docs + fixed attribute name error in cropping

Author: C-Achard

docs/res/model_instance_seg.rst

@@ -0,0 +1,14 @@
+model_workers.py
+===========================================
+
+
+Functions
+-------------
+
+binary_connected
+**************************************
+.. autofunction:: napari_cellseg_annotator.model_instance_seg::binary_connected
+
+binary_watershed
+**************************************
+.. autofunction:: napari_cellseg_annotator.model_instance_seg::binary_watershed

src/napari_cellseg_annotator/model_workers.py

@@ -41,7 +41,7 @@
 so instead, following the instructions in the guides below to have a worker with custom signals, I implemented
 a custom worker function."""
 
-
+# FutureReference():
 # https://python-forum.io/thread-31349.html
 # https://www.pythoncentral.io/pysidepyqt-tutorial-creating-your-own-signals-and-slots/
 # https://napari-staging-site.github.io/guides/stable/threading.html
@@ -100,7 +100,7 @@ def __init__(
         """
 
         super().__init__(self.inference)
-        self._signals = LogSignal()
+        self._signals = LogSignal() # add custom signals
         self.log_signal = self._signals.log_signal
         ###########################################
         ###########################################
@@ -310,6 +310,8 @@ def inference(self):
                     "model_name": self.model_dict["name"],
                 }
 
+        model.to("cpu")
+
 
 class TrainingWorker(GeneratorWorker):
     """A custom worker to run training jobs in.
@@ -693,6 +695,9 @@ def train(self):
             f"Train completed, best_metric: {best_metric:.4f} "
             f"at epoch: {best_metric_epoch}"
         )
+        model.to("cpu")
+        optimizer = None
+        del optimizer
         # del device
         # del model_id
         # del model_name

src/napari_cellseg_annotator/plugin_crop.py

@@ -158,9 +158,10 @@ def quicksave(self):
                     im_dir + "/" + im_filename + "_cropped_" + time + ".tif"
                 )
 
+            print(self.label)
             if self.label is not None:
                 im_filename = os.path.basename(self.label_path).split(".")[0]
-                im_dir = os.path.split(self.label_path)[0]
+                im_dir = os.path.split(self.label_path)[0] + "/cropped"
                 name = (
                     im_dir
                     + "/"
@@ -170,6 +171,7 @@ def quicksave(self):
                     + ".tif"
                 )
                 dat = viewer.layers["cropped_labels"].data
+                os.makedirs(im_dir, exist_ok=True)
                 imwrite(name, data=dat)
 
         else:
@@ -182,12 +184,14 @@ def quicksave(self):
                 dir_name = im_dir + "/volume_cropped_" + time
                 utils.save_stack(dat, dir_name, filetype=self.filetype)
 
+            print(self.label)
             if self.label is not None:
 
                 # im_filename = os.path.basename(self.image_path).split(".")[0]
                 im_dir = os.path.split(self.label_path)[0]
 
                 dir_name = im_dir + "/labels_cropped_" + time
+                print(f"dir name {dir_name}")
                 dat = viewer.layers["cropped_labels"].data
                 utils.save_stack(dat, dir_name, filetype=self.filetype)
 
@@ -231,7 +235,7 @@ def start(self):
         )
 
         if self.crop_labels:
-            self.labels = utils.load_images(
+            self.label = utils.load_images(
                 self.label_path, self.filetype, self.as_folder
             )
 
@@ -248,7 +252,7 @@ def start(self):
         )
 
         if self.crop_labels:
-            self.label_layer = vw.add_labels(self.labels, visible=False)
+            self.label_layer = vw.add_labels(self.label, visible=False)
 
         @magicgui(call_button="Quicksave")
         def save_widget():
@@ -301,9 +305,9 @@ def add_crop_sliders(self):
         )
 
         if self.crop_labels:
-            label_stack = self.labels
+            label_stack = self.label
             labels_crop_layer = vw.add_labels(
-                self.labels[:cropz, :cropy, :cropx],
+                self.label[:cropz, :cropy, :cropx],
                 name="cropped_labels",
                 scale=self.label_layer.scale,
             )