Improve LayerSelecter + Tooltips update (#64)

* Improved layer selecter code

- Better handling of removed/added layers independent of widget opening time
- Still missing layer renaming events handling

* Working layer rename

* Tooltips update

* Try to fix tests on Win

* Disable tests on Win for now

* Disable wandb for tests

* Small WandB improvement

* Change logger back to debug

* Fix layer addition and WandB error

* Fix bug with missing variable in some cases

* Fix WandB project name for WNet

* Fix make_csv

Author: C-Achard

napari_cellseg3d/_tests/test_plugin_utils.py

@@ -13,7 +13,7 @@ def test_utils_plugin(make_napari_viewer_proxy):
     view = make_napari_viewer_proxy()
     widget = Utilities(view)
 
-    image = rand_gen.random((10, 10, 10)).astype(np.uint8)
+    image = rand_gen.random((10, 10, 10))  # .astype(np.uint8)
     image_layer = view.add_image(image, name="image")
     label_layer = view.add_labels(image.astype(np.uint8), name="labels")
 

napari_cellseg3d/_tests/test_training.py

@@ -17,6 +17,8 @@
 )
 from napari_cellseg3d.config import MODEL_LIST
 
+WANDB_MODE = "disabled"
+
 im_path = Path(__file__).resolve().parent / "res/test.tif"
 im_path_str = str(im_path)
 lab_path = Path(__file__).resolve().parent / "res/test_labels.tif"

napari_cellseg3d/code_plugins/plugin_convert.py

@@ -363,6 +363,12 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
         self.container = self._build()
 
         self.function = clear_small_objects
+        self._set_tooltips()
+
+    def _set_tooltips(self):
+        self.size_for_removal_counter.setToolTip(
+            "Size of the objects to remove, in pixels."
+        )
 
     def _build(self):
         container = ui.ContainerWidget()
@@ -647,6 +653,15 @@ def __init__(self, viewer: "napari.viewer.Viewer", parent=None):
         self.container = self._build()
         self.function = threshold
 
+        self._set_tooltips()
+
+    def _set_tooltips(self):
+        self.binarize_counter.setToolTip(
+            "Value to use as threshold for binarization."
+            "For labels, use the highest ID you want to keep. All lower IDs will be removed."
+            "For images, use the intensity value (pixel value) to threshold the image."
+        )
+
     def _build(self):
         container = ui.ContainerWidget()
 

napari_cellseg3d/code_plugins/plugin_model_inference.py

@@ -281,6 +281,7 @@ def _set_tooltips(self):
         )
 
         thresh_desc = (
+            "NOT RECOMMENDED ON FIRST RUN - check results without first!\n"
             "Thresholding : all values in the image below the chosen probability"
             " threshold will be set to 0, and all others to 1."
         )
@@ -301,6 +302,7 @@ def _set_tooltips(self):
             "If enabled, data will be kept on the RAM rather than the VRAM.\nCan avoid out of memory issues with CUDA"
         )
         self.use_instance_choice.setToolTip(
+            "NOT RECOMMENDED ON FIRST RUN - check results without first!\n"
             "Instance segmentation will convert instance (0/1) labels to labels"
             " that attempt to assign an unique ID to each cell."
         )
@@ -653,6 +655,8 @@ def _display_results(self, result: InferenceResult):
                 if result.semantic_segmentation[channel].sum() > 0:
                     index_channel_least_labelled = channel
                     break
+                # if no channel has any label, use the first one
+                index_channel_least_labelled = 0
             viewer.dims.set_point(
                 0, index_channel_least_labelled
             )  # TODO(cyril: check if this is always the right axis

napari_cellseg3d/code_plugins/plugin_model_training.py

@@ -1247,7 +1247,7 @@ def on_finish(self):
         self.log.print_and_log("*" * 10)
         try:
             self._make_csv()
-        except ValueError as e:
+        except (ValueError, KeyError) as e:
             logger.warning(f"Error while saving CSV report: {e}")
 
         self.start_btn.setText("Start")
@@ -1375,11 +1375,11 @@ def _make_csv(self):
         try:
             self.loss_1_values["Loss"]
             supervised = True
-        except KeyError("Loss"):
+        except KeyError:
             try:
                 self.loss_1_values["SoftNCuts"]
                 supervised = False
-            except KeyError("SoftNCuts") as e:
+            except KeyError as e:
                 raise KeyError(
                     "Error when making csv. Check loss dict keys ?"
                 ) from e
@@ -1398,8 +1398,8 @@ def _make_csv(self):
                     "validation": val,
                 }
             )
-            if len(val) != len(self.loss_1_values):
-                err = f"Validation and loss values don't have the same length ! Got {len(val)} and {len(self.loss_1_values)}"
+            if len(val) != len(self.loss_1_values["Loss"]):
+                err = f"Validation and loss values don't have the same length ! Got {len(val)} and {len(self.loss_1_values['Loss'])}"
                 logger.error(err)
                 raise ValueError(err)
         else:

napari_cellseg3d/interface.py

@@ -1,7 +1,9 @@
 """User interface functions and aliases."""
+import contextlib
 import threading
 from functools import partial
 from typing import List, Optional
+from warnings import warn
 
 import napari
 
@@ -804,9 +806,12 @@ def __init__(
         self.layer_description.setVisible(False)
         # self.layer_list.setSizeAdjustPolicy(QComboBox.AdjustToContents) # use tooltip instead ?
 
+        # connect to LayerList events
         self._viewer.layers.events.inserted.connect(partial(self._add_layer))
         self._viewer.layers.events.removed.connect(partial(self._remove_layer))
+        self._viewer.layers.events.changed.connect(self._check_for_layers)
 
+        # update self.layer_list when layers are added or removed
         self.layer_list.currentIndexChanged.connect(self._update_tooltip)
         self.layer_list.currentTextChanged.connect(self._update_description)
 
@@ -816,20 +821,81 @@ def __init__(
         )
         self._check_for_layers()
 
+    def _get_all_layers(self):
+        return [
+            self.layer_list.itemText(i) for i in range(self.layer_list.count())
+        ]
+
     def _check_for_layers(self):
+        """Check for layers of the correct type and update the dropdown menu.
+
+        Also removes layers that have been removed from the viewer.
+        """
         for layer in self._viewer.layers:
-            if isinstance(layer, self.layer_type):
+            layer.events.name.connect(self._rename_layer)
+
+            if (
+                isinstance(layer, self.layer_type)
+                and layer.name not in self._get_all_layers()
+            ):
+                logger.debug(
+                    f"Layer {layer.name} - List : {self._get_all_layers()}"
+                )
+                # add new layers of correct type
                 self.layer_list.addItem(layer.name)
+                logger.debug(f"Layer {layer.name} has been added to the menu")
+                # break
+                # once added, check again for previously renamed layers
+                self._check_for_removed_layer(layer)
+
+            if layer.name in self._get_all_layers() and not isinstance(
+                layer, self.layer_type
+            ):
+                # remove layers of incorrect type
+                index = self.layer_list.findText(layer.name)
+                self.layer_list.removeItem(index)
+                logger.debug(
+                    f"Layer {layer.name} has been removed from the menu"
+                )
+
+        self._check_for_removed_layers()
+        self._update_tooltip()
+        self._update_description()
+
+    def _check_for_removed_layer(self, layer):
+        """Check if a specific layer has been removed from the viewer and must be removed from the menu."""
+        if isinstance(layer, str):
+            name = layer
+        elif isinstance(layer, self.layer_type):
+            name = layer.name
+        else:
+            logger.warning("Layer is not a string or a valid napari layer")
+            return
+
+        if name in self._get_all_layers() and name not in [
+            l.name for l in self._viewer.layers
+        ]:
+            index = self.layer_list.findText(name)
+            self.layer_list.removeItem(index)
+            logger.debug(f"Layer {name} has been removed from the menu")
+
+    def _check_for_removed_layers(self):
+        """Check for layers that have been removed from the viewer and must be removed from the menu."""
+        for layer in self._get_all_layers():
+            self._check_for_removed_layer(layer)
 
     def _update_tooltip(self):
         self.layer_list.setToolTip(self.layer_list.currentText())
 
     def _update_description(self):
         try:
             if self.layer_list.currentText() != "":
-                self.layer_description.setVisible(True)
-                shape_desc = f"Shape : {self.layer_data().shape}"
-                self.layer_description.setText(shape_desc)
+                try:
+                    shape_desc = f"Shape : {self.layer_data().shape}"
+                    self.layer_description.setText(shape_desc)
+                    self.layer_description.setVisible(True)
+                except AttributeError:
+                    self.layer_description.setVisible(False)
             else:
                 self.layer_description.setVisible(False)
         except KeyError:
@@ -841,6 +907,13 @@ def _add_layer(self, event):
         if isinstance(inserted_layer, self.layer_type):
             self.layer_list.addItem(inserted_layer.name)
 
+        # check for renaming
+        inserted_layer.events.name.connect(self._rename_layer)
+
+    def _rename_layer(self, _):
+        # on layer rename, check for removed/new layers
+        self._check_for_layers()
+
     def _remove_layer(self, event):
         removed_layer = event.value
 
@@ -867,15 +940,24 @@ def layer(self):
 
     def layer_name(self):
         """Returns the name of the layer selected in the dropdown menu."""
-        return self.layer_list.currentText()
+        try:
+            return self.layer_list.currentText()
+        except (KeyError, ValueError):
+            logger.warning("Layer list is empty")
+            return None
 
     def layer_data(self):
         """Returns the data of the layer selected in the dropdown menu."""
         if self.layer_list.count() < 1:
             logger.debug("Layer list is empty")
             return None
-
-        return self.layer().data
+        try:
+            return self.layer().data
+        except (KeyError, ValueError):
+            msg = f"Layer {self.layer_name()} has no data. Layer might have been renamed or removed."
+            logger.warning(msg)
+            warn(msg, stacklevel=1)
+            return None
 
 
 class FilePathWidget(QWidget):  # TODO include load as folder

napari_cellseg3d/utils.py

@@ -15,6 +15,7 @@
 LOGGER = logging.getLogger(__name__)
 ###############
 # Global logging level setting
+# SET TO INFO FOR RELEASE
 # LOGGER.setLevel(logging.DEBUG)
 LOGGER.setLevel(logging.INFO)
 ###############