IPKM/python-damaris
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fixed evil tab/spaces

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This commit is contained in:
Markus Rosenstihl 2014-11-26 13:19:23 +00:00
parent 059c059de7
commit aed38c1c89
2 changed files with 96 additions and 83 deletions
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30
src/data/DamarisFFT.py
View File

@ -5,9 +5,14 @@ import autophase
class DamarisFFT: class DamarisFFT:
def clip(self, start=None, stop=None): def clip(self, start=None, stop=None):
""" """
Method for clipping data, only the timesignal between start and stop :param float start: beginning of clipping
:param float stop: end of clipping
Method for clipping data, returns only the timesignal
between start and stop
is returned. is returned.
start and stop can be either time or frequency. The unit is automatically determined start and stop can be either time or frequency.
The unit is automatically determined
""" """
# check if start/stop order is properly # check if start/stop order is properly
if start > stop: if start > stop:
@ -15,12 +20,12 @@ class DamarisFFT:
# TODO swap values? # TODO swap values?
raise raise
# if one uses clip as a "placeholder" # if one uses clip as a "placeholder"
if start==None and stop==None: if start == None and stop == None:
return self return self
if start==None: if start == None:
start = 0 start = 0
if stop==None: if stop == None:
stop = -1 stop = -1
# check if data is fft which changes the start/stop units # check if data is fft which changes the start/stop units
# TODO should get nicer(failsafe), i.e. flags in the object? # TODO should get nicer(failsafe), i.e. flags in the object?
@ -50,12 +55,14 @@ class DamarisFFT:
Correct the baseline of your data by subtracting the mean of the Correct the baseline of your data by subtracting the mean of the
last_part fraction of your data. last_part fraction of your data.
:param float last_part: last section of your timesignal used to calculate baseline
last_part defaults to 0.1, i.e. last 10% of your data last_part defaults to 0.1, i.e. last 10% of your data
""" """
# TODO baselinecorrection for spectra after: # TODO baselinecorrection for spectra after:
# Heuer, A; Haeberlen, U.: J. Mag. Res.(1989) 85, Is 1, 79-94 # Heuer, A; Haeberlen, U.: J. Mag. Res.(1989) 85, Is 1, 79-94
# Should I create an empty object? # Should I create an empty object?
# I deided to do NOT a copy, but # I deided to do NOT a copy, but
# rather modify the object # rather modify the object
n = int(self.x.size*last_part) n = int(self.x.size*last_part)
for ch in xrange(len(self.y)): for ch in xrange(len(self.y)):
@ -80,7 +87,14 @@ class DamarisFFT:
""" """
def exp_window(self, line_broadening=10): def exp_window(self, line_broadening=10):
""" """
exponential window Exponential window function
:param float line_broadening: Applies apodization to time signal
.. math::
\\exp\\left(-\\pi\\cdot \\textsf{line_broadening} \\cdot t\\right)
""" """
apod = numpy.exp(-self.x*numpy.pi*line_broadening) apod = numpy.exp(-self.x*numpy.pi*line_broadening)
for i in range(2): for i in range(2):

149
src/gui/DamarisGUI.py
View File

@ -567,7 +567,7 @@ class DamarisGUI:
extensions_dict["res"]="unnamed" extensions_dict["res"]="unnamed"
else: else:
extensions_dict["res"]=os.path.splitext(os.path.basename(self.sw.res_script_filename))[0] extensions_dict["res"]=os.path.splitext(os.path.basename(self.sw.res_script_filename))[0]
# create new dump file name # create new dump file name
try: try:
self.dump_filename=actual_config.get("data_pool_name")%extensions_dict self.dump_filename=actual_config.get("data_pool_name")%extensions_dict
except ValueError,e: except ValueError,e:
@ -580,7 +580,7 @@ class DamarisGUI:
print "The dump filename is a directory, using filename 'DAMARIS_data_pool.h5'" print "The dump filename is a directory, using filename 'DAMARIS_data_pool.h5'"
self.dump_filename+=os.sep+"DAMARIS_data_pool.h5" self.dump_filename+=os.sep+"DAMARIS_data_pool.h5"
# compression # compression
self.dump_complib=actual_config.get("data_pool_complib",None) self.dump_complib=actual_config.get("data_pool_complib",None)
if self.dump_complib=="None": if self.dump_complib=="None":
self.dump_complib=None self.dump_complib=None
@ -589,7 +589,7 @@ class DamarisGUI:
else: else:
self.dump_complevel=0 self.dump_complevel=0
# time interval # time interval
self.dump_timeinterval=60*60*10 self.dump_timeinterval=60*60*10
try: try:
self.dump_timeinterval=int(60*float(actual_config["data_pool_write_interval"])) self.dump_timeinterval=int(60*float(actual_config["data_pool_write_interval"]))
@ -621,29 +621,29 @@ class DamarisGUI:
# init is finnished now # init is finnished now
# now it's time to create the hdf file # now it's time to create the hdf file
dump_file=None dump_file=None
if not os.path.isfile(self.dump_filename): if not os.path.isfile(self.dump_filename):
if not init: if not init:
print "dump file \"%s\" vanished unexpectedly, creating new one"%self.dump_filename print "dump file \"%s\" vanished unexpectedly, creating new one"%self.dump_filename
# have a look to the path and create necessary directories # have a look to the path and create necessary directories
dir_stack=[] dir_stack=[]
dir_trunk=os.path.dirname(os.path.abspath(self.dump_filename)) dir_trunk=os.path.dirname(os.path.abspath(self.dump_filename))
while dir_trunk!="" and not os.path.isdir(dir_trunk): while dir_trunk!="" and not os.path.isdir(dir_trunk):
dir_stack.append(os.path.basename(dir_trunk)) dir_stack.append(os.path.basename(dir_trunk))
dir_trunk=os.path.dirname(dir_trunk) dir_trunk=os.path.dirname(dir_trunk)
try: try:
while len(dir_stack): while len(dir_stack):
dir_trunk=os.path.join(dir_trunk, dir_stack.pop()) dir_trunk=os.path.join(dir_trunk, dir_stack.pop())
if os.path.isdir(dir_trunk): continue if os.path.isdir(dir_trunk): continue
os.mkdir(dir_trunk) os.mkdir(dir_trunk)
except OSError, e: except OSError, e:
print e print e
print "coud not create dump directory '%s', so hdf5 dumps disabled"%dir_trunk print "coud not create dump directory '%s', so hdf5 dumps disabled"%dir_trunk
self.dump_filename="" self.dump_filename=""
self.dump_timeinterval=0 self.dump_timeinterval=0
return True return True
# create new dump file # create new dump file
dump_file=tables.openFile(self.dump_filename,mode="w",title="DAMARIS experiment data") dump_file=tables.openFile(self.dump_filename,mode="w",title="DAMARIS experiment data")
# write scripts and other useful information # write scripts and other useful information
scriptgroup=dump_file.createGroup("/","scripts","Used Scripts") scriptgroup=dump_file.createGroup("/","scripts","Used Scripts")
@ -674,7 +674,7 @@ class DamarisGUI:
title="log messages", title="log messages",
filters=tables.Filters(complevel=9, complib='zlib')) filters=tables.Filters(complevel=9, complib='zlib'))
if dump_file is None and os.path.isfile(self.dump_filename) and tables.isPyTablesFile(self.dump_filename): if dump_file is None and os.path.isfile(self.dump_filename) and tables.isPyTablesFile(self.dump_filename):
# take some data from dump file and repack # take some data from dump file and repack
os.rename(self.dump_filename, self.dump_filename+".bak") os.rename(self.dump_filename, self.dump_filename+".bak")
old_dump_file=tables.openFile(self.dump_filename+".bak", mode="r+") old_dump_file=tables.openFile(self.dump_filename+".bak", mode="r+")
@ -687,13 +687,13 @@ class DamarisGUI:
# prepare for update # prepare for update
dump_file=tables.openFile(self.dump_filename, mode="r+") dump_file=tables.openFile(self.dump_filename, mode="r+")
if dump_file is None: if dump_file is None:
# exit! # exit!
print "coud not create dump directory '%s', so hdf5 dumps disabled"%dir_trunk print "coud not create dump directory '%s', so hdf5 dumps disabled"%dir_trunk
self.dump_filename="" self.dump_filename=""
self.dump_timeinterval=0 self.dump_timeinterval=0
return True return True
# no undo please! # no undo please!
if dump_file.isUndoEnabled(): if dump_file.isUndoEnabled():
dump_file.disableUndo() dump_file.disableUndo()
@ -1207,32 +1207,32 @@ class ScriptWidgets:
cursor_mark=textbuffer.get_insert() cursor_mark=textbuffer.get_insert()
cursor_iter=textbuffer.get_iter_at_mark(cursor_mark) cursor_iter=textbuffer.get_iter_at_mark(cursor_mark)
if textbuffer is self.experiment_script_textbuffer: if textbuffer is self.experiment_script_textbuffer:
line_indicator=self.experiment_script_line_indicator line_indicator=self.experiment_script_line_indicator
column_indicator=self.experiment_script_column_indicator column_indicator=self.experiment_script_column_indicator
if textbuffer is self.data_handling_textbuffer: if textbuffer is self.data_handling_textbuffer:
line_indicator=self.data_handling_line_indicator line_indicator=self.data_handling_line_indicator
column_indicator=self.data_handling_column_indicator column_indicator=self.data_handling_column_indicator
# do only necessary updates! # do only necessary updates!
li_range_new=textbuffer.get_end_iter().get_line()+1 li_range_new=textbuffer.get_end_iter().get_line()+1
if line_indicator.get_range()[1]!=li_range_new: if line_indicator.get_range()[1]!=li_range_new:
line_indicator.set_range(1, li_range_new) line_indicator.set_range(1, li_range_new)
ci_range_new=cursor_iter.get_chars_in_line()+1 ci_range_new=cursor_iter.get_chars_in_line()+1
if column_indicator.get_range()[1]!=ci_range_new: if column_indicator.get_range()[1]!=ci_range_new:
column_indicator.set_range(1, ci_range_new) column_indicator.set_range(1, ci_range_new)
cursor_line=cursor_iter.get_line()+1 cursor_line=cursor_iter.get_line()+1
cursor_lineoffset=cursor_iter.get_line_offset()+1 cursor_lineoffset=cursor_iter.get_line_offset()+1
if line_indicator.get_value()!=cursor_line: if line_indicator.get_value()!=cursor_line:
line_indicator.set_value(cursor_line) line_indicator.set_value(cursor_line)
if column_indicator.get_value()!=cursor_lineoffset: if column_indicator.get_value()!=cursor_lineoffset:
column_indicator.set_value(cursor_lineoffset) column_indicator.set_value(cursor_lineoffset)
return False return False
def textviews_keypress(self, widget, event, data = None): def textviews_keypress(self, widget, event, data = None):
""" """
helpful tab and return key functions helpful tab and return key functions
""" """
#print "keypress", event.state, event.keyval #print "keypress", event.state, event.keyval
if event.state&gtk.gdk.CONTROL_MASK!=0: if event.state&gtk.gdk.CONTROL_MASK!=0:
if event.keyval==gtk.gdk.keyval_from_name("c"): if event.keyval==gtk.gdk.keyval_from_name("c"):
if self.main_notebook.get_current_page() == 0: if self.main_notebook.get_current_page() == 0:
@ -1344,7 +1344,7 @@ class ScriptWidgets:
return 1 return 1
#self.textviews_moved(widget) #self.textviews_moved(widget)
return 0 return 0
def load_file_as_unicode(self, script_filename): def load_file_as_unicode(self, script_filename):
script_file = file(script_filename, "rU") script_file = file(script_filename, "rU")
@ -1734,10 +1734,10 @@ pygobject version %(pygobject)s
self.xml_gui.signal_connect("on_printer_setup_button_clicked", self.printer_setup_handler) self.xml_gui.signal_connect("on_printer_setup_button_clicked", self.printer_setup_handler)
for self.system_default_filename in self.system_default_filenames: for self.system_default_filename in self.system_default_filenames:
if self.system_default_filename: if self.system_default_filename:
if os.access(self.system_default_filename, os.R_OK): if os.access(self.system_default_filename, os.R_OK):
self.load_config(self.system_default_filename) self.load_config(self.system_default_filename)
else: else:
print "can not read system defaults from %s, ask your instrument responsible if required"%self.system_default_filename print "can not read system defaults from %s, ask your instrument responsible if required"%self.system_default_filename
self.config_from_system = self.get() self.config_from_system = self.get()
self.load_config() self.load_config()
@ -2064,7 +2064,7 @@ class MonitorWidgets:
def source_list_reset(self): def source_list_reset(self):
self.display_source_treestore.clear() self.display_source_treestore.clear()
self.source_list_add(u'None') self.source_list_add(u'None')
none_iter=self.source_list_find([u'None']) none_iter=self.source_list_find([u'None'])
if none_iter is not None: self.display_source_combobox.set_active_iter(none_iter) if none_iter is not None: self.display_source_combobox.set_active_iter(none_iter)
def source_list_find_one(self, model, iter, what): def source_list_find_one(self, model, iter, what):
@ -2286,8 +2286,8 @@ class MonitorWidgets:
self.displayed_data[0]==event.subject): self.displayed_data[0]==event.subject):
self.displayed_data=[None,None] self.displayed_data=[None,None]
none_iter=self.source_list_find([u'None']) none_iter=self.source_list_find([u'None'])
if none_iter is not None: self.display_source_combobox.set_active_iter(none_iter) if none_iter is not None: self.display_source_combobox.set_active_iter(none_iter)
# not necessary, because event will be submitted # not necessary, because event will be submitted
#self.clear_display() #self.clear_display()
self.source_list_remove(event.subject) self.source_list_remove(event.subject)
gtk.gdk.threads_leave() gtk.gdk.threads_leave()
@ -2334,7 +2334,7 @@ class MonitorWidgets:
self.clear_display() self.clear_display()
elif self.data_pool is None or new_data_name not in self.data_pool: elif self.data_pool is None or new_data_name not in self.data_pool:
none_iter=self.source_list_find([u'None']) none_iter=self.source_list_find([u'None'])
if none_iter is not None: self.display_source_combobox.set_active_iter(none_iter) if none_iter is not None: self.display_source_combobox.set_active_iter(none_iter)
self.display_source_path_label.set_label(u"") self.display_source_path_label.set_label(u"")
else: else:
new_data_struct=self.data_pool[new_data_name] new_data_struct=self.data_pool[new_data_name]
@ -2538,7 +2538,7 @@ class MonitorWidgets:
# Autoscaling activated? # Autoscaling activated?
elif self.display_autoscaling_checkbutton.get_active(): elif self.display_autoscaling_checkbutton.get_active():
xlim_min, xlim_max=self.matplot_axes.get_xlim() xlim_min, xlim_max=self.matplot_axes.get_xlim()
if xlim_min!= xmin or xlim_max!=xmax : if xlim_min!= xmin or xlim_max!=xmax :
self.matplot_axes.set_xlim(xmin, xmax) self.matplot_axes.set_xlim(xmin, xmax)
@ -2620,26 +2620,25 @@ class MonitorWidgets:
self.matplot_axes.set_ylabel("") self.matplot_axes.set_ylabel("")
# Any variables to be set? # Any variables to be set?
# if False: # if False:
# if isinstance(in_result, Accumulation): # if isinstance(in_result, Accumulation):
# descriptions = in_result.common_descriptions # descriptions = in_result.common_descriptions
# elif isinstance(in_result, ADC_Result): # elif isinstance(in_result, ADC_Result):
# descriptions = in_result.description # descriptions = in_result.description
# else: pass # else: pass
# actual_config = self.config.get() # actual_config = self.config.get()
# if (descriptions is not None) : #--markusro # if (descriptions is not None) : #--markusro
# print actual_config['pretty_descriptions'] # print actual_config['pretty_descriptions']
# pass # pass
# description_string = "" # description_string = ""
# for key in descriptions.keys(): # for key in descriptions.keys():
# description_string += "%s = %s\n" % (key,descriptions[key]) # description_string += "%s = %s\n" % (key,descriptions[key])
# self.matplot_axes.text(0.7,0.95, description_string[:-1], # self.matplot_axes.text(0.7,0.95, description_string[:-1],
# size=8, # size=8,
# transform=self.matplot_axes.transAxes, # transform=self.matplot_axes.transAxes,
# va='top', # va='top',
# backgroundcolor='white') # backgroundcolor='white')
# #
# Draw it! # Draw it!
self.matplot_canvas.draw_idle() self.matplot_canvas.draw_idle()
del in_result del in_result