tract_map

class TractMapProcessor(sample_manager: SampleManager | None = None, config_coordinator: ConfigCoordinator | None = None, channel: str = '', registration_processor=None)

Bases: ChannelPipelineOrchestrator

static transformation(coords, source_shape, resampled_shape, results_directories)

binarize(clip_low, clip_high)

compute_clip_range(pixel_percents=(70, 99.999))

create_test_dataset(slicing)

export_df(asset_sub_type=None)

get_registration_sequence_channels(stop_channel='atlas')

intensities_to_percentiles(low_intensity, high_intensity)

Convert two intensity thresholds to their percentile ranks (0‒100], using the same nearest-rank convention as compute_clip_range.

Parameters:

• low_intensity (scalar) – Intensity values (e.g. gray levels) whose positions in the global histogram are required.

• high_intensity (scalar) – Intensity values (e.g. gray levels) whose positions in the global histogram are required.

Returns

list[float]

[low_percentile, high_percentile]

label()

mask_to_coordinates(as_memmap=False)

parallel_transform(processes=-1)

plot_binarization_levels(low_spin_box, high_spin_box)

plot_binary(debug=False)

plot_tracts_3d_scatter_w_atlas_colors(raw=False, coordinates_from_debug=False, plot_onto_debug=False, parent=None)

plot_voxelized_counts()

run_pipeline(tuning=False)

setup(sample_manager, channel_name, registration_processor)

Attach a sample manager and mark this processor as ready.

Parameters:

sample_manager (SampleManager, optional) – If provided, replaces the currently stored sample manager. When None, the previously stored instance is reused.

Raises:

ValueError – If the config section identified by config_name is absent.

shift_coordinates()

Shift the coordinates by the cropping amount to get the values in whole sample reference frame

voxelize()

block_re = ('Processing block', re.compile('.*?Processing block \\d+/\\d+.*?\\selapsed time:\\s\\d+:\\d+:\\d+\\.\\d+'))

config_name = 'tract_map'

label_re = ('Labeling', re.compile('.*?Label: processing \\d+/\\d+.*?\\selapsed time:\\s\\d+:\\d+:\\d+\\.\\d+'))

where_re = ('Where', re.compile('.*?Where: processing \\d+/\\d+.*?\\selapsed time:\\s\\d+:\\d+:\\d+\\.\\d+'))

label_points_wrapper(annotator, coords)