copick-utils 0.5.0__tar.gz → 0.6.0__tar.gz

{copick_utils-0.5.0 → copick_utils-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: copick-utils
-Version: 0.5.0
+Version: 0.6.0
 Summary: Utilities for copick
 License: MIT
 Author: Kyle Harrington
@@ -15,7 +15,6 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Requires-Dist: copick (>=0.8.0)

{copick_utils-0.5.0 → copick_utils-0.6.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "copick-utils"
-version = "0.5.0"
+version = "0.6.0"
 description = "Utilities for copick"
 readme = "README.md"
 license = "MIT"
@@ -16,11 +16,11 @@ authors = [
 classifiers = [
   "Development Status :: 4 - Beta",
   "Programming Language :: Python",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: Implementation :: CPython",
   "Programming Language :: Python :: Implementation :: PyPy",
 ]

copick_utils-0.6.0/src/copick_utils/io/readers.py

@@ -0,0 +1,132 @@
+import numpy as np
+
+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))}" ) 
+        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)}")
+        if raise_error:
+            raise ValueError(message)
+        else:
+            print(message)
+            return None
+
+    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)
+
+    # 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) )
+        if raise_error:
+            raise ValueError(message)
+        else:
+            print(message)
+            return None
+
+    # 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')
+    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):
+                           
+    # 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)
+
+    if len(picks) == 0:
+        # Get all available segmentations with their metadata
+
+        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) )
+        if raise_error:
+            raise ValueError(message)
+        else:
+            print(message)
+            return None
+    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]
+
+        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')
+    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
+
+    # 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
+
+    # Return the array of coordinates
+    return coordinates