Merge pull request #8 from TheJacksonLaboratory/dev

Enabled navigation for labels

src/napari_activelearning/_interface.py

@@ -283,12 +283,16 @@ def _clear_layers_group(self):
         self.layers_group_name_cmb.setEnabled(False)
         self.use_as_input_chk.setEnabled(False)
         self.use_as_sampling_chk.setEnabled(False)
+        self.edit_scale_mdspn.axes = ""
+        self.edit_translate_mdspn.axes = ""
 
     def _clear_layer_channel(self):
         self.display_name_lbl.setText("None selected")
         self.edit_channel_spn.setValue(0)
         self.edit_channel_spn.setMaximum(0)
         self.edit_channel_spn.setEnabled(False)
+        self.edit_scale_mdspn.setEnabled(False)
+        self.edit_translate_mdspn.setEnabled(False)
 
     def _fill_image_group(self):
         self._clear_image_group()
@@ -355,13 +359,15 @@ def _fill_layer(self):
                 ax: ax_scl
                 for ax, ax_scl in zip(self._active_layer_channel.source_axes,
                                       self._active_layer_channel.scale)
+                if ax != "C"
             }
             self.edit_scale_mdspn.setEnabled(True)
 
             self.edit_translate_mdspn.sizes = {
                 ax: ax_scl
                 for ax, ax_scl in zip(self._active_layer_channel.source_axes,
                                       self._active_layer_channel.translate)
+                if ax != "C"
             }
             self.edit_translate_mdspn.setEnabled(True)
 
@@ -485,6 +491,7 @@ def _update_reference_info(self):
 
         else:
             self.generate_mask_btn.setEnabled(False)
+            self.patch_sizes_mspn.axes = ""
 
     def generate_mask_layer(self):
         self.generate_mask_btn.setEnabled(
@@ -697,7 +704,8 @@ def __init__(self):
             "Sampling top-left",
             "Sampling bottom-right"
         ])
-        self.labels_table_tw.itemSelectionChanged.connect(self.focus_region)
+        # self.labels_table_tw.itemSelectionChanged.connect(self.focus_region)
+        self.labels_table_tw.itemPressed.connect(self.focus_region)
 
         self.labels_table_tw.addTopLevelItem(self.labels_group_root)
         self.labels_group_root.setExpanded(True)
@@ -769,6 +777,11 @@ def focus_region(self, label: Optional[QTreeWidgetItem] = None,
             self._active_label_group 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)
+
     def edit_labels(self):
         editing = super(LabelsManagerWidget, self).edit_labels()
         self.commit_btn.setEnabled(editing)

src/napari_activelearning/_labels.py

@@ -223,8 +223,6 @@ def navigate(self, delta_patch_index=0, delta_image_index=0):
         if self._requires_commit:
             self.commit()
 
-        self._active_label.setSelected(False)
-
         self._active_label_group = self._active_label.parent()
         patch_index = self._active_label_group.indexOfChild(
             self._active_label
@@ -263,8 +261,10 @@ def navigate(self, delta_patch_index=0, delta_image_index=0):
 
         patch_index = patch_index % self._active_label_group.childCount()
 
+        self._active_label.setSelected(False)
         self._active_label = self._active_label_group.child(patch_index)
         self._active_label.setSelected(True)
+        self.focus_region(self._active_label)
 
     def focus_region(self, label: Optional[QTreeWidgetItem] = None,
                      edit_focused_label: bool = False):
@@ -302,18 +302,15 @@ def focus_region(self, label: Optional[QTreeWidgetItem] = None,
             self._active_image_group = self._active_layers_group.parent()
 
         current_center = [
-            int(pos * ax_scl)
+            pos * ax_scl
             for pos, ax_scl in zip(self._active_label.center,
                                    self._active_layer_channel.layer.scale)
         ]
 
         viewer = napari.current_viewer()
         viewer.dims.order = tuple(range(viewer.dims.ndim))
         viewer.camera.center = current_center
-        viewer.dims.current_step = tuple(current_center)
-        viewer.camera.zoom = 4 / min(
-            self._active_layer_channel.layer.scale
-        )
+        viewer.dims.current_step = tuple(map(int, current_center))
 
         for layer in viewer.layers:
             layer.visible = False

src/napari_activelearning/_layers.py

@@ -1323,9 +1323,6 @@ def set_active_item(self,
         elif isinstance(item, ImageGroup):
             self._active_image_group = item
 
-        else:
-            return
-
         self.layer_scale_editor.active_layer_channel =\
             self._active_layer_channel
 

src/napari_activelearning/_models.py

@@ -50,26 +50,25 @@ def __init__(self):
             self._channel_axis = 2
             self._channels = [0, 0]
 
-        def _model_init(self, pretrained_model=None):
-            if (pretrained_model is not None
-               and not os.path.exists(pretrained_model)):
-                pretrained_model = None
-
+        def _model_init(self):
             gpu = torch.cuda.is_available() and self._gpu
-            model_type = self._model_type if pretrained_model is None else None
+            if self._pretrained_model is None:
+                model_type = self._model_type
+            else:
+                model_type = None
 
             self._model = models.CellposeModel(
                 gpu=gpu,
                 model_type=model_type,
-                pretrained_model=pretrained_model
+                pretrained_model=self._pretrained_model
             )
             self._model.mkldnn = False
             self._model.net.mkldnn = False
 
             self._model_dropout = models.CellposeModel(
                 gpu=gpu,
                 model_type=model_type,
-                pretrained_model=pretrained_model
+                pretrained_model=self._pretrained_model
             )
             self._model_dropout.mkldnn = False
             self._model_dropout.net.mkldnn = False
@@ -87,7 +86,7 @@ def _model_init(self, pretrained_model=None):
 
         def _run_pred(self, img, *args, **kwargs):
             if self.refresh_model:
-                self._model_init(pretrained_model=self._pretrained_model)
+                self._model_init()
 
             x = self._transform(img)
 
@@ -100,7 +99,7 @@ def _run_pred(self, img, *args, **kwargs):
 
         def _run_eval(self, img, *args, **kwargs):
             if self.refresh_model:
-                self._model_init(pretrained_model=self._pretrained_model)
+                self._model_init()
 
             seg, _, _ = self._model.eval(img, diameter=None,
                                          flow_threshold=None,

src/napari_activelearning/_models_interface.py

@@ -18,7 +18,8 @@ def cellpose_segmentation_parameters(
                                         "max": 2**16}] = 2,
           channels: tuple[int, int] = (0, 0),
           pretrained_model: Annotated[Path, {"widget_type": "FileEdit",
-                                      "mode": "r"}] = Path(""),
+                                             "visible": False,
+                                             "mode": "r"}] = Path(""),
           model_type: Literal["custom",
                               "cyto",
                               "cyto2",
@@ -232,7 +233,7 @@ def _set_parameter(self, parameter_val, parameter_key=None):
                         .visible = False
                     self._pretrained_model = None
 
-            if getattr(self, parameter_key) != parameter_key:
+            if getattr(self, parameter_key) != parameter_val:
                 self.refresh_model = True
                 setattr(self, parameter_key, parameter_val)