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Merge branch 'more_bugs'

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This commit is contained in:
Dominik Demuth 2023-04-16 14:17:36 +02:00
commit 8e2ebfc765
11 changed files with 239 additions and 225 deletions
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2
AppImageBuilder.yml
View File

@ -44,6 +44,7 @@ AppDir:
- python3.9-minimal - python3.9-minimal
- python3-numpy - python3-numpy
- python3-scipy - python3-scipy
- gnuplot-nox
- python3-bsddb3 - python3-bsddb3
- python3-h5py - python3-h5py
- python3-pyqt5 - python3-pyqt5
@ -59,7 +60,6 @@ AppDir:
- qtbase5-dev-tools - qtbase5-dev-tools
- qtchooser - qtchooser
- pyqt5-dev-tools - pyqt5-dev-tools
- qtchooser
- libavahi-client3 - libavahi-client3
- libavahi-common-data - libavahi-common-data
- libavahi-common3 - libavahi-common3

15
src/gui_qt/data/datawidget/datawidget.py
View File

@ -1,5 +1,6 @@
from __future__ import annotations from __future__ import annotations
from nmreval.lib.logger import logger
from nmreval.lib.colors import available_cycles from nmreval.lib.colors import available_cycles
from .properties import PropWidget from .properties import PropWidget
@ -19,6 +20,7 @@ class DataTree(QtWidgets.QTreeWidget):
saveFits = QtCore.pyqtSignal(list) saveFits = QtCore.pyqtSignal(list)
extendFits = QtCore.pyqtSignal(list) extendFits = QtCore.pyqtSignal(list)
# noinspection PyUnresolvedReferences
def __init__(self, parent=None): def __init__(self, parent=None):
super().__init__(parent=parent) super().__init__(parent=parent)
@ -229,7 +231,7 @@ class DataTree(QtWidgets.QTreeWidget):
def sort(self, graph_item: QtWidgets.QTreeWidgetItem, mode: str = 'value'): def sort(self, graph_item: QtWidgets.QTreeWidgetItem, mode: str = 'value'):
graph_id = graph_item.data(0, QtCore.Qt.UserRole) graph_id = graph_item.data(0, QtCore.Qt.UserRole)
sets = self.management.get_attributes(graph_id, mode) sets = self.management.get_attributes(graph_id, mode)
sets = [el[0] for el in sorted(sets.items(), key=lambda x: x[1])] sets = [el[0] for el in sorted(sets.items(), key=lambda x: x[1])]
self.management.move_sets(sets, graph_id, graph_id, pos=-1) self.management.move_sets(sets, graph_id, graph_id, pos=-1)
@ -247,7 +249,6 @@ class DataTree(QtWidgets.QTreeWidget):
self.blockSignals(False) self.blockSignals(False)
def update_indexes(self): def update_indexes(self):
graph_cnt = -1 graph_cnt = -1
set_cnt = 0 set_cnt = 0
@ -342,7 +343,7 @@ class DataTree(QtWidgets.QTreeWidget):
self.setDragEnabled(idx.column() == 0) self.setDragEnabled(idx.column() == 0)
super().mousePressEvent(evt) super().mousePressEvent(evt)
def remove_item(self, ids: list): def remove_item(self, ids: list[str]):
iterator = QtWidgets.QTreeWidgetItemIterator(self) iterator = QtWidgets.QTreeWidgetItemIterator(self)
while iterator.value(): while iterator.value():
item = iterator.value() item = iterator.value()
@ -356,7 +357,10 @@ class DataTree(QtWidgets.QTreeWidget):
except AttributeError: except AttributeError:
idx = self.invisibleRootItem().indexOfChild(item) idx = self.invisibleRootItem().indexOfChild(item)
self.invisibleRootItem().takeChild(idx) self.invisibleRootItem().takeChild(idx)
self._checked_graphs.remove(_id) try:
self._checked_graphs.remove(_id)
except KeyError:
logger.warn(f'Graph {_id} already removed, skip')
iterator += 1 iterator += 1
@ -523,6 +527,7 @@ class DataWidget(QtWidgets.QWidget, Ui_DataWidget):
self.setupUi(self) self.setupUi(self)
self.tree = DataTree(self) self.tree = DataTree(self)
self.verticalLayout.addWidget(self.tree) self.verticalLayout.addWidget(self.tree)
# noinspection PyUnresolvedReferences
self.tree.selectionModel().selectionChanged.connect(lambda x, y: self.show_property(x)) self.tree.selectionModel().selectionChanged.connect(lambda x, y: self.show_property(x))
self.tree.keyChanged.connect(lambda x, y: self.keyChanged.emit(x, y)) self.tree.keyChanged.connect(lambda x, y: self.keyChanged.emit(x, y))
@ -550,7 +555,7 @@ class DataWidget(QtWidgets.QWidget, Ui_DataWidget):
self.tree.add_item(loi, gid) self.tree.add_item(loi, gid)
self.tree.blockSignals(False) self.tree.blockSignals(False)
def remove_item(self, key): def remove_item(self, key: list[str]):
self.tree.remove_item(key) self.tree.remove_item(key)
def show_property(self, _: QtCore.QModelIndex = None): def show_property(self, _: QtCore.QModelIndex = None):

7
src/gui_qt/fit/fitwindow.py
View File

@ -148,6 +148,13 @@ class QFitDialog(QtWidgets.QWidget, Ui_FitDialog):
Add name and id of dataset to list. Add name and id of dataset to list.
""" """
self.data_table.load(ids) self.data_table.load(ids)
# deselect all fit sets
for i in range(self.data_table.rowCount()):
data_id = self.data_table.item(i, 0).data(QtCore.Qt.UserRole+1)
if self._management[data_id].mode == 'fit':
self.data_table.item(i, 0).setCheckState(QtCore.Qt.Unchecked)
if self.models: if self.models:
for m in self.models.keys(): for m in self.models.keys():
self.data_table.add_model(m) self.data_table.add_model(m)

23
src/gui_qt/graphs/graphwindow.py
View File

@ -54,6 +54,8 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self._external_items = [] self._external_items = []
self.closable = True self.closable = True
self._block = False
self.log = [False, False] self.log = [False, False]
self.scene = self.plotItem.scene() self.scene = self.plotItem.scene()
@ -150,6 +152,16 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
return tuple(r) return tuple(r)
def block(self, state: bool):
self._block = state
if not self._block:
self.graphic.enableAutoRange()
self._update_zorder()
self.show_legend()
else:
self.graphic.disableAutoRange()
def add(self, name: str | list, plots: list): def add(self, name: str | list, plots: list):
if isinstance(name, str): if isinstance(name, str):
name = [name] name = [name]
@ -201,8 +213,9 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.listWidget.blockSignals(False) self.listWidget.blockSignals(False)
self._update_zorder() if not self._block:
self.show_legend() self._update_zorder()
self.show_legend()
def move_sets(self, sets: list, position: int): def move_sets(self, sets: list, position: int):
move_plots = [] move_plots = []
@ -484,6 +497,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.ymax_lineedit.setText('%.5g' % r[1][1]) self.ymax_lineedit.setText('%.5g' % r[1][1])
def _update_zorder(self): def _update_zorder(self):
print('update yorder')
for i, sid in enumerate(self.sets): for i, sid in enumerate(self.sets):
plt = self.real_plots[sid] plt = self.real_plots[sid]
if plt.zValue() != 2*i+1: if plt.zValue() != 2*i+1:
@ -501,6 +515,10 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.checkBox.setVisible(visible) self.checkBox.setVisible(visible)
def update_legend(self, sid, name): def update_legend(self, sid, name):
if self._block:
return
print('update legend')
self.listWidget.blockSignals(True) self.listWidget.blockSignals(True)
for i in range(self.listWidget.count()): for i in range(self.listWidget.count()):
@ -512,6 +530,7 @@ class QGraphWindow(QtWidgets.QGraphicsView, Ui_GraphWindow):
self.show_legend() self.show_legend()
def show_legend(self): def show_legend(self):
print('show legend')
if not self.legend.isVisible(): if not self.legend.isVisible():
return return

20
src/gui_qt/io/fcbatchreader.py
View File

@ -1,3 +1,5 @@
from __future__ import annotations
import pathlib import pathlib
from nmreval.io.fcbatchreader import FCReader from nmreval.io.fcbatchreader import FCReader
@ -31,6 +33,10 @@ class QFCReader(QtWidgets.QDialog, Ui_FCEval_dialog):
return super().eventFilter(src, evt) return super().eventFilter(src, evt)
def add_graphs(self, graphs: list[tuple[str, str]]):
for gid, graph_name in graphs:
self.graph_comboBox.addItem(graph_name, gid)
@QtCore.pyqtSlot(int, name='on_region_checkBox_stateChanged') @QtCore.pyqtSlot(int, name='on_region_checkBox_stateChanged')
def use_region(self, state: int): def use_region(self, state: int):
self.start_lineedit.setEnabled(state == QtCore.Qt.Checked) self.start_lineedit.setEnabled(state == QtCore.Qt.Checked)
@ -43,17 +49,17 @@ class QFCReader(QtWidgets.QDialog, Ui_FCEval_dialog):
infiles, _ = QtWidgets.QFileDialog.getOpenFileNames(caption='Select HDF files', infiles, _ = QtWidgets.QFileDialog.getOpenFileNames(caption='Select HDF files',
directory=str(self.path), directory=str(self.path),
filter='HDF files (*.h5)') filter='HDF files (*.h5)')
if infiles:
self.listWidget.addItems(infiles)
self.label.setText(str(pathlib.Path(infiles[-1]).parent))
else: else:
infiles = QtWidgets.QFileDialog.getExistingDirectory(caption='Select input directory', infiles = QtWidgets.QFileDialog.getExistingDirectory(caption='Select input directory',
directory=str(self.path), directory=str(self.path),
options=QtWidgets.QFileDialog.ShowDirsOnly) options=QtWidgets.QFileDialog.ShowDirsOnly)
infiles = [infiles] if infiles else infiles
if infiles: if infiles:
self.listWidget.addItem(infiles) self.listWidget.addItems(infiles)
self.label.setText(str(pathlib.Path(infiles).parent)) self.path = pathlib.Path(infiles[-1]).parent
self.label.setText(str(self.path))
@QtCore.pyqtSlot(name='on_savebutton_clicked') @QtCore.pyqtSlot(name='on_savebutton_clicked')
def save_path(self): def save_path(self):
@ -72,7 +78,7 @@ class QFCReader(QtWidgets.QDialog, Ui_FCEval_dialog):
self.close() self.close()
def read(self, items): def read(self, items):
region = (None, None) region = None
if self.region_box.isChecked(): if self.region_box.isChecked():
start = None start = None
if self.start_lineedit.text(): if self.start_lineedit.text():

58
src/gui_qt/lib/undos.py
View File

@ -1,3 +1,5 @@
from __future__ import annotations
import copy import copy
from numpy import argsort from numpy import argsort
@ -216,33 +218,55 @@ class DeleteGraphCommand(QtWidgets.QUndoCommand):
class DeleteCommand(QtWidgets.QUndoCommand): class DeleteCommand(QtWidgets.QUndoCommand):
def __init__(self, container, key, signal1, signal2): def __init__(self, container: dict, keys: list[str], graphs: dict, graphid: str,
signal1: QtCore.pyqtSignal, signal2: QtCore.pyqtSignal):
super().__init__('Delete data') super().__init__('Delete data')
self.__container = container self.__container = container
self.__value = self.__container[key] self.__graph_container = graphs
self.__key = key self.__graph_key = graphid
self.__value = {}
for k in keys:
self.__value[k] = self.__container[k]
self.__keys = tuple(keys)
self.__signal_add = signal1 self.__signal_add = signal1
self.__signal_remove = signal2 self.__signal_remove = signal2
def redo(self): def redo(self):
self.__signal_remove.emit(self.__key) # stop graph from rescaling and updating legend
if isinstance(self.__value, FitContainer): self.__graph_container[self.__graph_key].block(True)
try:
self.__container[self.__value.fitted_key]._fits.remove(self.__key) self.__signal_remove.emit(list(self.__keys[::-1]))
except KeyError: for sid in self.__keys[::-1]:
pass val = self.__value[sid]
del self.__container[self.__key]
if isinstance(val, FitContainer):
try:
self.__container[sid].fitted_key._fits.remove(sid)
except KeyError:
pass
del self.__container[sid]
self.__graph_container[self.__graph_key].block(False)
def undo(self): def undo(self):
self.__container[self.__key] = self.__value # stop graph from rescaling and updating legend
if isinstance(self.__value, FitContainer): self.__graph_container[self.__graph_key].block(True)
try:
self.__container[self.__value.fitted_key]._fits.append(self.__key)
except KeyError:
pass
self.__signal_add.emit([self.__key], self.__value.graph) for sid in self.__keys:
val = self.__value[sid]
self.__container[sid] = val
if isinstance(val, FitContainer):
try:
self.__container[val.fitted_key]._fits.append(sid)
except KeyError:
pass
self.__signal_add.emit(list(self.__keys), self.__graph_key)
self.__graph_container[self.__graph_key].block(False)
class EvalCommand(QtWidgets.QUndoCommand): class EvalCommand(QtWidgets.QUndoCommand):

12
src/gui_qt/main/mainwindow.py
View File

@ -254,6 +254,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
@QtCore.pyqtSlot(name='on_actionOpen_FC_triggered') @QtCore.pyqtSlot(name='on_actionOpen_FC_triggered')
def read_fc(self): def read_fc(self):
reader = QFCReader(path=self.path, parent=self) reader = QFCReader(path=self.path, parent=self)
reader.add_graphs(self.management.graphs.list())
reader.data_read.connect(self.management.add_new_data) reader.data_read.connect(self.management.add_new_data)
reader.exec() reader.exec()
@ -347,7 +348,7 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
@QtCore.pyqtSlot(str) @QtCore.pyqtSlot(str)
def remove_graph(self, gid: str): def remove_graph(self, gid: str):
self.datawidget.remove_item(gid) self.datawidget.remove_item([gid])
val_figure = self.valuewidget.connected_figure val_figure = self.valuewidget.connected_figure
self.valuewidget.remove_graph() self.valuewidget.remove_graph()
@ -732,10 +733,11 @@ class NMRMainWindow(QtWidgets.QMainWindow, Ui_BaseWindow):
self.datawidget.set_name(sid, self.management[sid].name) self.datawidget.set_name(sid, self.management[sid].name)
@QtCore.pyqtSlot(str) @QtCore.pyqtSlot(list)
def delete_data(self, sid): def delete_data(self, sid: list[str]):
if self.valuewidget.shown_set == sid: for key in sid:
self.tabWidget.setCurrentIndex(0) if self.valuewidget.shown_set == key:
self.tabWidget.setCurrentIndex(0)
self.datawidget.remove_item(sid) self.datawidget.remove_item(sid)

32
src/gui_qt/main/management.py
View File

@ -75,7 +75,7 @@ class UpperManagement(QtCore.QObject):
restoreGraph = QtCore.pyqtSignal(str) restoreGraph = QtCore.pyqtSignal(str)
deleteGraph = QtCore.pyqtSignal(str) deleteGraph = QtCore.pyqtSignal(str)
newData = QtCore.pyqtSignal(list, str) newData = QtCore.pyqtSignal(list, str)
deleteData = QtCore.pyqtSignal(str) deleteData = QtCore.pyqtSignal(list)
dataChanged = QtCore.pyqtSignal(str) dataChanged = QtCore.pyqtSignal(str)
fitFinished = QtCore.pyqtSignal(list) fitFinished = QtCore.pyqtSignal(list)
stopFit = QtCore.pyqtSignal() stopFit = QtCore.pyqtSignal()
@ -234,9 +234,17 @@ class UpperManagement(QtCore.QObject):
for k in plotkeys: for k in plotkeys:
self.data[k].graph = gid self.data[k].graph = gid
@QtCore.pyqtSlot(str) @QtCore.pyqtSlot(list)
def plot_from_graph(self, key: str): def plot_from_graph(self, key: list[str]):
self.graphs[self.data[key].graph].remove(key) sort_graph = {}
for sid in key:
v = self.data[sid].graph
if v not in sort_graph:
sort_graph[v] = []
sort_graph[v].append(sid)
for gid, sets in sort_graph.items():
self.graphs[gid].remove(sets)
@QtCore.pyqtSlot(list, str, str) @QtCore.pyqtSlot(list, str, str)
def move_sets(self, sets: list, dest: str, src: (str|list), pos: int = -1): def move_sets(self, sets: list, dest: str, src: (str|list), pos: int = -1):
@ -287,15 +295,26 @@ class UpperManagement(QtCore.QObject):
self.undostack.beginMacro('Delete') self.undostack.beginMacro('Delete')
rm_set_by_graph = {}
for k in rm_sets[::-1]: for k in rm_sets[::-1]:
if k in self.data: if k in self.data:
cmd = DeleteCommand(self.data, k, self.newData, self.deleteData) parent_graph = self.data[k].graph
self.undostack.push(cmd) if parent_graph not in rm_set_by_graph:
rm_set_by_graph[parent_graph] = []
rm_set_by_graph[parent_graph].append(k)
elif k in self.graphs: elif k in self.graphs:
rm_graphs.append(k) rm_graphs.append(k)
else: else:
logger.warning(f'delete_sets: {k} is not in data or graph found') logger.warning(f'delete_sets: {k} is not in data or graph found')
for gid, sid_list in rm_set_by_graph.items():
cmd = DeleteCommand(self.data, sid_list, self.graphs, gid, self.newData, self.deleteData)
self.undostack.push(cmd)
for k in rm_graphs: for k in rm_graphs:
cmd = DeleteGraphCommand(self.graphs, k, self.restoreGraph, self.deleteGraph) cmd = DeleteGraphCommand(self.graphs, k, self.restoreGraph, self.deleteGraph)
self.undostack.push(cmd) self.undostack.push(cmd)
@ -605,6 +624,7 @@ class UpperManagement(QtCore.QObject):
if not graph_id: if not graph_id:
graph_id = '' graph_id = ''
# TODO add flag that new window will not get focus, because it messes up the data_table in fitwindow
self.newData.emit(p_id_list, graph_id) self.newData.emit(p_id_list, graph_id)
def save_fit_parameter(self, fname: str | pathlib.Path, fit_sets: list[str] = None): def save_fit_parameter(self, fname: str | pathlib.Path, fit_sets: list[str] = None):

280
src/nmreval/io/fcbatchreader.py
View File

@ -2,6 +2,7 @@ from __future__ import annotations
import pathlib import pathlib
from matplotlib import pyplot as plt
# import matplotlib.pyplot as plt # import matplotlib.pyplot as plt
from scipy.optimize import curve_fit from scipy.optimize import curve_fit
import numpy as np import numpy as np
@ -25,8 +26,6 @@ class FCReader:
self.t_params = {} self.t_params = {}
self.f_params = {} self.f_params = {}
self._scipt_type = 'old'
def __call__(self, fname: (list | str | pathlib.Path)): def __call__(self, fname: (list | str | pathlib.Path)):
if isinstance(fname, (str, pathlib.Path)): if isinstance(fname, (str, pathlib.Path)):
self.fnames = [fname] self.fnames = [fname]
@ -77,9 +76,16 @@ class FCReader:
def _read_from_hdf(self, filename: (str | pathlib.Path)) -> dict: def _read_from_hdf(self, filename: (str | pathlib.Path)) -> dict:
_temp = {} _temp = {}
reader = HdfReader(filename) reader = HdfReader(filename)
mag_directory = 'mag' if self._scipt_type == 'old' else 'Magnetization'
for mag in reader.get_selected(mag_directory, dtype='points'): mag_directory = None
_temp[mag.value] = mag for m in ['Magnetization', 'mag']:
if m in reader:
mag_directory = m
break
if m is not None:
for mag in reader.get_selected(mag_directory, dtype='points'):
_temp[mag.value] = mag
return _temp return _temp
@ -97,21 +103,15 @@ class FCReader:
return _temp return _temp
@staticmethod def _read_signals(self, filename, region: tuple = None) -> dict:
def _read_signals(filename, region: tuple = None) -> dict:
reader = HdfReader(filename) reader = HdfReader(filename)
start = 0
stop = 30e-5
# This is one set with attributes to find default start:stop values # This is one set with attributes to find default start:stop values (with some
try: p = reader.parameters('/ABS_ACC_FID')
p = reader.parameters('/ABS_ACC_FID') start = p.get('stainte') or p.get('start') or 0
start = p['start'] stop = p.get('stointe') or p.get('stop') or 30e-5
stop = p['stop']
except:
pass
if region is None: if region == (None, None) or region is None:
region = (start, stop) region = (start, stop)
if region[0] is None: if region[0] is None:
@ -119,15 +119,45 @@ class FCReader:
if region[1] is None: if region[1] is None:
region = (region[0], stop) region = (region[0], stop)
sig = reader.get_selected('/data/B=*/ACC_ABS_FID*', dtype='signal')
_temp = {} _temp = {}
for s in sig: bevo_groups = reader['data'].children
pts = s.points([region]) no_bevo = False
b = s.group for grp in bevo_groups.values():
if b not in _temp: for k in grp.data():
_temp[b] = [] try:
# look for parameter, should be missing in older scripts
bevo = k.parameter['bevo']
except KeyError:
no_bevo = True
break
_temp[b].append([s.value, *[pp[1] for pp in pts]]) if str(k.parent) != 'ACC_ABS_FID_sig (group)':
continue
tevo = k.parameter['tevo']
s = reader.make_signal(k, flag='fid', value='tevo', group='bevo')
pts = s.points([region])
if bevo not in _temp:
_temp[bevo] = []
_temp[bevo].append((tevo, *[pp[1] for pp in pts]))
if no_bevo:
break
if no_bevo:
# hopefully only for old scripts
sig = reader.get_selected('/data/B=*/ACC_ABS_FID*', dtype='signal')
_temp = {}
for s in sig:
pts = s.points([region])
b = s.group
if b not in _temp:
_temp[b] = []
_temp[b].append([s.value, *[pp[1] for pp in pts]])
for b, m in sorted(_temp.items()): for b, m in sorted(_temp.items()):
m = np.array(m) m = np.array(m)
@ -148,9 +178,9 @@ class FCReader:
fit_path = fname_no_ext.joinpath('fit') fit_path = fname_no_ext.joinpath('fit')
fit_path.mkdir(parents=True, exist_ok=True) fit_path.mkdir(parents=True, exist_ok=True)
# if save_fig: if save_fig:
# image_path = fname_no_ext.joinpath('png') image_path = fname_no_ext.joinpath('png')
# image_path.mkdir(parents=True, exist_ok=True) image_path.mkdir(parents=True, exist_ok=True)
header = 'm0\tt1\tbeta\toff\n' header = 'm0\tt1\tbeta\toff\n'
@ -189,16 +219,16 @@ class FCReader:
np.savetxt(fit_path.joinpath(save_name), np.c_[xplot, yplot], np.savetxt(fit_path.joinpath(save_name), np.c_[xplot, yplot],
header=header+'\t'.join([f'{p}+/-{err}' for p, err in zip(p0, perr)])) header=header+'\t'.join([f'{p}+/-{err}' for p, err in zip(p0, perr)]))
# if save_fig: if save_fig:
# fig, ax = plt.subplots() fig, ax = plt.subplots()
# ax.set_xlabel('t / s') ax.set_xlabel('t / s')
# ax.set_ylabel('M') ax.set_ylabel('M')
# axheader = f'T1: {p0[2]:.4g}(+/-{perr[2]:.4g}) beta: {p0[3]:.4g}(+/-{perr[3]:.4g})' axheader = f'T1: {p0[2]:.4g}(+/-{perr[2]:.4g}) beta: {p0[3]:.4g}(+/-{perr[3]:.4g})'
# ax.set_title(f'f = {k:.4g} Hz\n{axheader}') ax.set_title(f'f = {k:.4g} Hz\n{axheader}')
# ax.semilogx(v.x, v.y, 'o') ax.semilogx(v.x, v.y, 'o')
# ax.semilogx(xplot, yplot, '-') ax.semilogx(xplot, yplot, '-')
# fig.savefig(image_path.joinpath(save_name).with_suffix('.png')) fig.savefig(image_path.joinpath(save_name).with_suffix('.png'))
# plt.close(fig) plt.close(fig)
freqs = np.asanyarray(freqs) freqs = np.asanyarray(freqs)
params = np.asanyarray(params) params = np.asanyarray(params)
@ -290,45 +320,45 @@ class FCReader:
path = pathlib.Path(path) path = pathlib.Path(path)
path.mkdir(parents=True, exist_ok=True) path.mkdir(parents=True, exist_ok=True)
# fig_mag, ax_mag = plt.subplots() fig_mag, ax_mag = plt.subplots()
# fig_t1, ax_t1 = plt.subplots() fig_t1, ax_t1 = plt.subplots()
# fig_beta, ax_beta = plt.subplots() fig_beta, ax_beta = plt.subplots()
#
# if kind == 'temp': if kind == 'temp':
# _params = self.t_params _params = self.t_params
# else: else:
# _params = self.f_params _params = self.f_params
#
# save_path = path.joinpath(kind) save_path = path.joinpath(kind)
# if not save_path.exists(): if not save_path.exists():
# save_path.mkdir(parents=True) save_path.mkdir(parents=True)
#
# for key, par in _params.items(): for key, par in _params.items():
# pl, = ax_mag.plot(par[:, 0], par[:, 1], 'o', label=key) pl, = ax_mag.plot(par[:, 0], par[:, 1], 'o', label=key)
# ax_mag.plot(par[:, 0], par[:, 3], 's', color=pl.get_color()) ax_mag.plot(par[:, 0], par[:, 3], 's', color=pl.get_color())
# ax_t1.plot(par[:, 0], par[:, 5], 'o', label=key) ax_t1.plot(par[:, 0], par[:, 5], 'o', label=key)
# ax_beta.plot(par[:, 0], par[:, 7], 'o', label=key) ax_beta.plot(par[:, 0], par[:, 7], 'o', label=key)
#
# for a in [ax_mag, ax_t1, ax_beta]: for a in [ax_mag, ax_t1, ax_beta]:
# if kind == 'freq': if kind == 'freq':
# a.legend(loc='upper left', bbox_to_anchor=(1, 1), ncol=2) a.legend(loc='upper left', bbox_to_anchor=(1, 1), ncol=2)
# a.set_xlabel('T / K') a.set_xlabel('T / K')
# else: else:
# a.set_xscale('log') a.set_xscale('log')
# a.legend(loc='upper left', bbox_to_anchor=(1, 1)) a.legend(loc='upper left', bbox_to_anchor=(1, 1))
# a.set_xlabel('f / Hz') a.set_xlabel('f / Hz')
#
# ax_t1.set_yscale('log') ax_t1.set_yscale('log')
# ax_t1.set_ylabel('T1 / s') ax_t1.set_ylabel('T1 / s')
# ax_beta.set_ylabel('beta') ax_beta.set_ylabel('beta')
# ax_mag.set_ylabel('M0 (squares), Offset (circles)') ax_mag.set_ylabel('M0 (squares), Offset (circles)')
#
# fig_beta.savefig(path.joinpath(f'beta_{kind}.png'), bbox_inches="tight") fig_beta.savefig(path.joinpath(f'beta_{kind}.png'), bbox_inches="tight")
# fig_mag.savefig(path.joinpath(f'mag_{kind}.png'), bbox_inches="tight") fig_mag.savefig(path.joinpath(f'mag_{kind}.png'), bbox_inches="tight")
# fig_t1.savefig(path.joinpath(f't1_{kind}.png'), bbox_inches="tight") fig_t1.savefig(path.joinpath(f't1_{kind}.png'), bbox_inches="tight")
# plt.close(fig_mag) plt.close(fig_mag)
# plt.close(fig_beta) plt.close(fig_beta)
# plt.close(fig_t1) plt.close(fig_t1)
def get_parameter(self, parameter='all', kind='freq', path=None, write=True, plot=True): def get_parameter(self, parameter='all', kind='freq', path=None, write=True, plot=True):
param_list = [] param_list = []
@ -389,101 +419,3 @@ class FCReader:
@staticmethod @staticmethod
def kww(x, m0, off, t1, beta): def kww(x, m0, off, t1, beta):
return m0 * np.exp(-(x/t1)**beta) + off return m0 * np.exp(-(x/t1)**beta) + off
class FCFileReader:
def __init__(self, fname: str):
self.filename = pathlib.Path(fname)
self._is_dir = self.filename.is_dir()
self._script_type = None
self.reader = None
if not self._is_dir:
self.reader = HdfReader(self.filename)
if 'mag' in self.reader:
self._script_type = 'old'
elif 'Magnetization' in self.reader:
self._script_type = '2022_09'
self._temperature = get_temperature(self.filename.stem)
def load_magnetization(self, region=None):
if self._is_dir:
_temp = self._read_from_dir()
else:
if region is None:
_temp = self._read_from_hdf()
else:
_temp = self._read_signals(region)
if not _temp:
raise OSError(-666, f'No magnetization found for {self.filename.name}.', self.filename.name)
def _read_from_hdf(self) -> dict:
_temp = {}
mag_directory = 'mag' if self._script_type == 'old' else 'Magnetization'
for mag in self.reader.get_selected(mag_directory, dtype='points'):
_temp[mag.value] = mag
return _temp
def _read_from_dir(self) -> dict:
fname_no_ext = self.filename.with_suffix('')
data_path = fname_no_ext / 'data'
_temp = {}
for mag in data_path.glob('*.dat'):
d = AsciiReader(mag).export()
for v in d:
_temp[v.value] = v
break
return _temp
def _read_signals(self, region: tuple = None) -> dict:
start = 0
stop = 30e-5
# This is one set with attributes to find default start:stop values
try:
p = self.reader.parameters('/ABS_ACC_FID')
start = p['start']
stop = p['stop']
except:
pass
if region is None:
region = (start, stop)
if region[0] is None:
region = (start, region[1])
if region[1] is None:
region = (region[0], stop)
sig = self.reader.get_selected('/data/B=*/ACC_ABS_FID*', dtype='signal')
_temp = {}
for s in sig:
pts = s.points([region])
b = s.group
if b not in _temp:
_temp[b] = []
_temp[b].append([s.value, *[pp[1] for pp in pts]])
for b, m in sorted(_temp.items()):
m = np.array(m)
_temp[b] = Points(x=m[:, 0], y=m[:, 1], value=b, name=f'B={b}').sort()
return _temp
if __name__ == '__main__':
from pprint import pprint
test = FCReader('/autohome/dominik/nmreval/testdata/fc_test/2022-09-15_1344_new_script.h5')
# test = FCReader('/autohome/dominik/nmreval/testdata/fc_test/314K_2015-09-03_1605.h5')
test.load_magnetization()
test.load_magnetization(region=(0, 10e-6))
# pprint(test.data)

11
src/nmreval/io/hdfreader.py
View File

@ -27,7 +27,7 @@ class HdfNode:
'num_signals', 'num_pts', 'num_grp', 'num_signals', 'num_pts', 'num_grp',
'title_parameter', 'parameter'] 'title_parameter', 'parameter']
def __init__(self, name, ref, parent): def __init__(self, name: str, ref, parent: HdfNode | None):
self.name = name self.name = name
self.type = 'group' self.type = 'group'
self.reference = ref self.reference = ref
@ -59,7 +59,6 @@ class HdfNode:
return key in self.children return key in self.children
def clear(self): def clear(self):
self.name = '' self.name = ''
self.type = 'group' self.type = 'group'
@ -281,16 +280,16 @@ class HdfReader(HdfNode):
for child in val.data(dtype=dtype): for child in val.data(dtype=dtype):
try: try:
if child.type == 'points': if child.type == 'points':
ret_val.append(self._make_point(child)) ret_val.append(self.make_point(child))
elif child.type == 'signal': elif child.type == 'signal':
ret_val.append(self._make_signal(child, flag=flag, value=value, group=group)) ret_val.append(self.make_signal(child, flag=flag, value=value, group=group))
except IOError: except IOError:
print('something went wrong for ' + child.name) print('something went wrong for ' + child.name)
continue continue
return ret_val return ret_val
def _make_point(self, node): def make_point(self, node):
data = self.file[node.reference] data = self.file[node.reference]
val = None val = None
@ -300,7 +299,7 @@ class HdfReader(HdfNode):
return Points(x=data['x'], y=data['y'], yerr=data['y_err'], name=node.name, value=val) return Points(x=data['x'], y=data['y'], yerr=data['y_err'], name=node.name, value=val)
def _make_signal(self, node, flag: str = 'fid', value: str = None, group: str = None): def make_signal(self, node, flag: str = 'fid', value: str = None, group: str = None):
if value is None: if value is None:
value = self._get_parameter_values(node, node.parameter) value = self._get_parameter_values(node, node.parameter)
else: else:

4
src/nmreval/models/basic.py
View File

@ -224,9 +224,9 @@ class ExpFunc:
@staticmethod @staticmethod
def func(x, c, x0, beta, pm: int = -1, mode: str = 'time'): def func(x, c, x0, beta, pm: int = -1, mode: str = 'time'):
if mode == 'time': if mode == 'time':
return c * np.exp(np.sign(pm) * (x0 * x) ** beta)
elif mode == 'rate':
return c * np.exp(np.sign(pm) * (x / x0) ** beta) return c * np.exp(np.sign(pm) * (x / x0) ** beta)
elif mode == 'rate':
return c * np.exp(np.sign(pm) * (x * x0) ** beta)
else: else:
raise ValueError('Unknown mode %s. Use either "rate" or "time".' % str(mode)) raise ValueError('Unknown mode %s. Use either "rate" or "time".' % str(mode))