Interface overhaul

.github/workflows/preview_metadata.yml

@@ -4,7 +4,7 @@ name: napari hub Preview Page # we use this name to find your preview page artif
 on:
   pull_request:
     branches:
-      - '**'
+      - 'test' # '**' for all
 
 jobs:
   preview-page:
@@ -16,6 +16,6 @@ jobs:
         uses: actions/checkout@v2
 
       - name: napari hub Preview Page Builder
-        uses: chanzuckerberg/napari-hub-preview-action@v0.1.5
+        uses: chanzuckerberg/napari-hub-preview-action@v0.1.6
         with:
           hub-ref: main

.github/workflows/test_and_deploy.yml

@@ -22,40 +22,41 @@ jobs:
     runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.8, 3.9, "3.10"]
+# platform: [ubuntu-latest, windows-latest, macos-latest]
+        platform: [windows-latest]
+        python-version: [3.8, 3.9] # 3.10
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      # these libraries enable testing on Qt on linux
+# these libraries enable testing on Qt on linux
       - uses: tlambert03/setup-qt-libs@v1
 
-      # strategy borrowed from vispy for installing opengl libs on windows
+# strategy borrowed from vispy for installing opengl libs on windows
       - name: Install Windows OpenGL
         if: runner.os == 'Windows'
         run: |
           git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
           powershell gl-ci-helpers/appveyor/install_opengl.ps1
           if (Test-Path -Path "C:\Windows\system32\opengl32.dll" -PathType Leaf) {Exit 0} else {Exit 1}
 
-      # note: if you need dependencies from conda, considering using
-      # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
-      # and
-      # tox-conda: https://github.com/tox-dev/tox-conda
+# note: if you need dependencies from conda, considering using
+# setup-miniconda: https://github.com/conda-incubator/setup-miniconda
+# and
+# tox-conda: https://github.com/tox-dev/tox-conda
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install setuptools tox tox-gh-actions
 
-      # this runs the platform-specific tests declared in tox.ini
+# this runs the platform-specific tests declared in tox.ini
       - name: Test with tox
-        uses: GabrielBB/xvfb-action@v1
+        uses: GabrielBB/xvfb-action@v1 # aganders3/headless-gui@v1
         with:
           run: python -m tox
         env:
@@ -65,9 +66,9 @@ jobs:
         uses: codecov/codecov-action@v2
 
   deploy:
-    # this will run when you have tagged a commit, starting with "v*"
-    # and requires that you have put your twine API key in your
-    # github secrets (see readme for details)
+# this will run when you have tagged a commit, starting with "v*"
+# and requires that you have put your twine API key in your
+# github secrets (see readme for details)
     needs: [test]
     runs-on: ubuntu-latest
     if: contains(github.ref, 'tags')

.gitignore

@@ -95,7 +95,12 @@ venv/
 ########
 #project specific
 #dataset, weights, old logos, requirements
-/napari_cellseg3d/models/dataset/
-/napari_cellseg3d/models/saved_weights/
+/napari_cellseg3d/code_models/models/dataset/
+/napari_cellseg3d/code_models/models/saved_weights/
 /docs/res/logo/old_logo/
 /reqs/
+/Loss_plots/
+notebooks/csv_cell_plot.html
+notebooks/full_plot.html
+*.csv
+*.png

docs/conf.py

@@ -52,7 +52,7 @@
 
 # General information about the project.
 project = "napari-cellseg3d"
-copyright = "2022, Cyril Achard, Maxime Vidal"
+copyright = "2022-2023, Cyril Achard, Maxime Vidal"
 author = "Cyril Achard, Maxime Vidal"
 
 # The version info for the project you're documenting, acts as replacement for

docs/index.rst

@@ -16,7 +16,7 @@ Welcome to napari-cellseg3d's documentation!
     :caption: Utilities :
 
     res/guides/metrics_module_guide
-    res/guides/convert_module_guide
+    res/guides/utils_module_guide
     res/guides/cropping_module_guide
 
 
@@ -34,8 +34,7 @@ Welcome to napari-cellseg3d's documentation!
     res/code/interface
     res/code/plugin_base
     res/code/plugin_review
-    res/code/launch_review
-    res/code/plugin_dock
+    res/code/plugin_review_dock
     res/code/plugin_crop
     res/code/plugin_convert
     res/code/plugin_metrics

docs/res/code/interface.rst

@@ -4,6 +4,27 @@ interface.py
 Classes
 -------------
 
+QWidgetSingleton
+**************************************
+.. autoclass:: napari_cellseg3d.interface::QWidgetSingleton
+    :members: __call__
+
+UtilsDropdown
+**************************************
+.. autoclass:: napari_cellseg3d.interface::UtilsDropdown
+    :members: __init__, dropdown_menu_call, show_utils_menu
+
+Log
+**************************************
+.. autoclass:: napari_cellseg3d.interface::Log
+    :members: __init__, write, replace_last_line, print_and_log, warn
+
+
+ContainerWidget
+**************************************
+.. autoclass:: napari_cellseg3d.interface::ContainerWidget
+    :members: __init__
+
 Button
 **************************************
 .. autoclass:: napari_cellseg3d.interface::Button
@@ -22,13 +43,13 @@ CheckBox
 AnisotropyWidgets
 **************************************
 .. autoclass:: napari_cellseg3d.interface::AnisotropyWidgets
-   :members: __init__, build, get_anisotropy_resolution_xyz, get_anisotropy_resolution_zyx, anisotropy_zoom_factor,is_enabled,toggle_permanent_visibility
+   :members: __init__, build, scaling_zyx, resolution_zyx, scaling_xyz, resolution_xyz,enabled
 
 
 FilePathWidget
 **************************************
 .. autoclass:: napari_cellseg3d.interface::FilePathWidget
-   :members: __init__, build, get_text_field, get_button, check_ready, set_required, update_field_color, set_description
+   :members: __init__, build, text_field, button, check_ready, required, update_field_color, tooltips
 
 ScrollArea
 **************************************
@@ -38,7 +59,7 @@ ScrollArea
 DoubleIncrementCounter
 **************************************
 .. autoclass:: napari_cellseg3d.interface::DoubleIncrementCounter
-   :members: __init__, set_precision, make_n
+   :members: __init__, precision, make_n
 
 IntIncrementCounter
 **************************************
@@ -49,22 +70,21 @@ IntIncrementCounter
 Functions
 -------------
 
-open_url
+handle_adjust_errors
 **************************************
-.. autofunction:: napari_cellseg3d.interface::open_url
-
+.. autofunction:: napari_cellseg3d.interface::handle_adjust_errors
 
-make_group
+handle_adjust_errors_wrapper
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_group
+.. autofunction:: napari_cellseg3d.interface::handle_adjust_errors_wrapper
 
-add_to_group
+open_url
 **************************************
-.. autofunction:: napari_cellseg3d.interface::add_to_group
+.. autofunction:: napari_cellseg3d.interface::open_url
 
-make_container
+make_group
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_container
+.. autofunction:: napari_cellseg3d.interface::make_group
 
 combine_blocks
 **************************************
@@ -74,6 +94,10 @@ add_blank
 **************************************
 .. autofunction:: napari_cellseg3d.interface::add_blank
 
+add_label
+**************************************
+.. autofunction:: napari_cellseg3d.interface::add_label
+
 toggle_visibility
 **************************************
 .. autofunction:: napari_cellseg3d.interface::toggle_visibility

docs/res/code/model_framework.rst

@@ -11,13 +11,13 @@ Class : ModelFramework
 
 Methods
 **********************
-.. autoclass:: napari_cellseg3d.model_framework::ModelFramework
-   :members:  __init__, load_dataset_paths,save_log, save_log_to_path,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
+.. autoclass:: napari_cellseg3d.code_models.model_framework::ModelFramework
+   :members:  __init__, send_log, save_log, save_log_to_path, display_status_report, create_train_dataset_dict, get_model, get_available_models, get_device, empty_cuda_cache
    :noindex:
 
 
 Attributes
 *********************
 
-.. autoclass:: napari_cellseg3d.model_framework::ModelFramework
-   :members:  _viewer, worker, docked_widgets, images_filepaths, labels_filepaths, results_path, model_path
+.. autoclass:: napari_cellseg3d.code_models.model_framework::ModelFramework
+   :members:  _viewer, worker, docked_widgets, images_filepaths, labels_filepaths, results_path

docs/res/code/model_instance_seg.rst

@@ -7,24 +7,24 @@ Functions
 
 binary_connected
 **************************************
-.. autofunction:: napari_cellseg3d.model_instance_seg::binary_connected
+.. autofunction:: napari_cellseg3d.code_models.model_instance_seg::binary_connected
 
 binary_watershed
 **************************************
-.. autofunction:: napari_cellseg3d.model_instance_seg::binary_watershed
+.. autofunction:: napari_cellseg3d.code_models.model_instance_seg::binary_watershed
 
 volume_stats
 **************************************
-.. autofunction:: napari_cellseg3d.model_instance_seg::volume_stats
+.. autofunction:: napari_cellseg3d.code_models.model_instance_seg::volume_stats
 
 clear_small_objects
 **************************************
-.. autofunction:: napari_cellseg3d.model_instance_seg::clear_small_objects
+.. autofunction:: napari_cellseg3d.code_models.model_instance_seg::clear_small_objects
 
 to_instance
 **************************************
-.. autofunction:: napari_cellseg3d.model_instance_seg::to_instance
+.. autofunction:: napari_cellseg3d.code_models.model_instance_seg::to_instance
 
 to_semantic
 **************************************
-.. autofunction:: napari_cellseg3d.model_instance_seg::to_semantic
+.. autofunction:: napari_cellseg3d.code_models.model_instance_seg::to_semantic

docs/res/code/model_workers.rst

@@ -10,7 +10,7 @@ Class : LogSignal
 
 Attributes
 ************************
-.. autoclass:: napari_cellseg3d.model_workers::LogSignal
+.. autoclass:: napari_cellseg3d.code_models.model_workers::LogSignal
    :members: log_signal
    :noindex:
 
@@ -24,7 +24,7 @@ Class : InferenceWorker
 
 Methods
 ************************
-.. autoclass:: napari_cellseg3d.model_workers::InferenceWorker
+.. autoclass:: napari_cellseg3d.code_models.model_workers::InferenceWorker
    :members: __init__, log, create_inference_dict, inference
    :noindex:
 
@@ -39,7 +39,7 @@ Class : TrainingWorker
 
 Methods
 ************************
-.. autoclass:: napari_cellseg3d.model_workers::TrainingWorker
+.. autoclass:: napari_cellseg3d.code_models.model_workers::TrainingWorker
    :members: __init__, log, train
    :noindex:
 

docs/res/code/plugin_base.rst

@@ -8,17 +8,15 @@ Class : BasePluginSingleImage
 
 Methods
 **********************
-.. autoclass:: napari_cellseg3d.plugin_base::BasePluginSingleImage
-   :members:  __init__, remove_from_viewer, show_dialog_images, show_dialog_labels, update_default
+.. autoclass:: napari_cellseg3d.code_plugins.plugin_base::BasePluginSingleImage
+   :members:  __init__, enable_utils_menu, remove_from_viewer, remove_docked_widgets
    :noindex:
 
-
-
 Attributes
 *********************
 
-.. autoclass:: napari_cellseg3d.plugin_base::BasePluginSingleImage
-   :members:  _viewer, image_path, label_path, filetype, file_handling_box
+.. autoclass:: napari_cellseg3d.code_plugins.plugin_base::BasePluginSingleImage
+   :members:  _viewer, image_path, label_path, image_layer_loader, label_layer_loader
 
 
 
@@ -29,13 +27,12 @@ Class : BasePluginFolder
 
 Methods
 ***********************
-.. autoclass:: napari_cellseg3d.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
+.. autoclass:: napari_cellseg3d.code_plugins.plugin_base::BasePluginFolder
+   :members:  __init__, load_dataset_paths,load_image_dataset,load_label_dataset
    :noindex:
 
-
 Attributes
 *********************
 
-.. autoclass:: napari_cellseg3d.plugin_base::BasePluginFolder
-   :members:  _viewer, images_filepaths, labels_filepaths,results_path, filetype_choice
+.. autoclass:: napari_cellseg3d.code_plugins.plugin_base::BasePluginFolder
+   :members:  _viewer, images_filepaths, labels_filepaths, results_path