[WIP] UI API overhaul + several features/fixes (#17)

* UI refactor + aniso convert + fixed review plots

- started cleaning up UI class/functions

- fixed incorrect plots when using anisotropy correction

- added anisotropy conversion to utils

- fixed errors in launching review in new viewer

* UI API refactor + aniso conversion + docs

* Update cropping_module_guide.rst

* Updated docs

* Feedback from PR #17 

- Improved conversion file path handling
- Edit for ambiguous desc. in framework model
- Changed training validation dropdown to spinbox

* Update requirements to have PyQT by default

* Update .gitignore

Author: C-Achard

.gitignore

@@ -8,8 +8,10 @@ __pycache__/
 
 # unwanted results files
 *.tif
+*.tiff
 napari_cellseg3d/_tests/res/*.csv
 *.pth
+*.db
 
 # Distribution / packaging
 .Python
@@ -97,4 +99,4 @@ venv/
 /napari_cellseg3d/models/saved_weights/
 /docs/res/logo/old_logo/
 /reqs/
-*.db
+

README.md

@@ -23,6 +23,11 @@ A napari plugin for 3D cell segmentation: training, inference, and data review.
 
 ## Installation
 
+Note : we recommend using conda to create a new environment for the plugin.
+
+    conda create --name python=3.8 napari-cellseg3d
+    conda activate napari-cellseg3d
+
 You can install `napari-cellseg3d` via [pip]:  
 
     pip install napari-cellseg3d

docs/conf.py

@@ -70,7 +70,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

docs/res/code/interface.rst

@@ -1,50 +1,75 @@
 interface.py
 =============
 
-Functions
+Classes
 -------------
 
-open_url
+Button
 **************************************
-.. autofunction:: napari_cellseg3d.interface::open_url
+.. autoclass:: napari_cellseg3d.interface::Button
+   :members: __init__, visibility_condition
 
+DropdownMenu
+**************************************
+.. autoclass:: napari_cellseg3d.interface::DropdownMenu
+   :members: __init__
 
-make_scrollable
+CheckBox
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_scrollable
+.. autoclass:: napari_cellseg3d.interface::CheckBox
+   :members: __init__
 
+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
 
-make_group
+
+FilePathWidget
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_group
+.. autoclass:: napari_cellseg3d.interface::FilePathWidget
+   :members: __init__, build, get_text_field, get_button, check_ready, set_required, update_field_color, set_description
 
-add_to_group
+ScrollArea
 **************************************
-.. autofunction:: napari_cellseg3d.interface::add_to_group
+.. autoclass:: napari_cellseg3d.interface::ScrollArea
+   :members: __init__, make_scrollable
 
-make_container
+DoubleIncrementCounter
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_container
+.. autoclass:: napari_cellseg3d.interface::DoubleIncrementCounter
+   :members: __init__, set_precision, make_n
+
+IntIncrementCounter
+**************************************
+.. autoclass:: napari_cellseg3d.interface::IntIncrementCounter
+   :members: __init__, make_n
 
 
-make_button
+Functions
+-------------
+
+open_url
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_button
+.. autofunction:: napari_cellseg3d.interface::open_url
+
 
-make_combobox
+make_group
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_combobox
+.. autofunction:: napari_cellseg3d.interface::make_group
 
-make_checkbox
+add_to_group
 **************************************
-.. autofunction:: napari_cellseg3d.interface::make_checkbox
+.. autofunction:: napari_cellseg3d.interface::add_to_group
 
+make_container
+**************************************
+.. autofunction:: napari_cellseg3d.interface::make_container
 
 combine_blocks
 **************************************
 .. autofunction:: napari_cellseg3d.interface::combine_blocks
 
-
 add_blank
 **************************************
 .. autofunction:: napari_cellseg3d.interface::add_blank

docs/res/guides/convert_module_guide.rst

@@ -17,6 +17,12 @@ You can :
 * Remove small objects :
     You can specify a size threshold in pixels; all objects smaller than this size will be removed in the image.
 
+* Resize anisotropic images :
+    Specifiy the resolution of your microscope to remove anisotropy from images.
+
+.. important:: Does not work for instance labels currently.
+
+
 .. figure:: ../images/converted_labels.png
    :scale: 30 %
    :align: center

docs/res/guides/cropping_module_guide.rst

@@ -25,6 +25,12 @@ Folders can be stacks of either .png or .tif files, ideally numbered with the in
 You can then choose the size of the cropped volume, which will be constant throughout the process; make sure it is correct beforehand.
 Setting a larger size than the size of the image will cause issues.
 
+You can also opt to correct the anisotropy if your image is anisotropic :
+simply set the resolution to the one of your microscope.
+
+.. important::
+    This will simply scale the image in the viewer, but saved images will **still be anisotropic.** To resize your image, see :doc:`convert_module_guide`
+
 Once you are ready, you can press **Start** to start the review process.
 
 

docs/res/guides/review_module_guide.rst

@@ -19,6 +19,12 @@ Launching the review process
 .. note::
     Only single 3D **.tif** files or 2D stacks of several **.png** or **.tif** in a folder are currently supported.
 
+* Anisotropic data :
+    This will scale the images to visually remove the anisotropy, so as to make review easier.
+
+.. important::
+    Results will still be saved as anisotropic images. If you wish to resize your images, see the :doc:`convert_module_guide`
+
 * CSV file name :
     You can then provide a model name, which will be used to name the csv file recording the status of each slice.
 

docs/res/logo/logo_alpha.png

@@ -5,23 +5,21 @@
 
 def test_launch_review(make_napari_viewer):
 
-        view = make_napari_viewer()
-        widget = rev.Reviewer(view)
+    view = make_napari_viewer()
+    widget = rev.Reviewer(view)
 
-        # widget.filetype_choice.setCurrentIndex(0)
+    # widget.filetype_choice.setCurrentIndex(0)
 
-        im_path = os.path.dirname(os.path.realpath(__file__)) + "/res/test.tif"
+    im_path = os.path.dirname(os.path.realpath(__file__)) + "/res/test.tif"
 
-        widget.image_path = im_path
-        widget.label_path = im_path
-
-        print(widget.image_path)
-        print(widget.label_path)
-        print(widget.as_folder)
-        print(widget.filetype)
-        widget.run_review()
-        widget._viewer.close()
-
-        assert widget._viewer is not None
+    widget.image_path = im_path
+    widget.label_path = im_path
 
+    print(widget.image_path)
+    print(widget.label_path)
+    print(widget.as_folder)
+    print(widget.filetype)
+    widget.run_review()
+    widget._viewer.close()
 
+    assert widget._viewer is not None