cellfinder 1.3.1__py3-none-any.whl → 1.3.3__py3-none-any.whl

cellfinder/core/classify/classify.py

@@ -68,6 +68,14 @@ def main(
         workers=workers,
     )
 
+    if trained_model and trained_model.suffix == ".h5":
+        print(
+            "Weights provided in place of the model, "
+            "loading weights into default model."
+        )
+        model_weights = trained_model
+        trained_model = None
+
     model = get_model(
         existing_model=trained_model,
         model_weights=model_weights,

cellfinder/napari/curation.py

@@ -113,7 +113,7 @@ class CurationWidget(QWidget):
         layer_names = [
             layer.name
             for layer in self.viewer.layers
-            if type(layer) == layer_type
+            if isinstance(layer, layer_type)
         ]
 
         if layer_names:
@@ -329,7 +329,7 @@ class CurationWidget(QWidget):
 
         if len(self.viewer.layers.selection) == 1:
             layer = list(self.viewer.layers.selection)[0]
-            if type(layer) == napari.layers.Points:
+            if isinstance(layer, napari.layers.Points):
                 if len(layer.data) > 0:
                     if point_type == "cell":
                         destination_layer = self.training_data_cell_layer

{cellfinder-1.3.1.dist-info → cellfinder-1.3.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.3.1
+Version: 1.3.3
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -23,37 +23,37 @@ Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: brainglobe-utils >=0.5.0
-Requires-Dist: brainglobe-napari-io >=0.3.4
+Requires-Dist: brainglobe-utils>=0.5.0
+Requires-Dist: brainglobe-napari-io>=0.3.4
 Requires-Dist: dask[array]
-Requires-Dist: fancylog >=0.0.7
+Requires-Dist: fancylog>=0.0.7
 Requires-Dist: natsort
 Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
-Requires-Dist: keras >=3.0.0
-Requires-Dist: torch >=2.1.0
+Requires-Dist: keras==3.5.0
+Requires-Dist: torch>=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm
 Provides-Extra: dev
-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-mock ; extra == 'dev'
-Requires-Dist: pytest-qt ; extra == 'dev'
-Requires-Dist: pytest-timeout ; extra == 'dev'
-Requires-Dist: pytest ; extra == 'dev'
-Requires-Dist: tox ; extra == 'dev'
+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-mock; extra == "dev"
+Requires-Dist: pytest-qt; extra == "dev"
+Requires-Dist: pytest-timeout; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: tox; extra == "dev"
 Provides-Extra: napari
-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: pooch >=1 ; extra == 'napari'
-Requires-Dist: qtpy ; extra == 'napari'
+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: pooch>=1; extra == "napari"
+Requires-Dist: qtpy; extra == "napari"
 
 [![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-1.3.1.dist-info → cellfinder-1.3.3.dist-info}/RECORD

@@ -5,7 +5,7 @@ cellfinder/core/main.py,sha256=t2mkq6iieEytbPckehBB43juwN5E-vhzstLSs620vdM,3625
 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=33ZvNDmgVabH_6p4jV9Xi8bLKwDZnVhzlImrL_TlnBk,3269
+cellfinder/core/classify/classify.py,sha256=uhvBGp3uFRp6uZeUtAIIS4BbIotQzZ_rql2zT_l-9Ok,3523
 cellfinder/core/classify/cube_generator.py,sha256=jC5aogTVy213PHouViSR9CgKkuOks3yk6csQC5kRoOE,17125
 cellfinder/core/classify/resnet.py,sha256=vGa85y_NcQnOXwAt5EtatLx5mrO8IoShCcNKtJ5-EFg,10034
 cellfinder/core/classify/tools.py,sha256=s5PEKAsZVbVuoferZ_nqMUM0f2bV_8WEKsdKe3SXEuE,2560
@@ -39,7 +39,7 @@ cellfinder/core/tools/tools.py,sha256=G8oDGNRuWkzEJDnnC4r3SNGgpVbqbelCZR5ODk9JRz
 cellfinder/core/train/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellfinder/core/train/train_yml.py,sha256=9QXv2wk24G8hYskMnBij7OngEELUWySK2fH4NFbYWw4,13260
 cellfinder/napari/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/napari/curation.py,sha256=nbxCwY2bhEPM15Wf3S_Ff8qGdLSWojr4X48mmAJqD3U,21447
+cellfinder/napari/curation.py,sha256=Pfif12RUIMExxPuIp9U0mW5-4QycciDlkVE8_9UMgpY,21455
 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
@@ -51,9 +51,9 @@ cellfinder/napari/detect/thread_worker.py,sha256=PWM3OE-FpK-dpdhaE_Gi-2lD3u8sL-S
 cellfinder/napari/train/__init__.py,sha256=xo4CK-DvSecInGEc2ohcTgQYlH3iylFnGvKTCoq2WkI,35
 cellfinder/napari/train/train.py,sha256=zJY7zKcLqDTDtD76thmbwViEU4tTFCmXZze-zHsTpoo,5941
 cellfinder/napari/train/train_containers.py,sha256=1wZ_GPe7B5XsLYs5XIx4m8GMw5KeVhg6SchhPtXu4V8,4386
-cellfinder-1.3.1.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
-cellfinder-1.3.1.dist-info/METADATA,sha256=tdKnKSv42LLsTm89qJdCx0EuRLSDj8XN1gzl8XuB8cM,7097
-cellfinder-1.3.1.dist-info/WHEEL,sha256=-oYQCr74JF3a37z2nRlQays_SX2MqOANoqVjBBAP2yE,91
-cellfinder-1.3.1.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
-cellfinder-1.3.1.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
-cellfinder-1.3.1.dist-info/RECORD,,
+cellfinder-1.3.3.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
+cellfinder-1.3.3.dist-info/METADATA,sha256=27H5g4lHvr3tyLQNPD7H3OnqUN2Y_LZFNOB15M9gS5s,7074
+cellfinder-1.3.3.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+cellfinder-1.3.3.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
+cellfinder-1.3.3.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
+cellfinder-1.3.3.dist-info/RECORD,,

{cellfinder-1.3.1.dist-info → cellfinder-1.3.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (71.0.3)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any