def main():
parser = argparse.ArgumentParser(
description="Restore orientation from CCTW parameter file")
parser.add_argument('-d', '--directory', required=True,
help='scan directory')
parser.add_argument('-e', '--entries', default=['f1', 'f2', 'f3'],
nargs='+', help='names of entries to be processed')
args = parser.parse_args()
for entry in args.entries:
reduce = NXReduce(entry, args.directory)
if os.path.exists(reduce.settings_file):
refine = NXRefine(reduce.entry)
refine.read_settings(reduce.settings_file)
refine.write_parameters()
if os.path.exists(reduce.transform_file):
refine.prepare_transform(reduce.transform_file)
if os.path.exists(reduce.masked_transform_file):
refine.prepare_transform(reduce.masked_transform_file,
mask=True)
reduce = NXMultiReduce(args.directory)
if os.path.exists(reduce.transform_file):
reduce.prepare_combine()
if os.path.exists(reduce.masked_transform_file):
reduce.mask = True
reduce.prepare_combine()
class TransformDialog(BaseDialog):
def __init__(self, parent=None):
super(TransformDialog, self).__init__(parent)
self.select_entry(self.initialize_grid)
self.refine = NXRefine()
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
header_font = QtGui.QFont()
header_font.setBold(True)
start_label = QtWidgets.QLabel('Start')
start_label.setFont(header_font)
grid.addWidget(start_label, 0, 1)
step_label = QtWidgets.QLabel('Step')
step_label.setFont(header_font)
grid.addWidget(step_label, 0, 2)
stop_label = QtWidgets.QLabel('Stop')
stop_label.setFont(header_font)
grid.addWidget(stop_label, 0, 3)
grid.addWidget(QtWidgets.QLabel('H:'), 1, 0)
grid.addWidget(QtWidgets.QLabel('K:'), 2, 0)
grid.addWidget(QtWidgets.QLabel('L:'), 3, 0)
self.start_h_box = QtWidgets.QLineEdit()
self.step_h_box = QtWidgets.QLineEdit()
self.stop_h_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_h_box, 1, 1)
grid.addWidget(self.step_h_box, 1, 2)
grid.addWidget(self.stop_h_box, 1, 3)
self.start_k_box = QtWidgets.QLineEdit()
self.step_k_box = QtWidgets.QLineEdit()
self.stop_k_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_k_box, 2, 1)
grid.addWidget(self.step_k_box, 2, 2)
grid.addWidget(self.stop_k_box, 2, 3)
self.start_l_box = QtWidgets.QLineEdit()
self.step_l_box = QtWidgets.QLineEdit()
self.stop_l_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_l_box, 3, 1)
grid.addWidget(self.step_l_box, 3, 2)
grid.addWidget(self.stop_l_box, 3, 3)
self.set_layout(self.entry_layout, grid,
self.checkboxes(('copy', 'Copy to all entries', True),
('mask', 'Create masked transform group', True),
('overwrite', 'Overwrite existing transforms', False)),
self.close_buttons(save=True))
self.setWindowTitle('Transforming Data')
try:
self.initialize_grid()
except Exception:
pass
def get_output_file(self, mask=False, entry=None):
if entry is None:
entry = self.entry
if mask:
return os.path.splitext(entry.data.nxsignal.nxfilename)[0]+'_masked_transform.nxs'
else:
return os.path.splitext(entry.data.nxsignal.nxfilename)[0]+'_transform.nxs'
def get_settings_file(self, entry=None):
if entry is None:
entry = self.entry
return os.path.splitext(entry.data.nxsignal.nxfilename)[0]+'_transform.pars'
def get_h_grid(self):
return (np.float32(self.start_h_box.text()),
np.float32(self.step_h_box.text()),
np.float32(self.stop_h_box.text()))
def get_k_grid(self):
return (np.float32(self.start_k_box.text()),
np.float32(self.step_k_box.text()),
np.float32(self.stop_k_box.text()))
def get_l_grid(self):
return (np.float32(self.start_l_box.text()),
np.float32(self.step_l_box.text()),
np.float32(self.stop_l_box.text()))
def initialize_grid(self):
self.refine = NXRefine(self.entry)
self.refine.initialize_grid()
self.start_h_box.setText('%g' % self.refine.h_start)
self.step_h_box.setText('%g' % self.refine.h_step)
self.stop_h_box.setText('%g' % self.refine.h_stop)
self.start_k_box.setText('%g' % self.refine.k_start)
self.step_k_box.setText('%g' % self.refine.k_step)
self.stop_k_box.setText('%g' % self.refine.k_stop)
self.start_l_box.setText('%g' % self.refine.l_start)
self.step_l_box.setText('%g' % self.refine.l_step)
self.stop_l_box.setText('%g' % self.refine.l_stop)
def write_parameters(self, output_file, settings_file):
self.refine.output_file = output_file
self.refine.settings_file = settings_file
self.refine.h_start, self.refine.h_step, self.refine.h_stop = self.get_h_grid()
self.refine.k_start, self.refine.k_step, self.refine.k_stop = self.get_k_grid()
self.refine.l_start, self.refine.l_step, self.refine.l_stop = self.get_l_grid()
self.refine.define_grid()
@property
def copy(self):
return self.checkbox['copy'].isChecked()
@property
def mask(self):
return self.checkbox['mask'].isChecked()
@property
def overwrite(self):
return self.checkbox['overwrite'].isChecked()
def accept(self):
try:
if 'transform' in self.entry and not self.overwrite:
self.display_message('Preparing Transform',
'Transform group already exists in %s' % self.entry.nxname)
return
if self.mask and 'masked_transform' in self.entry and not self.overwrite:
self.display_message('Preparing Transform',
'Masked transform group already exists in %s' % self.entry.nxname)
return
output_file = self.get_output_file()
settings_file = self.get_settings_file()
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(mask=True)
self.refine.prepare_transform(masked_output_file, mask=True)
self.refine.write_settings(settings_file)
if self.copy:
root = self.entry.nxroot
for entry in [e for e in root
if e != 'entry' and e != self.entry.nxname]:
if 'transform' in root[entry] and not self.overwrite:
self.display_message('Preparing Transform',
'Transform group already exists in %s' % entry)
return
if self.mask and 'masked_transform' in root[entry] and not self.overwrite:
self.display_message('Preparing Transform',
'Masked transform group already exists in %s' % entry)
return
self.refine = NXRefine(root[entry])
output_file = self.get_output_file(entry=root[entry])
settings_file = self.get_settings_file(entry=root[entry])
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(mask=True,
entry=root[entry])
self.refine.prepare_transform(masked_output_file, mask=True)
self.refine.write_settings(settings_file)
super(TransformDialog, self).accept()
except NeXusError as error:
report_error("Preparing Data Transform", error)
class TransformDialog(NXDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.select_entry(self.choose_entry)
self.Qgrid = QtWidgets.QGridLayout()
self.Qgrid.setSpacing(10)
headers = ['Axis', 'Q', 'dQ', 'N', 'Max']
width = [25, 50, 50, 25, 50]
column = 0
for header in headers:
label = NXLabel(header, bold=True, align='center')
self.Qgrid.addWidget(label, 0, column)
self.Qgrid.setColumnMinimumWidth(column, width[column])
column += 1
self.Qbox = {}
self.dQbox = {}
self.Nbox = {}
self.maxbox = {}
for i, label in enumerate(['H', 'K', 'L']):
self.Qgrid.addWidget(NXLabel(label, align='center'), i + 1, 0)
self.Qbox[label] = NXLineEdit(slot=self.calculate,
width=100,
align='right')
self.Qgrid.addWidget(self.Qbox[label], i + 1, 1)
self.dQbox[label] = NXLineEdit(slot=self.calculate,
width=100,
align='right')
self.Qgrid.addWidget(self.dQbox[label], i + 1, 2)
self.Nbox[label] = NXLabel(align='center')
self.Qgrid.addWidget(self.Nbox[label], i + 1, 3)
self.maxbox[label] = NXLabel(align='center')
self.Qgrid.addWidget(self.maxbox[label], i + 1, 4)
self.set_layout(self.entry_layout, self.close_buttons(save=True))
self.setWindowTitle('Transforming Data')
try:
self.initialize_grid()
except Exception:
pass
def choose_entry(self):
try:
refine = NXRefine(self.entry)
if refine.xp is None:
raise NeXusError("No peaks in entry")
except NeXusError as error:
report_error("Refining Lattice", error)
return
self.refine = refine
if self.layout.count() == 2:
self.insert_layout(1, self.Qgrid)
self.insert_layout(
2,
self.checkboxes(('copy', 'Copy to all entries', True),
('mask', 'Create masked transforms', True),
('overwrite', 'Overwrite transforms', False)))
self.refine.initialize_grid()
self.update_grid()
def update_grid(self):
self.Qbox['H'].setText(f"{self.refine.h_stop:g}")
self.Qbox['K'].setText(f"{self.refine.k_stop:g}")
self.Qbox['L'].setText(f"{self.refine.l_stop:g}")
self.dQbox['H'].setText(f"{self.refine.h_step:g}")
self.dQbox['K'].setText(f"{self.refine.k_step:g}")
self.dQbox['L'].setText(f"{self.refine.l_step:g}")
self.Nbox['H'].setText(f"{self.refine.h_shape:g}")
self.Nbox['K'].setText(f"{self.refine.k_shape:g}")
self.Nbox['L'].setText(f"{self.refine.l_shape:g}")
self.maxbox['H'].setText(f"{self.refine.Qmax / self.refine.astar:g}")
self.maxbox['K'].setText(f"{self.refine.Qmax / self.refine.bstar:g}")
self.maxbox['L'].setText(f"{self.refine.Qmax / self.refine.cstar:g}")
def calculate(self):
for label, rlu in [('H', self.refine.astar), ('K', self.refine.bstar),
('L', self.refine.cstar)]:
self.Nbox[label].setText(
int(
np.round(
2 * float(self.Qbox[label].text()) /
float(self.dQbox[label].text()), 2)) + 1)
self.maxbox[label].setText(f"{self.refine.Qmax / rlu:g}")
def get_output_file(self, mask=False, entry=None):
if entry is None:
entry = self.entry
if mask:
return os.path.splitext(
entry.data.nxsignal.nxfilename)[0] + '_masked_transform.nxs'
else:
return os.path.splitext(
entry.data.nxsignal.nxfilename)[0] + '_transform.nxs'
def get_settings_file(self, entry=None):
if entry is None:
entry = self.entry
return os.path.splitext(
entry.data.nxsignal.nxfilename)[0] + '_transform.pars'
def get_parameters(self, Q):
stop, step = float(self.Qbox[Q].text()), float(self.dQbox[Q].text())
return -stop, step, stop
def write_parameters(self, output_file, settings_file):
self.refine.output_file = output_file
self.refine.settings_file = settings_file
self.refine.h_start, self.refine.h_step, self.refine.h_stop = (
self.get_parameters('H'))
self.refine.k_start, self.refine.k_step, self.refine.k_stop = (
self.get_parameters('K'))
self.refine.l_start, self.refine.l_step, self.refine.l_stop = (
self.get_parameters('L'))
self.refine.define_grid()
@property
def copy(self):
return self.checkbox['copy'].isChecked()
@property
def mask(self):
return self.checkbox['mask'].isChecked()
@property
def overwrite(self):
return self.checkbox['overwrite'].isChecked()
def accept(self):
try:
if 'transform' in self.entry and not self.overwrite:
self.display_message(
"Preparing Transform",
f"Transform group already exists in {self.entry.nxname}")
return
if (self.mask and 'masked_transform' in self.entry
and not self.overwrite):
self.display_message(
"Preparing Transform",
"Masked transform group already exists in "
f"{self.entry.nxname}")
return
output_file = self.get_output_file()
settings_file = self.get_settings_file()
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(mask=True)
self.refine.prepare_transform(masked_output_file, mask=True)
self.refine.write_settings(settings_file)
if self.copy:
root = self.entry.nxroot
for entry in [
e for e in root
if e != 'entry' and e != self.entry.nxname
]:
if 'transform' in root[entry] and not self.overwrite:
self.display_message(
"Preparing Transform",
f"Transform group already exists in {entry}")
return
if (self.mask and 'masked_transform' in root[entry]
and not self.overwrite):
self.display_message(
"Preparing Transform",
f"Masked transform group already exists in {entry}"
)
return
self.refine = NXRefine(root[entry])
output_file = self.get_output_file(entry=root[entry])
settings_file = self.get_settings_file(entry=root[entry])
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(
mask=True, entry=root[entry])
self.refine.prepare_transform(masked_output_file,
mask=True)
self.refine.write_settings(settings_file)
super().accept()
except NeXusError as error:
report_error("Preparing Data Transform", error)
class TransformDialog(BaseDialog):
def __init__(self, parent=None):
super(TransformDialog, self).__init__(parent)
self.select_entry(self.initialize_grid)
self.refine = NXRefine()
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
header_font = QtGui.QFont()
header_font.setBold(True)
start_label = QtWidgets.QLabel('Start')
start_label.setFont(header_font)
grid.addWidget(start_label, 0, 1)
step_label = QtWidgets.QLabel('Step')
step_label.setFont(header_font)
grid.addWidget(step_label, 0, 2)
stop_label = QtWidgets.QLabel('Stop')
stop_label.setFont(header_font)
grid.addWidget(stop_label, 0, 3)
grid.addWidget(QtWidgets.QLabel('H:'), 1, 0)
grid.addWidget(QtWidgets.QLabel('K:'), 2, 0)
grid.addWidget(QtWidgets.QLabel('L:'), 3, 0)
self.start_h_box = QtWidgets.QLineEdit()
self.step_h_box = QtWidgets.QLineEdit()
self.stop_h_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_h_box, 1, 1)
grid.addWidget(self.step_h_box, 1, 2)
grid.addWidget(self.stop_h_box, 1, 3)
self.start_k_box = QtWidgets.QLineEdit()
self.step_k_box = QtWidgets.QLineEdit()
self.stop_k_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_k_box, 2, 1)
grid.addWidget(self.step_k_box, 2, 2)
grid.addWidget(self.stop_k_box, 2, 3)
self.start_l_box = QtWidgets.QLineEdit()
self.step_l_box = QtWidgets.QLineEdit()
self.stop_l_box = QtWidgets.QLineEdit()
grid.addWidget(self.start_l_box, 3, 1)
grid.addWidget(self.step_l_box, 3, 2)
grid.addWidget(self.stop_l_box, 3, 3)
self.set_layout(
self.entry_layout, grid,
self.checkboxes(
('copy', 'Copy to all entries', True),
('mask', 'Create masked transform group', True),
('overwrite', 'Overwrite existing transforms', False)),
self.close_buttons(save=True))
self.setWindowTitle('Transforming Data')
try:
self.initialize_grid()
except Exception:
pass
def get_output_file(self, mask=False):
if mask:
return os.path.splitext(self.entry.data.nxsignal.nxfilename
)[0] + '_masked_transform.nxs'
else:
return os.path.splitext(
self.entry.data.nxsignal.nxfilename)[0] + '_transform.nxs'
def get_settings_file(self):
return os.path.splitext(
self.entry.data.nxsignal.nxfilename)[0] + '_transform.pars'
def get_h_grid(self):
return (np.float32(self.start_h_box.text()),
np.float32(self.step_h_box.text()),
np.float32(self.stop_h_box.text()))
def get_k_grid(self):
return (np.float32(self.start_k_box.text()),
np.float32(self.step_k_box.text()),
np.float32(self.stop_k_box.text()))
def get_l_grid(self):
return (np.float32(self.start_l_box.text()),
np.float32(self.step_l_box.text()),
np.float32(self.stop_l_box.text()))
def initialize_grid(self):
self.refine = NXRefine(self.entry)
self.refine.initialize_grid()
self.start_h_box.setText('%g' % self.refine.h_start)
self.step_h_box.setText('%g' % self.refine.h_step)
self.stop_h_box.setText('%g' % self.refine.h_stop)
self.start_k_box.setText('%g' % self.refine.k_start)
self.step_k_box.setText('%g' % self.refine.k_step)
self.stop_k_box.setText('%g' % self.refine.k_stop)
self.start_l_box.setText('%g' % self.refine.l_start)
self.step_l_box.setText('%g' % self.refine.l_step)
self.stop_l_box.setText('%g' % self.refine.l_stop)
def write_parameters(self, output_file, settings_file):
self.refine.output_file = output_file
self.refine.settings_file = settings_file
self.refine.h_start, self.refine.h_step, self.refine.h_stop = self.get_h_grid(
)
self.refine.k_start, self.refine.k_step, self.refine.k_stop = self.get_k_grid(
)
self.refine.l_start, self.refine.l_step, self.refine.l_stop = self.get_l_grid(
)
self.refine.define_grid()
@property
def copy(self):
return self.checkbox['copy'].isChecked()
@property
def mask(self):
return self.checkbox['mask'].isChecked()
@property
def overwrite(self):
return self.checkbox['overwrite'].isChecked()
def accept(self):
try:
if 'transform' in self.entry and not self.overwrite:
self.display_message(
'Preparing Transform',
'Transform group already exists in %s' % self.entry.nxname)
return
if self.mask and 'masked_transform' in self.entry and not self.overwrite:
self.display_message(
'Preparing Transform',
'Masked transform group already exists in %s' %
self.entry.nxname)
return
output_file = self.get_output_file()
settings_file = self.get_settings_file()
self.write_parameters(output_file, settings_file)
self.refine.prepare_transform(output_file)
if self.mask:
masked_output_file = self.get_output_file(mask=True)
self.refine.prepare_transform(masked_output_file, mask=True)
self.refine.write_settings(settings_file)
if self.copy:
root = self.entry.nxroot
for entry in [
e for e in root
if e != 'entry' and e != self.entry.nxname
]:
if 'transform' in root[entry] and not self.overwrite:
self.display_message(
'Preparing Transform',
'Transform group already exists in %s' % entry)
return
if self.mask and 'masked_transform' in root[
entry] and not self.overwrite:
self.display_message(
'Preparing Transform',
'Masked transform group already exists in %s' %
entry)
return
self.refine = NXRefine(root[entry])
output = output_file.replace(self.entry.nxname, entry)
settings = settings_file.replace(self.entry.nxname, entry)
self.write_parameters(output, settings)
self.refine.prepare_transform(output)
if self.mask:
output = masked_output_file.replace(
self.entry.nxname, entry)
self.refine.prepare_transform(output, mask=True)
self.refine.write_settings(settings)
super(TransformDialog, self).accept()
except NeXusError as error:
report_error("Preparing Data Transform", error)