Napari GUI: Fix voxel size precision, font size, and rearrange widgets

plantseg/viewer/containers.py

@@ -1,12 +1,12 @@
 import webbrowser
 
 from PyQt5.QtCore import Qt
-from magicgui.widgets import MainWindow
+from magicgui.widgets import MainWindow, Label
 
 from plantseg.viewer.widget.dataprocessing import widget_cropping, widget_add_layers
 from plantseg.viewer.widget.dataprocessing import widget_label_processing
 from plantseg.viewer.widget.dataprocessing import widget_rescaling, widget_gaussian_smoothing
-from plantseg.viewer.widget.io import widget_open_file, export_stacks
+from plantseg.viewer.widget.io import widget_open_file, widget_export_stacks
 from plantseg.viewer.widget.predictions import widget_iterative_unet_predictions, widget_add_custom_model
 from plantseg.viewer.widget.predictions import widget_unet_predictions, widget_test_all_unet_predictions
 from plantseg.viewer.widget.predictions import widget_extra_pred_manager
@@ -19,6 +19,8 @@
 from plantseg.viewer.widget.segmentation import widget_simple_dt_ws
 from plantseg.viewer.widget.segmentation import widget_extra_seg_manager
 
+STYLE_SLIDER = "font-size: 9pt;"
+
 
 def setup_menu(container, path=None):
     def _callback():
@@ -33,19 +35,16 @@ def _callback():
     return container
 
 
-def get_main():
+def get_data_io():
     container = MainWindow(widgets=[widget_open_file,
-                                    export_stacks,
-                                    widget_split_and_merge_from_scribbles,
-                                    widget_clean_scribble,
-                                    widget_filter_segmentation,
-                                    ],
+                                    widget_export_stacks],
                            labels=False)
     container = setup_menu(container, path='https://hci-unihd.github.io/plant-seg/chapters/plantseg_interactive_napari/index.html')
     return container
 
 
 def get_preprocessing_workflow():
+    widget_cropping.crop_z.native.setStyleSheet(STYLE_SLIDER)
     container = MainWindow(widgets=[widget_gaussian_smoothing,
                                     widget_rescaling,
                                     widget_cropping,
@@ -65,22 +64,35 @@ def get_gasp_workflow():
     return container
 
 
+def get_extra_pred():
+    container = MainWindow(widgets=[widget_extra_pred_manager,
+                                    Label(),
+                                    widget_test_all_unet_predictions,
+                                    widget_iterative_unet_predictions,
+                                    widget_add_custom_model],
+                           labels=False)
+    container = setup_menu(container, path='https://hci-unihd.github.io/plant-seg/chapters/plantseg_interactive_napari/extra_pred.html')
+    return container
+
+
 def get_extra_seg():
     container = MainWindow(widgets=[widget_extra_seg_manager,
+                                    Label(),
                                     widget_dt_ws,
-                                    widget_lifted_multicut,
-                                    widget_fix_over_under_segmentation_from_nuclei,
-                                    widget_fix_false_positive_from_foreground_pmap],
+                                    widget_lifted_multicut],
                            labels=False)
     container = setup_menu(container, path='https://hci-unihd.github.io/plant-seg/chapters/plantseg_interactive_napari/extra_seg.html')
     return container
 
 
-def get_extra_pred():
-    container = MainWindow(widgets=[widget_extra_pred_manager,
-                                    widget_test_all_unet_predictions,
-                                    widget_iterative_unet_predictions,
-                                    widget_add_custom_model],
+def get_proofreading():
+    widget_fix_over_under_segmentation_from_nuclei.threshold.native.setStyleSheet(STYLE_SLIDER)
+    widget_fix_over_under_segmentation_from_nuclei.quantile.native.setStyleSheet(STYLE_SLIDER)
+    container = MainWindow(widgets=[widget_fix_over_under_segmentation_from_nuclei,
+                                    widget_fix_false_positive_from_foreground_pmap,
+                                    widget_split_and_merge_from_scribbles,
+                                    widget_clean_scribble,
+                                    widget_filter_segmentation],
                            labels=False)
-    container = setup_menu(container, path='https://hci-unihd.github.io/plant-seg/chapters/plantseg_interactive_napari/extra_pred.html')
+    container = setup_menu(container, path='https://hci-unihd.github.io/plant-seg/chapters/plantseg_interactive_napari/extra_seg.html')
     return container

plantseg/viewer/viewer.py

@@ -1,25 +1,25 @@
 import napari
 
-from plantseg.viewer.containers import get_extra_seg, get_extra_pred
-from plantseg.viewer.containers import get_gasp_workflow, get_preprocessing_workflow, get_main
+from plantseg.viewer.containers import get_extra_pred, get_extra_seg, get_proofreading
+from plantseg.viewer.containers import get_gasp_workflow, get_preprocessing_workflow, get_data_io
 from plantseg.viewer.logging import napari_formatted_logging
 from plantseg.viewer.widget.proofreading.proofreading import setup_proofreading_keybindings
 
 
 def run_viewer():
     viewer = napari.Viewer()
-    main_container = get_main()
-    main_w = viewer.window.add_dock_widget(main_container, name='Main')
+    main_container = get_data_io()
+    main_w = viewer.window.add_dock_widget(main_container, name='Data')
 
     setup_proofreading_keybindings(viewer)
 
-    for _containers, name in [(get_preprocessing_workflow(), 'Data - Processing'),
-                              (get_gasp_workflow(), 'UNet + Segmentation'),
-                              (get_extra_pred(), 'Extra-Pred'),
-                              (get_extra_seg(), 'Extra-Seg'),
-                              ]:
+    for _containers, name in [(get_preprocessing_workflow(), 'Preprocessing'),
+                              (get_gasp_workflow(), 'Main'),
+                              (get_extra_pred(), 'Prediction'),
+                              (get_extra_seg(), 'Segmentation'),
+                              (get_proofreading(), 'Proofreading')]:
         _container_w = viewer.window.add_dock_widget(_containers, name=name)
         viewer.window._qt_window.tabifyDockWidget(main_w, _container_w)
 
-    napari_formatted_logging('Plantseg is ready!', thread='Main', level='info')
+    napari_formatted_logging('Plantseg is ready!', thread='run_viewer', level='info')
     napari.run()

plantseg/viewer/widget/dataprocessing.py

@@ -66,10 +66,12 @@ class RescaleType(Enum):
           image={'label': 'Image or Label',
                  'tooltip': 'Layer to apply the rescaling.'},
           rescaling_factor={'label': 'Rescaling factor',
-                            'tooltip': 'Define the scaling factor to use for resizing the input image.'},
+                            'tooltip': 'Define the scaling factor to use for resizing the input image.',
+                            'options': {'step': 0.00001}},
           out_voxel_size={'label': 'Out voxel size',
                           'tooltip': 'Define the output voxel size. Units are same as imported, '
-                                     '(if units are missing default is "um").'},
+                                     '(if units are missing default is "um").',
+                          'options': {'step': 0.00001}},
           reference_layer={'label': 'Reference layer',
                            'tooltip': 'Rescale to same voxel size as selected layer.'},
           reference_model={'label': 'Reference model',

plantseg/viewer/widget/io.py

@@ -358,13 +358,13 @@ def checkout(*args):
     workflow_name={'label': 'Workflow name',
                    'tooltip': 'Name of the workflow object.'},
 )
-def export_stacks(images: List[Tuple[Layer, str]],
-                  directory: Path = Path.home(),
-                  export_format: str = 'tiff',
-                  rescale_to_original_resolution: bool = True,
-                  data_type: str = 'float32',
-                  workflow_name: str = 'workflow',
-                  ) -> None:
+def widget_export_stacks(images: List[Tuple[Layer, str]],
+                         directory: Path = Path.home(),
+                         export_format: str = 'tiff',
+                         rescale_to_original_resolution: bool = True,
+                         data_type: str = 'float32',
+                         workflow_name: str = 'workflow',
+                         ) -> None:
     export_name = []
 
     for i, (image, image_custom_name) in enumerate(images):
@@ -457,25 +457,25 @@ def export_stacks(images: List[Tuple[Layer, str]],
         napari_formatted_logging(f'Workflow correctly exported', thread='Export stack')
 
 
-export_stacks.directory.hide()
-export_stacks.export_format.hide()
-export_stacks.rescale_to_original_resolution.hide()
-export_stacks.data_type.hide()
-export_stacks.workflow_name.hide()
+widget_export_stacks.directory.hide()
+widget_export_stacks.export_format.hide()
+widget_export_stacks.rescale_to_original_resolution.hide()
+widget_export_stacks.data_type.hide()
+widget_export_stacks.workflow_name.hide()
 
 
-@export_stacks.images.changed.connect
+@widget_export_stacks.images.changed.connect
 def _on_images_changed(images_list: List[Tuple[Layer, str]]):
     images_list = return_value_if_widget(images_list)
     if len(images_list) > 0:
-        export_stacks.directory.show()
-        export_stacks.export_format.show()
-        export_stacks.rescale_to_original_resolution.show()
-        export_stacks.data_type.show()
-        export_stacks.workflow_name.show()
+        widget_export_stacks.directory.show()
+        widget_export_stacks.export_format.show()
+        widget_export_stacks.rescale_to_original_resolution.show()
+        widget_export_stacks.data_type.show()
+        widget_export_stacks.workflow_name.show()
     else:
-        export_stacks.directory.hide()
-        export_stacks.export_format.hide()
-        export_stacks.rescale_to_original_resolution.hide()
-        export_stacks.data_type.hide()
-        export_stacks.workflow_name.hide()
+        widget_export_stacks.directory.hide()
+        widget_export_stacks.export_format.hide()
+        widget_export_stacks.rescale_to_original_resolution.hide()
+        widget_export_stacks.data_type.hide()
+        widget_export_stacks.workflow_name.hide()

plantseg/viewer/widget/predictions.py

@@ -291,7 +291,7 @@ def _on_widget_iterative_unet_predictions_image_change(image: Image):
           new_model_name={'label': 'New model name'},
           model_location={'label': 'Model location',
                           'mode': 'd'},
-          resolution={'label': 'Resolution'},
+          resolution={'label': 'Resolution', 'options': {'step': 0.00001}},
           description={'label': 'Description'},
           dimensionality={'label': 'Dimensionality',
                           'tooltip': 'Dimensionality of the model (2D or 3D). '
@@ -339,12 +339,10 @@ def widget_add_custom_model(new_model_name: str = 'custom_model',
                                  "Iterative UNet": widget_iterative_unet_predictions,
                                  "Add Custom Model": widget_add_custom_model}
 
-for _widget in registered_extra_pred_widgets.values():
-    _widget.hide()
-
 
 @magicgui(auto_call=True,
           widget_name={'label': 'Widget Selection',
+                       'tooltip': 'Show only one widget if the Napari interface is too long.',
                        'choices': list(registered_extra_pred_widgets.keys())})
 def widget_extra_pred_manager(widget_name: str) -> None:
     napari_formatted_logging(f'Showing widget: {widget_name}', thread='Extra-Pred', level='info')
@@ -353,3 +351,12 @@ def widget_extra_pred_manager(widget_name: str) -> None:
             value.show()
         else:
             value.hide()
+
+TOO_MANY_WIDGES = False  # Set to True if there are too many widgets to show
+
+if TOO_MANY_WIDGES:
+    for _widget in registered_extra_pred_widgets.values():
+        _widget.hide()
+
+# widget_extra_pred_manager.enabled=TOO_MANY_WIDGES
+

plantseg/viewer/widget/segmentation.py

@@ -367,17 +367,12 @@ def widget_fix_false_positive_from_foreground_pmap(segmentation: Labels,
 
 
 register_extra_seg_widgets = {"Watershed": widget_dt_ws,
-                              "Lifted MultiCut": widget_lifted_multicut,
-                              "Fix Over/Under Segmentation from Nuclei": widget_fix_over_under_segmentation_from_nuclei,
-                              "Fix False Positives from Foreground Pmap": widget_fix_false_positive_from_foreground_pmap,
-                              }
-
-for _widget in register_extra_seg_widgets.values():
-    _widget.hide()
+                              "Lifted MultiCut": widget_lifted_multicut}
 
 
 @magicgui(auto_call=True,
           widget_name={'label': 'Widget Selection',
+                       'tooltip': 'Show only one widget if the Napari interface is too long.',
                        'choices': list(register_extra_seg_widgets.keys())})
 def widget_extra_seg_manager(widget_name: str) -> None:
     napari_formatted_logging(f'Showing {widget_name} widget',
@@ -388,3 +383,11 @@ def widget_extra_seg_manager(widget_name: str) -> None:
             value.show()
         else:
             value.hide()
+
+TOO_MANY_WIDGES = False  # Set to True if there are too many widgets to show
+
+if TOO_MANY_WIDGES:
+    for _widget in register_extra_seg_widgets.values():
+        _widget.hide()
+
+# widget_extra_seg_manager.enabled=TOO_MANY_WIDGES