Merge branch 'cy/training' into cy/wnet-train

Author: C-Achard

.github/workflows/test_and_deploy.yml

@@ -7,7 +7,6 @@ on:
   push:
     branches:
       - main
-      - cy/wnet-train
     tags:
       - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
   pull_request:

napari_cellseg3d/_tests/test_inference.py

@@ -66,6 +66,7 @@ def test_inference_on_folder():
     config.images_filepaths = [
         str(Path(__file__).resolve().parent / "res/test.tif")
     ]
+
     config.sliding_window_config.window_size = 8
 
     class mock_work:

napari_cellseg3d/_tests/test_models.py

@@ -27,7 +27,7 @@ def test_model_list():
     for model_name in MODEL_LIST:
         # if model_name=="test":
         #     continue
-        dims = 128
+        dims = 64
         test = MODEL_LIST[model_name](
             input_img_size=[dims, dims, dims],
             in_channels=1,

napari_cellseg3d/_tests/test_utils.py

@@ -1,7 +1,6 @@
 import random
 from functools import partial
 from pathlib import Path
-
 import numpy as np
 import pytest
 import torch

napari_cellseg3d/code_models/crf.py

@@ -7,8 +7,9 @@
 Philipp Krähenbühl and Vladlen Koltun
 NIPS 2011
 
-Implemented using the pydense libary available at https://github.com/kodalli/pydensecrf.
+Implemented using the pydense library available at https://github.com/kodalli/pydensecrf.
 """
+
 from warnings import warn
 
 try:

napari_cellseg3d/code_plugins/plugin_base.py

@@ -463,9 +463,10 @@ def _update_default_paths(self, path=None):
                 self.extract_dataset_paths(self.validation_filepaths),
                 self.results_path,
             ]
-            return
+            return utils.parse_default_path(self._default_path)
         if Path(path).is_dir():
             self._default_path.append(path)
+        return utils.parse_default_path(self._default_path)
 
     @staticmethod
     def extract_dataset_paths(paths):
@@ -476,8 +477,43 @@ def extract_dataset_paths(paths):
             return None
         return str(Path(paths[0]).parent)
 
+
     def _check_all_filepaths(self):
         self.image_filewidget.check_ready()
         self.labels_filewidget.check_ready()
         self.results_filewidget.check_ready()
         self.unsupervised_images_filewidget.check_ready()
+
+class BasePluginUtils(BasePluginFolder):
+    """Small subclass used to have centralized widgets layer and result path selection in utilities"""
+
+    save_path = None
+    utils_default_paths = [Path.home() / "cellseg3d"]
+
+    def __init__(
+        self,
+        viewer: napari.viewer.Viewer,
+        parent=None,
+        loads_images=True,
+        loads_labels=True,
+    ):
+        super().__init__(
+            viewer=viewer,
+            loads_images=loads_images,
+            loads_labels=loads_labels,
+            parent=parent,
+        )
+        if parent is not None:
+            self.setParent(parent)
+        self.parent = parent
+
+        self.layer = None
+        """Should contain the layer associated with the results of the utility widget"""
+
+    def _update_default_paths(self, path=None):
+        """Override to also update utilities' pool of default paths"""
+        default_path = super()._update_default_paths(path)
+        logger.debug(f"Trying to update default with {default_path}")
+        if default_path is not None:
+            self.utils_default_paths.append(default_path)
+