Open Source Stack for Raster Tiling in Custom Projections

This post is a high level look at the recent stack I built for a raster tiling set up. I am working out some kinks in my online and network delivery of cartographic products, so I thought it was time to set up a raster tiling service to access XYZ and WTMS services from my raster tile caches. I’ll be adding maps and zooms levels in the future, so check back now and again. Antarctica is on it’s way soon!

nz_from_basemap_service

Basic Demo Service using NZTM projection is here: https://xycarto.github.io/

See below for WMTS links

Raster tiling is not the only method, but it is still a viable choice for delivering nice looking maps online, serving across networks, and designing with raster data. I am particularly enamored with the quality of the visual outputs. For me, it is akin to the difference between music in vinyl and digital formats. In addition, the process is well documented and fairly straight forward. By virtue of having been around for a while, raster tiling has a wealth of information and standards to work with, delivery from S3 is a robust process, and there is nice integration with QGIS, Leaflet and Openlayers.

I break the stack in to three areas: analysis, rendering, and delivery

Analysis
QGIS: Sketching, QC, and general geospatial work.

GDAL: Processing raster data. Configuring your rasters in an optimal format from the beginning will greatly improve your rendering speeds. I recommend creating a good set of overviews and gathering everything into a virtual raster tile (VRT).

Postgres/PostGIS: Handling your vector data. Pulling all your data from a database significantly improves rendering speeds. Don’t forget to index!

Rendering
Tilemill/Mapnik XML: Yes, I still design using CartoCSS when working with raster data. I love the simplicity of the language. Tilemill is easy enough to containerize these days too. Tilemill exports into the Mapnik XML format, essential for my process further down the line. Here is how to hack Tilemill to work in a custom projection.

Mapnik: Support for using Mapnik XML

Mapnik with Python Bindings: Necessary for using Mapnik XML documents in MapProxy

MapProxy: MapProxy is a map server and tile renderer . It is easy to build on your machine, though I recommend using a container like Docker. Specifically, I use a hack provided by PalmerJ at Github to increase rendering speeds through multi-threading.

Delivery
Amazon S3: Simple Storage Service. Amazon is pretty cheap, free in many cases, and a good place for storing your tile cache. You get an easily accessed URL for your tiles and a home for your WMTS GetCapabilities document.

WMTS: For me, the real power in a base map service is the WMTS, so, below are two links to the WTMS service for you to set up in QGIS if you’d like to have a play. Here is a quick tutorial about how to set up WMTS if you are unfamiliar.

https://s3-ap-southeast-2.amazonaws.com/basemaps.temp/nz_colour_basemap/WMTSCapabilities.nz_colour_basemap.xml
https://s3-ap-southeast-2.amazonaws.com/basemaps.temp/nz_topo_basemap/WMTSCapabilities.nz_topo_basemap.xml

XYZ: Building a web map? If your tile cache is in S3, in a TMS structure, and public you should be able to access it via simple XYZ request like so:

https://{s3-your-region-here}/{your_bucket}/{project_name}/{projection}/{z}/{x}/{y}.png

Leaflet: Leaflet will handle all the XYZ requests to the server and allow for custom projections. Have a look here for the basic HTML, CSS and JS set up.

Experimenting with Hydrological Analysis using TauDEM

Blue Rivers Ordered

Over the past few years, I’ve played around with developing ordered rivers networks for different projects. I am not an expert in hydrology, but I can get close for cartographic purposes. I am an expert; however, in asking for help from those who know best and I rely on a lot of very smart people to guide me on my journey.

Recently, I decided to put together a visualization of ordered rivers for New Zealand. I came across a very nice data set offered through the Ministry for the Environment via the Koordinates website and thought I’d like to put it to use.

The rivers vis project made me wonder if I could build this base dataset myself using some of the recently released elevation data sets via the LINZ Data Service. The short answer to my question is “sorta”. Doing it open source is not an issue, but building an accurate ordered river centerline network is another story. This is a task I cannot take on as a solo project right now, but I could do a little experimentation. Below, I’ll offer some of methods and things I learned along the way.

Tools and Data

The method I tested used TauDEM and a 1m DEM raster accessed from the LINZ Data Service. I down sampled the DEM to 2m and 5m resolutions and used small areas for testing. Finding and open source tool was easy. I sorted through a few available methods and finally landed on “Terrain Analysis Using Digital Elevation Models” (TauDEM). There are additional methods through GRASS and SAGA GIS. I chose TauDEM because I never used it before.

Method Tested

To my knowledge, there is no open source tool where a person can put in a DEM and get a networked rivers centerline vector out the other side. It requires a number of steps to achieve your goal.

The basic run down to process the DEM is to:

  1. Fill sinks
  2. Determine flow directions
  3. Determine watersheds
  4. Determine flow accumulation
  5. Stream classification
  6. Export to vector

TauDEM does require a few extra steps to complete the process, but these steps are explained in the documentation of the tool. It was more about keeping all my variables in the right places and using them at the right time. I recommend using the variable names TauDEM provides.

BASH script here

Click the arrow to the left to view the full BASH script below:

#!bin/bash

#Rough sketch for building river centerlines. Rasters have been clipped prior

BASEPATH=/dir/path/to/base

raster_list=$( find $BASEPATH -name "*.tif" )

taudem_outputs=/dir/path/to/outputs

reso=resolution_number

for i in $raster_list
do


	INPUT_RASTER=$i

	file_name=$( basename $i )

	strip_input_extension=$( echo $file_name | sed 's/.tif//' )

	reso_name=$taudem_outputs/${strip_input_extension}_${reso}res

	gdal_translate -tr $reso $reso -of GTiff $i $reso_name.tif

	fel=${reso_name}_fel.tif
	p=${reso_name}_p.tif
	sd8=${reso_name}_sd8.tif
	ad8=${reso_name}_ad8.tif
	ang=${reso_name}_ang.tif
	slp=${reso_name}_slp.tif
	sca=${reso_name}_sca.tif
	sa=${reso_name}_sa.tif
	ssa=${reso_name}_ssa.tif
	src=${reso_name}_src.tif

	ord=${reso_name}_strahlerorder.tif 
	tree=${reso_name}_tree.dat
	coord=${reso_name}_coord.dat
	net=${reso_name}_network.shp
	w=${reso_name}_watershed.tif 

	processed_input_file=$reso_name.tif

	#TauDEM Commands
	mpiexec -n 8 pitremove -z $processed_input_file -fel $fel

	mpiexec -n 8 d8flowdir -fel $fel -p $p -sd8 $sd8 

	mpiexec -n 8 aread8 -p $p -ad8 $ad8 -nc

	mpiexec -n 8 dinfflowdir -fel $fel -ang $ang -slp $slp

	mpiexec -n 8 areadinf -ang $ang -sca $sca -nc

	mpiexec -n 8 slopearea -slp $slp -sca $sca -sa $sa

	mpiexec -n 8 d8flowpathextremeup -p $p -sa $sa -ssa $ssa -nc

	mpiexec -n 8 threshold -ssa $ssa -src $src

	mpiexec -n 8 streamnet -fel $fel -p $p -ad8 $ad8 -src $src -ord $ord -tree $tree -coord $coord -net $net -w $w

done

The script is a rough sketch, but does get results.

Challenges in the Process

One major challenge for this project was the size of the input DEM and my computers available RAM. I work primarily off a laptop. It’s a good machine but no match for a proper server set up with some spacious RAM. My laptop struggled with the large hi-resolution DEMs, so I needed to down-sample the images and choose a smaller test area to get it to work.

Clip the tiff with gdal_translate -projwin and down sample with -tr

gdal_translate -tr xres yres -projwin ulx uly lrx lry input.tif output.tif

The second challenge came up because I used a bounding box to clip my test regions. I recommend not doing this and instead clip your regions using a watershed boundary. Having square shapes for your test regions will give you very inaccurate and unhelpful results. For example, major channels in your DEM will be cut at the edges of your raster. You will not get accurate results.

Clipping a raster using a shapefile, like a watershed boundary, can be achieved using gdalwarp.

gdalwarp –cutline input.shp input.tif output.tif

Results

I ran my process and QCed the results against Aerial Imagery and a hillshade I developed from the DEM. The first run gave me good enough results to know I have a lot of work to do, but I did manage to develop a process I was happy with. The tool did a great job, but the accuracy of the DEM was a little more challenging. It’s a start. I captured a good number of river channels despite my incorrect usage of a square DEM, learned a lot about how DEM resolution affects outputs, and gained knowledge around how to spot troublesome artifacts.

Well Defined ChannelsImg 1: River capture in well defined channel.

From this experiment, there are a few ideas I’d like to explore further:

1. Accuracy of the DEM. The particular DEM I worked with had a number of ‘dams’ in the flows. Notably, bridges, culverts, vegetation artifacts, and other general errors that caused water to flow in interesting directions. When working with a data set like this, I am curious how manage these artifacts.

Road issueImg 1: River diversion at road.

Artifact issueImg 1: River diversion at culvert or bridge.

2. How to go beyond borders. This analysis can be broken down by watershed, but it will be necessary to link the outflows of those watersheds to the next for accurate results.

Edge issueImg 1: Flow not captured at edge.

3. As DEMs are released with better resolution, there is a need for scaled up computing power. The process needs a large amount of RAM. What is the best computational set up for capturing the largest area?

4. Did I do this correctly? I perform this task about once every two years and usually weekends when the surf is flat and the garden is weeded, so I am not an expert. There is a lot more research to be done to determine if I am using the tools to the best of their abilities.

Wellington Elevations: Interpolating the Bathymetry

It is important to note something from the very beginning. The interpolated bathymetry developed in this project does not reflect the actual bathymetry of the Wellington Harbour. It is my best guess based on the tools I had and the data I worked with. Furthermore, this interpolation is NOT the official product of any institution. It is an interpolation created by me only for the purposes of visualization.

welly_harbour-colour-and-aerial_FULLVIEW

Part of the goal when visualizing the Wellington landscape was to incorporate a better idea about what may be happening below the surface of the harbor. Various bathymetric scans in the past have gathered much of the information and institutions like NIWA have done the work visualizing that data. As for myself, I did not have access to those bathymetries; however, I did have a sounding point data set to work with, so I set about interpolating those points.

The data set, in CSV format, was over a million points; too dense for a single interpolation. I worked out a basic plan for the interpolation based on splitting the points into a grid, interpolate the smaller bits, then reassemble the grid tiles into a uniform bathymetry.

Conversion from CSV to shp
Using the open option (-oo) switch, OGR will convert CSV to shp seamlessly

ogr2ogr -s_srs EPSG:4167 -t_srs EPSG:4167 -oo X_POSSIBLE_NAMES=$xname* -oo Y_POSSIBLE_NAMES=$yname*  -f "ESRI Shapefile" $outputshapepath/$basenme.shp $i

Gridding the Shapefile
With the shapefile in place, I next needed to break it into smaller pieces for interpolation. For now, I create the grid by hand in QGIS using the ‘Create Grid’ function. This is found under Vector>Reasearch Tools>Create Grid. Determining a grid size that works best for the interpolation is a bit of trial and error. You want the largest size your interpolation can manage without crashing. Using the grid tool from QGIS in very convenient, in that it creates an attribute table of the xmin, xmax, ymin, ymax corrodinates for each tile in the grid. These attributes become very helpful during the interpolation process.

Interpolating the Points
I switched things up in the interpolation methods this time and tried out SAGA GIS. I have been looking for a while now for a fast and efficient method of interpolation that I could easily build into a scripted process. SAGA seemed like a good tool for this. The only drawback, I had a very hard time finding examples online about how to use this tool. My work around to was to test the tool in QGIS first. I noticed when the command would run, QGIS saved the last command in a log file. I found that log, copied out the command line function, and began to build my SAGA command for my script from there.

Here is look at the command I used:


saga_cmd grid_spline "Multilevel B-Spline Interpolation" -TARGET_DEFINITION 0 -SHAPES "$inputpoints" -FIELD "depth" -METHOD 0 -EPSILON 0.0001 -TARGET_USER_XMIN $xmin -TARGET_USER_XMAX $xmax -TARGET_USER_YMIN $ymin -TARGET_USER_YMAX $ymax -TARGET_USER_SIZE $reso -TARGET_USER_FITS 0 -TARGET_OUT_GRID "$rasteroutput/sdat/spline_${i}"

I tested a number of methods and landed on ‘grid_spline’ as producing the best results for the project. It was useful because it did a smooth interpolation across the large ‘nodata’ spaces.

Once the initial interpolation was complete, I needed to convert the output to GeoTIFF since SAGA exports in an .sdat format. Easy enough since GDAL_TRANSLATE recognizes the .sdat format. I then did my standard prepping and formatting for visualization:


gdal_translate "$iupput_sdat/IDW_${i}.sdat" "$output_tif/IDW_${i}.tif"
gdaldem hillshade -multidirectional -compute_edges "$output_tif/IDW_${i}.tif" "$ouput_hs/IDW_${i}.tif"
gdaladdo -ro "$output_tif/IDW_${i}.tif" 2 4 8 16 32 64 128
gdaladdo -ro "$ouput_hs/IDW_${i}.tif"2 4 8 16 32 64 128

Here is look at the interpolated harbour bathymetry, hillshaded, with Wellington 1m DEM hillshade added over top
welly_harbour_bw_all

And here is a look at the same bathy hillshade with coloring
welly_harbour_bw-and-aerial

Visualizing the Bathymetry
With the bathymetry, complete it was simply a matter of building it into the existing visualization I built for the Wellington Region. Learn more about the project here. The visualization was four steps:

Hillshade
addedbathy_bathyonlypng
Color
addedbathy_bathyonly_withcolor
Aerial Imagery
addedbathy_bathyonly_withcoloraerial
Then merge the models together
addedbathy_final

Easy as, eh? Let me know what you think!

Note: All imagery was produced during my time at Land Information New Zealand. Imagery licensing can be found here:
“Source: Land Information New Zealand (LINZ) and licensed by LINZ for re-use under the Creative Commons Attribution 4.0 International licence."

Building the Wellington Model with 1m DEM and DSM

As interest in LiDAR derived elevation increases, so grows the interest in the capabilities. LiDAR derived elevation data has been great for my visualization game and in helping me communicate the story out about what LiDAR can do. It all starts with a picture to get the imagination going.

wellyvation

The Wellington model derived for this project is part of an ongoing project to help increase the exposure of the Wellington 1m DEM/DSM elevation data derived from LiDAR. Step one for me is getting a working model built in QGIS, capturing still images, and increasing interest in the data.

I’ve talked about the processing of the elevation data for Wellington visualizations in the past, so for this post I’m only focusing on the blending of the data sets in building the model. This project is a good model since it encompasses a number of subtle techniques to get the model to stand out. This post is one of a two part series; the second post discusses the techniques used to derive and visualize the bathymetry for the surrounding harbor.

Let’s start with the base, Aerial Imagery.
wellyhabour_aerialonly

Blended with a hillshade
wellyhabour_aerial_withHS

DSM added for texture and context
wellyhabour_aerial_withDSMHS

Slope added to define some edges
wellyhabour_aerial_withDSMDEMSLOPEHS

Some darker shading added to the bathymetry to frame the elevation data
wellyhabour_aerial_withDSMDEMSLOPEHS_darkenframe

And finally some added bathymetry to lighten the edges at the shoreline enhancing the frame a bit more.
wellyhabour_aerial_withDSMDEMSLOPEHS_edgeframe

In the end there is some post-processing in Photoshop to lighten up the image. Honestly, this could have been done in QGIS, but I was being lazy. For the images produced, there was no need to retain the georeferencing, and when that is the case, I rely on Photoshop for color and light balancing.

The greatest difficultly in this project so far has been trying to create a universal model for the data set. I’m finding that as I visualize different regions using this model, I need to adjust the hillshading quite significantly to draw out different features. Take a look at the images here. It is the same model, but with the noticeably different gradients used in the hillshades. The techniques used for the images in this post worked well for the urban region shown, but fall apart as you move further out into the more mountainous regions. Much of the blending is too harsh and turns the mountains into a black muddled mess. I am almost there, but like any project, it takes a good bit of subtle tweaking of the blending to get a universal image to work.

The entire base mapping work is completed in QGIS. The elevation data was processed using GDAL and the bathymetric interpolations were produced SAGA GIS. There are no color palettes for this project. The aerial imagery does all the work in that department.

Base data can be found here:
DEM: https://data.linz.govt.nz/layer/53621-wellington-lidar-1m-dem-2013/
DSM: https://data.linz.govt.nz/layer/53592-wellington-lidar-1m-dsm-2013/
Aerial Imagery: https://data.linz.govt.nz/layer/51870-wellington-03m-rural-aerial-photos-2012-2013/

The next post covers the development of the bathymetry for the surrounding harbor. Thanks for having a look and let me know what you think.

Note: All imagery was produced during my time at Land Information New Zealand. Imagery licensing can be found here:
“Source: Land Information New Zealand (LINZ) and licensed by LINZ for re-use under the Creative Commons Attribution 4.0 International licence.”

The Rejects

Sometimes there is simply not enough room for all the ideas. Sometimes you want all the images to make it to the final round.

wairarapa

In a recent project to promote some of our elevation data, I was asked to present a number of ideas for a 2000mm x 900mm wall hanging. The piece was to act as a conversation starter and demonstrate some of the finer details elevation from LiDAR possesses.

In the end, the image above was the chosen candidate. Below are the drafts I initially presented for review. You can see the difference in treatment from the original ideas to the final product. Personally, I really enjoyed the images developed for the draft series, I liked the silvery undertones, and I thought it was a shame to merely let these images sit on my hard drive.
Below, you’ll find a brief description about a few challenges faced in the image development.

near_lake_ferry
nice_farm
masterton_region
random
draft_wairarapa

Artifacts and Finer Details
The hardest part of this job was drawing out the finer details of the chosen location. There was a strong interest in showing the ancient river bed; however, without a good bit of tweaking in the hillshades, the image is quite flat. After some trial and error, I found I could get a good contrast by limiting the hillshade values range to 170-190. That’s it, but the readability of the project really hinged on the simple tweak. It really made the details stand out.
That said, the gain in detail also revealed a significant artifact in the data. If you go back up and have a closer look, you will find diagonal depressions running across the images in equal intervals. These are lines from where the LiDAR scans overlap. I haven’t quite had the time to figure out how to remove these from the original data source, so for now I leave them in as conversational piece around improving LiDAR capture practices.
As usual, all map layout work was completed on QGIS, with the bulk of the data processing done using GDAL. The ‘Reject’ images for this post are direct exports from QGIS, with no manipulation apart from some down-sampling and cropping in Photoshop.

Base data can be found here:
DEM: https://data.linz.govt.nz/layer/53621-wellington-lidar-1m-dem-2013/
DSM: https://data.linz.govt.nz/layer/53592-wellington-lidar-1m-dsm-2013/
Aerial Imagery: https://data.linz.govt.nz/layer/51870-wellington-03m-rural-aerial-photos-2012-2013/

Hope you like and thanks for checking in!

Note: All imagery was produced during my time at Land Information New Zealand. Imagery licensing can be found here:
“Source: Land Information New Zealand (LINZ) and licensed by LINZ for re-use under the Creative Commons Attribution 4.0 International licence.”