cellfinder 1.4.0a0__py3-none-any.whl → 1.5.0__py3-none-any.whl

cellfinder/core/classify/classify.py

@@ -1,5 +1,6 @@
 import os
 from datetime import datetime
+from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import keras
@@ -68,7 +69,7 @@ def main(
         workers=workers,
     )
 
-    if trained_model and trained_model.suffix == ".h5":
+    if trained_model and Path(trained_model).suffix == ".h5":
         print(
             "Weights provided in place of the model, "
             "loading weights into default model."

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

@@ -266,22 +266,21 @@ class BallFilter:
         """
         if self.volume.shape[0]:
             if self.volume.shape[0] < self.kernel_z_size:
-                num_remaining_with_padding = 0
+                num_remaining_with_padding = self.volume.shape[0]
             else:
                 num_remaining = self.kernel_z_size - (self.middle_z_idx + 1)
                 num_remaining_with_padding = num_remaining + self.middle_z_idx
+            remaining_start = self.volume.shape[0] - num_remaining_with_padding
 
             self.volume = torch.cat(
-                [self.volume[-num_remaining_with_padding:, :, :], planes],
+                [self.volume[remaining_start:, :, :], planes],
                 dim=0,
             )
 
             if self.inside_brain_tiles is not None:
                 self.inside_brain_tiles = torch.cat(
                     [
-                        self.inside_brain_tiles[
-                            -num_remaining_with_padding:, :, :
-                        ],
+                        self.inside_brain_tiles[remaining_start:, :, :],
                         masks,
                     ],
                     dim=0,

cellfinder/napari/curation.py

@@ -8,11 +8,11 @@ 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
+from qt_niu.dialog import display_warning
+from qt_niu.interaction import add_button, add_combobox
 from qtpy import QtCore
 from qtpy.QtWidgets import (
     QComboBox,

cellfinder/napari/detect/detect.py

@@ -38,7 +38,7 @@ MIN_PLANES_ANALYSE = 0
 
 
 def get_heavy_widgets(
-    options: Dict[str, Any]
+    options: Dict[str, Any],
 ) -> Tuple[Callable, Callable, Callable]:
     # signal and other input are separated out from the main magicgui
     # parameter selections and are inserted as widget children in their own

{cellfinder-1.4.0a0.dist-info → cellfinder-1.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: cellfinder
-Version: 1.4.0a0
+Version: 1.5.0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -32,7 +32,7 @@ Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
-Requires-Dist: keras==3.5.0
+Requires-Dist: keras>=3.7.0
 Requires-Dist: torch!=2.4,>=2.1.0
 Requires-Dist: tifffile
 Requires-Dist: tqdm
@@ -47,6 +47,7 @@ Requires-Dist: pytest-timeout; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: tox; extra == "dev"
 Requires-Dist: pooch>=1; extra == "dev"
+Requires-Dist: qt-niu; extra == "dev"
 Provides-Extra: napari
 Requires-Dist: brainglobe-napari-io; extra == "napari"
 Requires-Dist: magicgui; extra == "napari"

{cellfinder-1.4.0a0.dist-info → cellfinder-1.5.0.dist-info}/RECORD

@@ -5,7 +5,7 @@ cellfinder/core/main.py,sha256=QiLo8qtK6hRT_cu-xSP9k93EE-dZjmb2xxocsY-hTwU,3836
 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=UN5j4-5RlsKNt9wd1A8udCjW4t-D4MySEyQ9BIkCckI,3529
+cellfinder/core/classify/classify.py,sha256=p3TvpnTVCVa9xCSgHm7QsgHeYeNZaoSbvf9fgZ3uF0c,3560
 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
@@ -20,7 +20,7 @@ cellfinder/core/detect/filters/plane/classical_filter.py,sha256=X5k266tbl9EHRVY5
 cellfinder/core/detect/filters/plane/plane_filter.py,sha256=6FbAjxgt39_RdGDXC_pQ9ndtZtknuHJeTWtbR8cReEA,6102
 cellfinder/core/detect/filters/plane/tile_walker.py,sha256=IiQibvWKnYlgl9h414fRklV7C2xZ0vXNmJ9t89DhYuI,4863
 cellfinder/core/detect/filters/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellfinder/core/detect/filters/volume/ball_filter.py,sha256=qIDo206f558B46tpxrOGXasP8VE6pZxju-duvhPRuNA,14440
+cellfinder/core/detect/filters/volume/ball_filter.py,sha256=aarEBD6z3ejhNMFdKqKEHi9zLPkopqA3HkzV9RGd7BA,14461
 cellfinder/core/detect/filters/volume/structure_detection.py,sha256=AIHq-5u5VFpKBBLEsE1Py-MlndbL8T0zXu0Bq2CI16Y,12916
 cellfinder/core/detect/filters/volume/structure_splitting.py,sha256=0LGE8cQ6EJIsKqWWmd087Q3At8m-PUDmmPjCZKV1TdY,10138
 cellfinder/core/detect/filters/volume/volume_filter.py,sha256=o9_4IsITedhqkhfwRsIhE53_zLNcFjgQzXbMMddH_q4,20544
@@ -41,21 +41,21 @@ cellfinder/core/tools/tools.py,sha256=opMGC5GBBsId0dmL8V0KQrI4U70w_D_KtGQYpZNeHY
 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=Pfif12RUIMExxPuIp9U0mW5-4QycciDlkVE8_9UMgpY,21455
+cellfinder/napari/curation.py,sha256=Egp56_ke1x1s1ZO9FK8oWgxG-xerBYWG76_V56JJ3eQ,21425
 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=AwTs76M9azutHhHj2yuaKErDEQ5F6pFbIIakBfzen6M,3824
 cellfinder/napari/detect/__init__.py,sha256=BD9Bg9NTAr6yRTq2A_p58U6j4w5wbY0sdXwhPJ3MSMY,34
-cellfinder/napari/detect/detect.py,sha256=VB3SLZvqJhjuypjpaZuV9JscQ-sE8yVHG8RzEsZWfeA,13809
+cellfinder/napari/detect/detect.py,sha256=EC71KN0AEr49hMjvS8yzvGvfRctqKqn_lNERyx9UAPc,13810
 cellfinder/napari/detect/detect_containers.py,sha256=j9NTsIyyDNrhlI2dc7hvc7QlxvI1NRHlCe137v7fsPg,5467
 cellfinder/napari/detect/thread_worker.py,sha256=PWM3OE-FpK-dpdhaE_Gi-2lD3u8sL-SJ13mp0pMhTyI,3078
 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-1.4.0a0.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
-cellfinder-1.4.0a0.dist-info/METADATA,sha256=X5NbLqZZpyJC2_JDAEo03MHDAjgzYN7SJsh_x2vkS48,7122
-cellfinder-1.4.0a0.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-cellfinder-1.4.0a0.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
-cellfinder-1.4.0a0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
-cellfinder-1.4.0a0.dist-info/RECORD,,
+cellfinder-1.5.0.dist-info/LICENSE,sha256=Tw8iMytIDXLSmcIUsbQmRWojstl9yOWsPCx6ZT6dZLY,1564
+cellfinder-1.5.0.dist-info/METADATA,sha256=3P9j6iSAWD_CVf4ho8C-RRX5Jf_r7A4mSaBfdeeNmTE,7158
+cellfinder-1.5.0.dist-info/WHEEL,sha256=nn6H5-ilmfVryoAQl3ZQ2l8SH5imPWFpm1A5FgEuFV4,91
+cellfinder-1.5.0.dist-info/entry_points.txt,sha256=cKKjU8GPiN-TRelG2sT2JCKAcB9XDCjP6g9atE9pSoY,247
+cellfinder-1.5.0.dist-info/top_level.txt,sha256=jyTQzX-tDjbsMr6s-E71Oy0IKQzmHTXSk4ZhpG5EDSE,11
+cellfinder-1.5.0.dist-info/RECORD,,

{cellfinder-1.4.0a0.dist-info → cellfinder-1.5.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.0)
+Generator: setuptools (75.8.1)
 Root-Is-Purelib: true
 Tag: py3-none-any