Merge remote-tracking branch 'origin/(WIP)_General_improvements' into (WIP)_General_improvements

# Conflicts:
#	docs/res/code/model_framework.rst
#	docs/res/plugin_base.rst
#	src/napari_cellseg_3d/plugin_metrics.py

Author: C-Achard

docs/index.rst

@@ -3,32 +3,40 @@ Welcome to napari-cellseg-3d's documentation!
 
 .. toctree::
     :maxdepth: 1
-    :caption: User guide:
+    :caption: Main modules guides:
 
     res/welcome
-    res/review_module_guide
-    res/inference_module_guide
-    res/training_module_guide
-    res/cropping_module_guide
-    res/custom_model_template
+    res/guides/review_module_guide
+    res/guides/inference_module_guide
+    res/guides/training_module_guide
+
+
+.. toctree::
+    :maxdepth: 1
+    :caption: Utilities & advanced guides:
+
+    res/guides/metrics_module_guide
+    res/guides/convert_module_guide
+    res/guides/cropping_module_guide
+    res/guides/custom_model_template
 
 
 .. toctree::
     :maxdepth: 1
     :caption: Source files:
 
-    res/interface
-    res/plugin_base
-    res/plugin_review
-    res/plugin_dock
-    res/plugin_crop
-    res/launch_review
-    res/model_framework
-    res/model_workers
-    res/model_instance_seg
-    res/plugin_model_inference
-    res/plugin_model_training
-    res/utils
+    res/code/interface
+    res/code/plugin_base
+    res/code/plugin_review
+    res/code/plugin_dock
+    res/code/plugin_crop
+    res/code/launch_review
+    res/code/model_framework
+    res/code/model_workers
+    res/code/model_instance_seg
+    res/code/plugin_model_inference
+    res/code/plugin_model_training
+    res/code/utils
 
 
 

docs/res/interface.rst docs/res/code/interface.rstdocs/res/interface.rst renamed to docs/res/code/interface.rst

@@ -1,3 +1,6 @@
+.. _model_framework.py_models_dict:
+
+
 model_framework.py
 ====================================================
 
@@ -13,7 +16,6 @@ Methods
    :noindex:
 
 
-
 Attributes
 *********************
 

docs/res/launch_review.rst docs/res/code/launch_review.rstdocs/res/launch_review.rst renamed to docs/res/code/launch_review.rst

@@ -13,6 +13,10 @@ binary_watershed
 **************************************
 .. autofunction:: napari_cellseg_3d.model_instance_seg::binary_watershed
 
+clear_small_objects
+**************************************
+.. autofunction:: napari_cellseg_annotator.model_instance_seg::clear_small_objects
+
 to_instance
 **************************************
 .. autofunction:: napari_cellseg_3d.model_instance_seg::to_instance

docs/res/model_framework.rst docs/res/code/model_framework.rstdocs/res/model_framework.rst renamed to docs/res/code/model_framework.rst

@@ -0,0 +1,39 @@
+plugin_base.py
+====================================================
+
+
+Class : BasePluginSingleImage
+----------------------------------------------------
+
+
+Methods
+**********************
+.. autoclass:: napari_cellseg_annotator.plugin_base::BasePluginSingleImage
+   :members:  __init__, remove_from_viewer, show_dialog_images, show_dialog_labels, update_default
+   :noindex:
+
+
+
+Attributes
+*********************
+
+.. autoclass:: napari_cellseg_annotator.plugin_base::BasePluginSingleImage
+   :members:  _viewer, image_path, label_path, filetype, file_handling_box
+
+
+Class : BasePluginFolder
+-------------------------------------------------------
+
+
+Methods
+***********************
+.. autoclass:: napari_cellseg_annotator.plugin_base::BasePluginFolder
+   :members:  __init__, remove_from_viewer,make_close_button,make_prev_button,make_next_button, load_dataset_paths,load_image_dataset,load_label_dataset,load_results_path, update_default,remove_docked_widgets
+   :noindex:
+
+
+Attributes
+*********************
+
+.. autoclass:: napari_cellseg_annotator.plugin_base::BasePluginFolder
+   :members:  _viewer, images_filepaths, labels_filepaths,results_path, filetype_choice