class RegionSeg(QGroupBox):
"""
Region segmentation method panel
"""
def __init__(
self,
parent,
calculate_volumes_default=CALCULATE_VOLUMES_DEFAULT,
summarise_volumes_default=SUMMARIZE_VOLUMES_DEFAULT,
brush_size=BRUSH_SIZE,
image_file_extension=IMAGE_FILE_EXT,
num_colors=NUM_COLORS,
):
super(RegionSeg, self).__init__()
self.parent = parent
self.calculate_volumes_default = calculate_volumes_default
self.summarise_volumes_default = summarise_volumes_default
# Brushes / ...
self.brush_size_default = BRUSH_SIZE # Keep track of default
self.brush_size = brush_size # Initialise
self.num_colors = num_colors
# File formats
self.image_file_extension = image_file_extension
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 toggle_region_panel(self):
# TODO: Change color scheme directly when theme is switched
# TODO: "text-align" property should follow constant SEGM_METHODS_PANEL_ALIGN
if self.region_panel.isVisible():
self.region_panel.setVisible(False)
if self.parent.viewer.theme == "dark":
self.parent.show_regionseg_button.setStyleSheet(
f"QPushButton {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
else:
self.parent.show_regionseg_button.setStyleSheet(
f"QPushButton {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
else:
self.region_panel.setVisible(True)
if self.parent.viewer.theme == "dark":
self.parent.show_regionseg_button.setStyleSheet(
f"QPushButton {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
else:
self.parent.show_regionseg_button.setStyleSheet(
f"QPushButton {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
def check_saved_region(self):
add_existing_region_segmentation(
self.parent.paths.regions_directory,
self.parent.viewer,
self.parent.label_layers,
self.image_file_extension,
)
def add_region(self):
print("Adding a new region\n")
self.region_panel.setVisible(True) # Should be visible by default!
add_new_region_layer(
self.parent.viewer,
self.parent.label_layers,
self.parent.base_layer.data,
self.brush_size,
self.num_colors,
)
def run_region_analysis(self):
if self.parent.label_layers:
print("Running region analysis")
worker = region_analysis(
self.parent.label_layers,
self.parent.atlas_layer.data,
self.parent.atlas,
self.parent.paths.regions_directory,
output_csv_file=self.parent.paths.region_summary_csv,
volumes=self.calculate_volumes_checkbox.isChecked(),
summarise=self.summarise_volumes_checkbox.isChecked(),
)
worker.start()
else:
print("No regions found")
class TrackSeg(QGroupBox):
"""
Track segmentation method panel
"""
def __init__(
self,
parent,
point_size=POINT_SIZE,
spline_size=SPLINE_SIZE,
track_file_extension=TRACK_FILE_EXT,
spline_points_default=SPLINE_POINTS_DEFAULT,
spline_smoothing_default=SPLINE_SMOOTHING_DEFAULT,
fit_degree_default=FIT_DEGREE_DEFAULT,
summarise_track_default=SUMMARISE_TRACK_DEFAULT,
):
super(TrackSeg, self).__init__()
self.parent = parent
self.tree = None
self.summarise_track_default = summarise_track_default
# Point / Spline fitting settings
self.point_size_default = POINT_SIZE # Keep track of default
self.point_size = point_size # Initialise
self.spline_points_default = spline_points_default
self.spline_size_default = SPLINE_SIZE # Keep track of default
self.spline_size = spline_size # Initialise
self.spline_smoothing_default = spline_smoothing_default
self.fit_degree_default = fit_degree_default
# File formats
self.track_file_extension = track_file_extension
# Initialise spline and spline names
self.splines = None
self.spline_names = None
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 toggle_track_panel(self):
# TODO: Change color scheme directly when theme is switched
# TODO: "text-align" property should follow constant SEGM_METHODS_PANEL_ALIGN
if self.track_panel.isVisible():
self.track_panel.setVisible(False)
if self.parent.viewer.theme == "dark":
self.parent.show_trackseg_button.setStyleSheet(
f"QPushButton {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #414851; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
else:
self.parent.show_trackseg_button.setStyleSheet(
f"QPushButton {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #d6d0ce; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
else:
self.track_panel.setVisible(True)
if self.parent.viewer.theme == "dark":
self.parent.show_trackseg_button.setStyleSheet(
f"QPushButton {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #7e868f; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
else:
self.parent.show_trackseg_button.setStyleSheet(
f"QPushButton {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
f"QPushButton:pressed {{ background-color: #fdf194; text-align:{SEGM_METHODS_PANEL_ALIGN};}}"
)
def check_saved_track(self):
track_files = glob(
str(self.parent.paths.tracks_directory) + "/*" +
self.track_file_extension)
if self.parent.paths.tracks_directory.exists() and track_files != []:
for track_file in track_files:
self.parent.track_layers.append(
add_existing_track_layers(
self.parent.viewer,
track_file,
self.point_size,
))
def add_track(self):
print("Adding a new track\n")
self.splines = None
self.spline_names = None
self.track_panel.setVisible(True) # Should be visible by default!
add_new_track_layer(
self.parent.viewer,
self.parent.track_layers,
self.point_size,
)
def add_surface_points(self):
if self.parent.track_layers:
print("Adding surface points (this may take a while)")
if self.tree is None:
self.create_brain_surface_tree()
for track_layer in self.parent.track_layers:
try:
_, index = self.tree.query(track_layer.data[0])
except IndexError:
print(
f"{track_layer.name} does not appear to hold any data")
continue
surface_point = self.tree.data[index]
track_layer.data = np.vstack((surface_point, track_layer.data))
print("Finished!\n")
else:
print("No tracks found.")
def create_brain_surface_tree(self):
self.tree = create_KDTree_from_image(self.parent.atlas_layer.data)
def run_track_analysis(self, override=False):
if self.parent.track_layers:
if not override:
choice = display_warning(
self.parent,
"About to analyse tracks",
"Existing files will be will be deleted. Proceed?",
)
else:
choice = True # for debugging
if choice:
print("Running track analysis")
self.splines, self.spline_names = track_analysis(
self.parent.viewer,
self.parent.atlas,
self.parent.paths.tracks_directory,
self.parent.track_layers,
self.spline_size,
spline_points=self.spline_points.value(),
fit_degree=self.fit_degree.value(),
spline_smoothing=self.spline_smoothing.value(),
summarise_track=self.summarise_track_checkbox.isChecked(),
)
print("Finished!\n")
else:
print("Preventing analysis as user chose 'Cancel'")
else:
print("No tracks found.")
