ccf_streamlines.projection.Isocortex3dProjector#

class ccf_streamlines.projection.Isocortex3dProjector(projection_file, surface_paths_file, thickness_type='unnormalized', layer_thicknesses=None, streamline_layer_thickness_file=None, hemisphere='both', view_space_for_other_hemisphere=False)#

Flattened projection of the common cortical framework with thickness

Parameters

  • projection_file (str) – File path to an HDF5 file containing the 2D projection information.

  • surface_paths_file (str) – File path to an HDF5 file containing information about the paths between the top and bottom of cortex.

  • thickness_type ({"unnormalized", "normalized_full", "normalized_layers"}) – Type of thickness normalization. If ‘unnormalized’, the thickness varies across the projection according to the length of the streamline. If ‘normalized_full’, the thickness (between pia and white matter) is consistent everywhere, but layer thicknesses can vary. If ‘normalized_layers’, layer thicknesses are consistent everywhere. Layers that are not present in a particular region are left empty in the projection.

  • layer_thicknesses (dict, optional) – Default None. Dictionary of layer thicknesses. Only used if thickness_type is normalized_layers.

  • streamline_layer_thickness_file (str, optional) – Default None. File path to an HDF5 file containing information about the layer thicknesses per streamline.

  • hemisphere ({"both", "left", "right"}) – Whether to create a final projection with both hemispheres (default) or just left or right.

  • view_space_for_other_hemisphere (bool, 'flatmap_dorsal', 'flatmap_butterfly', or int, optional) – If False (default), view is used as-is. If True, view is assumed to have the right half reserved for the other hemisphere, so that returning both hemispheres will result in a projection the size of the original view. This is valid for the ‘top’, ‘back’, ‘bottom’, and ‘front’ views. If the value is a str, it must be one of ‘flatmap_dorsal’, flatmap_butterfly’, ‘medial’, ‘side’, or ‘rotated’, which will use a preset value to place the hemispheres adjacent or near adjacent when used with the views of the same name. If an integer of value n, the right-most n voxels will be removed before combining both hemispheres to allow the user to customize the spacing.

__init__(projection_file, surface_paths_file, thickness_type='unnormalized', layer_thicknesses=None, streamline_layer_thickness_file=None, hemisphere='both', view_space_for_other_hemisphere=False)#

Methods

__init__(projection_file, surface_paths_file)

project_path_ordered_data(data)

Project 1D data corresponding to the list of streamlines

project_volume(volume[, thickness_type])

Create a flattened slab view of the volume.

reference_layer_thicknesses_in_voxels()

Get thicknesses of the reference layers in voxel units

Attributes

ISOCORTEX_LAYER_KEYS