README_3D

Instructions for producing Lake Erie bathymetry for STOQS databases using gmt-5.4.4, Meshlab, and InstantReality
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0. Download erie_lld.grd from https://www.ngdc.noaa.gov/mgg/greatlakes/erie.html

    wget https://www.ngdc.noaa.gov/mgg/greatlakes/erie/data/netcdf/erie_lld.grd.gz
    gunzip erie_lld.grd.gz

1. Create point cloud .asc file with 10x vertical exaggeration:

    grd2xyz erie_lld.grd ----FORMAT_FLOAT_OUT=%f | sed '/NaN/d' | awk '{print $1, $2, 10 * $3}' | mapproject -E --FORMAT_FLOAT_OUT=%f > erie_lld_10x.asc

2. Process in Meshlab:

    Copy erie_lld_10x.asc file locally to machine that has Meshlab
        File -> Import Mesh...
        Filters -> Point Set -> Compute normals for point sets (defaults)
        Filters -> Remeshing, Simplification and Reconstruction -> Screened Poisson Surface Reconstruction 
                                                                   (Reconstruction depth: 8, Minimum Number of Samples: 1.5, Interpolation Weight: 0)
        Filters -> Remeshing, Simplification and Reconstruction -> Simplification: Quadric Edge Collapse Decimation:
            - Target number of faces: 1,000,000
            - Preserve Normal
            - Preseve Topology
            - Optimal Position of Simplified Vertices
            - Planar Simplification
            - Post-simplification cleaning
        Filters -> Normals, Curvatures and Orientation -> Invert Faces Orientation
        * Cleanup - use editing tools (with plenty of intermediate saves)
        Filters -> Smoothing, Fairing and Deformation -> Laplacian smooth (surface preserve)
        File -> Export Mesh As... (save as file erie_lld_10x.ply)

3. Process with aopt:

    cd <working_dir>
    # On Mac aopt is in /Applications/Instant\ Player.app/Contents/MacOS/
    aopt -i erie_lld_10x.ply -F Scene -b erie_lld_10x.x3db
    aopt -i erie_lld_10x.x3db -f PrimitiveSet:creaseAngle:4 -V -Y "nodeType(Geometry)" -N erie_lld_10x.html

4. Copy to tmp directory on public stoqs server:

    scp erie_lld_10x.html stoqs.mbari.org:/tmp
    scp src*.src stoqs.mbari.org:/tmp

5. Log into stoqs.mbari.org, copy to new directory in html/x3d:

    mkdir /opt/docker_stoqs_vols/html/x3d/erie_lld_10x
    cd /opt/docker_stoqs_vols/html/x3d/erie_lld_10x
    cp /tmp/erie_lld_10x.html .
    cp /tmp/src*.src .

6. Edit /opt/docker_stoqs_vols/html/x3d/erie_lld_10x/erie_lld_10x.html to change material and https:

    <material diffuseColor='0.7 0.7 0.7' specularColor='0.1 0.1 0.1'></material>
    :%s#http:#https:#

7. View it at:

    http://stoqs.mbari.org/x3d/erie_lld_10x/erie_lld_10x.html

8. Create X3D scene file for inclusion in web apps:

    cp erie_lld_10x.html erie_lld_10x_scene.x3d

    - Edit erie_lld_10x_scene.x3d to remove all elements outside of the <scene>...</scene> element
    - For STOQS/Django to serve the .src files via AJAX the urls must be fully qualified:

    :%s#url='"src#url='"http://stoqs.mbari.org/x3d/erie_lld_10x/src#


--
Mike McCann
10 September 2019