Add apptainer

Add apptainer def file
Document Profile GL4bc is not available on X11GraphicsDevice error

README.md

@@ -4,68 +4,129 @@ MIT License
 
 Copyright (c) 2013-2021 Sherman Lo
 
-A *Java/Processing* implementation of the marching cubes algorithm, including normal averaging [[cite]](http://paulbourke.net/geometry/polygonise/). A sequence of binary `.png` files can be provided to show a 3D render of the resulting polygon.
+A *Java/Processing* implementation of the marching cubes algorithm, including
+normal averaging [[cite]](http://paulbourke.net/geometry/polygonise/). A
+sequence of binary `.png` files can be provided to show a 3D render of the
+resulting polygon.
 
 ![Binary images left, polygon render right](cover.jpg)
 
 ## How to Use
 
 **IMPORTANT**:
-- *Java* 8 is recommended as the latest *Java* versions are not compatible [[for example]](https://stackoverflow.com/questions/59217351/exception-while-setting-up-jogl-with-intellij).
 
-Download the `.jar` file from the release or compile it using the instructions below. Call the `.jar` file using
+- *Java* 8 is recommended as the latest *Java* versions are not compatible
+  [[for example]](https://stackoverflow.com/questions/59217351/exception-while-setting-up-jogl-with-intellij).
 
+Download the `.jar` file from the release or compile it using the instructions
+below. Call the `.jar` file using
+
+```shell
+java -jar marchingcubes-*-jar-with-dependencies.jar -file [FILE_NAME] [N_IMAGES]
 ```
-java -jar marchingcubes-1.0.0-jar-with-dependencies.jar -file [FILE_NAME] [N_IMAGES]
-```
-where `FILE_NAME` is the location of the mage sequence and any other prefixes of the `.png` files. Two digits and `.png` are appended to the file name. For example, providing `x/y` will search for the files `x/y00.png`, `x/y01.png` and so on. The parameter `N_IMAGES` is an integer, the number of images in the image sequence.
 
-Use the mouse (click, drag, scroll) to move the camera. Push the space bar to toggle the wire frame render.
+where `FILE_NAME` is the location of the mage sequence and any other prefixes of
+the `.png` files. Two digits and `.png` are appended to the file name. For
+example, providing `x/y` will search for the files `x/y00.png`, `x/y01.png` and
+so on. The parameter `N_IMAGES` is an integer, the number of images in the image
+sequence.
+
+Use the mouse (click, drag, scroll) to move the camera. Push the space bar to
+toggle the wire frame render.
 
 *Issues*:
-- An error may occur when exiting the program, this behaviour is expected. See discussions for further information: [[X11Util.Display: Shutdown]](https://discourse.processing.org/t/x11util-display-shutdown/7292), [[Can any one tell me why do I get this error while quitting any P3D seketch]](https://discourse.processing.org/t/can-any-one-tell-me-why-do-i-get-this-error-while-quitting-any-p3d-seketch/13800)
+
+- An error may occur when exiting the program, this behaviour is expected. See
+  discussions for further information:
+  [[X11Util.Display: Shutdown]](https://discourse.processing.org/t/x11util-display-shutdown/7292),
+  [[Can any one tell me why do I get this error while quitting any P3D seketch]](https://discourse.processing.org/t/can-any-one-tell-me-why-do-i-get-this-error-while-quitting-any-p3d-seketch/13800)
+- The following error may occur
+  `Profile GL4bc is not available on X11GraphicsDevice`. Setting
+  `export _JAVA_OPTIONS="-Djogl.disable.openglcore"` does fix this. See
+  discussions for further information:
+  [[Profile GL4bc is not available on X11GraphicsDevice]](https://groups.google.com/g/jaer-users/c/G6mZ7EXmiYQ),
+  [[Processing 3 OpenGL error when using P3D [SOLVED]
+  / Applications &Desktop Environments / Arch Linux Forums]](https://bbs.archlinux.org/viewtopic.php?id=268252)
 
 ## How to Compile
+
 *Maven* required.
 
 Clone this repository.
 
 Go to the repository and run
-```
+
+```shell
 mvn package
 ```
+
 and the `.jar` files are located in target/.
 
 ## Demos
 
-Demos, using SBFSEM images of a chromosome [[cite]](https://www.science.org/doi/10.1126/sciadv.1602231?intcmp=trendmd-adv), are provided by running
-```
-java -jar marchingcubes-1.0.0-jar-with-dependencies.jar [-option]
+Demos, using SBFSEM images of a chromosome
+[[cite]](https://www.science.org/doi/10.1126/sciadv.1602231?intcmp=trendmd-adv),
+are provided by running
+
+```shell
+java -jar marchingcubes-*-jar-with-dependencies.jar [-option]
 ```
+
 where `[-option]` can be one of the following:
 
 ### `-demo0`
+
 26 images of size 72 x 57
 
 ![Image of chromosome using demo0](demo0.png)
 
 ### `-demo1`
+
 28 images of size 174 x 222
 
 ![Image of chromosome using demo1](demo1.png)
 
 ### `-demo2`
+
 59 images of size 106 x 125
 
 ![Image of chromosome using demo2](demo2.png)
 
 ### `-demo3`
+
 - External shell (blue) created using 24 images of size 50 x 67
 - Internal features (red) created using 48 images of size 101 x 134
 
 ![Image of chromosome using demo3](demo3.png)
 
+## Apptainer
+
+The definition file `marchingcubes.def` is provided. Build the container using
+
+```shell
+apptainer build marchingcubes.sif marchingcubes.def
+```
+
+and run it using
+
+```shell
+apptainer run [--nv] [--env _JAVA_OPTIONS="-Djogl.disable.openglcore"] /
+  marchingcubes.sif -file [FILE_NAME] [N_IMAGES]
+```
+
+```shell
+apptainer run [--nv] [--env _JAVA_OPTIONS="-Djogl.disable.openglcore"] /
+  marchingcubes.sif [-option]
+```
+
+where `--nv` should be provided to use an Nvidia card and
+`--env _JAVA_OPTIONS="-Djogl.disable.openglcore"` may be required for fix some
+issues.
+
 ## References
 
-- Bourke, P. (1994). Polygonising a scalar field (Marching Cubes). http://paulbourke.net/geometry/polygonise/. Accessed September 2013.
-- Chen, B., Yusuf, M., Hashimoto, T., Estandarte, A.K., Thompson, G. and Robinson, I. (2017). Three-dimensional positioning and structure of chromosomes in a human prophase nucleus. *Science Advances*, 3(7):e1602231.
+- Bourke, P. (1994). Polygonising a scalar field (Marching Cubes).
+  <http://paulbourke.net/geometry/polygonise/>. Accessed September 2013.
+- Chen, B., Yusuf, M., Hashimoto, T., Estandarte, A.K., Thompson, G. and
+  Robinson, I. (2017). Three-dimensional positioning and structure of
+  chromosomes in a human prophase nucleus. *Science Advances*, 3(7):e1602231.

marchingcubes.def

@@ -0,0 +1,18 @@
+BootStrap: docker
+From: ubuntu
+
+%environment
+    export LC_ALL=C
+
+%post
+    apt update
+    apt install -y git
+    apt install -y openjdk-8-jdk
+    apt install -y maven
+    cd /usr/src
+    git clone --recurse-submodules  https://github.com/shermanlo77/marchingcubes.git
+    cd marchingcubes
+    mvn package
+
+%runscript
+    java -jar /usr/src/marchingcubes/target/marchingcubes-*-jar-with-dependencies.jar "$@"