cellfinder 1.1.0__py3-none-any.whl → 1.1.2__py3-none-any.whl

cellfinder/core/classify/cube_generator.py

@@ -197,9 +197,7 @@ class CubeGeneratorFromFile(Sequence):
         """
         return len(self.batches)
 
-    def __getitem__(
-        self, index: int
-    ) -> Union[
+    def __getitem__(self, index: int) -> Union[
         np.ndarray,
         Tuple[np.ndarray, List[Dict[str, float]]],
         Tuple[np.ndarray, Dict],
@@ -389,9 +387,7 @@ class CubeGeneratorFromDisk(Sequence):
         """
         return int(np.ceil(len(self.signal_list) / self.batch_size))
 
-    def __getitem__(
-        self, index: int
-    ) -> Union[
+    def __getitem__(self, index: int) -> Union[
         np.ndarray,
         Tuple[np.ndarray, List[Dict[str, float]]],
         Tuple[np.ndarray, Dict],

cellfinder/core/detect/detect.py

@@ -51,6 +51,16 @@ def calculate_parameters_in_pixels(
     ball_xy_size = int(round(ball_xy_size_um / mean_in_plane_pixel_size))
     ball_z_size = int(round(ball_z_size_um / float(voxel_sizes[0])))
 
+    if ball_z_size == 0:
+        raise ValueError(
+            "Ball z size has been calculated to be 0 voxels."
+            " This may be due to large axial spacing of your data or the "
+            "ball_z_size_um parameter being too small. "
+            "Please check input parameters are correct. "
+            "Note that cellfinder requires high resolution data in all "
+            "dimensions, so that cells can be detected in multiple "
+            "image planes."
+        )
     return soma_diameter, max_cluster_size, ball_xy_size, ball_z_size
 
 
@@ -76,11 +86,69 @@ def main(
     callback: Optional[Callable[[int], None]] = None,
 ) -> List[Cell]:
     """
+    Perform cell candidate detection on a 3D signal array.
+
     Parameters
     ----------
+    signal_array : numpy.ndarray
+        3D array representing the signal data.
+
+    start_plane : int
+        Index of the starting plane for detection.
+
+    end_plane : int
+        Index of the ending plane for detection.
+
+    voxel_sizes : Tuple[float, float, float]
+        Tuple of voxel sizes in each dimension (x, y, z).
+
+    soma_diameter : float
+        Diameter of the soma in physical units.
+
+    max_cluster_size : float
+        Maximum size of a cluster in physical units.
+
+    ball_xy_size : float
+        Size of the XY ball used for filtering in physical units.
+
+    ball_z_size : float
+        Size of the Z ball used for filtering in physical units.
+
+    ball_overlap_fraction : float
+        Fraction of overlap allowed between balls.
+
+    soma_spread_factor : float
+        Spread factor for soma size.
+
+    n_free_cpus : int
+        Number of free CPU cores available for parallel processing.
+
+    log_sigma_size : float
+        Size of the sigma for the log filter.
+
+    n_sds_above_mean_thresh : float
+        Number of standard deviations above the mean threshold.
+
+    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.
+
     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.
+
+    Returns
+    -------
+    List[Cell]
+        List of detected cells.
     """
     if not np.issubdtype(signal_array.dtype, np.integer):
         raise ValueError(
@@ -107,6 +175,7 @@ def main(
     if end_plane == -1:
         end_plane = len(signal_array)
     signal_array = signal_array[start_plane:end_plane]
+    signal_array = signal_array.astype(np.uint32)
 
     callback = callback or (lambda *args, **kwargs: None)
 
@@ -169,11 +238,11 @@ def main(
         # processes.
         cells = mp_3d_filter.process(async_results, locks, callback=callback)
 
-    print(
-        "Detection complete - all planes done in : {}".format(
-            datetime.now() - start_time
-        )
+    time_elapsed = datetime.now() - start_time
+    logger.debug(
+        f"All Planes done. Found {len(cells)} cells in {format(time_elapsed)}"
     )
+    print("Detection complete - all planes done in : {}".format(time_elapsed))
     return cells
 
 

cellfinder/core/detect/filters/plane/classical_filter.py

@@ -6,6 +6,31 @@ from scipy.signal import medfilt2d
 def enhance_peaks(
     img: np.ndarray, clipping_value: float, gaussian_sigma: float = 2.5
 ) -> np.ndarray:
+    """
+    Enhances the peaks (bright pixels) in an input image.
+
+    Parameters:
+    ----------
+    img : np.ndarray
+        Input image.
+    clipping_value : float
+        Maximum value for the enhanced image.
+    gaussian_sigma : float, optional
+        Standard deviation for the Gaussian filter. Default is 2.5.
+
+    Returns:
+    -------
+    np.ndarray
+        Enhanced image with peaks.
+
+    Notes:
+    ------
+    The enhancement process includes the following steps:
+    1. Applying a 2D median filter.
+    2. Applying a Laplacian of Gaussian filter (LoG).
+    3. Multiplying by -1 (bright spots respond negative in a LoG).
+    4. Rescaling image values to range from 0 to clipping value.
+    """
     type_in = img.dtype
     filtered_img = medfilt2d(img.astype(np.float64))
     filtered_img = gaussian_filter(filtered_img, gaussian_sigma)

cellfinder/core/detect/filters/volume/ball_filter.py

@@ -104,7 +104,7 @@ class BallFilter:
 
         # Stores the current planes that are being filtered
         self.volume = np.empty(
-            (plane_width, plane_height, ball_z_size), dtype=np.uint16
+            (plane_width, plane_height, ball_z_size), dtype=np.uint32
         )
         # Index of the middle plane in the volume
         self.middle_z_idx = int(np.floor(ball_z_size / 2))
@@ -165,7 +165,7 @@ class BallFilter:
         Get the plane in the middle of self.volume.
         """
         z = self.middle_z_idx
-        return np.array(self.volume[:, :, z], dtype=np.uint16)
+        return np.array(self.volume[:, :, z], dtype=np.uint32)
 
     def walk(self) -> None:  # Highly optimised because most time critical
         ball_radius = self.ball_xy_size // 2
@@ -327,6 +327,6 @@ def _walk(
                     THRESHOLD_VALUE,
                     kernel,
                 ):
-                    volume[
-                        ball_centre_x, ball_centre_y, middle_z
-                    ] = SOMA_CENTRE_VALUE
+                    volume[ball_centre_x, ball_centre_y, middle_z] = (
+                        SOMA_CENTRE_VALUE
+                    )

cellfinder/core/detect/filters/volume/structure_splitting.py

@@ -28,7 +28,7 @@ def coords_to_volume(
     expanded_shape = [
         dim_size + ball_diameter for dim_size in get_shape(xs, ys, zs)
     ]
-    volume = np.zeros(expanded_shape, dtype=np.uint16)
+    volume = np.zeros(expanded_shape, dtype=np.uint32)
 
     x_min, y_min, z_min = xs.min(), ys.min(), zs.min()
 
@@ -38,7 +38,7 @@ def coords_to_volume(
 
     # OPTIMISE: vectorize
     for rel_x, rel_y, rel_z in zip(relative_xs, relative_ys, relative_zs):
-        volume[rel_x, rel_y, rel_z] = 65534
+        volume[rel_x, rel_y, rel_z] = np.iinfo(volume.dtype).max - 1
     return volume
 
 
@@ -49,6 +49,26 @@ def ball_filter_imgs(
     ball_xy_size: int = 3,
     ball_z_size: int = 3,
 ) -> Tuple[np.ndarray, np.ndarray]:
+    """
+    Apply ball filtering to a 3D volume and detect cell centres.
+
+    Uses the `BallFilter` class to perform ball filtering on the volume
+    and the `CellDetector` class to detect cell centres.
+
+    Args:
+        volume (np.ndarray): The 3D volume to be filtered.
+        threshold_value (int): The threshold value for ball filtering.
+        soma_centre_value (int): The value representing the soma centre.
+        ball_xy_size (int, optional):
+            The size of the ball filter in the XY plane. Defaults to 3.
+        ball_z_size (int, optional):
+            The size of the ball filter in the Z plane. Defaults to 3.
+
+    Returns:
+        Tuple[np.ndarray, np.ndarray]:
+            A tuple containing the filtered volume and the cell centres.
+
+    """
     # OPTIMISE: reuse ball filter instance
 
     good_tiles_mask = np.ones((1, 1, volume.shape[2]), dtype=bool)
@@ -71,10 +91,10 @@ def ball_filter_imgs(
     )
 
     # FIXME: hard coded type
-    ball_filtered_volume = np.zeros(volume.shape, dtype=np.uint16)
+    ball_filtered_volume = np.zeros(volume.shape, dtype=np.uint32)
     previous_plane = None
     for z in range(volume.shape[2]):
-        bf.append(volume[:, :, z].astype(np.uint16), good_tiles_mask[:, :, z])
+        bf.append(volume[:, :, z].astype(np.uint32), good_tiles_mask[:, :, z])
         if bf.ready:
             bf.walk()
             middle_plane = bf.get_middle_plane()
@@ -89,11 +109,24 @@ def ball_filter_imgs(
 def iterative_ball_filter(
     volume: np.ndarray, n_iter: int = 10
 ) -> Tuple[List[int], List[np.ndarray]]:
+    """
+    Apply iterative ball filtering to the given volume.
+    The volume is eroded at each iteration, by subtracting 1 from the volume.
+
+    Parameters:
+        volume (np.ndarray): The input volume.
+        n_iter (int): The number of iterations to perform. Default is 10.
+
+    Returns:
+        Tuple[List[int], List[np.ndarray]]: A tuple containing two lists:
+            The structures found in each iteration.
+            The cell centres found in each iteration.
+    """
     ns = []
     centres = []
 
-    threshold_value = 65534
-    soma_centre_value = 65535
+    threshold_value = np.iinfo(volume.dtype).max - 1
+    soma_centre_value = np.iinfo(volume.dtype).max
 
     vol = volume.copy()  # TODO: check if required
 
@@ -131,6 +164,21 @@ def check_centre_in_cuboid(centre: np.ndarray, max_coords: np.ndarray) -> bool:
 def split_cells(
     cell_points: np.ndarray, outlier_keep: bool = False
 ) -> np.ndarray:
+    """
+    Split the given cell points into individual cell centres.
+
+    Args:
+        cell_points (np.ndarray): Array of cell points with shape (N, 3),
+            where N is the number of cell points and each point is represented
+            by its x, y, and z coordinates.
+        outlier_keep (bool, optional): Flag indicating whether to keep outliers
+            during the splitting process. Defaults to False.
+
+    Returns:
+        np.ndarray: Array of absolute cell centres with shape (M, 3),
+            where M is the number of individual cells and each centre is
+            represented by its x, y, and z coordinates.
+    """
     orig_centre = get_structure_centre(cell_points)
 
     xs = cell_points[:, 0]

cellfinder/core/detect/filters/volume/volume_filter.py

@@ -142,6 +142,10 @@ class VolumeFilter(object):
         )
 
         cells = []
+
+        logger.debug(
+            f"Processing {len(self.cell_detector.coords_maps.items())} cells"
+        )
         for cell_id, cell_points in self.cell_detector.coords_maps.items():
             cell_volume = len(cell_points)
 
@@ -191,6 +195,7 @@ class VolumeFilter(object):
                         )
                     )
 
+        logger.debug("Finished splitting cell clusters.")
         return cells
 
 

cellfinder/core/download/cli.py

@@ -3,7 +3,7 @@ from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
 from pathlib import Path
 
 from cellfinder.core.download import models
-from cellfinder.core.download.download import amend_cfg
+from cellfinder.core.download.download import amend_user_configuration
 
 home = Path.home()
 DEFAULT_DOWNLOAD_DIRECTORY = home / ".cellfinder"
@@ -65,7 +65,7 @@ def main():
         model_path = models.main(args.model, args.install_path)
 
     if not args.no_amend_config:
-        amend_cfg(new_model_path=model_path)
+        amend_user_configuration(new_model_path=model_path)
 
 
 if __name__ == "__main__":

cellfinder/core/download/download.py

@@ -7,8 +7,8 @@ from brainglobe_utils.general.config import get_config_obj
 from brainglobe_utils.general.system import disk_free_gb
 
 from cellfinder.core.tools.source_files import (
-    source_config_cellfinder,
-    source_custom_config_cellfinder,
+    default_configuration_path,
+    user_specific_configuration_path,
 )
 
 
@@ -75,16 +75,45 @@ def download(
         os.remove(download_path)
 
 
-def amend_cfg(new_model_path=None):
-    print("Ensuring custom config file is correct")
-
-    original_config = source_config_cellfinder()
-    new_config = source_custom_config_cellfinder()
-    if new_model_path is not None:
-        write_model_to_cfg(new_model_path, original_config, new_config)
+def amend_user_configuration(new_model_path=None) -> None:
+    """
+    Amends the user configuration to contain the configuration
+    in new_model_path, if specified.
 
+    Parameters
+    ----------
+    new_model_path : str, optional
+        The path to the new model configuration.
+    """
+    print("(Over-)writing custom user configuration")
 
-def write_model_to_cfg(new_model_path, orig_config, custom_config):
+    original_config = default_configuration_path()
+    new_config = user_specific_configuration_path()
+    if new_model_path is not None:
+        write_model_to_config(new_model_path, original_config, new_config)
+
+
+def write_model_to_config(new_model_path, orig_config, custom_config):
+    """
+    Update the model path in the custom configuration file, by
+    reading the lines in the original configuration file, replacing
+    the line starting with "model_path =" and writing these
+    lines to the custom file.
+
+    Parameters
+    ----------
+    new_model_path : str
+        The new path to the model.
+    orig_config : str
+        The path to the original configuration file.
+    custom_config : str
+        The path to the custom configuration file to be created.
+
+    Returns
+    -------
+    None
+
+    """
     config_obj = get_config_obj(orig_config)
     model_conf = config_obj["model"]
     orig_path = model_conf["model_path"]

cellfinder/core/main.py

@@ -2,6 +2,7 @@
 N.B imports are within functions to prevent tensorflow being imported before
 it's warnings are silenced
 """
+
 import os
 from typing import Callable, List, Optional, Tuple
 

cellfinder/core/tools/prep.py

@@ -3,6 +3,7 @@ prep
 ==================
 Functions to prepare files and directories needed for other functions
 """
+
 import os
 from pathlib import Path
 from typing import Optional
@@ -13,8 +14,8 @@ from brainglobe_utils.general.system import get_num_processes
 import cellfinder.core.tools.tf as tf_tools
 from cellfinder.core import logger
 from cellfinder.core.download import models as model_download
-from cellfinder.core.download.download import amend_cfg
-from cellfinder.core.tools.source_files import source_custom_config_cellfinder
+from cellfinder.core.download.download import amend_user_configuration
+from cellfinder.core.tools.source_files import user_specific_configuration_path
 
 home = Path.home()
 DEFAULT_INSTALL_PATH = home / ".cellfinder"
@@ -48,18 +49,18 @@ def prep_models(
     if model_weights_path is None:
         logger.debug("No model supplied, so using the default")
 
-        config_file = source_custom_config_cellfinder()
+        config_file = user_specific_configuration_path()
 
         if not Path(config_file).exists():
             logger.debug("Custom config does not exist, downloading models")
             model_path = model_download.main(model_name, install_path)
-            amend_cfg(new_model_path=model_path)
+            amend_user_configuration(new_model_path=model_path)
 
         model_weights = get_model_weights(config_file)
         if not model_weights.exists():
             logger.debug("Model weights do not exist, downloading")
             model_path = model_download.main(model_name, install_path)
-            amend_cfg(new_model_path=model_path)
+            amend_user_configuration(new_model_path=model_path)
             model_weights = get_model_weights(config_file)
     else:
         model_weights = Path(model_weights_path)

cellfinder/core/tools/source_files.py

@@ -1,9 +1,27 @@
 from pathlib import Path
 
 
-def source_config_cellfinder():
+def default_configuration_path():
+    """
+    Returns the default configuration path for cellfinder.
+
+    Returns:
+        Path: The default configuration path.
+    """
     return Path(__file__).parent.parent / "config" / "cellfinder.conf"
 
 
-def source_custom_config_cellfinder():
-    return Path(__file__).parent.parent / "config" / "cellfinder.conf.custom"
+def user_specific_configuration_path():
+    """
+    Returns the path to the user-specific configuration file for cellfinder.
+
+    This function returns the path to the user-specific configuration file
+    for cellfinder. The user-specific configuration file is located in the
+    user's home directory under the ".cellfinder" folder and is named
+    "cellfinder.conf.custom".
+
+    Returns:
+        Path: The path to the custom configuration file.
+
+    """
+    return Path.home() / ".cellfinder" / "cellfinder.conf.custom"

cellfinder/core/train/train_yml.py

@@ -338,7 +338,10 @@ def run(
 
     ensure_directory_exists(output_dir)
     model_weights = prep_model_weights(
-        install_path, model_weights, model, n_free_cpus
+        model_weights=model_weights,
+        install_path=install_path,
+        model_name=model,
+        n_free_cpus=n_free_cpus,
     )
 
     yaml_contents = parse_yaml(yaml_file)

cellfinder/napari/__init__.py

@@ -1,3 +0,0 @@
-__version__ = "0.0.20"
-__author__ = "Adam Tyson"
-__license__ = "GPL-3.0"

cellfinder/napari/curation.py

@@ -6,7 +6,10 @@ import numpy as np
 import tifffile
 from brainglobe_napari_io.cellfinder.utils import convert_layer_to_cells
 from brainglobe_utils.cells.cells import Cell
+from brainglobe_utils.general.system import delete_directory_contents
 from brainglobe_utils.IO.yaml import save_yaml
+from brainglobe_utils.qtpy.dialog import display_warning
+from brainglobe_utils.qtpy.interaction import add_button, add_combobox
 from magicgui.widgets import ProgressBar
 from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_info
@@ -20,8 +23,6 @@ from qtpy.QtWidgets import (
     QWidget,
 )
 
-from .utils import add_button, add_combobox, display_question
-
 # Constants used throughout
 WINDOW_HEIGHT = 750
 WINDOW_WIDTH = 1500
@@ -69,6 +70,7 @@ class CurationWidget(QWidget):
         self.output_directory: Optional[Path] = None
 
         self.setup_main_layout()
+        self.setup_keybindings()
 
         @self.viewer.layers.events.connect
         def update_layer_list(v: napari.viewer.Viewer):
@@ -173,33 +175,35 @@ class CurationWidget(QWidget):
             self.load_data_layout,
             "Training_data (non_cells)",
             self.point_layer_names,
-            4,
+            row=4,
             callback=self.set_training_data_non_cell,
         )
         self.mark_as_cell_button = add_button(
             "Mark as cell(s)",
             self.load_data_layout,
             self.mark_as_cell,
-            5,
+            row=5,
+            tooltip="Mark all selected points as non cell. Shortcut: 'c'",
         )
         self.mark_as_non_cell_button = add_button(
             "Mark as non cell(s)",
             self.load_data_layout,
             self.mark_as_non_cell,
-            5,
+            row=5,
             column=1,
+            tooltip="Mark all selected points as non cell. Shortcut: 'x'",
         )
         self.add_training_data_button = add_button(
             "Add training data layers",
             self.load_data_layout,
             self.add_training_data,
-            6,
+            row=6,
         )
         self.save_training_data_button = add_button(
             "Save training data",
             self.load_data_layout,
             self.save_training_data,
-            6,
+            row=6,
             column=1,
         )
         self.load_data_layout.setColumnMinimumWidth(0, COLUMN_WIDTH)
@@ -207,6 +211,10 @@ class CurationWidget(QWidget):
         self.load_data_panel.setVisible(True)
         self.layout.addWidget(self.load_data_panel, row, column, 1, 1)
 
+    def setup_keybindings(self):
+        self.viewer.bind_key("c", self.mark_as_cell)
+        self.viewer.bind_key("x", self.mark_as_non_cell)
+
     def set_signal_image(self):
         """
         Set signal layer from current signal text box selection.
@@ -245,9 +253,9 @@ class CurationWidget(QWidget):
             self.training_data_non_cell_layer = self.viewer.layers[
                 self.training_data_non_cell_choice.currentText()
             ]
-            self.training_data_non_cell_layer.metadata[
-                "point_type"
-            ] = Cell.UNKNOWN
+            self.training_data_non_cell_layer.metadata["point_type"] = (
+                Cell.UNKNOWN
+            )
             self.training_data_non_cell_layer.metadata["training_data"] = True
 
     def add_training_data(self):
@@ -256,7 +264,7 @@ class CurationWidget(QWidget):
 
         overwrite = False
         if self.training_data_cell_layer or self.training_data_non_cell_layer:
-            overwrite = display_question(
+            overwrite = display_warning(
                 self,
                 "Training data layers exist",
                 "Training data layers already exist,  "
@@ -303,10 +311,10 @@ class CurationWidget(QWidget):
         )
         self.training_data_non_cell_choice.setCurrentText(non_cell_name)
 
-    def mark_as_cell(self):
+    def mark_as_cell(self, viewer=None):
         self.mark_point_as_type("cell")
 
-    def mark_as_non_cell(self):
+    def mark_as_non_cell(self, viewer=None):
         self.mark_point_as_type("non-cell")
 
     def mark_point_as_type(self, point_type: str):
@@ -363,7 +371,10 @@ class CurationWidget(QWidget):
             )
 
     def save_training_data(
-        self, *, block: bool = False, prompt_for_directory: bool = True
+        self,
+        *,
+        block: bool = False,
+        prompt_for_directory: bool = True,
     ) -> None:
         """
         Parameters
@@ -373,16 +384,45 @@ class CurationWidget(QWidget):
         prompt_for_directory :
             If `True` show a file dialog for the user to select a directory.
         """
+
         if self.is_data_extractable():
             if prompt_for_directory:
                 self.get_output_directory()
+                # if the directory is not empty
+                if any(self.output_directory.iterdir()):
+                    choice = display_warning(
+                        self,
+                        "About to save training data",
+                        "Existing files will be will be deleted. Proceed?",
+                    )
+                    if not choice:
+                        return
             if self.output_directory is not None:
+                self.__prep_directories_for_save()
                 self.__extract_cubes(block=block)
                 self.__save_yaml_file()
                 show_info("Done")
 
             self.update_status_label("Ready")
 
+    def __prep_directories_for_save(self):
+        self.yaml_filename = self.output_directory / "training.yml"
+        self.cell_cube_dir = self.output_directory / "cells"
+        self.no_cell_cube_dir = self.output_directory / "non_cells"
+
+        self.__delete_existing_saved_training_data()
+
+    def __delete_existing_saved_training_data(self):
+        self.yaml_filename.unlink(missing_ok=True)
+        for directory in (
+            self.cell_cube_dir,
+            self.no_cell_cube_dir,
+        ):
+            if directory.exists():
+                delete_directory_contents(directory)
+            else:
+                directory.mkdir(exist_ok=True, parents=True)
+
     def __extract_cubes(self, *, block=False):
         """
         Parameters
@@ -489,18 +529,16 @@ class CurationWidget(QWidget):
         self.non_cells_to_extract = list(set(self.non_cells_to_extract))
 
     def __save_yaml_file(self):
-        # TODO: implement this in a portable way
-        yaml_filename = self.output_directory / "training.yml"
         yaml_section = [
             {
-                "cube_dir": str(self.output_directory / "cells"),
+                "cube_dir": str(self.cell_cube_dir),
                 "cell_def": "",
                 "type": "cell",
                 "signal_channel": 0,
                 "bg_channel": 1,
             },
             {
-                "cube_dir": str(self.output_directory / "non_cells"),
+                "cube_dir": str(self.no_cell_cube_dir),
                 "cell_def": "",
                 "type": "no_cell",
                 "signal_channel": 0,
@@ -509,7 +547,7 @@ class CurationWidget(QWidget):
         ]
 
         yaml_contents = {"data": yaml_section}
-        save_yaml(yaml_contents, yaml_filename)
+        save_yaml(yaml_contents, self.yaml_filename)
 
     def update_progress(self, attributes: dict):
         """
@@ -538,9 +576,15 @@ class CurationWidget(QWidget):
             "non_cells": self.non_cells_to_extract,
         }
 
-        for cell_type, cell_list in to_extract.items():
-            cell_type_output_directory = self.output_directory / cell_type
-            cell_type_output_directory.mkdir(exist_ok=True, parents=True)
+        directories = {
+            "cells": self.cell_cube_dir,
+            "non_cells": self.no_cell_cube_dir,
+        }
+
+        for cell_type in ["cells", "non_cells"]:
+            cell_type_output_directory = directories[cell_type]
+            cell_list = to_extract[cell_type]
+
             self.update_status_label(f"Saving {cell_type}...")
 
             cube_generator = CubeGeneratorFromFile(

cellfinder/napari/train/train.py

@@ -5,6 +5,7 @@ from magicgui import magicgui
 from magicgui.widgets import FunctionGui, PushButton
 from napari.qt.threading import thread_worker
 from napari.utils.notifications import show_info
+from qtpy.QtWidgets import QScrollArea
 
 from cellfinder.core.train.train_yml import run as train_yml
 from cellfinder.napari.utils import (
@@ -48,6 +49,7 @@ def training_widget() -> FunctionGui:
         **MiscTrainingInputs.widget_representation(),
         call_button=True,
         reset_button=dict(widget_type="PushButton", text="Reset defaults"),
+        scrollable=True,
     )
     def widget(
         header: dict,
@@ -175,4 +177,8 @@ def training_widget() -> FunctionGui:
             if value is not None:
                 getattr(widget, name).value = value
 
+    scroll = QScrollArea()
+    scroll.setWidget(widget._widget._qwidget)
+    widget._widget._qwidget = scroll
+
     return widget

cellfinder/napari/utils.py

@@ -1,18 +1,10 @@
-from typing import Callable, List, Optional, Tuple
+from typing import List, Tuple
 
 import napari
 import numpy as np
 import pandas as pd
 from brainglobe_utils.cells.cells import Cell
 from pkg_resources import resource_filename
-from qtpy.QtWidgets import (
-    QComboBox,
-    QLabel,
-    QLayout,
-    QMessageBox,
-    QPushButton,
-    QWidget,
-)
 
 brainglobe_logo = resource_filename(
     "cellfinder", "napari/images/brainglobe.png"
@@ -98,83 +90,3 @@ def cells_to_array(cells: List[Cell]) -> Tuple[np.ndarray, np.ndarray]:
     points = cells_df_as_np(df[df["type"] == Cell.CELL])
     rejected = cells_df_as_np(df[df["type"] == Cell.UNKNOWN])
     return points, rejected
-
-
-def add_combobox(
-    layout: QLayout,
-    label: str,
-    items: List[str],
-    row: int,
-    column: int = 0,
-    label_stack: bool = False,
-    callback=None,
-    width: int = 150,
-) -> Tuple[QComboBox, Optional[QLabel]]:
-    """
-    Add a selection box to *layout*.
-    """
-    if label_stack:
-        combobox_row = row + 1
-        combobox_column = column
-    else:
-        combobox_row = row
-        combobox_column = column + 1
-    combobox = QComboBox()
-    combobox.addItems(items)
-    if callback:
-        combobox.currentIndexChanged.connect(callback)
-    combobox.setMaximumWidth = width
-
-    if label is not None:
-        combobox_label = QLabel(label)
-        combobox_label.setMaximumWidth = width
-        layout.addWidget(combobox_label, row, column)
-    else:
-        combobox_label = None
-
-    layout.addWidget(combobox, combobox_row, combobox_column)
-    return combobox, combobox_label
-
-
-def add_button(
-    label: str,
-    layout: QLayout,
-    connected_function: Callable,
-    row: int,
-    column: int = 0,
-    visibility: bool = True,
-    minimum_width: int = 0,
-    alignment: str = "center",
-) -> QPushButton:
-    """
-    Add a button to *layout*.
-    """
-    button = QPushButton(label)
-    if alignment == "center":
-        pass
-    elif alignment == "left":
-        button.setStyleSheet("QPushButton { text-align: left; }")
-    elif alignment == "right":
-        button.setStyleSheet("QPushButton { text-align: right; }")
-
-    button.setVisible(visibility)
-    button.setMinimumWidth(minimum_width)
-    layout.addWidget(button, row, column)
-    button.clicked.connect(connected_function)
-    return button
-
-
-def display_question(widget: QWidget, title: str, message: str) -> bool:
-    """
-    Display a warning in a pop up that informs about overwriting files.
-    """
-    message_reply = QMessageBox.question(
-        widget,
-        title,
-        message,
-        QMessageBox.Yes | QMessageBox.Cancel,
-    )
-    if message_reply == QMessageBox.Yes:
-        return True
-    else:
-        return False

{cellfinder-1.1.0.dist-info → cellfinder-1.1.2.dist-info}/METADATA

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.1.0
+Version: 1.1.2
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
 Project-URL: Homepage, https://brainglobe.info/documentation/cellfinder/index.html
-Project-URL: Source Code, https://github.com/brainglobe/cellfinder-core
-Project-URL: Bug Tracker, https://github.com/brainglobe/cellfinder-core/issues
+Project-URL: Source Code, https://github.com/brainglobe/cellfinder
+Project-URL: Bug Tracker, https://github.com/brainglobe/cellfinder/issues
 Project-URL: Documentation, https://brainglobe.info/documentation/cellfinder/index.html
 Project-URL: User Support, https://forum.image.sc/tag/brainglobe
 Classifier: Development Status :: 4 - Beta
@@ -22,7 +22,8 @@ Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: brainglobe-utils
+Requires-Dist: brainglobe-utils >=0.4.2
+Requires-Dist: brainglobe-napari-io >=0.3.4
 Requires-Dist: dask[array]
 Requires-Dist: fancylog >=0.0.7
 Requires-Dist: natsort
@@ -39,7 +40,6 @@ Requires-Dist: black ; extra == 'dev'
 Requires-Dist: pre-commit ; extra == 'dev'
 Requires-Dist: pyinstrument ; extra == 'dev'
 Requires-Dist: pytest-cov ; extra == 'dev'
-Requires-Dist: pytest-lazy-fixture ; extra == 'dev'
 Requires-Dist: pytest-mock ; extra == 'dev'
 Requires-Dist: pytest-qt ; extra == 'dev'
 Requires-Dist: pytest-timeout ; extra == 'dev'
@@ -59,7 +59,7 @@ Requires-Dist: qtpy ; extra == 'napari'
 [![Downloads](https://pepy.tech/badge/cellfinder-core)](https://pepy.tech/project/cellfinder)
 [![Wheel](https://img.shields.io/pypi/wheel/cellfinder-core.svg)](https://pypi.org/project/cellfinder)
 [![Development Status](https://img.shields.io/pypi/status/cellfinder-core.svg)](https://github.com/brainglobe/cellfinder)
-[![Tests](https://img.shields.io/github/workflow/status/brainglobe/cellfinder-core/tests)](https://github.com/brainglobe/cellfinder/actions)
+[![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/cellfinder/test_and_deploy.yml?branch=main)](https://github.com/brainglobe/cellfinder/actions)
 [![codecov](https://codecov.io/gh/brainglobe/cellfinder-core/branch/main/graph/badge.svg?token=nx1lhNI7ox)](https://codecov.io/gh/brainglobe/cellfinder)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)

{cellfinder-1.1.0.dist-info → cellfinder-1.1.2.dist-info}/RECORD

@@ -1,63 +1,63 @@
 cellfinder/__init__.py,sha256=XwXxMZJgw62dOHhrAKMQk0CE3378WRQWoC-kpf5LLpE,935
 cellfinder/cli_migration_warning.py,sha256=gPtNrtnXvWpl5q0k_EGAQZg0DwcpCmuBTgpg56n5NfA,1578
 cellfinder/core/__init__.py,sha256=pRFuQsl78HEK0S6gvhJw70QLbjjSBzP-GFO0AtVaGtk,62
-cellfinder/core/main.py,sha256=LJTtx-cdbRwZZStMcd2tNxRIC_kWvbjvicBsJu4UNMs,3899
+cellfinder/core/main.py,sha256=3Wg4QvBUlaHq04Yltjg9FSiePAhtGeFL1C-6Z1SI0Gk,3900
 cellfinder/core/types.py,sha256=lTqWE4v0SMM0qLAZJdyAzqV1nLgDtobEpglNJcXt160,106
 cellfinder/core/classify/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/classify/augment.py,sha256=8dMbM7KhimM6NMgdMC53oHoCfYj1CIB-h3Yk8CZAxPw,6321
 cellfinder/core/classify/classify.py,sha256=y4EnHX3IpAUAfhGScoJGv2hLLpy6OtmGvkqxAow3_Kw,3046
-cellfinder/core/classify/cube_generator.py,sha256=01PAvXlcddSx8KY3VKKGlcWT6cPWP1Uaq0H9bYEf2uo,16614
+cellfinder/core/classify/cube_generator.py,sha256=4zMaa7bb7vr1QxBFpzqqitnWaNdzgEzZ2gt2xFeN37A,16586
 cellfinder/core/classify/resnet.py,sha256=976Qt0li7ySYx_w2m9QfRMaDAc0rEkA8rO9SYP5a6uw,10057
 cellfinder/core/classify/tools.py,sha256=UqABKS9KnkwR3PIhGRl7xHJbADP0mgVRSxXI5dybpqA,2547
 cellfinder/core/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/config/cellfinder.conf,sha256=5i8axif7ekMutKDiVnZRs-LiJrgVQljg_beltidqtNk,56
 cellfinder/core/detect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/core/detect/detect.py,sha256=mMrLt2mi01y6pxhipfuPDPBFGaPwHWkM7mdmTcGxPlg,6832
+cellfinder/core/detect/detect.py,sha256=bsiOPyxM3D_YZiYxqyauTxe7C4C2-rb_9yYiJiYaylM,9102
 cellfinder/core/detect/filters/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/detect/filters/setup_filters.py,sha256=sUyZ2dKbfwhn4YTq3kLVTHkckZZ460AVozLfoz7hJK8,2084
 cellfinder/core/detect/filters/plane/__init__.py,sha256=lybcPbVDnurEQeq2FiLq0zR8p_ztarQOlajhdh1Q2-4,40
-cellfinder/core/detect/filters/plane/classical_filter.py,sha256=SI-tgWzGvqUah_2bSeQnjWyK8Espz9q73-t4lQxjggE,626
+cellfinder/core/detect/filters/plane/classical_filter.py,sha256=Nton_nrvv6LhNlK10HnS0TIHsjapBiMJPURgzYh2myY,1331
 cellfinder/core/detect/filters/plane/plane_filter.py,sha256=PWcAHDKB3qn3i9aSmQzUTEi3tgmccrf24DipjnYbOg0,2746
 cellfinder/core/detect/filters/plane/tile_walker.py,sha256=lhKrq-MB35bR0_JYgj7WMR4otuaZ6XRDDhJhKyH1yS8,3001
 cellfinder/core/detect/filters/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/core/detect/filters/volume/ball_filter.py,sha256=lOpqugdDLuYgnZfLFHfXy667pblgrVIe-lT1TxqPQCI,11173
+cellfinder/core/detect/filters/volume/ball_filter.py,sha256=nNGYAjDWst4Ufh6o6LAb5CVi5hFqYi2ObyrwgChbkQw,11175
 cellfinder/core/detect/filters/volume/structure_detection.py,sha256=8lSyDFiqn5lYoE_mDLpXTUOsWGVm2-suGttZBdDAqmA,9152
-cellfinder/core/detect/filters/volume/structure_splitting.py,sha256=8CHQ7Qgwb1KYbOFsgzo-vOR3LjpTXSxyGFltcisNxDo,5693
-cellfinder/core/detect/filters/volume/volume_filter.py,sha256=Ul3ikwCGJqmkjFArCcXOJ_4ayLSP9v7X35KlbQrLWd4,6704
+cellfinder/core/detect/filters/volume/structure_splitting.py,sha256=VuXKAOHG6f63ommPxZC08JRoegbQgZUReZAmvY5nm_U,7656
+cellfinder/core/detect/filters/volume/volume_filter.py,sha256=nBc9kZhsZ2jsyuzizXcx6s0i5-Vc7BfUfDqtIxhGUSo,6873
 cellfinder/core/download/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/core/download/cli.py,sha256=XgWU_a_cA-3dOyWmrR_cB6KdOoJmWoINRo9_QXy9mEg,1777
-cellfinder/core/download/download.py,sha256=wf-vWuINuj2Lng4JczXTjOzWf8kSIi2wKfxumd4mp0s,3002
+cellfinder/core/download/cli.py,sha256=uejrDBoveybeyMq-tcn8460r2Hf3iC1FhpEC2sXs7EI,1807
+cellfinder/core/download/download.py,sha256=k7DZwox6UWhL4Efz1CK0VqG6jNVkotcomKHMZIlunTQ,3797
 cellfinder/core/download/models.py,sha256=mLb6wAUn-tH1FtgvQU6ooLXqXetTP4D5Jd4_gPN-kJo,1359
 cellfinder/core/tools/IO.py,sha256=q-euCP1s3iuWYvD2V72sPSBfwr5A1ETcL6Z_K41mLV0,1235
 cellfinder/core/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/tools/array_operations.py,sha256=LDbqWA_N2YtxeKS877QYdJRL2FCMC1R1ExJtdb6-vEA,3371
 cellfinder/core/tools/geometry.py,sha256=xlEQQmVQ9jcXqRzUqU554P8VxkaWkc5J_YhjkkKlI0Q,1124
 cellfinder/core/tools/image_processing.py,sha256=z27bGjf3Iv3G4Nt1OYzpEnIYQNc4nNomj_QitqvZB78,2269
-cellfinder/core/tools/prep.py,sha256=OdE722NIIBE_zAYum_h7oPZf1WXFDdkdof-_4p4QKPQ,2505
-cellfinder/core/tools/source_files.py,sha256=J3gThEoJGaNeJXHUG3finw0kg4qQ_zuLJ9i5O-2srp4,249
+cellfinder/core/tools/prep.py,sha256=A1tfHZmkGFpbb7cjLdfP8KavZNqRwzdum92NW8Et01o,2553
+cellfinder/core/tools/source_files.py,sha256=NCPeA_kvnPWgS_fxWarc-9nBNjxkgL1xMFg-Co_kPlA,791
 cellfinder/core/tools/system.py,sha256=6iSOLrz2mtKgOIdwjp_VS0-74XQCuaQYCvWAViJgEus,2232
 cellfinder/core/tools/tf.py,sha256=jNU97-gIB51rLube9EoZ9bREkbqWRk-xPZhDTXG_jE4,1713
 cellfinder/core/tools/tiff.py,sha256=NzIz6wq2GzxmcIhawFMwZADe-uQO2rIG46H7xkpGKLs,2899
 cellfinder/core/tools/tools.py,sha256=G8oDGNRuWkzEJDnnC4r3SNGgpVbqbelCZR5ODk9JRzs,4867
 cellfinder/core/train/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/core/train/train_yml.py,sha256=n-mvcPM6u413JpzW7S6ow-5dJC2hEPGkezvXzT0yXhA,13139
-cellfinder/napari/__init__.py,sha256=STu4EgG0BBSD2yXQUVgP2coXt1LZLsCEP3SI-latdcM,73
-cellfinder/napari/curation.py,sha256=2n8_M2Wqr1JyP19V4-vZyiYmZbv61tzzu4WF-n5OKfs,19844
+cellfinder/core/train/train_yml.py,sha256=TO_8e6Uz1S-P49o53gB_4i97Afz6RCHqmyyIrA70TZ8,13214
+cellfinder/napari/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+cellfinder/napari/curation.py,sha256=jz7GekuuzOdwiEFLarvvO5Bho68k8eL7AjObMdEoPXw,21447
 cellfinder/napari/input_container.py,sha256=tkm0dkPt7kSL8Xkvs1fh8M6vKWw57QLIt_wv74HFkGk,2150
 cellfinder/napari/napari.yaml,sha256=WMR1CIAmYIVyQngbdbomTRZLvlDbb6LxsXsvTRClQnE,921
 cellfinder/napari/sample_data.py,sha256=oUST23q09MM8dxHbUCmO0AjtXG6OlR_32LLqP0EU2UA,732
-cellfinder/napari/utils.py,sha256=m8kmpkebS5_S71uMs1OTEMX0ndjnEZtglfkhRnP57-g,4765
+cellfinder/napari/utils.py,sha256=mCy4Lr_gE2wWgRUSEiApNUjgLLAz0SSahTZnmUnRbgQ,2592
 cellfinder/napari/detect/__init__.py,sha256=BD9Bg9NTAr6yRTq2A_p58U6j4w5wbY0sdXwhPJ3MSMY,34
 cellfinder/napari/detect/detect.py,sha256=Jr4-lDGIntwcxSQ1Ne4xoA0SaKd4kf4zUT8MPyyO5ic,7443
 cellfinder/napari/detect/detect_containers.py,sha256=C_tN7qwWNHhYFRRn_2yQ7QDyxpj3pQXLZalO0UQ_cbw,5020
 cellfinder/napari/detect/thread_worker.py,sha256=BchLapCyML4SBDfihsqNLvqGM8FVcXEejaGg8MSkMCs,2604
 cellfinder/napari/images/brainglobe.png,sha256=IT2zfikD2vKTOg--e6bMRHr5mC2x3s-eOt_t0eblvQ0,21216
 cellfinder/napari/train/__init__.py,sha256=xo4CK-DvSecInGEc2ohcTgQYlH3iylFnGvKTCoq2WkI,35
-cellfinder/napari/train/train.py,sha256=CF5im8kYbO4oMkvNVoCJ5KM28gdBHM9Vqy9bsaAhxrA,5886
+cellfinder/napari/train/train.py,sha256=Cv8ivPWZoJJ-Iq1vW1JUmViaSnBPeqs07jBvZfOZQLc,6061
 cellfinder/napari/train/train_containers.py,sha256=mYI_M1QssWgPBpkqViqgj1Ls32lVRUAjt6OGTqcrKI4,4390
-cellfinder-1.1.0.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
-cellfinder-1.1.0.dist-info/METADATA,sha256=RmB9QJEct2Ax-9kuF18H1ml_HtVeUQcIoWNLrrwbpds,6633
-cellfinder-1.1.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-cellfinder-1.1.0.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
-cellfinder-1.1.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
-cellfinder-1.1.0.dist-info/RECORD,,
+cellfinder-1.1.2.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
+cellfinder-1.1.2.dist-info/METADATA,sha256=uP0C6fbKBWInZTmOxAfR24SIgOomzbvZZW82CYjXYXI,6652
+cellfinder-1.1.2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+cellfinder-1.1.2.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
+cellfinder-1.1.2.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
+cellfinder-1.1.2.dist-info/RECORD,,

{cellfinder-1.1.0.dist-info → cellfinder-1.1.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any