cellfinder 1.6.0__tar.gz → 1.7.0__tar.gz

{cellfinder-1.6.0 → cellfinder-1.7.0}/.github/workflows/test_and_deploy.yml

@@ -86,6 +86,15 @@ jobs:
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           use-xvfb: true
 
+      # Run tests on napari main if this is a scheduled run
+      - name: Run tests on napari main
+        if: github.event_name == 'schedule'
+        uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
+          tox-args: '-e napari-dev'
+
       - name: Notify slack on scheduled failure
         if: failure() && github.event_name == 'schedule'
         uses: ravsamhq/notify-slack-action@v2

{cellfinder-1.6.0 → cellfinder-1.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cellfinder
-Version: 1.6.0
+Version: 1.7.0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -33,7 +33,7 @@ Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: keras>=3.7.0
-Requires-Dist: torch!=2.4,>=2.1.0
+Requires-Dist: torch>=2.4.1
 Requires-Dist: tifffile
 Requires-Dist: tqdm
 Requires-Dist: qt-niu
@@ -56,6 +56,7 @@ Requires-Dist: napari-plugin-engine>=0.1.4; extra == "napari"
 Requires-Dist: napari[pyqt5]; extra == "napari"
 Requires-Dist: pooch>=1; extra == "napari"
 Requires-Dist: qtpy; extra == "napari"
+Dynamic: license-file
 
 [![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)
 [![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/cli_migration_warning.py

@@ -1,5 +1,7 @@
 import argparse
 
+from cellfinder.core import logger
+
 BRAINGLOBE_WORKFLOWS = "https://github.com/brainglobe/brainglobe-workflows"
 NEW_NAME = "brainmapper"
 BLOG_POST = "https://brainglobe.info/blog/version1/core_and_napari_merge.html"
@@ -36,7 +38,7 @@ def cli_catch() -> None:
         ),
     )
 
-    print(
+    logger.warning(
         "Hey, it looks like you're trying to run the old command-line tool.",
         "This workflow has been renamed and moved -",
         " you can now find it in the brainglobe-workflows package:\n",

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/core/classify/classify.py

@@ -70,7 +70,7 @@ def main(
     )
 
     if trained_model and Path(trained_model).suffix == ".h5":
-        print(
+        logger.warning(
             "Weights provided in place of the model, "
             "loading weights into default model."
         )
@@ -103,7 +103,7 @@ def main(
         points_list.append(cell)
 
     time_elapsed = datetime.now() - start_time
-    print(
+    logger.info(
         "Classfication complete - all points done in : {}".format(time_elapsed)
     )
 

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/core/classify/tools.py

@@ -47,9 +47,19 @@ def get_model(
                 f"Setting model weights according to: {model_weights}",
             )
             if model_weights is None:
-                raise OSError("`model_weights` must be provided")
-            model.load_weights(model_weights)
-        return model
+                raise OSError(
+                    "`model_weights` must be provided for inference "
+                    "or continued training."
+                )
+            try:
+                model.load_weights(model_weights)
+            except (OSError, ValueError) as e:
+                raise ValueError(
+                    f"Error loading weights: {model_weights}.\n"
+                    "Provided weights don't match the model architecture.\n"
+                ) from e
+
+    return model
 
 
 def make_lists(

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/core/detect/detect.py

@@ -48,8 +48,7 @@ def main(
     save_planes: bool = False,
     plane_directory: Optional[str] = None,
     batch_size: Optional[int] = None,
-    torch_device: str = "cpu",
-    use_scipy: bool = True,
+    torch_device: Optional[str] = None,
     split_ball_xy_size: int = 3,
     split_ball_z_size: int = 3,
     split_ball_overlap_fraction: float = 0.8,
@@ -121,9 +120,9 @@ def main(
         becomes slower.
 
     torch_device : str, optional
-        The device on which to run the computation. By default, it's "cpu".
-        To run on a gpu, specify the PyTorch device name, such as "cuda" to
-        run on the first GPU.
+        The device on which to run the computation. If not specified (None),
+        "cuda" will be used if a GPU is available, otherwise "cpu".
+        You can also manually specify "cuda" or "cpu".
 
     callback : Callable[int], optional
         A callback function that is called every time a plane has finished
@@ -135,6 +134,8 @@ def main(
         List of detected cells.
     """
     start_time = datetime.now()
+    if torch_device is None:
+        torch_device = "cuda" if torch.cuda.is_available() else "cpu"
     if batch_size is None:
         if torch_device == "cpu":
             batch_size = 4
@@ -155,6 +156,12 @@ def main(
     end_plane = min(len(signal_array), end_plane)
 
     torch_device = torch_device.lower()
+    # Use SciPy filtering on CPU (better performance); use PyTorch on GPU
+    if torch_device != "cuda":
+        use_scipy = True
+    else:
+        use_scipy = False
+
     batch_size = max(batch_size, 1)
     # brainmapper can pass them in as str
     voxel_sizes = list(map(float, voxel_sizes))
@@ -231,6 +238,5 @@ def main(
 
     time_elapsed = datetime.now() - start_time
     s = f"Detection complete. Found {len(cells)} cells in {time_elapsed}"
-    logger.debug(s)
-    print(s)
+    logger.info(s)
     return cells

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/core/download/download.py

@@ -6,6 +6,7 @@ import pooch
 from brainglobe_utils.general.config import get_config_obj
 
 from cellfinder import DEFAULT_CELLFINDER_DIRECTORY
+from cellfinder.core import logger
 from cellfinder.core.tools.source_files import (
     default_configuration_path,
     user_specific_configuration_path,
@@ -74,7 +75,7 @@ def amend_user_configuration(new_model_path=None) -> None:
     new_model_path : Path, optional
         The path to the new model configuration.
     """
-    print("(Over-)writing custom user configuration")
+    logger.info("(Over-)writing custom user configuration")
 
     original_config = default_configuration_path()
     new_config = user_specific_configuration_path()

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/core/main.py

@@ -37,7 +37,7 @@ def main(
     skip_classification: bool = False,
     detected_cells: List[Cell] = None,
     classification_batch_size: Optional[int] = None,
-    classification_torch_device: str = "cpu",
+    torch_device: Optional[str] = None,
     *,
     detect_callback: Optional[Callable[[int], None]] = None,
     classify_callback: Optional[Callable[[int], None]] = None,
@@ -77,7 +77,7 @@ def main(
             log_sigma_size,
             n_sds_above_mean_thresh,
             batch_size=classification_batch_size,
-            torch_device=classification_torch_device,
+            torch_device=torch_device,
             callback=detect_callback,
         )
 

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/core/tools/threading.py

@@ -15,6 +15,7 @@ Typical example::
 
     from cellfinder.core.tools.threading import ThreadWithException, \\
         EOFSignal, ProcessWithException
+    from cellfinder.core import logger
     import torch
 
 
@@ -63,7 +64,7 @@ Typical example::
                     # thread exited for whatever reason (not exception)
                     break
 
-                print(f"Thread processed tensor {i}")
+                logger.debug(f"Thread processed tensor {i}")
         finally:
             # whatever happens, make sure thread is told to finish so it
             # doesn't get stuck
@@ -248,8 +249,8 @@ class ExceptionWithQueueMixIn:
             ...         # do something with the msg
             ...         pass
             ... except ExecutionFailure as e:
-            ...     print(f"got exception {type(e.__cause__)}")
-            ...     print(f"with message {e.__cause__.args[0]}")
+            ...     logger.error(f"got exception {type(e.__cause__)}")
+            ...     logger.error(f"with message {e.__cause__.args[0]}")
         """
         msg, value = self.from_thread_queue.get(block=True, timeout=timeout)
         if msg == "eof":

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/core/train/train_yaml.py

@@ -3,9 +3,6 @@ main
 ===============
 
 Trains a network based on a yaml file specifying cubes of cells/non cells.
-
-N.B imports are within functions to prevent tensorflow being imported before
-it's warnings are silenced
 """
 
 import os
@@ -29,12 +26,16 @@ from brainglobe_utils.general.system import (
 from brainglobe_utils.IO.cells import find_relevant_tiffs
 from brainglobe_utils.IO.yaml import read_yaml_section
 from fancylog import fancylog
+from keras.callbacks import CSVLogger, ModelCheckpoint, TensorBoard
 from sklearn.model_selection import train_test_split
 
 import cellfinder.core as program_for_log
 from cellfinder.core import logger
+from cellfinder.core.classify.cube_generator import CubeGeneratorFromDisk
 from cellfinder.core.classify.resnet import layer_type
+from cellfinder.core.classify.tools import get_model, make_lists
 from cellfinder.core.download.download import DEFAULT_DOWNLOAD_DIRECTORY
+from cellfinder.core.tools.prep import prep_model_weights
 
 depth_type = Literal["18", "34", "50", "101", "152"]
 
@@ -316,16 +317,6 @@ def run(
     save_progress=False,
     epochs=100,
 ):
-    from keras.callbacks import (
-        CSVLogger,
-        ModelCheckpoint,
-        TensorBoard,
-    )
-
-    from cellfinder.core.classify.cube_generator import CubeGeneratorFromDisk
-    from cellfinder.core.classify.tools import get_model, make_lists
-    from cellfinder.core.tools.prep import prep_model_weights
-
     start_time = datetime.now()
 
     ensure_directory_exists(output_dir)

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/napari/curation.py

@@ -95,6 +95,22 @@ class CurationWidget(QWidget):
                 self.training_data_non_cell_choice, self.point_layer_names
             )
 
+        @self.viewer.layers.events.removed.connect
+        def _remove_selection_layers(event: QtCore.QEvent):
+            """
+            Set internal background, signal, training data cell,
+            and training data non-cell layers to None when they
+            are removed from the napari viewer GUI.
+            """
+            if event.value == self.signal_layer:
+                self.signal_layer = None
+            if event.value == self.background_layer:
+                self.background_layer = None
+            if event.value == self.training_data_cell_layer:
+                self.training_data_cell_layer = None
+            if event.value == self.training_data_non_cell_layer:
+                self.training_data_non_cell_layer = None
+
     @staticmethod
     def _update_combobox_options(combobox: QComboBox, options_list: List[str]):
         original_text = combobox.currentText()

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/napari/detect/detect.py

@@ -261,6 +261,7 @@ def detect_widget() -> FunctionGui:
         end_plane: int,
         n_free_cpus: int,
         analyse_local: bool,
+        use_gpu: bool,
         debug: bool,
         reset_button,
     ) -> None:
@@ -315,6 +316,8 @@ def detect_widget() -> FunctionGui:
             How many CPU cores to leave free
         analyse_local : bool
             Only analyse planes around the current position
+        use_gpu : bool
+            If True, use GPU for processing (if available); otherwise, use CPU.
         debug : bool
             Increase logging
         reset_button :
@@ -389,7 +392,7 @@ def detect_widget() -> FunctionGui:
             end_plane = len(signal_image.data)
 
         misc_inputs = MiscInputs(
-            start_plane, end_plane, n_free_cpus, analyse_local, debug
+            start_plane, end_plane, n_free_cpus, analyse_local, use_gpu, debug
         )
 
         worker = Worker(

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/napari/detect/detect_containers.py

@@ -1,8 +1,9 @@
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from pathlib import Path
 from typing import List, Optional
 
 import numpy
+import torch
 from brainglobe_utils.cells.cells import Cell
 
 from cellfinder.napari.input_container import InputContainer
@@ -30,7 +31,7 @@ class DataInputs(InputContainer):
             self.voxel_size_x,
         )
         # del operator doesn't affect self, because asdict creates a copy of
-        # fields.
+        # the dict.
         del data_input_dict["voxel_size_z"]
         del data_input_dict["voxel_size_y"]
         del data_input_dict["voxel_size_x"]
@@ -144,10 +145,13 @@ class MiscInputs(InputContainer):
     end_plane: int = 0
     n_free_cpus: int = 2
     analyse_local: bool = False
+    use_gpu: bool = field(default_factory=lambda: torch.cuda.is_available())
     debug: bool = False
 
     def as_core_arguments(self) -> dict:
         misc_input_dict = super().as_core_arguments()
+        misc_input_dict["torch_device"] = "cuda" if self.use_gpu else "cpu"
+        del misc_input_dict["use_gpu"]
         del misc_input_dict["debug"]
         del misc_input_dict["analyse_local"]
         return misc_input_dict
@@ -162,5 +166,11 @@ class MiscInputs(InputContainer):
                 "n_free_cpus", custom_label="Number of free CPUs"
             ),
             analyse_local=dict(value=cls.defaults()["analyse_local"]),
+            use_gpu=dict(
+                widget_type="CheckBox",
+                label="Use GPU",
+                value=cls.defaults()["use_gpu"],
+                enabled=torch.cuda.is_available(),
+            ),
             debug=dict(value=cls.defaults()["debug"]),
         )

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/napari/input_container.py

@@ -1,8 +1,18 @@
 from abc import abstractmethod
-from dataclasses import asdict, dataclass
+from dataclasses import dataclass, fields
 from typing import Optional
 
 
+def asdict_no_copy(obj: dataclass) -> dict:
+    """
+    Similar to `asdict`, except it makes no copies of the field values.
+    asdict will do a deep copy of field values that are non-basic objects.
+
+    It still creates a new dict to return, though.
+    """
+    return {field.name: getattr(obj, field.name) for field in fields(obj)}
+
+
 @dataclass
 class InputContainer:
     """Base for classes that contain inputs
@@ -23,7 +33,7 @@ class InputContainer:
         # Derived classes are not expected to be particularly
         # slow to instantiate, so use the default constructor
         # to avoid code repetition.
-        return asdict(cls())
+        return asdict_no_copy(cls())
 
     @abstractmethod
     def as_core_arguments(self) -> dict:
@@ -32,10 +42,10 @@ class InputContainer:
         The implementation provided here can be re-used in derived classes, if
         convenient.
         """
-        # note that asdict returns a new instance of a dict,
+        # note that asdict_no_copy returns a new instance of a dict,
         # so any subsequent modifications of this dict won't affect the class
         # instance
-        return asdict(self)
+        return asdict_no_copy(self)
 
     @classmethod
     def _custom_widget(

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/napari/train/train.py

@@ -25,14 +25,14 @@ def run_training(
     optional_training_inputs: OptionalTrainingInputs,
     misc_training_inputs: MiscTrainingInputs,
 ):
-    print("Running training")
+    show_info("Running training...")
     train_yaml(
         **training_data_inputs.as_core_arguments(),
         **optional_network_inputs.as_core_arguments(),
         **optional_training_inputs.as_core_arguments(),
         **misc_training_inputs.as_core_arguments(),
     )
-    print("Finished!")
+    show_info("Training finished!")
 
 
 def training_widget() -> FunctionGui:
@@ -60,7 +60,6 @@ def training_widget() -> FunctionGui:
         continue_training: bool,
         augment: bool,
         tensorboard: bool,
-        save_weights: bool,
         save_checkpoints: bool,
         save_progress: bool,
         epochs: int,
@@ -96,9 +95,6 @@ def training_widget() -> FunctionGui:
             Augment the training data to improve generalisation
         tensorboard : bool
             Log to output_directory/tensorboard
-        save_weights : bool
-            Only store the model weights, and not the full model
-            Useful to save storage space
         save_checkpoints : bool
             Store the model at intermediate points during training
         save_progress : bool
@@ -133,7 +129,6 @@ def training_widget() -> FunctionGui:
             continue_training,
             augment,
             tensorboard,
-            save_weights,
             save_checkpoints,
             save_progress,
             epochs,
@@ -147,6 +142,7 @@ def training_widget() -> FunctionGui:
         if yaml_files[0] == Path.home():  # type: ignore
             show_info("Please select a YAML file for training")
         else:
+            show_info("Starting training process...")
             worker = run_training(
                 training_data_inputs,
                 optional_network_inputs,

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder/napari/train/train_containers.py

@@ -75,7 +75,6 @@ class OptionalTrainingInputs(InputContainer):
     continue_training: bool = False
     augment: bool = True
     tensorboard: bool = False
-    save_weights: bool = False
     save_checkpoints: bool = True
     save_progress: bool = True
     epochs: int = 100
@@ -98,7 +97,6 @@ class OptionalTrainingInputs(InputContainer):
             continue_training=cls._custom_widget("continue_training"),
             augment=cls._custom_widget("augment"),
             tensorboard=cls._custom_widget("tensorboard"),
-            save_weights=cls._custom_widget("save_weights"),
             save_checkpoints=cls._custom_widget("save_checkpoints"),
             save_progress=cls._custom_widget("save_progress"),
             epochs=cls._custom_widget("epochs"),

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cellfinder
-Version: 1.6.0
+Version: 1.7.0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -33,7 +33,7 @@ Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: keras>=3.7.0
-Requires-Dist: torch!=2.4,>=2.1.0
+Requires-Dist: torch>=2.4.1
 Requires-Dist: tifffile
 Requires-Dist: tqdm
 Requires-Dist: qt-niu
@@ -56,6 +56,7 @@ Requires-Dist: napari-plugin-engine>=0.1.4; extra == "napari"
 Requires-Dist: napari[pyqt5]; extra == "napari"
 Requires-Dist: pooch>=1; extra == "napari"
 Requires-Dist: qtpy; extra == "napari"
+Dynamic: license-file
 
 [![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)
 [![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)

{cellfinder-1.6.0 → cellfinder-1.7.0}/cellfinder.egg-info/requires.txt

@@ -8,7 +8,7 @@ numpy
 scikit-image
 scikit-learn
 keras>=3.7.0
-torch!=2.4,>=2.1.0
+torch>=2.4.1
 tifffile
 tqdm
 qt-niu

{cellfinder-1.6.0 → cellfinder-1.7.0}/pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
     "scikit-image",
     "scikit-learn",
     "keras>=3.7.0",
-    "torch>=2.1.0,!=2.4",
+    "torch>=2.4.1",
     "tifffile",
     "tqdm",
     "qt-niu"
@@ -113,7 +113,7 @@ 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{311,312,313}
+envlist = py{311,312,313}, napari-dev
 isolated_build = true
 
 [gh-actions]
@@ -139,4 +139,6 @@ passenv =
     NUMPY_EXPERIMENTAL_ARRAY_FUNCTION
     PYVISTA_OFF_SCREEN
     BRAINGLOBE_TEST_DATA_DIR
+deps =
+    napari-dev: git+https://github.com/napari/napari
 """