def add_saving_panel(self, row):
"""
Saving/Export panel
"""
self.save_data_panel = QGroupBox()
self.save_data_layout = QGridLayout()
self.export_button = add_button(
"To brainrender",
self.save_data_layout,
self.export_to_brainrender,
0,
0,
visibility=False,
)
self.save_button = add_button("Save",
self.save_data_layout,
self.save,
0,
1,
visibility=False)
self.save_data_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)
self.save_data_panel.setLayout(self.save_data_layout)
self.layout.addWidget(self.save_data_panel, row, 0, 1, 2)
self.save_data_panel.setVisible(False)
def add_loading_panel(self, row, column=0):
"""
Loading panel:
- Load project (sample space)
- Load project (atlas space)
- Atlas chooser
"""
self.load_data_panel = QGroupBox("Load data")
self.load_data_layout = QGridLayout()
self.load_data_layout.setSpacing(15)
self.load_data_layout.setContentsMargins(10, 10, 10, 10)
self.load_data_layout.setAlignment(QtCore.Qt.AlignBottom)
self.load_button = add_button(
"Load project (sample space)",
self.load_data_layout,
self.load_brainreg_directory_sample,
0,
0,
visibility=False,
minimum_width=COLUMN_WIDTH,
alignment=LOADING_PANEL_ALIGN,
)
self.load_button_standard = add_button(
"Load project (atlas space)",
self.load_data_layout,
self.load_brainreg_directory_standard,
1,
0,
visibility=False,
minimum_width=COLUMN_WIDTH,
alignment=LOADING_PANEL_ALIGN,
)
self.add_atlas_menu(self.load_data_layout)
self.load_data_layout.setColumnMinimumWidth(0, COLUMN_WIDTH)
self.load_data_panel.setLayout(self.load_data_layout)
self.load_data_panel.setVisible(True)
self.layout.addWidget(self.load_data_panel, row, column, 1, 1)
# buttons made visible after adding to main widget, preventing them
# from briefly appearing in a separate window
self.load_button.setVisible(True)
self.load_button_standard.setVisible(True)
def add_loading_panel(self, row, column=0):
"""
Loading panel:
- Load project (sample space)
- Load project (atlas space)
- Atlas chooser
"""
self.load_data_panel = QGroupBox("Load data")
self.load_data_layout = QGridLayout()
self.load_data_layout.setSpacing(15)
self.load_data_layout.setContentsMargins(10, 10, 10, 10)
self.load_data_layout.setAlignment(QtCore.Qt.AlignBottom)
self.load_button = add_button(
"Load project (sample space)",
self.load_data_layout,
self.load_brainreg_directory_sample,
0,
0,
minimum_width=COLUMN_WIDTH,
alignment=LOADING_PANEL_ALIGN,
)
self.load_button_standard = add_button(
"Load project (atlas space)",
self.load_data_layout,
self.load_brainreg_directory_standard,
1,
0,
minimum_width=COLUMN_WIDTH,
alignment=LOADING_PANEL_ALIGN,
)
self.add_atlas_menu(self.load_data_layout)
self.load_data_layout.setColumnMinimumWidth(0, COLUMN_WIDTH)
self.load_data_panel.setLayout(self.load_data_layout)
self.load_data_panel.setVisible(True)
self.layout.addWidget(self.load_data_panel, row, column, 1, 1)
def add_segmentation_methods_panel(self, row, column=1):
"""
Segmentation methods chooser panel:
Toggle visibility of segmentation
methods
"""
self.toggle_methods_panel = QGroupBox("Segmentation")
self.toggle_methods_layout = QGridLayout()
self.toggle_methods_layout.setContentsMargins(10, 10, 10, 10)
self.toggle_methods_layout.setSpacing(5)
self.toggle_methods_layout.setAlignment(QtCore.Qt.AlignBottom)
self.show_trackseg_button = add_button(
"Track tracing",
self.toggle_methods_layout,
self.track_seg.toggle_track_panel,
0,
1,
minimum_width=COLUMN_WIDTH,
alignment=SEGM_METHODS_PANEL_ALIGN,
)
self.show_trackseg_button.setEnabled(False)
self.show_regionseg_button = add_button(
"Region segmentation",
self.toggle_methods_layout,
self.region_seg.toggle_region_panel,
1,
1,
minimum_width=COLUMN_WIDTH,
alignment=SEGM_METHODS_PANEL_ALIGN,
)
self.show_regionseg_button.setEnabled(False)
self.toggle_methods_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)
self.toggle_methods_panel.setLayout(self.toggle_methods_layout)
self.toggle_methods_panel.setVisible(True)
self.layout.addWidget(self.toggle_methods_panel, row, column, 1, 1)
def add_region_panel(self, row):
self.region_panel = QGroupBox("Region analysis")
region_layout = QGridLayout()
add_button(
"Add region",
region_layout,
self.add_region,
2,
0,
)
add_button(
"Analyse regions",
region_layout,
self.run_region_analysis,
2,
1,
)
self.calculate_volumes_checkbox = add_checkbox(
region_layout,
self.calculate_volumes_default,
"Calculate volumes",
0,
)
self.summarise_volumes_checkbox = add_checkbox(
region_layout,
self.summarise_volumes_default,
"Summarise volumes",
1,
)
region_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)
self.region_panel.setLayout(region_layout)
self.parent.layout.addWidget(self.region_panel, row, 0, 1, 2)
self.region_panel.setVisible(False)
def add_track_panel(self, row):
self.track_panel = QGroupBox("Track tracing")
track_layout = QGridLayout()
add_button(
"Add surface points",
track_layout,
self.add_surface_points,
5,
1,
)
add_button(
"Add track",
track_layout,
self.add_track,
6,
0,
)
add_button(
"Trace tracks",
track_layout,
self.run_track_analysis,
6,
1,
)
self.summarise_track_checkbox = add_checkbox(
track_layout,
self.summarise_track_default,
"Summarise",
0,
)
self.fit_degree = add_int_box(
track_layout,
self.fit_degree_default,
1,
5,
"Fit degree",
1,
)
self.spline_smoothing = add_float_box(
track_layout,
self.spline_smoothing_default,
0,
1,
"Spline smoothing",
0.1,
2,
)
self.spline_points = add_int_box(
track_layout,
self.spline_points_default,
1,
10000,
"Spline points",
3,
)
track_layout.setColumnMinimumWidth(1, COLUMN_WIDTH)
self.track_panel.setLayout(track_layout)
self.parent.layout.addWidget(self.track_panel, row, 0, 1, 2)
self.track_panel.setVisible(False)
def add_loading_panel(self, row, column=0):
"""
Loading panel:
- Load project (sample space)
- Load project (atlas space)
- Atlas chooser
"""
self.load_data_panel = QGroupBox("Load data")
self.load_data_layout = QGridLayout()
self.load_data_layout.setSpacing(15)
self.load_data_layout.setContentsMargins(10, 10, 10, 10)
self.load_data_layout.setAlignment(QtCore.Qt.AlignBottom)
# self.load_cellfinder_dir_button = add_button(
# "Load cellfinder project",
# self.load_data_layout,
# self.get_cellfinder_directory,
# 0,
# 0,
# minimum_width=COLUMN_WIDTH,
# )
# self.load_background_button = add_button(
# "Load background",
# self.load_data_layout,
# self.get_background,
# 1,
# 0,
# minimum_width=COLUMN_WIDTH,
# )
self.load_signal_button = add_button(
"Load signal",
self.load_data_layout,
self.get_signal,
2,
0,
minimum_width=COLUMN_WIDTH,
)
self.add_cells_button = add_button(
"Add cell count",
self.load_data_layout,
self.add_cell_count,
3,
0,
minimum_width=COLUMN_WIDTH,
)
self.add_cells_button = add_button(
"Load cell count",
self.load_data_layout,
self.load_cells,
4,
0,
minimum_width=COLUMN_WIDTH,
)
self.save_cells_button = add_button(
"Save cells",
self.load_data_layout,
self.save_cell_count,
5,
0,
minimum_width=COLUMN_WIDTH,
)
self.analyse_cells_button = add_button(
"Analyse cells",
self.load_data_layout,
self.analyse_cells,
6,
0,
minimum_width=COLUMN_WIDTH,
)
self.load_data_layout.setColumnMinimumWidth(0, COLUMN_WIDTH)
self.load_data_panel.setLayout(self.load_data_layout)
self.load_data_panel.setVisible(True)
self.layout.addWidget(self.load_data_panel, row, column, 1, 1)