Merge pull request #46 from C-Achard/(WIP)_General_improvements

General improvements

Author: C-Achard

.github/workflows/build_docs.yml

@@ -0,0 +1,25 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    # Standard drop-in approach that should work for most people.
+    - uses: ammaraskar/sphinx-action@master
+      with:
+        pre-build-command: "pip install -r dev.requirements.txt"
+        docs-folder: "docs/"
+
+    - name: GitHub Pages action
+      uses: peaceiris/[email protected]
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/_build/html

.gitignore

@@ -91,5 +91,5 @@ venv/
 ########
 #project specific
 #dataset
-/src/napari_cellseg_annotator/models/dataset/
-/src/napari_cellseg_annotator/models/saved_weights/
+/src/napari_cellseg_3d/models/dataset/
+/src/napari_cellseg_3d/models/saved_weights/

README.md

@@ -1,13 +1,13 @@
-# napari-cellseg-annotator
+# napari-cellseg-3d
 
-[![License](https://img.shields.io/pypi/l/napari-cellseg-annotator.svg?color=green)](https://github.com/C_Achard/napari-cellseg-annotator/raw/main/LICENSE)
-[![PyPI](https://img.shields.io/pypi/v/napari-cellseg-annotator.svg?color=green)](https://pypi.org/project/napari-cellseg-annotator)
-[![Python Version](https://img.shields.io/pypi/pyversions/napari-cellseg-annotator.svg?color=green)](https://python.org)
-[![tests](https://github.com/C_Achard/napari-cellseg-annotator/workflows/tests/badge.svg)](https://github.com/C_Achard/napari-cellseg-annotator/actions)
-[![codecov](https://codecov.io/gh/C_Achard/napari-cellseg-annotator/branch/main/graph/badge.svg)](https://codecov.io/gh/C_Achard/napari-cellseg-annotator)
-[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cellseg-annotator)](https://napari-hub.org/plugins/napari-cellseg-annotator)
+[![License](https://img.shields.io/pypi/l/napari-cellseg-3d.svg?color=green)](https://github.com/C_Achard/napari-cellseg-3d/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-cellseg-3d.svg?color=green)](https://pypi.org/project/napari-cellseg-3d)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-cellseg-3d.svg?color=green)](https://python.org)
+[![tests](https://github.com/C_Achard/napari-cellseg-3d/workflows/tests/badge.svg)](https://github.com/C_Achard/napari-cellseg-3d/actions)
+[![codecov](https://codecov.io/gh/C_Achard/napari-cellseg-3d/branch/main/graph/badge.svg)](https://codecov.io/gh/C_Achard/napari-cellseg-3d)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-cellseg-3d)](https://napari-hub.org/plugins/napari-cellseg-3d)
 
-annotator for cell segmentation
+plugin for cell segmentation
 
 ----------------------------------
 
@@ -32,9 +32,9 @@ If you get errors from MONAI regarding missing readers, please see [MONAI's opti
 
 ## Installation
 
-You can install `napari-cellseg-annotator` via [pip]:
+You can install `napari-cellseg-3d` via [pip]:
 
-    pip install napari-cellseg-annotator
+    pip install napari-cellseg-3d
 
 For local installation, please run:
 
@@ -52,7 +52,7 @@ To use the plugin, please run:
 ```
 napari
 ```
-Then go into Plugins > napari-cellseg-annotator, and choose which tool to use.
+Then go into Plugins > napari-cellseg-3d, and choose which tool to use.
 
 - **Review**: This module allows you to review your labels, from predictions or manual labeling, and correct them if needed. It then saves the status of each file in a csv, for easier monitoring.
 - **Infer**: This module allows you to use pre-trained segmentation algorithms on volumes to automatically label cells.
@@ -75,7 +75,7 @@ the coverage at least stays the same before you submit a pull request.
 ## License
 
 Distributed under the terms of the [MIT] license,
-"napari-cellseg-annotator" is free and open source software
+"napari-cellseg-3d" is free and open source software
 
 ## Issues
 

docs/conf.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# napari-cellseg-annotator documentation build configuration file, created by
+# napari-cellseg-3d documentation build configuration file, created by
 # sphinx-quickstart on Thu Oct  1 00:43:18 2015.
 #
 # This file is execfile()d with the current directory set to its
@@ -51,7 +51,7 @@
 main_doc = "index"
 
 # General information about the project.
-project = "napari-cellseg-annotator"
+project = "napari-cellseg-3d"
 copyright = "2022, Cyril Achard, Maxime Vidal"
 author = "Cyril Achard, Maxime Vidal"
 
@@ -266,7 +266,7 @@
     (
         main_doc,
         "napari-cookiecutterplugin_name",
-        "napari-cellseg-annotator Documentation",
+        "napari-cellseg-3d Documentation",
         [author],
         1,
     )
@@ -285,7 +285,7 @@
     (
         main_doc,
         "napari-cookiecutterplugin_name",
-        "napari-cellseg-annotator Documentation",
+        "napari-cellseg-3d Documentation",
         author,
         "napari-cookiecutterplugin_name",
         "One line description of project.",

docs/index.rst

@@ -1,34 +1,42 @@
-Welcome to napari-cellseg-annotator's documentation!
+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/code/interface.rst

@@ -0,0 +1,71 @@
+interface.py
+=============
+
+Functions
+-------------
+
+open_url
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::open_url
+
+
+make_scrollable
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::make_scrollable
+
+
+make_group
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::make_group
+
+
+make_container_widget
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::make_container_widget
+
+
+make_button
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::make_button
+
+make_combobox
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::make_combobox
+
+make_checkbox
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::make_checkbox
+
+
+combine_blocks
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::combine_blocks
+
+
+add_blank
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::add_blank
+
+
+open_file_dialog
+**************************************
+.. autofunction:: napari_cellseg_3d.interface::open_file_dialog
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

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

@@ -7,4 +7,4 @@ Functions
 launch_review
 *******************************
 
-.. autofunction:: napari_cellseg_annotator.launch_review::launch_review
+.. autofunction:: napari_cellseg_3d.launch_review::launch_review

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

@@ -1,3 +1,6 @@
+.. _model_framework.py_models_dict:
+
+
 model_framework.py
 ====================================================
 
@@ -8,14 +11,13 @@ Class : ModelFramework
 
 Methods
 **********************
-.. autoclass:: napari_cellseg_annotator.model_framework::ModelFramework
-   :members:  __init__,load_dataset_paths,save_log,get_model, get_loss,display_status_report,load_dataset_paths,create_train_dataset_dict, load_image_dataset, load_label_dataset,load_results_path,load_model_path,get_device, update_default, close
+.. autoclass:: napari_cellseg_3d.model_framework::ModelFramework
+   :members:  __init__,load_dataset_paths,save_log,get_model, get_loss,display_status_report,load_dataset_paths,create_train_dataset_dict, load_image_dataset, load_label_dataset,load_results_path,load_model_path,get_device, update_default, remove_from_viewer
    :noindex:
 
 
-
 Attributes
 *********************
 
-.. autoclass:: napari_cellseg_annotator.model_framework::ModelFramework
+.. autoclass:: napari_cellseg_3d.model_framework::ModelFramework
    :members:  _viewer, worker, docked_widgets, images_filepaths, labels_filepaths, results_path, model_path

docs/res/code/model_instance_seg.rst

@@ -0,0 +1,26 @@
+model_instance_seg.py
+===========================================
+
+
+Functions
+-------------
+
+binary_connected
+**************************************
+.. autofunction:: napari_cellseg_3d.model_instance_seg::binary_connected
+
+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
+
+to_semantic
+**************************************
+.. autofunction:: napari_cellseg_3d.model_instance_seg::to_semantic

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

@@ -10,7 +10,7 @@ Class : LogSignal
 
 Attributes
 ************************
-.. autoclass:: napari_cellseg_annotator.model_workers::LogSignal
+.. autoclass:: napari_cellseg_3d.model_workers::LogSignal
    :members: log_signal
    :noindex:
 
@@ -24,7 +24,7 @@ Class : InferenceWorker
 
 Methods
 ************************
-.. autoclass:: napari_cellseg_annotator.model_workers::InferenceWorker
+.. autoclass:: napari_cellseg_3d.model_workers::InferenceWorker
    :members: __init__, log, create_inference_dict, inference
    :noindex:
 
@@ -39,7 +39,7 @@ Class : TrainingWorker
 
 Methods
 ************************
-.. autoclass:: napari_cellseg_annotator.model_workers::TrainingWorker
+.. autoclass:: napari_cellseg_3d.model_workers::TrainingWorker
    :members: __init__, log, train
    :noindex: