Licensing is open-source as always!
- Software: GPLv3
- Data: CC-BY-SA 4.0 Intl
- Database: ODbL
- Database contents: DbCL
- Documentation: GFDL
The terrain_aggregator
is a general-purpose terrain aggregation workflow.
This workflow produces a single, uniform, and seamless raster terrain dataset at the highest quality available.
This workflow aggregates terrain tiles from a variety of raster DEM tilesets to a single uniform projection.
The total processing time to aggregate tiles on a small-country scale (~1.6M km2) takes at most 15 days compute time back-to-front, or about 1600 node-hours of computational time.
D. Hardesty Lewis, S. A. Pierce, P. Passalacqua, et al (2022), terrain_aggregator
, GitHub
https://doi.org/10.5281/zenodo.7005059
The typical engineering analysis in 2022 using terrain data involves some very common preprocessing steps, detailed below. Because of significant differences in Lidar data product standards and metadata quality, these steps can be prone to error and headache.
-
determining available raster imagery from different data hubs, usually (from a Texas point-of-view) :
- TNRIS's Data Hub : all available raster imagery organized by collection in Texas
- USGS's National Map Downloader : highest quality raster imagery organized by resolution across the U.S.
- NOAA's Digital Coast : raster imagery organized by project along U.S. coast
- In practice, in Texas this means downloading individual tiles from TNRIS's Data Hub.
-
reviewing characteristics of available raster imagery in a study area, usually :
- resolution : pixel width by pixel height, usually in meters
- year : when imagery was collected
- quality : measure of data quality, such as the USGS's Topographic Data Quality Levels (QLs)
-
selecting source imagery tiles from projects based on these characteristics
- In practice, in Texas this means selecting the highest resolution data first, then the most recent year.
-
aggregating disparate raster imagery by some combination of the following steps :
- transforming, to unify characteristics from this table :
characteristic description spatial reference system projection + datum including unit of measurement (e.g. NAD83 / UTM zone 14N + NAVD88 height (m)) pixel data type data type of the pixel values of the tile (e.g. float, integer, etc.) color interpretation human interpretation of color (e.g. black, RGB, etc.) - mosaicking, to unify characteristics from this table :
characteristic description geographic extent boundary box of the tile pixel width width of spatial resolution (usually in meters) pixel height height of spatial resolution (usually in meters) - retiling, to unify characteristics from this table :
characteristic description tile width width of each tile (in pixels) tile height height of each tile (in pixels) - In practice, transforming & mosaicking must be done in a very careful order to prevent common raster transformation issues.
-
cropping uniform dataset to some bounding unit of analysis, usually one of the following :
- watershed - a natural boundary
- county - a political boundary
- tile - a simple boundary
- tile-delineated watershed - a simplified natural boundary
- tile-delineated county - a simplified political boundary
- In practice, for flood modelling usually a tile-delineated watershed is taken.
-
applying domain-specific engineering analysis, such as :
- Height Above Nearest Drainage (HAND)
- HEC-RAS
- etc.
- In practice, for flood modelling HEC-RAS is the gold standard and by far the most commonly used.
The terrain_aggregator
produces a single, uniform, and seamless terrain dataset at the highest available resolution and the best available year.
This greatly simplifies steps 1.-4. above, enabling engineers and consultants to far more rapidly work directly with the data they need.
Here is the new, simpler workflow starting from the single_seamless_elevation
product that the terrain_aggregator
produces :
-
determine
single_seamless_elevation
coverage from a single data hub !- TNRIS/TDIS's Terrain Data Downloader : in-development elevation data organized by tile in Texas
- The
single_seamless_elevation
is in development; availabity & coverage may vary
-
select terrain tiles by coverage !
- No need to familiarize yourself with minutia about each raster collection!
- No need to worry about upstream metadata issues!
-
mosaic selected tiles to your preferred resolution !
- Because tiles are served out at a single, highest available resolution, you can choose to :
- use the highest-resolution data available, or
- upscale to a common resolution of analysis, such as 1-meter
- Because tiles are served out at a single, highest available resolution, you can choose to :
-
crop uniform dataset to your study area !
- No need if you use tile-delineated boundaries!
-
apply your engineering analysis !
@TACC now hosts TNRIS Lidar tiles for TACC users.
To begin using TACC resources, please create a TACC account at the following page:
https://portal.tacc.utexas.edu/account-request
Once you have a TACC account, submit a ticket at the following page and CC [email protected]
https://portal.tacc.utexas.edu/tacc-consulting
Intermediate retiling results are available :
- on Stampede2 at :
stampede2.tacc.utexas.edu:/scratch/04950/dhl/TNRIS-Lidar/TNRIS-Lidar-retiling/srid_colorinterp_pixeltype.csv.d/3083.vrt.d
- and on Corral at :
data.tacc.utexas.edu:/corral/projects/TDIS/TNRIS-Lidar-retiling/TX_scale
Here is a Shapefile of the extent of each TNRIS Lidar tile:
https://utexas.box.com/v/tnris-lidar-tiles-shp
This shapefile is projected in NAD83(2011) / Texas Centric Albers Equal Area (EPSG:6579):
https://spatialreference.org/ref/epsg/nad83-texas-centric-albers-equal-area/
Each tile has the following attributes:
Attribute | Description |
---|---|
rast | a reference address to the raster tile on Stampede2 |
filename | TRNIS Lidar tilename |
absolutepath | TNRIS Lidar tile absolute path on Stampede2 |
project | TNRIS Lidar project parent directory name |
srid | corrected SRID/EPSG code of the tile |
srid_orig | originally found SRID/EPSG code of the tile |
pixeltype | datatype of the pixels of the tile (float, integer, etc) |
envelope | polygon of the extent of the tile projected in the corrected EPSG |
centroid | centroid of the envelope projected in the corrected EPSG |
centroid_albers | centroid of the envelope projected in EPSG:6579 |
x | longitude of the centroid projected in EPSG:6579 |
y | latitude of the centroid projected in EPSG:6579 |
width | width of the tile in pixels |
height | height of the tile in pixels |
pixelwidth | width of each pixel in EPSG:6579 units (m) |
pixelheight | height of each pixel in EPSG:6579 units (m) |
colorinterp | color interpretation of the raster tile |
- Singularity & dhardestylewis's PostGIS-GDAL/OGR Singularity image
- Conda & dhardestylewis's GDAL/OGR Conda environment
- AWS CLI
This Singularity image includes support for the following 3 PostgreSQL - GDAL/OGR translators:
raster2pgsql
: to create a PostgreSQL script to add rasters to a PostgreSQL tableshp2pgsql
: to create a PostgreSQL script to add features from a Shapefile to a PostgreSQL tablepgsql2shp
: to create a Shapefile from an existing PostgreSQL table
To download this Singularity image, use the following commands from the Stampede2 command line:
## to enter a computational node: Singularity cannot be used from a development node
idev
## to load the pre-existing Singularity module from TACC's module repository
module load tacc-singularity
## to download this Singularity image from the online Docker Hub image repository
cd $WORK
singularity pull docker://dhardestylewis/postgis:14-3.2-gdalogr
To clone this Git repository, use the following commands from the Stampede2 command line:
git clone https://github.com/dhardestylewis/terrain_aggregator.git
cd terrain_aggregator
export TERRAIN_AGGREGATOR=$(pwd)
See [below](# Accessing the latest TNRIS Lidar database) to access the existing terrain_aggregator
database hosted on Stampede2 @TACC.
A copy of the TNRIS Lidar DEM database is kept on this GitHub repo under TNRIS-Lidar-Tiles.sql.d/
To create TNRIS Lidar PostgreSQL database from the copy hosted here on GitHub, use the following commands from the Stampede2 command line:
## Load Singularity module
module load tacc-singularity
## Start Postgres database
SINGULARITYENV_POSTGRES_PASSWORD=pgpass SINGULARITYENV_PGDATA=$WORK/pgdata SINGULARIRTYENV_PGOPTIONS="-c 'custom.scratch=${SCRATCH}'" singularity run --cleanenv --bind $SCRATCH:/var $WORK/postgis_14-3.2-gdalogr.sif &
## Upload TNRIS Lidar table to database
for filename in $(ls ${TERRAIN_AGGREGATOR}/TNRIS-Lidar-Tiles.sql.d/*.sql); do SINGULARITYENV_POSTGRES_PASSWORD=pgpass SINGULARITYENV_PGDATA=$WORK/pgdata SINGULARIRTYENV_PGOPTIONS="-c 'custom.scratch=${SCRATCH}'" singularity exec --cleanenv --bind $SCRATCH:/var $WORK/postgis_14-3.2-gdalogr.sif psql -U postgres -d postgres -h 127.0.0.1 -f ${filename}; done
## Connect to the Postgres database
SINGULARITYENV_POSTGRES_PASSWORD=pgpass SINGULARITYENV_PGDATA=$WORK/pgdata SINGULARIRTYENV_PGOPTIONS="-c 'custom.scratch=${SCRATCH}'" singularity exec --cleanenv --bind $SCRATCH:/var $WORK/postgis_14-3.2-gdalogr.sif psql -U postgres -d postgres -h 127.0.0.1
Please submit a ticket if you don't have permission to access this database and be sure to CC [email protected]
https://portal.tacc.utexas.edu/tacc-consulting
Note : Please wait for the following output before trying to access this database:
LOG: database system is ready to accept connections
To connect to the existing TNRIS Lidar PostgreSQL database, use the following commands from the Stampede2 command line:
## Load Singularity module
module load tacc-singularity
## Start Postgres database
SINGULARITYENV_POSTGRES_PASSWORD=pgpass SINGULARITYENV_PGDATA=/work2/04950/dhl/stampede2/pgdata SINGULARIRTYENV_PGOPTIONS="-c 'custom.scratch=${SCRATCH}'" singularity run --cleanenv --bind $SCRATCH:/var $WORK/postgis_14-3.2-gdalogr.sif &
## Connect to the Postgres database
SINGULARITYENV_POSTGRES_PASSWORD=pgpass SINGULARITYENV_PGDATA=/work2/04950/dhl/stampede2/pgdata SINGULARIRTYENV_PGOPTIONS="-c 'custom.scratch=${SCRATCH}'" singularity exec --cleanenv --bind $SCRATCH:/var $WORK/postgis_14-3.2-gdalogr.sif psql -U postgres -d postgres -h 127.0.0.1
Please submit a ticket if you don't have permission to access this database and be sure to CC [email protected]
https://portal.tacc.utexas.edu/tacc-consulting
Note : Please wait for the following output before trying to access this database:
LOG: database system is ready to accept connections
To populate the database with newly added tiles, the following commands can be used to generate a list of raster tiles to add to the table
From the command line outside the Singularity container:
cds
mkdir tnris-lidardata
cd tnris-lidardata
export TNRIS_LIDAR_DATA=$(pwd)
cd ..
aws s3 cp s3://tnris-public-data/production-data/ tnris-lidardata --recursive
For reference, TNRIS's AWS S3 bucket of their Lidar data can be publicly accessed at the following URL:
First we gather a list of tiles that we want to record in the database. From the parent directory of TNRIS Lidar data, on the command line outside the Singularity container:
find $(pwd) -maxdepth 4 -type f -wholename "*/dem/*.tif" -o -wholename "*/dem/*.img" -o -wholename "*/dem/*.dem" > $WORK/find_dem_tiles.csv
sort -u $WORK/find_dem_tiles.csv > $WORK/find_dem_tiles-sorted.csv
mv $WORK/find_dem_tiles-sorted.csv $WORK/find_dem_tiles.csv
Then we gather a list of existing tiles in the database. From the PostgreSQL database:
/* replace the following CSV path with your equivalent */
COPY (SELECT absolutepath FROM tnris_lidar_tiles ORDER BY absolutepath) TO current_setting('custom.scratch')||'/select_all_dem_tiles.csv' (FORMAT csv) ;
We compare lists to find which tiles are not currently in the database. From the command line outside of the Singularity container:
comm -23 $SCRATCH/find_dem_tiles.csv $SCRATCH/select_all_dem_tiles.csv > $WORK/missing_dem_tiles.csv
## Run raster2pgsql from the Singularity image
SINGULARITYENV_POSTGRES_PASSWORD=pgpass SINGULARITYENV_PGDATA=$WORK/pgdata singularity exec --cleanenv --bind $SCRATCH:/var $WORK/postgis_14-3.2-gdalogr.sif bash
We upload the tiles to the database. From the command line inside the Singularity container:
raster2pgsql -R -F -Y -I -M -e $(cat $WORK/missing_dem_tiles.csv | tr "\n" " ") public.missing_dem_tiles > $WORK/missing_dem_tiles.sql
## Once this is done, load the tiles' metadata to the PostgreSQL database using the following command
psql -U postgres -d postgres -h 127.0.0.1 -f $WORK/missing_dem_tiles.sql
From the PostgreSQL database:
CREATE TABLE missing_dem_tiles_paths (absolutepath text) ;
/* Be sure to replace the following CSV path with your specific CSV path */
COPY missing_dem_tiles_paths FROM '$WORK/missing_dem_tiles.csv' WITH (FORMAT csv) ;
From the command line outside the Singularity container:
## Add the following columns to the table:
## - project
## - filename
## - absolutepath
## - srid_orig
## - srid
## - pixeltype
## - x
## - y
## - width
## - height
## and populate the following columns with metadata:
## - project : TNRIS Lidar project parent directory name
## - filename : TRNIS Lidar tilename
## - absolutepath : TNRIS Lidar tile absolute path on Stampede2
## - srid_orig : originally found SRID/EPSG code of the tile
## - srid : corrected SRID/EPSG code of the tile
## - pixeltype : datatype of the pixels of the tile (float, integer, etc)
## - width : width of the tile in pixels
## - height : height of the tile in pixels
## - pixelwidth : width of each pixel in EPSG:6579 (m)
## - pixelheight : height of each pixel in EPSG:6579 (m)
psql -U postgres -d postgres -h 127.0.0.1 -f $TNRIS_LIDAR_POSTGRESQL/tnris_lidar_tiles_update.sql.d/tnris_lidar_tiles_update0.sql
psql -U postgres -d postgres -h 127.0.0.1 -f $TNRIS_LIDAR_POSTGRESQL/tnris_lidar_tiles_update.sql.d/tnris_lidar_tiles_update1.sql
From the PostgreSQL database:
/* Check to see if the GDAL driver failed to find any of the tiles' projections */
SELECT COUNT(DISTINCT(absolutepath)) FROM missing_dem_tiles WHERE srid_orig = 0 ;
/* If any tiles are found above, it will be necessary to correct the projection information for these tiles. I leave it to the user to determine how to do that. I provide the `srid` column to record corrected projections. Once all of the tiles' projections have been corrected, the following selection should return 0 */
SELECT COUNT(DISTINCT(absolutepath)) FROM missing_dem_tiles WHERE srid = 0 ;
From the command line outside the Singularity container:
## Populate the following columns with correct(ed) metadata:
## - rast : raster tile geometry in the corrected SRID/EPSG code)
## - envelope : envelope of the raster tile
## - envelope_albers : envelope reprojected to NAD83(2011) / Texas Centric Albers Equal Area
## - centroid : centroid of the envelope
## - centroid_albers : centroid reprojected to NAD83(2011) / Texas Centric Albers Equal Area
## - x : latitudinal coordinate of the centroid in original projection
## - y : longitudinal coordinate of the centroid in the orignal projection
psql -U postgres -d postgres -h 127.0.0.1 -f $TNRIS_LIDAR_POSTGRESQL/tnris_lidar_tiles_update.sql.d/tnris_lidar_tiles_update2.sql
## It is necessary to set the `colorinterp` attribute separately
From the PostgreSQL database:
/* Join the original table with the missing tiles table */
CREATE TABLE updated_tnris_lidar_tiles AS (SELECT rast, filename, absolutepath, project, srid, srid_orig, pixeltype, envelope, envelope_albers, centroid, centroid_albers, x, y, width, height FROM tnris_lidar_tiles UNION SELECT rast, filename, absolutepath, project, srid, srid_orig, pixeltype, envelope, envelope_albers, centroid, centroid_albers, x, y, width, height FROM missing_dem_tiles) ;
DROP TABLE tnris_lidar_tiles ;
DROP TABLE missing_dem_tiles ;
ALTER TABLE updated_tnris_lidar_tiles RENAME TO tnris_lidar_tiles ;
Once this table is corrected, the following command can be run from the command line inside the Singularity container to generate a new TNRIS Lidar availability file:
pgsql2shp -f $WORK/TNRIS-Lidar-Corrected_availability_file.shp -h 127.0.0.1 -P pgpass -u postgres -g envelope_albers -k postgres public.tnris_lidar_tiles
QAQC : Keep in mind that a visual inspection of the resulting Shapefile is necessary in order to ensure that the tiles are all now in the correct projection.
From the PostgreSQL database:
/* Replace with your preferred location below */
COPY (SELECT DISTINCT(srid) FROM tnris_lidar_tiles) TO current_setting('custom.scratch')||'/distinct_srid.csv' (FORMAT csv) ;
Create and activate the Conda environment from the command line outside the Singularity container:
conda env create -f $TNRIS_LIDAR_POSTGRESQL/gdal.yml
conda activate gdal
From the command line outside the Singularity container:
## Please note that any tiles whose pixeltype != Float32 will need to be pre-treated with the following command before starting this workflow.
## Thus far, ~142 tiles from the following two projects are impacted:
## - capcog-2007-140cm-caldwell-travis-williamson
## - usgs-2016-70cm-middle-brazos-lake-whitney
# gdal_translate -ot Float32 src_dataset dst_dataset.vrt
## It will be necessary to substitute in these VRTs for the source tiles in the following `gdalbuildvrt` file lists
## Create a file list of each tileset grouped by SRID/EPSG code:
while read srid; do psql -d postgres -t -A -F"," -c "SELECT absolutepath FROM tnris_lidar_tiles WHERE srid = ${srid}" > ${srid}.srid ; done < $TNRIS_LIDAR_POSTGRESQL/distinct_srid.csv
## Conduct a `gdalbuildvrt` for each unique EPSG:
for filename in $(ls *.srid); do gdalbuildvrt -allow_projection_difference -vrtnodata -9999. -a_srs EPSG:$(basename ${filename} .srid) -input_file_list ${filename} -overwrite ${filename}.vrt; done
## Conduct a `gdal_translate` for each unique EPSG's VRT:
for filename in $(ls *.srid); do gdal_translate -of VRT -colorinterp gray ${filename}.vrt ${filename}-translated.vrt; done
## Conduct a `gdalwarp` for each unique EPSG's VRT:
for filename in $(ls *.srid); do gdalwarp -t_srs EPSG:6579 -multi -overwrite -setci ${filename}-translated.vrt ${filename}-warped.vrt; done
## EPSGs 2277-2279 will require manual intervention in order to tile successfully.
## They have a vertical datum of NAVD88 (ftUS).
## Run the following command to shift their pixel values to NAVD88 (m):
for filename in $(ls 227[7-9].srid); do gdalwarp -s_srs EPSG:$(basename ${filename} .srid)+6360 -t_srs EPSG:6579+5703 -multi -overwrite -setci ${filename}-translated.vrt ${filename}-warped.vrt; done
## Conduct a `gdalbuildvrt` to create a VRT of warped VRTs:
gdalbuildvrt -resolution user -tr 1 1 -allow_projection_difference 6579-warped.vrt $(ls -r *-warped.vrt)
## Conduct a retiling:
mkdir 6579-warped.d
gdal_retile.py -tileIndex 6579-warped.shp -csv 6579-warped.csv -levels 20 -resume -targetDir 6579-warped.d 6579-warped.vrt
## Create a VRT of the retiles:
gdalbuildvrt -resolution user -tr 1 1 6579-warped.d.vrt 6579-warped.d/*.tif
1) intel/18.0.2 3) impi/18.0.2 5) autotools/1.1 7) cmake/3.16.1 9) TACC
2) libfabric/1.7.0 4) git/2.24.1 6) python2/2.7.15 8) xalt/2.10.2
https://www.gnu.org/licenses/fdl-1.3.en.html
Copyright (C) 2022 Daniel Hardesty Lewis.
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- I. Preserve the section Entitled "History", Preserve its Title, and add to it an item stating at least the title, year, new authors, and publisher of the Modified Version as given on the Title Page. If there is no section Entitled "History" in the Document, create one stating the title, year, authors, and publisher of the Document as given on its Title Page, then add an item describing the Modified Version as stated in the previous sentence.
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You may add a section Entitled "Endorsements", provided it contains nothing but endorsements of your Modified Version by various parties—for example, statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard.
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The combined work need only contain one copy of this License, and multiple identical Invariant Sections may be replaced with a single copy. If there are multiple Invariant Sections with the same name but different contents, make the title of each such section unique by adding at the end of it, in parentheses, the name of the original author or publisher of that section if known, or else a unique number. Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work.
In the combination, you must combine any sections Entitled "History" in the various original documents, forming one section Entitled "History"; likewise combine any sections Entitled "Acknowledgements", and any sections Entitled "Dedications". You must delete all sections Entitled "Endorsements".
You may make a collection consisting of the Document and other documents released under this License, and replace the individual copies of this License in the various documents with a single copy that is included in the collection, provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects.
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A compilation of the Document or its derivatives with other separate and independent documents or works, in or on a volume of a storage or distribution medium, is called an "aggregate" if the copyright resulting from the compilation is not used to limit the legal rights of the compilation's users beyond what the individual works permit. When the Document is included in an aggregate, this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document.
If the Cover Text requirement of section 3 is applicable to these copies of the Document, then if the Document is less than one half of the entire aggregate, the Document's Cover Texts may be placed on covers that bracket the Document within the aggregate, or the electronic equivalent of covers if the Document is in electronic form. Otherwise they must appear on printed covers that bracket the whole aggregate.
Translation is considered a kind of modification, so you may distribute translations of the Document under the terms of section 4. Replacing Invariant Sections with translations requires special permission from their copyright holders, but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections. You may include a translation of this License, and all the license notices in the Document, and any Warranty Disclaimers, provided that you also include the original English version of this License and the original versions of those notices and disclaimers. In case of a disagreement between the translation and the original version of this License or a notice or disclaimer, the original version will prevail.
If a section in the Document is Entitled "Acknowledgements", "Dedications", or "History", the requirement (section 4) to Preserve its Title (section 1) will typically require changing the actual title.
You may not copy, modify, sublicense, or distribute the Document except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense, or distribute it is void, and will automatically terminate your rights under this License.
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.
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To use this License in a document you have written, include a copy of the License in the document and put the following copyright and license notices just after the title page:
Copyright (C) YEAR YOUR NAME.
Permission is granted to copy, distribute and/or modify this document
under the terms of the GNU Free Documentation License, Version 1.3
or any later version published by the Free Software Foundation;
with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
A copy of the license is included in the section entitled "GNU
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If you have Invariant Sections, Front-Cover Texts and Back-Cover Texts, replace the "with … Texts." line with this:
with the Invariant Sections being LIST THEIR TITLES, with the
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If you have Invariant Sections without Cover Texts, or some other combination of the three, merge those two alternatives to suit the situation.
If your document contains nontrivial examples of program code, we recommend releasing these examples in parallel under your choice of free software license, such as the GNU General Public License, to permit their use in free software.