def __init__(self, parent=None):
super(ImportDialog, self).__init__(parent)
try:
import spec2nexus
except ImportError:
raise NeXusError("Please install the 'spec2nexus' module")
self.accepted = False
self.import_file = None # must set in self.get_data()
self.spec = None
# progress bar is updated via calls to pdate_progress()
self.progress_bar = QtWidgets.QProgressBar()
self.progress_bar.setVisible(False)
status_layout = QtWidgets.QHBoxLayout()
status_layout.addWidget(self.progress_bar)
status_layout.addStretch()
status_layout.addWidget(self.close_buttons())
self.layout = QtWidgets.QVBoxLayout()
self.layout.addLayout(self.filebox())
self.layout.addLayout(self.scanbox())
self.layout.addLayout(status_layout)
self.setLayout(self.layout)
self.setWindowTitle("Import " + str(filetype))
def make_filter_box(self):
filter_box = QtWidgets.QWidget()
layout = QtWidgets.QGridLayout()
layout.setSpacing(10)
prefix_label = QtWidgets.QLabel('File Prefix')
self.prefix_box = QtWidgets.QLineEdit()
self.prefix_box.editingFinished.connect(self.set_range)
extension_label = QtWidgets.QLabel('File Extension')
self.extension_box = QtWidgets.QLineEdit()
self.extension_box.editingFinished.connect(self.set_extension)
suffix_label = QtWidgets.QLabel('File Suffix')
self.suffix_box = QtWidgets.QLineEdit('')
self.suffix_box.editingFinished.connect(self.get_prefixes)
layout.addWidget(prefix_label, 0, 0)
layout.addWidget(self.prefix_box, 0, 1)
layout.addWidget(extension_label, 0, 2)
layout.addWidget(self.extension_box, 0, 3)
layout.addWidget(suffix_label, 0, 4)
layout.addWidget(self.suffix_box, 0, 5)
self.prefix_combo = QtWidgets.QComboBox()
self.prefix_combo.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
self.prefix_combo.activated.connect(self.choose_prefix)
self.extension_combo = QtWidgets.QComboBox()
self.extension_combo.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
self.extension_combo.activated.connect(self.choose_extension)
layout.addWidget(self.prefix_combo, 1, 1, alignment=QtCore.Qt.AlignHCenter)
layout.addWidget(self.extension_combo, 1, 3, alignment=QtCore.Qt.AlignHCenter)
filter_box.setLayout(layout)
filter_box.setVisible(False)
return filter_box
def __init__(self, parent=None):
super(FindDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.parameters = GridParameters()
self.parameters.add('threshold', '', 'Threshold')
self.parameters.add('first', '', 'First Frame')
self.parameters.add('last', '', 'Last Frame')
find_layout = QtWidgets.QHBoxLayout()
self.find_button = QtWidgets.QPushButton('Find Peaks')
self.find_button.clicked.connect(self.find_peaks)
self.peak_count = QtWidgets.QLabel()
self.peak_count.setVisible(False)
find_layout.addStretch()
find_layout.addWidget(self.find_button)
find_layout.addWidget(self.peak_count)
find_layout.addStretch()
self.set_layout(self.entry_layout,
self.parameters.grid(),
find_layout,
self.progress_layout(save=True))
self.progress_bar.setVisible(False)
self.progress_bar.setValue(0)
self.set_title('Find Peaks')
self.reduce = None
def __init__(self, parent=None):
super(ImportDialog, self).__init__(parent)
self.layout = QtWidgets.QVBoxLayout()
self.layout.addLayout(self.directorybox())
self.filter_box = self.make_filterbox()
self.layout.addWidget(self.filter_box)
self.rangebox = self.make_rangebox()
self.layout.addWidget(self.rangebox)
status_layout = QtWidgets.QHBoxLayout()
self.progress_bar = QtWidgets.QProgressBar()
status_layout.addWidget(self.progress_bar)
self.progress_bar.setVisible(False)
status_layout.addStretch()
status_layout.addWidget(self.buttonbox())
self.layout.addLayout(status_layout)
self.setLayout(self.layout)
self.setWindowTitle("Import " + str(filetype))
def __init__(self, parent=None):
super().__init__(parent=parent)
try:
from globusonline.catalog.client.examples.catalog_wrapper import \
CatalogWrapper
except ImportError:
raise NeXusError("Cannot import globusonline package")
token_file = os.path.join(os.path.expanduser('~'), '.nexpy',
'globusonline', 'gotoken.txt')
self.wrap = CatalogWrapper(token='file', token_file=token_file)
_, self.catalogs = self.wrap.catalogClient.get_catalogs()
catalog_layout = QtWidgets.QHBoxLayout()
self.catalog_box = QtWidgets.QComboBox()
for catalog in self.catalogs:
try:
self.catalog_box.addItem(catalog['config']['name'])
except Exception:
pass
self.catalog_box.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
catalog_button = QtWidgets.QPushButton("Choose Catalog")
catalog_button.clicked.connect(self.get_catalog)
catalog_layout.addWidget(self.catalog_box)
catalog_layout.addWidget(catalog_button)
self.layout = QtWidgets.QVBoxLayout()
self.layout.addLayout(catalog_layout)
self.layout.addWidget(self.close_buttons())
self.setLayout(self.layout)
self.setWindowTitle("Import " + str(filetype))
def __init__(self, parent=None):
super(ImportDialog, self).__init__(parent)
self.file_type = None
layout = QtWidgets.QVBoxLayout()
layout.addLayout(self.filebox())
title_layout = QtWidgets.QHBoxLayout()
title_label = NXLabel('Title')
self.title_box = NXLineEdit()
title_layout.addWidget(title_label)
title_layout.addWidget(self.title_box)
layout.addLayout(title_layout)
energy_layout = QtWidgets.QHBoxLayout()
energy_label = NXLabel('Incident Energy')
self.energy_box = NXLineEdit()
self.energy_box.setFixedWidth(150)
energy_layout.addWidget(energy_label)
energy_layout.addWidget(self.energy_box)
energy_layout.addStretch()
layout.addLayout(energy_layout)
step_layout = QtWidgets.QHBoxLayout()
Q_label = NXLabel('dQ')
self.Q_box = NXLineEdit()
self.Q_box.setFixedWidth(75)
E_label = NXLabel('dE')
self.E_box = NXLineEdit()
self.E_box.setFixedWidth(75)
self.convert_box = QtWidgets.QCheckBox('Convert to S(Q,E)')
self.convert_box.setChecked(False)
step_layout.addWidget(self.convert_box)
step_layout.addStretch()
step_layout.addWidget(Q_label)
step_layout.addWidget(self.Q_box)
step_layout.addWidget(E_label)
step_layout.addWidget(self.E_box)
step_layout.addStretch()
layout.addLayout(step_layout)
layout.addWidget(self.close_buttons())
self.setLayout(layout)
self.setWindowTitle("Import "+str(filetype))
def new_checkbox(self, slot=None):
checkbox = QtWidgets.QCheckBox()
checkbox.setCheckState(QtCore.Qt.Unchecked)
checkbox.setEnabled(True)
if slot:
checkbox.stateChanged.connect(slot)
return checkbox
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 add_grid_headers(self):
self.header_grid = QtWidgets.QGridLayout()
self.header_widget = NXWidget()
self.header_widget.set_layout(self.header_grid)
row = 0
columns = [
'Scan', 'data', 'link', 'copy', 'max', 'find', 'refine', 'prepare',
'transform', 'masked_transform', 'combine', 'masked_combine',
'pdf', 'masked_pdf', 'overwrite', 'sync'
]
header = {}
for col, column in enumerate(columns):
header[column] = NXLabel(column,
bold=True,
width=75,
align='center')
if column == 'transform' or column == 'combine' or column == 'pdf':
self.header_grid.addWidget(header[column], row, col, 1, 2,
QtCore.Qt.AlignHCenter)
elif 'masked' not in column:
self.header_grid.addWidget(header[column], row, col)
header[column].setAlignment(QtCore.Qt.AlignHCenter)
row = 1
columns = 3 * ['regular', 'masked']
for col, column in enumerate(columns):
header[column] = NXLabel(column, width=75, align='center')
self.header_grid.addWidget(header[column], row, col + 8)
self.header_grid.setSpacing(0)
self.header_widget.setFixedHeight(60)
self.insert_layout(2, self.header_widget)
def make_output_box(self):
"""
Creates a text box and button for selecting the output file.
"""
output_box = QtWidgets.QWidget()
layout = QtWidgets.QHBoxLayout()
file_button = QtWidgets.QPushButton("Choose Output File")
file_button.clicked.connect(self.choose_output_file)
self.output_file = QtWidgets.QLineEdit(self)
self.output_file.setMinimumWidth(300)
layout.addWidget(file_button)
layout.addWidget(self.output_file)
output_box.setLayout(layout)
output_box.setVisible(False)
return output_box
def scanbox(self):
'''create widgets for specifying scan range to import'''
scanminlabel = QtWidgets.QLabel("Min. Scan")
self.scanmin = QtWidgets.QLineEdit()
self.scanmin.setFixedWidth(100)
self.scanmin.setAlignment(QtCore.Qt.AlignRight)
scanmaxlabel = QtWidgets.QLabel("Max. Scan")
self.scanmax = QtWidgets.QLineEdit()
self.scanmax.setFixedWidth(100)
self.scanmax.setAlignment(QtCore.Qt.AlignRight)
scanbox = QtWidgets.QHBoxLayout()
scanbox.addWidget(scanminlabel)
scanbox.addWidget(self.scanmin)
scanbox.addWidget(scanmaxlabel)
scanbox.addWidget(self.scanmax)
return scanbox
def get_dataset(self):
self.dataset_id = self.get_dataset_id(self.dataset_box.currentText())
_, self.members = self.wrap.catalogClient.get_members(
self.catalog_id, self.dataset_id)
member_layout = QtWidgets.QHBoxLayout()
self.member_box = QtWidgets.QComboBox()
for member in self.members:
try:
self.member_box.addItem(member['data_uri'])
except Exception:
pass
self.member_box.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
member_button = QtWidgets.QPushButton("Choose Member")
member_button.clicked.connect(self.get_member)
member_layout.addWidget(self.member_box)
member_layout.addWidget(member_button)
self.layout.insertLayout(2, member_layout)
def get_catalog(self):
self.catalog_id = self.get_catalog_id(self.catalog_box.currentText())
_, self.datasets = self.wrap.catalogClient.get_datasets(
self.catalog_id)
dataset_layout = QtWidgets.QHBoxLayout()
self.dataset_box = QtWidgets.QComboBox()
for dataset in self.datasets:
try:
self.dataset_box.addItem(dataset['name'])
except Exception:
pass
self.dataset_box.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
dataset_button = QtWidgets.QPushButton("Choose Dataset")
dataset_button.clicked.connect(self.get_dataset)
dataset_layout.addWidget(self.dataset_box)
dataset_layout.addWidget(dataset_button)
self.layout.insertLayout(1, dataset_layout)
def make_rangebox(self):
rangebox = QtWidgets.QWidget()
layout = QtWidgets.QHBoxLayout()
rangeminlabel = NXLabel("Min. index")
self.rangemin = NXLineEdit()
self.rangemin.setFixedWidth(150)
self.rangemin.setAlignment(QtCore.Qt.AlignRight)
rangemaxlabel = NXLabel("Max. index")
self.rangemax = NXLineEdit()
self.rangemax.setFixedWidth(150)
self.rangemax.setAlignment(QtCore.Qt.AlignRight)
layout.addWidget(rangeminlabel)
layout.addWidget(self.rangemin)
layout.addStretch()
layout.addWidget(rangemaxlabel)
layout.addWidget(self.rangemax)
rangebox.setLayout(layout)
rangebox.setVisible(False)
return rangebox
def __init__(self, parent=None):
super(ImportDialog, self).__init__(parent)
skippedbox = QtWidgets.QHBoxLayout()
skippedlabel = QtWidgets.QLabel("No. of skipped rows")
self.skiprows = QtWidgets.QLineEdit()
self.skiprows.setText('0')
self.skiprows.setFixedWidth(20)
skippedbox.addWidget(skippedlabel)
skippedbox.addWidget(self.skiprows)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(self.filebox())
layout.addLayout(skippedbox)
layout.addWidget(self.buttonbox())
self.setLayout(layout)
self.setWindowTitle("Import "+str(filetype))
def __init__(self, parent=None):
super(StackDialog, self).__init__(parent)
status_layout = QtWidgets.QHBoxLayout()
self.progress_bar = QtWidgets.QProgressBar()
status_layout.addWidget(self.progress_bar)
self.progress_bar.setVisible(False)
status_layout.addStretch()
status_layout.addWidget(self.close_buttons(save=True))
self.set_layout(self.directorybox(),
self.make_filter_box(),
self.make_range_box(),
self.make_output_box(),
status_layout)
self.setLayout(self.layout)
self.set_title('Stack Images')
self.suffix = ''
def __init__(self, parent=None):
super(OrientationDialog, self).__init__(parent)
self.select_entry(self.choose_entry)
self.refine = NXRefine(self.entry)
self.refine.read_parameters()
self.parameters = GridParameters()
self.parameters.add('phi_start', self.refine.phi, 'Phi Start (deg)')
self.parameters.add('phi_step', self.refine.phi_step, 'Phi Step (deg)')
self.parameters.add('chi', self.refine.chi, 'Chi (deg)')
self.parameters.add('omega', self.refine.omega, 'Omega (deg)')
self.parameters.add('polar', self.refine.polar_max,
'Max. Polar Angle (deg)')
self.parameters.add('polar_tolerance', self.refine.polar_tolerance,
'Polar Angle Tolerance')
self.parameters.add('peak_tolerance', self.refine.peak_tolerance,
'Peak Angle Tolerance')
action_buttons = self.action_buttons(
('Generate Grains', self.generate_grains),
('List Peaks', self.list_peaks))
self.grain_layout = QtWidgets.QHBoxLayout()
self.grain_combo = QtWidgets.QComboBox()
self.grain_combo.setSizeAdjustPolicy(
QtWidgets.QComboBox.AdjustToContents)
self.grain_combo.currentIndexChanged.connect(self.set_grain)
self.grain_textbox = QtWidgets.QLabel()
self.grain_layout.addWidget(self.grain_combo)
self.grain_layout.addStretch()
self.grain_layout.addWidget(self.grain_textbox)
bottom_layout = QtWidgets.QHBoxLayout()
self.result_textbox = QtWidgets.QLabel()
bottom_layout.addWidget(self.result_textbox)
bottom_layout.addStretch()
bottom_layout.addWidget(self.close_buttons())
self.set_layout(self.entry_layout, self.parameters.grid(),
action_buttons, bottom_layout)
self.set_title('Defining Orientation')
def scanbox(self):
"""Create widgets for specifying scan range to import."""
scanminlabel = NXLabel("Min. Scan")
self.scanmin = NXLineEdit(width=100, align='right')
scanmaxlabel = NXLabel("Max. Scan")
self.scanmax = NXLineEdit(width=100, align='right')
scanbox = QtWidgets.QHBoxLayout()
scanbox.addWidget(scanminlabel)
scanbox.addWidget(self.scanmin)
scanbox.addWidget(scanmaxlabel)
scanbox.addWidget(self.scanmax)
return scanbox
def __init__(self, parent=None):
super(MaximumDialog, self).__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 = QtWidgets.QLabel('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 __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 update(self):
if not self.sample_directory:
raise NeXusError("No sample directory declared")
if self.grid:
self.delete_grid(self.grid)
# Map from wrapper files to scan directories
wrapper_files = {
w: self.get_scan(w)
for w in sorted([
os.path.join(self.sample_directory, filename)
for filename in os.listdir(self.sample_directory)
if self.is_valid(filename)
],
key=natural_sort)
}
self.grid = QtWidgets.QGridLayout()
self.insert_layout(2, self.grid)
self.grid.setSpacing(1)
row = 0
columns = [
'Scan', 'data', 'link', 'max', 'find', 'copy', 'refine',
'transform', 'masked_transform', 'combine', 'masked_combine',
'pdf', 'overwrite', 'reduce', 'sync'
]
header = {}
for col, column in enumerate(columns):
header[column] = QtWidgets.QLabel(column)
header[column].setFont(self.bold_font)
header[column].setFixedWidth(75)
if column == 'transform' or column == 'combine':
self.grid.addWidget(header[column], row, col, 1, 2,
QtCore.Qt.AlignHCenter)
elif 'masked' not in column:
self.grid.addWidget(header[column], row, col)
header[column].setAlignment(QtCore.Qt.AlignHCenter)
row = 1
columns = ['regular', 'masked', 'regular', 'masked']
for col, column in enumerate(columns):
header[column] = QtWidgets.QLabel(column)
header[column].setFixedWidth(75)
header[column].setAlignment(QtCore.Qt.AlignHCenter)
self.grid.addWidget(header[column], row, col + 7)
self.scans = {}
self.scans_backup = {}
# Create (unchecked) checkboxes
for wrapper_file, scan in wrapper_files.items():
scan_label = os.path.basename(scan)
row += 1
status = {}
status['scan'] = QtWidgets.QLabel(scan_label)
if self.parent_file == wrapper_file:
status['scan'].setStyleSheet('font-weight:bold')
status['data'] = self.new_checkbox()
status['link'] = self.new_checkbox()
status['max'] = self.new_checkbox()
status['find'] = self.new_checkbox()
status['copy'] = self.new_checkbox()
status['refine'] = self.new_checkbox()
status['transform'] = self.new_checkbox()
status['masked_transform'] = self.new_checkbox()
status['combine'] = self.new_checkbox()
status['masked_combine'] = self.new_checkbox()
status['pdf'] = self.new_checkbox()
status['overwrite'] = self.new_checkbox(self.select_scans)
status['reduce'] = self.new_checkbox(self.select_scans)
status['sync'] = self.new_checkbox()
self.grid.addWidget(status['scan'], row, 0, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['data'], row, 1, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['link'], row, 2, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['max'], row, 3, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['find'], row, 4, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['copy'], row, 5, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['refine'], row, 6,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['transform'], row, 7,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['masked_transform'], row, 8,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['combine'], row, 9,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['masked_combine'], row, 10,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['pdf'], row, 11, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['overwrite'], row, 12,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['reduce'], row, 13,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['sync'], row, 14, QtCore.Qt.AlignCenter)
self.scans[scan] = status
row += 1
self.grid.addWidget(QtWidgets.QLabel('All'), row, 0,
QtCore.Qt.AlignCenter)
all_boxes = {}
all_boxes['link'] = self.new_checkbox(
lambda: self.select_status('link'))
all_boxes['max'] = self.new_checkbox(lambda: self.select_status('max'))
all_boxes['find'] = self.new_checkbox(
lambda: self.select_status('find'))
all_boxes['copy'] = self.new_checkbox(
lambda: self.select_status('copy'))
all_boxes['refine'] = self.new_checkbox(
lambda: self.select_status('refine'))
all_boxes['transform'] = self.new_checkbox(
lambda: self.select_status('transform'))
all_boxes['masked_transform'] = self.new_checkbox(
lambda: self.select_status('masked_transform'))
all_boxes['combine'] = self.new_checkbox(
lambda: self.select_status('combine'))
all_boxes['masked_combine'] = self.new_checkbox(
lambda: self.select_status('masked_combine'))
all_boxes['pdf'] = self.new_checkbox(lambda: self.select_status('pdf'))
all_boxes['overwrite'] = self.new_checkbox(self.select_all)
all_boxes['reduce'] = self.new_checkbox(self.select_all)
all_boxes['sync'] = self.new_checkbox(self.select_all)
self.grid.addWidget(all_boxes['link'], row, 2, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['max'], row, 3, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['find'], row, 4, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['copy'], row, 5, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['refine'], row, 6, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['transform'], row, 7,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['masked_transform'], row, 8,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['combine'], row, 9,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['masked_combine'], row, 10,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['pdf'], row, 11, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['overwrite'], row, 12,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['reduce'], row, 13,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['sync'], row, 14, QtCore.Qt.AlignCenter)
self.all_scans = all_boxes
self.start_progress((0, len(wrapper_files)))
# Populate the checkboxes based on the entries in nxdb.File
for i, (wrapper, scan) in enumerate(wrapper_files.items()):
status = self.scans[scan]
status['data'].setEnabled(False)
f = nxdb.get_file(wrapper)
for task_name in nxdb.task_names:
# Database columns use nx* names while columns don't
if task_name.startswith('nx'):
col_name = task_name[2:]
else:
col_name = task_name
checkbox = status[col_name]
file_status = getattr(f, task_name)
if file_status == nxdb.DONE:
checkbox.setCheckState(QtCore.Qt.Checked)
checkbox.setEnabled(False)
elif file_status == nxdb.IN_PROGRESS:
checkbox.setCheckState(QtCore.Qt.PartiallyChecked)
checkbox.setEnabled(True)
elif file_status == nxdb.QUEUED:
checkbox.setCheckState(QtCore.Qt.PartiallyChecked)
checkbox.setEnabled(False)
elif file_status == nxdb.FAILED:
checkbox.setCheckState(QtCore.Qt.Unchecked)
checkbox.setEnabled(True)
# TODO: do i need to account for last?
if status['data'].checkState() == QtCore.Qt.Unchecked:
self.disable_status(status)
self.update_progress(i)
self.stop_progress()
self.backup_scans()
return self.grid
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 update(self):
if not self.sample_directory:
raise NeXusError("No sample directory declared")
if self.grid:
self.delete_grid(self.grid)
del self.grid_widget
if self.scroll_area:
self.scroll_area.close()
self.scroll_area.deleteLater()
# Map from wrapper files to scan directories
wrapper_files = {
w: self.get_scan(w)
for w in sorted([
os.path.join(self.sample_directory, filename)
for filename in os.listdir(self.sample_directory)
if self.is_valid(filename)
],
key=natural_sort)
}
self.grid = QtWidgets.QGridLayout()
self.grid_widget = NXWidget()
self.grid_widget.set_layout(self.grid, 'stretch')
self.scroll_area = NXScrollArea(self.grid_widget)
self.scroll_area.setMinimumSize(1250, 300)
self.insert_layout(3, self.scroll_area)
self.grid.setSpacing(1)
self.scans = {}
self.scans_backup = {}
row = 0
# Create (unchecked) checkboxes
for wrapper_file, scan in wrapper_files.items():
scan_label = os.path.basename(scan)
status = {}
status['scan'] = NXLabel(scan_label)
if self.parent_file == wrapper_file:
status['scan'].setStyleSheet('font-weight:bold')
status['entries'] = []
status['data'] = self.new_checkbox()
status['link'] = self.new_checkbox()
status['copy'] = self.new_checkbox()
status['max'] = self.new_checkbox()
status['find'] = self.new_checkbox()
status['refine'] = self.new_checkbox()
status['prepare'] = self.new_checkbox()
status['transform'] = self.new_checkbox()
status['masked_transform'] = self.new_checkbox()
status['combine'] = self.new_checkbox()
status['masked_combine'] = self.new_checkbox()
status['pdf'] = self.new_checkbox()
status['masked_pdf'] = self.new_checkbox()
status['overwrite'] = self.new_checkbox(self.select_scans)
status['sync'] = self.new_checkbox()
self.grid.addWidget(status['scan'], row, 0, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['data'], row, 1, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['link'], row, 2, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['copy'], row, 3, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['max'], row, 4, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['find'], row, 5, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['refine'], row, 6,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['prepare'], row, 7,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['transform'], row, 8,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['masked_transform'], row, 9,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['combine'], row, 10,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['masked_combine'], row, 11,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['pdf'], row, 12, QtCore.Qt.AlignCenter)
self.grid.addWidget(status['masked_pdf'], row, 13,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['overwrite'], row, 14,
QtCore.Qt.AlignCenter)
self.grid.addWidget(status['sync'], row, 15, QtCore.Qt.AlignCenter)
self.scans[scan] = status
row += 1
self.grid.addWidget(NXLabel('All'), row, 0, QtCore.Qt.AlignCenter)
all_boxes = {}
all_boxes['link'] = self.new_checkbox(
lambda: self.select_status('link'))
all_boxes['copy'] = self.new_checkbox(
lambda: self.select_status('copy'))
all_boxes['max'] = self.new_checkbox(lambda: self.select_status('max'))
all_boxes['find'] = self.new_checkbox(
lambda: self.select_status('find'))
all_boxes['refine'] = self.new_checkbox(
lambda: self.select_status('refine'))
all_boxes['prepare'] = self.new_checkbox(
lambda: self.select_status('prepare'))
all_boxes['transform'] = self.new_checkbox(
lambda: self.select_status('transform'))
all_boxes['masked_transform'] = self.new_checkbox(
lambda: self.select_status('masked_transform'))
all_boxes['combine'] = self.new_checkbox(
lambda: self.select_status('combine'))
all_boxes['masked_combine'] = self.new_checkbox(
lambda: self.select_status('masked_combine'))
all_boxes['pdf'] = self.new_checkbox(lambda: self.select_status('pdf'))
all_boxes['masked_pdf'] = self.new_checkbox(
lambda: self.select_status('masked_pdf'))
all_boxes['overwrite'] = self.new_checkbox(self.select_all)
all_boxes['sync'] = self.new_checkbox(self.select_all)
self.grid.addWidget(all_boxes['link'], row, 2, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['copy'], row, 3, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['max'], row, 4, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['find'], row, 5, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['refine'], row, 6, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['prepare'], row, 7,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['transform'], row, 8,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['masked_transform'], row, 9,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['combine'], row, 10,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['masked_combine'], row, 11,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['pdf'], row, 12, QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['masked_pdf'], row, 13,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['overwrite'], row, 14,
QtCore.Qt.AlignCenter)
self.grid.addWidget(all_boxes['sync'], row, 15, QtCore.Qt.AlignCenter)
self.all_scans = all_boxes
self.start_progress((0, len(wrapper_files)))
# Populate the checkboxes based on the entries in self.db.File
for i, (wrapper, scan) in enumerate(wrapper_files.items()):
status = self.scans[scan]
status['data'].setEnabled(False)
f = self.db.get_file(wrapper)
status['entries'] = f.get_entries()
for task_name in self.db.task_names:
# Database columns use nx* names while columns don't
if task_name.startswith('nx'):
col_name = task_name[2:]
else:
col_name = task_name
checkbox = status[col_name]
file_status = getattr(f, task_name)
if file_status == self.db.DONE:
checkbox.setCheckState(QtCore.Qt.Checked)
checkbox.setEnabled(False)
elif file_status == self.db.IN_PROGRESS:
checkbox.setCheckState(QtCore.Qt.PartiallyChecked)
checkbox.setEnabled(True)
checkbox.setStyleSheet("color: green")
elif file_status == self.db.QUEUED:
checkbox.setCheckState(QtCore.Qt.PartiallyChecked)
checkbox.setEnabled(True)
checkbox.setStyleSheet("color: blue")
elif file_status == self.db.FAILED:
checkbox.setCheckState(QtCore.Qt.PartiallyChecked)
checkbox.setEnabled(True)
checkbox.setStyleSheet("color: red")
if status['data'].checkState() == QtCore.Qt.Unchecked:
for task in [
'link', 'max', 'find', 'prepare', 'transform',
'masked_transform'
]:
status[task].setEnabled(False)
self.update_progress(i)
self.stop_progress()
self.backup_scans()
return self.grid
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.refine.assign_rings()
self.rings = self.refine.make_rings()
self.ring_list = self.refine.get_ring_list()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = NXLineEdit(self.refine.primary,
width=80,
align='right')
self.secondary_box = NXLineEdit(self.refine.secondary,
width=80,
align='right')
orient_button = NXPushButton('Orient', self.choose_peaks)
orient_layout = self.make_layout(NXLabel('Primary'),
self.primary_box,
NXLabel('Secondary'),
self.secondary_box,
'stretch',
orient_button,
align='right')
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.status_text = NXLabel(f'Score: {self.refine.score():.4f}')
self.tolerance_box = NXLineEdit(self.refine.hkl_tolerance,
width=80,
slot=self.update_table,
align='right')
self.tolerance_box.setMaxLength(5)
export_button = NXPushButton('Export', self.export_peaks)
save_button = NXPushButton('Save', self.save_orientation)
close_button = NXPushButton('Close', self.close_peaks_box)
close_layout = self.make_layout(self.status_text, 'stretch',
NXLabel('Threshold'),
self.tolerance_box, 'stretch',
export_button, save_button,
close_button)
self.peaks_box.set_layout(orient_layout, self.table_view, close_layout)
self.peaks_box.set_title(f'{self.refine.name} Peak Table')
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
def list_orientations(self):
message_box = BaseDialog(self)
message_box.setMinimumWidth(600)
message_box.setMinimumHeight(600)
header = [
'i', 'x', 'y', 'z', 'Polar', 'Azi', 'Intensity', 'H', 'K', 'L',
'Diff'
]
peak_list = self.refine.get_peaks()
self.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
refine_button = QtWidgets.QPushButton('Refine')
refine_button.clicked.connect(self.refine_orientation)
restore_button = QtWidgets.QPushButton('Restore')
restore_button.clicked.connect(self.restore_orientation)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
orient_layout.addWidget(refine_button)
orient_layout.addWidget(restore_button)
grid = QtWidgets.QGridLayout()
grid.setSpacing(10)
self.lattice = GridParameters()
self.lattice.add('a', self.refine.a, 'a', False)
self.lattice.add('b', self.refine.b, 'b', False)
self.lattice.add('c', self.refine.c, 'c', False)
self.lattice.add('alpha', self.refine.alpha, 'alpha', False)
self.lattice.add('beta', self.refine.beta, 'beta', False)
self.lattice.add('gamma', self.refine.gamma, 'gamma', False)
p = self.lattice['a']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['b']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['c']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 0, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 0, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 0, 8, QtCore.Qt.AlignHCenter)
p = self.lattice['alpha']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 0, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 1, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 2, QtCore.Qt.AlignHCenter)
p = self.lattice['beta']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 3, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 4, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 5, QtCore.Qt.AlignHCenter)
p = self.lattice['gamma']
p.box.setFixedWidth(80)
label, value, checkbox = p.label, p.value, p.vary
grid.addWidget(p.label, 1, 6, QtCore.Qt.AlignRight)
grid.addWidget(p.box, 1, 7, QtCore.Qt.AlignHCenter)
grid.addWidget(p.checkbox, 1, 8, QtCore.Qt.AlignHCenter)
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)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addLayout(grid)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' %
self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(
self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(message_box.close)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
message_box.setLayout(layout)
message_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
message_box.adjustSize()
message_box.show()
self.plotview = None
def list_peaks(self):
if self.peaks_box is not None and self.table_model is not None:
self.update_table()
return
self.peaks_box = BaseDialog(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.refine.assign_rings()
self.rings = self.refine.get_ring_hkls()
orient_layout = QtWidgets.QHBoxLayout()
if self.refine.primary is None:
self.refine.primary = 0
if self.refine.secondary is None:
self.refine.secondary = 1
self.primary_box = QtWidgets.QLineEdit(str(self.refine.primary))
self.primary_box.setAlignment(QtCore.Qt.AlignRight)
self.primary_box.setFixedWidth(80)
self.secondary_box = QtWidgets.QLineEdit(str(self.refine.secondary))
self.secondary_box.setAlignment(QtCore.Qt.AlignRight)
self.secondary_box.setFixedWidth(80)
orient_button = QtWidgets.QPushButton('Orient')
orient_button.clicked.connect(self.orient)
orient_layout.addStretch()
orient_layout.addWidget(QtWidgets.QLabel('Primary'))
orient_layout.addWidget(self.primary_box)
orient_layout.addWidget(QtWidgets.QLabel('Secondary'))
orient_layout.addWidget(self.secondary_box)
orient_layout.addStretch()
orient_layout.addWidget(orient_button)
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)
layout = QtWidgets.QVBoxLayout()
layout.addLayout(orient_layout)
layout.addWidget(self.table_view)
close_layout = QtWidgets.QHBoxLayout()
self.status_text = QtWidgets.QLabel('Score: %.4f' %
self.refine.score())
self.tolerance_box = QtWidgets.QLineEdit(str(
self.refine.hkl_tolerance))
self.tolerance_box.setAlignment(QtCore.Qt.AlignRight)
self.tolerance_box.setMaxLength(5)
self.tolerance_box.editingFinished.connect(self.update_table)
self.tolerance_box.setFixedWidth(80)
save_button = QtWidgets.QPushButton('Save Orientation')
save_button.clicked.connect(self.save_orientation)
close_button = QtWidgets.QPushButton('Close Window')
close_button.clicked.connect(self.close_peaks_box)
close_layout.addWidget(self.status_text)
close_layout.addStretch()
close_layout.addWidget(QtWidgets.QLabel('Threshold'))
close_layout.addWidget(self.tolerance_box)
close_layout.addStretch()
close_layout.addWidget(save_button)
close_layout.addStretch()
close_layout.addWidget(close_button)
layout.addLayout(close_layout)
self.peaks_box.setLayout(layout)
self.peaks_box.setWindowTitle('%s Peak Table' % self.entry.nxtitle)
self.peaks_box.adjustSize()
self.peaks_box.show()
self.plotview = None
