cellfinder 1.3.0rc0__tar.gz → 1.3.0rc2__tar.gz

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc2}/.github/workflows/test_and_deploy.yml

@@ -48,11 +48,11 @@ jobs:
         # Include one windows and two macOS (intel based and arm based) runs
         include:
           - os: macos-13
-            python-version: "3.10"
+            python-version: "3.11"
           - os: macos-latest
-            python-version: "3.10"
+            python-version: "3.11"
           - os: windows-latest
-            python-version: "3.10"
+            python-version: "3.11"
 
     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: "3.10"
+          python-version: "3.11"
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
@@ -125,10 +125,10 @@ jobs:
         with:
           repository: 'brainglobe/brainglobe-workflows'
 
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v3
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install test dependencies
         run: |

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc2}/.github/workflows/test_include_guard.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install cellfinder via pip
         run: python -m pip install -e "."

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc0
+Version: 1.3.0rc2
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -18,6 +18,7 @@ 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: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc2}/cellfinder/__init__.py

@@ -26,8 +26,8 @@ except PackageNotFoundError as e:
 
 # Set the Keras backend to torch
 os.environ["KERAS_BACKEND"] = "torch"
+os.environ["PYTORCH_ENABLE_MPS_FALLBACK"] = "1"
 
-__author__ = "Adam Tyson, Christian Niedworok, Charly Rousseau"
 __license__ = "BSD-3-Clause"
 
 DEFAULT_CELLFINDER_DIRECTORY = Path.home() / ".brainglobe" / "cellfinder"

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc2}/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-1.3.0rc0 → cellfinder-1.3.0rc2}/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-1.3.0rc0 → cellfinder-1.3.0rc2}/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-1.3.0rc0 → cellfinder-1.3.0rc2}/cellfinder/core/tools/system.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 
+import keras
 from brainglobe_utils.general.exceptions import CommandLineInputError
 
 
@@ -80,3 +81,12 @@ def memory_in_bytes(memory_amount, unit):
         )
     else:
         return memory_amount * 10 ** supported_units[unit]
+
+
+def force_cpu():
+    """
+    Forces the CPU to be used, even if a GPU is available
+    """
+    keras.src.backend.common.global_state.set_global_attribute(
+        "torch_device", "cpu"
+    )

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc2}/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-1.3.0rc0 → cellfinder-1.3.0rc2}/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-1.3.0rc0 → cellfinder-1.3.0rc2}/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-1.3.0rc0 → cellfinder-1.3.0rc2}/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-1.3.0rc0 → cellfinder-1.3.0rc2}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.0rc0
+Version: 1.3.0rc2
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -18,6 +18,7 @@ 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: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown

cellfinder-1.3.0rc2/cellfinder.egg-info/SOURCES.txt

@@ -0,0 +1,68 @@
+.gitignore
+CITATION.cff
+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+.github/workflows/test_and_deploy.yml
+.github/workflows/test_include_guard.yaml
+.napari/config.yml
+cellfinder/__init__.py
+cellfinder/cli_migration_warning.py
+cellfinder.egg-info/PKG-INFO
+cellfinder.egg-info/SOURCES.txt
+cellfinder.egg-info/dependency_links.txt
+cellfinder.egg-info/entry_points.txt
+cellfinder.egg-info/requires.txt
+cellfinder.egg-info/top_level.txt
+cellfinder/core/__init__.py
+cellfinder/core/main.py
+cellfinder/core/types.py
+cellfinder/core/classify/__init__.py
+cellfinder/core/classify/augment.py
+cellfinder/core/classify/classify.py
+cellfinder/core/classify/cube_generator.py
+cellfinder/core/classify/resnet.py
+cellfinder/core/classify/tools.py
+cellfinder/core/config/__init__.py
+cellfinder/core/config/cellfinder.conf
+cellfinder/core/detect/__init__.py
+cellfinder/core/detect/detect.py
+cellfinder/core/detect/filters/__init__.py
+cellfinder/core/detect/filters/setup_filters.py
+cellfinder/core/detect/filters/plane/__init__.py
+cellfinder/core/detect/filters/plane/classical_filter.py
+cellfinder/core/detect/filters/plane/plane_filter.py
+cellfinder/core/detect/filters/plane/tile_walker.py
+cellfinder/core/detect/filters/volume/__init__.py
+cellfinder/core/detect/filters/volume/ball_filter.py
+cellfinder/core/detect/filters/volume/structure_detection.py
+cellfinder/core/detect/filters/volume/structure_splitting.py
+cellfinder/core/detect/filters/volume/volume_filter.py
+cellfinder/core/download/__init__.py
+cellfinder/core/download/cli.py
+cellfinder/core/download/download.py
+cellfinder/core/tools/__init__.py
+cellfinder/core/tools/array_operations.py
+cellfinder/core/tools/geometry.py
+cellfinder/core/tools/image_processing.py
+cellfinder/core/tools/prep.py
+cellfinder/core/tools/source_files.py
+cellfinder/core/tools/system.py
+cellfinder/core/tools/tiff.py
+cellfinder/core/tools/tools.py
+cellfinder/core/train/__init__.py
+cellfinder/core/train/train_yml.py
+cellfinder/napari/__init__.py
+cellfinder/napari/curation.py
+cellfinder/napari/input_container.py
+cellfinder/napari/napari.yaml
+cellfinder/napari/sample_data.py
+cellfinder/napari/utils.py
+cellfinder/napari/detect/__init__.py
+cellfinder/napari/detect/detect.py
+cellfinder/napari/detect/detect_containers.py
+cellfinder/napari/detect/thread_worker.py
+cellfinder/napari/train/__init__.py
+cellfinder/napari/train/train.py
+cellfinder/napari/train/train_containers.py

{cellfinder-1.3.0rc0 → cellfinder-1.3.0rc2}/pyproject.toml

@@ -16,6 +16,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "Topic :: Scientific/Engineering :: Image Recognition",
 ]
 requires-python = ">=3.9"
@@ -121,16 +122,8 @@ python =
 
 [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

cellfinder-1.3.0rc0/cellfinder/core/config/cellfinder.conf.custom

@@ -1,3 +0,0 @@
-[model]
-    model_path = '/home/adam/.cellfinder/model_weights/resnet50_tv.h5'
-    model_type = '50-layer'