Empty raster at selection step

[MathieuChailloux]

Occurrs even if selection is not empty

[nussano24]

Hi,

I've run into a problem regarding rasters produced in the selection phase, but I'm not sure it's the same problem you encountered.
During selection phase, the vector layer is created correctly. After the rasterize step, the raster produced seemed empty, with the scale in the symbology panel indicating values ranging from -32 768 to 32 767. An error is shown in the plug-in logs :

[info] Calling processing algorithm 'gdal:rasterize'
[2025-05-16 10:21:40] [info] GDAL command:
[2025-05-16 10:21:40] [info] GDAL command output:
[2025-05-16 10:21:45] [internal error] Process returned error code 1
[2025-05-16 10:21:45] [Unexpected error] : Process returned error code 1
[2025-05-16 10:21:46] [info] Results: {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_raster.tif'}
[2025-05-16 10:21:46] [info] Call to rasterize successful, performed in 6.223242998123169 seconds

Seeing the call to rasterize sucessfull, I was thinking of a symbology problem and that values where corect in the raster, I continued with the merge step, that either return once again an empty raster, or crash QGIS with an access violation error.
The logs when it returns an empty raster :

[info] Calling processing algorithm 'gdal:merge'
[2025-05-16 10:36:24] [info] GDAL command:
[2025-05-16 10:36:24] [info] GDAL command output:
[2025-05-16 10:36:26] [internal error] Traceback (most recent call last): File "C:\OSGeo4W\apps\Python312\Scripts\gdal_merge.py", line 12, in
[2025-05-16 10:36:26] [internal error] sys.exit(main(sys.argv)) ^^^^^^^^^^^^^^ File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo_utils\gdal_merge.py", line 657, in main return gdal_merge(argv) ^^^^^^^^^^^^^^^^ File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo_utils\gdal_merge.py", line 397, in gdal_merge return _gdal_merge(argv=argv) ^^^^^^^^^^^^^^^^^^^^^^ File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo_utils\gdal_merge.py", line 642, in _gdal_merge fi.copy_into(t_fh, band, band, nodata, verbose) File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo_utils\gdal_merge.py", line 348, in copy_into return raster_copy( ^^^^^^^^^^^^ File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo_utils\gdal_merge.py", line 95, in raster_copy return raster_copy_with_mask( ^^^^^^^^^^^^^^^^^^^^^^ File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo_utils\gdal_merge.py", line 187, in raster_copy_with_mask data_dst = t_band.ReadAsArray(t_xoff, t_yoff, t_xsize, t_ysize) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo\gdal.py", line 8265, in ReadAsArray
[2025-05-16 10:36:26] [internal error] return gdal_array.BandReadAsArray(self, xoff, yoff, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo\gdal_array.py", line 636, in BandReadAsArray
[2025-05-16 10:36:26] [internal error] _RaiseException() File "C:\OSGeo4W\apps\Python312\Lib\site-packages\osgeo\gdal_array.py", line 347, in _RaiseException
[2025-05-16 10:36:26] [internal error] raise RuntimeError(gdal.GetLastErrorMsg()) RuntimeError
[2025-05-16 10:36:26] [internal error] Process returned error code 1
[2025-05-16 10:36:26] [info] Results: {'OUTPUT': 'C:/.../workfolder/Subnetworks/Blanche/Blanche_merged.tif'}
[2025-05-16 10:36:26] [info] Call to merge successful, performed in 2.5725700855255127 seconds

The crash report :

Windows fatal exception: access violation

Current thread 0x00000f4c (most recent call first):
File "C:\Users/user/AppData/Roaming/QGIS/QGIS3\profiles\Debug biodisp/python/plugins\BioDispersal\qgis_lib_mc\feedbacks.py", line 205 in setProgressText
QGuiApplication.processEvents()
File "C:\Users/user/AppData/Roaming/QGIS/QGIS3\profiles\Debug biodisp/python/plugins\BioDispersal\qgis_lib_mc\feedbacks.py", line 197 in setSubText
self.setProgressText(txt)
File "C:\Users/user/AppData/Roaming/QGIS/QGIS3\profiles\Debug biodisp/python/plugins\BioDispersal\qgis_lib_mc\feedbacks.py", line 187 in endSection
self.setSubText("DONE")
File "C:\Users/user/AppData/Roaming/QGIS/QGIS3\profiles\Debug biodisp/python/plugins\BioDispersal\steps\fusion.py", line 172 in applyItemsWithContext
feedback.endSection()
File "C:\Users/user/AppData/Roaming/QGIS/QGIS3\profiles\Debug biodisp/python/plugins\BioDispersal\qgis_lib_mc\abstract_model.py", line 1236 in applyItems
self.model.applyItemsWithContext(None,self.dlg.feedback,indexes)
File "C:\Users/user/AppData/Roaming/QGIS/QGIS3\profiles\Debug biodisp/python/plugins\BioDispersal\BioDispersal.py", line 253 in run
result = dlg.exec_()

Due to the crashes, I have not yet tested if the next steps present problems or not.

Info on my installation of QGIS :

QGIS Info
QGIS Version: 3.40.4-Bratislava
QGIS code revision: 4dd7d7e969
Compiled against Qt: 5.15.13
Running against Qt: 5.15.13
Compiled against GDAL: 3.10.2
Running against GDAL: 3.10.2

The entire process run smoothly on QGIS version 3.34.13 (GDAL version 3.9.3)

[MathieuChailloux]

BioDispersal.zip

Can you try to re-install BioDispersal from attached zip ?
Someone reported a similar error, if this fix works for you I will publish this version.

Regards,
Mathieu

[nussano24]

Hi,
It does not seem to fix the issue. The selection step and the fusion steps still show the same errors and the crash is still happening.
Do you need additionnal information ?
Have a great day

[MathieuChailloux]

Can you show me the rasterize options used ?
You can copy the whole log panel with debug mode activated.

[nussano24]

The rasterized options are as follows :

parameters : {'ALL_TOUCH': True, 'BURN': None, 'DATA_TYPE': 1, 'EXTENT': '408736.5250931235,455877.9001571437,6687818.600247109,6740000.041378646[EPSG:2154]', 'FIELD': 'Code', 'HEIGHT': 10.0, 'INPUT': 'C:/.../workfolder/Groups/zh/zh_vector.shp', 'NODATA': '-9999', 'OPTIONS': 'BIGTIFF=IF_SAFER|COMPRESS=LZW|NUM_THREADS=ALL_CPUS', 'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_raster.tif', 'UNITS': 1, 'WIDTH': 10.0, 'EXTRA': '-at'}

Here are the logs when the selection step is launched :

[2025-05-21 11:05:23] [info] ******** BEGIN : Selection
[2025-05-21 11:05:23] [debug] extent_path = C:....\workfolder\Données\Site\Site_tampon_15km.shp
[2025-05-21 11:05:23] [debug] mode_val
[2025-05-21 11:05:23] [debug] parameters : {'INPUT': 'C:\....\workfolder\Données\ZH\Zones_humides_fus.shp', 'EXPR': '', 'CLASS': 'zh', 'CODE': 51, 'OUTPUT': 'C:/Users/user/AppData/Local/Temp/processing_EmHpsr/1e420943360f489aaaadd8d0b5e0e81d/selected.gpkg'}
[2025-05-21 11:05:23] [info] Calling processing algorithm 'BioDispersal:selectvexpr'
[2025-05-21 11:05:23] [debug] complete_name = BioDispersal:selectvexpr
[2025-05-21 11:05:23] [debug] feedback = ProgressMultiStepFeedback
[2025-05-21 11:05:23] [debug] input =
[2025-05-21 11:05:23] [debug] encoding 1 = UTF-8
[2025-05-21 11:05:23] [debug] extension = .shp
[2025-05-21 11:05:23] [debug] system = Windows
[2025-05-21 11:05:23] [debug] encoding 2 = windows-1252
[2025-05-21 11:05:23] [debug] Expression =
[2025-05-21 11:05:29] [info] Résultats: {'OUTPUT': 'C:/Users/user/AppData/Local/Temp/processing_EmHpsr/1e420943360f489aaaadd8d0b5e0e81d/selected.gpkg'}
[2025-05-21 11:05:29] [debug] res1 = {'OUTPUT': 'C:/Users/user/AppData/Local/Temp/processing_EmHpsr/1e420943360f489aaaadd8d0b5e0e81d/selected.gpkg'}
[2025-05-21 11:05:29] [info] Call to selectvexpr successful, performed in 6.144959926605225 seconds
[2025-05-21 11:05:29] [debug] res = {'OUTPUT': 'C:/Users/user/AppData/Local/Temp/processing_EmHpsr/1e420943360f489aaaadd8d0b5e0e81d/selected.gpkg'}
[2025-05-21 11:05:29] [debug] output = C:/Users/user/AppData/Local/Temp/processing_EmHpsr/1e420943360f489aaaadd8d0b5e0e81d/selected.gpkg
[2025-05-21 11:05:29] [debug] output type =
[2025-05-21 11:05:29] [debug] End run selectvexpr
[2025-05-21 11:05:29] [debug] parameters : {'INPUT': 'C:/Users/user/AppData/Local/Temp/processing_EmHpsr/1e420943360f489aaaadd8d0b5e0e81d/selected.gpkg', 'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_vector.shp', 'TARGET_CRS': }
[2025-05-21 11:05:29] [info] Calling processing algorithm 'native:reprojectlayer'
[2025-05-21 11:05:29] [debug] complete_name = native:reprojectlayer
[2025-05-21 11:05:29] [debug] feedback = ProgressMultiStepFeedback
[2025-05-21 11:05:34] [info] Résultats: {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_vector.shp'}
[2025-05-21 11:05:34] [debug] res1 = {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_vector.shp'}
[2025-05-21 11:05:34] [info] Call to reprojectlayer successful, performed in 4.602636814117432 seconds
[2025-05-21 11:05:34] [debug] res = {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_vector.shp'}
[2025-05-21 11:05:34] [debug] output = C:/.../workfolder/Groups/zh/zh_vector.shp
[2025-05-21 11:05:34] [debug] output type =
[2025-05-21 11:05:34] [debug] End run reprojectlayer
[2025-05-21 11:05:34] [debug] parameters : {'ALL_TOUCH': True, 'BURN': None, 'DATA_TYPE': 1, 'EXTENT': '408736.5250931235,455877.9001571437,6687818.600247109,6740000.041378646[EPSG:2154]', 'FIELD': 'Code', 'HEIGHT': 10.0, 'INPUT': 'C:/.../workfolder/Groups/zh/zh_vector.shp', 'NODATA': '-9999', 'OPTIONS': 'BIGTIFF=IF_SAFER|COMPRESS=LZW|NUM_THREADS=ALL_CPUS', 'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_raster.tif', 'UNITS': 1, 'WIDTH': 10.0, 'EXTRA': '-at'}
[2025-05-21 11:05:34] [info] Calling processing algorithm 'gdal:rasterize'
[2025-05-21 11:05:34] [debug] complete_name = gdal:rasterize
[2025-05-21 11:05:34] [debug] feedback = ProgressMultiStepFeedback
[2025-05-21 11:05:34] [info] Commande GDAL :
[2025-05-21 11:05:34] [debug] gdal_rasterize -l zh_vector -a Code -tr 10.0 10.0 -a_nodata -9999.0 -te 408736.5250931235 6687818.600247109 455877.9001571437 6740000.041378646 -ot Int16 -of GTiff -co BIGTIFF=IF_SAFER -co COMPRESS=LZW -co NUM_THREADS=ALL_CPUS -at C:/.../workfolder/Groups/zh/zh_vector.shp C:/.../workfolder/Groups/zh/zh_raster.tif
[2025-05-21 11:05:34] [info] Sortie de commande GDAL :
[2025-05-21 11:05:36] [internal error] Le processus a renvoyé le code erreur 1
[2025-05-21 11:05:36] [debug] pluginExcHook
[2025-05-21 11:05:36] [debug] Ignoring custom exception : Le processus a renvoyé le code erreur 1
[2025-05-21 11:05:36] [debug] [loadNTab] 7
[2025-05-21 11:05:36] [debug] Help file = C:\Users/user/AppData/Roaming/QGIS/QGIS3\profiles\Debug biodisp/python/plugins\BioDispersal\help\logHelp-fr.html
[2025-05-21 11:05:36] [debug] path = C:\Users\user\AppData\Roaming\QGIS\QGIS3\profiles\Debug biodisp\python\plugins\BioDispersal\help\logHelp-fr.html
[2025-05-21 11:05:36] [debug] pathparts = ('C:\', 'Users', 'user', 'AppData', 'Roaming', 'QGIS', 'QGIS3', 'profiles', 'Debug biodisp', 'python', 'plugins', 'BioDispersal', 'help', 'logHelp-fr.html')
[2025-05-21 11:05:36] [debug] focusLogTab 28179
[2025-05-21 11:05:36] [info] Résultats: {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_raster.tif'}
[2025-05-21 11:05:36] [debug] res1 = {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_raster.tif'}
[2025-05-21 11:05:36] [info] Call to rasterize successful, performed in 2.437906503677368 seconds
[2025-05-21 11:05:36] [debug] res = {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh_raster.tif'}
[2025-05-21 11:05:36] [debug] output = C:/.../workfolder/Groups/zh/zh_raster.tif
[2025-05-21 11:05:36] [debug] output type =
[2025-05-21 11:05:36] [debug] End run rasterize
[2025-05-21 11:05:36] [debug] extentLayerType = Vector
[2025-05-21 11:05:36] [debug] parameters : {'ALPHA_BAND': False, 'CROP_TO_CUTLINE': True, 'DATA_TYPE': 0, 'INPUT': 'C:/.../workfolder/Groups/zh/zh_raster.tif', 'KEEP_RESOLUTION': False, 'MASK': 'C:\...\workfolder\Données\Site\Site_tampon_15km.shp', 'NODATA': '-9999', 'OPTIONS': 'BIGTIFF=IF_SAFER|COMPRESS=LZW|NUM_THREADS=ALL_CPUS', 'OUTPUT': 'C:/.../workfolder/Groups/zh/zh.tif', 'SET_RESOLUTION': True, 'X_RESOLUTION': 10.0, 'Y_RESOLUTION': 10.0}
[2025-05-21 11:05:36] [info] Calling processing algorithm 'gdal:cliprasterbymasklayer'
[2025-05-21 11:05:36] [debug] complete_name = gdal:cliprasterbymasklayer
[2025-05-21 11:05:36] [debug] feedback = ProgressMultiStepFeedback
[2025-05-21 11:05:37] [info] Commande GDAL :
[2025-05-21 11:05:37] [debug] gdalwarp -overwrite -of GTiff -tr 10.0 10.0 -tap -cutline C:...\workfolder\Données\Site\Site_tampon_15km.shp -cl Site_tampon_15km -crop_to_cutline -dstnodata -9999.0 -co BIGTIFF=IF_SAFER -co COMPRESS=LZW -co NUM_THREADS=ALL_CPUS C:/.../workfolder/Groups/zh/zh_raster.tif C:/.../workfolder/Groups/zh/zh.tif
[2025-05-21 11:05:37] [info] Sortie de commande GDAL :
[2025-05-21 11:05:38] [debug] Creating output file that is 4715P x 5220L. Using internal nodata values (e.g. -9999) for image C:/.../workfolder/Groups/zh/zh_raster.tif. Processing C:/.../workfolder/Groups/zh/zh_raster.tif [1/1] : 0...10...20...30...40...50...60...70...80...90...100 - done.
[2025-05-21 11:05:38] [info] Processus terminé avec succès.
[2025-05-21 11:05:38] [info] Résultats: {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh.tif'}
[2025-05-21 11:05:38] [debug] res1 = {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh.tif'}
[2025-05-21 11:05:38] [info] Call to cliprasterbymasklayer successful, performed in 1.853100299835205 seconds
[2025-05-21 11:05:38] [debug] res = {'OUTPUT': 'C:/.../workfolder/Groups/zh/zh.tif'}
[2025-05-21 11:05:38] [debug] output = C:/.../workfolder/Groups/zh/zh.tif
[2025-05-21 11:05:38] [debug] output type =
[2025-05-21 11:05:38] [debug] End run cliprasterbymasklayer
[2025-05-21 11:05:38] [info] ******** END : Selection in 15.609335899353027 seconds

Hope this helps,

[MathieuChailloux]

This should have been fixed by previous zip.
What is your installed BioDispersal versions ?
If version is 1.3 and not 1.3.1 please try to reinstall BioDispersal from zip file above, otherwise I will resend you a version.

Regards,
Mathieu

[nussano24]

I tried again this morning and it's working. I must have done the previous test on the wrong version without the fix. The merging step seems to run smoothly too. Thanks a lot for the help and sorry for the confusion.
Have a great rest of your day !