params

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

class AtlasParams(tab, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: UiParameter

build_params_dict()

connect()

Connect GUI slots here

handle_atlas_resolution_changed(state)

notify_atlas_id_changed()

update_atlas_resolution()

property atlas_base_name

atlas_folder: str

atlas_id: str

publishes = <ClearMap.Utils.event_bus.Publishes object>

structure_tree_id: str

class BatchParameters(tab, *, event_bus: EventBus, preferences=None, get_view=None, apply_patch=None)

Bases: UiParameter

add_group(name: str | None = None) → None

Add a new empty group (called by SamplePickerDialog and similar wizards).

build_params_dict() → dict

cfg_to_ui()

connect()

Connect GUI slots here

get_all_paths() → list[str]

get_paths(gp_idx: int) → list[str]

remove_current_group()

set_paths(gp_idx: int, paths: list[str]) → None

cfg_subtree = None

property group_names: list[str]

groups: dict[str, list[str]]

property n_groups: int

publishes = <ClearMap.Utils.event_bus.Publishes object>

results_folder: str

class BatchProcessingParams(tab, *, event_bus: EventBus, preferences=None, get_view=None, apply_patch=None)

Bases: BatchParameters

Essentially BatchParameters with processing steps

align: bool

cfg_subtree = ['batch_processing']

count_cells: bool

run_vasculature: bool

class BlockProcessingParams(tab, *, cfg_prefix: list[str], event_bus: EventBus, get_view=None, apply_patch=None)

Bases: UiParameter

Generic block-processing parameters (n_processes + size_min / size_max / overlap).

You can attach this to any ‘block_processing’ subtree by passing cfg_prefix. tab is expected to be the BlockProcessingParamsWidget for that step.

build_params_dict()

property cfg_subtree

n_processes: int

overlap: int | None

size_max: int | None

size_min: int | None

class CellMapParams(tab, sample_params, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelsUiParameterCollection

add_channel(channel_name, data_type=None)

add_perf_channel(channel_name: str)

Called from the tab once the channel UI page exists.

pop(channel_name: str)

property params

class ChannelCellMapParams(tab, channel, *, main_params, event_bus: EventBus, dtype=<class 'numpy.uint16'>, get_view=None, apply_patch=None)

Bases: ChannelUiParameter, OrthoviewerSlicingMixin

build_params_dict()

cast_max_from_ui(cfg_vals)

After sentinel mapping back to tokens (None/’auto’), push upper to dtype.max.

connect()

Connect GUI slots here

handle_advanced_state_changed(state)

handle_colocalization_compatible_changed(state)

background_correction_diameter: List[int]

cell_filter_intensity: List[int]

cell_filter_size: List[int]

property cfg_subtree

colocalization_compatible: bool

crop_x: List[int]

crop_y: List[int]

crop_z: List[int]

detect_cells: bool

detection_threshold: int

filter_cells: bool

h_max: int | None

maxima_shape: int

n_detected_cells: int

n_filtered_cells: int

plot_detected_cells: bool

plot_when_finished: bool

save_shape: bool

voxelization_radii: List[int]

voxelization_weights: str | None

voxelize: bool

class ChannelCellMapPerformanceParams(tab: QWidget, channel_name: str, *, event_bus: EventBus, name_widget_name: str | None = None, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: ChannelUiParameter

Links per-channel detection.block_processing performance to the UI widget.

build_params_dict()

property cfg_subtree

n_processes: int

overlap: int | None

size_max: int

size_min: int

class ChannelColocalizationParams(tab, channel, *, main_params, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelUiParameter

build_params_dict()

property cfg_subtree

max_particle_distance: float

n_processes: int

particle_diameter: int

relative_overlap_threshold: float

voxel_number_overlap_threshold: int

class ChannelRegistrationParams(tab, channel_name, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelUiParameter

static scale_landmarks(value: int)

Scale the weight of the landmarks using an exponential function so that the ratio between the weights follows a geometric progression with the slider value

Parameters:

value (int) – The value of the slider (between 0 and 100)

Returns

float

The scaled weight (between 0 and max_ratio)

build_params_dict()

connect()

Connect GUI slots here

handle_landmarks_weight_changed(idx: int, value: int)

handle_params_files_changed()

property cfg_subtree

property n_registration_files: int

property params_files

publishes = <ClearMap.Utils.event_bus.Publishes object>

property use_landmarks_for

class ChannelStitchingParams(tab, channel, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: UiParameterCollection

compute_layout()

Checks if the layout should be computed for this channel. This is the case if the layout channel is the current channel. If the config has not been pushed to the ui yet, it will use the config directly.

Returns

bool

Whether the stitching layout should be computed for this channel

connect()

handle_layout_channel_changed(layout_changed_event: UiLayoutChannelChanged)

handle_use_existing_layout_changed(use_existing_layout_event: UiUseExistingLayoutChanged)

property params

class ChannelTractMapParams(tab, channel, *, main_params, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelUiParameter, OrthoviewerSlicingMixin

build_params_dict()

binarize: bool

property cfg_subtree

clip_range: List[int]

clipping_decimation_ratio: int

clipping_percents: List[float]

crop_x: List[int]

crop_y: List[int]

crop_z: List[int]

display_decimation_ratio: int

export_df: bool

extract_coordinates: bool

label_coordinates: bool

transform_coordinates: bool

voxelization_radii: List[int]

voxelize: bool

class ColocalizationParams(tab, sample_params, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelsUiParameterCollection

add_channel(channel_name, data_type=None)

property params

class GeneralChannelStitchingParams(tab: QWidget, channel_name: str, *, event_bus: EventBus, name_widget_name: str | None = None, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: ChannelUiParameter

build_params_dict()

refresh_layout_channel_items()

Populate and keep in sync the layoutChannelComboBox items.

property cfg_subtree

layout_channel: str

publishes = <ClearMap.Utils.event_bus.Publishes object>

property run

use_existing_layout: bool

use_npy: bool

class GraphFilterParams(*, main_params, widget, graph, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: UiParameter

connect()

Connect GUI slots here

get_default_property_value()

get_property_value()

handle_property_name_changed()

suffix()

update_properties()

property cfg_subtree

property combine_operator_name

Read the action from the following combine button .. rubric:: Returns

property current_dtype

property filter_type

property property_name

class GroupAnalysisParams(tab, *, event_bus: EventBus, preferences=None, get_view=None, apply_patch=None)

Bases: BatchParameters

Essentially batch parameters with comparisons

cfg_to_ui()

set_channels_provider(provider: Callable[[], list[str]])

set_on_plot_group(handler: Callable[[str], None])

set_pipelines(pipelines: list[str])

set_suffixes_provider(provider: Callable[[], list[str]])

cfg_subtree = ['group_analysis']

property comparisons: list[Tuple[str, str]]

compute_sd_and_effect_size: bool

density_suffix: str

pipeline: str

property selected_comparisons: list[Tuple[str, str]]

class NProcessesParams(tab, *, cfg_path: list[str], event_bus: EventBus, get_view=None, apply_patch=None)

Bases: UiParameter

Minimal helper for performance.<step>.n_processes

build_params_dict()

property cfg_subtree

n_processes: int

class PreferencesParams(tab: QWidget, *, event_bus: EventBus, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: UiParameter

build_params_dict()

cfg_subtree = ['machine']

font_size: int

lut: str

pattern_finder_min_n_files: int

start_folder: str

start_full_screen: bool

three_d_plot_bg: str

verbosity: str

class RegistrationParams(tab, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelsUiParameterCollection

add_channel(channel_name, data_type=None)

get_channel_name(channel_idx)

property params

publishes = <ClearMap.Utils.event_bus.Publishes object>

class RigidChannelStitchingParams(tab: QWidget, channel_name: str, *, event_bus: EventBus, name_widget_name: str | None = None, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: ChannelUiParameter

build_params_dict()

set_enabled(state)

set_visible(state)

background_level: int

background_pixels: int

property cfg_subtree

max_shifts_x: List[int]

max_shifts_y: List[int]

max_shifts_z: List[int]

projection_thickness: List[int]

skip: bool

x_overlap: int

y_overlap: int

class SampleChannelParameters(tab, channel_name, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelUiParameter

build_params_dict()

cfg_to_ui()

connect()

Connect GUI slots here

handle_name_changed(old_name: str, new_name: str)

handle_orientation_changed(_)

set_geometry_settings_from_options(items)

validate_orientation(orientation)

property cfg_subtree

comments: str

data_type: str

extension: str

geometry_settings_from: str

property orientation

path: str

publishes = <ClearMap.Utils.event_bus.Publishes object>

resolution: List[float]

slice_x: List[int]

slice_y: List[int]

slice_z: List[int]

wavelength: int | None

class SampleParameters(tab, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelsUiParameterCollection

Class that links the sample params file to the UI

add_channel(channel_name: str)

cfg_to_ui()

ensure_channel_param(channel_name: str)

get_channel_name(channel_idx)

handle_channel_rename_request(old_name: str, new_name: str, requester: SampleChannelParameters) → None

Orchestrate rename:

1. Update parent-owned state (dict key, tab text) so synchronous cascade sees consistent state

2. Ask child to write its config

3. Verify and revert on failure

Parameters:

• old_name (str) – The current name of the channel to rename. This must be a key in self.channel_params.

• new_name (str) – The desired name for the channel. This must be a valid channel name.

• requester (SampleChannelParameters) – The sub tab (channel) that triggered this rename. This is needed to route the config change and to revert the UI if something goes wrong.

propagate_params(channel)

reconcile_from_config()

Makes channels in UI match view (i.e. config).

request_add_channel(channel_name: str)

cfg_subtree: List[str] = ['sample']

property config_channels

property params

publishes = <ClearMap.Utils.event_bus.Publishes object>

class SharedRegistrationParams(tab: QWidget, *, event_bus: EventBus, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: UiParameter

build_params_dict()

class SharedSampleParams(tab: QWidget, *, event_bus: EventBus, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: UiParameter

Links the shared sample parameters (i.e. independent of channel like folder, sample_id…) 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

default_tile_extension

The extension of the tile files

Type:

str

build_params_dict()

cfg_subtree = ['sample']

property channels

default_tile_extension: str

sample_id: str

src_folder: str

use_id_as_prefix: bool

class SharedVesselBinarizationParams(tab: QWidget, *, event_bus: EventBus, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: UiParameter

build_params_dict()

set_plotable_channels(channels)

fill_combined: bool

plot_channel_1: str

plot_channel_2: str

plot_step_1: str

plot_step_2: str

class StitchingParams(tab, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelsUiParameterCollection

Class that groups all the parameters related to the stitching of the sample (i.e. rigid and wobbly stitching)

add_channel(channel_name, data_type=None)

Add a channel to the stitching parameters if not already present.

Warning

This only adds the channel to the config — it does not create the UI elements. UI creation is handled by the tab’s add_channel_tab() method.

Parameters:

• channel_name (str) – The name of the channel to add.

• data_type (str, optional)

compute_layout(channel)

create_missing_channels_from_view(desired_channels: tuple)

get_channels_to_run()

handle_layout_channel_changed(channel, layout_channel)

materialize_channel(ch)

prune_obsolete_channels(desired_channels: tuple)

reconcile_children_from_view(*_)

Ensure we have one ChannelStitchingParams per stitching.channels entry.

set_channels_to_run(channels)

property params

publishes = <ClearMap.Utils.event_bus.Publishes object>

class TractMapParams(tab, sample_params, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelsUiParameterCollection

add_channel(channel_name, data_type=None)

property params

class TractMapPerformanceParams(tab: QWidget, *, event_bus: EventBus, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: UiParameter

tract_map.performance.<section> → performanceGroupBox widgets. Shared (not per-channel) in v3.1.

build_params_dict()

cfg_subtree = ['tract_map', 'performance']

class VesselBinarizationParams(tab: QWidget, channel_name: str, *, event_bus: EventBus, name_widget_name: str | None = None, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: ChannelUiParameter

apply_pipeline_to_config(pipeline: LinearPipeline) → None

Write step order and enabled flags from pipeline to config. Called by the tab whenever the pipeline widget changes.

build_params_dict()

cfg_to_ui() → None

pipeline_from_config() → LinearPipeline

Reconstruct a LinearPipeline from config run flags and step_order. Falls back to BINARIZATION_STEPS insertion order when step_order is absent (e.g. legacy config).

post_connect() → None

Create and wire the LinearPipelineWidget after ParamLink connections are established. The widget replaces the run_* checkboxes and is owned here because it drives config writes via apply_pipeline_to_config.

binarization_clip_range: List[int]

binarization_threshold: int

property cfg_subtree

property n_steps

run_binarization: bool

run_binary_filling: bool

run_deep_filling: bool

run_smoothing: bool

class VesselBinarizationPerformanceParams(tab: QWidget, channel_name: str, *, event_bus: EventBus, name_widget_name: str | None = None, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: ChannelUiParameter

build_params_dict()

property cfg_subtree

n_processes: int

overlap: int | None

size_max: int

size_min: int

class VesselGraphParams(tab, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: UiParameter

add_graph_filter_params(widget, graph)

build_params_dict()

compute_filter_suffix()

annotate: bool

arteries_min_noise_edges: int

artery_intensity_min: float

artery_trace_radius_um: float

build: bool

cfg_subtree = ['vasculature']

clean: bool

distance_to_surface_min: float

final_min_vein_radius: float

max_arteries_tracing_iterations: int

max_veins_tracing_iterations: int

min_artery_component_edges: int

min_vein_component_edges: int

property n_filters

permissive_min_vein_radius: float

publishes = <ClearMap.Utils.event_bus.Publishes object>

reduce: bool

restrictive_min_vein_radius: float

skeletonize: bool

transform: bool

use_arteries: bool

vein_intensity_min: float

vein_intensity_range_on_arteries_channel: List[int]

vein_trace_radius_um: float

class VesselGraphPerformanceParams(tab: QWidget, *, event_bus: EventBus, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: UiParameter

Graph construction performance parameters. Global — graph operates on the combined binary, not per-channel. Widgets are created dynamically in VasculatureTab._setup_graph_perf() before VesselParams is instantiated.

build_params_dict() → dict

cfg_subtree = ['vasculature', 'performance', 'graph_construction']

class VesselParams(tab, sample_params, *, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: ChannelsUiParameterCollection

add_channel(channel_name, data_type=None)

add_perf_channel(channel_name: str)

Called from the tab once the channel UI page exists.

get_selected_steps_and_channels()

pop(channel_name: str)

property params

class VesselVisualizationParams(tab, *, sample_params=None, event_bus: EventBus, get_view=None, apply_patch=None)

Bases: UiParameter, OrthoviewerSlicingMixin

build_params_dict()

set_structure_id(structure_widget)

crop_x: List[int]

crop_y: List[int]

crop_z: List[int]

graph_step: str

pipeline: str | None = 'TubeMap'

plot_type: str

vertex_degrees: str

voxelization_size: List[int]

weight_by_radius: bool

class WobblyChannelStitchingParams(tab: QWidget, channel_name: str, *, event_bus: EventBus, name_widget_name: str | None = None, get_view: Callable[[], Mapping[str, Any]] | None = None, apply_patch: Callable[[dict], None] | None = None)

Bases: ChannelUiParameter

build_params_dict()

set_enabled(state)

set_visible(state)

property cfg_subtree

max_shifts_x: List[int]

max_shifts_y: List[int]

max_shifts_z: List[int]

skip: bool

slice_pixel_size: int | None

slice_valid_range: List[int]

stack_pixel_size: int | None

stack_valid_range: list