cellfinder 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

cellfinder/__init__.py

@@ -1,3 +1,7 @@
-__version__ = "0.7.0"
-__author__ = "Adam Tyson, Christian Niedworok, Charly Rousseau"
-__license__ = "BSD-3-Clause"
+from importlib.metadata import metadata
+
+__version__ = metadata("cellfinder")["version"]
+__author__ = metadata("cellfinder")["author-email"]
+__license__ = metadata("cellfinder")["license"]
+
+del metadata

cellfinder/main.py

@@ -42,7 +42,7 @@ def cells_exist(points_file):
 
 def main():
     suppress_tf_logging(tf_suppress_log_messages)
-    from brainreg.main import main as register
+    from brainreg.core.main import main as register
 
     from cellfinder.tools import prep
 

cellfinder/tools/parser.py

@@ -16,8 +16,8 @@ from brainglobe_utils.general.numerical import (
     check_positive_float,
     check_positive_int,
 )
-from brainreg.cli import atlas_parse, geometry_parser, niftyreg_parse
-from brainreg.cli import backend_parse as brainreg_backend_parse
+from brainreg.core.cli import atlas_parse, geometry_parser, niftyreg_parse
+from brainreg.core.cli import backend_parse as brainreg_backend_parse
 from cellfinder_core.download.cli import (
     download_directory_parser,
     model_parser,

cellfinder/tools/prep.py

@@ -14,7 +14,7 @@ from pathlib import PurePath
 from bg_atlasapi import BrainGlobeAtlas
 from brainglobe_utils.general.exceptions import CommandLineInputError
 from brainglobe_utils.general.system import ensure_directory_exists
-from brainreg.paths import Paths as BrainRegPaths
+from brainreg.core.paths import Paths as BrainRegPaths
 from fancylog import fancylog
 
 import cellfinder as program_for_log

cellfinder/tools/tools.py

@@ -80,9 +80,9 @@ def get_number_of_bins_nd(array_size, binning):
     :param binning: How many pixels in each edge of nD equal sized bins
     :return:
     """
-    if type(array_size) is tuple:
+    if isinstance(array_size, tuple):
         bins = [int(size / binning) for size in array_size]
-    elif type(array_size) is dict:
+    elif isinstance(array_size, dict):
         bins = [int(size / binning) for size in array_size.values()]
     else:
         raise NotImplementedError(

{cellfinder-0.7.0.dist-info → cellfinder-0.8.0.dist-info}/METADATA

@@ -1,13 +1,43 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 0.7.0
+Version: 0.8.0
 Summary: Automated 3D cell detection and registration of whole-brain images
-Home-page: https://brainglobe.info/cellfinder
-Author: Adam Tyson, Christian Niedworok, Charly Rousseau
-Author-email: code@adamltyson.com
-Project-URL: Source Code, https://github.com/brainglobe/cellfinder
-Project-URL: Bug Tracker, https://github.com/brainglobe/cellfinder/issues
-Project-URL: Documentation, https://docs.brainglobe.info/cellfinder
+Author: Christian Niedworok, Charly Rousseau
+Author-email: Adam Tyson <code@adamltyson.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2020, University College London
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        * Redistributions of source code must retain the above copyright notice, this
+          list of conditions and the following disclaimer.
+        
+        * Redistributions in binary form must reproduce the above copyright notice,
+          this list of conditions and the following disclaimer in the documentation
+          and/or other materials provided with the distribution.
+        
+        * Neither the name of the copyright holder nor the names of its
+          contributors may be used to endorse or promote products derived from
+          this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: source, https://github.com/brainglobe/cellfinder
+Project-URL: bug_tracker, https://github.com/brainglobe/cellfinder/issues
+Project-URL: homepage, https://brainglobe.info
+Project-URL: documentation, https://brainglobe.info/documentation/cellfinder
 Classifier: Development Status :: 3 - Alpha
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Operating System :: Microsoft :: Windows :: Windows 10
@@ -18,16 +48,16 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: brainreg
-Requires-Dist: cellfinder-core (>=0.2.4)
+Requires-Dist: brainreg >=1.0.0
+Requires-Dist: cellfinder-core >=0.2.4
 Requires-Dist: configobj
-Requires-Dist: fancylog (>=0.0.7)
+Requires-Dist: fancylog >=0.0.7
 Requires-Dist: imio
-Requires-Dist: brainglobe-utils (>=0.2.5)
-Requires-Dist: multiprocessing-logging (>=0.3.4)
+Requires-Dist: brainglobe-utils >=0.2.5
+Requires-Dist: multiprocessing-logging >=0.3.4
 Requires-Dist: natsort
 Requires-Dist: numpy
 Requires-Dist: pandas
@@ -40,10 +70,9 @@ Requires-Dist: black ; extra == 'dev'
 Requires-Dist: pytest-cov ; extra == 'dev'
 Requires-Dist: pytest ; extra == 'dev'
 Requires-Dist: gitpython ; extra == 'dev'
-Requires-Dist: coverage (>=5.0.3) ; extra == 'dev'
-Requires-Dist: bump2version ; extra == 'dev'
+Requires-Dist: coverage >=5.0.3 ; extra == 'dev'
 Requires-Dist: pre-commit ; extra == 'dev'
-Requires-Dist: flake8 ; extra == 'dev'
+Requires-Dist: setuptools-scm ; extra == 'dev'
 Provides-Extra: napari
 Requires-Dist: napari[pyside2] ; extra == 'napari'
 Requires-Dist: brainglobe-napari-io ; extra == 'napari'

{cellfinder-0.7.0.dist-info → cellfinder-0.8.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
-cellfinder/__init__.py,sha256=Y0Iscj_uSldCL3OCYBpfjPquQ-dH2VAwtb1p4Mixr7s,115
-cellfinder/main.py,sha256=tMuq_GWHs8dsEew0RwwwKeDsFby9sZXvv5rSE354E5E,7385
+cellfinder/__init__.py,sha256=TOTszmwu6-ukckrUEstKsi1A0Yt6aue2P5OPE2NVt0U,203
+cellfinder/main.py,sha256=pIWLWp-rGp2-xDf6E9ehXyt9mjJMYTW8I0KWjBWCq4o,7390
 cellfinder/analyse/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/analyse/analyse.py,sha256=8Wf3nUpBqGdu2PuJFIzdHHDnrkSDsk0WZRUj5COCaM0,11010
 cellfinder/export/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -13,16 +13,13 @@ cellfinder/figures/figures.py,sha256=ughsNeTM6YnBtRakNfMB_jmPOTzaOgpqFdb28SZH4Ts
 cellfinder/figures/heatmap.py,sha256=ayKbv-vDhnpdv5vYIayEwzDmU_rmyzPQ7TknRvcouec,1951
 cellfinder/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/tools/image_processing.py,sha256=z27bGjf3Iv3G4Nt1OYzpEnIYQNc4nNomj_QitqvZB78,2269
-cellfinder/tools/parser.py,sha256=1kwryFA7hEBKrsbXkW0iEl03AAGqi4Ss7RkCkv9-l_c,13567
-cellfinder/tools/prep.py,sha256=bCEdUCsq_1sew_owuCCtEPn3YlEvTRu9WbePLzqGUk4,11119
+cellfinder/tools/parser.py,sha256=7FJFUi3OJcSpuXm1ikZIJIFen2_Y8FtI-13T-ZIzGiI,13577
+cellfinder/tools/prep.py,sha256=7SqxBdzP4U3tH4oWkYo7vnC79tgqLS5PTDW-KWwjyt4,11124
 cellfinder/tools/system.py,sha256=6iSOLrz2mtKgOIdwjp_VS0-74XQCuaQYCvWAViJgEus,2232
-cellfinder/tools/tools.py,sha256=0HqnTg0S1avKMQtb2SkiG43jvLTa-QhxNlujvztpubI,3627
-cellfinder/train/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/train/curation.py,sha256=qVwjqONEOPIMb0m4QDe5nCw86Rzt_LF3-2HFeQGrjbI,10588
-cellfinder/train/curation_old.py,sha256=peduW8pDuOlhqSoj91EXcy0bb3z7G1h8IdRvie-JxJ4,9019
-cellfinder-0.7.0.dist-info/LICENSE,sha256=zyXpitCrNwvc33VKBFomd9v6Ahi9x1H5fvfXDxCblM0,1525
-cellfinder-0.7.0.dist-info/METADATA,sha256=F7E6erjHB8V8-7aTwa7X_gPMvBi3yNg2oVvVt2F6bTU,9900
-cellfinder-0.7.0.dist-info/WHEEL,sha256=AtBG6SXL3KF_v0NxLf0ehyVOh0cold-JbJYXNGorC6Q,92
-cellfinder-0.7.0.dist-info/entry_points.txt,sha256=g7ZJi8oEOOxNuA3BXT_fAm9RKWtEZ3Vah6M-SlFt2wk,162
-cellfinder-0.7.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
-cellfinder-0.7.0.dist-info/RECORD,,
+cellfinder/tools/tools.py,sha256=Km4Y1p3yQOYi_dyTOZthJXcvUintIzTUYwDkuXGNc0A,3635
+cellfinder-0.8.0.dist-info/LICENSE,sha256=zyXpitCrNwvc33VKBFomd9v6Ahi9x1H5fvfXDxCblM0,1525
+cellfinder-0.8.0.dist-info/METADATA,sha256=LiFR_CUo5hxSYUBO4Un2NrdWc50ymOuym472Syi63ss,11634
+cellfinder-0.8.0.dist-info/WHEEL,sha256=Xo9-1PvkuimrydujYJAjF7pCkriuXBpUPEjma1nZyJ0,92
+cellfinder-0.8.0.dist-info/entry_points.txt,sha256=n3M2y93q1QNL0MnYqyaJ5yWl8j4YJ-OHitghTwiGuvk,52
+cellfinder-0.8.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
+cellfinder-0.8.0.dist-info/RECORD,,

{cellfinder-0.7.0.dist-info → cellfinder-0.8.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.0)
+Generator: bdist_wheel (0.41.3)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cellfinder-0.8.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+cellfinder = cellfinder.main:main

cellfinder/train/curation.py

@@ -1,355 +0,0 @@
-import json
-from pathlib import Path
-
-import napari
-import numpy as np
-from bg_atlasapi import BrainGlobeAtlas
-from brainglobe_utils.cells.cells import Cell
-from brainglobe_utils.general.system import get_sorted_file_paths
-from brainglobe_utils.IO.cells import save_cells
-from brainreg.paths import Paths as BrainregPaths
-from brainreg_segment.layout.gui_elements import add_button
-from napari.utils.io import magic_imread
-from napari_cellfinder.cellfinder import get_cell_arrays
-from qtpy import QtCore
-from qtpy.QtWidgets import QFileDialog, QGridLayout, QGroupBox, QLabel, QWidget
-
-from cellfinder.analyse.analyse import run_analysis
-from cellfinder.main import get_downsampled_space
-
-# Constants used throughout
-WINDOW_HEIGHT = 750
-WINDOW_WIDTH = 1500
-COLUMN_WIDTH = 150
-
-
-class CurationWidget(QWidget):
-    def __init__(
-        self,
-        viewer,
-    ):
-        super(CurationWidget, self).__init__()
-
-        self.viewer = viewer
-
-        self.background_layer = []
-        self.background_path = ""
-
-        self.signal_layer = []
-        self.signal_path = ""
-
-        self.directory = ""
-        self.output_directory = None
-
-        self.setup_main_layout()
-
-    def setup_main_layout(self):
-        """
-        Construct main layout of widget
-        """
-        self.layout = QGridLayout()
-        self.layout.setContentsMargins(10, 10, 10, 10)
-        self.layout.setAlignment(QtCore.Qt.AlignTop)
-        self.layout.setSpacing(4)
-
-        self.add_loading_panel(1)
-
-        self.status_label = QLabel()
-        self.status_label.setText("Ready")
-        self.layout.addWidget(self.status_label, 5, 0)
-
-        self.setLayout(self.layout)
-
-    def add_loading_panel(self, row, column=0):
-        """
-        Loading panel:
-            - Load project (sample space)
-            - Load project (atlas space)
-            - Atlas chooser
-        """
-        self.load_data_panel = QGroupBox("Load data")
-        self.load_data_layout = QGridLayout()
-        self.load_data_layout.setSpacing(15)
-        self.load_data_layout.setContentsMargins(10, 10, 10, 10)
-        self.load_data_layout.setAlignment(QtCore.Qt.AlignBottom)
-
-        # self.load_cellfinder_dir_button = add_button(
-        #     "Load cellfinder project",
-        #     self.load_data_layout,
-        #     self.get_cellfinder_directory,
-        #     0,
-        #     0,
-        #     minimum_width=COLUMN_WIDTH,
-        # )
-
-        # self.load_background_button = add_button(
-        #     "Load background",
-        #     self.load_data_layout,
-        #     self.get_background,
-        #     1,
-        #     0,
-        #     minimum_width=COLUMN_WIDTH,
-        # )
-
-        self.load_signal_button = add_button(
-            "Load signal",
-            self.load_data_layout,
-            self.get_signal,
-            2,
-            0,
-            minimum_width=COLUMN_WIDTH,
-        )
-
-        self.add_cells_button = add_button(
-            "Add cell count",
-            self.load_data_layout,
-            self.add_cell_count,
-            3,
-            0,
-            minimum_width=COLUMN_WIDTH,
-        )
-
-        self.add_cells_button = add_button(
-            "Load cell count",
-            self.load_data_layout,
-            self.load_cells,
-            4,
-            0,
-            minimum_width=COLUMN_WIDTH,
-        )
-
-        self.save_cells_button = add_button(
-            "Save cells",
-            self.load_data_layout,
-            self.save_cell_count,
-            5,
-            0,
-            minimum_width=COLUMN_WIDTH,
-        )
-        self.analyse_cells_button = add_button(
-            "Analyse cells",
-            self.load_data_layout,
-            self.analyse_cells,
-            6,
-            0,
-            minimum_width=COLUMN_WIDTH,
-        )
-
-        self.load_data_layout.setColumnMinimumWidth(0, COLUMN_WIDTH)
-        self.load_data_panel.setLayout(self.load_data_layout)
-        self.load_data_panel.setVisible(True)
-        self.layout.addWidget(self.load_data_panel, row, column, 1, 1)
-
-    def get_cellfinder_directory(self):
-        self.status_label.setText("Loading...")
-        options = QFileDialog.Options()
-        options |= QFileDialog.DontUseNativeDialog
-        cellfinder_directory = QFileDialog.getExistingDirectory(
-            self,
-            "Select cellfinder directory",
-            options=options,
-        )
-
-        if not cellfinder_directory:
-            return
-
-        if self.directory != cellfinder_directory:
-            self.directory = Path(cellfinder_directory)
-        else:
-            print(f"{str(cellfinder_directory)} already loaded.")
-            return
-
-        # Otherwise, proceed loading brainreg dir
-        self.load_cellfinder_directory()
-        self.status_label.setText("Ready...")
-
-    def load_cellfinder_directory(self):
-        try:
-            self.viewer.open(str(self.directory), plugin="cellfinder")
-        except ValueError:
-            print(
-                f"The directory ({self.directory}) does not appear to be "
-                f"a cellfinder directory, please try again."
-            )
-            return
-
-    def get_background(self):
-        self.background_layer, self.background_path = self.get_data(
-            name="background", visible=False
-        )
-
-    def get_signal(self):
-        self.signal_layer, self.signal_path = self.get_data(name="signal")
-        self.status_label.setText("Ready")
-
-    def get_data(self, name="", visible=True):
-        self.status_label.setText("Loading...")
-        options = QFileDialog.Options()
-        options |= QFileDialog.DontUseNativeDialog
-        directory = QFileDialog.getExistingDirectory(
-            self,
-            f"Select {name} channel",
-            options=options,
-        )
-
-        if not directory:
-            return
-
-        if self.directory != directory:
-            self.directory = Path(directory)
-        else:
-            print(f"{str(directory)} already loaded.")
-            return
-
-        return self.load_data(name=name, visible=visible), directory
-
-    def load_data(self, name="", visible=True):
-        try:
-            img_paths = get_sorted_file_paths(
-                self.directory, file_extension=".tif"
-            )
-            images = magic_imread(img_paths, use_dask=True, stack=True)
-            return self.viewer.add_image(images)
-            # return self.viewer.open(
-            #     str(self.directory), name=name, visible=visible
-            # )
-        except ValueError:
-            print(
-                f"The directory ({self.directory}) cannot be "
-                f"loaded, please try again."
-            )
-            return
-
-    def add_cell_count(self):
-        self.cell_layer = self.viewer.add_points(
-            np.empty((0, 3)),
-            symbol="ring",
-            n_dimensional=True,
-            size=10,
-            opacity=0.6,
-            face_color="lightgoldenrodyellow",
-            name="cells",
-        )
-
-    def load_cells(self):
-        options = QFileDialog.Options()
-        options |= QFileDialog.DontUseNativeDialog
-        filename = QFileDialog.getOpenFileName(
-            self,
-            "Select cell file...",
-            filter="cellfinder xml files (*.xml)",
-            options=options,
-        )
-        cells, _ = get_cell_arrays(filename[0])
-
-        self.cell_layer = self.viewer.add_points(
-            cells,
-            symbol="ring",
-            n_dimensional=True,
-            size=10,
-            opacity=0.6,
-            face_color="lightgoldenrodyellow",
-            name="cells",
-        )
-
-    def save_cell_count(self):
-        self.status_label.setText("Saving cells")
-        print("Saving cells")
-        self.get_output_directory()
-        filename = self.output_directory / "cells.xml"
-
-        cells_to_save = []
-        for idx, point in enumerate(self.cell_layer.data):
-            cell = Cell([point[2], point[1], point[0]], Cell.CELL)
-            cells_to_save.append(cell)
-
-        save_cells(cells_to_save, str(filename))
-
-        self.status_label.setText("Ready")
-        print("Done!")
-
-    def get_output_directory(self):
-        if self.output_directory is None:
-            options = QFileDialog.Options()
-            options |= QFileDialog.DontUseNativeDialog
-            self.output_directory = QFileDialog.getExistingDirectory(
-                self,
-                "Select output directory",
-                options=options,
-            )
-            self.output_directory = Path(self.output_directory)
-
-    def analyse_cells(self):
-        self.status_label.setText("Analysing cells")
-        print("Analysing cells")
-
-        self.get_output_directory()
-        self.get_brainreg_directory()
-
-        analyse_cell_positions(
-            self.cell_layer.data,
-            self.brainreg_directory,
-            self.signal_path,
-            self.output_directory,
-        )
-        self.status_label.setText("Ready")
-
-    def get_brainreg_directory(self):
-        options = QFileDialog.Options()
-        options |= QFileDialog.DontUseNativeDialog
-        self.brainreg_directory = QFileDialog.getExistingDirectory(
-            self,
-            "Select brainreg directory",
-            options=options,
-        )
-
-
-def analyse_cell_positions(
-    points, brainreg_directory, signal_path, output_directory
-):
-    brainreg_paths = BrainregPaths(brainreg_directory)
-
-    with open(brainreg_paths.metadata_path) as json_file:
-        metadata = json.load(json_file)
-
-    atlas = BrainGlobeAtlas(metadata["atlas"])
-
-    downsampled_space = get_downsampled_space(
-        atlas, brainreg_paths.boundaries_file_path
-    )
-    deformation_field_paths = [
-        brainreg_paths.deformation_field_0,
-        brainreg_paths.deformation_field_1,
-        brainreg_paths.deformation_field_2,
-    ]
-
-    run_analysis(
-        points,
-        signal_path,
-        metadata["orientation"],
-        metadata["voxel_sizes"],
-        atlas,
-        deformation_field_paths,
-        downsampled_space,
-        output_directory / "downsampled.points",
-        output_directory / "atlas.points",
-        output_directory / "points.npy",
-        brainreg_paths.volume_csv_path,
-        output_directory / "all_points.csv",
-        output_directory / "summary.csv",
-    )
-
-    print("Done")
-
-
-def main():
-    print("Loading curation GUI.\n ")
-    with napari.gui_qt():
-        viewer = napari.Viewer(title="Curation GUI")
-        viewer.window.resize(WINDOW_WIDTH, WINDOW_HEIGHT)
-        widget = CurationWidget(viewer)
-        viewer.window.add_dock_widget(widget, name="Curation", area="right")
-
-
-if __name__ == "__main__":
-    main()

cellfinder/train/curation_old.py

@@ -1,287 +0,0 @@
-from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
-from pathlib import Path
-
-import napari
-import numpy as np
-from brainglobe_utils.cells.cells import Cell
-from brainglobe_utils.general.list import unique_elements_lists
-from brainglobe_utils.general.system import (
-    ensure_directory_exists,
-    get_sorted_file_paths,
-)
-from brainglobe_utils.IO.cells import cells_xml_to_df, get_cells, save_cells
-from brainglobe_utils.IO.yaml import save_yaml
-from napari.utils.io import magic_imread
-from qtpy.QtWidgets import QApplication
-
-import cellfinder.tools.parser as cellfinder_parse
-from cellfinder.extract.extract_cubes import main as extract_cubes_main
-
-OUTPUT_NAME = "curated_cells.xml"
-CURATED_POINTS = []
-
-
-def parser():
-    parser = ArgumentParser(formatter_class=ArgumentDefaultsHelpFormatter)
-    parser = curation_parser(parser)
-    parser = cellfinder_parse.pixel_parser(parser)
-    parser = cellfinder_parse.misc_parse(parser)
-    parser = cellfinder_parse.cube_extract_parse(parser)
-    return parser
-
-
-def curation_parser(parser):
-    parser.add_argument(
-        dest="signal_image_paths", type=str, help="Signal images"
-    )
-    parser.add_argument(
-        dest="background_image_paths",
-        type=str,
-        help="Background images",
-    )
-
-    parser.add_argument(
-        dest="cells_xml", type=str, help="Path to the .xml cell file"
-    )
-    parser.add_argument(
-        "--output",
-        "-o",
-        type=str,
-        default=None,
-        help="Output directory for curation results",
-    )
-    parser.add_argument(
-        "--symbol", type=str, default="ring", help="Marker symbol."
-    )
-    parser.add_argument(
-        "--marker-size", type=int, default=15, help="Marker size."
-    )
-    parser.add_argument(
-        "--opacity", type=float, default=0.6, help="Opacity of the markers."
-    )
-    return parser
-
-
-def get_cell_labels_arrays(
-    cells_file, new_order=[2, 1, 0], type_column="type"
-):
-    df = cells_xml_to_df(cells_file)
-
-    labels = df[type_column]
-    labels = labels.to_numpy()
-    cells_df = df.drop(columns=[type_column])
-    cells = cells_df[cells_df.columns[new_order]]
-    cells = cells.to_numpy()
-
-    # convert to boolean
-    labels = labels == 2
-    return cells, labels
-
-
-def main():
-    args = parser().parse_args()
-    # args = define_pixel_sizes(args)
-
-    if args.output is None:
-        output = Path(args.cells_xml)
-        output_directory = output.parent
-        print(
-            f"No output directory given, so setting output "
-            f"directory to: {output_directory}"
-        )
-    else:
-        output_directory = Path(args.output)
-
-    ensure_directory_exists(str(output_directory))
-    output_filename = output_directory / OUTPUT_NAME
-
-    img_paths = get_sorted_file_paths(
-        args.signal_image_paths, file_extension=".tif"
-    )
-    cells, labels = get_cell_labels_arrays(args.cells_xml)
-
-    properties = {"cell": labels}
-
-    with napari.gui_qt():
-        viewer = napari.Viewer(title="Cellfinder cell curation")
-        images = magic_imread(img_paths, use_dask=True, stack=True)
-        viewer.add_image(images)
-        face_color_cycle = ["lightskyblue", "lightgoldenrodyellow"]
-        viewer.add_points(
-            cells,
-            properties=properties,
-            symbol=args.symbol,
-            n_dimensional=True,
-            size=args.marker_size,
-            face_color="cell",
-            face_color_cycle=face_color_cycle,
-            name="Cell candidates",
-        )
-
-        @viewer.bind_key("t")
-        def toggle_point_property(viewer):
-            """Toggle point type"""
-            selected_points = list(viewer.layers[1].selected_data)
-            if selected_points:
-                selected_properties = viewer.layers[1].properties["cell"][
-                    selected_points
-                ]
-                toggled_properties = np.logical_not(selected_properties)
-                viewer.layers[1].properties["cell"][
-                    selected_points
-                ] = toggled_properties
-
-                # Add curated cells to list
-                CURATED_POINTS.extend(selected_points)
-                print(
-                    f"{len(selected_points)} points "
-                    f"toggled and added to the list "
-                )
-
-                # refresh the properties colour
-                viewer.layers[1].refresh_colors(update_color_mapping=False)
-
-        @viewer.bind_key("c")
-        def confirm_point_property(viewer):
-            """Confirm point type"""
-            selected_points = list(viewer.layers[1].selected_data)
-            if selected_points:
-                # Add curated cells to list
-                CURATED_POINTS.extend(selected_points)
-                print(
-                    f"{len(selected_points)} points "
-                    f"confirmed and added to the list "
-                )
-
-        @viewer.bind_key("Alt-Q")
-        def save_curation(viewer):
-            """Save file"""
-            if not CURATED_POINTS:
-                print("No cells have been confirmed or toggled, not saving")
-            else:
-                unique_cells = unique_elements_lists(CURATED_POINTS)
-                points = viewer.layers[1].data[unique_cells]
-                labels = viewer.layers[1].properties["cell"][unique_cells]
-                labels = labels.astype("int")
-                labels = labels + 1
-
-                cells_to_save = []
-                for idx, point in enumerate(points):
-                    cell = Cell([point[2], point[1], point[0]], labels[idx])
-                    cells_to_save.append(cell)
-
-                print(f"Saving results to: {output_filename}")
-                save_cells(cells_to_save, output_filename)
-                print("Done!")
-
-        @viewer.bind_key("Alt-E")
-        def start_cube_extraction(viewer):
-            """Extract cubes for training"""
-
-            if not output_filename.exists():
-                print(
-                    "No curation results have been saved. "
-                    "Please save before extracting cubes"
-                )
-            else:
-                print(f"Saving cubes to: {output_directory}")
-                run_extraction(
-                    output_filename,
-                    output_directory,
-                    args.signal_image_paths,
-                    args.background_image_paths,
-                    args.cube_depth,
-                    args.cube_width,
-                    args.cube_height,
-                    args.voxel_sizes,
-                    args.network_voxel_sizes,
-                    args.max_ram,
-                    args.n_free_cpus,
-                    args.save_empty_cubes,
-                )
-
-                print("Saving yaml file to use for training")
-                save_yaml_file(output_directory)
-
-                print("Closing window")
-                QApplication.closeAllWindows()
-                print(
-                    "Finished! You may now annotate more "
-                    "datasets, or go straight to training"
-                )
-
-
-def run_extraction(
-    output_filename,
-    output_directory,
-    signal_paths,
-    background_paths,
-    cube_depth,
-    cube_width,
-    cube_height,
-    voxel_sizes,
-    network_voxel_sizes,
-    max_ram,
-    n_free_cpus,
-    save_empty_cubes,
-):
-    planes_paths = {}
-    planes_paths[0] = get_sorted_file_paths(
-        signal_paths, file_extension=".tif"
-    )
-    planes_paths[1] = get_sorted_file_paths(
-        background_paths, file_extension=".tif"
-    )
-
-    all_candidates = get_cells(str(output_filename))
-
-    cells = [c for c in all_candidates if c.is_cell()]
-    non_cells = [c for c in all_candidates if not c.is_cell()]
-
-    to_extract = {"cells": cells, "non_cells": non_cells}
-
-    for cell_type, cell_list in to_extract.items():
-        print(f"Extracting type: {cell_type}")
-        cell_type_output_directory = output_directory / cell_type
-        print(f"Saving to: {cell_type_output_directory}")
-        ensure_directory_exists(str(cell_type_output_directory))
-        extract_cubes_main(
-            cell_list,
-            cell_type_output_directory,
-            planes_paths,
-            cube_depth,
-            cube_width,
-            cube_height,
-            voxel_sizes,
-            network_voxel_sizes,
-            max_ram,
-            n_free_cpus,
-            save_empty_cubes,
-        )
-
-
-def save_yaml_file(output_directory):
-    yaml_filename = output_directory / "training.yml"
-    yaml_section = [
-        {
-            "cube_dir": str(output_directory / "cells"),
-            "cell_def": "",
-            "type": "cell",
-            "signal_channel": 0,
-            "bg_channel": 1,
-        },
-        {
-            "cube_dir": str(output_directory / "non_cells"),
-            "cell_def": "",
-            "type": "no_cell",
-            "signal_channel": 0,
-            "bg_channel": 1,
-        },
-    ]
-
-    yaml_contents = {"data": yaml_section}
-    save_yaml(yaml_contents, yaml_filename)
-
-
-if __name__ == "__main__":
-    main()

cellfinder-0.7.0.dist-info/entry_points.txt

@@ -1,4 +0,0 @@
-[console_scripts]
-cellfinder = cellfinder.main:main
-cellfinder_curate = cellfinder.train.curation_old:main
-cellfinder_curate_new = cellfinder.train.curation:main