def write_parameters(self):
if self.entry.nxfilemode == 'r':
display_message("NeXus file opened as readonly")
return
elif ('nxrefine' in self.entry
or 'orientation_matrix' in self.entry['instrument/detector']):
if not self.confirm_action('Overwrite existing refinement?'):
return
self.transfer_parameters()
polar_angles, azimuthal_angles = self.refine.calculate_angles(
self.refine.xp, self.refine.yp)
self.refine.write_angles(polar_angles, azimuthal_angles)
self.refine.write_parameters()
reduce = NXReduce(self.entry)
reduce.record_start('nxrefine')
reduce.record('nxrefine', fit_report='\n'.join(self.fit_report))
reduce.logger.info('Orientation refined in NeXpy')
reduce.record_end('nxrefine')
root = self.entry.nxroot
entries = [
entry for entry in root.entries
if entry != 'entry' and entry != self.entry.nxname
]
if entries and self.confirm_action(
f'Copy orientation to other entries? ({", ".join(entries)})',
answer='yes'):
om = self.entry['instrument/detector/orientation_matrix']
for entry in entries:
root[entry]['instrument/detector/orientation_matrix'] = om
self.define_data()
if len(self.paths) > 0:
self.update_scaling()
def write_parameters(self):
self.transfer_parameters()
polar_angles, azimuthal_angles = self.refine.calculate_angles(
self.refine.xp, self.refine.yp)
self.refine.write_angles(polar_angles, azimuthal_angles)
self.refine.write_parameters()
reduce = NXReduce(self.entry)
reduce.record('nxrefine', fit_report='\n'.join(self.fit_report))
root = self.entry.nxroot
entries = [entry for entry in root.entries if entry != 'entry']
if entries and self.confirm_action(
'Copy orientation to other entries? (%s)' %
(', '.join(entries))):
om = self.entry['instrument/detector/orientation_matrix']
for entry in entries:
root[entry]['instrument/detector/orientation_matrix'] = om
class FindDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
default = NXSettings().settings['nxreduce']
self.parameters = GridParameters()
self.parameters.add('threshold', default['threshold'], 'Threshold')
self.parameters.add('first', default['first'], 'First Frame')
self.parameters.add('last', default['last'], 'Last Frame')
self.parameters.add('min_pixels', default['min_pixels'],
'Minimum Pixels in Peak')
self.parameters.grid()
self.find_button = NXPushButton('Find Peaks', self.find_peaks)
self.find_layout = self.make_layout(self.action_buttons(
('Find Peaks', self.find_peaks), ('List Peaks', self.list_peaks)),
align='center')
self.set_layout(self.entry_layout,
self.close_layout(save=True, progress=True))
self.set_title('Find Peaks')
self.reduce = None
self.refine = None
self.peaks_box = None
def choose_entry(self):
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid_layout)
self.insert_layout(2, self.find_layout)
self.reduce = NXReduce(self.entry)
self.refine = NXRefine(self.entry)
self.refine.polar_max = self.refine.two_theta_max()
if self.reduce.first is not None:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
else:
try:
self.parameters['last'].value = self.reduce.shape[0]
except Exception:
pass
self.parameters['threshold'].value = self.reduce.threshold
@property
def threshold(self):
try:
return int(self.parameters['threshold'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def first(self):
try:
return int(self.parameters['first'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def last(self):
try:
return int(self.parameters['last'].value)
except Exception as error:
report_error("Finding Peaks", error)
@property
def min_pixels(self):
try:
return int(self.parameters['min_pixels'].value)
except Exception as error:
report_error("Finding Peaks", error)
def find_peaks(self):
if is_file_locked(self.reduce.data_file):
return
self.start_thread()
self.reduce = NXReduce(self.entry,
threshold=self.threshold,
first=self.first,
last=self.last,
min_pixels=self.min_pixels,
find=True,
overwrite=True,
gui=True)
self.reduce.moveToThread(self.thread)
self.reduce.start.connect(self.start_progress)
self.reduce.update.connect(self.update_progress)
self.reduce.result.connect(self.get_peaks)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxfind)
self.thread.start()
def get_peaks(self, peaks):
self.peaks = peaks
self.status_message.setText(f'{len(self.peaks)} peaks found')
self.status_message.setVisible(True)
self.refine.xp = np.array([peak.x for peak in peaks])
self.refine.yp = np.array([peak.y for peak in peaks])
self.refine.zp = np.array([peak.z for peak in peaks])
self.refine.intensity = np.array([peak.intensity for peak in peaks])
self.refine.polar_angle, self.refine.azimuthal_angle = (
self.refine.calculate_angles(self.refine.xp, self.refine.yp))
self.update_table()
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def list_peaks(self):
if self.peaks_box in self.mainwindow.dialogs:
self.update_table()
return
self.peaks_box = NXDialog(self)
self.peaks_box.setMinimumWidth(600)
self.peaks_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.table_view = QtWidgets.QTableView()
self.table_model = NXTableModel(self, peak_list, header)
self.table_view.setModel(self.table_model)
self.table_view.resizeColumnsToContents()
self.table_view.horizontalHeader().stretchLastSection()
self.table_view.setSelectionBehavior(
QtWidgets.QAbstractItemView.SelectRows)
self.table_view.doubleClicked.connect(self.plot_peak)
self.table_view.setSortingEnabled(True)
self.table_view.sortByColumn(0, QtCore.Qt.AscendingOrder)
self.peaks_box.set_layout(self.table_view,
self.close_buttons(close=True))
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def update_table(self):
if self.peaks_box not in self.mainwindow.dialogs:
return
elif self.table_model is None:
self.close_peaks_box()
self.list_peaks()
self.table_model.peak_list = self.refine.get_peaks()
rows, columns = len(self.table_model.peak_list), 11
self.table_model.dataChanged.emit(
self.table_model.createIndex(0, 0),
self.table_model.createIndex(rows - 1, columns - 1))
self.table_view.resizeColumnsToContents()
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.setVisible(True)
def plot_peak(self):
row = self.table_view.currentIndex().row()
data = self.entry.data
i, x, y, z = [
self.table_view.model().peak_list[row][i] for i in range(4)
]
signal = data.nxsignal
xmin, xmax = max(0, x - 200), min(x + 200, signal.shape[2])
ymin, ymax = max(0, y - 200), min(y + 200, signal.shape[1])
zmin, zmax = max(0, z - 20), min(z + 20, signal.shape[0])
zslab = np.s_[zmin:zmax, ymin:ymax, xmin:xmax]
if 'Peak Plot' in self.plotviews:
self.plotview = self.plotviews['Peak Plot']
else:
self.plotview = NXPlotView('Peak Plot')
self.plotview.plot(data[zslab], log=True)
self.plotview.ax.set_title(f'{data.nxtitle}: Peak {i}')
self.plotview.ztab.maxbox.setValue(z)
self.plotview.aspect = 'equal'
self.plotview.crosshairs(x, y, color='r', linewidth=0.5)
def close_peaks_box(self):
try:
self.peaks_box.close()
except Exception:
pass
self.peaks_box = None
def accept(self):
try:
self.reduce.write_peaks(self.peaks)
self.reduce.record('nxfind',
threshold=self.threshold,
first_frame=self.first,
last_frame=self.last,
min_pixels=self.min_pixels,
peak_number=len(self.peaks))
self.reduce.record_end('nxfind')
super().accept()
except Exception as error:
report_error("Finding Peaks", error)
def reject(self):
self.stop()
super().reject()
class PrepareDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
default = NXSettings().settings['nxreduce']
self.parameters = GridParameters()
self.parameters.add('first', default['first'], 'First Frame')
self.parameters.add('last', default['last'], 'Last Frame')
self.parameters.add('threshold1', '2', 'Threshold 1')
self.parameters.add('horizontal1', '11', 'Horizontal Size 1')
self.parameters.add('threshold2', '0.8', 'Threshold 2')
self.parameters.add('horizontal2', '51', 'Horizontal Size 2')
self.parameters.grid()
self.prepare_button = NXPushButton('Prepare Mask', self.prepare_mask)
self.plot_button = NXPushButton('Plot Mask', self.plot_mask)
self.prepare_layout = self.make_layout(self.prepare_button,
self.plot_button,
align='center')
self.plot_button.setVisible(False)
self.set_layout(self.entry_layout,
self.close_layout(save=True, progress=True))
self.set_title('Prepare 3D Mask')
self.reduce = None
self.mask = None
self.plotview = None
def choose_entry(self):
if self.layout.count() == 2:
self.insert_layout(1, self.parameters.grid_layout)
self.insert_layout(2, self.prepare_layout)
self.reduce = NXReduce(self.entry)
self.parameters['first'].value = self.reduce.first
self.parameters['last'].value = self.reduce.last
@property
def first(self):
try:
return int(self.parameters['first'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def last(self):
try:
return int(self.parameters['last'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def threshold1(self):
try:
return float(self.parameters['threshold1'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def horizontal1(self):
try:
return int(self.parameters['horizontal1'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def threshold2(self):
try:
return float(self.parameters['threshold2'].value)
except Exception as error:
report_error("Preparing Mask", error)
@property
def horizontal2(self):
try:
return int(self.parameters['horizontal2'].value)
except Exception as error:
report_error("Preparing Mask", error)
def prepare_mask(self):
if is_file_locked(self.reduce.data_file):
return
self.start_thread()
self.reduce = NXReduce(self.entry,
prepare=True,
first=self.first,
last=self.last,
overwrite=True,
gui=True)
self.reduce.mask_parameters['threshold_1'] = self.threshold1
self.reduce.mask_parameters['threshold_1'] = self.threshold1
self.reduce.mask_parameters['horizontal_size_1'] = self.horizontal1
self.reduce.mask_parameters['threshold_2'] = self.threshold2
self.reduce.mask_parameters['horizontal_size_2'] = self.horizontal2
self.reduce.moveToThread(self.thread)
self.reduce.start.connect(self.start_progress)
self.reduce.update.connect(self.update_progress)
self.reduce.result.connect(self.get_mask)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxprepare)
self.thread.start()
def get_mask(self, mask):
self.mask = mask
self.status_message.setText("Mask complete")
self.status_message.setVisible(True)
self.plot_button.setVisible(True)
def plot_mask(self):
self.plotview = NXPlotView('3D Mask')
self.plotview.plot(
NXdata(self.mask,
self.reduce.data.nxaxes,
title=f"3D Mask: {self.reduce.name}"))
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def accept(self):
try:
if self.mask is None:
raise NeXusError("No mask has been created")
elif self.entry.nxfilemode == 'r':
raise NeXusError("NeXus file opened as readonly")
self.reduce.write_mask(self.mask)
self.reduce.record('nxprepare',
masked_file=self.reduce.mask_file,
threshold1=self.threshold1,
horizontal1=self.horizontal1,
threshold2=self.threshold2,
horizontal2=self.horizontal2,
process='nxprepare_mask')
self.reduce.record_end('nxprepare')
super().accept()
except Exception as error:
report_error("Preparing Mask", error)
def reject(self):
self.stop()
super().reject()
class MaximumDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('first', '', 'First Frame')
self.parameters.add('last', '', 'Last Frame')
self.output = NXLabel('Maximum Value:')
self.set_layout(
self.entry_layout, self.output, self.parameters.grid(),
self.action_buttons(('Find Maximum', self.find_maximum)),
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Find Maximum Value')
self.reduce = None
def choose_entry(self):
self.reduce = NXReduce(self.entry)
self.maximum = self.reduce.maximum
if self.reduce.first:
self.parameters['first'].value = self.reduce.first
if self.reduce.last:
self.parameters['last'].value = self.reduce.last
@property
def first(self):
try:
_first = np.int32(self.parameters['first'].value)
if _first >= 0:
return _first
else:
return None
except Exception as error:
return None
@property
def last(self):
try:
_last = np.int32(self.parameters['last'].value)
if _last > 0:
return _last
else:
return None
except Exception as error:
return None
@property
def maximum(self):
return np.float(self.output.text().split()[-1])
@maximum.setter
def maximum(self, value):
self.output.setText(f'Maximum Value: {value}')
def find_maximum(self):
if is_file_locked(self.reduce.data_file):
return
self.start_thread()
self.reduce = NXReduce(self.entry,
first=self.first,
last=self.last,
maxcount=True,
overwrite=True,
gui=True)
self.reduce.moveToThread(self.thread)
self.reduce.start.connect(self.start_progress)
self.reduce.update.connect(self.update_progress)
self.reduce.result.connect(self.get_maximum)
self.reduce.stop.connect(self.stop)
self.thread.started.connect(self.reduce.nxmax)
self.thread.finished.connect(self.stop)
self.thread.start(QtCore.QThread.LowestPriority)
def get_maximum(self, maximum):
self.maximum = maximum
def stop(self):
self.stop_progress()
if self.thread and self.thread.isRunning():
self.reduce.stopped = True
self.stop_thread()
def accept(self):
try:
self.reduce.write_maximum(self.maximum)
self.reduce.record('nxmax',
maximum=self.maximum,
first_frame=self.first,
last_frame=self.last)
self.reduce.record_end('nxmax')
self.stop()
super().accept()
except Exception as error:
report_error("Finding Maximum", error)
def reject(self):
self.stop()
super().reject()