Visualization Tools & Apps

FigureGen

FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps. In contrast to the other Visualization Applications in the Workspace, FigureGen is not an interactive but rather it submits a batch job and output files are returned to the user.

More detailed information and FigureGen user documentation can be found on the FigureGen website.

How to Submit a FigureGen Job in the Workspace

  • Select the FigureGen application from the Visualization tab in the Workspace.
  • Locate your Input Directory (Folder) with your input files that are in the Data Depot and follow the onscreen directions to enter this directory in the form.
  • Enter the FigureGen input file (.inp) into the form.
  • Enter a maximum job runtime in the form. See guidance on form for selecting a runtime.
  • Enter a job name.
  • Enter an output archive location or use the default provided.
  • Click Run to submit your job.
  • Check the job status by clicking on the arrow in the upper right of the job submission form.

Hazmapper User Guide

Moved to GIS Tools: Hazmapper.

Kalpana

Kalpana is a Python library which primarily converts ADCIRC NetCDF output files to GIS-compatible shapefiles. Secondary functions are not available in the DesignSafe application. It was developed by the Coastal and Computational Hydraulics Team at North Carolina State University. More information regarding Kalpana can be found at:

Submitting a Job

On the Web Portal

Generating contours for a single case is simple through the web interface. The following information is required:

  • ADCIRC File. See the reference table below. Generic NetCDF files may also be accepted, if formatted appropriately.
  • Variable. Preceded by flag --var. The variable of interest from the NetCDF file. See the reference table below.
  • Contour levels. Preceded by flag --levels. Separated by spaces, the minimum contour, maximum contour, and step size.
  • Vertical units out. m or ft
  • Vertical units in. m or ft
  • Time Steps. Preceded by flag --timesteps. For time-varying files, specific time steps to extract are provided, separated by spaces. Otherwise, all are exported.

After this, generic allocation and archiving preferences are available. Since Kalpana is a serial program, it does not make sense to run on multiple nodes. However, additional cores may provide additional memory to process very large files.

Reference Table for Common ADCIRC Files
File Description Variables of Interest
fort.63.nc Time-dependent water elevation depth, zeta
fort.64.nc Time-dependent water velocity depth, u-vel, v-vel
fort.73.nc Time-dependent air pressure depth, pressure
fort.74.nc Time-dependent wind velocity depth, windx, windy
maxele.63.nc Maximum water elevation depth, time_of_zeta_max, zeta_max
maxvel.63.nc Maximum water velocity depth, time_of_vel_max, vel_max
maxwvel.63.nc Maximum wind velocity depth, time_of_wind_max, wind_max
swan_HS.63.nc Significant wave height swan_HS
swan_HS_max.63.nc Maximum significant wave height swan_HS_max
swan_TPS.63.nc Peak wave period swan_TPS
swan_TPS_max.63.nc Maximum peak wave period swan_TPS_max
swan_TMM10.63.nc Mean wave period swan_TMM10

Advanced Functionality with Tapis

To generate shapefiles for an ensemble, or to modify advanced Kalpana settings, submit JSON job requests using TapiPy. Descriptions for each flag are available in the Tapis app specification or the source file on GitHub, see function nc2shp).

Paraview

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. Using ParaView in the Workspace, you will be running interactively in a GUI.

More detailed information and ParaView user documentation can be found on the ParaView website.

How to Start a Paraview Interactive Session in the Workspace

  • Select the ParaView application from the Visualization tab in the Workspace.
  • Locate the directory containing your data files in the Data Depot and follow the onscreen directions to enter this as your Working Directory.
  • Select your desired desktop resolution from the dropdown menu.
  • Enter a maximum job runtime in the form. See guidance on form for selecting a runtime.
  • Enter a job name.
  • Enter an output archive location or use the default provided.
  • Select the number of nodes to be used for your job. Larger data files run more efficiently on higher node counts.
  • Click Run to start your interactive session.
  • Be sure to exit the Paraview application when you are finished with the session or any files saved will not be archived with the job.

Potree Converter

The Potree Converter converts point clouds to a format compatible with the Potree Viewer. Several options are available for you to customize your conversion, and can be found on the Potree Converter Github site.

POTREE Converter can be found under Visualization tab in DesignSafe Workspace. This application converts non-proprietary point cloud data formats (e.g. las, laz, binary ply, xyz or ptx) to a POTREE readable data structure (octree). The output directory from this application can next be visualized in POTREE Viewer.

How to Submit a Potree Converter Job in the Workspace

Similar to most applications in DesignSafe, you will have to fill out a form to submit your job that asks for following information:

  1. File/Folder to be converted:
    You can simply drag and drop either a file or a folder containing multiple point cloud files from Data Depot Browser (to the left of this form) in this place.
  2. Extra arguments passed into the converter:
    “-p index” should be passed as a minimum in this section. This creates a html index file which is necessary for POTREE viewer to run. Additionally, you will be able to pass more arguments. For instance, you can type the name of the output directory shown as below -p index –outdir OUT_DIR_NAME. Please note that the output directory will be placed in “MyData.”
  3. Job name:
    You will need to provide a recognizable name for this job.

The job log files will be stored at archive folder in “Mydata”: {username}/archive/jobs/\({YYYY-MM-DD}/\)-${JOB_ID}

When the form is completed, you can click “Launch” to submit your job. The job status can be monitored to the right of this form. It will change from “Pending” to “Staged”, “Submitted” and “Running” before it is successfully “Finished.”

Potree Converter FAQ

  1. My job’s status will change swiftly from Running to Finished with no converted output directory?

    This most likely means that the process is not completed and the job is failed. This is usually as a result of the presense of special characters (e.g. * ^, !, $, % and etc.) in your input file or directory. Please re-submit a job after removing these characters by renaming the input files or directory. If the problem persists, please submit a ticket for further assistance.
  2. I want to convert a file/folder located in My Projects. What should I do?

    From the Data Depot Browser to the left of job submission form, you can browse to your desired project and select the file/folder to be converted.

Potree Viewer

Potree Viewer is a point cloud viewer that enables exploration and measurement of very large LiDAR datasets and is designed to be efficient in a web browser. Use the Potree Converter to first convert your point cloud data to a format compatible with the Potree Viewer.

How to Start a Potree Interactive Session in the Workspace

  • Select the Potree Viewer application from the Visualization tab in the Workspace.
  • Locate the folder containing your data files in the Data Depot and follow the onscreen directions to enter this folder into the form.
  • Enter a maximum job runtime in the form. While this field is required in the form it is not actually used, simply enter any time using the time format shown.
  • Enter a job name.
  • Enter an output archive location or use the default provided.
  • Click Run to start your interactive session.

General Potree Viewing Instructions

You can upload the data, run the Potree converter and then create a Potree Viewer website where you can view the data in your web browser (Best with Chrome). Here are some examples you can explore:

(1) RidgeCrest Earthquake Fault Rupture - (DOI: https://doi.org/10.17603/ds2-wfgc-a575)

https://agave.designsafe-ci.org/geo/v2/assets/72/961e37b1-a0ac-47b9-9161-b977c0eb92e5/index.html

https://agave.designsafe-ci.org/geo/v2/assets/72/077e6d23-930b-4b20-9c04-f7c92503f751/index.html

(2) Alaska Anchorage Rockslope - (DOI: https://doi.org/10.17603/ds2-jmfv-9171)

https://agave.designsafe-ci.org/geo/v2/assets/104/cfc136e1-e91c-40d2-8d8e-c010da0f9656/index.html

(3) SfM Point Cloud (University of Washington Campus):

https://agave.designsafe-ci.org/geo/v2/assets/80/8f4c3c75-a0b0-44f1-a858-e1949802cf6e/index.html

Note for best viewing, be sure to turn on eye dome lighting in the appearance tab and increase the point budget. You can also change the coloring of point clouds by clicking on index under object which will bring various coloring objects under attribute menu. For instance, you can select "Elevation" and set the minimum and maximum range for a coloring scheme.

Potree Point Cloud Cross-section Tutorial

Note that the locations of the tools and options will vary somewhat in different version of potree, but the process is similar. The current version of potree Viewer in DesignSafe is 1.6. The figure below shows examples of tools in version 1.6.

To view data in potree, the following mouse movements are used to navigate the scene.

  • Double Click- sets center of rotation and zooms into that point.
  • Left Click, hold and move mouse, rotates the view
  • Middle Scroll Wheel – Zooms in and out
  • Right Click, hold and move mouse pans in the scene

Potree enables you to extract cross sections of the data. To extract those cross sections, do the following:

  • Click on the menu button (3 horizontal lines) in the upper left-hand corner of the view window.
  • Scroll down to the "Tools" bar and click.
  • Select the tool icon that looks like a multicolored M.
  • When you mouse over the point cloud data, you should now see a red ball attached to your mouse cursor. This allows you to drop nodes and establish the location of your profile.
  • When you want to finalize your profile double click on the last node. Once a profile is finalized, you can still change its location by clicking on the red nodes and dragging them to a different location.

  • Now, return to the side menu and click on the "Measurements" bar. You should see a Profile item with coordinates listed. Click the "show 2D profile" button. This is also where you can delete profiles by clicking the red X.
  • A profile of the lidar data should now be visible at the bottom of the screen. The profile will also update in real time if you move the profile throughout the data.
  • The save button in the upper right corner of the profile window will download a las file containing the points from the profile. This is useful for extracting the data you want to use for further analysis.

QGIS Desktop User Guide

Moved to GIS Tools: QGIS.

Taggit User Guide: Basic Image Browsing and Mapping

Moved to GIS Tools: Taggit: Basic Image Browsing and Mapping.

Taggit User Guide: Grouping and Tagging Image Files

Moved to GIS Tools: Taggit: Grouping and Tagging Image Files.

VisIt

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations. VisIt contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured, adaptive and unstructured meshes. Owing to its customizable plugin design, VisIt is capable of visualizing data from over 120 different scientific data formats.

More detailed information and VisIt user documentation can be found on the VisIt website.

How to Start a VisIt Interactive Session in the Workspace

  • Select the VisIt application from the Visualization tab in the Workspace.
  • Locate the directory containing your data files in the Data Depot and follow the onscreen directions to enter this as your Working Directory.
  • Select your desired desktop resolution from the dropdown menu.
  • Enter a maximum job runtime in the form. While this field is required in the form it is not actually used, simply enter any time using the time format shown.
  • Enter a job name.
  • Enter an output archive location or use the default provided.
  • Select the number of nodes to be used for your job. Larger data files run more efficiently on higher node counts.
  • Click Run to start your interactive session.
  • Be sure to exit the Paraview application when you are finished with the session or any files saved will not be archived with the job.