renamed plugin + changed logo + added transfer learning + custom weights + added new trailmap from 3dunet

Author: C-Achard

.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

@@ -1,4 +1,4 @@
-Welcome to napari-cellseg-annotator's documentation!
+Welcome to napari-cellseg-3d's documentation!
 ===============================================================
 
 .. toctree::

docs/res/custom_model_template.rst

@@ -3,7 +3,7 @@
 Advanced : Declaring a custom model
 =============================================
 
-To add a custom model, you will need a **.py** file with the following structure to be placed in the *src/napari_cellseg_annotator/models* folder:
+To add a custom model, you will need a **.py** file with the following structure to be placed in the *src/napari_cellseg_3d/models* folder:
 
 
 ::
@@ -15,7 +15,7 @@ To add a custom model, you will need a **.py** file with the following structure
 
     def get_weights_file():
         return "weights_file.pth" # name of the weights file for the model,
-        # which should be in *src/napari_cellseg_annotator/models/saved_weights*
+        # which should be in *src/napari_cellseg_3d/models/saved_weights*
 
 
     def get_output(model, input):

docs/res/interface.rst

@@ -6,50 +6,50 @@ Functions
 
 open_url
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::open_url
+.. autofunction:: napari_cellseg_3d.interface::open_url
 
 
 make_scrollable
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::make_scrollable
+.. autofunction:: napari_cellseg_3d.interface::make_scrollable
 
 
 make_group
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::make_group
+.. autofunction:: napari_cellseg_3d.interface::make_group
 
 
 make_container_widget
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::make_container_widget
+.. autofunction:: napari_cellseg_3d.interface::make_container_widget
 
 
 make_button
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::make_button
+.. autofunction:: napari_cellseg_3d.interface::make_button
 
 make_combobox
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::make_combobox
+.. autofunction:: napari_cellseg_3d.interface::make_combobox
 
 make_checkbox
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::make_checkbox
+.. autofunction:: napari_cellseg_3d.interface::make_checkbox
 
 
 combine_blocks
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::combine_blocks
+.. autofunction:: napari_cellseg_3d.interface::combine_blocks
 
 
 add_blank
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::add_blank
+.. autofunction:: napari_cellseg_3d.interface::add_blank
 
 
 open_file_dialog
 **************************************
-.. autofunction:: napari_cellseg_annotator.interface::open_file_dialog
+.. autofunction:: napari_cellseg_3d.interface::open_file_dialog
 
 
 

docs/res/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

@@ -8,7 +8,7 @@ Class : ModelFramework
 
 Methods
 **********************
-.. autoclass:: napari_cellseg_annotator.model_framework::ModelFramework
+.. 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:
 
@@ -17,5 +17,5 @@ Methods
 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/model_instance_seg.rst

@@ -7,16 +7,16 @@ Functions
 
 binary_connected
 **************************************
-.. autofunction:: napari_cellseg_annotator.model_instance_seg::binary_connected
+.. autofunction:: napari_cellseg_3d.model_instance_seg::binary_connected
 
 binary_watershed
 **************************************
-.. autofunction:: napari_cellseg_annotator.model_instance_seg::binary_watershed
+.. autofunction:: napari_cellseg_3d.model_instance_seg::binary_watershed
 
 to_instance
 **************************************
-.. autofunction:: napari_cellseg_annotator.model_instance_seg::to_instance
+.. autofunction:: napari_cellseg_3d.model_instance_seg::to_instance
 
 to_semantic
 **************************************
-.. autofunction:: napari_cellseg_annotator.model_instance_seg::to_semantic
+.. autofunction:: napari_cellseg_3d.model_instance_seg::to_semantic

docs/res/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: