cellfinder 1.3.0rc1__tar.gz → 1.3.1__tar.gz

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/.github/workflows/test_and_deploy.yml

@@ -44,15 +44,15 @@ jobs:
       matrix:
         # Run all supported Python versions on linux
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         # Include one windows and two macOS (intel based and arm based) runs
         include:
           - os: macos-13
-            python-version: "3.11"
+            python-version: "3.12"
           - os: macos-latest
-            python-version: "3.11"
+            python-version: "3.12"
           - os: windows-latest
-            python-version: "3.11"
+            python-version: "3.12"
 
     steps:
       - name: Cache brainglobe directory
@@ -98,7 +98,7 @@ jobs:
       # Run test suite with numba disabled
       - uses: neuroinformatics-unit/actions/test@v2
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
@@ -125,10 +125,10 @@ jobs:
         with:
           repository: 'brainglobe/brainglobe-workflows'
 
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v3
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install test dependencies
         run: |

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/.github/workflows/test_include_guard.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: '3.12'
 
       - name: Install cellfinder via pip
         run: python -m pip install -e "."

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc1
+Version: 1.3.1
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -16,11 +16,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 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
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: brainglobe-utils>=0.5.0
@@ -101,8 +101,14 @@ pip install cellfinder>=1.0.0
 Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
 See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
 
-## Contributing
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
-If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).
+## Citation
+If you find this package useful, and use it in your research, please cite the following paper:
+> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
+[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 
-If you are interested in contributing to cellfinder (thank you!) - please head over to our [developer documentation](https://brainglobe.info/community/developers/index.html).
+**If you use this, or any other tools in the brainglobe suite, please
+ [let us know](https://brainglobe.info/contact.html), and
+ we'd be happy to promote your paper/talk etc.**

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/README.md

@@ -44,8 +44,14 @@ pip install cellfinder>=1.0.0
 Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
 See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
 
-## Contributing
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
-If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).
+## Citation
+If you find this package useful, and use it in your research, please cite the following paper:
+> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
+[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 
-If you are interested in contributing to cellfinder (thank you!) - please head over to our [developer documentation](https://brainglobe.info/community/developers/index.html).
+**If you use this, or any other tools in the brainglobe suite, please
+ [let us know](https://brainglobe.info/contact.html), and
+ we'd be happy to promote your paper/talk etc.**

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/__init__.py

@@ -26,6 +26,7 @@ except PackageNotFoundError as e:
 
 # Set the Keras backend to torch
 os.environ["KERAS_BACKEND"] = "torch"
+os.environ["PYTORCH_ENABLE_MPS_FALLBACK"] = "1"
 
 __license__ = "BSD-3-Clause"
 

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/core/classify/classify.py

@@ -1,4 +1,5 @@
 import os
+from datetime import datetime
 from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import keras
@@ -50,6 +51,8 @@ def main(
     # Too many workers doesn't increase speed, and uses huge amounts of RAM
     workers = get_num_processes(min_free_cpu_cores=n_free_cpus)
 
+    start_time = datetime.now()
+
     logger.debug("Initialising cube generator")
     inference_generator = CubeGeneratorFromFile(
         points,
@@ -90,6 +93,11 @@ def main(
         cell.type = predictions[idx] + 1
         points_list.append(cell)
 
+    time_elapsed = datetime.now() - start_time
+    print(
+        "Classfication complete - all points done in : {}".format(time_elapsed)
+    )
+
     return points_list
 
 

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/core/classify/cube_generator.py

@@ -40,7 +40,7 @@ class CubeGeneratorFromFile(Sequence):
         background_array: types.array,
         voxel_sizes: Tuple[int, int, int],
         network_voxel_sizes: Tuple[int, int, int],
-        batch_size: int = 16,
+        batch_size: int = 64,
         cube_width: int = 50,
         cube_height: int = 50,
         cube_depth: int = 20,
@@ -345,7 +345,7 @@ class CubeGeneratorFromDisk(Sequence):
         signal_list: List[Union[str, Path]],
         background_list: List[Union[str, Path]],
         labels: Optional[List[int]] = None,  # only if training or validating
-        batch_size: int = 16,
+        batch_size: int = 64,
         shape: Tuple[int, int, int] = (50, 50, 20),
         channels: int = 2,
         classes: int = 2,

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/core/detect/filters/volume/structure_splitting.py

@@ -74,6 +74,7 @@ def ball_filter_imgs(
     good_tiles_mask = np.ones((1, 1, volume.shape[2]), dtype=np.bool_)
 
     plane_width, plane_height = volume.shape[:2]
+    current_z = ball_z_size // 2
 
     bf = BallFilter(
         plane_width,
@@ -86,9 +87,7 @@ def ball_filter_imgs(
         threshold_value=threshold_value,
         soma_centre_value=soma_centre_value,
     )
-    cell_detector = CellDetector(
-        plane_width, plane_height, start_z=ball_z_size // 2
-    )
+    cell_detector = CellDetector(plane_width, plane_height, start_z=current_z)
 
     # FIXME: hard coded type
     ball_filtered_volume = np.zeros(volume.shape, dtype=np.uint32)
@@ -98,7 +97,11 @@ def ball_filter_imgs(
         if bf.ready:
             bf.walk()
             middle_plane = bf.get_middle_plane()
-            ball_filtered_volume[:, :, z] = middle_plane[:]
+
+            # first valid middle plane is the current_z, not z
+            ball_filtered_volume[:, :, current_z] = middle_plane[:]
+            current_z += 1
+
             # DEBUG: TEST: transpose
             previous_plane = cell_detector.process(
                 middle_plane.copy(), previous_plane
@@ -134,7 +137,10 @@ def iterative_ball_filter(
         vol, cell_centres = ball_filter_imgs(
             vol, threshold_value, soma_centre_value
         )
-        vol -= 1
+
+        # vol is unsigned, so can't let zeros underflow to max value
+        vol[:, :, :] = np.where(vol != 0, vol - 1, 0)
+
         n_structures = len(cell_centres)
         ns.append(n_structures)
         centres.append(cell_centres)

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/core/main.py

@@ -18,7 +18,7 @@ def main(
     trained_model: Optional[os.PathLike] = None,
     model_weights: Optional[os.PathLike] = None,
     model: model_type = "resnet50_tv",
-    batch_size: int = 32,
+    batch_size: int = 64,
     n_free_cpus: int = 2,
     network_voxel_sizes: Tuple[int, int, int] = (5, 1, 1),
     soma_diameter: int = 16,

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/napari/curation.py

@@ -54,7 +54,7 @@ class CurationWidget(QWidget):
         self.save_empty_cubes = save_empty_cubes
         self.max_ram = max_ram
         self.voxel_sizes = [5, 2, 2]
-        self.batch_size = 32
+        self.batch_size = 64
         self.viewer = viewer
 
         self.signal_layer = None

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/napari/detect/detect.py

@@ -253,8 +253,9 @@ def detect_widget() -> FunctionGui:
         max_cluster_size: int,
         classification_options,
         skip_classification: bool,
-        trained_model: Optional[Path],
         use_pre_trained_weights: bool,
+        trained_model: Optional[Path],
+        batch_size: int,
         misc_options,
         start_plane: int,
         end_plane: int,
@@ -298,6 +299,8 @@ def detect_widget() -> FunctionGui:
             should be attempted
         use_pre_trained_weights : bool
             Select to use pre-trained model weights
+        batch_size : int
+            How many points to classify at one time
         skip_classification : bool
             If selected, the classification step is skipped and all cells from
             the detection stage are added
@@ -372,7 +375,10 @@ def detect_widget() -> FunctionGui:
         if use_pre_trained_weights:
             trained_model = None
         classification_inputs = ClassificationInputs(
-            skip_classification, use_pre_trained_weights, trained_model
+            skip_classification,
+            use_pre_trained_weights,
+            trained_model,
+            batch_size,
         )
 
         if analyse_local:

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/napari/detect/detect_containers.py

@@ -114,6 +114,7 @@ class ClassificationInputs(InputContainer):
     skip_classification: bool = False
     use_pre_trained_weights: bool = True
     trained_model: Optional[Path] = Path.home()
+    batch_size: int = 64
 
     def as_core_arguments(self) -> dict:
         args = super().as_core_arguments()
@@ -131,6 +132,7 @@ class ClassificationInputs(InputContainer):
             skip_classification=dict(
                 value=cls.defaults()["skip_classification"]
             ),
+            batch_size=dict(value=cls.defaults()["batch_size"]),
         )
 
 

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder/napari/detect/thread_worker.py

@@ -72,10 +72,10 @@ class Worker(WorkerBase):
         def classify_callback(batch: int) -> None:
             self.update_progress_bar.emit(
                 "Classifying cells",
-                # Default cellfinder-core batch size is 32. This seems to give
+                # Default cellfinder-core batch size is 64. This seems to give
                 # a slight underestimate of the number of batches though, so
                 # allow for batch number to go over this
-                max(self.npoints_detected // 32 + 1, batch + 1),
+                max(self.npoints_detected // 64 + 1, batch + 1),
                 batch + 1,
             )
 

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc1
+Version: 1.3.1
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -16,11 +16,11 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 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
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: brainglobe-utils>=0.5.0
@@ -101,8 +101,14 @@ pip install cellfinder>=1.0.0
 Be sure to specify a version greater than version `v1.0.0` - prior to this version the `cellfinder` package had a very different structure that is incompatible with BrainGlobe version 1 and the other tools in the BrainGlobe suite.
 See [our blog posts](https://brainglobe.info/blog/) for more information on the release of BrainGlobe version 1.
 
-## Contributing
+## Seeking help or contributing
+We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the [contact page of our website](https://brainglobe.info/contact.html).
 
-If you have encountered a bug whilst using cellfinder, please [open an issue on GitHub](https://github.com/brainglobe/cellfinder/issues).
+## Citation
+If you find this package useful, and use it in your research, please cite the following paper:
+> Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M. and Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets’ PLOS Computational Biology, 17(5), e1009074
+[https://doi.org/10.1371/journal.pcbi.1009074](https://doi.org/10.1371/journal.pcbi.1009074)
 
-If you are interested in contributing to cellfinder (thank you!) - please head over to our [developer documentation](https://brainglobe.info/community/developers/index.html).
+**If you use this, or any other tools in the brainglobe suite, please
+ [let us know](https://brainglobe.info/contact.html), and
+ we'd be happy to promote your paper/talk etc.**

{cellfinder-1.3.0rc1 → cellfinder-1.3.1}/pyproject.toml

@@ -14,12 +14,12 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "brainglobe-utils>=0.5.0",
     "brainglobe-napari-io>=0.3.4",
@@ -79,7 +79,7 @@ requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = 'setuptools.build_meta'
 
 [tool.black]
-target-version = ['py39', 'py310','py311']
+target-version = ['py310','py311', 'py312']
 skip-string-normalization = false
 line-length = 79
 
@@ -111,27 +111,19 @@ markers = ["slow: marks tests as slow (deselect with '-m \"not slow\"')"]
 legacy_tox_ini = """
 # For more information about tox, see https://tox.readthedocs.io/en/latest/
 [tox]
-envlist = py{39,310,311}
+envlist = py{310,311,312}
 isolated_build = true
 
 [gh-actions]
 python =
-    3.9: py39
     3.10: py310
     3.11: py311
+    3.12: py312
 
 [testenv]
 commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml
-deps =
-    pytest
-    pytest-cov
-    pytest-mock
-    pytest-timeout
-    # Even though napari is a requirement for cellfinder.napari, we have to
-    # ensure it is installed with the default Qt backend here.
-    napari[all]
-    pytest-qt
 extras =
+    dev
     napari
 setenv =
     KERAS_BACKEND = torch