Bird vs. Fish

Latest Error

I’m getting this error after a 137 /panfs/roc/msisoft/R/3.6.0/lib64/R/bin/BATCH: line 60: 30473 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 It ends on this line… fr <- sapply(1:nrow(forest),function(y) fasterize(forest[y,], cr[[1]])) Since smaller memory processes run without error, I can only assume that storing a vector of larger cropped rasters is the problem. So, onto a […]

Best Practices for Big Polygon Data Sets

Some common, useful formats for storing this type of information… CSV GeoJSON/TopoJSON GML KML MySQL/SQLite/SpatiaLite/PostGIS NetCDF SVG VRT ESRI shape file ESRI feature class It can also be advantageous to abstract data in memory to work with it. I had never heard of GMT or VPF until now but I’m curious about them! A colleague […]

GDAL Warp Adventure

I’m working with a colleague on processing a raster, in order to define patches by connectivity rules. The input raster was a habitat suitability model, where… 1 = suitable habitat 0 = unsuitable habitat 255 = background “no data” value So, we needed to ultimately make the “1s” into patches. To do this, we needed […]

Linux + GDAL Tricks

I needed to merge a bunch of shape files into one. These files were all in a folder, but each shape file was in a separate sub-folder. So I copied them all into a folder together to merge them. First I navigated to the folder that had all the sub folders, and then I ran… […]

Yellow Rail Notes

From the COSEWIC report (direct quotes): Yellow Rails have such a narrow tolerance of water levels for breeding that any given location may be suitable in one year but not the next, especially in prairie regions, where the species mainly occurs in seasonal wetlands (Prescott et al. 2003). An occupied marsh in southern Manitoba was partly destroyed […]

GDAL Polygonize in Action!

#!/bin/bash for VARIABLE in ./test_export/*.tif; do gdal_translate -of GTiff -a_nodata 0 “$VARIABLE” “PPR_no/$(basename “$VARIABLE” .tif).tif” gdal_sieve.py -st 2 -8 “PPR_no/$(basename “$VARIABLE” .tif).tif” gdal_polygonize.py -8 “PPR_no/$(basename “$VARIABLE” .tif).tif” -f “ESRI Shapefile” “shapefile/$(basename “$VARIABLE” .tif).shp” rm “PPR_no/$(basename “$VARIABLE” .tif).tif” ogr2ogr -f “ESRI Shapefile” -progress “shapefiles/$(basename “$VARIABLE” .tif).shp” “shapefile/$(basename “$VARIABLE” .tif).shp” -t_srs “EPSG:5070” done listofmodisdays=`ls shapefiles/*.shp | cut […]

Aurora

I’m so happy my parents got to cross northern lights off their bucket list!

Esrey Park

I already want to revisit this neat lakeside park to snorkel!

Keweenaw

Today, I kicked off a long weekend vacation with my parents! We decided to take a little road trip somewhere none of us had been. Apparently, pipe vesicles can be found on the bluffs just north of Bessemer. “The traps from Bessemer to North Bessemer appear to be older than any beds exposed north…Elongate, so-called […]

Parallel Raster Extraction

This is my job submission script for the raster extraction. #!/bin/bash -l #PBS -l walltime=48:00:00,nodes=1:ppn=24,mem=61gb #PBS -m abe #PBS -M myaddress@email.com module load gdal/2.0.1 module load proj module load R module load ompi module load udunits module load geos export OMP_NUM_THREADS=1 mpirun -v -hostfile $PBS_NODEFILE -np 1 R –slave CMD BATCH ./extract.R /dev/stdout This is […]