Merge pull request #1 from joda01/init

chore: Initial commit
joda01 · Jul 14, 2024 · e96b0c2 · e96b0c2
2 parents 1816952 + bdc9cc9
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diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
@@ -0,0 +1 @@
+FROM joda001/imagec-doc:v1.0.0 AS live
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -0,0 +1,31 @@
+// For format details, see https://aka.ms/vscode-remote/devcontainer.json or this file's README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.117.1/containers/cpp
+{
+	// docker run   your_image_name
+	"name": "imagec-doc",
+	"dockerFile": "Dockerfile",
+	"runArgs": [
+		"--cap-add=SYS_PTRACE",
+		"--security-opt",
+		"seccomp=unconfined",
+		"--gpus=all"
+	],
+	"customizations": {
+		// Set *default* container specific settings.json values on container create.
+		"settings": {
+			"terminal.integrated.shell.linux": "/bin/bash"
+		},
+		// Add the IDs of extensions you want installed when the container is created.
+		"vscode": {
+			"extensions": [
+				"ms-vscode.cpptools",
+				"llvm-vs-code-extensions.vscode-clangd",
+				"GrapeCity.gc-excelviewer",
+				"streetsidesoftware.code-spell-checker",
+				"vscjava.vscode-java-pack",
+				"xaver.clang-format",
+				"felgo.felgo"
+			]
+		}
+	}
+}
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -0,0 +1 @@
+@joda01
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+ - package-ecosystem: "devcontainers"
+   directory: "/"
+   schedule:
+     interval: weekly
diff --git a/.github/workflows/cmake-multi-platform.yml b/.github/workflows/cmake-multi-platform.yml
@@ -0,0 +1,72 @@
+name: C++ Build
+
+on:
+  push:
+    branches:
+      - main
+      - init
+    tags:
+      - '*'
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build-doc:
+    runs-on: ubuntu-22.04
+    container: 
+      image: joda001/imagec-doc:v1.0.0
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Build imagec-doc
+        env:
+          TAG_NAME: "${{ github.ref_name }}"
+        run: |
+          make html
+
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: imagec-doc-html
+          path: _build
+          if-no-files-found: error
+
+
+  release:
+    needs:
+      - build-windows
+      - build-linux
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: imagec-doc-html
+          path: _build
+
+
+      - name: Upload to imagec.org
+        if: startsWith(github.ref, 'refs/tags/')
+        env:
+          SSH_KEY: ${{ secrets.SSH_KEY_IMAGEC }}
+          SERVER_NAME : ${{ secrets.SERVER_NAME_IMAGEC }}
+        run: |
+          echo "$SSH_KEY" > ssh_key_for_github
+          chmod 400 ssh_key_for_github
+          scp -o StrictHostKeyChecking=no -i ssh_key_for_github _build/* github@$SERVER_NAME:/var/www/html/doc/*
+          rm -rf ssh_key_for_github
+
+
+      
+
+
+
+
+
+
+
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,10 @@
+FROM sphinxdoc/sphinx AS live
+
+RUN pip install readthedocs-sphinx-search==0.3.2
+RUN pip install myst-parser==2.0.0
+RUN pip install sphinx-rtd-theme==1.3.0
+RUN pip install sphinx-design==0.5.0
+
+FROM live as build
+
+RUN apt-get update && apt-get install -y git
diff --git a/README.md b/README.md
@@ -1,58 +1,15 @@
 # imageC Doc
 
-This contains the source for imageC's documentation, hosted at https://imagec.readthedocs.io
+This contains the source for imageC's documentation, hosted at https://imagec-doc.readthedocs.io/en/latest/
 
 ## Building locally
 
-To build this locally, create a virtual environment, eg:
+1) Start in docker image `joda001/imagec-doc:v1.0.0`
+2) Execute `make html`
 
-```bash
-python -m venv ./venv
-. ./venv/bin/activate
-```
 
-or using conda/mamba:
+### Deploy build docker image
 
-```bash
-conda env create -n qupath-docs python=3.12
-conda activate qupath-docs
-```
-
-Then install the requirements for this repo:
-
-```bash
-pip install -r requirements.txt
-```
-
-You'll also need the command line tool `Make` (e.g., [GNU Make](https://www.gnu.org/software/make/)).
-
-Then, you can run `make` to see available build options.
-`make html` will make the HTML version of the website, which is probably the
-most useful option. The built HTML files will be in `_build/html`, and can
-be opened in a web browser without running a local HTTP server.
-
-Alternatively, you can install `sphinx-autobuild` and `watchfiles`
-into your virtual environment to run a HTTP server and have the HTML files
-automatically rebuilt when any changes are made:
-
-```bash
-sphinx-autobuild . _build/html
-```
-
-## License
-
-All original content here is shared under a Creative Commons license ([CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/)).
-
-Here's the formal bit:
-
----
-
-<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons Licence" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />Except where otherwise noted, this website is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
-
----
-
-In some places, the docs include public images from other sources, e.g. within screenshots.
-For download links and information about their licenses, see [the Acknowledgements page](https://qupath.readthedocs.io/en/stable/docs/intro/acknowledgements.html).
-
-> All this refers only to the documentation on this repo. 
-> For license info about the QuPath *software*, see https://github.com/qupath/qupath
+docker build --target live -t joda001/imagec-doc:live .
+docker build --target build -t joda001/imagec-doc:v1.0.0 .
+docker push  joda001/imagec-doc:v1.0.0
diff --git a/conf.py b/conf.py
@@ -17,8 +17,8 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'imageC'
-copyright = '2023-2024, imageC doc authors'
+project = 'EVAnalyzer2'
+copyright = '2023-2024, Joachim Danmayr'
 author = 'imageC authors'
 
 
@@ -76,6 +76,7 @@
 .. |vertical_ellipsis| unicode:: 0x22EE
 
 .. |copyright| unicode:: 0xA9
+
 """
 
 myst_enable_extensions = [
@@ -101,8 +102,8 @@
 
 html_favicon = 'docs/images/imagec.ico'
 
-release = '0.5.1'
-version = '0.5'
+release = '1.0.0-alpha.103'
+version = '1.0.0-alpha.103'
 
 # myst_heading_anchors = 2
 

diff --git a/docs/images/imagec.ico b/docs/images/imagec.ico
diff --git a/docs/images/imagec_128.png b/docs/images/imagec_128.png
diff --git a/docs/intro/about.md b/docs/intro/about.md
@@ -1,16 +1,24 @@
-# What is QuPath?
+# What is imageC?
 
-**QuPath is open source software for bioimage analysis.**
+**imageC is open source software for high throughput bioimage analysis.**
 
-QuPath is often used for **digital pathology** applications because it offers a powerful set of tools for working with **whole slide images** - but it can be applied to lots of other kinds of image as well.
+imageC is often used for **single vesicle quantification** applications because it offers a powerful set of templates optimized for working the **EV field** - but it can be applied to lots of other kinds of image and applications as well.
 
 Features include:
 
-- Powerful annotation & visualization tools using a modern JavaFX interface
-- Built-in algorithms for common tasks, including cell and tissue detection
-- Interactive machine learning, both for object and pixel classification
-- Compatibility with other popular open tools, including ImageJ, OpenCV, Java Topology Suite and OMERO
-- Support for many image formats through Bio-Formats and OpenSlide, including whole slide images and multiplexed data
-- Groovy scripting for customization and deeper data interrogation
+- [BioFormats support](https://github.com/ome/bioformats)  
+- [OME-XML support](https://docs.openmicroscopy.org/)      
+- XLSX report generation                                   
+- Max. channels                                            
+- Max image size                                           
+- Support for big tiff                                     
+- AI based object detection                                
+- Database based result processing                         
+- Heatmap generation                                       
+- Image density map generation                             
+- In image object marker                                   
+- Built-in reporting tool                                  
+- Side by side image comparison                            
 
-To find out more, check out the [original publication introducing QuPath](https://doi.org/10.1038/s41598-017-17204-5) or {doc}`dive into the tutorials <../tutorials/index>` to see some of what it can do.
+
+To find out more, check out the [original publication introducing imageC](https://pubmed.ncbi.nlm.nih.gov/36437554/) or {doc}`dive into the tutorials <../tutorials/index>` to see some of what it can do.
diff --git a/docs/intro/acknowledgements.md b/docs/intro/acknowledgements.md
@@ -1,115 +1,16 @@
 # License & Acknowledgements
 
-QuPath is open-source software, available under the [GNU General Public License v3.0](https://github.com/qupath/qupath/blob/main/LICENSE).
-For more info, check out [QuPath's GitHub repo](https://github.com/qupath/qupath).
+imageC is open-source software, available under the [GNU Affero General Public License v3.0](https://github.com/joda01/imagec/blob/main/LICENSE).
+For more info, check out [imageC's GitHub repo](https://github.com/joda01/imagec).
 
-All original content in the QuPath documentation you're reading now is shared under a Creative Commons attribution license.
+All original content in the imageC documentation you're reading now is shared under a Creative Commons attribution license.
 You're free to reuse it, but we'd ask that you attribute the source -- and preferably include a link to this website, so that people know where to find the latest version.
 
-Here's the formal bit:
-
 ---
 
 <a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons Licence" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />Except where otherwise noted, this website is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
 
 ---
 
-Please note that there is some derived content where other licenses could apply.
-Specifically, many of the screenshots were created using public images from other sources.
-
-The sources and terms of reuse for these images are summarized in the table below:
-
-::::{list-table}
-:header-rows: 1
-:align: center
-
-* - Image
-  - Source
-  - Reuse
-* - :::{figure} images/CMU-1.jpg
-    :height: 100px
-    :class: shadow-image
-
-    CMU-1.svs
-    :::
-
-  - [OpenSlide (Aperio)](http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/)
-  - CC0 1.0
-* - :::{figure} images/CMU-2.jpg
-    :height: 100px
-    :class: shadow-image
-
-    CMU-2.svs
-    :::
-
-  - [OpenSlide (Aperio)](http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/)
-  - CC0 1.0
-* - :::{figure} images/CMU-3.jpg
-    :height: 100px
-    :class: shadow-image
-
-    CMU-3.svs
-    :::
-
-  - [OpenSlide (Aperio)](http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/)
-  - CC0 1.0
-* - :::{figure} images/OS-1.jpg
-    :height: 100px
-    :class: shadow-image
-
-    OS-1.ndpi
-    :::
-
-  - [OpenSlide (Hamamatsu)](http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/)
-  - Freely-distributable
-* - :::{figure} images/OS-2.jpg
-    :height: 100px
-    :class: shadow-image
-
-    OS-2.ndpi
-    :::
-
-  - [OpenSlide (Hamamatsu)](http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/)
-  - Freely-distributable
-* - :::{figure} images/OS-3.jpg
-    :height: 100px
-    :class: shadow-image
-
-    OS-3.ndpi
-    :::
-
-  - [OpenSlide (Hamamatsu)](http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/)
-  - Freely-distributable
-* - :::{figure} images/LuCa-7color_[13860,52919]_1x1component_data.jpg
-    :height: 100px
-    :class: shadow-image
-
-    LuCa-7color_[13860,52919]_1x1
-    :::
-
-  - [Perkin Elmer](https://downloads.openmicroscopy.org/images/Vectra-QPTIFF/perkinelmer/)
-  - CC-BY 4.0
-* - :::{figure} images/LuCa-7color_[17572,60173]_3x3component_data.jpg
-    :height: 100px
-    :class: shadow-image
-
-    LuCa-7color_[17572,60173]_3x3
-    :::
-
-  - [Perkin Elmer](https://downloads.openmicroscopy.org/images/Vectra-QPTIFF/perkinelmer/)
-  - CC-BY 4.0
-* - :::{figure} images/LuCa-7color_Scan1.jpg
-    :height: 100px
-    :class: shadow-image
-
-    LuCa-7color_Scan1.qptiff
-    :::
-
-  - [Perkin Elmer](https://downloads.openmicroscopy.org/images/Vectra-QPTIFF/perkinelmer/)
-  - CC-BY 4.0
-::::
-
-Additionally, the icons used in QuPath are exported as PNG for use in the docs.
-Most are original, but some are free icons from [Font Awesome](https://github.com/FortAwesome/Font-Awesome).
-
-To find the source of any specific icon, see [`IconFactory.java`](https://github.com/qupath/qupath/blob/6bd29f9586a9b34759498854ad8f36920dfa386b/qupath-gui-fx/src/main/java/qupath/lib/gui/tools/IconFactory.java).
+Additionally, the icons used in imageC are exported as PNG for use in the docs.
+Most are original, but some are free icons from [icons8](https://icons8.de/).