feat: modularize workflows

Author: keejkrej

MANIFEST.in

@@ -26,8 +26,8 @@ prune publications
 prine notebooks
 prune FijiMacros
 
-exclude cellacdc/models/YeastMate/detectron2
-exclude cellacdc/models/YeastMate/pycocotools
+exclude cellacdc/segmenters/YeastMate/detectron2
+exclude cellacdc/segmenters/YeastMate/pycocotools
 
 exclude requirements.txt
 exclude not_installed_requirements.txt

cellacdc/__init__.py

@@ -410,19 +410,25 @@ def printl(*objects, pretty=False, is_decorator=False, idx=1, **kwargs):
 
 parent_path = os.path.dirname(cellacdc_path)
 html_path = os.path.join(cellacdc_path, '_html')
-models_path = os.path.join(cellacdc_path, 'models')
-promptable_models_path = os.path.join(cellacdc_path, 'promptable_models')
+segmenters_path = os.path.join(cellacdc_path, 'segmenters')
+segmenters_promptable_path = os.path.join(cellacdc_path, 'segmenters_promptable')
 data_path = os.path.join(parent_path, 'data')
 resources_folderpath = os.path.join(cellacdc_path, 'resources')
 resources_filepath = os.path.join(cellacdc_path, 'resources_light.qrc')
 logs_path = os.path.join(user_profile_path, '.acdc-logs')
 acdc_fiji_path = os.path.join(user_profile_path, 'acdc-fiji')
 acdc_ffmpeg_path = os.path.join(user_profile_path, 'acdc-ffmpeg')
 resources_path = os.path.join(cellacdc_path, 'resources_light.qrc')
-models_list_file_path = os.path.join(settings_folderpath, 'custom_models_paths.ini')
-promptable_models_list_file_path = os.path.join(
+segmenters_list_file_path = os.path.join(
+    settings_folderpath, 'custom_models_paths.ini'
+)
+segmenters_promptable_list_file_path = os.path.join(
     settings_folderpath, 'custom_promptable_models_paths.ini'
 )
+models_path = segmenters_path
+promptable_models_path = segmenters_promptable_path
+models_list_file_path = segmenters_list_file_path
+promptable_models_list_file_path = segmenters_promptable_list_file_path
 favourite_func_metrics_csv_path = os.path.join(
     settings_folderpath, 'favourite_func_metrics.csv'
 )
@@ -806,4 +812,30 @@ def inner_function(self, *args, **kwargs):
 single_pos_index_cols = (
     'experiment_folderpath', 
     'Position_n'
-)
+)
+
+# Public modular API (scripting entry points)
+from cellacdc.domain import ExperimentSession, PositionSession  # noqa: E402
+
+try:
+    from cellacdc.api import (  # noqa: E402
+        AnnotationViewer,
+        current_viewer,
+        imshow,
+        open_session,
+        run,
+        view_intensity,
+        view_labels,
+        view_path,
+        view_session,
+    )
+except ImportError:
+    AnnotationViewer = None  # type: ignore
+    current_viewer = None  # type: ignore
+    imshow = None  # type: ignore
+    open_session = None  # type: ignore
+    run = None  # type: ignore
+    view_intensity = None  # type: ignore
+    view_labels = None  # type: ignore
+    view_path = None  # type: ignore
+    view_session = None  # type: ignore

cellacdc/_run.py

@@ -369,7 +369,7 @@ def download_model_params():
     if parser_args['StarDistModelsDownload'] or parser_args['AllModelsDownload']:
         print('[INFO]: Downloading StarDist models...')
         try:
-            from cellacdc.models import STARDIST_MODELS
+            from cellacdc.segmenters import STARDIST_MODELS
             from stardist.models import StarDist2D, StarDist3D
             for model_type in [StarDist2D, StarDist3D]:
                 for model_name in STARDIST_MODELS: