gdal_merge.bat Runtime Error. QGIS 3.4.3 Standalone Installers for 32 and 64 bit Windows systems

[gabrieldeluca]

On clean installs of the QGIS 3.4.3 Standallone Installers for 32 and 64 bit builds for Windows systems, the GDAL Merge tool produces images with only zero values in all pixels when the result is saved to a temporary file (if not, the merged file is well generated but the command output is the same).

Log:

Processing algorithm…
Algorithm 'Merge' starting…
Input parameters:
{ 'DATA_TYPE' : 5, 'INPUT' : ['D:/test/merge/S44E170.hgt','D:/test/merge/S44E171.hgt'], 'NODATA_INPUT' : None, 'NODATA_OUTPUT' : None, 'OPTIONS' : '', 'OUTPUT' : 'C:/Users/Gabriel/AppData/Local/Temp/processing_6e5c1804cb924bf882b2ccc82074d4cc/3b8fd4e987774e5fb55ea11a62d9420c/OUTPUT.tif', 'PCT' : False, 'SEPARATE' : False }

GDAL command:
cmd.exe /C gdal_merge.bat -ot Float32 -of GTiff -o C:/Users/Gabriel/AppData/Local/Temp/processing_6e5c1804cb924bf882b2ccc82074d4cc/3b8fd4e987774e5fb55ea11a62d9420c/OUTPUT.tif --optfile C:/Users/Gabriel/AppData/Local/Temp/processing_6e5c1804cb924bf882b2ccc82074d4cc\mergeInputFiles.txt
GDAL command output:
0RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa

Traceback (most recent call last):

File "C:\PROGRA~1\QGIS3~1.4\bin\gdal_merge.py", line 611, in <module>

sys.exit(main())

File "C:\PROGRA~1\QGIS3~1.4\bin\gdal_merge.py", line 596, in main

fi.copy_into(t_fh, band, band, nodata)

File "C:\PROGRA~1\QGIS3~1.4\bin\gdal_merge.py", line 343, in copy_into

nodata_arg)

File "C:\PROGRA~1\QGIS3~1.4\bin\gdal_merge.py", line 124, in raster_copy

m_band)

File "C:\PROGRA~1\QGIS3~1.4\bin\gdal_merge.py", line 180, in raster_copy_with_mask

t_xsize, t_ysize)

File "C:\PROGRA~1\QGIS3~1.4\apps\Python27\lib\site-packages\osgeo\gdal.py", line 2635, in ReadAsArray

from osgeo import gdalnumeric

File "C:\PROGRA~1\QGIS3~1.4\apps\Python27\lib\site-packages\osgeo\gdalnumeric.py", line 2, in <module>

from osgeo.gdal_array import *

File "C:\PROGRA~1\QGIS3~1.4\apps\Python27\lib\site-packages\osgeo\gdal_array.py", line 17, in <module>

_gdal_array = swig_import_helper()

File "C:\PROGRA~1\QGIS3~1.4\apps\Python27\lib\site-packages\osgeo\gdal_array.py", line 16, in swig_import_helper

return importlib.import_module('_gdal_array')

File "C:\PROGRA~1\QGIS3~1.4\apps\Python27\lib\importlib\__init__.py", line 37, in import_module

__import__(name)

ImportError: No module named _gdal_array

Execution completed in 1.81 seconds
Results:
{'OUTPUT': <QgsProcessingOutputLayerDefinition {'sink':C:/Users/Gabriel/AppData/Local/Temp/processing_6e5c1804cb924bf882b2ccc82074d4cc/3b8fd4e987774e5fb55ea11a62d9420c/OUTPUT.tif, 'createOptions': {'fileEncoding': 'System'}}>}

Loading resulting layers
Algorithm 'Merge' finished

---

Manually solved from the OSGeo4W.bat (as Administrator) shell:

C:\Windows\System32>python -m pip install -U numpy
Collecting numpy
  Using cached https://files.pythonhosted.org/packages/74/a4/1bae5948ac37ee6769ffdf01fef3e1c731981574d4d416e2876070441688/numpy-1.15.4-cp27-none-win_amd64.whl
Installing collected packages: numpy
  Found existing installation: numpy 1.12.1+mkl
    Uninstalling numpy-1.12.1+mkl:
      Successfully uninstalled numpy-1.12.1+mkl
Successfully installed numpy-1.15.4

After that, Merge tool works fine and without error logs.

---

Tested with the builds:

​http://download.osgeo.org/qgis/windows/QGIS-OSGeo4W-3.4.3-1-Setup-x86.exe

​http://download.osgeo.org/qgis/windows/QGIS-OSGeo4W-3.4.3-1-Setup-x86_64.exe

in Windows 7 and Windows 10, with the following data:

​https://dds.cr.usgs.gov/srtm/version2_1/SRTM3/Islands/S44E170.hgt.zip

​https://dds.cr.usgs.gov/srtm/version2_1/SRTM3/Islands/S44E171.hgt.zip

---

Reports found: ​SE Getting black square after merging two rasters in QGIS

​QGIS #20835

[gabrieldeluca]

Erratum:

• Wehere it says "Standallone", it should be read "Standalone".
• The correct link to the original question in GIS Stack Exchange is: ​https://gis.stackexchange.com/questions/307195/getting-black-square-after-merging-two-rasters-in-qgis

[vesnikos]

This also affects the normal execution of any gdal/python (i.e gdal_calc) from the osgeo console.

Installing previous versions of numpy from the console doesn't solve the problem.

[Andreas Müller]

I have the same error now with python-numpy 2.7-1.7.0-1 and gdal 2.4.1-1. QGIS is 3.4.9 and 3.8.0, 32 bit

EDIT: Today, tested with 3.4.10, still does not work. Some processing tools fail too.

[Andreas Müller]

See my comment above...