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Visualization: Difference between revisions
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* [https://itk.org/Wiki/VTK/Tutorials VTK tutorials] | * [https://itk.org/Wiki/VTK/Tutorials VTK tutorials] | ||
=== 3D Slicer === | === 3D Slicer === <!--T:139--> | ||
3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. | 3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization. Built over two decades through support from the National Institutes of Health and a worldwide developer community, Slicer brings free, powerful cross-platform processing tools to physicians, researchers, and the general public. | ||
* [https://www.slicer.org/wiki/Documentation/4.10 3D Slicer user manual] | * [https://www.slicer.org/wiki/Documentation/4.10 3D Slicer user manual] | ||
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Start VisIt on your laptop and in Options -> Host profiles... edit the connection nickname (let's call it Cloud West), the VM host name, path to VisIt installation (/home/centos/visit) and your username on the VM, and enable tunneling through ssh. Don't forget to save settings with Options -> Save Settings. Then opening a file (File -> Open file... -> Host = Cloud West) you should see the VM's filesystem. Load a file and try to visualize it. Data processing and rendering should be done on the VM, while the result and the GUI controls will be displayed on your laptop. | Start VisIt on your laptop and in Options -> Host profiles... edit the connection nickname (let's call it Cloud West), the VM host name, path to VisIt installation (/home/centos/visit) and your username on the VM, and enable tunneling through ssh. Don't forget to save settings with Options -> Save Settings. Then opening a file (File -> Open file... -> Host = Cloud West) you should see the VM's filesystem. Load a file and try to visualize it. Data processing and rendering should be done on the VM, while the result and the GUI controls will be displayed on your laptop. | ||
== yt rendering on clusters == | == yt rendering on clusters == <!--T:140--> | ||
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To install [http://yt-project.org yt] for CPU rendering on a cluster in your own directory, please do | To install [http://yt-project.org yt] for CPU rendering on a cluster in your own directory, please do | ||
$ module load python | $ module load python | ||
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$ pip install mpi4py | $ pip install mpi4py | ||
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Then, in normal use, simply load the environment and start python | Then, in normal use, simply load the environment and start python | ||
$ source ~/astro/bin/activate # load the environment | $ source ~/astro/bin/activate # load the environment | ||
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$ deactivate | $ deactivate | ||
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We assume that you have downloaded the sample dataset Enzo_64 from http://yt-project.org/data. Start with the following script `grids.py` to render 90 frames rotating the dataset around the vertical axis | We assume that you have downloaded the sample dataset Enzo_64 from http://yt-project.org/data. Start with the following script `grids.py` to render 90 frames rotating the dataset around the vertical axis | ||
import yt | import yt | ||
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sc.save('frame%04d.png' % (i+1), sigma_clip=4) | sc.save('frame%04d.png' % (i+1), sigma_clip=4) | ||
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and the job submission script `yt-mpi.sh` | and the job submission script `yt-mpi.sh` | ||
#!/bin/bash | #!/bin/bash | ||
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srun python grids.py | srun python grids.py | ||
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Then submit the job with `sbatch yt-mpi.sh`, wait for it to finish, and then create a movie at 30fps | Then submit the job with `sbatch yt-mpi.sh`, wait for it to finish, and then create a movie at 30fps | ||
$ ffmpeg -r 30 -i frame%04d.png -c:v libx264 -pix_fmt yuv420p -vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" grids.mp4 | $ ffmpeg -r 30 -i frame%04d.png -c:v libx264 -pix_fmt yuv420p -vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" grids.mp4 | ||
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=== Webinars and other short presentations === <!--T:10--> | === Webinars and other short presentations === <!--T:10--> | ||
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[https://westgrid.github.io/trainingMaterials/tools/visualization/ WestGrid's visualization training materials page] has embedded video recordings and slides from the following webinars: | [https://westgrid.github.io/trainingMaterials/tools/visualization/ WestGrid's visualization training materials page] has embedded video recordings and slides from the following webinars: | ||
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* “Using YT for analysis and visualization of volumetric data” | * “Using YT for analysis and visualization of volumetric data” | ||
* “Scientific visualization with Plotly” | * “Scientific visualization with Plotly” | ||