copick-utils 0.6.1__py3-none-any.whl → 1.0.0__py3-none-any.whl

copick_utils-1.0.0.dist-info/RECORD

@@ -0,0 +1,71 @@
+copick_utils/__init__.py,sha256=kFQ8LThoKCfUlzlQkmifSsrvL9z0Wamtr7jQ_MLQWA8,135
+copick_utils/cli/__init__.py,sha256=51i1xC-N2laWLdZLdpsKMSB9LdO3BEdqDdWIbyxJ8f0,634
+copick_utils/cli/clipmesh.py,sha256=M1MP8lw16diGHajipFXbZDQ4ZrsTvFiqAaHji0Smmtc,6172
+copick_utils/cli/clippicks.py,sha256=7lmEZj8GDyVqc9l_rvGhAFTYWUhSEnwZcWu8w9LStBU,5857
+copick_utils/cli/clipseg.py,sha256=atx01VUBdk5xLSwEHh43bN7HEKV2bjVgDmaNaLwJQ5E,6437
+copick_utils/cli/conversion_commands.py,sha256=7I729S_9R7l67NzwfKaEWZAxcq0NbBhflZHKxTXaZhk,1045
+copick_utils/cli/enclosed.py,sha256=gsJxapWCqH4IOMDyTTd_akv4L1qzuBfbRJEDBES6Wik,7209
+copick_utils/cli/filter_components.py,sha256=hOs8h0648Ws-rzVxTh7w8Futjk4aEOpavoqrJMvr-2Q,6163
+copick_utils/cli/fit_spline.py,sha256=BdLujzR9sen6IGlmZ9pGbhqs6Kjzk5MuAgmq3ewyMhk,6491
+copick_utils/cli/hull.py,sha256=EpcgQB1-BM0iIyDE7Hj8Gpws8qgjsozSuoIFxCNog80,4666
+copick_utils/cli/input_output_selection.py,sha256=DFsV52h9D6Y8fi7eIkULPAW5NQOfX8ssymU25gBMP34,2537
+copick_utils/cli/logical_commands.py,sha256=Cdt9tFVTXmJZIdqORQgrfYqFLUxN-xiC1bRETs0s32k,861
+copick_utils/cli/mesh2picks.py,sha256=BXCGvc9C1G71O6j15IhMj9EH279blBZh4zC_wbEbKBE,5604
+copick_utils/cli/mesh2seg.py,sha256=cViBvsvrwBpIkTUZudB0IuM869FILQi1n7AmydN6mRs,6118
+copick_utils/cli/meshop.py,sha256=E9PMMu6ueTPH9NudsRYTJIy5mBnmJNulS6C-GlqIqLc,9575
+copick_utils/cli/picks2ellipsoid.py,sha256=A28VjDQsQPfCR8jNrmSkMemPQce4dGSn_bH9QqLsamk,6025
+copick_utils/cli/picks2mesh.py,sha256=SsCURExY2NvtPlHncnWj5QKWd0mRNpve6YEqCHXUKVo,6316
+copick_utils/cli/picks2plane.py,sha256=09IXCQUoiLPKCFH6LQ3uaDsFY9bzj1i0C_jbcxvRx-g,5428
+copick_utils/cli/picks2seg.py,sha256=94Up--yLJ-2G9jW61pTfpbMrggcLEPIQ4bUbCJ2_dzk,4682
+copick_utils/cli/picks2sphere.py,sha256=P-xFFDJdEowxHF20aLMO2Xymv7VHAaP4paBbgPWeqCE,5924
+copick_utils/cli/picks2surface.py,sha256=vXprZa3tHndSE3Sp1yPOEqyv2kRkAbV7QlHjF8oE1zg,5712
+copick_utils/cli/picksin.py,sha256=SD32-BJoxB2dGQU54ksuq2rCmcGjnQLldE0hrnV8pLA,5485
+copick_utils/cli/picksout.py,sha256=odm2JeTyDzBrXkr2SCsbE3REGj589bCgPOq3ldj8soA,5568
+copick_utils/cli/processing_commands.py,sha256=s9Mn0mvKQ60XQN6o6eyO2x7qZX_Hpq0K3kPwMuLHlKY,576
+copick_utils/cli/seg2mesh.py,sha256=9fv3zaVHxAS4VhhlvU6qJ7W7wWjAYDedzDNeiaMZxTk,4732
+copick_utils/cli/seg2picks.py,sha256=05RUsOJETnOc9zMmW_x3DVr1t2F01w2e2R8sAaJrHg8,4549
+copick_utils/cli/segop.py,sha256=K_ju0MB4n-k5-wkOI7gOvkHCUslgHZCZUOFn-k2ta9M,9372
+copick_utils/cli/separate_components.py,sha256=m0c5v4ZXSeoUURcVoY7jCE6I_jGbTdZXqEoLUiURIHs,5670
+copick_utils/cli/skeletonize.py,sha256=CV_J9nibqLpKmckNRG6-7zlq6ROqPBLk166yDzhxJ5w,5646
+copick_utils/cli/util.py,sha256=tne45hU9dL0AepQhV9KKqkKjAMAfweR9_GLGHJnisnc,18011
+copick_utils/cli/validbox.py,sha256=Z-HY73QnWwxL-cLHLiIWNnYz4t-4jf63ho8pfk38xXU,5364
+copick_utils/converters/__init__.py,sha256=f3_UJJ2jJqkOAaEy6y4i3x1baFZEem9aTrGGdBQgXFQ,1701
+copick_utils/converters/converter_common.py,sha256=DVcneXPrrjdsQtshDKLHVr1oHT8lG4yl-3h0_0UBSoo,21475
+copick_utils/converters/ellipsoid_from_picks.py,sha256=UKfF0CUWVDiqR4KWo1KSNgn6YW2460zIMGifVdJjUMc,12717
+copick_utils/converters/lazy_converter.py,sha256=pyoxnXqaSNE8KWMe8_XHfswm996TjUqj1sTucDMv8u4,20037
+copick_utils/converters/mesh_from_picks.py,sha256=5fPYVnij18p-6y0MuZLNWO7AFOSGEY3iBpR18nst0ZY,7614
+copick_utils/converters/mesh_from_segmentation.py,sha256=KeLdk909fXLodwnqf-x1NAe9ghvbPEjilaWLURB_J_g,3626
+copick_utils/converters/picks_from_mesh.py,sha256=PkYIz09FMQGos1Ab1IjzJkaqHGtx11Sw7vKYyXkTISA,18422
+copick_utils/converters/picks_from_segmentation.py,sha256=fRPOFtFzKZ12kfYHT5yLXSTw8DitlXmaPlbtHXtY2-E,5807
+copick_utils/converters/plane_from_picks.py,sha256=a2DV5PtH0mWsrZZIjzB9SuMeToh_fH1nU9BSS_KuNRU,9041
+copick_utils/converters/segmentation_from_mesh.py,sha256=IPrvtSaFT8QNOGidWHDeaeJa7g78G6aAzhUgvDISsrs,10145
+copick_utils/converters/segmentation_from_picks.py,sha256=OtA5GAePcKc3k1_oQXY7-H1vA515GWLONqVJmC_LdN0,10709
+copick_utils/converters/sphere_from_picks.py,sha256=jwoXYV00hNR1Qjw0id9hVf9R2EmNzzQVSA7iAAsEHBw,11431
+copick_utils/converters/surface_from_picks.py,sha256=PHRVtdaDikygT3kmTJKUnw2Gvj_QPsRI6sxMlye9nKY,11886
+copick_utils/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+copick_utils/features/skimage.py,sha256=Sz-348tTT44lLS825z14iIOM3L_tALXQctUF1HbnWnw,4209
+copick_utils/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+copick_utils/io/readers.py,sha256=bE7IBPohNjsFgD6HRPTrWte6OjaJ0NrF4RS8Dwgf3nA,5435
+copick_utils/io/writers.py,sha256=iYyNkpBgrD0_N0N-LoyCOfIrk46WHWocKvkUUQYXMRg,2985
+copick_utils/logical/__init__.py,sha256=coOdLd7vH6TCsoHj9T1Hj5hqnfiGM5CrVkmjVB-HdbM,1181
+copick_utils/logical/distance_operations.py,sha256=cVn8YywwrgNEaKJxnZ6KbsJwwx7fJ2VDDaUEgat0b9A,24071
+copick_utils/logical/enclosed_operations.py,sha256=f388K37vS4wCN5D0FL5lnvO29pd23pmC0LlXhNuNsS0,8583
+copick_utils/logical/mesh_operations.py,sha256=hra0SiA0tsvEYbY4ldCl-e0nUUpND2dSdGkAIdJhXPY,14041
+copick_utils/logical/point_operations.py,sha256=a2KrTqSuXeb-GNvFywN7iDuATkTDsSz0CsLSWhJeG80,10848
+copick_utils/logical/segmentation_operations.py,sha256=AlPHq3t7Hw46svW6qBnr3i1PPulcNvDNikoYD7_RnrI,12090
+copick_utils/pickers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+copick_utils/pickers/grid_picker.py,sha256=KKfdv3fDmeY7XwqiVADRQJibr1eyjYoG9ZpaihcrgHw,2345
+copick_utils/process/__init__.py,sha256=ERh5Ka4vU0_ub4_UZFDWOXbr-my79s3RekfS9dV41wE,1227
+copick_utils/process/connected_components.py,sha256=9h_Feu3wxYWW84evaUmW73_UY0fGmTszS55R8oljjEo,13601
+copick_utils/process/filter_components.py,sha256=dU0l0PJ6ZejY6ANqsrDRtQ1RevdKWn6Txl4nr0sBq14,10587
+copick_utils/process/hull.py,sha256=tLah4_fcwIuiy9Kaly5sVVDHltGBh6euyO3i9W99pms,3191
+copick_utils/process/skeletonize.py,sha256=gLQgQdYlyuqFHyC19vzx8-gna15UiAM_1i85hF-mkMg,11713
+copick_utils/process/spline_fitting.py,sha256=6pBr4w7cKZb5xaKaU3b1R5A6cIVDrCTRKTVVUL4vDSI,25025
+copick_utils/process/validbox.py,sha256=5uEbVjmyNJxp__2XJal1jP7Ecpqv2uZsBkAy26zpxx8,9494
+copick_utils/util/__init__.py,sha256=V76KYVdhERpiXkCsaap4WQBbvfXG04x3vGvdSayzpmk,190
+copick_utils/util/config_models.py,sha256=vzih8OsmvKQk8rULYyY6f6yiRHUnk48KKrCES5Pvq4w,21964
+copick_utils-1.0.0.dist-info/METADATA,sha256=dd7zA7C50YZXDF2qOOwlffYrh93CTSNK_Dokse4Uti4,4562
+copick_utils-1.0.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+copick_utils-1.0.0.dist-info/entry_points.txt,sha256=qDi4JAAncjmkB86tEivSpc9QVr6YbdFC3T0SwIabNaM,1504
+copick_utils-1.0.0.dist-info/licenses/LICENSE,sha256=3UHKsYd99Gh_qf1a9s8G5sdKqafgbGs5WIMoeX0OcdY,1105
+copick_utils-1.0.0.dist-info/RECORD,,

copick_utils-1.0.0.dist-info/entry_points.txt

@@ -0,0 +1,29 @@
+[copick.convert.commands]
+mesh2picks = copick_utils.cli.conversion_commands:mesh2picks
+mesh2seg = copick_utils.cli.conversion_commands:mesh2seg
+picks2ellipsoid = copick_utils.cli.conversion_commands:picks2ellipsoid
+picks2mesh = copick_utils.cli.conversion_commands:picks2mesh
+picks2plane = copick_utils.cli.conversion_commands:picks2plane
+picks2seg = copick_utils.cli.conversion_commands:picks2seg
+picks2sphere = copick_utils.cli.conversion_commands:picks2sphere
+picks2surface = copick_utils.cli.conversion_commands:picks2surface
+seg2mesh = copick_utils.cli.conversion_commands:seg2mesh
+seg2picks = copick_utils.cli.conversion_commands:seg2picks
+
+[copick.logical.commands]
+clipmesh = copick_utils.cli.logical_commands:clipmesh
+clippicks = copick_utils.cli.logical_commands:clippicks
+clipseg = copick_utils.cli.logical_commands:clipseg
+enclosed = copick_utils.cli.logical_commands:enclosed
+meshop = copick_utils.cli.logical_commands:meshop
+picksin = copick_utils.cli.logical_commands:picksin
+picksout = copick_utils.cli.logical_commands:picksout
+segop = copick_utils.cli.logical_commands:segop
+
+[copick.process.commands]
+filter_components = copick_utils.cli.processing_commands:filter_components
+fit_spline = copick_utils.cli.processing_commands:fit_spline
+hull = copick_utils.cli.processing_commands:hull
+separate_components = copick_utils.cli.processing_commands:separate_components
+skeletonize = copick_utils.cli.processing_commands:skeletonize
+validbox = copick_utils.cli.processing_commands:validbox

copick_utils/segmentation/picks_from_segmentation.py

@@ -1,81 +0,0 @@
-import numpy as np
-import scipy.ndimage as ndi
-from skimage.measure import regionprops
-from skimage.morphology import ball, binary_dilation, binary_erosion
-from skimage.segmentation import watershed
-
-
-def picks_from_segmentation(
-    segmentation,
-    segmentation_idx,
-    maxima_filter_size,
-    min_particle_size,
-    max_particle_size,
-    session_id,
-    user_id,
-    pickable_object,
-    run,
-    voxel_spacing=1,
-):
-    """
-    Process a specific label in the segmentation, extract centroids, and save them as picks.
-
-    Args:
-        segmentation (np.ndarray): Multilabel segmentation array.
-        segmentation_idx (int): The specific label from the segmentation to process.
-        maxima_filter_size (int): Size of the maximum detection filter.
-        min_particle_size (int): Minimum size threshold for particles.
-        max_particle_size (int): Maximum size threshold for particles.
-        session_id (str): Session ID for pick saving.
-        user_id (str): User ID for pick saving.
-        pickable_object (str): The name of the object to save picks for.
-        run: A Copick run object that manages pick saving.
-        voxel_spacing (int): The voxel spacing used to scale pick locations (default 1).
-    """
-    # Create a binary mask for the specific segmentation label
-    binary_mask = (segmentation == segmentation_idx).astype(int)
-
-    # Skip if the segmentation label is not present
-    if np.sum(binary_mask) == 0:
-        print(f"No segmentation with label {segmentation_idx} found.")
-        return
-
-    # Structuring element for erosion and dilation
-    struct_elem = ball(1)
-    eroded = binary_erosion(binary_mask, struct_elem)
-    dilated = binary_dilation(eroded, struct_elem)
-
-    # Distance transform and local maxima detection
-    distance = ndi.distance_transform_edt(dilated)
-    local_max = distance == ndi.maximum_filter(
-        distance,
-        footprint=np.ones((maxima_filter_size, maxima_filter_size, maxima_filter_size)),
-    )
-
-    # Watershed segmentation
-    markers, _ = ndi.label(local_max)
-    watershed_labels = watershed(-distance, markers, mask=dilated)
-
-    # Extract region properties and filter based on particle size
-    all_centroids = []
-    for region in regionprops(watershed_labels):
-        if min_particle_size <= region.area <= max_particle_size:
-            all_centroids.append(region.centroid)
-
-    # Save centroids as picks
-    if all_centroids:
-        pick_set = run.new_picks(pickable_object, session_id, user_id)
-
-        positions = np.array(all_centroids)[:, [2, 1, 0]] * voxel_spacing
-        pick_set.from_numpy(positions=positions)
-        pick_set.store()
-
-        print(f"Centroids for label {segmentation_idx} saved successfully.")
-        return pick_set
-    else:
-        print(f"No valid centroids found for label {segmentation_idx}.")
-        return None
-
-
-# Example call to the function
-# picks_from_segmentation(segmentation_array, label_id, 9, 1000, 50000, session_id, user_id, pickable_object_name, run_object)

copick_utils-0.6.1.dist-info/RECORD

@@ -1,14 +0,0 @@
-copick_utils/__init__.py,sha256=FqcMzBIYexR9TCNHvUyjKXblBOdEaa9-pt1fv8TNEcA,135
-copick_utils/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-copick_utils/features/skimage.py,sha256=Sz-348tTT44lLS825z14iIOM3L_tALXQctUF1HbnWnw,4209
-copick_utils/io/readers.py,sha256=bE7IBPohNjsFgD6HRPTrWte6OjaJ0NrF4RS8Dwgf3nA,5435
-copick_utils/io/writers.py,sha256=iYyNkpBgrD0_N0N-LoyCOfIrk46WHWocKvkUUQYXMRg,2985
-copick_utils/pickers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-copick_utils/pickers/grid_picker.py,sha256=KKfdv3fDmeY7XwqiVADRQJibr1eyjYoG9ZpaihcrgHw,2345
-copick_utils/segmentation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-copick_utils/segmentation/picks_from_segmentation.py,sha256=Pu3079P4LNJPQAEwsYdrJ3K_X_i1zmo_xxbu16goKAo,3007
-copick_utils/segmentation/segmentation_from_picks.py,sha256=oeP9NdOYcRATbpeKf3SkbdqbRuUEZCOPArl-KBseYc0,6991
-copick_utils-0.6.1.dist-info/METADATA,sha256=GXk4KjbVjumU8HK6nCwUuWjqR9AMrV4Vc_32S2GR5IQ,4246
-copick_utils-0.6.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-copick_utils-0.6.1.dist-info/licenses/LICENSE,sha256=3UHKsYd99Gh_qf1a9s8G5sdKqafgbGs5WIMoeX0OcdY,1105
-copick_utils-0.6.1.dist-info/RECORD,,