Merge pull request #14 from TheJacksonLaboratory/dev

Fixing labels manager interface

src/napari_activelearning/_acquisition.py

@@ -246,7 +246,7 @@ def fine_tune(self, dataset_metadata_list: Iterable[
             dataset = zds.ZarrDataset(
                 list(dataset_metadata.values()),
                 return_positions=False,
-                draw_same_chunk=True,
+                draw_same_chunk=False,
                 patch_sampler=StaticPatchSampler(
                     patch_size=patch_sizes,
                     top_lefts=top_lefts,

src/napari_activelearning/_interface.py

@@ -794,7 +794,17 @@ def edit_labels(self):
     def commit(self):
         super(LabelsManagerWidget, self).commit()
         self.commit_btn.setEnabled(False)
-        self.edit_labels_btn.setEnabled(True)
+        self.edit_labels_btn.setEnabled(self._active_label is not None)
+
+        self.prev_img_btn.setEnabled(self._active_label is not None)
+        self.prev_patch_btn.setEnabled(self._active_label is not None)
+        self.next_patch_btn.setEnabled(self._active_label is not None)
+        self.next_img_btn.setEnabled(self._active_label is not None)
+
+        self.remove_labels_btn.setEnabled(self._active_label is not None)
+        self.remove_labels_group_btn.setEnabled(
+            self._active_label_group is not None
+        )
 
 
 class TunableMethodWidget(TunableMethod, QWidget):

src/napari_activelearning/_labels.py

@@ -123,13 +123,17 @@ def remove_managed_label_group(self, label_group: LabelGroup):
             if not self.managed_layers[layer]:
                 self.managed_layers.pop(layer)
 
+        self.setSelected(True)
+
     def remove_managed_layer(self, event):
         removed_layer = event.value
 
         label_group_list = self.managed_layers.get(removed_layer, [])
         for label_group in label_group_list:
             self.removeChild(label_group)
 
+        self.setSelected(True)
+
     def addChild(self, child: QTreeWidgetItem):
         if isinstance(child, LabelGroup):
             if child.layer_channel:
@@ -151,11 +155,15 @@ def removeChild(self, child: QTreeWidgetItem):
 
         super(LabelGroupRoot, self).removeChild(child)
 
+        self.setSelected(True)
+
     def takeChild(self, index: int):
         child = super(LabelGroupRoot, self).takeChild(index)
         if isinstance(child, LabelGroup) and child.layer_channel:
             self.remove_managed_label_group(child)
 
+        self.setSelected(True)
+
         return child
 
     def takeChildren(self):
@@ -164,6 +172,8 @@ def takeChildren(self):
             if isinstance(child, LabelGroup) and child.layer_channel:
                 self.remove_managed_label_group(child)
 
+        self.setSelected(True)
+
         return children
 
 
@@ -189,6 +199,50 @@ def __init__(self):
             self.commit
         )
 
+    def _load_label_data(self, input_filename, data_group=None):
+        if isinstance(input_filename, (Path, str)):
+            spec = {
+                'driver': 'zarr',
+                'kvstore': {
+                    'driver': 'file',
+                    'path': str(Path(input_filename) / data_group),
+                },
+            }
+
+            ts_array = ts.open(spec).result()
+
+            self._transaction = ts.Transaction()
+
+            label_data = ts_array.with_transaction(self._transaction)
+            selection = ts.d[:][self._active_label.position].translate_to[0]
+            label_data = label_data[selection]
+
+        elif isinstance(input_filename, MultiScaleData):
+            label_data = np.array(
+                input_filename[0][self._active_label.position]
+            )
+        else:
+            label_data = np.array(input_filename[self._active_label.position])
+
+        return label_data
+
+    def _write_label_data(self, label_data: np.ndarray):
+        if self._active_layers_group:
+            segmentation_channel = self._active_layers_group.child(0)
+            segmentation_channel_layer = segmentation_channel.layer
+            if isinstance(segmentation_channel.layer.data, MultiScaleData):
+                segmentation_channel_data =\
+                    segmentation_channel_layer.data[0]
+            else:
+                segmentation_channel_data = segmentation_channel_layer.data
+
+        if isinstance(self._transaction, ts.Transaction):
+            self._transaction.commit_async()
+        elif (self._active_label.position is not None
+                and segmentation_channel_data is not None):
+            segmentation_channel_data[self._active_label.position] =\
+                label_data
+
     def add_labels(self, layer_channel: LayerChannel,
                    labels: Iterable[LabelItem]):
         new_label_group = LabelGroup(layer_channel)
@@ -212,7 +266,14 @@ def remove_labels(self):
         self._active_label_group.removeChild(self._active_label)
         if not self._active_label_group.childCount():
             self.remove_labels_group()
+        else:
+            self._active_label_group.setSelected(True)
+
+        for child in map(lambda idx: self.labels_group_root.child(idx),
+                         range(self.labels_group_root.childCount())):
+            child.setSelected(False)
 
+        self._active_label = None
         self._requires_commit = False
         self.commit()
 
@@ -221,6 +282,14 @@ def remove_labels_group(self):
             return
 
         self.labels_group_root.removeChild(self._active_label_group)
+
+        for child in map(lambda idx: self.labels_group_root.child(idx),
+                         range(self.labels_group_root.childCount())):
+            child.setSelected(False)
+
+        self.labels_group_root.setSelected(True)
+        self._active_label_group = None
+
         self._requires_commit = False
         self.commit()
 
@@ -277,7 +346,7 @@ def focus_region(self, label: Optional[QTreeWidgetItem] = None,
 
         if isinstance(label, list) and len(label):
             label = label[0]
-        elif not isinstance(label, LabelItem):
+        elif not isinstance(label, (LabelItem, LabelGroup)):
             label = None
 
         self._active_label_group = None
@@ -361,33 +430,11 @@ def edit_labels(self):
         input_filename = self._active_layers_group.source_data
         data_group = self._active_layers_group.data_group
 
-        if isinstance(input_filename, (Path, str)):
-            spec = {
-                'driver': 'zarr',
-                'kvstore': {
-                    'driver': 'file',
-                    'path': str(Path(input_filename) / data_group),
-                },
-            }
-
-            ts_array = ts.open(spec).result()
-
-            self._transaction = ts.Transaction()
-
-            lazy_data = ts_array.with_transaction(self._transaction)
-            lazy_data =\
-                lazy_data[ts.d[:][self._active_label.position].translate_to[0]]
-
-        elif isinstance(input_filename, MultiScaleData):
-            lazy_data = np.array(
-                input_filename[0][self._active_label.position]
-            )
-        else:
-            lazy_data = np.array(input_filename[self._active_label.position])
+        label_data = self._load_label_data(input_filename, data_group)
 
         viewer = napari.current_viewer()
         self._active_edit_layer = viewer.add_labels(
-            lazy_data,
+            label_data,
             name="Labels edit",
             blending="translucent_no_depth",
             opacity=0.7,
@@ -415,21 +462,22 @@ def commit(self):
             if self._active_edit_layer:
                 edit_data = self._active_edit_layer.data
 
-            if self._active_layers_group:
-                segmentation_channel = self._active_layers_group.child(0)
-                segmentation_channel_layer = segmentation_channel.layer
-                if isinstance(segmentation_channel.layer.data, MultiScaleData):
-                    segmentation_channel_data =\
-                        segmentation_channel_layer.data[0]
-                else:
-                    segmentation_channel_data = segmentation_channel_layer.data
-
-            if isinstance(self._transaction, ts.Transaction):
-                self._transaction.commit_async()
-            elif (self._active_label.position is not None
-                  and segmentation_channel_data is not None):
-                segmentation_channel_data[self._active_label.position] =\
-                    edit_data
+            # if self._active_layers_group:
+            #     segmentation_channel = self._active_layers_group.child(0)
+            #     segmentation_channel_layer = segmentation_channel.layer
+            #     if isinstance(segmentation_channel.layer.data, MultiScaleData):
+            #         segmentation_channel_data =\
+            #             segmentation_channel_layer.data[0]
+            #     else:
+            #         segmentation_channel_data = segmentation_channel_layer.data
+
+            # if isinstance(self._transaction, ts.Transaction):
+            #     self._transaction.commit_async()
+            # elif (self._active_label.position is not None
+            #       and segmentation_channel_data is not None):
+            #     segmentation_channel_data[self._active_label.position] =\
+            #         edit_data
+            self._write_label_data(edit_data)
 
         viewer = napari.current_viewer()
         if (self._active_edit_layer

src/napari_activelearning/_layers.py

@@ -869,6 +869,14 @@ def remove_managed_layer(self, event):
             if not image_group.childCount():
                 self.removeChild(image_group)
 
+            if image_group.labels_group:
+                if image_group.labels_group.parent():
+                    image_group.labels_group.parent().removeChild(
+                        image_group.labels_group
+                    )
+
+                image_group.labels_group = None
+
         if not self.managed_layers[removed_layer]:
             self.managed_layers.pop(removed_layer)
 

src/napari_activelearning/_utils.py

@@ -249,7 +249,7 @@ def get_dataloader(
     train_dataset = zds.ZarrDataset(
         list(dataset_metadata.values()),
         return_positions=True,
-        draw_same_chunk=True,
+        draw_same_chunk=False,
         patch_sampler=patch_sampler,
         shuffle=shuffle
     )