Separate requirements in files and folders (#451)

- Reduced the requirements to the basic packages, add extra requirements in `ui_env.yml` file
- Update readme, contributing, documentation

Author: DanicaSTFC

.github/workflows/docker_build_test_publish.yml

@@ -33,5 +33,5 @@ jobs:
       - name: Run docker container with tests
         shell: bash -l {0}
         run: |
-          docker run --rm --entrypoint /bin/bash -v /home/runner/work/CILViewer/CILViewer:/root/source_code  cil-viewer -c "source ./mambaforge/etc/profile.d/conda.sh && conda activate cilviewer_webapp && conda install cil-data pytest -c ccpi && python -m pytest /root/source_code/Wrappers/Python -k 'not test_version and not test_cli_resample and not test_CILViewerBase and not test_CILViewer3D and not test_viewer_main_windows and not test_ui_dialogs'"
+          docker run --rm --entrypoint /bin/bash -v /home/runner/work/CILViewer/CILViewer:/root/source_code  cil-viewer -c "source ./mambaforge/etc/profile.d/conda.sh && conda activate cilviewer_webapp && conda install cil-data pytest pyside2 eqt>=1.0.0 -c ccpi && python -m pytest /root/source_code/Wrappers/Python -k 'not test_version and not test_cli_resample and not test_CILViewerBase and not test_CILViewer3D and not test_viewer_main_windows and not test_ui_dialogs'"
     # TODO: publish to come later

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 ## vx.x.x
 
+Requirements:
+- Reduced the requirements to the basic packages, add extra requirements in `ui_env.yml` file #451
+
+Documentation:
+- Update readme, contributing, documentation #451
+
 Build and CI:
  - Renamed mambaforge to miniforge to fix docker action #446
  - Use ubuntu v22.04 in the actions #446

CONTRIBUTING.md

@@ -2,21 +2,33 @@
 Contribute to the repository by opening a pull request.
 
 ## Local
-Develop code locally by cloning the source code and installing it.
-
+Clone the source code.
 ```sh
-# Clone (download) source code
 git clone git@github.com:TomographicImaging/CILViewer.git
+```
+Navigate the folder.
+```sh
 cd CILViewer
-# Install
-pip install ./Wrappers/Python
+```
+
+Create a new environment. 
+```sh
+conda env create –f Wrappers/Python/conda-recipe/environment.yml
+```
+Activate the environment.
+```sh
+conda activate cilviewer
+```
+Install the package.
+```sh
+pip install ./Wrappers/Python --no-dependencies
 ```
 
 ### Run tests
 Before merging a pull request, all tests must pass. 
 Install the required packages:
 ```sh
-pip install pytest pillow
+conda install eqt pillow pyside2 pytest -c ccpi cil-data=22.0.0
 ```
 Tests can be run locally from the repository folder
 ```sh

Documentation/documentation.md

@@ -0,0 +1,58 @@
+# CILViewer Documentation
+
+## Using the 2D and 3D Viewers keyboard interactors
+
+### **2D Viewer keybindings**
+The interactive viewer CILViewer2D provides:
+  - Keyboard Interactions:
+    - 'h' display the help
+    - 'x' slices on the YZ plane
+    - 'y' slices on the XZ plane
+    - 'z' slices on the XY
+    - 'a' auto window/level to accomodate all values
+    - 's' save render to PNG (current_render.png)
+    - 'l' plots horizontal and vertical profiles of the displayed image at the pointer location
+    - 'i' toggles interpolation
+  - slice up/down: mouse scroll (10 x pressing SHIFT)
+  - Window/Level: ALT + Right Mouse Button + drag
+  - Pan: CTRL + Right Mouse Button + drag
+  - Zoom: SHIFT + Right Mouse Button + drag (up: zoom in, down: zoom out)
+  - Pick: Left Mouse Click
+  - ROI (square): 
+    - Create ROI: CTRL + Left Mouse Button 
+    - Resize ROI: Left Mouse Button on outline + drag
+    - Translate ROI: Middle Mouse Button within ROI
+    - Delete ROI: ALT + Left Mouse Button
+
+### Demonstration on head dataset[1]
+
+| 2D viewer	| Zoom 	| Slice X + Pick 	|
+|-----	|---	|---	|
+|![Window/Level](pics/windowLevel.png)|![Zoom](pics/zoom.png)|![Slice X + Pick](pics/sliceXPick.png)|
+
+| ROI | Line profiles |
+|---	|---	|
+|![ROI](pics/ROI.png)|![line](pics/line.png)|
+
+### **3D Viewer keybindings**
+The interactive 3D viewer CILViewer provides:
+  - Keyboard Interactions:
+    - 'h' display the help
+    - 'x' slices on the YZ plane
+    - 'y' slices on the XZ plane
+    - 'z' slices on the XY
+    - 'r' save render to current_render.png
+    - 's' toggle visibility of slice
+    - 'v' toggle visibility of volume render
+    - 'c' activates volume render clipping plane widget, for slicing through a volume.
+    - 'a' whole image Auto Window/Level on the slice.
+    - 'i' interpolation of the slice.
+  - Slice: Mouse Scroll
+  - Zoom: Right Mouse + Move Up/Down
+  - Pan: Middle Mouse Button + Move or Shift + Left Mouse + Move
+  - Adjust Camera: Left Mouse + Move
+  - Rotate: Ctrl + Left Mouse + Move
+
+## References
+
+[1] The head dataset is avaiable in [CIL-Data as 'head.mha'](https://github.com/TomographicImaging/CIL-Data) along with its license.