No module named '_gdal_array'

[pzuniga]

Dear Researchers,

In the "Process" frame, clicking "GET OUTPUTS" gives the message "No module named '_gdal_array'" and cannot "DISPLAY OUTPUTS".

Thanks you

kind regards

Pablo

[dfguerrerom]

@pzuniga, the problem is related to a gdal cached wheel being installed in our virtual environment, we are working to find a prompt solution. Thanks for reporting.

[dfguerrerom]

Some findings here:

• the reported error was related to the gdal installation in the biota UI venv:
  • biota package is using gdal.Open.ds.ReadAsArray()() method to open and return images as Numpy arrays (check https://github.com/OSGeo/gdal/tree/master/swig/python#numpy).
  • the array support is only installed by python gdal binding if Numpy is installed before, the installation will check if it is installed, if not, it will skip the array support.
  • there is no way to change the package installation order in this repo since SEPAL deals with this.
  • pip doesn't ensure that the installation order in requirements.txt is the same order as the packages are listed.
  • adding gdal[numpy] extra_require doesn't work in gdal==3.4.3. There is a patched version that does this https://github.com/OSGeo/gdal/issues/2158.

To give a prompt I've decided to modify our forked version of biota and use rasterio to open images and return the Numpy array, it's been done here https://github.com/dfguerrerom/biota/commit/64286f4f627082135d5445cddf257a16be082b9b.

[dfguerrerom]

@pzuniga I'm closing this since was fixed with https://github.com/dfguerrerom/biota/commit/64286f4f627082135d5445cddf257a16be082b9b.