GRASS i.gensig and i.maxlik

[qgib]

Author Name: Patrice Carbonneau (Patrice Carbonneau)
Original Redmine Issue: 19539
Affected QGIS version: 3.2.1
Redmine category:processing/grass

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I am having major issues with GRASS and SAGA processing tools. This report is about GRASS tools for classification. When running through the procedure, i.gensig runs but closes. I can't see the log file. It does produce a signature and I have attached it. In the error log, there seems to be a problem with this signature, it's the first mention of errors. Then it seems that the tool cannot find the raster image group it created. Full error log is below:

Algorithm 'i.maxlik' starting…
Input parameters:
{ 'GRASS_RASTER_FORMAT_META' : '', 'GRASS_RASTER_FORMAT_OPT' : '', 'GRASS_REGION_CELLSIZE_PARAMETER' : 0, 'GRASS_REGION_PARAMETER' : None, 'input' : ['C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/ff682a87d4e341358eec94aa0e0179d9/B.sdat','C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/597d0f6b759947919cd4d5cd53bfc2b5/G.sdat','C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/33c61bf0bbb1409d9b79545684848d28/R.sdat'], 'output' : 'C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/4b51fe8a7282498dbeec1b4398b973f9/output.tif', 'reject' : 'C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/d9f1b86081ba42f194b0153ad8499cea/reject.tif', 'signaturefile' : 'D:/DeepRiverscapes/Qtest_signatures_split.txt' }

g.proj -c proj4="+proj=utm +zone=31 +datum=WGS84 +units=m +no_defs"
r.external input="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\ff682a87d4e341358eec94aa0e0179d9\B.sdat" band=1 output="rast_5b640d296aee516" --overwrite -o
r.external input="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\597d0f6b759947919cd4d5cd53bfc2b5\G.sdat" band=1 output="rast_5b640d296aee517" --overwrite -o
r.external input="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\33c61bf0bbb1409d9b79545684848d28\R.sdat" band=1 output="rast_5b640d296aee518" --overwrite -o
g.region n=800.0 s=0.0 e=1228.0 w=0.0 res=1.0
i.group group=group_5b640d296b69419 subgroup=subgroup_5b640d296b69420 input=rast_5b640d296aee516,rast_5b640d296aee517,rast_5b640d296aee518
MD C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\grassdata\temp_location\PERMANENT\group\group_5b640d296b69419\subgroup\subgroup_5b640d296b69420\sig
COPY /Y D:/DeepRiverscapes/Qtest_signatures_split.txt C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\grassdata\temp_location\PERMANENT\group\group_5b640d296b69419\subgroup\subgroup_5b640d296b69420\sig\Qtest_signatures_split.txt
i.maxlik signaturefile="Qtest_signatures_split.txt" group="group_5b640d296b69419" subgroup="subgroup_5b640d296b69420" output=output6b078ef4b4c4478fb568df68904c2d81 reject=reject6b078ef4b4c4478fb568df68904c2d81 --overwrite
g.region raster=output6b078ef4b4c4478fb568df68904c2d81
r.out.gdal -t -m input="output6b078ef4b4c4478fb568df68904c2d81" output="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\4b51fe8a7282498dbeec1b4398b973f9\output.tif" format="GTiff" createopt="TFW=YES,COMPRESS=LZW" --overwrite
g.region raster=reject6b078ef4b4c4478fb568df68904c2d81
r.out.gdal -t -m input="reject6b078ef4b4c4478fb568df68904c2d81" output="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\d9f1b86081ba42f194b0153ad8499cea\reject.tif" format="GTiff" createopt="TFW=YES,COMPRESS=LZW" --overwrite
Cleaning up temporary files...
Starting GRASS GIS...
WARNING: Concurrent mapset locking is not supported on Windows
Executing <C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\grassdata\grass_batch_job.cmd> ...

C:\PROGRA1\QGIS31.2\bin>chcp 1252 1>NUL

C:\PROGRA1\QGIS31.2\bin>g.proj -c proj4="+proj=utm +zone=31 +datum=WGS84 +units=m +no_defs"
Default region was updated to the new projection, but if you have multiple mapsets g.region -d should be run in each to update the region from the default
Projection information updated

C:\PROGRA1\QGIS31.2\bin>r.external input="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\ff682a87d4e341358eec94aa0e0179d9\B.sdat" band=1 output="rast_5b640d296aee516" --overwrite -o
Over-riding projection check
Reading band 1 of 1...
r.external complete. Link to raster map <rast_5b640d296aee516> created.

C:\PROGRA1\QGIS31.2\bin>r.external input="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\597d0f6b759947919cd4d5cd53bfc2b5\G.sdat" band=1 output="rast_5b640d296aee517" --overwrite -o
Over-riding projection check
Reading band 1 of 1...
r.external complete. Link to raster map <rast_5b640d296aee517> created.

C:\PROGRA1\QGIS31.2\bin>r.external input="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\33c61bf0bbb1409d9b79545684848d28\R.sdat" band=1 output="rast_5b640d296aee518" --overwrite -o
Over-riding projection check
Reading band 1 of 1...
r.external complete. Link to raster map <rast_5b640d296aee518> created.

C:\PROGRA1\QGIS31.2\bin>g.region n=800.0 s=0.0 e=1228.0 w=0.0 res=1.0

C:\PROGRA1\QGIS31.2\bin>i.group group=group_5b640d296b69419 subgroup=subgroup_5b640d296b69420 input=rast_5b640d296aee516,rast_5b640d296aee517,rast_5b640d296aee518
Adding raster map rast_5b640d296aee516@PERMANENT to group
Adding raster map rast_5b640d296aee517@PERMANENT to group
Adding raster map rast_5b640d296aee518@PERMANENT to group
Adding raster map rast_5b640d296aee516@PERMANENT to subgroup
Adding raster map rast_5b640d296aee517@PERMANENT to subgroup
Adding raster map rast_5b640d296aee518@PERMANENT to subgroup

C:\PROGRA1\QGIS31.2\bin>MD C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\grassdata\temp_location\PERMANENT\group\group_5b640d296b69419\subgroup\subgroup_5b640d296b69420\sig

C:\PROGRA1\QGIS31.2\bin>COPY /Y D:/DeepRiverscapes/Qtest_signatures_split.txt C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\grassdata\temp_location\PERMANENT\group\group_5b640d296b69419\subgroup\subgroup_5b640d296b69420\sig\Qtest_signatures_split.txt
The syntax of the command is incorrect.

C:\PROGRA1\QGIS31.2\bin>i.maxlik signaturefile="Qtest_signatures_split.txt" group="group_5b640d296b69419" subgroup="subgroup_5b640d296b69420" output=output6b078ef4b4c4478fb568df68904c2d81 reject=reject6b078ef4b4c4478fb568df68904c2d81 --overwrite
ERROR: Unable to open signature file <Qtest_signatures_split.txt>

C:\PROGRA1\QGIS31.2\bin>g.region raster=output6b078ef4b4c4478fb568df68904c2d81
ERROR: Raster map not found

C:\PROGRA1\QGIS31.2\bin>r.out.gdal -t -m input="output6b078ef4b4c4478fb568df68904c2d81" output="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\4b51fe8a7282498dbeec1b4398b973f9\output.tif" format="GTiff" createopt="TFW=YES,COMPRESS=LZW" --overwrite
ERROR: Raster map or group not found

C:\PROGRA1\QGIS31.2\bin>g.region raster=reject6b078ef4b4c4478fb568df68904c2d81
ERROR: Raster map not found

C:\PROGRA1\QGIS31.2\bin>r.out.gdal -t -m input="reject6b078ef4b4c4478fb568df68904c2d81" output="C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\d9f1b86081ba42f194b0153ad8499cea\reject.tif" format="GTiff" createopt="TFW=YES,COMPRESS=LZW" --overwrite
ERROR: Raster map or group not found

C:\PROGRA1\QGIS31.2\bin>exit
Execution of <C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\grassdata\grass_batch_job.cmd> finished.
Cleaning up temporary files...
Press any key to continue . . .
Execution completed in 2.35 seconds
Results:
{'output': <QgsProcessingOutputLayerDefinition {'sink':C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/4b51fe8a7282498dbeec1b4398b973f9/output.tif, 'createOptions': {'fileEncoding': 'System'}}>,
'reject': <QgsProcessingOutputLayerDefinition {'sink':C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/d9f1b86081ba42f194b0153ad8499cea/reject.tif, 'createOptions': {'fileEncoding': 'System'}}>}

Loading resulting layers
The following layers were not correctly generated.

• C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/4b51fe8a7282498dbeec1b4398b973f9/output.tif
• C:/Users/patca/AppData/Local/Temp/processing_7c97d6ddd9dd4aeb9964c897acb1336d/d9f1b86081ba42f194b0153ad8499cea/reject.tif

You can check the 'Log Messages Panel' in QGIS main window to find more information about the execution of the algorithm.

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• Qtest_signatures_split.txt (Patrice Carbonneau)
• Qtest_modified.aux.xml (Patrice Carbonneau)
• Qtest2_class.dbf (Patrice Carbonneau)
• Qtest2_class.shp (Patrice Carbonneau)
• Qtest2_class.shx (Patrice Carbonneau)
• Qtest2_class.prj (Patrice Carbonneau)
• Qtest2_class.qpj (Patrice Carbonneau)
• Qtest_Classes.dbf (Patrice Carbonneau)
• Qtest_modified (Patrice Carbonneau)

[qgib]

Author Name: Giovanni Manghi (@gioman)

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Does it work on QGIS LTR?

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• status_id was changed from Open to Feedback

[qgib]

Author Name: Nyall Dawson (@nyalldawson)

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The problem comes in the command:

COPY /Y D:/DeepRiverscapes/Qtest_signatures_split.txt C:\Users\patca\AppData\Local\Temp\processing_7c97d6ddd9dd4aeb9964c897acb1336d\grassdata\temp_location\PERMANENT\group\group_5b640d296b69419\subgroup\subgroup_5b640d296b69420\sig\Qtest_signatures_split.txt 

I suspect it's the unix style path with / which is tripping this up. Investigating now...

[qgib]

Author Name: sarah david (sarah david)

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[qgib]

Author Name: Patrice Carbonneau (Patrice Carbonneau)

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Giovanni Manghi wrote:

Does it work on QGIS LTR?

I don't know. Haven't got it installed. I use some new features in 3.2 quite a bit so would rather get 3.2 working.

[qgib]

Author Name: Giovanni Manghi (@gioman)

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Patrice Carbonneau wrote:

Giovanni Manghi wrote:

Does it work on QGIS LTR?

I don't know. Haven't got it installed. I use some new features in 3.2 quite a bit so would rather get 3.2 working.

but 3.* is NOT LTR yet, for important work people should still rely on the table version if QGIS.

[qgib]

Author Name: Nyall Dawson (@nyalldawson)

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Can you please share some small test data which I can use to create a unit test protecting this? (With a trial bug fix every raster I throw at it results in grass errors relating to the classification itself, not a processing error!).

[qgib]

Author Name: Patrice Carbonneau (Patrice Carbonneau)

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Ok, here is a test data set. I uploaded a vector in ESRI format and an image. These are the files I used to run i.gensig and (with the rsulting signature file, run i.maxlik.

Thanks

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• 13059 was configured as Qtest2_class.dbf
• 13058 was configured as Qtest_modified.aux.xml
• 13060 was configured as Qtest2_class.shp
• 13065 was configured as Qtest_modified
• 13064 was configured as Qtest_Classes.dbf
• 13063 was configured as Qtest2_class.qpj
• 13062 was configured as Qtest2_class.prj
• 13061 was configured as Qtest2_class.shx

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• Qtest2_class.dbf (Patrice Carbonneau)
• Qtest_modified.aux.xml (Patrice Carbonneau)
• Qtest2_class.shp (Patrice Carbonneau)
• Qtest_modified (Patrice Carbonneau)
• Qtest_Classes.dbf (Patrice Carbonneau)
• Qtest2_class.qpj (Patrice Carbonneau)
• Qtest2_class.prj (Patrice Carbonneau)
• Qtest2_class.shx (Patrice Carbonneau)

[qgib]

Author Name: Jürgen Fischer (@jef-n)

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• status_id was changed from Feedback to Open

[qgib]

Author Name: Alexander Bruy (@alexbruy)

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Already fixed.

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• resolution was changed from to fixed/implemented
• status_id was changed from Open to Closed