Save selected layers to folder

src/box_manager/_qt/OrganizeLayer.py

@@ -230,7 +230,7 @@ def _save_ui(self):
             "dummyf": QLabel(self),
             "suffix": QLineEdit(self),
         }
-        self.save_layers["layer"].addItems([""])
+        self.save_layers["layer"].addItems(["Selected"])
         self.save_layers["dimension"].addItems(["", "2D", "3D"])
         self.save_layers["type"].addItems(["", "Particles", "Filaments"])
         self.save_layers["suffix"].setPlaceholderText("e.g., _suffix")
@@ -333,10 +333,7 @@ def _add_ui(self):
 
     @Slot()
     def _run_save(self,path=None):
-        cur_format = self.save_layers["format"].currentText().split(" ", 1)[0]
-        cur_layer = self.napari_viewer.layers[
-            self.save_layers["layer"].currentText()
-        ]
+
 
         cur_spacing = self.save_layers["inter-box distance"].text()
         cur_type = self.save_layers["type"].currentText()
@@ -356,13 +353,28 @@ def _run_save(self,path=None):
             self.saved_dir_path = os.getcwd()
             return
 
-        napari_get_writer(
-            self.saved_dir_path,
-            [cur_layer.as_layer_data_tuple()],
-            cur_format,
-            self.save_layers["suffix"].text() + cur_format,
-            cur_spacing=int(cur_spacing),
-        )
+
+        cur_format = self.save_layers["format"].currentText().split(" ", 1)[0]
+        sel_layer = self.save_layers["layer"].currentText()
+        layers_to_write = []
+        if sel_layer == "Selected":
+            for cur_layer in self.napari_viewer.layers.selection:
+                if len(cur_layer.data) == 0:
+                    continue
+                layers_to_write.append(cur_layer)
+        else:
+            cur_layer = self.napari_viewer.layers[sel_layer]
+            layers_to_write.append(cur_layer)
+
+        for cur_layer in layers_to_write:
+            napari_get_writer(
+                self.saved_dir_path,
+                [cur_layer.as_layer_data_tuple()],
+                cur_format,
+                self.save_layers["suffix"].text() + cur_format,
+                cur_spacing=int(cur_spacing),
+            )
+
 
     @Slot(object)
     def _update_link_combo(self, *_):
@@ -393,7 +405,7 @@ def _update_layer_combo(self, *_):
             if isinstance(entry, (napari.layers.Shapes, napari.layers.Points))
         ]
         self.save_layers["layer"].clear()
-        self.save_layers["layer"].addItems([""] + names)
+        self.save_layers["layer"].addItems(["Selected"] + names)
         try:
             self.save_layers["layer"].setCurrentText(
                 self.napari_viewer.layers.selection.active.name
@@ -413,6 +425,9 @@ def _save_layer_changed(self, _):
     def _update_format(self, _=None, is_layer=False):
         cur_layer = self.save_layers["layer"].currentText()
 
+        if cur_layer == "Selected":
+            return
+
         if not cur_layer:
             self.save_run_btn.setEnabled(False)
             for name, widget in self.save_layers.items():

src/box_manager/io/cbox.py

@@ -172,6 +172,9 @@ def _make_df_data_filament(
         feature_map["angle"] = "_Angle"
         other_interpolation_cols.append("_Angle")
 
+    if coordinates.size == 0:
+        return {"cryolo": pd.DataFrame(columns=coord_columns), "filament_vertices": pd.DataFrame(columns=coord_columns)}
+
     empty_data = copy.deepcopy(data)
     filaments = []
     entry = 0
@@ -220,12 +223,15 @@ def _make_df_data_filament(
     else:
         coordinates[:, [0, 1]] = coordinates[:, [1, 0]]
 
+
     verts = pd.DataFrame(
         coordinates, columns=coord_columns+["_filamentid"]
     )
     verts["_Width"] = box_size
     verts["_Height"] = box_size
+
     result = {"cryolo": pd.concat(filaments), "filament_vertices": verts}
+
     return result
 
 

src/box_manager/io/io_utils.py

@@ -251,7 +251,7 @@ def to_napari_image(
         original_path = path
         path = sorted(glob.glob(path))  # type: ignore
 
-        if not os.path.exists(original_path):
+        if not os.path.exists(original_path) and is_2d_stack==False:
             raise FileNotFoundError(original_path)
 
     else:
@@ -272,6 +272,7 @@ def to_napari_image(
     file_size = (
         sum(os.stat(file_name).st_size for file_name in path) / 1024**3
     )
+
     if len(path) > 1 and file_size > PROXY_THRESHOLD_GB:
         data = LoaderProxy(path, load_image, do_normalize)
     else:
@@ -570,8 +571,10 @@ def convert_shape_filament_layer_to_boxlayer(
             [[filid] * len(d) for filid, d in enumerate(data)]
         )
     )
-
-    data = np.concatenate(data)
+    if len(data) > 0:
+        data = np.concatenate(data)
+    else:
+        data = np.empty((0,0))
 
     return data, meta