def on_action_save_config_yaml_triggered(self):
selected_file, selected_filter = QFileDialog.getSaveFileName(
self.ui, 'Save Configuration', HexrdConfig().working_dir,
'YAML files (*.yml)')
if selected_file:
HexrdConfig().working_dir = str(Path(selected_file).parent)
return HexrdConfig().save_instrument_config(selected_file)
def live_update(self, enabled):
previous = HexrdConfig().live_update
HexrdConfig().set_live_update(enabled)
if enabled:
HexrdConfig().rerender_needed.connect(self.update_all)
# Only disconnect if we were previously enabled. i.e. the signal was connected
elif previous:
HexrdConfig().rerender_needed.disconnect(self.update_all)
def on_action_save_imageseries_triggered(self):
if not HexrdConfig().has_images():
msg = ('No ImageSeries available for saving.')
QMessageBox.warning(self.ui, 'HEXRD', msg)
return
if ImageLoadManager().unaggregated_images:
ims_dict = ImageLoadManager().unaggregated_images
else:
ims_dict = HexrdConfig().imageseries_dict
if len(ims_dict) > 1:
# Have the user choose an imageseries to save
names = list(ims_dict.keys())
name, ok = QInputDialog.getItem(self.ui, 'HEXRD',
'Select ImageSeries', names, 0,
False)
if not ok:
# User canceled...
return
else:
name = list(ims_dict.keys())[0]
selected_file, selected_filter = QFileDialog.getSaveFileName(
self.ui, 'Save ImageSeries',
HexrdConfig().working_dir,
'HDF5 files (*.h5 *.hdf5);; NPZ files (*.npz)')
if selected_file:
HexrdConfig().working_dir = os.path.dirname(selected_file)
if selected_filter.startswith('HDF5'):
selected_format = 'hdf5'
elif selected_filter.startswith('NPZ'):
selected_format = 'frame-cache'
kwargs = {}
if selected_format == 'hdf5':
# A path must be specified. Set it ourselves for now.
kwargs['path'] = 'imageseries'
elif selected_format == 'frame-cache':
# Get the user to pick a threshold
result, ok = QInputDialog.getDouble(self.ui, 'HEXRD',
'Choose Threshold', 10, 0,
1e12, 3)
if not ok:
# User canceled...
return
kwargs['threshold'] = result
# This needs to be specified, but I think it just needs
# to be the same as the file name...
kwargs['cache_file'] = selected_file
HexrdConfig().save_imageseries(ims_dict.get(name), name,
selected_file, selected_format,
**kwargs)
def update_labels(self):
# Make sure tilt labels reflect current euler convention
if HexrdConfig().euler_angle_convention is None:
a, b, c = 'xyz'
else:
a, b, c = HexrdConfig().euler_angle_convention['axes_order']
self.ui.label_tilt_2.setText(str.upper(a + ':'))
self.ui.label_tilt_0.setText(str.upper(b + ':'))
self.ui.label_tilt_1.setText(str.upper(c + ':'))
def on_action_export_polar_plot_triggered(self):
selected_file, selected_filter = QFileDialog.getSaveFileName(
self.ui, 'Save Polar Image',
HexrdConfig().working_dir,
'HDF5 files (*.h5 *.hdf5);; NPZ files (*.npz)')
if selected_file:
HexrdConfig().working_dir = os.path.dirname(selected_file)
return self.ui.image_tab_widget.export_polar_plot(selected_file)
def create_masks_list(self):
self.masks = {}
for v, i in enumerate(HexrdConfig().polar_masks_line_data):
if not any(np.array_equal(m, v) for m in self.masks.values()):
self.masks['mask_' + str(i)] = copy.copy(v)
if HexrdConfig().threshold_mask_status:
self.threshold_name = 'threshold'
self.masks['threshold'] = HexrdConfig().threshold_mask
self.visible = copy.copy(self.masks)
def setup_connections(self):
HexrdConfig().overlay_config_changed.connect(self.update_overlays)
HexrdConfig().show_saturation_level_changed.connect(
self.show_saturation)
HexrdConfig().detector_transform_modified.connect(
self.on_detector_transform_modified)
HexrdConfig().rerender_detector_borders.connect(
self.draw_detector_borders)
HexrdConfig().beam_vector_changed.connect(self.beam_vector_changed)
def setup_connections(self):
self.ui.table.selectionModel().selectionChanged.connect(
self.update_selections)
HexrdConfig().active_material_modified.connect(
self.active_material_modified)
HexrdConfig().material_renamed.connect(self.update_material_name)
HexrdConfig().update_reflections_tables.connect(
self.update_table_if_name_matches)
def path_exists(self, f):
try:
imageseries.open(f,
'hdf5',
path=HexrdConfig().hdf5_path[0],
dataname=HexrdConfig().hdf5_path[1])
return True
except:
return False
def orientation(self):
# This automatically converts from Euler angle conventions
values = [x.value() for x in self.orientation_widgets]
if HexrdConfig().euler_angle_convention is not None:
values = np.radians(values)
convention = HexrdConfig().euler_angle_convention
self.convert_angle_convention(values, convention, None)
return values
def run_apply_polar_mask(self, line_data):
for line in line_data:
name = create_unique_name(
HexrdConfig().polar_masks_line_data, 'polar_mask_0')
HexrdConfig().polar_masks_line_data[name] = line.copy()
HexrdConfig().visible_masks.append(name)
create_polar_mask([line.copy()], name)
HexrdConfig().polar_masks_changed.emit()
self.new_mask_added.emit(self.image_mode)
def orientation(self, v):
# This automatically converts to Euler angle conventions
if HexrdConfig().euler_angle_convention is not None:
v = copy.deepcopy(v)
convention = HexrdConfig().euler_angle_convention
self.convert_angle_convention(v, None, convention)
for i, w in enumerate(self.orientation_widgets):
blocker = QSignalBlocker(w) # noqa: F841
w.setValue(v[i])
def load_instrument_config(self):
temp = tempfile.NamedTemporaryFile(delete=False, suffix='.yml')
self.config_file = temp.name
HexrdConfig().save_instrument_config(self.config_file)
fname = f'default_{self.instrument.lower()}_config.yml'
with resource_loader.resource_path(
hexrd.ui.resources.calibration, fname) as f:
for overlay in HexrdConfig().overlays:
overlay['visible'] = False
HexrdConfig().load_instrument_config(f, import_raw=True)
def beam_vector_changed(self):
if not self.iviewer or not hasattr(self.iviewer, 'instr'):
return
# Re-draw all overlays from scratch
HexrdConfig().clear_overlay_data()
bvec = HexrdConfig().instrument_config['beam']['vector']
self.iviewer.instr.beam_vector = (bvec['azimuth'], bvec['polar_angle'])
self.update_overlays()
def on_action_open_config_triggered(self):
selected_file, selected_filter = QFileDialog.getOpenFileName(
self.ui, 'Load Configuration',
HexrdConfig().working_dir, 'YAML files (*.yml)')
if selected_file:
HexrdConfig().load_instrument_config(selected_file)
self.cal_tree_view.rebuild_tree()
self.calibration_config_widget.update_gui_from_config()
self.update_all(clear_canvases=True)
def tth_tol(self, v):
v = np.radians(v)
if self.material.planeData.tThWidth == v:
# Just return...
return
self.material.planeData.tThWidth = v
HexrdConfig().material_tth_width_modified.emit(self.material.name)
HexrdConfig().flag_overlay_updates_for_material(self.material.name)
HexrdConfig().overlay_config_changed.emit()
def on_action_open_materials_triggered(self):
selected_file, selected_filter = QFileDialog.getOpenFileName(
self.ui, 'Load Materials File', HexrdConfig().working_dir,
'HDF5 files (*.h5 *.hdf5)')
if selected_file:
HexrdConfig().working_dir = os.path.dirname(selected_file)
HexrdConfig().load_materials(selected_file)
self.materials_panel.update_gui_from_config()
self.materials_panel.update_structure_tab()
def modify_material_name(self, new_name):
names = HexrdConfig().materials.keys()
if new_name in names:
# Just ignore it
return
old_name = HexrdConfig().active_material_name()
HexrdConfig().rename_material(old_name, new_name)
self.update_gui_from_config()
def import_material(self):
selected_file, selected_filter = QFileDialog.getOpenFileName(
self.ui, 'Import Material',
HexrdConfig().working_dir, 'CIF files (*.cif)')
if selected_file:
HexrdConfig().working_dir = os.path.dirname(selected_file)
HexrdConfig().import_material(selected_file)
self.update_gui_from_config()
self.update_structure_tab()
def setup_processing_options(self):
self.state = HexrdConfig().load_panel_state
self.num_dets = len(HexrdConfig().detector_names)
self.state.setdefault('agg', UI_AGG_INDEX_NONE)
self.state.setdefault(
'trans', [UI_TRANS_INDEX_NONE for x in range(self.num_dets)])
self.state.setdefault(
'dark', [UI_DARK_INDEX_NONE for x in range(self.num_dets)])
self.state.setdefault(
'dark_files', [None for x in range(self.num_dets)])
def select_quaternion_grid_file(self):
title = 'Select quaternion grid file'
filters = 'NPY files (*.npy)'
selected_file, selected_filter = QFileDialog.getOpenFileName(
self.ui, title,
HexrdConfig().working_dir, filters)
if selected_file:
HexrdConfig().working_dir = str(Path(selected_file).parent)
self.quaternion_grid_file = selected_file
def snip_width_pixels():
from hexrd.ui.hexrd_config import HexrdConfig
pixel_size_tth = HexrdConfig().polar_pixel_size_tth
snip_width_deg = HexrdConfig().polar_snip1d_width
# Convert the snip width into pixels using pixel_size_tth
# Always round up
return math.ceil(snip_width_deg / pixel_size_tth)
def load_aps_imageseries(self, detectors, directory_names):
HexrdConfig().imageseries_dict.clear()
for name, d in zip(detectors, directory_names):
try:
ims = self.open_directory(d)
HexrdConfig().imageseries_dict[name] = ims
except (Exception, IOError) as error:
msg = ('ERROR - Could not read file: \n' + str(error))
QMessageBox.warning(None, 'HEXRD', msg)
return
def write_instrument_to_hexrd_config(self, instr):
iconfig = HexrdConfig().instrument_config_none_euler_convention
# Add this so the calibration crystal gets written
cal_crystal = iconfig.get('calibration_crystal')
output_dict = instr.write_config(calibration_dict=cal_crystal)
# Convert back to whatever convention we were using before
eac = HexrdConfig().euler_angle_convention
if eac is not None:
convert_tilt_convention(output_dict, None, eac)
# Add the saturation levels, as they seem to be missing
sl = 'saturation_level'
for det in output_dict['detectors'].keys():
output_dict['detectors'][det][sl] = iconfig['detectors'][det][sl]
# Save the previous iconfig to restore the statuses
prev_iconfig = HexrdConfig().config['instrument']
# Update the config
HexrdConfig().config['instrument'] = output_dict
# This adds in any missing keys. In particular, it is going to
# add in any "None" detector distortions
HexrdConfig().set_detector_defaults_if_missing()
# Add status values
HexrdConfig().add_status(output_dict)
# Set the previous statuses to be the current statuses
HexrdConfig().set_statuses_from_prev_iconfig(prev_iconfig)
def load_images(self, image_names):
HexrdConfig().emit_update_status_bar('Loading image view...')
if (self.mode != ViewType.raw
or len(image_names) != len(self.axes_images)):
# Either we weren't in image mode before, we have a different
# number of images, or there are masks to apply. Clear and re-draw.
self.clear()
self.mode = ViewType.raw
cols = 1
if len(image_names) > 1:
cols = 2
rows = math.ceil(len(image_names) / cols)
idx = HexrdConfig().current_imageseries_idx
for i, name in enumerate(image_names):
img = HexrdConfig().image(name, idx)
# Apply any masks
for mask_name, (det, mask) in HexrdConfig().raw_masks.items():
if (mask_name in HexrdConfig().visible_masks
and det == name):
img[~mask] = 0
axis = self.figure.add_subplot(rows, cols, i + 1)
axis.set_title(name)
self.axes_images.append(
axis.imshow(img, cmap=self.cmap, norm=self.norm))
axis.autoscale(False)
self.raw_axes.append(axis)
self.figure.tight_layout()
else:
idx = HexrdConfig().current_imageseries_idx
for i, name in enumerate(image_names):
img = HexrdConfig().image(name, idx)
# Apply any masks
for mask_name, (det, mask) in HexrdConfig().raw_masks.items():
if (mask_name in HexrdConfig().visible_masks
and det == name):
img[~mask] = 0
self.axes_images[i].set_data(img)
# This will call self.draw()
self.show_saturation()
# This will be used for drawing the rings
self.iviewer = raw_iviewer()
# Set the detectors to draw
self.iviewer.detectors = [x.get_title() for x in self.raw_axes]
self.update_overlays()
msg = 'Image view loaded!'
HexrdConfig().emit_update_status_bar(msg)
def remove_current_material(self):
# Don't allow the user to remove all of the materials
if len(HexrdConfig().materials.keys()) == 1:
msg = 'Cannot remove all materials. Add another first.'
QMessageBox.warning(self.ui, 'HEXRD', msg)
return
name = self.current_material()
HexrdConfig().remove_material(name)
self.material_editor_widget.material = HexrdConfig().active_material
self.update_gui_from_config()
def _save_config(self, extension, filter):
selected_file, selected_filter = QFileDialog.getSaveFileName(
self.ui, 'Save Configuration',
HexrdConfig().working_dir, filter)
if selected_file:
if Path(selected_file).suffix != extension:
selected_file += extension
HexrdConfig().working_dir = str(Path(selected_file).parent)
return HexrdConfig().save_instrument_config(selected_file)
def on_action_open_config_file_triggered(self):
selected_file, selected_filter = QFileDialog.getOpenFileName(
self.ui, 'Load Configuration',
HexrdConfig().working_dir, 'HEXRD files (*.hexrd *.yml)')
if selected_file:
path = Path(selected_file)
HexrdConfig().working_dir = str(path.parent)
HexrdConfig().load_instrument_config(str(path))
self.update_config_gui()
def change_directory(self):
caption = HexrdConfig().images_dirtion = 'Select directory for images'
new_dir = QFileDialog.getExistingDirectory(self.ui,
caption,
dir=self.parent_dir)
if new_dir:
HexrdConfig().working_dir = new_dir
self.parent_dir = new_dir
self.ui.pwd.setText(self.parent_dir)
self.ui.pwd.setToolTip(self.parent_dir)
def load_dummy_images(self, initial=False):
HexrdConfig().clear_images(initial)
detectors = HexrdConfig().detector_names
iconfig = HexrdConfig().instrument_config
for det in detectors:
cols = iconfig['detectors'][det]['pixels']['columns']
rows = iconfig['detectors'][det]['pixels']['rows']
shape = (rows, cols)
data = np.ones(shape, dtype=np.uint8)
ims = imageseries.open(None, 'array', data=data)
HexrdConfig().imageseries_dict[det] = ims