pumapy.segmentation¶
pumapy.segmentation.ccl¶
Functions to relying on Connected Component Labeling (CCL)
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pumapy.segmentation.ccl.
fill_closed_pores
(workspace, solid_cutoff, fill_value, return_pores=False)[source]¶ Identify the porespace and fill closed porosity
- Parameters
workspace (pumapy.Workspace) – domain
solid_cutoff ((int, int)) – specify the solid range to discard from pores identification
fill_value (int) – value to fill closed porosity with
return_pores (bool) – specifies whether to return identified pores
- Returns
filled workspace with IDs set as: 0 for void, 1 for solid, fill_value for added filler material. In addition, if return_pores==True, then it also returns the porespace marked as: 0 solid, 1 largest pore (likely open porosity), >1 other pores
- Return type
pumapy.Workspace
- Example
>>> import pumapy as puma >>> ws = puma.generate_random_spheres((100, 100, 100), diameter=20, porosity=0.8, allow_intersect=True, segmented=False) >>> puma.render_volume(ws[:ws.matrix.shape[0] // 2]) >>> ws.binarize_range((1, 250)) >>> puma.render_volume(ws[:ws.matrix.shape[0] // 2]) >>> filled_ws, pores = puma.fill_closed_pores(ws, (1, 1), fill_value=2, return_pores=True) >>> puma.render_volume(pores, cutoff=(0, pores.max()), cmap='jet')
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pumapy.segmentation.ccl.
identify_porespace
(workspace, solid_cutoff, connectivity=None)[source]¶ Identify the porespace
- Parameters
workspace (pumapy.Workspace) – domain
solid_cutoff ((int, int)) – specify the solid range to discard from pores identification
connectivity – Maximum number of orthogonal hops to consider a pixel/voxel as a neighbor
(None automatically gives full connectivity of
input.ndim
, which for 3D domain is 3, for 2D is 2) :type connectivity: int or None :return: porespace marked as: 0 solid, 1 largest pore (likely open porosity), >1 other pores :rtype: np.ndarray- Example
>>> import pumapy as puma >>> ws = puma.generate_sphere((100, 100, 100), (50, 50, 50), 40, segmented=False) >>> ws.binarize_range((1, 253)) >>> puma.render_volume(ws[:ws.matrix.shape[0] // 2], cutoff=(0, 255)) >>> pores = puma.identify_porespace(ws, (1, 1)) >>> puma.render_volume(pores[:pores.shape[0] // 2], cutoff=(0, pores.max()))
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pumapy.segmentation.ccl.
remove_rbms
(workspace, void_id, direction)[source]¶ Rigid Body Movements (RBMs) removal in segmented domain
- Parameters
workspace (pumapy.Workspace) – domain
void_id (int) – specify the void ID to discard from RBMs identification
direction (str) – Cartesian direction that has to be connected, options: ‘x’, ‘y’, ‘z’
- Returns
workspace without the possible RBMs determined by not being connected from side to side
- Return type
pumapy.Workspace
- Example
>>> import pumapy as puma >>> workspace = puma.import_3Dtiff(puma.path_to_example_file("100_fiberform.tif")) >>> new_ws = puma.remove_rbms(workspace, void_cutoff=(0, 103), direction='y') >>> puma.render_volume(workspace, (104, 255), solid_color=(1,1,1)) >>> puma.render_volume(new_ws, (1, new_ws.max()), solid_color=(1,1,1))