def get_parameters_to_save(self, config):
for subsection in config[self.parameter_section_name]:
parameters_keep_tmp = config.get(self.parameter_section_name,
subsection).split(",")
self.parameters_keep = self.parameters_keep + parameters_keep_tmp
self.parameters_keep = unique_elements_lists(self.parameters_keep)
if self._strip_spaces:
self.parameters_keep = strip_spaces_list(self.parameters_keep)
def summary_run(args):
# if args.structures_file_path is None:
# args.structures_file_path = get_structures_path()
# reference_structures_table = pd.read_csv(args.structures_file_path)
# else:
# raise NotImplementedError(
# "Only the Allen adult mouse atlas is " "currently supported."
# )
reference_structures_table = pd.read_csv(get_structures_path())
if not args.regions and not args.regions_list:
# regions = list(pd.read_csv(args.structures_file_path)["name"])
regions = list(pd.read_csv(get_structures_path())["name"])
else:
regions = []
if args.regions:
regions = regions + args.regions
if args.regions_list:
regions = regions + list(pd.read_csv(args.regions_list)["name"])
regions = remove_empty_string(regions)
regions = unique_elements_lists(regions)
csvs_folder = args.csv_dir
destination_folder = os.path.join(args.csv_dir, "summary")
csvs_names = [f for f in os.listdir(csvs_folder) if f.endswith(".csv")]
if len(csvs_names) == 0:
raise FileNotFoundError(
"No CSV files were found in the directory: "
"{}. Please check the arguments".format(csvs_folder))
csvs_paths = [os.path.join(csvs_folder, f) for f in csvs_names]
if not os.path.exists(destination_folder):
os.makedirs(destination_folder)
for csv_file_path in csvs_paths:
print("CSV file: {}".format(os.path.basename(csv_file_path)))
summary = make_summary_df_for_brain(
csv_file_path,
regions,
reference_structures_table,
sum_regions=args.sum_regions,
)
filename = os.path.basename(csv_file_path)
dest_path = os.path.join(destination_folder, filename)
summary.to_csv(dest_path, index=False)
print("Done!")
def save_curation(viewer):
"""Save file"""
if not CURATED_POINTS:
print("No cells have been confirmed or toggled, not saving")
else:
unique_cells = unique_elements_lists(CURATED_POINTS)
points = viewer.layers[1].data[unique_cells]
labels = viewer.layers[1].properties["cell"][unique_cells]
labels = labels.astype("int")
labels = labels + 1
cells_to_save = []
for idx, point in enumerate(points):
cell = Cell([point[2], point[1], point[0]], labels[idx])
cells_to_save.append(cell)
print(f"Saving results to: {output_filename}")
save_cells(cells_to_save, output_filename)
def analyse_region_brain_areas(
label_layer,
destination_directory,
annotations,
hemispheres,
structures_reference_df,
extension=".csv",
ignore_empty=True,
):
"""
:param label_layer: napari labels layer (with segmented regions)
:param np.array annotations: numpy array of the brain area annotations
:param np.array hemispheres: numpy array of hemipshere annotations
:param structures_reference_df: Pandas dataframe with "id" column (matching
the values in "annotations" and a "name column"
:param ignore_empty: If True, don't analyse empty regions
"""
data = label_layer.data
if ignore_empty:
if data.sum() == 0:
return
# swap data back to original orientation from napari orientation
data = np.swapaxes(data, 2, 0)
name = label_layer.name
masked_annotations = data.astype(bool) * annotations
# TODO: don't hardcode hemisphere value. Get from atlas config
annotations_left, annotations_right = lateralise_atlas(
masked_annotations,
hemispheres,
left_hemisphere_value=2,
right_hemisphere_value=1,
)
unique_vals_left, counts_left = np.unique(annotations_left,
return_counts=True)
unique_vals_right, counts_right = np.unique(annotations_right,
return_counts=True)
voxel_volume = get_voxel_volume(source_custom_config_amap())
voxel_volume_in_mm = voxel_volume / (1000**3)
df = initialise_df(
"structure_name",
"left_volume_mm3",
"left_percentage_of_total",
"right_volume_mm3",
"right_percentage_of_total",
"total_volume_mm3",
"percentage_of_total",
)
sampled_structures = unique_elements_lists(
list(unique_vals_left) + list(unique_vals_right))
total_volume_region = get_total_volume_regions(unique_vals_left,
unique_vals_right,
counts_left, counts_right)
for atlas_value in sampled_structures:
if atlas_value != 0:
try:
df = add_structure_volume_to_df(
df,
atlas_value,
structures_reference_df,
unique_vals_left,
unique_vals_right,
counts_left,
counts_right,
voxel_volume_in_mm,
total_volume_voxels=total_volume_region,
)
except UnknownAtlasValue:
print(
"Value: {} is not in the atlas structure reference file. "
"Not calculating the volume".format(atlas_value))
filename = destination_directory / (name + extension)
df.to_csv(filename, index=False)
def analyse_region_brain_areas(
label_layer,
atlas_layer_data,
hemispheres,
destination_directory,
atlas,
extension=".csv",
ignore_empty=True,
):
"""
:param label_layer: napari labels layer (with segmented regions)
:param ignore_empty: If True, don't analyse empty regions
"""
data = label_layer.data
if ignore_empty:
if data.sum() == 0:
return
name = label_layer.name
masked_annotations = data.astype(bool) * atlas_layer_data
annotations_left, annotations_right = lateralise_atlas_image(
masked_annotations,
hemispheres,
left_hemisphere_value=atlas.left_hemisphere_value,
right_hemisphere_value=atlas.right_hemisphere_value,
)
unique_vals_left, counts_left = np.unique(annotations_left,
return_counts=True)
unique_vals_right, counts_right = np.unique(annotations_right,
return_counts=True)
voxel_volume_in_mm = np.prod(atlas.resolution) / (1000**3)
df = initialise_df(
"structure_name",
"left_volume_mm3",
"left_percentage_of_total",
"right_volume_mm3",
"right_percentage_of_total",
"total_volume_mm3",
"percentage_of_total",
)
sampled_structures = unique_elements_lists(
list(unique_vals_left) + list(unique_vals_right))
total_volume_region = get_total_volume_regions(unique_vals_left,
unique_vals_right,
counts_left, counts_right)
for atlas_value in sampled_structures:
if atlas_value != 0:
try:
df = add_structure_volume_to_df(
df,
atlas_value,
atlas.structures,
unique_vals_left,
unique_vals_right,
counts_left,
counts_right,
voxel_volume_in_mm,
total_volume_voxels=total_volume_region,
)
except KeyError:
print(f"Value: {atlas_value} is not in the atlas structure"
f" reference file. Not calculating the volume")
filename = destination_directory / (name + extension)
df.to_csv(filename, index=False)
def test_unique_elements_list():
list_in = [1, 2, 2, "a", "b", 1, "a", "dog"]
unique_list = [1, 2, "a", "b", "dog"]
assert list_tools.unique_elements_lists(list_in) == unique_list