copick 0.4.0__tar.gz

copick-0.4.0/.gitignore

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copick-0.4.0/.pre-commit-config.yaml

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+repos:
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 23.9.1
+  hooks:
+  - id: black
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.0.292
+  hooks:
+  - id: ruff
+    args:
+    - --fix
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+  - id: check-toml
+  - id: check-yaml
+  - id: check-json
+  - id: check-merge-conflict
+  - id: end-of-file-fixer
+  - id: trailing-whitespace

copick-0.4.0/LICENSE

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+MIT License
+
+Copyright (c) 2024 Utz Ermel
+
+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.

copick-0.4.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: copick
+Version: 0.4.0
+Summary: Definitions for a collaborative cryoET annotation tool.
+Project-URL: Repository, https://github.com/uermel/copick.git
+Project-URL: Issues, https://github.com/uermel/copick/issues
+Author-email: "Utz H. Ermel" <utz.ermel@czii.org>, "Kyle I. S. Harrington" <kyle@kyleharrington.com>
+License: MIT License
+        
+        Copyright (c) 2024 Utz Ermel
+        
+        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,collaborative,copick,cryo-et,cryoet,segmentation,tomography
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.10
+Requires-Dist: fsspec
+Requires-Dist: numpy
+Requires-Dist: pydantic
+Requires-Dist: qtpy
+Requires-Dist: trimesh
+Requires-Dist: zarr
+Provides-Extra: dev
+Requires-Dist: black; extra == 'dev'
+Requires-Dist: ipython; extra == 'dev'
+Requires-Dist: notebook; extra == 'dev'
+Requires-Dist: pre-commit; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# copick
+Definitions for a collaborative cryoET annotation tool.
+
+## Data Spec
+
+Shared data is organized as follows:
+
+```
+[copick_root]/
+|-- copick_config.json (spec: src/models.py:CopickConfig)
+|-- ParticleMrcs/
+    |-- [object_id]_[object_name].mrc (index: src/models.py:CopickConfig.pickable_objects.object_name)
+|-- ExperimentRuns
+    |-- [run_name]/ (index: src/io/copick_models.py:CopickPicks.runs)
+        |-- VoxelSpacing[xx.yyy]/
+        |   |-- [tomotype].zarr/
+        |   |   |-- [multiscale subdirectories according to OME-NGFF spec at 100%, 50% and 25% scale]
+        |   |-- [tomotype]_[feature_type]_features.zarr/
+        |       |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale]
+        |-- VoxelSpacing[x2.yy2]/
+        |   |-- [tomotype].zarr/
+        |   |   |-- [multiscale subdirectories according to OME-NGFF spec at 100%, 50% and 25% scale]
+        |   |-- [tomotype]_[feature_type]_features.zarr/
+        |       |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale]
+        |-- Picks/
+        |   |-- [user_id | tool_name]_[session_id | 0]_[object_name].json (spec: src/models.py:CopickPicks)
+        |-- Meshes/
+        |   |-- [user_id | tool_name]_[session_id | 0]_[object_name].glb (spec: src/models.py:TBD)
+        |-- Segmentations/
+            |-- [xx.yyy]_[user_id | tool_name]_[session_id | 0]_[object_name].zarr (spec: src/models.py:TBD)
+            |   |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale, 50% and 25% scale]
+            |-- [xx.yyy]_[user_id | tool_name]_[session_id | 0]_[name]-multilabel.zarr (spec: src/models.py:TBD)
+                |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale, 50% and 25% scale]
+```
+
+## Sample Data
+
+A test set is hosted on [zenodo](https://doi.org/10.5281/zenodo.10905908).
+
+The fsspec implementation allows the dataset to be split into a static and an overlay part. The static part is read-only
+and contains the original data. The overlay part is read-write and contains the user-specific annotations.
+
+### Config for identical location
+
+```json
+{
+    "name": "test",
+    "description": "A test project.",
+    "version": "1.0.0",
+
+    "pickable_objects": [
+        {
+            "name": "proteasome",
+            "is_particle": true,
+            "pdb_id": "3J9I",
+            "label": 1,
+            "color": [255, 0, 0, 255]
+        },
+        {
+            "name": "ribosome",
+            "is_particle": true,
+            "pdb_id": "7P6Z",
+            "label": 2,
+            "color": [0, 255, 0, 255]
+        },
+        {
+            "name": "membrane",
+            "is_particle": false,
+            "label": 3,
+            "color": [0, 0, 0, 255]
+        }
+    ],
+
+    "overlay_root": "local:///PATH/TO/sample_project",
+    "static_root": "local:///PATH/TO/sample_project",
+
+    "overlay_fs_args": {
+        "auto_mkdir": true
+    }
+}
+```
+
+### Config for static remote and mutable local dataset
+
+This has the additional `s3fs` requirement.
+
+```json
+{
+    "name": "test",
+    "description": "A test project.",
+    "version": "1.0.0",
+
+    "pickable_objects": [
+        {
+            "name": "proteasome",
+            "is_particle": true,
+            "pdb_id": "3J9I",
+            "label": 1,
+            "color": [255, 0, 0, 255]
+        },
+        {
+            "name": "ribosome",
+            "is_particle": true,
+            "pdb_id": "7P6Z",
+            "label": 2,
+            "color": [0, 255, 0, 255]
+        },
+        {
+            "name": "membrane",
+            "is_particle": false,
+            "label": 3,
+            "color": [0, 0, 0, 255]
+        }
+    ],
+
+    "overlay_root": "local:///PATH/TO/sample_project",
+    "static_root": "s3://bucket/path/to/sample_project",
+
+    "overlay_fs_args": {
+        "auto_mkdir": true
+    }
+}
+```
+
+### API overview
+```python
+from copick.impl.filesystem import CopickRootFSSpec
+import zarr
+
+# Project root
+root = CopickRootFSSpec.from_file("/PATH/TO/sample_project/copick_config_filesystem.json")
+
+## Root API
+root.config # CopickConfig object
+root.runs # List of run objects (lazy loading from filesystem location(s))
+root.get_run("run_name") # Get a run by name
+run = root.new_run("run_name") # Create a new run (appends to the list of runs and creates directory in overlay fs location)
+root.refresh() # Refresh the list of runs from filesystem location(s)
+
+## Run API
+# Hierarchical objects (lazy loading from filesystem location(s))
+run.picks # List of pick objects
+run.meshes # List of mesh objects
+run.segmentations # List of segmentation objects
+run.voxel_spacings # List of voxel spacing objects
+
+# Create new objects
+run.new_pick("user_id", "session_id", "object_name") # Create a new pick object (appends to the list of picks and creates file in overlay fs location)
+run.new_mesh("user_id", "session_id", "object_name") # Create a new mesh object (appends to the list of meshes and creates file in overlay fs location)
+run.new_segmentation("user_id", "session_id") # Create a new segmentation object (appends to the list of segmentations and creates zarr file in overlay fs location)
+run.new_voxel_spacing(10.000) # Create a new voxel spacing object (appends to the list of voxel spacings and creates directory in overlay fs location)
+
+# Get objects by name
+run.get_picks(object_name="object_name") # Get all picks (list) for this run with a given object name
+# ... similar for meshes, segmentations, voxel spacings
+
+## Pick API
+pick = run.picks[0] # Get a pick object
+pick.points # List of CopickPoint objects
+
+## Mesh API
+mesh = run.meshes[0] # Get a mesh object
+mesh.mesh # Trimesh scene object
+
+## Segmentation API
+segmentation = run.segmentations[0] # Get a segmentation object
+segmentation.zarr() # zarr.storage.FSStore object
+
+## VoxelSpacing API
+voxel_spacing = run.voxel_spacings[0] # Get a voxel spacing object
+voxel_spacing.tomograms # List of CopickTomogram objects
+
+## Tomogram API
+tomogram = voxel_spacing.tomograms[0] # Get a tomogram object
+tomogram.zarr() # zarr.storage.FSStore object
+tomogram.features # List of CopickTomogramFeature objects
+
+
+# Example usage
+# List of runs
+print(root.runs)
+
+# Points
+print(root.runs[0].picks[0].points)
+
+# List of meshes
+print(root.runs[0].meshes)
+
+# List of segmentations
+print(root.runs[0].segmentations)
+
+# List of voxel spacings
+print(root.runs[0].voxel_spacings)
+
+# List of tomograms
+print(root.runs[0].voxel_spacings[0].tomograms)
+
+# Get Zarr store for a tomogram
+print(zarr.open_group(root.runs[0].voxel_spacings[0].tomograms[0].zarr()).info)
+
+# Get Zarr store for a tomogram feature
+print(root.runs[0].voxel_spacings[0].tomograms[1].features)
+print(zarr.open_group(root.runs[0].voxel_spacings[0].tomograms[1].features[0].zarr()).info)
+
+# Get a pick file's contents
+print(root.runs[0].picks[0].load())
+
+# Get a mesh file's contents
+print(root.runs[0].meshes[0].mesh)
+
+# Get a Zarr store for a segmentation
+print(root.runs[0].segmentations[0].path)
+print(zarr.open_group(root.runs[0].segmentations[0].zarr()).info)
+
+```

copick-0.4.0/README.md

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+# copick
+Definitions for a collaborative cryoET annotation tool.
+
+## Data Spec
+
+Shared data is organized as follows:
+
+```
+[copick_root]/
+|-- copick_config.json (spec: src/models.py:CopickConfig)
+|-- ParticleMrcs/
+    |-- [object_id]_[object_name].mrc (index: src/models.py:CopickConfig.pickable_objects.object_name)
+|-- ExperimentRuns
+    |-- [run_name]/ (index: src/io/copick_models.py:CopickPicks.runs)
+        |-- VoxelSpacing[xx.yyy]/
+        |   |-- [tomotype].zarr/
+        |   |   |-- [multiscale subdirectories according to OME-NGFF spec at 100%, 50% and 25% scale]
+        |   |-- [tomotype]_[feature_type]_features.zarr/
+        |       |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale]
+        |-- VoxelSpacing[x2.yy2]/
+        |   |-- [tomotype].zarr/
+        |   |   |-- [multiscale subdirectories according to OME-NGFF spec at 100%, 50% and 25% scale]
+        |   |-- [tomotype]_[feature_type]_features.zarr/
+        |       |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale]
+        |-- Picks/
+        |   |-- [user_id | tool_name]_[session_id | 0]_[object_name].json (spec: src/models.py:CopickPicks)
+        |-- Meshes/
+        |   |-- [user_id | tool_name]_[session_id | 0]_[object_name].glb (spec: src/models.py:TBD)
+        |-- Segmentations/
+            |-- [xx.yyy]_[user_id | tool_name]_[session_id | 0]_[object_name].zarr (spec: src/models.py:TBD)
+            |   |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale, 50% and 25% scale]
+            |-- [xx.yyy]_[user_id | tool_name]_[session_id | 0]_[name]-multilabel.zarr (spec: src/models.py:TBD)
+                |-- [multiscale subdirectories according to OME-NGFF spec at 100% scale, 50% and 25% scale]
+```
+
+## Sample Data
+
+A test set is hosted on [zenodo](https://doi.org/10.5281/zenodo.10905908).
+
+The fsspec implementation allows the dataset to be split into a static and an overlay part. The static part is read-only
+and contains the original data. The overlay part is read-write and contains the user-specific annotations.
+
+### Config for identical location
+
+```json
+{
+    "name": "test",
+    "description": "A test project.",
+    "version": "1.0.0",
+
+    "pickable_objects": [
+        {
+            "name": "proteasome",
+            "is_particle": true,
+            "pdb_id": "3J9I",
+            "label": 1,
+            "color": [255, 0, 0, 255]
+        },
+        {
+            "name": "ribosome",
+            "is_particle": true,
+            "pdb_id": "7P6Z",
+            "label": 2,
+            "color": [0, 255, 0, 255]
+        },
+        {
+            "name": "membrane",
+            "is_particle": false,
+            "label": 3,
+            "color": [0, 0, 0, 255]
+        }
+    ],
+
+    "overlay_root": "local:///PATH/TO/sample_project",
+    "static_root": "local:///PATH/TO/sample_project",
+
+    "overlay_fs_args": {
+        "auto_mkdir": true
+    }
+}
+```
+
+### Config for static remote and mutable local dataset
+
+This has the additional `s3fs` requirement.
+
+```json
+{
+    "name": "test",
+    "description": "A test project.",
+    "version": "1.0.0",
+
+    "pickable_objects": [
+        {
+            "name": "proteasome",
+            "is_particle": true,
+            "pdb_id": "3J9I",
+            "label": 1,
+            "color": [255, 0, 0, 255]
+        },
+        {
+            "name": "ribosome",
+            "is_particle": true,
+            "pdb_id": "7P6Z",
+            "label": 2,
+            "color": [0, 255, 0, 255]
+        },
+        {
+            "name": "membrane",
+            "is_particle": false,
+            "label": 3,
+            "color": [0, 0, 0, 255]
+        }
+    ],
+
+    "overlay_root": "local:///PATH/TO/sample_project",
+    "static_root": "s3://bucket/path/to/sample_project",
+
+    "overlay_fs_args": {
+        "auto_mkdir": true
+    }
+}
+```
+
+### API overview
+```python
+from copick.impl.filesystem import CopickRootFSSpec
+import zarr
+
+# Project root
+root = CopickRootFSSpec.from_file("/PATH/TO/sample_project/copick_config_filesystem.json")
+
+## Root API
+root.config # CopickConfig object
+root.runs # List of run objects (lazy loading from filesystem location(s))
+root.get_run("run_name") # Get a run by name
+run = root.new_run("run_name") # Create a new run (appends to the list of runs and creates directory in overlay fs location)
+root.refresh() # Refresh the list of runs from filesystem location(s)
+
+## Run API
+# Hierarchical objects (lazy loading from filesystem location(s))
+run.picks # List of pick objects
+run.meshes # List of mesh objects
+run.segmentations # List of segmentation objects
+run.voxel_spacings # List of voxel spacing objects
+
+# Create new objects
+run.new_pick("user_id", "session_id", "object_name") # Create a new pick object (appends to the list of picks and creates file in overlay fs location)
+run.new_mesh("user_id", "session_id", "object_name") # Create a new mesh object (appends to the list of meshes and creates file in overlay fs location)
+run.new_segmentation("user_id", "session_id") # Create a new segmentation object (appends to the list of segmentations and creates zarr file in overlay fs location)
+run.new_voxel_spacing(10.000) # Create a new voxel spacing object (appends to the list of voxel spacings and creates directory in overlay fs location)
+
+# Get objects by name
+run.get_picks(object_name="object_name") # Get all picks (list) for this run with a given object name
+# ... similar for meshes, segmentations, voxel spacings
+
+## Pick API
+pick = run.picks[0] # Get a pick object
+pick.points # List of CopickPoint objects
+
+## Mesh API
+mesh = run.meshes[0] # Get a mesh object
+mesh.mesh # Trimesh scene object
+
+## Segmentation API
+segmentation = run.segmentations[0] # Get a segmentation object
+segmentation.zarr() # zarr.storage.FSStore object
+
+## VoxelSpacing API
+voxel_spacing = run.voxel_spacings[0] # Get a voxel spacing object
+voxel_spacing.tomograms # List of CopickTomogram objects
+
+## Tomogram API
+tomogram = voxel_spacing.tomograms[0] # Get a tomogram object
+tomogram.zarr() # zarr.storage.FSStore object
+tomogram.features # List of CopickTomogramFeature objects
+
+
+# Example usage
+# List of runs
+print(root.runs)
+
+# Points
+print(root.runs[0].picks[0].points)
+
+# List of meshes
+print(root.runs[0].meshes)
+
+# List of segmentations
+print(root.runs[0].segmentations)
+
+# List of voxel spacings
+print(root.runs[0].voxel_spacings)
+
+# List of tomograms
+print(root.runs[0].voxel_spacings[0].tomograms)
+
+# Get Zarr store for a tomogram
+print(zarr.open_group(root.runs[0].voxel_spacings[0].tomograms[0].zarr()).info)
+
+# Get Zarr store for a tomogram feature
+print(root.runs[0].voxel_spacings[0].tomograms[1].features)
+print(zarr.open_group(root.runs[0].voxel_spacings[0].tomograms[1].features[0].zarr()).info)
+
+# Get a pick file's contents
+print(root.runs[0].picks[0].load())
+
+# Get a mesh file's contents
+print(root.runs[0].meshes[0].mesh)
+
+# Get a Zarr store for a segmentation
+print(root.runs[0].segmentations[0].path)
+print(zarr.open_group(root.runs[0].segmentations[0].zarr()).info)
+
+```