Patches and difficulties with multispec maps

Firstly, I must just say what a fantastic piece of software this is. Very versatile and perfect for my uses.

I am having some issues with the multispec outputs when going through the different available indices. There are patches where the data is definitely incorrect and I am not sure if this is perhaps a processing issue or a drone issue (DJI P4 Multi).

image

There are a number of green and red areas that are inconsistent with the real world and as you can see, the areas look like they are missing data. When I open the individual blue band only in GIS, the grey scale data matches the patches you see here, but only on the blue band. The other band are all fine.

This is a flight over an indigenous forest where alien vegetation is starting to encroach. It is not possible at this time to upload all the images but I will as soon as I have a better connection.

Any thoughts?

Thanks again for a brilliant piece of software!

Processing task output bellow:

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Blending texture patches 100%… done. (Took 12.514s)
Generating texture atlases:
Sorting texture patches… done.

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Working on atlas 7 100%… done.
Finalizing texture atlases… done. (Took: 0s)
Building objmodel:
Saving model… done.
Whole texturing procedure took: 50.066s
[INFO] Finished mvs_texturing stage
[INFO] Running odm_georeferencing stage
[INFO] Georeferencing point cloud
[INFO] running pdal translate -i “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_filterpoints\point_cloud.ply” -o “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.laz” ferry transformation --filters.ferry.dimensions=“views => UserData” --writers.las.compression=“lazip” --filters.transformation.matrix=“1 0 0 645725.0 0 1 0 6238045.0 0 0 1 0 0 0 0 1” --writers.las.offset_x=645725.0 --writers.las.offset_y=6238045.0 --writers.las.offset_z=0 --writers.las.a_srs="+proj=utm +zone=34 +south +datum=WGS84 +units=m +no_defs +type=crs"
[INFO] Calculating cropping area and generating bounds shapefile from point cloud
[INFO] running pdal translate -i “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.laz” -o “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.decimated.las” decimation --filters.decimation.step=80
[INFO] running pdal info --boundary --filters.hexbin.edge_size=1 --filters.hexbin.threshold=0 “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.decimated.las” > “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.boundary.json”
[INFO] running pdal info --summary “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.laz” > “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.summary.json”
[INFO] running ogr2ogr -overwrite -f GPKG -a_srs “+proj=utm +zone=34 +south +datum=WGS84 +units=m +no_defs” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.bounds.gpkg” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.bounds.geojson”
[INFO] Creating Entwine Point Tile output
[INFO] running untwine --temp_dir “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\entwine_pointcloud-tmp” --files “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.laz” --output_dir “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\entwine_pointcloud”
[INFO] Finished odm_georeferencing stage
[INFO] Running odm_dem stage
[WARNING] Maximum resolution set to 2.0 * (GSD - 10.0%) (7.52 cm / pixel, requested resolution was 5.00 cm / pixel)
[INFO] Classify: False
[INFO] Create DSM: False
[INFO] Create DTM: False
[INFO] DEM input file C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.laz found: True
[WARNING] DEM will not be generated
[INFO] Finished odm_dem stage
[INFO] Running odm_orthophoto stage
[INFO] running “C:\WebODM\resources\app\apps\ODM\SuperBuild\install\bin\odm_orthophoto” -inputFiles “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_texturing_25d\odm_textured_model_geo.obj”,“C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_texturing_25d\green\odm_textured_model_geo.obj”,“C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_texturing_25d\red\odm_textured_model_geo.obj”,“C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_texturing_25d\rededge\odm_textured_model_geo.obj”,“C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_texturing_25d\nir\odm_textured_model_geo.obj” -logFile “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto_log.txt” -outputFile “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto_render.tif” -resolution 20.0 -outputCornerFile “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto_corners.txt” -bands Blue,Green,Red,RedEdge,NIR
[INFO] Creating GeoTIFF
[INFO] running gdal_translate -a_ullr 645603.3245697021 6238172.8519973755 645910.1986694336 6237890.419189453 -co TILED=YES -co COMPRESS=DEFLATE -co PREDICTOR=2 -co BIGTIFF=IF_SAFER -co BLOCKXSIZE=512 -co BLOCKYSIZE=512 -co NUM_THREADS=8 -a_srs “+proj=utm +zone=34 +south +datum=WGS84 +units=m +no_defs +type=crs” --config GDAL_CACHEMAX 38.55% --config GDAL_TIFF_INTERNAL_MASK YES “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto_render.tif” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.tif” > “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\gdal_translate_log.txt”
[INFO] Cropping C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.tif
[INFO] running gdalwarp -cutline “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.bounds.gpkg” -crop_to_cutline -co TILED=YES -co COMPRESS=DEFLATE -co PREDICTOR=2 -co BIGTIFF=IF_SAFER -co BLOCKXSIZE=512 -co BLOCKYSIZE=512 -co NUM_THREADS=8 -dstalpha “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.original.tif” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.tif” --config GDAL_CACHEMAX 38.35%
Using band 6 of source image as alpha.
Creating output file that is 6008P x 5541L.
Processing C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.original.tif [1/1] : 0…10…20…30…40…50…60…70…80…90…100 - done.
[INFO] Optimizing C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.tif as Cloud Optimized GeoTIFF
[INFO] running gdal_translate -of COG -co NUM_THREADS=8 -co BLOCKSIZE=256 -co COMPRESS=DEFLATE -co PREDICTOR=2 -co BIGTIFF=IF_SAFER -co RESAMPLING=NEAREST --config GDAL_CACHEMAX 38.7% --config GDAL_NUM_THREADS 8 “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.tif” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto_cogeo.tif”
Input file size is 6008, 5541
0…10…20…30…40…50…60…70…80…90…100 - done.
[INFO] Finished odm_orthophoto stage
[INFO] Running odm_report stage
[INFO] Exporting shots.geojson
[INFO] Wrote C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_report\shots.geojson
[INFO] running pdal info --dimensions “X,Y,Z” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.laz” > “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.info.json”
[INFO] running pdal translate -i “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.laz” -o “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.tif” --writer gdal --writers.gdal.resolution=0.21927857142864793 --writers.gdal.data_type=uint8_t --writers.gdal.dimension=UserData --writers.gdal.output_type=max --writers.gdal.radius=0.3101067296521914
[INFO] Cropping C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.tif
[INFO] running gdalwarp -cutline “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_georeferencing\odm_georeferenced_model.bounds.gpkg” -crop_to_cutline -co TILED=YES -co COMPRESS=DEFLATE -co PREDICTOR=2 -co BIGTIFF=IF_SAFER -co BLOCKXSIZE=512 -co BLOCKYSIZE=512 -co NUM_THREADS=8 “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.original.tif” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.tif” --config GDAL_CACHEMAX 39.7%
Creating output file that is 1369P x 1262L.
Processing C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.original.tif [1/1] : 0Using internal nodata values (e.g. 255) for image C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.original.tif.
Copying nodata values from source C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.original.tif to destination C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.tif.
…10…20…30…40…50…60…70…80…90…100 - done.
[INFO] running gdaldem color-relief “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.tif” “C:\WebODM\resources\app\apps\ODM\opendm\report\overlap_color_map.txt” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\overlap.png” -of PNG -alpha
0…10…20…30…40…50…60…70…80…90…100 - done.
[INFO] running gdal_translate -of png “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_orthophoto\odm_orthophoto.tif” “C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\opensfm\stats\ortho.png” -outsize 1400 0 -b 1 -b 2 -b 3 -a_nodata 0 --config GDAL_CACHEMAX 39.75%
Warning 6: PNG driver doesn’t support data type Float32. Only eight bit (Byte) and sixteen bit (UInt16) bands supported. Defaulting to Byte

Input file size is 6008, 5541
0…10…20…30…40…50…60…70…80…90…100 - done.
[INFO] Exporting report to C:\WebODM\resources\app\apps\NodeODM\data\ec147476-1056-4ac8-82d1-a93d0ed0a9cd\odm_report\report.pdf
2021-11-11 14:23:58,410 DEBUG: Final doc sections size summary:
2021-11-11 14:23:58,410 DEBUG: - header.size: 9.0B
2021-11-11 14:23:58,410 DEBUG: - pages.size: 4.1KiB
2021-11-11 14:23:58,410 DEBUG: - resources.fonts.size: 199.0B
2021-11-11 14:23:58,418 DEBUG: - resources.images.size: 4.2MiB
2021-11-11 14:23:58,418 DEBUG: - resources.dict.size: 204.0B
2021-11-11 14:23:58,418 DEBUG: - info.size: 55.0B
2021-11-11 14:23:58,418 DEBUG: - catalog.size: 104.0B
2021-11-11 14:23:58,418 DEBUG: - xref.size: 670.0B
2021-11-11 14:23:58,418 DEBUG: - trailer.size: 67.0B
[INFO] Finished odm_report stage
[INFO] Running odm_postprocess stage
[INFO] Post Processing
[INFO] Finished odm_postprocess stage
[INFO] No more stages to run
[INFO] MMMMMMMMMMMNNNMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMNNNMMMMMMMMMMM
[INFO] MMMMMMdo:…—…/sNMMMMMMMMMMMMMMMMMMMMMMMMMMNs/…—…:odMMMMMM
[INFO] MMMMy-.odNMMMMMNy//mMMMMMMMMMMMMMMMMMMMMMMm//hNMMMMMNdo.-yMMMM
[INFO] MMN/sMMMMMMMMMNNMm/yMMMMMMMMMMMMMMMMMMMMy/mMNNMMMMMMMMNs/MMM
[INFO] MM/ hMMMMMMMMNs.+MMM/ dMMMMMMMMMMMMMMMMMMh +MMM+.sNMMMMMMMMh +MM
[INFO] MN /MMMMMMNo/./mMMMMN :MMMMMMMMMMMMMMMMMM: NMMMMm/./oNMMMMMM: NM
[INFO] Mm +MMMMMN+ /MMMMMMM-MMMMMMMMMMMMMMMMMM-MMMMMMM: oNMMMMM+ mM
[INFO] MM…NMMNs./mNMMMMMMMy sMMMMMMMMMMMMMMMMMMo hMMMMMMMNm/.sNMMN-MM [INFO] MMd:mMNomMMMMMMMMMy:MMMMMMMNmmmmNMMMMMMN:hMMMMMMMMMdoNMm-dMM [INFO] MMMm:.omMMMMMMMMNh/ sdmmho/.-``-/sddh+ /hNMMMMMMMMdo.:mMMM [INFO] MMMMMd+--/osss+:-:/ :- .ym+ hmo``:-` `+:-:ossso/-:+dMMMMM [INFO] MMMMMMMNmhysosydmNMo /ds`/NMM+ hMMd..dh. sMNmdysosyhmNMMMMMMM [INFO] MMMMMMMMMMMMMMMMMMMs .:-:``hmmN+ yNmds -:.:`-NMMMMMMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMMMMMMN.-mNm- //:::. -:://: +mMd`-NMMMMMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMMMMMM+ dMMN -MMNNN+ yNNNMN :MMMs sMMMMMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMMMMMM`.mmmy /mmmmm/ smmmmm``mmmh :MMMMMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMMMMMM``:::- ./////. -:::::` :::: -MMMMMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMMMMMM:`mNNd /NNNNN+ hNNNNN .NNNy +MMMMMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMMMMMMd`/MMM.`ys+//. -/+oso +MMN.`mMMMMMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMMMMMMMy /o:- `oyhd/ shys+ `-:s-`hMMMMMMMMMMMMMMMMMM [INFO] MMMMMMMMNmdhhhdmNMMM` +d+ sMMM+ hMMN:`hh- sMMNmdhhhdmNMMMMMMMM [INFO] MMMMMms:::/++//::+ho .+- /dM+ hNh- +/` -h+:://++/::/smMMMMM [INFO] MMMN+./hmMMMMMMNds- ./oso:.``:. :-``.:os+- -sdNMMMMMMmy:.oNMMM [INFO] MMm-.hMNhNMMMMMMMMNo`/MMMMMNdhyyyyhhdNMMMM+`oNMMMMMMMMNhNMh.-mMM [INFO] MM:`mMMN/-sNNMMMMMMMo yMMMMMMMMMMMMMMMMMMy sMMMMMMMNNs-/NMMm`:MM [INFO] Mm /MMMMMd/.-oMMMMMMN :MMMMMMMMMMMMMMMMMM-`MMMMMMMo-./dMMMMM/ NM [INFO] Mm /MMMMMMm:-`sNMMMMN :MMMMMMMMMMMMMMMMMM-`MMMMMNs`-/NMMMMMM/ NM [INFO] MM:`mMMMMMMMMd/-sMMMo yMMMMMMMMMMMMMMMMMMy sMMMs-/dMMMMMMMMd`:MM [INFO] MMm-.hMMMMMMMMMdhMNo`+MMMMMMMMMMMMMMMMMMMM+`oNMhdMMMMMMMMMh.-mMM [INFO] MMMNo./hmNMMMMMNms--yMMMMMMMMMMMMMMMMMMMMMMy--smNMMMMMNmy/.oNMMM [INFO] MMMMMms:-:/+++/:-+hMMMMMMMMMMMMMMMMMMMMMMMMMNh+-:/+++/:-:smMMMMM [INFO] MMMMMMMMNdhhyhdmMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMmdhyhhmNMMMMMMMM [INFO] MMMMMMMMMMMMMMMNNNNNMMMMMMNNNNNNMMMMMMMMNNMMMMMMMNNMMMMMMMMMMMMM [INFO] MMMMMMMMMMMMMh/-...-+dMMMm......:+hMMMMs../MMMMMo..sMMMMMMMMMMMM [INFO] MMMMMMMMMMMM/ /yhy- sMMm -hhy/ :NMM+ oMMMy /MMMMMMMMMMMM [INFO] MMMMMMMMMMMy /MMMMN` NMm /MMMMo +MM: .` yMd :MMMMMMMMMMMM
[INFO] MMMMMMMMMMM+ sMMMMM: hMm /MMMMd -MM- /s h.d- -MMMMMMMMMMMM
[INFO] MMMMMMMMMMMs +MMMMM. mMm /MMMMy /MM. +M/ yM: MMMMMMMMMMMM [INFO] MMMMMMMMMMMN- smNm/ +MMm :NNdo .mMMoMM+/yMM/ MMMMMMMMMMMM [INFO] MMMMMMMMMMMMNo- :yMMMm :sNMMM sMMMMMMM+ NMMMMMMMMMMM
[INFO] MMMMMMMMMMMMMMMNmmNMMMMMMMNmmmmNMMMMMMMNNMMMMMMMMMNNMMMMMMMMMMMM
[INFO] ODM app finished - Thu Nov 11 14:23:58 2021
100 - done.
Compressing all.zip

Done

1 Like

Any particular reason you’ve selected VARI despite having a multispectral sensor with an infrared band?