Merge pull request #50 from IMSY-DKFZ/develop

package release v0.2.2

.github/workflows/build.yml

@@ -88,8 +88,6 @@ jobs:
         uses: actions/[email protected]
       - name: Documentation
         run: |
-          sudo apt install doxygen graphviz
-          sudo pip3 install -U sphinx furo breathe
-          cd docs
-          doxygen Doxyfile
-          make html
+          sudo apt install doxygen
+          sudo pip3 install -U mkdocs mkdocs-glightbox mkdocs-material mkdocstrings[python] mkdoxy
+          mkdocs build

.readthedocs.yaml

@@ -5,14 +5,7 @@ build:
   tools: {python: "3.10"}
   jobs:
     post_create_environment:
-      - pip install -U furo breathe
-    pre_build:
-        - cd docs && doxygen Doxyfile
-  apt_packages:
-      - doxygen
-      - graphviz
+      - pip install -U mkdocs mkdocs-glightbox mkdocs-material mkdocstrings[python] mkdoxy
 
-sphinx:
-  builder: html
-  configuration: docs/source/conf.py
-  fail_on_warning: false
+mkdocs:
+   configuration: mkdocs.yml

CHANGELOG.md

@@ -23,6 +23,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 -
 
+## [0.2.2]
+
+### Added
+
+- Adds image viewer tab to open recorded .b2nd files and scroll over images.
+- Adds missing camera models to JSON file.
+- Adds documentation for all classes in XiLens.
+
+### Changed
+
+- All displaying operations run from a thread, and only calls the main thread when the process images are to be displayed.
+- Restructures UI for a more clear use and structures controls inside a toolbox.
+- Limits frequency at which images are displayed to avoid locking the UI. Images are still recorded at full speed.
+- Defines per-camera property to control which channels are used for rGB representation of the raw spectral data.
+- Moves from using Sphix to Mkdocs to build documentation.
+- Modifies signals for some text input such that ENTER does not need to be pressed for changes to take effect.
+
+### Removed
+
+- Removes command line options that are no longer needed such as white, dark, model file, etc.
+
+### Fixed
+
+- Fixes UI responsiveness hindered by temperature thread.
+- Fixes opening files that only have one image stored.
+
 ## [0.2.1]
 
 ### Added

CITATION.cff

@@ -11,6 +11,6 @@ authors:
 - family-names: "Maier-Hein"
   given-names: "Lena"
 title: "XiLens"
-version: 0.2.1
+version: 0.2.2
 url: "https://github.com/IMSY-DKFZ/xilens"
 doi: 10.5281/zenodo.13305567

CMakeLists.txt

@@ -5,7 +5,7 @@
 # CMake project configuration
 #-----------------------------------------------------------------------------------------------------------------------
 cmake_minimum_required(VERSION 3.5)
-project(xilens VERSION 0.2.1)
+project(xilens VERSION 0.2.2)
 
 #-----------------------------------------------------------------------------------------------------------------------
 # Language definitions

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 # Avoid Docker build freeze due to region selection
 ENV DEBIAN_FRONTEND=noninteractive
@@ -38,7 +38,6 @@ RUN dpkg -i xilens*.deb
 # run tests
 ENV QT_QPA_PLATFORM offscreen
 RUN xvfb-run -a --server-args="-screen 0 1024x768x24" ctest --output-on-failure
-RUN gcovr --html --exclude-unreachable-branches --print-summary -o coverage.html -e '/.*cmake-build.*/.*' --root ../
 
 # run application
-CMD QT_GRAPHICSSYSTEM="native" QT_X11_NO_MITSHM=1 /home/xilens/build/xilens /home/caffe/models/susi/imec_patchnet_4_LAYER_in_vivo.prototxt /home/caffe/models/susi/model_20SNR_20stain_3patch.caffemodel /home/caffe/models/susi/white.tif /home/caffe/models/susi/dark.tif
+CMD QT_GRAPHICSSYSTEM="native" QT_X11_NO_MITSHM=1 /home/xilens/build/xilens