Hi Pietr,

I understand. My images come from a hyperspectral camera, so there is no CRS (I do not know how to state an arbitrary euclidean space and maybe that would create other problems, so I use to define a fake utm CRS for display in QGIS). 
I cannot use your workaround regularly as the images are huge (that one was just an example). I will modify my scripts so that I work in envi format where it is easy to just edit the hdr file (have tried modifying the GTiff with gdal_edit.py but found lots of complications). 
The problem is for all the images I already have. I will keep doing the cropping in R whenever I need it (although croping in R is unbearably slow and pkcrop is fast). 
Thanks a lot for pktools!
(BTW, please think on https://savannah.nongnu.org/bugs/?56332)

I have a geotif raster with no projection that I display in QGIS stating epsg:25831. I then digitize a polygon in epsg: 25831
(see attached screenshot). 
I then run pkcrop: 
pkcrop -i testin2.tif -sband 1 -eband 4 -e test.shp -of "ENVI" -o test2out.raw 
which results on an ENVI raster file that is all 0 (same for any format) 

Same problem even for selecting bands: 
pkcrop -i testin2.tif -sband 1 -eband 3  -of GTiff -o test2out2.tif 
All 0

I've put the necessary input files here: 
https://www.dropbox.com/sh/xnhute0nnsvdpet/AAC1ZHzSgFOVN7QouL2XZhWda

Best,
Agus
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