Refactoring for fun, don't merge!

.gitignore

@@ -62,10 +62,10 @@ cellacdc/metrics/*
 !cellacdc/metrics/CV.py
 !cellacdc/metrics/combine_metrics_example.py
 !cellacdc/metrics/channel_indipendent_metric_example.py
-cellacdc/models/beno
-cellacdc/models/Simone_cellpose
+cellacdc/segmenters/beno
+cellacdc/segmenters/Simone_cellpose
 cellacdc/timon_tests
-cellacdc/models/test_segm_model
+cellacdc/segmenters/test_segm_model
 cellacdc/trackers/example
 cellacdc/test_qt_app.py
 cellacdc/test_qthread.py
@@ -98,7 +98,7 @@ UserManual/*
 # Ignore models folder but keep the folder with placeholder.txt dummy file
 models/*
 !models/placeholder.txt
-cellacdc/models/*/model/*
+cellacdc/segmenters/*/model/*
 
 # Hide placeholder.txt dummy file (probably works only on Linux)
 !models/.placeholder.txt

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

README.rst

@@ -192,6 +192,57 @@ Alternatively, you can also use **Cite this repository** button on the right
 ribbon of the GitHub page.
 
 
+Using Cell-ACDC from a script
+=============================
+
+Cell-ACDC can be launched from a Python script or notebook with a napari-style
+API. Install the GUI dependencies first:
+
+.. code-block:: bash
+
+   pip install "cellacdc[gui]"
+
+Build a unified :class:`ExperimentData` object from arrays or from a path, then
+pass it to the viewer:
+
+.. code-block:: python
+
+   import cellacdc
+   import numpy as np
+
+   image = np.zeros((100, 128, 128), dtype=np.uint16)  # T, Y, X
+   data = cellacdc.ExperimentData.from_arrays(image, axes="tyx")
+   viewer = cellacdc.Viewer(data)
+   cellacdc.run()
+
+The convenience helper mirrors ``napari.imshow`` and returns both the viewer
+and the data object:
+
+.. code-block:: python
+
+   data = cellacdc.ExperimentData.from_arrays(image, axes="tyx")
+   viewer, data = cellacdc.imshow(data)
+   cellacdc.run()
+
+Path-based loading:
+
+.. code-block:: python
+
+   data = cellacdc.ExperimentData.from_path("/path/to/experiment")
+   viewer, data = cellacdc.imshow(data)
+   cellacdc.run()
+
+Optional ``labels`` can be supplied when creating data from arrays. When no
+``workspace`` path is given, Cell-ACDC uses a temporary folder so segmentation
+outputs can still be saved from the GUI.
+
+In a Jupyter notebook with ``%gui qt``, ``cellacdc.run()`` is a no-op because
+IPython already runs the Qt event loop.
+
+For view-only inspection of arrays without segmentation, use
+``cellacdc.plot.imshow`` instead.
+
+
 **IMPORTANT**: when citing Cell-ACDC make sure to also cite the paper of the 
 segmentation models and trackers you used! 
 See `here <https://cell-acdc.readthedocs.io/en/latest/citation.html>`__ 

cellacdc/QtScoped.py

@@ -2,62 +2,72 @@
 
 from qtpy.QtWidgets import QAbstractSlider, QStyle
 
+
 def SliderNoAction():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderNoAction.value
     else:
         return QAbstractSlider.SliderAction.SliderNoAction
 
+
 def SliderSingleStepAdd():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderSingleStepAdd.value
     else:
         return QAbstractSlider.SliderAction.SliderSingleStepAdd
 
+
 def SliderSingleStepSub():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderSingleStepSub.value
     else:
         return QAbstractSlider.SliderAction.SliderSingleStepSub
 
+
 def SliderPageStepAdd():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderPageStepAdd.value
     else:
         return QAbstractSlider.SliderAction.SliderPageStepAdd
 
+
 def SliderPageStepSub():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderPageStepAdd.value
     else:
         return QAbstractSlider.SliderAction.SliderPageStepAdd
 
+
 def SliderToMinimum():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderPageStepAdd.value
     else:
         return QAbstractSlider.SliderAction.SliderPageStepAdd
 
+
 def SliderToMaximum():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderPageStepAdd.value
     else:
         return QAbstractSlider.SliderAction.SliderPageStepAdd
 
+
 def SliderMove():
     if PYQT6:
         return QAbstractSlider.SliderAction.SliderMove.value
     else:
         return QAbstractSlider.SliderAction.SliderMove
 
+
 def QStyleCC_ScrollBar():
     if PYQT6:
         return QStyle.ComplexControl.CC_ScrollBar
     else:
         return QStyle.CC_ScrollBar
 
+
 def QStyleSC_ScrollBarSubLine():
     if PYQT6:
         return QStyle.SubControl.SC_ScrollBarSubLine
     else:
-        return QStyle.SC_ScrollBarSubLine
+        return QStyle.SC_ScrollBarSubLine