cellfinder 1.6.0__tar.gz → 1.8.0__tar.gz

{cellfinder-1.6.0 → cellfinder-1.8.0}/.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-1.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cellfinder
-Version: 1.6.0
+Version: 1.8.0
 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
@@ -53,9 +53,10 @@ Requires-Dist: brainglobe-napari-io; extra == "napari"
 Requires-Dist: magicgui; extra == "napari"
 Requires-Dist: napari-ndtiffs; extra == "napari"
 Requires-Dist: napari-plugin-engine>=0.1.4; extra == "napari"
-Requires-Dist: napari[pyqt5]; extra == "napari"
+Requires-Dist: napari[pyqt5]>=0.6.1; 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-1.8.0}/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-1.8.0}/cellfinder/core/classify/classify.py

@@ -19,8 +19,8 @@ def main(
     signal_array: types.array,
     background_array: types.array,
     n_free_cpus: int,
-    voxel_sizes: Tuple[int, int, int],
-    network_voxel_sizes: Tuple[int, int, int],
+    voxel_sizes: Tuple[float, float, float],
+    network_voxel_sizes: Tuple[float, float, float],
     batch_size: int,
     cube_height: int,
     cube_width: int,
@@ -29,12 +29,58 @@ def main(
     model_weights: Optional[os.PathLike],
     network_depth: depth_type,
     max_workers: int = 3,
+    pin_memory: bool = False,
     *,
     callback: Optional[Callable[[int], None]] = None,
 ) -> List[Cell]:
     """
     Parameters
     ----------
+
+    points: List of Cell objects
+        The potential cells to classify.
+    signal_array : numpy.ndarray or dask array
+        3D array representing the signal data in z, y, x order.
+    background_array : numpy.ndarray or dask array
+        3D array representing the signal data in z, y, x order.
+    n_free_cpus : int
+        How many CPU cores to leave free.
+    voxel_sizes : 3-tuple of floats
+        Size of your voxels in the z, y, and x dimensions.
+    network_voxel_sizes : 3-tuple of floats
+        Size of the pre-trained network's voxels in the z, y, and x dimensions.
+    batch_size : int
+        How many potential cells to classify at one time. The GPU/CPU
+        memory must be able to contain at once this many data cubes for
+        the models. For performance-critical applications, tune to maximize
+        memory usage without running out. Check your GPU/CPU memory to verify
+        it's not full.
+    cube_height: int
+        The height of the data cube centered on the cell used for
+        classification. Defaults to `50`.
+    cube_width: int
+        The width of the data cube centered on the cell used for
+        classification. Defaults to `50`.
+    cube_depth: int
+        The depth of the data cube centered on the cell used for
+        classification. Defaults to `20`.
+    trained_model : Optional[Path]
+        Trained model file path (home directory (default) -> pretrained
+        weights).
+    model_weights : Optional[Path]
+        Model weights path (home directory (default) -> pretrained
+        weights).
+    network_depth: str
+        The network depth to use during classification. Defaults to `"50"`.
+    max_workers: int
+        The number of sub-processes to use for data loading / processing.
+        Defaults to 8.
+    pin_memory: bool
+        Pins data to be sent to the GPU to the CPU memory. This allows faster
+        GPU data speeds, but can only be used if the data used by the GPU can
+        stay in the CPU RAM while the GPU uses it. I.e. there's enough RAM.
+        Otherwise, if there's a risk of the RAM being paged, it shouldn't be
+        used. Defaults to False.
     callback : Callable[int], optional
         A callback function that is called during classification. Called with
         the batch number once that batch has been classified.
@@ -70,7 +116,7 @@ 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 +149,7 @@ 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-1.8.0}/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-1.8.0}/cellfinder/core/detect/detect.py

@@ -48,12 +48,12 @@ def main(
     save_planes: bool = False,
     plane_directory: Optional[str] = None,
     batch_size: Optional[int] = None,
-    torch_device: str = "cpu",
-    use_scipy: bool = True,
-    split_ball_xy_size: int = 3,
-    split_ball_z_size: int = 3,
+    torch_device: Optional[str] = None,
+    pin_memory: bool = False,
+    split_ball_xy_size: float = 6,
+    split_ball_z_size: float = 15,
     split_ball_overlap_fraction: float = 0.8,
-    split_soma_diameter: int = 7,
+    n_splitting_iter: int = 10,
     *,
     callback: Optional[Callable[[int], None]] = None,
 ) -> List[Cell]:
@@ -62,69 +62,80 @@ def main(
 
     Parameters
     ----------
-    signal_array : numpy.ndarray
-        3D array representing the signal data.
-
+    signal_array : numpy.ndarray or dask array
+        3D array representing the signal data in z, y, x order.
     start_plane : int
-        Index of the starting plane for detection.
-
+        First plane index to process (inclusive, to process a subset of the
+        data).
     end_plane : int
-        Index of the ending plane for detection.
-
-    voxel_sizes : Tuple[float, float, float]
-        Tuple of voxel sizes in each dimension (z, y, x).
-
+        Last plane index to process (exclusive, to process a subset of the
+        data).
+    voxel_sizes : 3-tuple of floats
+        Size of your voxels in the z, y, and x dimensions (microns).
     soma_diameter : float
-        Diameter of the soma in physical units.
-
+        The expected in-plane (xy) soma diameter (microns).
     max_cluster_size : float
-        Maximum size of a cluster in physical units.
-
+        Largest detected cell cluster (in cubic um) where splitting
+        should be attempted. Clusters above this size will be labeled
+        as artifacts.
     ball_xy_size : float
-        Size of the XY ball used for filtering in physical units.
-
+        3d filter's in-plane (xy) filter ball size (microns).
     ball_z_size : float
-        Size of the Z ball used for filtering in physical units.
-
+        3d filter's axial (z) filter ball size (microns).
     ball_overlap_fraction : float
-        Fraction of overlap allowed between balls.
-
+        3d filter's fraction of the ball filter needed to be filled by
+        foreground voxels, centered on a voxel, to retain the voxel.
     soma_spread_factor : float
-        Spread factor for soma size.
-
+        Cell spread factor for determining the largest cell volume before
+        splitting up cell clusters. Structures with spherical volume of
+        diameter `soma_spread_factor * soma_diameter` or less will not be
+        split.
     n_free_cpus : int
-        Number of free CPU cores available for parallel processing.
-
+        How many CPU cores to leave free.
     log_sigma_size : float
-        Size of the sigma for the log filter.
-
+        Gaussian filter width (as a fraction of soma diameter) used during
+        2d in-plane Laplacian of Gaussian filtering.
     n_sds_above_mean_thresh : float
-        Number of standard deviations above the mean threshold.
-
+        Intensity threshold (the number of standard deviations above
+        the mean) of the filtered 2d planes used to mark pixels as
+        foreground or background.
     outlier_keep : bool, optional
         Whether to keep outliers during detection. Defaults to False.
-
     artifact_keep : bool, optional
         Whether to keep artifacts during detection. Defaults to False.
-
     save_planes : bool, optional
         Whether to save the planes during detection. Defaults to False.
-
     plane_directory : str, optional
         Directory path to save the planes. Defaults to None.
-
-    batch_size : int, optional
-        The number of planes to process in each batch. Defaults to 1.
-        For CPU, there's no benefit for a larger batch size. Only a memory
-        usage increase. For CUDA, the larger the batch size the better the
-        performance. Until it fills up the GPU memory - after which it
-        becomes slower.
-
+    batch_size: int
+        The number of planes of the original data volume to process at
+        once. The GPU/CPU memory must be able to contain this many planes
+        for all the filters. For performance-critical applications, tune to
+        maximize memory usage without running out. Check your GPU/CPU memory
+        to verify it's not full.
     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".
+    pin_memory: bool
+        Pins data to be sent to the GPU to the CPU memory. This allows faster
+        GPU data speeds, but can only be used if the data used by the GPU can
+        stay in the CPU RAM while the GPU uses it. I.e. there's enough RAM.
+        Otherwise, if there's a risk of the RAM being paged, it shouldn't be
+        used. Defaults to False.
+    split_ball_xy_size: float
+        Similar to `ball_xy_size`, except the value to use for the 3d
+        filter during cluster splitting.
+    split_ball_z_size: float
+        Similar to `ball_z_size`, except the value to use for the 3d filter
+        during cluster splitting.
+    split_ball_overlap_fraction: float
+        Similar to `ball_overlap_fraction`, except the value to use for the
+        3d filter during cluster splitting.
+    n_splitting_iter: int
+        The number of iterations to run the 3d filtering on a cluster. Each
+        iteration reduces the cluster size by the voxels not retained in
+        the previous iteration.
     callback : Callable[int], optional
         A callback function that is called every time a plane has finished
         being processed. Called with the plane number that has finished.
@@ -132,9 +143,11 @@ def main(
     Returns
     -------
     List[Cell]
-        List of detected cells.
+        List of detected cell candidates.
     """
     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 +168,12 @@ 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))
@@ -180,19 +199,16 @@ def main(
         plane_directory=plane_directory,
         batch_size=batch_size,
         torch_device=torch_device,
+        pin_memory=pin_memory,
+        n_splitting_iter=n_splitting_iter,
     )
 
     # replicate the settings specific to splitting, before we access anything
     # of the original settings, causing cached properties
     kwargs = dataclasses.asdict(settings)
-    kwargs["ball_z_size_um"] = split_ball_z_size * settings.z_pixel_size
-    kwargs["ball_xy_size_um"] = (
-        split_ball_xy_size * settings.in_plane_pixel_size
-    )
+    kwargs["ball_z_size_um"] = split_ball_z_size
+    kwargs["ball_xy_size_um"] = split_ball_xy_size
     kwargs["ball_overlap_fraction"] = split_ball_overlap_fraction
-    kwargs["soma_diameter_um"] = (
-        split_soma_diameter * settings.in_plane_pixel_size
-    )
     # always run on cpu because copying to gpu overhead is likely slower than
     # any benefit for detection on smallish volumes
     kwargs["torch_device"] = "cpu"
@@ -231,6 +247,5 @@ 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-1.8.0}/cellfinder/core/detect/filters/plane/plane_filter.py

@@ -39,7 +39,7 @@ class TileProcessor:
         Number of standard deviations above the mean threshold to use for
         determining whether a voxel is bright.
     log_sigma_size : float
-        Size of the sigma for the gaussian filter.
+        Size of the Gaussian sigma for the Laplacian of Gaussian filtering.
     soma_diameter : float
         Diameter of the soma in voxels.
     torch_device: str

{cellfinder-1.6.0 → cellfinder-1.8.0}/cellfinder/core/detect/filters/setup_filters.py

@@ -80,23 +80,28 @@ class DetectionSettings:
 
     voxel_sizes: Tuple[float, float, float] = (1.0, 1.0, 1.0)
     """
-    Tuple of voxel sizes in each dimension (z, y, x). We use this to convert
-    from `um` to pixel sizes.
+    Tuple of voxel sizes (microns) in each dimension (z, y, x). We use this
+    to convert from `um` to pixel sizes.
     """
 
     soma_spread_factor: float = 1.4
-    """Spread factor for soma size - how much it may stretch in the images."""
+    """
+    Cell spread factor for determining the largest cell volume before
+    splitting up cell clusters. Structures with spherical volume of
+    diameter `soma_spread_factor * soma_diameter` or less will not be
+    split.
+    """
 
     soma_diameter_um: float = 16
     """
-    Diameter of a typical soma in um. Bright areas larger than this will be
-    split.
+    Diameter of a typical soma in-plane (xy) in microns.
     """
 
     max_cluster_size_um3: float = 100_000
     """
-    Maximum size of a cluster (bright area) that will be processed, in um.
-    Larger bright areas are skipped as artifacts.
+    Largest detected cell cluster (in cubic um) where splitting
+    should be attempted. Clusters above this size will be labeled
+    as artifacts.
     """
 
     ball_xy_size_um: float = 6
@@ -116,17 +121,21 @@ class DetectionSettings:
 
     ball_overlap_fraction: float = 0.6
     """
-    Fraction of overlap between a bright area and the spherical kernel,
-    for the area to be considered a single ball.
+    Fraction of the 3d ball filter needed to be filled by foreground voxels,
+    centered on a voxel, to retain the voxel.
     """
 
     log_sigma_size: float = 0.2
-    """Size of the sigma for the 2d Gaussian filter."""
+    """
+    Gaussian filter width (as a fraction of soma diameter) used during
+    2d in-plane Laplacian of Gaussian filtering.
+    """
 
     n_sds_above_mean_thresh: float = 10
     """
-    Number of standard deviations above the mean intensity to use for a
-    threshold to define bright areas. Below it, it's not considered bright.
+    Intensity threshold (the number of standard deviations above
+    the mean) of the filtered 2d planes used to mark pixels as
+    foreground or background.
     """
 
     outlier_keep: bool = False
@@ -180,6 +189,14 @@ class DetectionSettings:
     to run on the first GPU.
     """
 
+    pin_memory: bool = False
+    """
+    Pins data to be sent to the GPU to the CPU memory. This allows faster GPU
+    data speeds, but can only be used if the data used by the GPU can stay in
+    the CPU RAM while the GPU uses it. I.e. there's enough RAM. Otherwise, if
+    there's a risk of the RAM being paged, it shouldn't be used.
+    """
+
     n_free_cpus: int = 2
     """
     Number of free CPU cores to keep available and not use during parallel
@@ -191,6 +208,8 @@ class DetectionSettings:
     """
     During the structure splitting phase we iteratively shrink the bright areas
     and re-filter with the 3d filter. This is the number of iterations to do.
+    Each iteration reduces the cluster size by the voxels not retained in the
+    previous iteration.
 
     This is a maximum because we also stop if there are no more structures left
     during any iteration.

{cellfinder-1.6.0 → cellfinder-1.8.0}/cellfinder/core/detect/filters/volume/ball_filter.py

@@ -78,11 +78,11 @@ class BallFilter:
     ----------
     plane_height, plane_width : int
         Height/width of the planes.
-    ball_xy_size : int
-        Diameter of the spherical kernel in the x/y dimensions.
-    ball_z_size : int
-        Diameter of the spherical kernel in the z dimension.
-        Equal to the number of planes stacked to filter
+    ball_xy_size : float
+        Diameter of the spherical kernel (in microns) in the x/y dimensions.
+    ball_z_size : float
+        Diameter of the spherical kernel in the z dimension in microns.
+        Determines the number of planes stacked to filter
         the central plane of the stack.
     overlap_fraction : float
         The fraction of pixels within the spherical kernel that

{cellfinder-1.6.0 → cellfinder-1.8.0}/cellfinder/core/detect/filters/volume/structure_splitting.py

@@ -1,3 +1,4 @@
+from copy import copy
 from typing import List, Tuple, Type
 
 import numpy as np
@@ -224,6 +225,7 @@ def split_cells(
             where M is the number of individual cells and each centre is
             represented by its x, y, and z coordinates.
     """
+    settings = copy(settings)
     # these points are in x, y, z order columnwise, in absolute pixels
     orig_centre = get_structure_centre(cell_points)
 

{cellfinder-1.6.0 → cellfinder-1.8.0}/cellfinder/core/detect/filters/volume/volume_filter.py

@@ -140,7 +140,7 @@ class VolumeFilter:
             tensor = torch.empty(
                 (batch_size, *self.settings.plane_shape),
                 dtype=torch_dtype,
-                pin_memory=not cpu,
+                pin_memory=not cpu and self.settings.pin_memory,
                 device="cpu",
             )
 

{cellfinder-1.6.0 → cellfinder-1.8.0}/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()