not os.path.isfile(self.executable):
|
||||||
|
raise AssertionError("could not find backend %s "%self.executable)
|
||||||
|
if not os.access(self.executable,os.X_OK):
|
||||||
|
raise AssertionError("insufficient rights for backend %s execution"%self.executable)
|
||||||
|
if not os.path.isdir(self.spool_dir):
|
||||||
|
try:
|
||||||
|
os.makedirs(os.path.abspath(self.spool_dir))
|
||||||
|
except OSError,e:
|
||||||
|
print e
|
||||||
|
raise AssertionError("could not create backend's spool directory %s "%self.spool_dir)
|
||||||
|
|
||||||
|
# remove stale state filenames
|
||||||
|
if sys.platform.startswith("linux") or sys.platform.startswith("darwin"):
|
||||||
|
old_state_files=glob.glob(os.path.join(self.spool_dir,"*.state"))
|
||||||
|
statelinepattern=re.compile("<state name=\"([^\"]+)\" pid=\"([^\"]+)\" starttime=\"([^\"]+)\">")
|
||||||
|
for statefilename in old_state_files:
|
||||||
|
statefile=file(statefilename,"r")
|
||||||
|
statelines=statefile.readlines()
|
||||||
|
statefile.close
|
||||||
|
del statefile
|
||||||
|
core_pid=None
|
||||||
|
for l in statelines:
|
||||||
|
matched=statelinepattern.match(l)
|
||||||
|
if matched:
|
||||||
|
core_pid=int(matched.group(2))
|
||||||
|
break
|
||||||
|
if core_pid is not None:
|
||||||
|
if os.path.isdir("/proc/%d"%core_pid):
|
||||||
|
raise AssertionError("found backend with pid %d (state file %s) in same spool dir"%(core_pid,statefilename))
|
||||||
|
else:
|
||||||
|
print "removing stale backend state file", statefilename
|
||||||
|
os.remove(statefilename)
|
||||||
|
else:
|
||||||
|
print "todo: take care of existing backend state files"
|
||||||
|
|
||||||
|
self.result_reader = ResultReader.BlockingResultReader(self.spool_dir,
|
||||||
|
no=0,
|
||||||
|
result_pattern=self.result_pattern,
|
||||||
|
clear_jobs=clear_jobs,
|
||||||
|
clear_results=clear_results)
|
||||||
|
self.experiment_writer = ExperimentWriter.ExperimentWriterWithCleanup(self.spool_dir,
|
||||||
|
no=0,
|
||||||
|
job_pattern=self.experiment_pattern,
|
||||||
|
inform_last_job=self.result_reader)
|
||||||
|
|
||||||
|
self.quit_flag=threading.Event()
|
||||||
|
self.raised_exception=None
|
||||||
|
|
||||||
|
def run(self):
|
||||||
|
# take care of older logfiles
|
||||||
|
self.core_output_filename=os.path.join(self.spool_dir,"logdata")
|
||||||
|
if os.path.isfile(self.core_output_filename):
|
||||||
|
i=0
|
||||||
|
max_logs=100
|
||||||
|
while os.path.isfile(self.core_output_filename+".%02d"%i):
|
||||||
|
i+=1
|
||||||
|
while (i>=max_logs):
|
||||||
|
i-=1
|
||||||
|
os.remove(self.core_output_filename+".%02d"%i)
|
||||||
|
for j in xrange(i):
|
||||||
|
os.rename(self.core_output_filename+".%02d"%(i-j-1),self.core_output_filename+".%02d"%(i-j))
|
||||||
|
os.rename(self.core_output_filename, self.core_output_filename+".%02d"%0)
|
||||||
|
# create logfile
|
||||||
|
self.core_output=file(self.core_output_filename,"w")
|
||||||
|
|
||||||
|
# again look out for existing state files
|
||||||
|
state_files=glob.glob(os.path.join(self.spool_dir,"*.state"))
|
||||||
|
if state_files:
|
||||||
|
self.raised_exception="found other state file(s) in spool directory: "+",".join(state_files)
|
||||||
|
self.quit_flag.set()
|
||||||
|
return
|
||||||
|
|
||||||
|
# start backend
|
||||||
|
if sys.platform.startswith("linux") or sys.platform.startswith("darwin"):
|
||||||
|
self.core_input=subprocess.Popen([self.executable, "--spool", self.spool_dir],
|
||||||
|
stdout=self.core_output,
|
||||||
|
stderr=self.core_output)
|
||||||
|
|
||||||
|
if sys.platform=="win32":
|
||||||
|
cygwin_root_key=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\Cygnus Solutions\\Cygwin\\mounts v2\\/")
|
||||||
|
cygwin_path=_winreg.QueryValueEx(cygwin_root_key,"native")[0]
|
||||||
|
os.environ["PATH"]+=";"+os.path.join(cygwin_path,"bin")+";"+os.path.join(cygwin_path,"lib")
|
||||||
|
self.core_input=subprocess.Popen("\"" + self.executable + "\"" + " --spool "+self.spool_dir,
|
||||||
|
stdout=self.core_output,
|
||||||
|
stderr=self.core_output)
|
||||||
|
|
||||||
|
# wait till state file shows up
|
||||||
|
timeout=10
|
||||||
|
# to do: how should I know core's state name????!!!!!
|
||||||
|
self.statefilename=None
|
||||||
|
state_files=glob.glob(os.path.join(self.spool_dir,"*.state"))
|
||||||
|
while len(state_files)==0:
|
||||||
|
if timeout<0 or self.core_input is None or self.core_input.poll() is not None or self.quit_flag.isSet():
|
||||||
|
# look into core log file and include contents
|
||||||
|
log_message=''
|
||||||
|
self.core_input=None
|
||||||
|
if os.path.isfile(self.core_output_filename):
|
||||||
|
# to do include log data
|
||||||
|
log_message='\n'+''.join(file(self.core_output_filename,"r").readlines()[:10])
|
||||||
|
if not log_message:
|
||||||
|
log_message=" no error message from core"
|
||||||
|
self.core_output.close()
|
||||||
|
self.raised_exception="no state file appeared or backend died away:"+log_message
|
||||||
|
print self.raised_exception
|
||||||
|
self.quit_flag.set()
|
||||||
|
return
|
||||||
|
time.sleep(0.05)
|
||||||
|
timeout-=0.05
|
||||||
|
state_files=glob.glob(os.path.join(self.spool_dir,"*.state"))
|
||||||
|
|
||||||
|
# save the one
|
||||||
|
if len(state_files)>1:
|
||||||
|
print "did find more than one state file, taking first one!"
|
||||||
|
self.statefilename=state_files[0]
|
||||||
|
|
||||||
|
# read state file
|
||||||
|
statefile=file(self.statefilename,"r")
|
||||||
|
statelines=statefile.readlines()
|
||||||
|
statefile=None
|
||||||
|
statelinepattern=re.compile("<state name=\"([^\"]+)\" pid=\"([^\"]+)\" starttime=\"([^\"]+)\">")
|
||||||
|
self.core_pid=-1
|
||||||
|
for l in statelines:
|
||||||
|
matched=statelinepattern.match(l)
|
||||||
|
if matched:
|
||||||
|
self.core_pid=int(matched.group(2))
|
||||||
|
break
|
||||||
|
|
||||||
|
# wait on flag and look after backend
|
||||||
|
while not self.quit_flag.isSet() and self.is_busy():
|
||||||
|
self.quit_flag.wait(0.1)
|
||||||
|
|
||||||
|
if self.quit_flag.isSet():
|
||||||
|
self.stop_queue()
|
||||||
|
while self.is_busy():
|
||||||
|
time.sleep(0.1)
|
||||||
|
|
||||||
|
if not self.is_busy():
|
||||||
|
if self.core_input is not None:
|
||||||
|
backend_result=self.core_input.poll()
|
||||||
|
wait_loop_counter=0
|
||||||
|
while backend_result is None:
|
||||||
|
# waiting in tenth of a second
|
||||||
|
time.sleep(0.1)
|
||||||
|
wait_loop_counter+=1
|
||||||
|
backend_result=self.core_input.poll()
|
||||||
|
if backend_result is not None: break
|
||||||
|
if wait_loop_counter==10:
|
||||||
|
print "sending termination signal to backend process"
|
||||||
|
self.send_signal("SIGTERM")
|
||||||
|
elif wait_loop_counter==20:
|
||||||
|
print "sending kill signal to backend process"
|
||||||
|
self.send_signal("SIGKILL")
|
||||||
|
elif wait_loop_counter>30:
|
||||||
|
print "no longer waiting for backend shutdown"
|
||||||
|
break
|
||||||
|
|
||||||
|
if backend_result is None:
|
||||||
|
print "backend dit not end properly, please stop it manually"
|
||||||
|
elif backend_result>0:
|
||||||
|
print "backend returned ", backend_result
|
||||||
|
elif backend_result<0:
|
||||||
|
sig_name=filter(lambda x: x.startswith("SIG") and \
|
||||||
|
x[3]!="_" and \
|
||||||
|
(type(signal.__dict__[x])is types.IntType) and \
|
||||||
|
signal.__dict__[x]==-backend_result,
|
||||||
|
dir(signal))
|
||||||
|
if sig_name:
|
||||||
|
print "backend was terminated by signal ",sig_name[0]
|
||||||
|
else:
|
||||||
|
print "backend was terminated by signal no",-backend_result
|
||||||
|
self.core_input = None
|
||||||
|
self.core_pid = None
|
||||||
|
|
||||||
|
# the experiment handler should stop
|
||||||
|
if self.experiment_writer is not None:
|
||||||
|
# self.experiment_writer.
|
||||||
|
self.experiment_writer=None
|
||||||
|
|
||||||
|
# tell result reader, game is over...
|
||||||
|
#self.result_reader.stop_no=self.experiment_writer.no
|
||||||
|
if self.result_reader is not None:
|
||||||
|
self.result_reader.poll_time=-1
|
||||||
|
self.result_reader=None
|
||||||
|
|
||||||
|
def clear_job(self,no):
|
||||||
|
jobfilename=os.path.join(self.spool_dir,"job.%09d")
|
||||||
|
resultfilename=os.path.join(self.spool_dir,"job.%09d.result")
|
||||||
|
if os.path.isfile(jobfilename):
|
||||||
|
os.remove(jobfilename)
|
||||||
|
if os.path.isfile(resultfilename):
|
||||||
|
os.remove(resultfilename)
|
||||||
|
|
||||||
|
def get_messages(self):
|
||||||
|
# return pending messages
|
||||||
|
if self.core_output.tell()==os.path.getsize(self.core_output_filename):
|
||||||
|
return None
|
||||||
|
return self.core_output.read()
|
||||||
|
|
||||||
|
def restart_queue(self):
|
||||||
|
self.send_signal("SIGUSR1")
|
||||||
|
|
||||||
|
def stop_queue(self):
|
||||||
|
self.send_signal("SIGQUIT")
|
||||||
|
# assumes success
|
||||||
|
#self.core_pid=None
|
||||||
|
#self.core_input=None
|
||||||
|
|
||||||
|
def abort(self):
|
||||||
|
# abort execution
|
||||||
|
self.send_signal("SIGTERM")
|
||||||
|
# assumes success
|
||||||
|
#self.core_pid=None
|
||||||
|
#self.core_input=None
|
||||||
|
|
||||||
|
def send_signal(self, sig):
|
||||||
|
if self.core_pid is None:
|
||||||
|
print "BackendDriver.send_signal is called with core_pid=None"
|
||||||
|
return
|
||||||
|
try:
|
||||||
|
if sys.platform[:5]=="linux":
|
||||||
|
os.kill(self.core_pid,signal.__dict__[sig])
|
||||||
|
if sys.platform[:7]=="win32":
|
||||||
|
# reg_handle=_winreg.ConnectRegistry(None,_winreg.HKEY_LOCAL_MACHINE)
|
||||||
|
cygwin_root_key=_winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, "SOFTWARE\\Cygnus Solutions\\Cygwin\\mounts v2\\/")
|
||||||
|
cygwin_path=_winreg.QueryValueEx(cygwin_root_key,"native")[0]
|
||||||
|
kill_command=os.path.join(cygwin_path,"bin","kill.exe")
|
||||||
|
os.popen("%s -%s %d"%(kill_command,sig,self.core_pid))
|
||||||
|
except OSError, e:
|
||||||
|
print "could not send signal %s to core: %s"%(sig, str(e))
|
||||||
|
|
||||||
|
|
||||||
|
def is_busy(self):
|
||||||
|
"Checks for state file"
|
||||||
|
return self.statefilename is not None and os.path.isfile(self.statefilename) and \
|
||||||
|
self.core_input is not None and self.core_input.poll() is None
|
||||||
|
|
||||||
|
#file_list = glob.glob(os.path.join(self.spool_dir, self.core_state_file))
|
||||||
|
#if len(file_list) != 0:
|
||||||
|
# return True
|
||||||
|
#else:
|
||||||
|
# return False
|
||||||
|
|
||||||
|
|
||||||
|
def get_exp_writer(self):
|
||||||
|
return self.experiment_writer
|
||||||
|
|
||||||
|
def get_res_reader(self):
|
||||||
|
return self.result_reader
|
||||||
|
|
||||||
|
def __del__(self):
|
||||||
|
# stop core and wait for it
|
||||||
|
if self.core_pid is not None:
|
||||||
|
try:
|
||||||
|
self.abort()
|
||||||
|
except OSError:
|
||||||
|
pass
|
||||||
|
self.core_input=None
|
||||||
|
if self.core_output:
|
||||||
|
self.core_output.close()
|
||||||
|
self.core_output=None
|
||||||
BIN
src/gui/DAMARIS.ico
Normal file
BIN
src/gui/DAMARIS.ico
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 11 KiB |
BIN
src/gui/DAMARIS.png
Normal file
BIN
src/gui/DAMARIS.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 664 B |
2880
src/gui/DamarisGUI.py
Normal file
2880
src/gui/DamarisGUI.py
Normal file
File diff suppressed because it is too large
Load Diff
95
src/gui/ExperimentHandling.py
Normal file
95
src/gui/ExperimentHandling.py
Normal file
@ -0,0 +1,95 @@
|
|||||||
|
import threading
|
||||||
|
import StringIO
|
||||||
|
import traceback
|
||||||
|
import sys
|
||||||
|
import time
|
||||||
|
from damaris.experiments.Experiment import Quit
|
||||||
|
from damaris.experiments import Experiment
|
||||||
|
|
||||||
|
class ExperimentHandling(threading.Thread):
|
||||||
|
"""
|
||||||
|
runs the experiment script in sandbox
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self, script, exp_writer, data):
|
||||||
|
threading.Thread.__init__(self, name="experiment handler")
|
||||||
|
self.script=script
|
||||||
|
self.writer=exp_writer
|
||||||
|
self.data=data
|
||||||
|
self.quit_flag = threading.Event()
|
||||||
|
if self.data is not None:
|
||||||
|
self.data["__recentexperiment"]=-1
|
||||||
|
|
||||||
|
def synchronize(self, before=0, waitsteps=0.1):
|
||||||
|
while (self.data["__recentexperiment"]>self.data["__recentresult"]+before) and not self.quit_flag.isSet():
|
||||||
|
self.quit_flag.wait(waitsteps)
|
||||||
|
if self.quit_flag.isSet():
|
||||||
|
raise StopIteration
|
||||||
|
|
||||||
|
def run(self):
|
||||||
|
dataspace={}
|
||||||
|
exp_classes = __import__('damaris.experiments', dataspace, dataspace, ['Experiment'])
|
||||||
|
for name in dir(exp_classes):
|
||||||
|
if name[:2]=="__" and name[-2:]=="__": continue
|
||||||
|
dataspace[name]=exp_classes.__dict__[name]
|
||||||
|
del exp_classes
|
||||||
|
|
||||||
|
dataspace["data"]=self.data
|
||||||
|
dataspace["synchronize"]=self.synchronize
|
||||||
|
self.raised_exception = None
|
||||||
|
self.location = None
|
||||||
|
exp_iterator=None
|
||||||
|
try:
|
||||||
|
exec self.script in dataspace
|
||||||
|
except Exception, e:
|
||||||
|
self.raised_exception=e
|
||||||
|
self.location=traceback.extract_tb(sys.exc_info()[2])[-1][1:3]
|
||||||
|
traceback_file=StringIO.StringIO()
|
||||||
|
traceback.print_tb(sys.exc_info()[2], None, traceback_file)
|
||||||
|
self.traceback=traceback_file.getvalue()
|
||||||
|
traceback_file=None
|
||||||
|
return
|
||||||
|
if "experiment" in dataspace:
|
||||||
|
try:
|
||||||
|
exp_iterator=dataspace["experiment"]()
|
||||||
|
except Exception, e:
|
||||||
|
self.raised_exception=e
|
||||||
|
self.location=traceback.extract_tb(sys.exc_info()[2])[-1][1:3]
|
||||||
|
traceback_file=StringIO.StringIO()
|
||||||
|
traceback.print_tb(sys.exc_info()[2], None, traceback_file)
|
||||||
|
self.traceback=traceback_file.getvalue()
|
||||||
|
traceback_file=None
|
||||||
|
return
|
||||||
|
while exp_iterator is not None and not self.quit_flag.isSet():
|
||||||
|
# get next experiment from script
|
||||||
|
try:
|
||||||
|
job=exp_iterator.next()
|
||||||
|
except StopIteration:
|
||||||
|
break
|
||||||
|
except Exception, e:
|
||||||
|
self.raised_exception=e
|
||||||
|
self.location=traceback.extract_tb(sys.exc_info()[2])[-1][1:3]
|
||||||
|
traceback_file=StringIO.StringIO()
|
||||||
|
traceback.print_tb(sys.exc_info()[2], None, traceback_file)
|
||||||
|
self.traceback=traceback_file.getvalue()
|
||||||
|
traceback_file=None
|
||||||
|
break
|
||||||
|
# send it
|
||||||
|
self.writer.send_next(job)
|
||||||
|
# write a note
|
||||||
|
if isinstance(job, Experiment):
|
||||||
|
if self.data is not None:
|
||||||
|
self.data["__recentexperiment"]=job.job_id+0
|
||||||
|
# relax for a short time
|
||||||
|
if "__resultsinadvance" in self.data and self.data["__resultsinadvance"]+100<job.job_id:
|
||||||
|
self.quit_flag.wait(0.05)
|
||||||
|
if self.quit_flag.isSet():
|
||||||
|
data_sapce=None
|
||||||
|
exp_iterator=None
|
||||||
|
break
|
||||||
|
|
||||||
|
self.writer.send_next(Quit(), quit=True)
|
||||||
|
# do not count quit job (is this a good idea?)
|
||||||
|
dataspace=None
|
||||||
|
self.exp_iterator=None
|
||||||
|
self.writer=None
|
||||||
66
src/gui/ExperimentWriter.py
Normal file
66
src/gui/ExperimentWriter.py
Normal file
@ -0,0 +1,66 @@
|
|||||||
|
import os
|
||||||
|
import os.path
|
||||||
|
import shutil
|
||||||
|
from damaris.experiments import Experiment
|
||||||
|
|
||||||
|
class ExperimentWriter:
|
||||||
|
"""
|
||||||
|
writes experiments in propper way to spool directory
|
||||||
|
"""
|
||||||
|
def __init__(self, spool, no=0, job_pattern="job.%09d", inform_last_job=None):
|
||||||
|
self.spool=spool
|
||||||
|
self.job_pattern=job_pattern
|
||||||
|
self.no=no
|
||||||
|
self.inform_last_job=inform_last_job
|
||||||
|
# test if spool exists
|
||||||
|
if not os.path.isdir(spool):
|
||||||
|
os.mkdir(spool)
|
||||||
|
|
||||||
|
def send_next(self, job, quit=False):
|
||||||
|
"""
|
||||||
|
"""
|
||||||
|
if quit and self.inform_last_job is not None:
|
||||||
|
self.inform_last_job.stop_no=self.no
|
||||||
|
self.inform_last_job=None
|
||||||
|
job.job_id=self.no
|
||||||
|
job_filename=os.path.join(self.spool,self.job_pattern%self.no)
|
||||||
|
f=file(job_filename+".tmp","w")
|
||||||
|
f.write(job.write_xml_string())
|
||||||
|
f.flush()
|
||||||
|
f.close() # explicit close under windows necessary (don't know why)
|
||||||
|
del f
|
||||||
|
# this implementation tries to satisfiy msvc filehandle caching
|
||||||
|
os.rename(job_filename+".tmp", job_filename)
|
||||||
|
#shutil.copyfile(job_filename+".tmp", job_filename)
|
||||||
|
#try:
|
||||||
|
# os.unlink(job_filename+".tmp")
|
||||||
|
#except OSError:
|
||||||
|
# print "could not delete temporary file %s.tmp"%job_filename
|
||||||
|
|
||||||
|
self.no+=1
|
||||||
|
|
||||||
|
def __del__(self):
|
||||||
|
if self.inform_last_job is not None:
|
||||||
|
self.inform_last_job.stop_no=self.no-1
|
||||||
|
self.inform_last_job=None
|
||||||
|
|
||||||
|
class ExperimentWriterWithCleanup(ExperimentWriter):
|
||||||
|
"""
|
||||||
|
writes experiments and cleans up in front of queue
|
||||||
|
"""
|
||||||
|
def __init__(self, spool, no=0, job_pattern="job.%09d", inform_last_job=None):
|
||||||
|
ExperimentWriter.__init__(self, spool, no, job_pattern, inform_last_job=inform_last_job)
|
||||||
|
self.delete_no_files(self.no)
|
||||||
|
|
||||||
|
def send_next(self, job, quit=False):
|
||||||
|
self.delete_no_files(self.no+1)
|
||||||
|
ExperimentWriter.send_next(self,job,quit)
|
||||||
|
|
||||||
|
def delete_no_files(self,no):
|
||||||
|
"""
|
||||||
|
delete everything with this job number
|
||||||
|
"""
|
||||||
|
filename=os.path.join(self.spool,(self.job_pattern%no))
|
||||||
|
if os.path.isfile(filename): os.unlink(filename)
|
||||||
|
if os.path.isfile(filename+".tmp"): os.unlink(filename+".tmp")
|
||||||
|
if os.path.isfile(filename+".result"): os.unlink(filename+".result")
|
||||||
78
src/gui/ResultHandling.py
Normal file
78
src/gui/ResultHandling.py
Normal file
@ -0,0 +1,78 @@
|
|||||||
|
import threading
|
||||||
|
import StringIO
|
||||||
|
import sys
|
||||||
|
import os
|
||||||
|
import os.path
|
||||||
|
import traceback
|
||||||
|
from damaris.data import Resultable
|
||||||
|
|
||||||
|
class ResultHandling(threading.Thread):
|
||||||
|
"""
|
||||||
|
runs the result script in sandbox
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self, script_data, result_iterator, data_pool):
|
||||||
|
threading.Thread.__init__(self,name="result handler")
|
||||||
|
self.script=script_data
|
||||||
|
self.results=result_iterator
|
||||||
|
self.data_space=data_pool
|
||||||
|
self.quit_flag=self.results.quit_flag
|
||||||
|
if self.data_space is not None:
|
||||||
|
self.data_space["__recentresult"]=-1
|
||||||
|
|
||||||
|
def run(self):
|
||||||
|
# execute it
|
||||||
|
dataspace={}
|
||||||
|
data_classes = __import__('damaris.data', dataspace, dataspace, ['*'])
|
||||||
|
for name in dir(data_classes):
|
||||||
|
if name[:2]=="__" and name[-2:]=="__": continue
|
||||||
|
dataspace[name]=data_classes.__dict__[name]
|
||||||
|
del data_classes
|
||||||
|
dataspace["results"]=self
|
||||||
|
dataspace["data"]=self.data_space
|
||||||
|
self.raised_exception=None
|
||||||
|
self.location = None
|
||||||
|
try:
|
||||||
|
exec self.script in dataspace
|
||||||
|
except Exception, e:
|
||||||
|
self.raised_exception=e
|
||||||
|
self.location=traceback.extract_tb(sys.exc_info()[2])[-1][1:3]
|
||||||
|
traceback_file=StringIO.StringIO()
|
||||||
|
traceback.print_tb(sys.exc_info()[2], None, traceback_file)
|
||||||
|
self.traceback=traceback_file.getvalue()
|
||||||
|
traceback_file=None
|
||||||
|
return
|
||||||
|
if not "result" in dataspace:
|
||||||
|
dataspace=None
|
||||||
|
return
|
||||||
|
try:
|
||||||
|
dataspace["result"]()
|
||||||
|
except Exception, e:
|
||||||
|
self.raised_exception=e
|
||||||
|
self.location=traceback.extract_tb(sys.exc_info()[2])[-1][1:3]
|
||||||
|
traceback_file=StringIO.StringIO()
|
||||||
|
traceback.print_tb(sys.exc_info()[2], None, traceback_file)
|
||||||
|
self.traceback=traceback_file.getvalue()
|
||||||
|
traceback_file=None
|
||||||
|
dataspace=None
|
||||||
|
|
||||||
|
def __iter__(self):
|
||||||
|
if self.quit_flag.isSet():
|
||||||
|
self.results=None
|
||||||
|
return
|
||||||
|
for i in self.results:
|
||||||
|
if hasattr(self.results, "in_advance"):
|
||||||
|
self.data_space["__resultsinadvance"]=self.results.in_advance
|
||||||
|
if self.quit_flag.isSet():
|
||||||
|
self.results=None
|
||||||
|
return
|
||||||
|
if isinstance(i, Resultable.Resultable):
|
||||||
|
if self.data_space is not None:
|
||||||
|
self.data_space["__recentresult"]=i.job_id+0
|
||||||
|
yield i
|
||||||
|
if self.quit_flag.isSet():
|
||||||
|
self.results=None
|
||||||
|
return
|
||||||
|
|
||||||
|
def stop(self):
|
||||||
|
self.quit_flag.set()
|
||||||
576
src/gui/ResultReader.py
Normal file
576
src/gui/ResultReader.py
Normal file
@ -0,0 +1,576 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
#############################################################################
|
||||||
|
# #
|
||||||
|
# Name: Class ResultReader #
|
||||||
|
# #
|
||||||
|
#############################################################################
|
||||||
|
|
||||||
|
import os
|
||||||
|
import os.path
|
||||||
|
import glob
|
||||||
|
import time
|
||||||
|
import sys
|
||||||
|
import base64
|
||||||
|
import numpy
|
||||||
|
|
||||||
|
try:
|
||||||
|
import xml.etree.cElementTree
|
||||||
|
ELEMENT_TREE = True
|
||||||
|
except:
|
||||||
|
import xml.parsers.expat
|
||||||
|
ELEMENT_TREE = False
|
||||||
|
|
||||||
|
import threading
|
||||||
|
from datetime import datetime
|
||||||
|
|
||||||
|
from damaris.data import ADC_Result
|
||||||
|
from damaris.data import Error_Result
|
||||||
|
from damaris.data import Temp_Result
|
||||||
|
from damaris.data import Config_Result
|
||||||
|
|
||||||
|
class ResultReader:
|
||||||
|
"""
|
||||||
|
starts at some point and returns result objects until none are there
|
||||||
|
"""
|
||||||
|
CONFIG_TYPE = 3
|
||||||
|
TEMP_TYPE = 2
|
||||||
|
ADCDATA_TYPE = 1
|
||||||
|
ERROR_TYPE = 0
|
||||||
|
|
||||||
|
def __init__(self, spool_dir=".", no=0, result_pattern="job.%09d.result", clear_jobs=False, clear_results=False):
|
||||||
|
self.spool_dir = spool_dir
|
||||||
|
self.start_no = no
|
||||||
|
self.no = self.start_no
|
||||||
|
self.result_pattern = result_pattern
|
||||||
|
self.clear_jobs=clear_jobs
|
||||||
|
self.clear_results=clear_results
|
||||||
|
self.quit_flag=threading.Event() # asychronous quit flag
|
||||||
|
|
||||||
|
def __iter__(self):
|
||||||
|
"""
|
||||||
|
get next job with iterator
|
||||||
|
"""
|
||||||
|
expected_filename=os.path.join(self.spool_dir,self.result_pattern%(self.no))
|
||||||
|
while os.access(expected_filename,os.R_OK):
|
||||||
|
yield self.get_result_object(expected_filename)
|
||||||
|
# purge result file
|
||||||
|
if self.clear_results:
|
||||||
|
if os.path.isfile(expected_filename): os.remove(expected_filename)
|
||||||
|
if self.clear_jobs:
|
||||||
|
if os.path.isfile(expected_filename[:-7]): os.remove(expected_filename[:-7])
|
||||||
|
self.no+=1
|
||||||
|
expected_filename=os.path.join(self.spool_dir,self.result_pattern%(self.no))
|
||||||
|
return
|
||||||
|
|
||||||
|
def get_result_object(self, in_filename):
|
||||||
|
"""
|
||||||
|
get result object
|
||||||
|
"""
|
||||||
|
# class-intern result-object currently being processed
|
||||||
|
retries=0
|
||||||
|
result_file=None
|
||||||
|
while result_file is None:
|
||||||
|
try:
|
||||||
|
result_file = file(in_filename, "r")
|
||||||
|
except IOError, e:
|
||||||
|
if retries>10:
|
||||||
|
raise e
|
||||||
|
print e, "retry", retries
|
||||||
|
time.sleep(0.05)
|
||||||
|
retries+=1
|
||||||
|
|
||||||
|
# get date of last modification
|
||||||
|
self.result_job_date = datetime.fromtimestamp(os.stat(in_filename)[8])
|
||||||
|
if ELEMENT_TREE:
|
||||||
|
self.__parseFile = self.__parseFile_cETree
|
||||||
|
else:
|
||||||
|
self.__parseFile = self.__parseFile_expat
|
||||||
|
|
||||||
|
self.__parseFile (result_file)
|
||||||
|
|
||||||
|
result_file.close()
|
||||||
|
result_file = None
|
||||||
|
|
||||||
|
r=self.result
|
||||||
|
self.result = None
|
||||||
|
|
||||||
|
return r
|
||||||
|
|
||||||
|
def __parseFile_cETree(self, in_file):
|
||||||
|
self.result = None
|
||||||
|
self.in_description_section=False
|
||||||
|
self.result_description = { }
|
||||||
|
self.result_job_number = None
|
||||||
|
# Job Date is set in __read_file()
|
||||||
|
self.__filetype = None
|
||||||
|
for elem in xml.etree.cElementTree.ElementTree(file=in_file).getiterator():
|
||||||
|
if elem.tag == 'result':
|
||||||
|
self.result_job_number = int(elem.get("job"))
|
||||||
|
pass
|
||||||
|
|
||||||
|
elif elem.tag == 'description':
|
||||||
|
if elem.text!=None:
|
||||||
|
self.result_description = {}
|
||||||
|
self.in_description_section=True
|
||||||
|
self.in_description_data=()
|
||||||
|
for an_item in elem.getchildren():
|
||||||
|
self.in_description_data = (an_item.get("key"), an_item.get("type"), an_item.text)
|
||||||
|
# make item contents to dictionary item:
|
||||||
|
k,t,v=self.in_description_data
|
||||||
|
self.in_description_data=()
|
||||||
|
if t == "None":
|
||||||
|
self.result_description[k]=None
|
||||||
|
if t == "Float":
|
||||||
|
self.result_description[k]=float(v)
|
||||||
|
elif t == "Int":
|
||||||
|
self.result_description[k]=int(v)
|
||||||
|
elif t == "Long":
|
||||||
|
self.result_description[k]=long(v)
|
||||||
|
elif t == "Complex":
|
||||||
|
self.result_description[k]=complex(v)
|
||||||
|
elif t == "Boolean":
|
||||||
|
self.result_description[k]=bool(v)
|
||||||
|
elif t == "String":
|
||||||
|
self.result_description[k]=v
|
||||||
|
else:
|
||||||
|
# Anything else will be handled as a string
|
||||||
|
# Probably "repr".
|
||||||
|
self.result_description[k]=v
|
||||||
|
|
||||||
|
elif elem.tag == 'adcdata':
|
||||||
|
self.__filetype = ResultReader.ADCDATA_TYPE
|
||||||
|
self.adc_result_trailing_chars = ""
|
||||||
|
|
||||||
|
if self.result is None:
|
||||||
|
self.result = ADC_Result()
|
||||||
|
# None: new guess for adc data encoding
|
||||||
|
# "a": ascii
|
||||||
|
# "b": base64
|
||||||
|
self.adc_data_encoding = None
|
||||||
|
|
||||||
|
self.result.set_sampling_rate(float(elem.get("rate")))
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
self.result.set_nChannels(int(elem.get("channels")))
|
||||||
|
|
||||||
|
self.result.set_description_dictionary(self.result_description.copy())
|
||||||
|
title = "ADC-Result: job-id=%d"%int(self.result_job_number)
|
||||||
|
if len(self.result_description) > 0:
|
||||||
|
for k,v in self.result_description.iteritems():
|
||||||
|
title += ", %s=%s"%(k,v)
|
||||||
|
self.result.set_title(title)
|
||||||
|
self.result_description = None
|
||||||
|
self.adc_result_sample_counter = 0
|
||||||
|
self.adc_result_parts = [] # will contain arrays of sampled intervals, assumes same sample rate
|
||||||
|
else:
|
||||||
|
if float(elem.get("rate")) != self.result.get_sampling_rate():
|
||||||
|
print "sample rate different in ADC_Result, found %f, former value %f"%\
|
||||||
|
(float(in_attribute["rate"]),self.result.get_sampling_rate())
|
||||||
|
new_samples = int(elem.get("samples"))
|
||||||
|
self.adc_result_sample_counter += new_samples
|
||||||
|
|
||||||
|
self.adc_result_trailing_chars = "".join(elem.text.splitlines())
|
||||||
|
tmp_string = base64.standard_b64decode(self.adc_result_trailing_chars)
|
||||||
|
self.adc_result_trailing_chars = None
|
||||||
|
tmp = numpy.fromstring(tmp_string,dtype='Int16')
|
||||||
|
tmp_string = None
|
||||||
|
self.adc_result_parts.append(tmp)
|
||||||
|
tmp = None
|
||||||
|
# we do not need this adcdata anymore, delete it
|
||||||
|
elem.clear()
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
elif elem.tag == 'error':
|
||||||
|
self.__filetype = ResultReader.ERROR_TYPE
|
||||||
|
|
||||||
|
self.result = Error_Result()
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
|
||||||
|
self.result.set_description_dictionary(self.result_description.copy())
|
||||||
|
self.result.set_error_message(elem.text)
|
||||||
|
|
||||||
|
elif elem.tag == 'temp':
|
||||||
|
self.__filetype = ResultReader.TEMP_TYPE
|
||||||
|
|
||||||
|
self.result = Error_Result()
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
|
||||||
|
elif elem.tag == 'conf':
|
||||||
|
self.__filetype = ResultReader.CONF_TYPE
|
||||||
|
|
||||||
|
self.result = Error_Result()
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
|
||||||
|
# xml file was traversed now prepare the data in one go
|
||||||
|
# prepare result data
|
||||||
|
if self.result is not None and \
|
||||||
|
self.__filetype == ResultReader.ADCDATA_TYPE and \
|
||||||
|
self.adc_result_sample_counter>0:
|
||||||
|
# fill the ADC_Result with collected data
|
||||||
|
# x data
|
||||||
|
self.result.x=numpy.arange(self.adc_result_sample_counter, dtype="Float64")/\
|
||||||
|
self.result.get_sampling_rate()
|
||||||
|
self.result.y = []
|
||||||
|
nChannels = self.result.get_nChannels()
|
||||||
|
# initialise the y arrays
|
||||||
|
for i in xrange(nChannels):
|
||||||
|
self.result.y.append(numpy.empty(self.adc_result_sample_counter, dtype='Int16'))
|
||||||
|
# remove from result stack
|
||||||
|
tmp_index = 0
|
||||||
|
while self.adc_result_parts:
|
||||||
|
tmp_part=self.adc_result_parts.pop(0)
|
||||||
|
tmp_size = tmp_part.size/nChannels
|
||||||
|
|
||||||
|
for i in xrange(nChannels):
|
||||||
|
# split interleaved data
|
||||||
|
self.result.y[i][tmp_index:tmp_index+tmp_size] = tmp_part[i::nChannels]
|
||||||
|
self.result.y[i][tmp_index:tmp_index+tmp_size] = tmp_part[i::nChannels]
|
||||||
|
|
||||||
|
if self.result.index != []:
|
||||||
|
self.result.index.append((tmp_index, tmp_index+tmp_size-1))
|
||||||
|
else:
|
||||||
|
self.result.index = [(0,tmp_size-1)]
|
||||||
|
tmp_index += tmp_size
|
||||||
|
self.result.cont_data=True
|
||||||
|
tmp_part = None
|
||||||
|
|
||||||
|
def __parseFile_expat(self, in_file):
|
||||||
|
"Parses the given file, adding it to the result-queue"
|
||||||
|
|
||||||
|
self.result = None
|
||||||
|
self.in_description_section=False
|
||||||
|
self.result_description = { }
|
||||||
|
self.result_job_number = None
|
||||||
|
# Job Date is set in __read_file()
|
||||||
|
self.__filetype = None
|
||||||
|
|
||||||
|
# Expat XML-Parser & Binding handlers
|
||||||
|
self.xml_parser = xml.parsers.expat.ParserCreate()
|
||||||
|
self.xml_parser.StartElementHandler = self.__xmlStartTagFound
|
||||||
|
self.xml_parser.CharacterDataHandler = self.__xmlCharacterDataFound
|
||||||
|
self.xml_parser.EndElementHandler = self.__xmlEndTagFound
|
||||||
|
self.element_stack=[]
|
||||||
|
|
||||||
|
try:
|
||||||
|
# short version, but pyexpat buffers are awfully small
|
||||||
|
# self.xml_parser.ParseFile(in_file)
|
||||||
|
# read all, at least try
|
||||||
|
databuffer=in_file.read(-1)
|
||||||
|
# test wether really everything was read...
|
||||||
|
databuffer2=in_file.read(self.xml_parser.buffer_size)
|
||||||
|
if databuffer2=="":
|
||||||
|
# parse everything at once
|
||||||
|
self.xml_parser.Parse(databuffer,True)
|
||||||
|
else:
|
||||||
|
# do the first part ...
|
||||||
|
self.xml_parser.Parse(databuffer,False)
|
||||||
|
databuffer=databuffer2
|
||||||
|
# ... and again and again
|
||||||
|
while databuffer!="":
|
||||||
|
self.xml_parser.Parse(databuffer,False)
|
||||||
|
databuffer=in_file.read(-1)
|
||||||
|
self.xml_parser.Parse("",True)
|
||||||
|
except xml.parsers.expat.ExpatError, e:
|
||||||
|
print "result file %d: xml parser '%s' error at line %d, offset %d"%(self.no,
|
||||||
|
xml.parsers.expat.ErrorString(e.code),
|
||||||
|
e.lineno,
|
||||||
|
e.offset)
|
||||||
|
self.result = None
|
||||||
|
|
||||||
|
del databuffer
|
||||||
|
self.xml_parser.StartElementHandler=None
|
||||||
|
self.xml_parser.EndElementHandler=None
|
||||||
|
self.xml_parser.CharacterDataHandler=None
|
||||||
|
del self.xml_parser
|
||||||
|
|
||||||
|
# prepare result data
|
||||||
|
if self.result is not None and \
|
||||||
|
self.__filetype == ResultReader.ADCDATA_TYPE and \
|
||||||
|
self.adc_result_sample_counter>0:
|
||||||
|
# fill the ADC_Result with collected data
|
||||||
|
self.result.x=numpy.arange(self.adc_result_sample_counter, dtype="Float64")/\
|
||||||
|
self.result.get_sampling_rate()
|
||||||
|
self.result.y=[]
|
||||||
|
self.result.index=[]
|
||||||
|
for i in xrange(2):
|
||||||
|
self.result.y.append(numpy.empty((self.adc_result_sample_counter,), dtype="Int16"))
|
||||||
|
tmp_sample_counter=0
|
||||||
|
while self.adc_result_parts:
|
||||||
|
tmp_part=self.adc_result_parts.pop(0)
|
||||||
|
tmp_size=tmp_part.size/2
|
||||||
|
self.result.y[0][tmp_sample_counter:tmp_sample_counter+tmp_size]=tmp_part[::2]
|
||||||
|
self.result.y[1][tmp_sample_counter:tmp_sample_counter+tmp_size]=tmp_part[1::2]
|
||||||
|
self.result.index.append((tmp_sample_counter,tmp_sample_counter+tmp_size-1))
|
||||||
|
tmp_sample_counter+=tmp_size
|
||||||
|
self.result.cont_data=True
|
||||||
|
|
||||||
|
# Callback when a xml start tag is found
|
||||||
|
def __xmlStartTagFound(self, in_name, in_attribute):
|
||||||
|
|
||||||
|
# General Result-Tag
|
||||||
|
if in_name == "result":
|
||||||
|
self.result_job_number = int(in_attribute["job"])
|
||||||
|
# Job-Date is set in __read_file()
|
||||||
|
|
||||||
|
# Description
|
||||||
|
elif in_name == "description":
|
||||||
|
# old style description:
|
||||||
|
if len(in_attribute)!=0:
|
||||||
|
self.result_description = in_attribute.copy()
|
||||||
|
self.in_description_section=True
|
||||||
|
self.in_description_data=()
|
||||||
|
|
||||||
|
elif self.in_description_section and in_name == "item":
|
||||||
|
self.in_description_data=[in_attribute["key"], in_attribute["type"], ""]
|
||||||
|
|
||||||
|
# ADC_Results
|
||||||
|
elif in_name == "adcdata":
|
||||||
|
self.__filetype = ResultReader.ADCDATA_TYPE
|
||||||
|
|
||||||
|
self.adc_result_trailing_chars = ""
|
||||||
|
|
||||||
|
if self.result is None:
|
||||||
|
self.result = ADC_Result()
|
||||||
|
# None: new guess for adc data encoding
|
||||||
|
# "a": ascii
|
||||||
|
# "b": base64
|
||||||
|
self.adc_data_encoding = None
|
||||||
|
|
||||||
|
self.result.set_sampling_rate(float(in_attribute["rate"]))
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
|
||||||
|
self.result.set_description_dictionary(self.result_description.copy())
|
||||||
|
title="ADC-Result: job-id=%d"%int(self.result_job_number)
|
||||||
|
if len(self.result_description)>0:
|
||||||
|
for k,v in self.result_description.iteritems():
|
||||||
|
title+=", %s=%s"%(k,v)
|
||||||
|
self.result.set_title(title)
|
||||||
|
self.result_description=None
|
||||||
|
self.adc_result_sample_counter = 0
|
||||||
|
self.adc_result_parts=[] # will contain arrays of sampled intervals, assumes same sample rate
|
||||||
|
else:
|
||||||
|
if float(in_attribute["rate"])!=self.result.get_sampling_rate():
|
||||||
|
print "sample rate different in ADC_Result, found %f, former value %f"%\
|
||||||
|
(float(in_attribute["rate"]),self.result.get_sampling_rate())
|
||||||
|
new_samples=int(in_attribute["samples"])
|
||||||
|
self.adc_result_sample_counter += new_samples
|
||||||
|
|
||||||
|
# version depends on the inclusion of http://bugs.python.org/issue1137
|
||||||
|
if sys.hexversion>=0x020501f0:
|
||||||
|
# extend buffer to expected base64 size (2 channels, 2 byte)
|
||||||
|
required_buffer=int(new_samples*4/45+1)*62
|
||||||
|
if self.xml_parser.buffer_size < required_buffer:
|
||||||
|
try:
|
||||||
|
self.xml_parser.buffer_size=required_buffer
|
||||||
|
except AttributeError:
|
||||||
|
pass
|
||||||
|
|
||||||
|
# pass all chardata as one block
|
||||||
|
self.xml_parser.buffer_text = True
|
||||||
|
# do not change the contents
|
||||||
|
self.xml_parser.returns_unicode=False
|
||||||
|
|
||||||
|
# Error_Results
|
||||||
|
elif in_name == "error":
|
||||||
|
self.__filetype = ResultReader.ERROR_TYPE
|
||||||
|
|
||||||
|
self.result = Error_Result()
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
|
||||||
|
self.result.set_description_dictionary(self.result_description.copy())
|
||||||
|
|
||||||
|
# Temp_Results
|
||||||
|
elif in_name == "temp":
|
||||||
|
self.__filetype = ResultReader.TEMP_TYPE
|
||||||
|
|
||||||
|
self.result = Temp_Result()
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
|
||||||
|
# Config_Results
|
||||||
|
elif in_name == "conf":
|
||||||
|
self.__filetype = ResultReader.CONFIG_TYPE
|
||||||
|
|
||||||
|
self.result = Config_Result()
|
||||||
|
self.result.set_job_id(self.result_job_number)
|
||||||
|
self.result.set_job_date(self.result_job_date)
|
||||||
|
|
||||||
|
# maintain the stack
|
||||||
|
self.element_stack.append(in_name)
|
||||||
|
|
||||||
|
def __xmlCharacterDataFound(self, in_cdata):
|
||||||
|
|
||||||
|
if self.in_description_section and len(self.in_description_data):
|
||||||
|
self.in_description_data[2]+=in_cdata
|
||||||
|
|
||||||
|
# ADC_Result
|
||||||
|
elif self.__filetype == ResultReader.ADCDATA_TYPE and self.element_stack[-1]=="adcdata":
|
||||||
|
self.adc_result_trailing_chars+=in_cdata
|
||||||
|
|
||||||
|
# Error_Result
|
||||||
|
elif self.__filetype == ResultReader.ERROR_TYPE:
|
||||||
|
tmp_string = self.result.get_error_message()
|
||||||
|
if tmp_string is None: tmp_string = ""
|
||||||
|
|
||||||
|
tmp_string += in_cdata
|
||||||
|
self.result.set_error_message(tmp_string)
|
||||||
|
|
||||||
|
# Temp_Results
|
||||||
|
elif self.__filetype == ResultReader.TEMP_TYPE:
|
||||||
|
pass
|
||||||
|
|
||||||
|
# Config_Results
|
||||||
|
elif self.__filetype == ResultReader.CONFIG_TYPE:
|
||||||
|
pass
|
||||||
|
|
||||||
|
def __xmlEndTagFound(self, in_name):
|
||||||
|
|
||||||
|
# maintain the stack
|
||||||
|
self.element_stack.pop()
|
||||||
|
|
||||||
|
if in_name == "adcdata":
|
||||||
|
|
||||||
|
# ADC_Result
|
||||||
|
if self.__filetype == ResultReader.ADCDATA_TYPE:
|
||||||
|
# detect type of data encoding from first line
|
||||||
|
if self.adc_data_encoding is None:
|
||||||
|
self.adc_result_trailing_chars=self.adc_result_trailing_chars.strip()
|
||||||
|
first_line_end=self.adc_result_trailing_chars.find("\n")
|
||||||
|
first_line=""
|
||||||
|
if first_line_end!=-1:
|
||||||
|
first_line=self.adc_result_trailing_chars[:first_line_end]
|
||||||
|
else:
|
||||||
|
first_line=self.adc_result_trailing_chars
|
||||||
|
if len(first_line.lstrip("-0123456789 \t\n\r"))==0:
|
||||||
|
try:
|
||||||
|
map(int,filter(len,first_line.split()))
|
||||||
|
except ValueError,e:
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
self.adc_data_encoding="a"
|
||||||
|
if self.adc_data_encoding is None and len(first_line)%4==0:
|
||||||
|
try:
|
||||||
|
base64.standard_b64decode(first_line)
|
||||||
|
except TypeError:
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
self.adc_data_encoding="b"
|
||||||
|
if self.adc_data_encoding is None:
|
||||||
|
print "unknown ADC data format \"%s\""%first_line
|
||||||
|
|
||||||
|
tmp=None
|
||||||
|
if self.adc_data_encoding=="a":
|
||||||
|
values=map(int,self.adc_result_trailing_chars.split())
|
||||||
|
tmp=numpy.array(values, dtype="Int16")
|
||||||
|
elif self.adc_data_encoding=="b":
|
||||||
|
tmp_string=base64.standard_b64decode(self.adc_result_trailing_chars)
|
||||||
|
tmp=numpy.fromstring(tmp_string, dtype="Int16")
|
||||||
|
del tmp_string
|
||||||
|
else:
|
||||||
|
print "unknown ADC data format"
|
||||||
|
|
||||||
|
self.adc_result_trailing_chars=""
|
||||||
|
self.adc_result_parts.append(tmp)
|
||||||
|
del tmp
|
||||||
|
return
|
||||||
|
|
||||||
|
elif in_name == "description":
|
||||||
|
self.in_description_section=False
|
||||||
|
|
||||||
|
elif self.in_description_section and in_name == "item":
|
||||||
|
# make item contents to dictionary item:
|
||||||
|
k,t,v=self.in_description_data
|
||||||
|
self.in_description_data=()
|
||||||
|
if t == "None":
|
||||||
|
self.result_description[k]=None
|
||||||
|
if t == "Float":
|
||||||
|
self.result_description[k]=float(v)
|
||||||
|
elif t == "Int":
|
||||||
|
self.result_description[k]=int(v)
|
||||||
|
elif t == "Long":
|
||||||
|
self.result_description[k]=long(v)
|
||||||
|
elif t == "Complex":
|
||||||
|
self.result_description[k]=complex(v)
|
||||||
|
elif t == "Boolean":
|
||||||
|
self.result_description[k]=bool(v)
|
||||||
|
elif t == "String":
|
||||||
|
self.result_description[k]=v
|
||||||
|
else:
|
||||||
|
# Anything else will be handled as a string
|
||||||
|
# Probably "repr".
|
||||||
|
self.result_description[k]=v
|
||||||
|
|
||||||
|
elif in_name == "result":
|
||||||
|
pass
|
||||||
|
|
||||||
|
# Error_Result
|
||||||
|
elif self.__filetype == ResultReader.ERROR_TYPE:
|
||||||
|
pass
|
||||||
|
|
||||||
|
# Temp_Result
|
||||||
|
elif self.__filetype == ResultReader.TEMP_TYPE:
|
||||||
|
pass
|
||||||
|
|
||||||
|
# Config_Result
|
||||||
|
elif self.__filetype == ResultReader.CONFIG_TYPE:
|
||||||
|
pass
|
||||||
|
|
||||||
|
class BlockingResultReader(ResultReader):
|
||||||
|
"""
|
||||||
|
to follow an active result stream
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self, spool_dir=".", no=0, result_pattern="job.%09d.result", clear_jobs=False, clear_results=False):
|
||||||
|
ResultReader.__init__(self, spool_dir, no, result_pattern, clear_jobs=clear_jobs, clear_results=clear_results)
|
||||||
|
self.stop_no=None # end of job queue
|
||||||
|
self.poll_time=0.1 # sleep interval for polling results, <0 means no polling and stop
|
||||||
|
self.in_advance=0
|
||||||
|
|
||||||
|
def __iter__(self):
|
||||||
|
"""
|
||||||
|
get next job with iterator
|
||||||
|
block until result is available
|
||||||
|
"""
|
||||||
|
expected_filename=os.path.join(self.spool_dir,self.result_pattern%(self.no))
|
||||||
|
while (not self.quit_flag.isSet()) and (self.stop_no is None or self.stop_no>self.no):
|
||||||
|
if not os.access(expected_filename,os.R_OK):
|
||||||
|
# stop polling, if required
|
||||||
|
if self.poll_time<0: break
|
||||||
|
self.quit_flag.wait(self.poll_time)
|
||||||
|
continue
|
||||||
|
|
||||||
|
# find pending results
|
||||||
|
self.in_advance=max(self.no,self.in_advance)
|
||||||
|
in_advance_filename=os.path.join(self.spool_dir,self.result_pattern%(self.in_advance+1))
|
||||||
|
while os.access(in_advance_filename, os.R_OK) and (self.stop_no is None or self.stop_no>self.in_advance+1):
|
||||||
|
# do not more than 100 results in advance at one glance
|
||||||
|
if self.in_advance>self.no+100: break
|
||||||
|
self.in_advance+=1
|
||||||
|
in_advance_filename=os.path.join(self.spool_dir,self.result_pattern%(self.in_advance+1))
|
||||||
|
|
||||||
|
if self.quit_flag.isSet(): break
|
||||||
|
r=self.get_result_object(expected_filename)
|
||||||
|
if self.quit_flag.isSet(): break
|
||||||
|
|
||||||
|
if self.quit_flag.isSet(): break
|
||||||
|
yield r
|
||||||
|
|
||||||
|
if self.clear_results:
|
||||||
|
if os.path.isfile(expected_filename): os.remove(expected_filename)
|
||||||
|
if self.clear_jobs:
|
||||||
|
if os.path.isfile(expected_filename[:-7]): os.remove(expected_filename[:-7])
|
||||||
|
|
||||||
|
self.no+=1
|
||||||
|
expected_filename=os.path.join(self.spool_dir,self.result_pattern%(self.no))
|
||||||
|
|
||||||
|
return
|
||||||
|
|
||||||
|
def quit(self):
|
||||||
|
self.quit_flag.set()
|
||||||
0
src/gui/__init__.py
Normal file
0
src/gui/__init__.py
Normal file
2106
src/gui/damaris.glade
Normal file
2106
src/gui/damaris.glade
Normal file
File diff suppressed because it is too large
Load Diff
8
src/gui/damaris.gladep
Normal file
8
src/gui/damaris.gladep
Normal file
@ -0,0 +1,8 @@
|
|||||||
|
<?xml version="1.0" standalone="no"?> <!--*- mode: xml -*-->
|
||||||
|
<!DOCTYPE glade-project SYSTEM "http://glade.gnome.org/glade-project-2.0.dtd">
|
||||||
|
|
||||||
|
<glade-project>
|
||||||
|
<name>damaris-gui</name>
|
||||||
|
<program_name>damaris</program_name>
|
||||||
|
<gnome_support>FALSE</gnome_support>
|
||||||
|
</glade-project>
|
||||||
681
src/gui/gtkcodebuffer.py
Normal file
681
src/gui/gtkcodebuffer.py
Normal file
@ -0,0 +1,681 @@
|
|||||||
|
""" This module contains the PyGTKCodeBuffer-class. This class is a
|
||||||
|
specialisation of the gtk.TextBuffer and enables syntax-highlighting for
|
||||||
|
PyGTK's TextView-widget.
|
||||||
|
|
||||||
|
To use the syntax-highlighting feature you have load a syntax-definition or
|
||||||
|
specify your own. To load one please read the docs for the SyntaxLoader()
|
||||||
|
class. """
|
||||||
|
|
||||||
|
|
||||||
|
# This library is free software: you can redistribute it and/or modify
|
||||||
|
# it under the terms of the GNU Lesser General Public License as published by
|
||||||
|
# the Free Software Foundation, either version 3 of the License, or
|
||||||
|
# (at your option) any later version.
|
||||||
|
#
|
||||||
|
# This program is distributed in the hope that it will be useful,
|
||||||
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||||
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||||
|
# GNU Lesser General Public License for more details.
|
||||||
|
#
|
||||||
|
# You should have received a copy of the GNU Lesser General Public License
|
||||||
|
# along with this program. If not, see <http://www.gnu.org/licenses/>.
|
||||||
|
|
||||||
|
|
||||||
|
import gtk
|
||||||
|
import pango
|
||||||
|
import re
|
||||||
|
import sys
|
||||||
|
import os.path
|
||||||
|
import xml.sax
|
||||||
|
import imp
|
||||||
|
from xml.sax.handler import ContentHandler
|
||||||
|
from xml.sax.saxutils import unescape
|
||||||
|
|
||||||
|
__version__ = "1.0RC2"
|
||||||
|
__author__ = "Hannes Matuschek <hmatuschek@gmail.com>"
|
||||||
|
|
||||||
|
|
||||||
|
# defined the default styles
|
||||||
|
DEFAULT_STYLES = {
|
||||||
|
'DEFAULT': {'font': 'monospace'},
|
||||||
|
'comment': {'foreground': '#0000FF'},
|
||||||
|
'preprocessor': {'foreground': '#A020F0',
|
||||||
|
'weight': pango.WEIGHT_BOLD},
|
||||||
|
'keyword': {'foreground': '#A52A2A',
|
||||||
|
'weight': pango.WEIGHT_BOLD},
|
||||||
|
'special': {'foreground': '#006600'},
|
||||||
|
'mark1': {'foreground': '#008B8B'},
|
||||||
|
'mark2': {'foreground': '#6A5ACD'},
|
||||||
|
'string': {'foreground': '#CC00CC'},
|
||||||
|
'number': {'foreground': '#CC00CC'},
|
||||||
|
'datatype': {'foreground': '#2E8B57',
|
||||||
|
'weight': pango.WEIGHT_BOLD},
|
||||||
|
'function': {'foreground': '#008A8C'},
|
||||||
|
|
||||||
|
'link': {'foreground': '#0000FF',
|
||||||
|
'underline': pango.UNDERLINE_SINGLE}}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def _main_is_frozen():
|
||||||
|
""" Internal used function. """
|
||||||
|
return (hasattr(sys, "frozen") or # new py2exe
|
||||||
|
hasattr(sys, "importers") # old py2exe
|
||||||
|
or imp.is_frozen("__main__")) # tools/freeze
|
||||||
|
|
||||||
|
|
||||||
|
if _main_is_frozen():
|
||||||
|
this_module_path = os.path.dirname(sys.executable)
|
||||||
|
else:
|
||||||
|
this_module_path = os.path.abspath(os.path.dirname(__file__))
|
||||||
|
|
||||||
|
|
||||||
|
# defines default-search paths for syntax-files
|
||||||
|
SYNTAX_PATH = [ os.path.join('.', 'syntax'),
|
||||||
|
this_module_path,
|
||||||
|
os.path.join(os.path.expanduser('~'),".pygtkcodebuffer"),
|
||||||
|
os.path.join(sys.prefix,"share","pygtkcodebuffer","syntax")]
|
||||||
|
|
||||||
|
|
||||||
|
# enable/disable debug-messages
|
||||||
|
DEBUG_FLAG = False
|
||||||
|
|
||||||
|
|
||||||
|
#
|
||||||
|
# Some log functions...
|
||||||
|
# (internal used)
|
||||||
|
def _log_debug(msg):
|
||||||
|
if not DEBUG_FLAG:
|
||||||
|
return
|
||||||
|
sys.stderr.write("DEBUG: ")
|
||||||
|
sys.stderr.write(msg)
|
||||||
|
sys.stderr.write("\n")
|
||||||
|
|
||||||
|
def _log_warn(msg):
|
||||||
|
sys.stderr.write("WARN: ")
|
||||||
|
sys.stderr.write(msg)
|
||||||
|
sys.stderr.write("\n")
|
||||||
|
|
||||||
|
def _log_error(msg):
|
||||||
|
sys.stderr.write("ERROR: ")
|
||||||
|
sys.stderr.write(msg)
|
||||||
|
sys.stderr.write("\n")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def add_syntax_path(path_or_list):
|
||||||
|
""" This function adds one (string) or many (list of strings) paths to the
|
||||||
|
global search-paths for syntax-files. """
|
||||||
|
global SYNTAX_PATH
|
||||||
|
# handle list of strings
|
||||||
|
if isinstance(path_or_list, (list, tuple)):
|
||||||
|
for i in range(len(path_or_list)):
|
||||||
|
SYNTAX_PATH.insert(0, path_or_list[-i])
|
||||||
|
# handle single string
|
||||||
|
elif isinstance(path_or_list, basestring):
|
||||||
|
SYNTAX_PATH.insert(0, path_or_list)
|
||||||
|
# handle attr-error
|
||||||
|
else:
|
||||||
|
raise TypeError, "Argument must be path-string or list of strings"
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class Pattern:
|
||||||
|
""" More or less internal used class representing a pattern. You may use
|
||||||
|
this class to "hard-code" your syntax-definition. """
|
||||||
|
|
||||||
|
def __init__(self, regexp, style="DEFAULT", group=0, flags=""):
|
||||||
|
""" The constructor takes at least on argument: the regular-expression.
|
||||||
|
|
||||||
|
The optional kwarg style defines the style applied to the string
|
||||||
|
matched by the regexp.
|
||||||
|
|
||||||
|
The kwarg group may be used to define which group of the regular
|
||||||
|
expression will be used for highlighting (Note: This means that only
|
||||||
|
the selected group will be highlighted but the complete pattern must
|
||||||
|
match!)
|
||||||
|
|
||||||
|
The optional kwarg flags specifies flags for the regular expression.
|
||||||
|
Look at the Python lib-ref for a list of flags and there meaning."""
|
||||||
|
# assemble re-flag
|
||||||
|
flags += "ML"; flag = 0
|
||||||
|
|
||||||
|
_log_debug("init rule %s -> %s (%s)"%(regexp, style, flags))
|
||||||
|
|
||||||
|
for char in flags:
|
||||||
|
if char == 'M': flag |= re.M
|
||||||
|
if char == 'L': flag |= re.L
|
||||||
|
if char == 'S': flag |= re.S
|
||||||
|
if char == 'I': flag |= re.I
|
||||||
|
if char == 'U': flag |= re.U
|
||||||
|
if char == 'X': flag |= re.X
|
||||||
|
|
||||||
|
# compile re
|
||||||
|
try: self._regexp = re.compile(regexp, flag)
|
||||||
|
except re.error, e:
|
||||||
|
raise Exception("Invalid regexp \"%s\": %s"%(regexp,str(e)))
|
||||||
|
|
||||||
|
self._group = group
|
||||||
|
self.tag_name = style
|
||||||
|
|
||||||
|
|
||||||
|
def __call__(self, txt, start, end):
|
||||||
|
m = self._regexp.search(txt)
|
||||||
|
if not m: return None
|
||||||
|
|
||||||
|
mstart, mend = m.start(self._group), m.end(self._group)
|
||||||
|
s = start.copy(); s.forward_chars(mstart)
|
||||||
|
e = start.copy(); e.forward_chars(mend)
|
||||||
|
|
||||||
|
return (s,e)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class KeywordList(Pattern):
|
||||||
|
""" This class may be used for hard-code a syntax-definition. It specifies
|
||||||
|
a pattern for a keyword-list. This simplifies the definition of
|
||||||
|
keyword-lists. """
|
||||||
|
|
||||||
|
def __init__(self, keywords, style="keyword", flags=""):
|
||||||
|
""" The constructor takes at least on argument: A list of strings
|
||||||
|
specifying the keywords to highlight.
|
||||||
|
|
||||||
|
The optional kwarg style specifies the style used to highlight these
|
||||||
|
keywords.
|
||||||
|
|
||||||
|
The optional kwarg flags specifies the flags for the
|
||||||
|
(internal generated) regular-expression. """
|
||||||
|
regexp = "(?:\W|^)(%s)\W"%("|".join(keywords),)
|
||||||
|
Pattern.__init__(self, regexp, style, group=1, flags=flags)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class String:
|
||||||
|
""" This class may be used to hard-code a syntax-definition. It simplifies
|
||||||
|
the definition of a "string". A "string" is something that consists of
|
||||||
|
a start-pattern and an end-pattern. The end-pattern may be content of
|
||||||
|
the string if it is escaped. """
|
||||||
|
|
||||||
|
def __init__(self, starts, ends, escape=None, style="string"):
|
||||||
|
""" The constructor needs at least two arguments: The start- and
|
||||||
|
end-pattern.
|
||||||
|
|
||||||
|
The optional kwarg escape specifies a escape-sequence escaping the
|
||||||
|
end-pattern.
|
||||||
|
|
||||||
|
The optional kwarg style specifies the style used to highlight the
|
||||||
|
string. """
|
||||||
|
try:
|
||||||
|
self._starts = re.compile(starts)
|
||||||
|
except re.error, e:
|
||||||
|
raise Exception("Invalid regexp \"%s\": %s"%(regexp,str(e)))
|
||||||
|
|
||||||
|
if escape:
|
||||||
|
end_exp = "[^%(esc)s](?:%(esc)s%(esc)s)*%(end)s"
|
||||||
|
end_exp = end_exp%{'esc':escape*2,'end':ends}
|
||||||
|
else:
|
||||||
|
end_exp = ends
|
||||||
|
|
||||||
|
try:
|
||||||
|
self._ends = re.compile(end_exp)
|
||||||
|
except re.error, e:
|
||||||
|
raise Exception("Invalid regexp \"%s\": %s"%(regexp,str(e)))
|
||||||
|
|
||||||
|
self.tag_name = style
|
||||||
|
|
||||||
|
|
||||||
|
def __call__(self, txt, start, end):
|
||||||
|
start_match = self._starts.search(txt)
|
||||||
|
if not start_match: return
|
||||||
|
|
||||||
|
start_it = start.copy()
|
||||||
|
start_it.forward_chars(start_match.start(0))
|
||||||
|
end_it = end.copy()
|
||||||
|
|
||||||
|
end_match = self._ends.search(txt, start_match.end(0)-1)
|
||||||
|
if end_match:
|
||||||
|
end_it.set_offset(start.get_offset()+end_match.end(0))
|
||||||
|
|
||||||
|
return start_it, end_it
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class LanguageDefinition:
|
||||||
|
""" This class is a container class for all rules (Pattern, KeywordList,
|
||||||
|
...) specifying the language. You have to used this class if you like
|
||||||
|
to hard-code your syntax-definition. """
|
||||||
|
|
||||||
|
def __init__(self, rules):
|
||||||
|
""" The constructor takes only one argument: A list of rules (i.e
|
||||||
|
Pattern, KeywordList and String). """
|
||||||
|
self._grammar = rules
|
||||||
|
self._styles = dict()
|
||||||
|
|
||||||
|
|
||||||
|
def __call__(self, buf, start, end=None):
|
||||||
|
# if no end given -> end of buffer
|
||||||
|
if not end: end = buf.get_end_iter()
|
||||||
|
|
||||||
|
mstart = mend = end
|
||||||
|
mtag = None
|
||||||
|
txt = buf.get_slice(start, end)
|
||||||
|
|
||||||
|
# search min match
|
||||||
|
for rule in self._grammar:
|
||||||
|
# search pattern
|
||||||
|
m = rule(txt, start, end)
|
||||||
|
if not m: continue
|
||||||
|
|
||||||
|
# prefer match with smallest start-iter
|
||||||
|
if m[0].compare(mstart) < 0:
|
||||||
|
mstart, mend = m
|
||||||
|
mtag = rule.tag_name
|
||||||
|
continue
|
||||||
|
|
||||||
|
if m[0].compare(mstart)==0 and m[1].compare(mend)>0:
|
||||||
|
mstart, mend = m
|
||||||
|
mtag = rule.tag_name
|
||||||
|
continue
|
||||||
|
|
||||||
|
return (mstart, mend, mtag)
|
||||||
|
|
||||||
|
|
||||||
|
def get_styles(self):
|
||||||
|
return self._styles
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class SyntaxLoader(ContentHandler, LanguageDefinition):
|
||||||
|
""" This class loads a syntax definition. There have to be a file
|
||||||
|
named LANGUAGENAME.xml in one of the directories specified in the
|
||||||
|
global path-list. You may add a directory using the add_syntax_path()
|
||||||
|
function. """
|
||||||
|
|
||||||
|
# some translation-tables for the style-defs:
|
||||||
|
style_weight_table = {'ultralight': pango.WEIGHT_ULTRALIGHT,
|
||||||
|
'light': pango.WEIGHT_LIGHT,
|
||||||
|
'normal': pango.WEIGHT_NORMAL,
|
||||||
|
'bold': pango.WEIGHT_BOLD,
|
||||||
|
'ultrabold': pango.WEIGHT_ULTRABOLD,
|
||||||
|
'heavy': pango.WEIGHT_HEAVY}
|
||||||
|
style_variant_table = {'normal': pango.VARIANT_NORMAL,
|
||||||
|
'smallcaps': pango.VARIANT_SMALL_CAPS}
|
||||||
|
style_underline_table = {'none': pango.UNDERLINE_NONE,
|
||||||
|
'single': pango.UNDERLINE_SINGLE,
|
||||||
|
'double': pango.UNDERLINE_DOUBLE}
|
||||||
|
style_style_table = {'normal': pango.STYLE_NORMAL,
|
||||||
|
'oblique': pango.STYLE_OBLIQUE,
|
||||||
|
'italic': pango.STYLE_ITALIC}
|
||||||
|
style_scale_table = {
|
||||||
|
'xx_small': pango.SCALE_XX_SMALL,
|
||||||
|
'x_small': pango.SCALE_X_SMALL,
|
||||||
|
'small': pango.SCALE_SMALL,
|
||||||
|
'medium': pango.SCALE_MEDIUM,
|
||||||
|
'large': pango.SCALE_LARGE,
|
||||||
|
'x_large': pango.SCALE_X_LARGE,
|
||||||
|
'xx_large': pango.SCALE_XX_LARGE,
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
def __init__(self, lang_name):
|
||||||
|
""" The constructor takes only one argument: the language name.
|
||||||
|
The constructor tries to load the syntax-definition from a
|
||||||
|
syntax-file in one directory of the global path-list.
|
||||||
|
|
||||||
|
An instance of this class IS a LanguageDefinition. You can pass it
|
||||||
|
to the constructor of the CodeBuffer class. """
|
||||||
|
LanguageDefinition.__init__(self, [])
|
||||||
|
ContentHandler.__init__(self)
|
||||||
|
|
||||||
|
# search for syntax-files:
|
||||||
|
fname = None
|
||||||
|
for syntax_dir in SYNTAX_PATH:
|
||||||
|
fname = os.path.join(syntax_dir, "%s.xml"%lang_name)
|
||||||
|
if os.path.isfile(fname): break
|
||||||
|
|
||||||
|
_log_debug("Loading syntaxfile %s"%fname)
|
||||||
|
|
||||||
|
if not os.path.isfile(fname):
|
||||||
|
raise Exception("No snytax-file for %s found!"%lang_name)
|
||||||
|
|
||||||
|
xml.sax.parse(fname, self)
|
||||||
|
|
||||||
|
|
||||||
|
# Dispatch start/end - document/element and chars
|
||||||
|
def startDocument(self):
|
||||||
|
self.__stack = []
|
||||||
|
|
||||||
|
def endDocument(self):
|
||||||
|
del self.__stack
|
||||||
|
|
||||||
|
def startElement(self, name, attr):
|
||||||
|
self.__stack.append( (name, attr) )
|
||||||
|
if hasattr(self, "start_%s"%name):
|
||||||
|
handler = getattr(self, "start_%s"%name)
|
||||||
|
handler(attr)
|
||||||
|
|
||||||
|
def endElement(self, name):
|
||||||
|
if hasattr(self, "end_%s"%name):
|
||||||
|
handler = getattr(self, "end_%s"%name)
|
||||||
|
handler()
|
||||||
|
del self.__stack[-1]
|
||||||
|
|
||||||
|
def characters(self, txt):
|
||||||
|
if not self.__stack: return
|
||||||
|
name, attr = self.__stack[-1]
|
||||||
|
|
||||||
|
if hasattr(self, "chars_%s"%name):
|
||||||
|
handler = getattr(self, "chars_%s"%name)
|
||||||
|
handler(txt)
|
||||||
|
|
||||||
|
|
||||||
|
# Handle regexp-patterns
|
||||||
|
def start_pattern(self, attr):
|
||||||
|
self.__pattern = ""
|
||||||
|
self.__group = 0
|
||||||
|
self.__flags = ''
|
||||||
|
self.__style = attr['style']
|
||||||
|
if 'group' in attr.keys(): self.__group = int(attr['group'])
|
||||||
|
if 'flags' in attr.keys(): self.__flags = attr['flags']
|
||||||
|
|
||||||
|
def end_pattern(self):
|
||||||
|
rule = Pattern(self.__pattern, self.__style, self.__group, self.__flags)
|
||||||
|
self._grammar.append(rule)
|
||||||
|
del self.__pattern
|
||||||
|
del self.__group
|
||||||
|
del self.__flags
|
||||||
|
del self.__style
|
||||||
|
|
||||||
|
def chars_pattern(self, txt):
|
||||||
|
self.__pattern += unescape(txt)
|
||||||
|
|
||||||
|
|
||||||
|
# handle keyword-lists
|
||||||
|
def start_keywordlist(self, attr):
|
||||||
|
self.__style = "keyword"
|
||||||
|
self.__flags = ""
|
||||||
|
if 'style' in attr.keys():
|
||||||
|
self.__style = attr['style']
|
||||||
|
if 'flags' in attr.keys():
|
||||||
|
self.__flags = attr['flags']
|
||||||
|
self.__keywords = []
|
||||||
|
|
||||||
|
def end_keywordlist(self):
|
||||||
|
kwlist = KeywordList(self.__keywords, self.__style, self.__flags)
|
||||||
|
self._grammar.append(kwlist)
|
||||||
|
del self.__keywords
|
||||||
|
del self.__style
|
||||||
|
del self.__flags
|
||||||
|
|
||||||
|
def start_keyword(self, attr):
|
||||||
|
self.__keywords.append("")
|
||||||
|
|
||||||
|
def end_keyword(self):
|
||||||
|
if not self.__keywords[-1]:
|
||||||
|
del self.__keywords[-1]
|
||||||
|
|
||||||
|
def chars_keyword(self, txt):
|
||||||
|
parent,pattr = self.__stack[-2]
|
||||||
|
if not parent == "keywordlist": return
|
||||||
|
self.__keywords[-1] += unescape(txt)
|
||||||
|
|
||||||
|
|
||||||
|
#handle String-definitions
|
||||||
|
def start_string(self, attr):
|
||||||
|
self.__style = "string"
|
||||||
|
self.__escape = None
|
||||||
|
if 'escape' in attr.keys():
|
||||||
|
self.__escape = attr['escape']
|
||||||
|
if 'style' in attr.keys():
|
||||||
|
self.__style = attr['style']
|
||||||
|
self.__start_pattern = ""
|
||||||
|
self.__end_pattern = ""
|
||||||
|
|
||||||
|
def end_string(self):
|
||||||
|
strdef = String(self.__start_pattern, self.__end_pattern,
|
||||||
|
self.__escape, self.__style)
|
||||||
|
self._grammar.append(strdef)
|
||||||
|
del self.__style
|
||||||
|
del self.__escape
|
||||||
|
del self.__start_pattern
|
||||||
|
del self.__end_pattern
|
||||||
|
|
||||||
|
def chars_starts(self, txt):
|
||||||
|
self.__start_pattern += unescape(txt)
|
||||||
|
|
||||||
|
def chars_ends(self, txt):
|
||||||
|
self.__end_pattern += unescape(txt)
|
||||||
|
|
||||||
|
|
||||||
|
# handle style
|
||||||
|
def start_style(self, attr):
|
||||||
|
self.__style_props = dict()
|
||||||
|
self.__style_name = attr['name']
|
||||||
|
|
||||||
|
def end_style(self):
|
||||||
|
self._styles[self.__style_name] = self.__style_props
|
||||||
|
del self.__style_props
|
||||||
|
del self.__style_name
|
||||||
|
|
||||||
|
def start_property(self, attr):
|
||||||
|
self.__style_prop_name = attr['name']
|
||||||
|
|
||||||
|
def chars_property(self, value):
|
||||||
|
value.strip()
|
||||||
|
|
||||||
|
# convert value
|
||||||
|
if self.__style_prop_name in ['font','foreground','background',]:
|
||||||
|
pass
|
||||||
|
|
||||||
|
elif self.__style_prop_name == 'variant':
|
||||||
|
if not value in self.style_variant_table.keys():
|
||||||
|
Exception("Unknown style-variant: %s"%value)
|
||||||
|
value = self.style_variant_table[value]
|
||||||
|
|
||||||
|
elif self.__style_prop_name == 'underline':
|
||||||
|
if not value in self.style_underline_table.keys():
|
||||||
|
Exception("Unknown underline-style: %s"%value)
|
||||||
|
value = self.style_underline_table[value]
|
||||||
|
|
||||||
|
elif self.__style_prop_name == 'scale':
|
||||||
|
if not value in self.style_scale_table.keys():
|
||||||
|
Exception("Unknown scale-style: %s"%value)
|
||||||
|
value = self.style_scale_table[value]
|
||||||
|
|
||||||
|
elif self.__style_prop_name == 'weight':
|
||||||
|
if not value in self.style_weight_table.keys():
|
||||||
|
Exception("Unknown style-weight: %s"%value)
|
||||||
|
value = self.style_weight_table[value]
|
||||||
|
|
||||||
|
elif self.__style_prop_name == 'style':
|
||||||
|
if not value in self.style_style_table[value]:
|
||||||
|
Exception("Unknwon text-style: %s"%value)
|
||||||
|
value = self.style_style_table[value]
|
||||||
|
|
||||||
|
else:
|
||||||
|
raise Exception("Unknown style-property %s"%self.__style_prop_name)
|
||||||
|
|
||||||
|
# store value
|
||||||
|
self.__style_props[self.__style_prop_name] = value
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
class CodeBuffer(gtk.TextBuffer):
|
||||||
|
""" This class extends the gtk.TextBuffer to support syntax-highlighting.
|
||||||
|
You can use this class like a normal TextBuffer. """
|
||||||
|
|
||||||
|
def __init__(self, table=None, lang=None, styles={}):
|
||||||
|
""" The constructor takes 3 optional arguments.
|
||||||
|
|
||||||
|
table specifies a tag-table associated with the TextBuffer-instance.
|
||||||
|
This argument will be passed directly to the constructor of the
|
||||||
|
TextBuffer-class.
|
||||||
|
|
||||||
|
lang specifies the language-definition. You have to load one using
|
||||||
|
the SyntaxLoader-class or you may hard-code your syntax-definition
|
||||||
|
using the LanguageDefinition-class.
|
||||||
|
|
||||||
|
styles is a dictionary used to extend or overwrite the default styles
|
||||||
|
provided by this module (DEFAULT_STYLE) and any language specific
|
||||||
|
styles defined by the LanguageDefinition. """
|
||||||
|
gtk.TextBuffer.__init__(self, table)
|
||||||
|
|
||||||
|
# default styles
|
||||||
|
self.styles = DEFAULT_STYLES
|
||||||
|
|
||||||
|
# update styles with lang-spec:
|
||||||
|
if lang:
|
||||||
|
self.styles.update(lang.get_styles())
|
||||||
|
# update styles with user-defined
|
||||||
|
self.styles.update(styles)
|
||||||
|
|
||||||
|
# create tags
|
||||||
|
for name, props in self.styles.items():
|
||||||
|
style = dict(self.styles['DEFAULT']) # take default
|
||||||
|
style.update(props) # and update with props
|
||||||
|
self.create_tag(name, **style)
|
||||||
|
|
||||||
|
# store lang-definition
|
||||||
|
self._lang_def = lang
|
||||||
|
|
||||||
|
self.connect_after("insert-text", self._on_insert_text)
|
||||||
|
self.connect_after("delete-range", self._on_delete_range)
|
||||||
|
self.connect('apply-tag', self._on_apply_tag)
|
||||||
|
|
||||||
|
self._apply_tags = False
|
||||||
|
|
||||||
|
|
||||||
|
def _on_apply_tag(self, buf, tag, start, end):
|
||||||
|
# FIXME This is a hack! It allows apply-tag only while
|
||||||
|
# _on_insert_text() and _on_delete_range()
|
||||||
|
if not self._apply_tags:
|
||||||
|
self.emit_stop_by_name('apply-tag')
|
||||||
|
return True
|
||||||
|
|
||||||
|
_log_debug("tag \"%s\" as %s"%(self.get_slice(start,end), tag.get_property("name")))
|
||||||
|
|
||||||
|
|
||||||
|
def _on_insert_text(self, buf, it, text, length):
|
||||||
|
# if no syntax defined -> nop
|
||||||
|
if not self._lang_def: return False
|
||||||
|
|
||||||
|
it = it.copy()
|
||||||
|
it.backward_chars(length)
|
||||||
|
|
||||||
|
if not it.begins_tag():
|
||||||
|
it.backward_to_tag_toggle(None)
|
||||||
|
_log_debug("Not tag-start -> moved iter to %i (%s)"%(it.get_offset(), it.get_char()))
|
||||||
|
|
||||||
|
if it.begins_tag(self.get_tag_table().lookup("DEFAULT")):
|
||||||
|
it.backward_to_tag_toggle(None)
|
||||||
|
_log_debug("Iter at DEFAULT-start -> moved to %i (%s)"%(it.get_offset(), it.get_char()))
|
||||||
|
|
||||||
|
self._apply_tags = True
|
||||||
|
self.update_syntax(it)
|
||||||
|
self._apply_tags = False
|
||||||
|
|
||||||
|
|
||||||
|
def _on_delete_range(self, buf, start, end):
|
||||||
|
# if no syntax defined -> nop
|
||||||
|
if not self._lang_def: return False
|
||||||
|
|
||||||
|
start = start.copy()
|
||||||
|
if not start.begins_tag():
|
||||||
|
start.backward_to_tag_toggle(None)
|
||||||
|
|
||||||
|
self._apply_tags = True
|
||||||
|
self.update_syntax(start)
|
||||||
|
self._apply_tags = False
|
||||||
|
|
||||||
|
|
||||||
|
def update_syntax(self, start, end=None):
|
||||||
|
""" More or less internal used method to update the
|
||||||
|
syntax-highlighting. """
|
||||||
|
# if no lang set
|
||||||
|
if not self._lang_def: return
|
||||||
|
_log_debug("Update syntax from %i"%start.get_offset())
|
||||||
|
|
||||||
|
# if not end defined
|
||||||
|
if not end: end = self.get_end_iter()
|
||||||
|
|
||||||
|
# We do not use recursion -> long files exceed rec-limit!
|
||||||
|
finished = False
|
||||||
|
while not finished:
|
||||||
|
# search first rule matching txt[start..end]
|
||||||
|
mstart, mend, tagname = self._lang_def(self, start, end)
|
||||||
|
|
||||||
|
# optimisation: if mstart-mend is allready tagged with tagname
|
||||||
|
# -> finished
|
||||||
|
if tagname: #if something found
|
||||||
|
tag = self.get_tag_table().lookup(tagname)
|
||||||
|
if mstart.begins_tag(tag) and mend.ends_tag(tag) and not mstart.equal(start):
|
||||||
|
self.remove_all_tags(start,mstart)
|
||||||
|
self.apply_tag_by_name("DEFAULT", start, mstart)
|
||||||
|
_log_debug("Optimized: Found old tag at %i (%s)"%(mstart.get_offset(), mstart.get_char()))
|
||||||
|
# finish
|
||||||
|
finished = True
|
||||||
|
continue
|
||||||
|
|
||||||
|
# remove all tags from start..mend (mend == buffer-end if no match)
|
||||||
|
self.remove_all_tags(start, mend)
|
||||||
|
# make start..mstart = DEFAUL (mstart == buffer-end if no match)
|
||||||
|
if not start.equal(mstart):
|
||||||
|
_log_debug("Apply DEFAULT")
|
||||||
|
self.apply_tag_by_name("DEFAULT", start, mstart)
|
||||||
|
|
||||||
|
# nothing found -> finished
|
||||||
|
if not tagname:
|
||||||
|
finished = True
|
||||||
|
continue
|
||||||
|
|
||||||
|
# apply tag
|
||||||
|
_log_debug("Apply %s"%tagname)
|
||||||
|
self.apply_tag_by_name(tagname, mstart, mend)
|
||||||
|
|
||||||
|
start = mend
|
||||||
|
|
||||||
|
if start == end:
|
||||||
|
finished = True
|
||||||
|
continue
|
||||||
|
|
||||||
|
|
||||||
|
def reset_language(self, lang_def):
|
||||||
|
""" Reset the currently used language-definition. """
|
||||||
|
# remove all tags from complete text
|
||||||
|
start = self.get_start_iter()
|
||||||
|
self.remove_all_tags(start, self.get_end_iter())
|
||||||
|
# store lexer
|
||||||
|
self._lang_def = lang_def
|
||||||
|
# update styles from lang_def:
|
||||||
|
if self._lang_def:
|
||||||
|
self.update_styles(self._lang_def.get_styles())
|
||||||
|
# and ...
|
||||||
|
self._apply_tags = True
|
||||||
|
self.update_syntax(start)
|
||||||
|
self._apply_tags = False
|
||||||
|
|
||||||
|
|
||||||
|
def update_styles(self, styles):
|
||||||
|
""" Update styles. This method may be used to reset any styles at
|
||||||
|
runtime. """
|
||||||
|
self.styles.update(styles)
|
||||||
|
|
||||||
|
table = self.get_tag_table()
|
||||||
|
for name, props in styles.items():
|
||||||
|
style = self.styles['DEFAULT']
|
||||||
|
style.update(props)
|
||||||
|
# if tagname is unknown:
|
||||||
|
if not table.lookup(name):
|
||||||
|
_log_debug("Create tag: %s (%s)"%(name, style))
|
||||||
|
self.create_tag(name, **style)
|
||||||
|
else: # update tag
|
||||||
|
tag = table.lookup(name)
|
||||||
|
_log_debug("Update tag %s with (%s)"%(name, style))
|
||||||
|
map(lambda i: tag.set_property(i[0],i[1]), style.items())
|
||||||
|
|
||||||
|
|
||||||
210
src/gui/python.xml
Normal file
210
src/gui/python.xml
Normal file
@ -0,0 +1,210 @@
|
|||||||
|
<?xml version="1.0"?>
|
||||||
|
<!--
|
||||||
|
This syntax-file was generated by sourceview2codebuffer.xsl from
|
||||||
|
GtkSourceView's Python-syntax-file!
|
||||||
|
|
||||||
|
This transformation is not perfect so it may need some hand-word to fix
|
||||||
|
minor issues in this file.
|
||||||
|
|
||||||
|
You can get sourceview2codebuffer.xsl from http://pygtkcodebuffer.googlecode.com/.
|
||||||
|
-->
|
||||||
|
<syntax>
|
||||||
|
<string style="string" escape="\"><starts>([uUrR]|[uU][rR]|[rR][uU])?"""</starts><ends>"""</ends></string>
|
||||||
|
<string style="string" escape="\"><starts>([uUrR]|[uU][rR]|[rR][uU])?'''</starts><ends>'''</ends></string>
|
||||||
|
<string style="string" escape="\"><starts>([uUrR]|[uU][rR]|[rR][uU])?"</starts><ends>"</ends></string>
|
||||||
|
<string style="string" escape="\"><starts>([uUrR]|[uU][rR]|[rR][uU])?'</starts><ends>'</ends></string>
|
||||||
|
|
||||||
|
<keywordlist style="preprocessor">
|
||||||
|
<keyword>import</keyword>
|
||||||
|
<keyword>from</keyword>
|
||||||
|
<keyword>as</keyword>
|
||||||
|
<keyword>False</keyword>
|
||||||
|
<keyword>None</keyword>
|
||||||
|
<keyword>True</keyword>
|
||||||
|
<keyword>__name__</keyword>
|
||||||
|
<keyword>__debug__</keyword>
|
||||||
|
</keywordlist>
|
||||||
|
|
||||||
|
<keywordlist style="keyword">
|
||||||
|
<keyword>def</keyword>
|
||||||
|
<keyword>class</keyword>
|
||||||
|
<keyword>return</keyword>
|
||||||
|
</keywordlist>
|
||||||
|
|
||||||
|
<keywordlist style="keyword">
|
||||||
|
<keyword>and</keyword>
|
||||||
|
<keyword>assert</keyword>
|
||||||
|
<keyword>break</keyword>
|
||||||
|
<keyword>continue</keyword>
|
||||||
|
<keyword>del</keyword>
|
||||||
|
<keyword>elif</keyword>
|
||||||
|
<keyword>else</keyword>
|
||||||
|
<keyword>except</keyword>
|
||||||
|
<keyword>exec</keyword>
|
||||||
|
<keyword>finally</keyword>
|
||||||
|
<keyword>for</keyword>
|
||||||
|
<keyword>global</keyword>
|
||||||
|
<keyword>if</keyword>
|
||||||
|
<keyword>in</keyword>
|
||||||
|
<keyword>is</keyword>
|
||||||
|
<keyword>lambda</keyword>
|
||||||
|
<keyword>not</keyword>
|
||||||
|
<keyword>or</keyword>
|
||||||
|
<keyword>pass</keyword>
|
||||||
|
<keyword>print</keyword>
|
||||||
|
<keyword>raise</keyword>
|
||||||
|
<keyword>try</keyword>
|
||||||
|
<keyword>while</keyword>
|
||||||
|
<keyword>yield</keyword>
|
||||||
|
</keywordlist>
|
||||||
|
|
||||||
|
<keywordlist style="special">
|
||||||
|
<keyword>ArithmeticError</keyword>
|
||||||
|
<keyword>AssertionError</keyword>
|
||||||
|
<keyword>AttributeError</keyword>
|
||||||
|
<keyword>EnvironmentError</keyword>
|
||||||
|
<keyword>EOFError</keyword>
|
||||||
|
<keyword>Exception</keyword>
|
||||||
|
<keyword>FloatingPointError</keyword>
|
||||||
|
<keyword>ImportError</keyword>
|
||||||
|
<keyword>IndentationError</keyword>
|
||||||
|
<keyword>IndexError</keyword>
|
||||||
|
<keyword>IOError</keyword>
|
||||||
|
<keyword>KeyboardInterrupt</keyword>
|
||||||
|
<keyword>KeyError</keyword>
|
||||||
|
<keyword>LookupError</keyword>
|
||||||
|
<keyword>MemoryError</keyword>
|
||||||
|
<keyword>NameError</keyword>
|
||||||
|
<keyword>NotImplementedError</keyword>
|
||||||
|
<keyword>OSError</keyword>
|
||||||
|
<keyword>OverflowError</keyword>
|
||||||
|
<keyword>ReferenceError</keyword>
|
||||||
|
<keyword>RuntimeError</keyword>
|
||||||
|
<keyword>StandardError</keyword>
|
||||||
|
<keyword>StopIteration</keyword>
|
||||||
|
<keyword>SyntaxError</keyword>
|
||||||
|
<keyword>SystemError</keyword>
|
||||||
|
<keyword>SystemExit</keyword>
|
||||||
|
<keyword>TabError</keyword>
|
||||||
|
<keyword>TypeError</keyword>
|
||||||
|
<keyword>UnboundLocalError</keyword>
|
||||||
|
<keyword>UnicodeDecodeError</keyword>
|
||||||
|
<keyword>UnicodeEncodeError</keyword>
|
||||||
|
<keyword>UnicodeError</keyword>
|
||||||
|
<keyword>UnicodeTranslateError</keyword>
|
||||||
|
<keyword>ValueError</keyword>
|
||||||
|
<keyword>WindowsError</keyword>
|
||||||
|
<keyword>ZeroDivisionError</keyword>
|
||||||
|
|
||||||
|
<keyword>Warning</keyword>
|
||||||
|
<keyword>UserWarning</keyword>
|
||||||
|
<keyword>DeprecationWarning</keyword>
|
||||||
|
<keyword>PendingDeprecationWarning</keyword>
|
||||||
|
<keyword>SyntaxWarning</keyword>
|
||||||
|
<keyword>OverflowWarning</keyword>
|
||||||
|
<keyword>RuntimeWarning</keyword>
|
||||||
|
<keyword>FutureWarning</keyword>
|
||||||
|
|
||||||
|
<keyword>__import__</keyword>
|
||||||
|
<keyword>abs</keyword>
|
||||||
|
<keyword>apply</keyword>
|
||||||
|
<keyword>basestring</keyword>
|
||||||
|
<keyword>bool</keyword>
|
||||||
|
<keyword>buffer</keyword>
|
||||||
|
<keyword>callable</keyword>
|
||||||
|
<keyword>chr</keyword>
|
||||||
|
<keyword>classmethod</keyword>
|
||||||
|
<keyword>cmp</keyword>
|
||||||
|
<keyword>coerce</keyword>
|
||||||
|
<keyword>compile</keyword>
|
||||||
|
<keyword>complex</keyword>
|
||||||
|
<keyword>delattr</keyword>
|
||||||
|
<keyword>dict</keyword>
|
||||||
|
<keyword>dir</keyword>
|
||||||
|
<keyword>divmod</keyword>
|
||||||
|
<keyword>enumerate</keyword>
|
||||||
|
<keyword>eval</keyword>
|
||||||
|
<keyword>execfile</keyword>
|
||||||
|
<keyword>file</keyword>
|
||||||
|
<keyword>filter</keyword>
|
||||||
|
<keyword>float</keyword>
|
||||||
|
<keyword>getattr</keyword>
|
||||||
|
<keyword>globals</keyword>
|
||||||
|
<keyword>hasattr</keyword>
|
||||||
|
<keyword>hash</keyword>
|
||||||
|
<keyword>hex</keyword>
|
||||||
|
<keyword>id</keyword>
|
||||||
|
<keyword>input</keyword>
|
||||||
|
<keyword>int</keyword>
|
||||||
|
<keyword>intern</keyword>
|
||||||
|
<keyword>isinstance</keyword>
|
||||||
|
<keyword>issubclass</keyword>
|
||||||
|
<keyword>iter</keyword>
|
||||||
|
<keyword>len</keyword>
|
||||||
|
<keyword>list</keyword>
|
||||||
|
<keyword>locals</keyword>
|
||||||
|
<keyword>long</keyword>
|
||||||
|
<keyword>map</keyword>
|
||||||
|
<keyword>max</keyword>
|
||||||
|
<keyword>min</keyword>
|
||||||
|
<keyword>object</keyword>
|
||||||
|
<keyword>oct</keyword>
|
||||||
|
<keyword>open</keyword>
|
||||||
|
<keyword>ord</keyword>
|
||||||
|
<keyword>pow</keyword>
|
||||||
|
<keyword>property</keyword>
|
||||||
|
<keyword>range</keyword>
|
||||||
|
<keyword>raw_input</keyword>
|
||||||
|
<keyword>reduce</keyword>
|
||||||
|
<keyword>reload</keyword>
|
||||||
|
<keyword>repr</keyword>
|
||||||
|
<keyword>round</keyword>
|
||||||
|
<keyword>setattr</keyword>
|
||||||
|
<keyword>slice</keyword>
|
||||||
|
<keyword>staticmethod</keyword>
|
||||||
|
<keyword>str</keyword>
|
||||||
|
<keyword>sum</keyword>
|
||||||
|
<keyword>super</keyword>
|
||||||
|
<keyword>tuple</keyword>
|
||||||
|
<keyword>type</keyword>
|
||||||
|
<keyword>unichr</keyword>
|
||||||
|
<keyword>unicode</keyword>
|
||||||
|
<keyword>vars</keyword>
|
||||||
|
<keyword>xrange</keyword>
|
||||||
|
<keyword>zip</keyword>
|
||||||
|
</keywordlist>
|
||||||
|
|
||||||
|
<!-- Some Experiment keywords -->
|
||||||
|
<keywordlist style="special">
|
||||||
|
<keyword>set_pfg</keyword>
|
||||||
|
<keyword>set_pfg_wt</keyword>
|
||||||
|
<keyword>set_description</keyword>
|
||||||
|
<keyword>get_description</keyword>
|
||||||
|
<keyword>set_phase</keyword>
|
||||||
|
<keyword>set_frequency</keyword>
|
||||||
|
<keyword>ttl_pulse</keyword>
|
||||||
|
<keyword>rf_pulse</keyword>
|
||||||
|
<keyword>state_start</keyword>
|
||||||
|
<keyword>state_end</keyword>
|
||||||
|
<keyword>loop_start</keyword>
|
||||||
|
<keyword>loop_end</keyword>
|
||||||
|
<keyword>set_pts_local</keyword>
|
||||||
|
<keyword>wait</keyword>
|
||||||
|
<keyword>record</keyword>
|
||||||
|
</keywordlist>
|
||||||
|
|
||||||
|
<keywordlist style="datatype">
|
||||||
|
<keyword>Accumulation</keyword>
|
||||||
|
<keyword>Experiment</keyword>
|
||||||
|
<keyword>ADC_Result</keyword>
|
||||||
|
<keyword>MeasurementResult</keyword>
|
||||||
|
<keyword>AccumulatedValue</keyword>
|
||||||
|
</keywordlist>
|
||||||
|
|
||||||
|
<pattern style="comment">#.*$</pattern>
|
||||||
|
<pattern style="datatype">\bself\b</pattern>
|
||||||
|
<pattern style="number">\b([1-9][0-9]*|0)([Uu]([Ll]|LL|ll)?|([Ll]|LL|ll)[Uu]?)?\b</pattern>
|
||||||
|
<pattern style="number">\b([0-9]+[Ee][-]?[0-9]+|([0-9]*\.[0-9]+|[0-9]+\.)([Ee][-]?[0-9]+)?)[fFlL]?</pattern>
|
||||||
|
<pattern style="number">\b0[0-7]+([Uu]([Ll]|LL|ll)?|([Ll]|LL|ll)[Uu]?)?\b</pattern>
|
||||||
|
<pattern style="number">\b0[xX][0-9a-fA-F]+([Uu]([Ll]|LL|ll)?|([Ll]|LL|ll)[Uu]?)?\b</pattern>
|
||||||
|
</syntax>
|
||||||
152
src/gui/script_interface.py
Normal file
152
src/gui/script_interface.py
Normal file
@ -0,0 +1,152 @@
|
|||||||
|
#! /usr/bin/env python
|
||||||
|
|
||||||
|
import time
|
||||||
|
import sys
|
||||||
|
import os
|
||||||
|
import os.path
|
||||||
|
import tables
|
||||||
|
import damaris.data.DataPool as DataPool
|
||||||
|
import damaris.gui.ResultReader as ResultReader
|
||||||
|
import damaris.gui.ExperimentWriter as ExperimentWriter
|
||||||
|
import damaris.gui.BackendDriver as BackendDriver
|
||||||
|
import damaris.gui.ResultHandling as ResultHandling
|
||||||
|
import damaris.gui.ExperimentHandling as ExperimentHandling
|
||||||
|
|
||||||
|
def some_listener(event):
|
||||||
|
if event.subject=="__recentexperiment" or event.subject=="__recentresult":
|
||||||
|
r=event.origin.get("__recentresult",-1)+1
|
||||||
|
e=event.origin.get("__recentexperiment",-1)+1
|
||||||
|
if e!=0:
|
||||||
|
ratio=100.0*r/e
|
||||||
|
else:
|
||||||
|
ratio=100.0
|
||||||
|
print "\r%d/%d (%.0f%%)"%(r,e,ratio),
|
||||||
|
|
||||||
|
|
||||||
|
class ScriptInterface:
|
||||||
|
|
||||||
|
def __init__(self, exp_script=None, res_script=None, backend_executable=None, spool_dir="spool"):
|
||||||
|
self.exp_script=exp_script
|
||||||
|
self.res_script=res_script
|
||||||
|
self.backend_executable=backend_executable
|
||||||
|
self.spool_dir=os.path.abspath(spool_dir)
|
||||||
|
self.exp_handling=self.res_handling=None
|
||||||
|
|
||||||
|
self.exp_writer=self.res_reader=self.back_driver=None
|
||||||
|
if self.backend_executable is not None:
|
||||||
|
self.back_driver=BackendDriver.BackendDriver(self.backend_executable, spool_dir)
|
||||||
|
if self.exp_script: self.exp_writer=self.back_driver.get_exp_writer()
|
||||||
|
if self.res_script: self.res_reader=self.back_driver.get_res_reader()
|
||||||
|
else:
|
||||||
|
self.back_driver=None
|
||||||
|
if self.exp_script: self.exp_writer=ExperimentWriter.ExperimentWriter(spool_dir)
|
||||||
|
if self.res_script: self.res_reader=ResultReader.ResultReader(spool_dir)
|
||||||
|
|
||||||
|
self.data=DataPool()
|
||||||
|
|
||||||
|
|
||||||
|
def runScripts(self):
|
||||||
|
# get script engines
|
||||||
|
if self.exp_script and self.exp_writer:
|
||||||
|
self.exp_handling=ExperimentHandling.ExperimentHandling(self.exp_script, self.exp_writer, self.data)
|
||||||
|
if self.res_script and self.res_reader:
|
||||||
|
self.res_handling=ResultHandling.ResultHandling(self.res_script, self.res_reader, self.data)
|
||||||
|
|
||||||
|
# start them
|
||||||
|
if self.exp_handling: self.exp_handling.start()
|
||||||
|
if self.back_driver is not None: self.back_driver.start()
|
||||||
|
if self.res_handling: self.res_handling.start()
|
||||||
|
|
||||||
|
def waitForScriptsEnding(self):
|
||||||
|
# time of last dump
|
||||||
|
dump_interval=600
|
||||||
|
next_dump_time=time.time()+dump_interval
|
||||||
|
# keyboard interrupts are handled in extra cleanup loop
|
||||||
|
try:
|
||||||
|
while filter(None,[self.exp_handling,self.res_handling,self.back_driver]):
|
||||||
|
time.sleep(0.1)
|
||||||
|
if time.time()>next_dump_time:
|
||||||
|
self.dump_data("pool/data_pool.h5")
|
||||||
|
next_dump_time+=dump_interval
|
||||||
|
|
||||||
|
if self.exp_handling is not None:
|
||||||
|
if not self.exp_handling.isAlive():
|
||||||
|
self.exp_handling.join()
|
||||||
|
if self.exp_handling.raised_exception:
|
||||||
|
print ": experiment script failed at line %d (function %s): %s"%(self.exp_handling.location[0],
|
||||||
|
self.exp_handling.location[1],
|
||||||
|
self.exp_handling.raised_exception)
|
||||||
|
else:
|
||||||
|
print ": experiment script finished"
|
||||||
|
self.exp_handling = None
|
||||||
|
|
||||||
|
if self.res_handling is not None:
|
||||||
|
if not self.res_handling.isAlive():
|
||||||
|
self.res_handling.join()
|
||||||
|
if self.res_handling.raised_exception:
|
||||||
|
print ": result script failed at line %d (function %s): %s"%(self.res_handling.location[0],
|
||||||
|
self.res_handling.location[1],
|
||||||
|
self.res_handling.raised_exception)
|
||||||
|
else:
|
||||||
|
print ": result script finished"
|
||||||
|
self.res_handling = None
|
||||||
|
|
||||||
|
if self.back_driver is not None:
|
||||||
|
if not self.back_driver.isAlive():
|
||||||
|
print ": backend finished"
|
||||||
|
self.back_driver=None
|
||||||
|
|
||||||
|
except KeyboardInterrupt:
|
||||||
|
still_running=filter(None,[self.exp_handling,self.res_handling,self.back_driver])
|
||||||
|
for r in still_running:
|
||||||
|
r.quit_flag.set()
|
||||||
|
|
||||||
|
for r in still_running:
|
||||||
|
r.join()
|
||||||
|
|
||||||
|
def dump_data(self, filename):
|
||||||
|
try:
|
||||||
|
# write data from pool
|
||||||
|
dump_file=tables.openFile(filename,mode="w",title="DAMARIS experiment data")
|
||||||
|
self.data.write_hdf5(dump_file, complib='zlib', complevel=6)
|
||||||
|
# write scripts
|
||||||
|
scriptgroup=dump_file.createGroup("/","scripts","Used Scripts")
|
||||||
|
dump_file.createArray(scriptgroup,"experiment_script", self.exp_script)
|
||||||
|
dump_file.createArray(scriptgroup,"result_script", self.res_script)
|
||||||
|
dump_file.createArray(scriptgroup,"backend_executable", self.backend_executable)
|
||||||
|
dump_file.createArray(scriptgroup,"spool_directory", self.spool_dir)
|
||||||
|
dump_file.flush()
|
||||||
|
dump_file.close()
|
||||||
|
dump_file=None
|
||||||
|
# todo
|
||||||
|
except Exception,e:
|
||||||
|
print "dump failed", e
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
if __name__=="__main__":
|
||||||
|
|
||||||
|
if len(sys.argv)==1:
|
||||||
|
print "%s: data_handling_script [spool directory]"%sys.argv[0]
|
||||||
|
sys.exit(1)
|
||||||
|
if len(sys.argv)==3:
|
||||||
|
spool_dir=os.getcwd()
|
||||||
|
else:
|
||||||
|
spool_dir=sys.argv[3]
|
||||||
|
|
||||||
|
expscriptfile=open(sys.argv[1])
|
||||||
|
expscript=expscriptfile.read()
|
||||||
|
resscriptfile=open(sys.argv[2])
|
||||||
|
resscript=resscriptfile.read()
|
||||||
|
|
||||||
|
si=ScriptInterface(expscript, resscript,"/usr/lib/damaris/backends/Mobilecore", spool_dir)
|
||||||
|
|
||||||
|
si.data.register_listener(some_listener)
|
||||||
|
|
||||||
|
si.runScripts()
|
||||||
|
|
||||||
|
si.waitForScriptsEnding()
|
||||||
|
|
||||||
|
si.dump_data("data_pool.h5")
|
||||||
|
|
||||||
|
si=None
|
||||||
0
src/tools/__init__.py
Normal file
0
src/tools/__init__.py
Normal file
119
src/tools/eurotherm.py
Normal file
119
src/tools/eurotherm.py
Normal file
@ -0,0 +1,119 @@
|
|||||||
|
import serial
|
||||||
|
import re
|
||||||
|
import operator
|
||||||
|
|
||||||
|
|
||||||
|
DEBUG=False
|
||||||
|
|
||||||
|
reply_pattern = re.compile(r"\x02..(.*)\x03.", re.DOTALL)
|
||||||
|
# example answer '\x02PV279.8\x03/'
|
||||||
|
# [EOT] = \x04
|
||||||
|
# [STX] = \x02
|
||||||
|
# [ENQ] = \x05
|
||||||
|
# [ETX] = \x03
|
||||||
|
# [ACK] = \x06
|
||||||
|
# BCC = checksum
|
||||||
|
|
||||||
|
standard_device='0011'
|
||||||
|
EOT = '\x04'
|
||||||
|
STX = '\x02'
|
||||||
|
ENQ = '\x05'
|
||||||
|
ETX = '\x03'
|
||||||
|
ACK = '\x06'
|
||||||
|
NAK = '\x15'
|
||||||
|
|
||||||
|
|
||||||
|
"""
|
||||||
|
Paramter read example:
|
||||||
|
|
||||||
|
Master: [EOT]0011PV[ENQ]
|
||||||
|
Instrument: [STX]PV16.4[ETX]{BCC}
|
||||||
|
|
||||||
|
Writing data:
|
||||||
|
|
||||||
|
Master: [EOT] {GID}{GID}{UID}{UID}[STX]{CHAN}(c1)(c2)<DATA>[ETX](BCC)
|
||||||
|
|
||||||
|
"""
|
||||||
|
|
||||||
|
def checksum(message):
|
||||||
|
bcc = (reduce(operator.xor, map(ord,message)))
|
||||||
|
return chr(bcc)
|
||||||
|
|
||||||
|
class Eurotherm(object):
|
||||||
|
def __init__(self, serial_device, baudrate = 19200):
|
||||||
|
self.device = standard_device
|
||||||
|
# timeout: 110 ms to get all answers.
|
||||||
|
self.s = serial.Serial(serial_device,
|
||||||
|
baudrate = baudrate,
|
||||||
|
bytesize=7,
|
||||||
|
parity='E',
|
||||||
|
stopbits=1,
|
||||||
|
timeout=0.11)
|
||||||
|
self._expect_len = 50
|
||||||
|
|
||||||
|
def send_read_param(self, param):
|
||||||
|
self.s.write(EOT + self.device + param + ENQ)
|
||||||
|
|
||||||
|
def read_param(self, param):
|
||||||
|
self.s.flushInput()
|
||||||
|
self.send_read_param(param)
|
||||||
|
answer = self.s.read(self._expect_len)
|
||||||
|
m = reply_pattern.search(answer)
|
||||||
|
if m is None:
|
||||||
|
# Reading _expect_len bytes was not enough...
|
||||||
|
answer += self.s.read(200)
|
||||||
|
m = reply_pattern.search(answer)
|
||||||
|
if m is not None:
|
||||||
|
self._expect_len = len(answer)
|
||||||
|
return m.group(1)
|
||||||
|
else:
|
||||||
|
print "received:", repr(answer)
|
||||||
|
return None
|
||||||
|
|
||||||
|
def write_param(self, mnemonic, data):
|
||||||
|
if len(mnemonic) > 2:
|
||||||
|
raise ValueError
|
||||||
|
bcc = checksum(mnemonic + data + ETX)
|
||||||
|
mes = EOT+self.device+STX+mnemonic+data+ETX+bcc
|
||||||
|
if DEBUG:
|
||||||
|
for i in mes:
|
||||||
|
print i,hex(ord(i))
|
||||||
|
self.s.flushInput()
|
||||||
|
self.s.write(mes)
|
||||||
|
answer = self.s.read(1)
|
||||||
|
# print "received:", repr(answer)
|
||||||
|
if answer == "":
|
||||||
|
# raise IOError("No answer from device")
|
||||||
|
return None
|
||||||
|
return answer[-1] == ACK
|
||||||
|
|
||||||
|
def get_current_temperature(self):
|
||||||
|
temp = self.read_param('PV')
|
||||||
|
if temp is None:
|
||||||
|
temp = "0"
|
||||||
|
return temp
|
||||||
|
|
||||||
|
def set_temperature(self, temperature):
|
||||||
|
return self.write_param('SL', str(temperature))
|
||||||
|
|
||||||
|
def get_setpoint_temperature(self):
|
||||||
|
return self.read_param('SL')
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
import time
|
||||||
|
delta=5
|
||||||
|
date = time.strftime('%Y-%m-%d')
|
||||||
|
f = open('templog_%s'%date,'w')
|
||||||
|
f.write('# Start time: %s\n#delta t : %.1f s\n'%(time.asctime(), delta))
|
||||||
|
et = Eurotherm("/dev/ttyUSB0")
|
||||||
|
while True:
|
||||||
|
for i in xrange(120):
|
||||||
|
time.sleep(delta)
|
||||||
|
#t = time.strftime()
|
||||||
|
T = et.get_current_temperature()
|
||||||
|
|
||||||
|
l = '%f %s\n'%(time.time(),T)
|
||||||
|
print time.asctime(), T
|
||||||
|
f.write(l)
|
||||||
|
f.flush()
|
||||||
|
f.write('# MARK -- %s --\n'%(time.asctime()))
|
||||||
127
src/tools/ranges.py
Normal file
127
src/tools/ranges.py
Normal file
@ -0,0 +1,127 @@
|
|||||||
|
import numpy as N
|
||||||
|
import sys
|
||||||
|
if sys.version_info > (2,6,0):
|
||||||
|
import numbers
|
||||||
|
else:
|
||||||
|
pass
|
||||||
|
|
||||||
|
if sys.version_info > (2,6,0):
|
||||||
|
def lin_range(start,stop,step):
|
||||||
|
if isinstance(step, numbers.Integral):
|
||||||
|
return N.linspace(start,stop,step)
|
||||||
|
else:
|
||||||
|
return N.arange(start,stop,step)
|
||||||
|
else:
|
||||||
|
def lin_range(start,stop,step):
|
||||||
|
return N.arange(start,stop,step)
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def log_range(start, stop, stepno):
|
||||||
|
if (start<=0 or stop<=0 or stepno<1):
|
||||||
|
raise ValueError("start, stop must be positive and stepno must be >=1")
|
||||||
|
return N.logspace(N.log10(start),N.log10(stop), num=stepno)
|
||||||
|
|
||||||
|
|
||||||
|
def staggered_range(some_range, size=3):
|
||||||
|
m=0
|
||||||
|
if isinstance(some_range, N.ndarray):
|
||||||
|
is_numpy = True
|
||||||
|
some_range = list(some_range)
|
||||||
|
else:
|
||||||
|
is_numpy = False
|
||||||
|
new_list=[]
|
||||||
|
for k in xrange(len(some_range)):
|
||||||
|
for i in xrange(size):
|
||||||
|
try:
|
||||||
|
index = (m*size)
|
||||||
|
new_list.append(some_range.pop(index))
|
||||||
|
except IndexError:
|
||||||
|
break
|
||||||
|
m+=1
|
||||||
|
if is_numpy:
|
||||||
|
new_list = N.asarray(new_list+some_range)
|
||||||
|
else:
|
||||||
|
new_list+=some_range
|
||||||
|
return new_list
|
||||||
|
|
||||||
|
|
||||||
|
def combine_ranges(*ranges):
|
||||||
|
new_list = []
|
||||||
|
for r in ranges:
|
||||||
|
new_list.extend(r)
|
||||||
|
return new_list
|
||||||
|
|
||||||
|
combined_ranges=combine_ranges
|
||||||
|
|
||||||
|
def interleaved_range(some_list, left_out):
|
||||||
|
"""
|
||||||
|
in first run, do every n-th, then do n-1-th of the remaining values and so on...
|
||||||
|
"""
|
||||||
|
m=0
|
||||||
|
new_list = []
|
||||||
|
for j in xrange(left_out):
|
||||||
|
for i in xrange(len(some_list)):
|
||||||
|
if (i*left_out+m) < len(some_list):
|
||||||
|
new_list.append(some_list[i*left_out+m])
|
||||||
|
else:
|
||||||
|
m+=1
|
||||||
|
break
|
||||||
|
if isinstance(some_list, N.ndarray):
|
||||||
|
new_list = N.array(new_list)
|
||||||
|
return new_list
|
||||||
|
|
||||||
|
|
||||||
|
# These are the generators
|
||||||
|
def lin_range_iter(start,stop, step):
|
||||||
|
this_one=float(start)+0.0
|
||||||
|
if step>0:
|
||||||
|
while (this_one<=float(stop)):
|
||||||
|
yield this_one
|
||||||
|
this_one+=float(step)
|
||||||
|
else:
|
||||||
|
while (this_one>=float(stop)):
|
||||||
|
yield this_one
|
||||||
|
this_one+=float(step)
|
||||||
|
|
||||||
|
|
||||||
|
def log_range_iter(start, stop, stepno):
|
||||||
|
if (start<=0 or stop<=0 or stepno<1):
|
||||||
|
raise ValueError("start, stop must be positive and stepno must be >=1")
|
||||||
|
if int(stepno)==1:
|
||||||
|
factor=1.0
|
||||||
|
else:
|
||||||
|
factor=(stop/start)**(1.0/int(stepno-1))
|
||||||
|
for i in xrange(int(stepno)):
|
||||||
|
yield start*(factor**i)
|
||||||
|
|
||||||
|
def staggered_range_iter(some_range, size = 1):
|
||||||
|
"""
|
||||||
|
size=1: do one, drop one, ....
|
||||||
|
size=n: do 1 ... n, drop n+1 ... 2*n
|
||||||
|
in a second run the dropped values were done
|
||||||
|
"""
|
||||||
|
left_out=[]
|
||||||
|
try:
|
||||||
|
while True:
|
||||||
|
for i in xrange(size):
|
||||||
|
yield some_range.next()
|
||||||
|
for i in xrange(size):
|
||||||
|
left_out.append(some_range.next())
|
||||||
|
except StopIteration:
|
||||||
|
pass
|
||||||
|
|
||||||
|
# now do the droped ones
|
||||||
|
for i in left_out:
|
||||||
|
yield i
|
||||||
|
|
||||||
|
def combined_ranges_iter(*ranges):
|
||||||
|
"""
|
||||||
|
iterate over one range after the other
|
||||||
|
"""
|
||||||
|
for r in ranges:
|
||||||
|
for i in r:
|
||||||
|
yield i
|
||||||
|
|
||||||
|
combine_ranges_iter=combined_ranges_iter
|
||||||
|
|
||||||
30
src/tools/signal.py
Normal file
30
src/tools/signal.py
Normal file
@ -0,0 +1,30 @@
|
|||||||
|
import math
|
||||||
|
|
||||||
|
__all__ = ['rotate_signal']
|
||||||
|
|
||||||
|
|
||||||
|
def rotate_signal(timesignal, angle):
|
||||||
|
"Rotate <timesignal> by <angle> degrees"
|
||||||
|
# implicit change to float arrays!
|
||||||
|
if timesignal.get_number_of_channels()!=2:
|
||||||
|
raise Exception("rotation defined only for 2 channels")
|
||||||
|
# simple case 0, 90, 180, 270 degree
|
||||||
|
reduced_angle=divmod(angle, 90)
|
||||||
|
if abs(reduced_angle[1])<1e-6:
|
||||||
|
reduced_angle=reduced_angle[0]%4
|
||||||
|
if reduced_angle==0:
|
||||||
|
return
|
||||||
|
elif reduced_angle==1:
|
||||||
|
timesignal.y[1]*=-1
|
||||||
|
timesignal.y=[timesignal.y[1],timesignal.y[0]]
|
||||||
|
elif reduced_angle==2:
|
||||||
|
timesignal.y[0]*=-1
|
||||||
|
timesignal.y[1]*=-1
|
||||||
|
elif reduced_angle==3:
|
||||||
|
timesignal.y[0]*=-1
|
||||||
|
timesignal.y=[timesignal.y[1],timesignal.y[0]]
|
||||||
|
else:
|
||||||
|
sin_angle=math.sin(angle/180.0*math.pi)
|
||||||
|
cos_angle=math.cos(angle/180.0*math.pi)
|
||||||
|
timesignal.y=[cos_angle*timesignal.y[0]-sin_angle*timesignal.y[1],
|
||||||
|
sin_angle*timesignal.y[0]+cos_angle*timesignal.y[1]]
|
||||||
97
tests/datatest.py
Normal file
97
tests/datatest.py
Normal file
@ -0,0 +1,97 @@
|
|||||||
|
import sys
|
||||||
|
import numpy
|
||||||
|
import math
|
||||||
|
import os.path
|
||||||
|
import unittest
|
||||||
|
|
||||||
|
print "running tests on modules in source directory"
|
||||||
|
# assume, script is in tests directory and we are testing modules in src
|
||||||
|
sys.path[0:0]=[os.path.join(os.path.dirname(sys.argv[0]), "..", "src", "data")]
|
||||||
|
from MeasurementResult import *
|
||||||
|
|
||||||
|
class TestAccumulatedValueClass(unittest.TestCase):
|
||||||
|
|
||||||
|
def setUp(self):
|
||||||
|
# is called before each test
|
||||||
|
pass
|
||||||
|
|
||||||
|
def testInitialization_Empty(self):
|
||||||
|
a=AccumulatedValue()
|
||||||
|
self.assert_(a.mean() is None)
|
||||||
|
self.assert_(a.mean_error() is None)
|
||||||
|
self.assert_(a.sigma() is None)
|
||||||
|
self.assert_(a.n==0)
|
||||||
|
|
||||||
|
def testInitialization_1Value(self):
|
||||||
|
a=AccumulatedValue(0)
|
||||||
|
self.assert_(a.mean()==0)
|
||||||
|
self.assertAlmostEqual(a.mean_error(),0)
|
||||||
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self.assertAlmostEqual(a.sigma(),0)
|
||||||
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self.assert_(a.n==1)
|
||||||
|
|
||||||
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def testInitialization_2Values(self):
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a=AccumulatedValue(1, 0.1)
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|
self.assert_(a.mean(),1.0)
|
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self.assertAlmostEqual(a.mean_error(), 0.1)
|
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self.assertAlmostEqual(a.sigma(), 0.1*math.sqrt(2.0))
|
||||||
|
self.assert_(a.n==2)
|
||||||
|
|
||||||
|
def testInitialization_3Values(self):
|
||||||
|
a=AccumulatedValue(1, 0.1, 10)
|
||||||
|
self.assertAlmostEqual(a.mean(),1)
|
||||||
|
self.assertAlmostEqual(a.mean_error(), 0.1)
|
||||||
|
self.assertAlmostEqual(a.sigma(), 0.1*math.sqrt(10.0))
|
||||||
|
self.assert_(a.n==10)
|
||||||
|
|
||||||
|
def testStatistics(self):
|
||||||
|
test_dataset=numpy.arange(10.0)
|
||||||
|
a=AccumulatedValue()
|
||||||
|
for i in test_dataset:
|
||||||
|
a+=i
|
||||||
|
self.assert_(a.n==len(test_dataset))
|
||||||
|
# sum x_i/n
|
||||||
|
self.assertAlmostEqual(a.mean(), test_dataset.mean())
|
||||||
|
# std_dev_n-1 x_i= sqrt(sum (x-xmean)**2/(n-1))
|
||||||
|
self.assertAlmostEqual(a.sigma(), math.sqrt(((test_dataset-a.mean())**2).sum()/(len(test_dataset)-1.)))
|
||||||
|
# std_dev_n-1 x_i/sqrt(n)
|
||||||
|
self.assertAlmostEqual(a.mean_error(), a.sigma()/math.sqrt(len(test_dataset)))
|
||||||
|
|
||||||
|
def tearDown(self):
|
||||||
|
# is called after each test
|
||||||
|
pass
|
||||||
|
|
||||||
|
class TestMeasurementResult(unittest.TestCase):
|
||||||
|
|
||||||
|
def testImplicitCast(self):
|
||||||
|
# check wether other data types will be converted to AccumulatedValue
|
||||||
|
m=MeasurementResult("TestData")
|
||||||
|
m[1.0]
|
||||||
|
m[2.0]=2
|
||||||
|
self.assert_(isinstance(m[1.0], AccumulatedValue))
|
||||||
|
self.assert_(isinstance(m[2.0], AccumulatedValue))
|
||||||
|
|
||||||
|
def testUninitalizedEntries(self):
|
||||||
|
# assure that entries with no data are listed as xdata
|
||||||
|
m=MeasurementResult("TestData")
|
||||||
|
a=m[2.0]
|
||||||
|
self.assert_(isinstance(a, AccumulatedValue))
|
||||||
|
self.assert_(2.0 in m)
|
||||||
|
self.assert_(2.0 not in m.get_xdata())
|
||||||
|
m[2.0]+=1
|
||||||
|
self.assert_(2.0 in m.get_xdata())
|
||||||
|
|
||||||
|
def testZeroError(self):
|
||||||
|
# AccumulatedValues with only one Accumulation should have 0 error
|
||||||
|
m=MeasurementResult("TestData")
|
||||||
|
m[0.0]
|
||||||
|
m[1.0]=AccumulatedValue()
|
||||||
|
m[2.0]=0
|
||||||
|
m[3.0]=AccumulatedValue(0,1.0)
|
||||||
|
k,v,e=m.get_errorplotdata()
|
||||||
|
self.assert_(2.0 in k and 3.0 in k)
|
||||||
|
self.assert_(1.0 not in k and 0.0 not in k)
|
||||||
|
self.assertAlmostEqual(e[k==2.0][0], 0)
|
||||||
|
self.assertAlmostEqual(e[k==3.0][0], 1.0)
|
||||||
|
|
||||||
|
if __name__=="__main__":
|
||||||
|
unittest.main()
|
||||||
Loading…
Reference in New Issue
Block a user