copick-utils 0.6.0__py3-none-any.whl → 0.6.1__py3-none-any.whl

copick_utils/__init__.py

@@ -1,3 +1,4 @@
 # SPDX-FileCopyrightText: 2024-present Kyle Harrington <czi@kyleharrington.com>
 #
 # SPDX-License-Identifier: MIT
+__version__ = "0.6.1"

copick_utils/features/skimage.py

@@ -1,19 +1,30 @@
 import numpy as np
-from skimage.feature import multiscale_basic_features
 import zarr
 from numcodecs import Blosc
+from skimage.feature import multiscale_basic_features
+
 
-def compute_skimage_features(tomogram, feature_type, copick_root, intensity=True, edges=True, texture=True, sigma_min=0.5, sigma_max=16.0, feature_chunk_size=None):
+def compute_skimage_features(
+    tomogram,
+    feature_type,
+    copick_root,
+    intensity=True,
+    edges=True,
+    texture=True,
+    sigma_min=0.5,
+    sigma_max=16.0,
+    feature_chunk_size=None,
+):
     """
     Processes the tomogram chunkwise and computes the multiscale basic features.
     Allows for optional feature chunk size.
     """
-    image = zarr.open(tomogram.zarr(), mode='r')['0']
+    image = zarr.open(tomogram.zarr(), mode="r")["0"]
     input_chunk_size = feature_chunk_size if feature_chunk_size else image.chunks
     chunk_size = input_chunk_size if len(input_chunk_size) == 3 else input_chunk_size[1:]
-    
+
     overlap = int(chunk_size[0] / 2)
-    
+
     print(f"Processing image with shape {image.shape}")
     print(f"Using chunk size: {chunk_size}, overlap: {overlap}")
 
@@ -25,7 +36,7 @@ def compute_skimage_features(tomogram, feature_type, copick_root, intensity=True
         edges=edges,
         texture=texture,
         sigma_min=sigma_min,
-        sigma_max=sigma_max
+        sigma_max=sigma_max,
     )
     num_features = test_features.shape[-1]
 
@@ -43,10 +54,10 @@ def compute_skimage_features(tomogram, feature_type, copick_root, intensity=True
     out_array = zarr.create(
         shape=(num_features, *image.shape),
         chunks=feature_chunk_size,
-        dtype='float32',
-        compressor=Blosc(cname='zstd', clevel=3, shuffle=2),
+        dtype="float32",
+        compressor=Blosc(cname="zstd", clevel=3, shuffle=2),
         store=feature_store,
-        overwrite=True
+        overwrite=True,
     )
 
     # Process each chunk
@@ -67,7 +78,7 @@ def compute_skimage_features(tomogram, feature_type, copick_root, intensity=True
                     edges=edges,
                     texture=texture,
                     sigma_min=sigma_min,
-                    sigma_max=sigma_max
+                    sigma_max=sigma_max,
                 )
 
                 # Adjust indices for overlap
@@ -78,7 +89,12 @@ def compute_skimage_features(tomogram, feature_type, copick_root, intensity=True
                 # Ensure contiguous array and correct slicing
                 contiguous_chunk = np.ascontiguousarray(chunk_features[z_slice, y_slice, x_slice].transpose(3, 0, 1, 2))
 
-                out_array[0:num_features, z:z + chunk_size[0], y:y + chunk_size[1], x:x + chunk_size[2]] = contiguous_chunk
+                out_array[
+                    0:num_features,
+                    z : z + chunk_size[0],
+                    y : y + chunk_size[1],
+                    x : x + chunk_size[2],
+                ] = contiguous_chunk
 
     print(f"Features saved under feature type '{feature_type}'")
     return copick_features
@@ -91,6 +107,10 @@ if __name__ == "__main__":
         tomogram=tomo,
         feature_type="skimageFeatures",
         copick_root=root,
-        intensity=True, edges=True, texture=True, sigma_min=0.5, sigma_max=16.0,
-        feature_chunk_size=None  # Default to detected chunk size
+        intensity=True,
+        edges=True,
+        texture=True,
+        sigma_min=0.5,
+        sigma_max=16.0,
+        feature_chunk_size=None,  # Default to detected chunk size
     )

copick_utils/io/readers.py

@@ -1,33 +1,34 @@
 import numpy as np
 
-def tomogram(run, 
-             voxel_size: float = 10, 
-             algorithm: str = 'wbp',
-             raise_error: bool = False):
-    
+
+def tomogram(run, voxel_size: float = 10, algorithm: str = "wbp", raise_error: bool = False):
     voxel_spacing_obj = run.get_voxel_spacing(voxel_size)
 
     if voxel_spacing_obj is None:
         # Query Avaiable Voxel Spacings
         availableVoxelSpacings = [tomo.voxel_size for tomo in run.voxel_spacings]
 
-        # Report to the user which voxel spacings they can use 
-        message = (f"[Warning] No tomogram found for {run.name} with voxel size {voxel_size} and tomogram type {algorithm}"
-                   f"Available spacings are: {', '.join(map(str, availableVoxelSpacings))}" ) 
+        # Report to the user which voxel spacings they can use
+        message = (
+            f"[Warning] No tomogram found for {run.name} with voxel size {voxel_size} and tomogram type {algorithm}"
+            f"Available spacings are: {', '.join(map(str, availableVoxelSpacings))}"
+        )
         if raise_error:
             raise ValueError(message)
         else:
             print(message)
             return None
-    
+
     tomogram = voxel_spacing_obj.get_tomogram(algorithm)
     if tomogram is None:
         # Get available algorithms
         availableAlgorithms = [tomo.tomo_type for tomo in run.get_voxel_spacing(voxel_size).tomograms]
-        
+
         # Report to the user which algorithms are available
-        message = (f"[Warning] No tomogram found for {run.name} with voxel size {voxel_size} and tomogram type {algorithm}"
-                   f"Available algorithms are: {', '.join(availableAlgorithms)}")
+        message = (
+            f"[Warning] No tomogram found for {run.name} with voxel size {voxel_size} and tomogram type {algorithm}"
+            f"Available algorithms are: {', '.join(availableAlgorithms)}"
+        )
         if raise_error:
             raise ValueError(message)
         else:
@@ -36,32 +37,29 @@ def tomogram(run,
 
     return tomogram.numpy()
 
-def segmentation(run, 
-                 voxel_spacing: float,
-                 segmentation_name: str, 
-                 session_id=None,
-                 user_id=None,
-                 raise_error = False):
 
-    seg = run.get_segmentations(name=segmentation_name, 
-                                session_id = session_id,
-                                user_id = user_id,
-                                voxel_size = voxel_spacing)
+def segmentation(run, voxel_spacing: float, segmentation_name: str, session_id=None, user_id=None, raise_error=False):
+    seg = run.get_segmentations(
+        name=segmentation_name,
+        session_id=session_id,
+        user_id=user_id,
+        voxel_size=voxel_spacing,
+    )
 
     # No Segmentations Are Available, Result in Error
     if len(seg) == 0:
         # Get all available segmentations with their metadata
         available_segs = run.get_segmentations(voxel_size=voxel_spacing)
         seg_info = [(s.name, s.user_id, s.session_id) for s in available_segs]
-        
+
         # Format the information for display
-        seg_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" 
-                      for name, uid, sid in seg_info]
-        
-        message = ( f'\nNo segmentation found matching:\n'
-                    f'  name: {segmentation_name}, user_id: {user_id}, session_id: {session_id}\n'
-                    f'Available segmentations in {run.name} are:\n  ' + 
-                    '\n  '.join(seg_details) )
+        seg_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in seg_info]
+
+        message = (
+            f"\nNo segmentation found matching:\n"
+            f"  name: {segmentation_name}, user_id: {user_id}, session_id: {session_id}\n"
+            f"Available segmentations in {run.name} are:\n  " + "\n  ".join(seg_details)
+        )
         if raise_error:
             raise ValueError(message)
         else:
@@ -70,20 +68,24 @@ def segmentation(run,
 
     # No Segmentations Are Available, Result in Error
     if len(seg) > 1:
-        print(f'[Warning] More Than 1 Segmentation is Available for the Query Information. '
-              f'Available Segmentations are: {seg} '
-              f'Defaulting to Loading: {seg[0]}\n')
+        print(
+            f"[Warning] More Than 1 Segmentation is Available for the Query Information. "
+            f"Available Segmentations are: {seg} "
+            f"Defaulting to Loading: {seg[0]}\n",
+        )
     seg = seg[0]
 
     return seg.numpy()
 
-def coordinates(run,                     # CoPick run object containing the segmentation data
-                name: str,               # Name of the object or protein for which coordinates are being extracted
-                user_id: str,            # Identifier of the user that generated the picks
-                session_id: str = None,  # Identifier of the session that generated the picks
-                voxel_size: float = 10,  # Voxel size of the tomogram, used for scaling the coordinates
-                raise_error: bool = False):
-                           
+
+def coordinates(
+    run,  # CoPick run object containing the segmentation data
+    name: str,  # Name of the object or protein for which coordinates are being extracted
+    user_id: str,  # Identifier of the user that generated the picks
+    session_id: str = None,  # Identifier of the session that generated the picks
+    voxel_size: float = 10,  # Voxel size of the tomogram, used for scaling the coordinates
+    raise_error: bool = False,
+):
     # Retrieve the pick points associated with the specified object and user ID
     picks = run.get_picks(object_name=name, user_id=user_id, session_id=session_id)
 
@@ -92,15 +94,15 @@ def coordinates(run,                     # CoPick run object containing the segm
 
         available_picks = run.get_picks()
         picks_info = [(s.pickable_object_name, s.user_id, s.session_id) for s in available_picks]
-        
+
         # Format the information for display
-        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" 
-                      for name, uid, sid in picks_info]
-        
-        message = ( f'\nNo picks found matching:\n'
-                    f'  name: {name}, user_id: {user_id}, session_id: {session_id}\n'
-                    f'Available picks are:\n  '  
-                    + '\n  '.join(picks_details) )
+        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
+
+        message = (
+            f"\nNo picks found matching:\n"
+            f"  name: {name}, user_id: {user_id}, session_id: {session_id}\n"
+            f"Available picks are:\n  " + "\n  ".join(picks_details)
+        )
         if raise_error:
             raise ValueError(message)
         else:
@@ -109,24 +111,25 @@ def coordinates(run,                     # CoPick run object containing the segm
     elif len(picks) > 1:
         # Format pick information for display
         picks_info = [(p.pickable_object_name, p.user_id, p.session_id) for p in picks]
-        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" 
-                        for name, uid, sid in picks_info]
+        picks_details = [f"(name: {name}, user_id: {uid}, session_id: {sid})" for name, uid, sid in picks_info]
 
-        print(f'[Warning] More than 1 pick is available for the query information.'
-              f'\nAvailable picks are:\n  ' + 
-              '\n  '.join(picks_details) +
-              f'\nDefaulting to loading:\n {picks[0]}\n')
+        print(
+            "[Warning] More than 1 pick is available for the query information."
+            "\nAvailable picks are:\n  " + "\n  ".join(picks_details) + f"\nDefaulting to loading:\n {picks[0]}\n",
+        )
     points = picks[0].points
 
     # Initialize an array to store the coordinates
-    nPoints = len(picks[0].points)                      # Number of points retrieved
-    coordinates = np.zeros([len(picks[0].points), 3])   # Create an empty array to hold the (z, y, x) coordinates
+    nPoints = len(picks[0].points)  # Number of points retrieved
+    coordinates = np.zeros([len(picks[0].points), 3])  # Create an empty array to hold the (z, y, x) coordinates
 
     # Iterate over all points and convert their locations to coordinates in voxel space
     for ii in range(nPoints):
-        coordinates[ii,] = [points[ii].location.z / voxel_size,   # Scale z-coordinate by voxel size
-                            points[ii].location.y / voxel_size,   # Scale y-coordinate by voxel size
-                            points[ii].location.x / voxel_size]   # Scale x-coordinate by voxel size
+        coordinates[ii,] = [
+            points[ii].location.z / voxel_size,  # Scale z-coordinate by voxel size
+            points[ii].location.y / voxel_size,  # Scale y-coordinate by voxel size
+            points[ii].location.x / voxel_size,
+        ]  # Scale x-coordinate by voxel size
 
     # Return the array of coordinates
     return coordinates

copick_utils/io/writers.py

@@ -1,12 +1,7 @@
-from typing import Any, Dict, List
 import numpy as np
 
-def tomogram(
-    run,
-    input_volume,
-    voxel_size=10,
-    algorithm="wbp"
-):
+
+def tomogram(run, input_volume, voxel_size=10, algorithm="wbp"):
     """
     Writes a volumetric tomogram into an OME-Zarr format within a Copick directory.
 
@@ -26,17 +21,17 @@ def tomogram(
     copick.Tomogram
         The created or modified tomogram object.
     """
-    
+
     # Retrieve or create voxel spacing
     voxel_spacing = run.get_voxel_spacing(voxel_size)
     if voxel_spacing is None:
         voxel_spacing = run.new_voxel_spacing(voxel_size=voxel_size)
-    
+
     # Check if We Need to Create a New Tomogram for Given Algorithm
     tomogram = voxel_spacing.get_tomogram(algorithm)
     if tomogram is None:
         tomogram = voxel_spacing.new_tomogram(tomo_type=algorithm)
-    
+
     # Write the tomogram data
     tomogram.from_numpy(input_volume)
 
@@ -48,7 +43,7 @@ def segmentation(
     name="segmentation",
     session_id="0",
     voxel_size=10,
-    multilabel=True
+    multilabel=True,
 ):
     """
     Writes a segmentation into an OME-Zarr format within a Copick directory.
@@ -75,7 +70,7 @@ def segmentation(
     copick.Segmentation
         The created or modified segmentation object.
     """
-    
+
     # Retrieve or create a segmentation
     segmentations = run.get_segmentations(name=name, user_id=user_id, session_id=session_id)
 
@@ -86,11 +81,11 @@ def segmentation(
             name=name,
             session_id=session_id,
             is_multilabel=multilabel,
-            user_id=user_id
+            user_id=user_id,
         )
     else:
         # Overwrite the current segmentation at the specified voxel size if it exists
         segmentation = next(seg for seg in segmentations if seg.voxel_size == voxel_size)
-    
+
     # Write the segmentation data
     segmentation.from_numpy(segmentation_volume, dtype=np.uint8)

copick_utils/pickers/grid_picker.py

@@ -2,6 +2,7 @@ import numpy as np
 import zarr
 from copick.models import CopickPoint
 
+
 def grid_picker(pickable_obj, run, tomogram, grid_spacing_factor, session_id="0", user_id="gridPicker"):
     """
     Creates a grid of picks for a pickable object based on a tomogram and grid spacing factor.
@@ -28,14 +29,14 @@ def grid_picker(pickable_obj, run, tomogram, grid_spacing_factor, session_id="0"
     grid_spacing = radius * grid_spacing_factor
 
     # Open the highest resolution of the tomogram
-    image = zarr.open(tomogram.zarr(), mode='r')['0']
+    image = zarr.open(tomogram.zarr(), mode="r")["0"]
 
     # Create a grid of points
     points = []
     for z in np.arange(0, image.shape[0], grid_spacing):
         for y in np.arange(0, image.shape[1], grid_spacing):
             for x in np.arange(0, image.shape[2], grid_spacing):
-                points.append(CopickPoint(location={'x': x, 'y': y, 'z': z}))
+                points.append(CopickPoint(location={"x": x, "y": y, "z": z}))
 
     # Save the picks
     pick_set = run.new_picks(obj_name, session_id, user_id)
@@ -45,6 +46,7 @@ def grid_picker(pickable_obj, run, tomogram, grid_spacing_factor, session_id="0"
     print(f"Saved {len(points)} grid points for object {obj_name}.")
     return pick_set
 
+
 if __name__ == "__main__":
     import copick
 
@@ -65,5 +67,4 @@ if __name__ == "__main__":
     tomogram = voxel_spacing_obj.get_tomogram(tomo_type)
 
     for pickable_obj in root.pickable_objects:
-        create_grid_of_picks(pickable_obj, run, tomogram, grid_spacing_factor, session_id, user_id)
-
+        grid_picker(pickable_obj, run, tomogram, grid_spacing_factor, session_id, user_id)

copick_utils/segmentation/picks_from_segmentation.py

@@ -1,11 +1,22 @@
 import numpy as np
 import scipy.ndimage as ndi
-from skimage.segmentation import watershed
 from skimage.measure import regionprops
-from skimage.morphology import binary_erosion, binary_dilation, ball
+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):
+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.
 
@@ -36,7 +47,10 @@ def picks_from_segmentation(segmentation, segmentation_idx, maxima_filter_size,
 
     # 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))))
+    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)
@@ -55,7 +69,7 @@ def picks_from_segmentation(segmentation, segmentation_idx, maxima_filter_size,
         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:

copick_utils/segmentation/segmentation_from_picks.py

@@ -1,13 +1,9 @@
 import numpy as np
 import zarr
 from scipy.ndimage import zoom
-import copick
 
-def from_picks(pick,
-               seg_volume,
-               radius: float = 10.0,
-               label_value: int = 1,
-               voxel_spacing: float = 10):
+
+def from_picks(pick, seg_volume, radius: float = 10.0, label_value: int = 1, voxel_spacing: float = 10):
     """
     Paints picks into a segmentation volume as spheres.
 
@@ -26,12 +22,13 @@ def from_picks(pick,
     Returns:
     --------
     numpy.ndarray
-        The modified segmentation volume with spheres inserted at pick locations.    
+        The modified segmentation volume with spheres inserted at pick locations.
     """
+
     def create_sphere(shape, center, radius, val):
         zc, yc, xc = center
         z, y, x = np.indices(shape)
-        distance_sq = (x - xc)**2 + (y - yc)**2 + (z - zc)**2
+        distance_sq = (x - xc) ** 2 + (y - yc) ** 2 + (z - zc) ** 2
         sphere = np.zeros(shape, dtype=np.float32)
         sphere[distance_sq <= radius**2] = val
         return sphere
@@ -48,7 +45,11 @@ def from_picks(pick,
     # Paint each pick as a sphere
     for point in pick.points:
         # Convert the pick's location from angstroms to voxel units
-        cx, cy, cz = point.location.x / voxel_spacing, point.location.y / voxel_spacing, point.location.z / voxel_spacing
+        cx, cy, cz = (
+            point.location.x / voxel_spacing,
+            point.location.y / voxel_spacing,
+            point.location.z / voxel_spacing,
+        )
 
         # Calculate subarray bounds
         xLow, xHigh = get_relative_target_coordinates(cx, delta, seg_volume.shape[2])
@@ -65,7 +66,10 @@ def from_picks(pick,
         sphere = create_sphere(subarray_shape, local_center, radius_voxel, label_value)
 
         # Assign Sphere to Segmentation Target Volume
-        seg_volume[zLow:zHigh, yLow:yHigh, xLow:xHigh] = np.maximum(seg_volume[zLow:zHigh, yLow:yHigh, xLow:xHigh], sphere)
+        seg_volume[zLow:zHigh, yLow:yHigh, xLow:xHigh] = np.maximum(
+            seg_volume[zLow:zHigh, yLow:yHigh, xLow:xHigh],
+            sphere,
+        )
 
     return seg_volume
 
@@ -79,7 +83,17 @@ def downsample_to_exact_shape(array, target_shape):
     return zoom(array, zoom_factors, order=0)
 
 
-def segmentation_from_picks(radius, painting_segmentation_name, run, voxel_spacing, tomo_type, pickable_object, pick_set, user_id="paintedPicks", session_id="0"):
+def segmentation_from_picks(
+    radius,
+    painting_segmentation_name,
+    run,
+    voxel_spacing,
+    tomo_type,
+    pickable_object,
+    pick_set,
+    user_id="paintedPicks",
+    session_id="0",
+):
     """
     Paints picks from a run into a multiscale segmentation array, representing them as spheres in 3D space.
 
@@ -115,7 +129,13 @@ def segmentation_from_picks(radius, painting_segmentation_name, run, voxel_spaci
         raise ValueError("Tomogram not found for the given parameters.")
 
     # Use copick to create a new segmentation if one does not exist
-    segs = run.get_segmentations(user_id=user_id, session_id=session_id, is_multilabel=True, name=painting_segmentation_name, voxel_size=voxel_spacing)
+    segs = run.get_segmentations(
+        user_id=user_id,
+        session_id=session_id,
+        is_multilabel=True,
+        name=painting_segmentation_name,
+        voxel_size=voxel_spacing,
+    )
     if len(segs) == 0:
         seg = run.new_segmentation(voxel_spacing, painting_segmentation_name, session_id, True, user_id=user_id)
     else:
@@ -142,7 +162,7 @@ def segmentation_from_picks(radius, painting_segmentation_name, run, voxel_spaci
     segmentation_group[highest_res_name][:] = highest_res_seg
 
     # Downsample to create lower resolution scales
-    multiscale_metadata = tomogram_zarr.attrs.get('multiscales', [{}])[0].get('datasets', [])
+    multiscale_metadata = tomogram_zarr.attrs.get("multiscales", [{}])[0].get("datasets", [])
     for level_index, level_metadata in enumerate(multiscale_metadata):
         if level_index == 0:
             continue
@@ -154,7 +174,13 @@ def segmentation_from_picks(radius, painting_segmentation_name, run, voxel_spaci
         scaled_array = downsample_to_exact_shape(highest_res_seg, expected_shape)
 
         # Create/overwrite the Zarr array for this level
-        segmentation_group.create_dataset(level_name, shape=expected_shape, data=scaled_array, dtype=np.uint16, overwrite=True)
+        segmentation_group.create_dataset(
+            level_name,
+            shape=expected_shape,
+            data=scaled_array,
+            dtype=np.uint16,
+            overwrite=True,
+        )
 
         segmentation_group[level_name][:] = scaled_array
 

{copick_utils-0.6.0.dist-info → copick_utils-0.6.1.dist-info}/METADATA

@@ -1,15 +1,25 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: copick-utils
-Version: 0.6.0
+Version: 0.6.1
 Summary: Utilities for copick
-License: MIT
-Author: Kyle Harrington
-Author-email: czi@kyleharrington.com
-Requires-Python: >=3.9
+Project-URL: Repository, https://github.com/KyleHarrington/copick-utils.git
+Project-URL: Issues, https://github.com/KyleHarrington/copick-utils/issues
+Project-URL: Documentation, https://github.com/KyleHarrington/copick-utils#readme
+Author-email: Kyle Harrington <czi@kyleharrington.com>, Jonathan Schwartz <jonathan.schwartz@czii.org>
+License: MIT License
+        
+        Copyright (c) 2024-present Kyle Harrington <czi@kyleharrington.com>
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+License-File: LICENSE
+Keywords: annotation,copick,cryo-et,cryoet,tomography,utilities
 Classifier: Development Status :: 4 - Beta
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
@@ -17,10 +27,14 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
-Requires-Dist: copick (>=0.8.0)
-Project-URL: Documentation, https://github.com/KyleHarrington/copick-utils#readme
-Project-URL: Issues, https://github.com/KyleHarrington/copick-utils/issues
-Project-URL: Source, https://github.com/KyleHarrington/copick-utils
+Requires-Python: >=3.9
+Requires-Dist: copick>=0.8.0
+Provides-Extra: dev
+Requires-Dist: black>=25.1.0; extra == 'dev'
+Requires-Dist: hatch-vcs>=0.4.0; extra == 'dev'
+Requires-Dist: hatchling>=1.25.0; extra == 'dev'
+Requires-Dist: pre-commit>=4.2.0; extra == 'dev'
+Requires-Dist: ruff>=0.12.0; extra == 'dev'
 Description-Content-Type: text/markdown
 
 # copick-utils
@@ -69,4 +83,3 @@ This project adheres to the Contributor Covenant [code of conduct](https://githu
 ## Reporting Security Issues
 
 If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
-

copick_utils-0.6.1.dist-info/RECORD

@@ -0,0 +1,14 @@
+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,,

{copick_utils-0.6.0.dist-info → copick_utils-0.6.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any

copick_utils/__about__.py

@@ -1,4 +0,0 @@
-# SPDX-FileCopyrightText: 2024-present Kyle Harrington <czi@kyleharrington.com>
-#
-# SPDX-License-Identifier: MIT
-__version__ = "0.0.1"

copick_utils-0.6.0.dist-info/RECORD

@@ -1,15 +0,0 @@
-copick_utils/__about__.py,sha256=7D13PJEcpdhEa6RrlKLt7IEkoVVVGuzqHJb5MQxgLiI,135
-copick_utils/__init__.py,sha256=v-RIkEuGuAXivakLMrneraDQd7cWN7zsdGLmjwLtDDw,113
-copick_utils/features/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-copick_utils/features/skimage.py,sha256=t38jpu-ntC7Zw--1qSxWhGIg9e02RLhVBZEySIa5dQs,4036
-copick_utils/io/readers.py,sha256=ajqe64e5tp67iZoqSV6AsjpGX25Rdz_q0tX8qXVVp7g,5902
-copick_utils/io/writers.py,sha256=KhdZUUZrZR02bzS5SWM9q-u4y2s1qxcySwN3MN5j5YA,3055
-copick_utils/pickers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-copick_utils/pickers/grid_picker.py,sha256=NhFbWxMQREb0fLKTho4602yzH7zE6DCkJY94dgJ-gIQ,2353
-copick_utils/segmentation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-copick_utils/segmentation/picks_from_segmentation.py,sha256=Ne_RYfnEFaV_qwNw4uOwPfLLgGxHMEQ2uecp9X2_EVc,2951
-copick_utils/segmentation/segmentation_from_picks.py,sha256=3oIlFWRAR904j5IpC5Fo8Y4gP9iL6qUiwybRgJvhzmc,6820
-copick_utils-0.6.0.dist-info/LICENSE.txt,sha256=3UHKsYd99Gh_qf1a9s8G5sdKqafgbGs5WIMoeX0OcdY,1105
-copick_utils-0.6.0.dist-info/METADATA,sha256=TwbWK0CmHk8pB7tI401f3khfIG8mMEtTENOg2b1brOY,2742
-copick_utils-0.6.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-copick_utils-0.6.0.dist-info/RECORD,,