params#

All the classes that define parameters or group thereof for the tabs of the graphical interface

exception ParamsOrientationError[source]#: Bases: ValueError

class AlignmentParams(tab, src_folder=None)[source]#

Bases: UiParameterCollection

Class that groups all the parameters related to the alignment of the sample This includes stitching and registration

fix_cfg_file(f_path)[source]#: Fix the file if it was copied from defaults, tailor to current sample

property all_stitching_params#

property params#

property pipeline_name#

class BatchParameters(tab, src_folder=None, preferences=None)[source]#

Bases: UiParameter

add_group()[source]#

cfg_to_ui()[source]#

connect()[source]#: Connect GUI slots here

connect_groups()[source]#

get_all_paths()[source]#

get_gp_ctrls(ctrl_name)[source]#

get_paths(gp)[source]#

handle_add_src_folder_clicked()[source]#

handle_remove_src_folder_clicked()[source]#

handle_results_folder_changed()[source]#

remove_group()[source]#

set_paths(gp, paths)[source]#

property gp_add_folder_buttons#

property gp_group_name_ctrls#

property gp_list_widget#

property gp_remove_folder_buttons#

property group_names#

property groups#

property n_groups#

property results_folder#

class BatchProcessingParams(tab, src_folder=None, preferences=None)[source]#

Bases: BatchParameters

Essentially BatchParameters with processing steps

property align#

property count_cells#

property run_vaculature#

class CellMapParams(tab, sample_params=None, preprocessing_params=None, src_folder=None)[source]#

Bases: UiParameter

cfg_to_ui()[source]#

connect()[source]#: Connect GUI slots here

handle_background_correction_diameter_changed(val)[source]#

handle_filter_intensity_changed(_)[source]#

reverse_scale_axis(val, axis='x')[source]#

scale_axis(val, axis='x')[source]#

property background_correction_diameter#

property cell_filter_intensity#

cell_filter_size: List[int]#

crop_x_max: int#

crop_x_min: int#

crop_y_max: int#

crop_y_min: int#

crop_z_max: int#

crop_z_min: int#

detect_cells: bool#

detection_threshold: int#

filter_cells: bool#

maxima_shape: int#

plot_detected_cells: bool#

plot_when_finished: bool#

property ratios#

save_shape: bool#

property slice_tuples#

property slicing#

voxelization_radii: List[int]#

voxelize: bool#

class GeneralStitchingParams(tab, src_folder=None)[source]#

Bases: UiParameter

connect()[source]#: Connect GUI slots here

handle_convert_output_changed(state)[source]#

conversion_fmt: str#

convert_arteries: bool#

property convert_output#

convert_raw: bool#

preview_arteries: bool#

preview_raw: bool#

run_arteries: bool#

run_raw: bool#

use_npy: bool#

class GroupAnalysisParams(tab, src_folder=None, preferences=None)[source]#

Bases: BatchParameters

Essentially batch parameters with comparisons

cfg_to_ui()[source]#

connect_groups()[source]#

update_comparisons()[source]#

property comparisons#

Returns

The list of all possible pairs of groups

property selected_comparisons#

class PreferencesParams(tab, src_folder=None)[source]#

Bases: UiParameter

cfg_to_ui()[source]#

chunk_size_max: int#

chunk_size_min: int#

chunk_size_overlap: int#

property font_family#

font_size: int#

property lut#

property n_processes_binarization#

property n_processes_cell_detection#

property n_processes_file_conv#

property n_processes_resampling#

property n_processes_stitching#

pattern_finder_min_n_files: int#

start_folder: str#

start_full_screen: bool#

property three_d_plot_bg#

property verbosity#

class RegistrationParams(tab, src_folder=None)[source]#

Bases: UiParameter

connect()[source]#: Connect GUI slots here

handle_atlas_id_changed()[source]#

handle_atlas_resolution_changed(state)[source]#

handle_structure_tree_id_changed()[source]#

property atlas_base_name#

atlas_folder: str#

property atlas_id#

atlas_id_changed#

property atlas_resolution#

atlas_structure_tree_id_changed#

channel_affine_file_path: str#

ref_affine_file_path: str#

ref_bspline_file_path: str#

skip_resampling: bool#

property structure_tree_id#

class RigidStitchingParams(tab, src_folder=None)[source]#

Bases: UiParameter

connect()[source]#: Connect GUI slots here

handle_projection_thickness_changed()[source]#

background_level: int#

background_pixels: int#

max_shifts_x: List[int]#

max_shifts_y: List[int]#

max_shifts_z: List[int]#

property projection_thickness#

skip: bool#

x_overlap: int#

y_overlap: int#

class SampleParameters(tab, src_folder=None)[source]#

Bases: UiParameter

Class that links the sample params file to the UI

sample_id#

The ID of the sample. This must be unique

Type:: str

use_id_as_prefix#

Whether to use the sample ID as a prefix for the output files

Type:: bool

tile_extension#

The extension of the tile files

Type:: str

raw_path#

The path to the raw data. This is typically an expression that will be expanded by ClearMap

Type:: str

autofluo_path#

The path to the autofluorescence data. This is typically an expression that will be expanded by ClearMap

Type:: str

arteries_path#

The path to the arteries data. This is typically an expression that will be expanded by ClearMap

Type:: str

raw_resolution#

The resolution (sampling) of the raw data

Type:: List[float]

arteries_resolution#

The resolution (sampling) of the arteries data

Type:: List[float]

autofluorescence_resolution#

The resolution (sampling) of the autofluorescence data

Type:: List[float]

slice_x#

The slice in the x dimension

Type:: List[int]

slice_y#

The slice in the y dimension

Type:: List[int]

slice_z#

The slice in the z dimension

Type:: List[int]

orientation#

The orientation of the data (x, y, z) as a tuple of integers (1, 2, 3), (3, 1, 2) … Negative values are allowed to indicate a flip of the axis

Type:: List[int]

cfg_to_ui()[source]#

connect()[source]#: Connect GUI slots here

fix_cfg_file(f_path)[source]#: Fix the file if it was copied from defaults, tailor to current sample

handle_orientation_changed(val)[source]#

handle_raw_path_changed()[source]#

handle_sample_id_changed(id_=None)[source]#

arteries_path: str#

arteries_resolution: List[float]#

autofluo_path: str#

autofluorescence_resolution: List[float]#

property orientation#

property raw_path#

raw_resolution: List[float]#

property sample_id#

slice_x: List[int]#

slice_y: List[int]#

slice_z: List[int]#

tile_extension: str#

use_id_as_prefix: bool#

class VesselBinarizationParams(tab, src_folder=None)[source]#

Bases: UiParameter

connect()[source]#: Connect GUI slots here

handle_arteries_binarization_threshold_changed()[source]#

handle_raw_binarization_threshold_changed()[source]#

arteries_binarization_clip_range: List[int]#

property arteries_binarization_threshold#

binary_fill_arteries: bool#

binary_fill_raw: bool#

fill_combined: bool#

fill_main_channel: bool#

fill_secondary_channel: bool#

property n_steps#

plot_channel_1: str#

plot_channel_2: str#

plot_step_1: str#

plot_step_2: str#

raw_binarization_clip_range: List[int]#

property raw_binarization_threshold#

run_arteries_binarization: bool#

run_raw_binarization: bool#

smooth_arteries: bool#

smooth_raw: bool#

class VesselGraphParams(tab, src_folder=None)[source]#

Bases: UiParameter

connect()[source]#: Connect GUI slots here

annotate: bool#

arteries_min_radius: float#

build: bool#

clean: bool#

final_min_vein_radius: float#

max_arteries_tracing_iterations: int#

max_veins_tracing_iterations: int#

min_artery_size: int#

min_vein_size: int#

permissive_min_vein_radius: float#

reduce: bool#

restrictive_min_vein_radius: float#

skeletonize: bool#

transform: bool#

use_arteries: bool#

vein_intensity_range_on_arteries_channel: List[int]#

class VesselParams(tab, sample_params, preprocessing_params, src_folder=None)[source]#

Bases: UiParameterCollection

property params#

class VesselVisualizationParams(tab, sample_params=None, preprocessing_params=None, src_folder=None)[source]#

Bases: UiParameter

connect()[source]#: Connect GUI slots here

reverse_scale_axis(val, axis='x')[source]#

scale_axis(val, axis='x')[source]#

set_structure_id(structure_widget)[source]#

crop_x_max: int#

crop_x_min: int#

crop_y_max: int#

crop_y_min: int#

crop_z_max: int#

crop_z_min: int#

graph_step: str#

plot_type: str#

property ratios#

property slice_tuples#

property slicing#

vertex_degrees: str#

voxelization_size: List[int]#

weight_by_radius: bool#

class WobblyStitchingParams(tab, src_folder=None)[source]#

Bases: UiParameter

connect()[source]#: Connect GUI slots here

max_shifts_x: List[int]#

max_shifts_y: List[int]#

max_shifts_z: List[int]#

skip: bool#

slice_pixel_size: int#

slice_range: List[int]#

valid_range: list#