Storing multiple GeoTiffs in HDF5 file in Python

Question

I want to store multiple GeoTiff files in one HDF5 file to use it for further analysis since the function I am supposed to use can just deal with HDF5 (so basically like a raster stack in R but stored in a HDF5). I have to use Python. I am relatively new to HDF5 format (and geoanalysis in Python generally) and don't really know how to approach this issue. Especially keeping the geolocation/projection inforation seems tricky to me. So far I tried:

import h5py
import rasterio

r1 = rasterio.open("filename.tif")
r2 = rasterio.open("filename2.tif")

with h5py.File('path/test.h5', 'w') as hdf:
    hdf.create_dataset('GeoTiff1', data=r1)
    hdf.create_dataset('GeoTiff2', data=r2)

Yielding the following errror:

TypeError: Object dtype dtype('O') has no native HDF5 equivalent

I am pretty sure this not at all the correct approach and I'm happy about any suggestions.

Answer 1

What you can try is to do this:

import numpy as np
spec_dtype = h5py.special_dtype(vlen=np.dtype('float64'))

Just make a spec_dtype variable with float64 type then apply this to create_dataset:

with h5py.File('path/test.h5', 'w') as hdf:
    hdf.create_dataset('GeoTiff1', data=r1,, dtype=spec_dtype)
    hdf.create_dataset('GeoTiff2', data=r2,, dtype=spec_dtype)

Apply these and hopefully it will work.

Answer 2

Using HDFql in Python, your use-case could be solved as follows:

import HDFql

HDFql.execute("SHOW FILE SIZE filename.tif, filename2.tif")

HDFql.cursor_next()

HDFql.execute("CREATE DATASET path/test.h5 GeoTiff1 AS OPAQUE(%d) VALUES FROM BINARY FILE filename.tif" % HDFql.cursor_get_bigint())

HDFql.cursor_next()

HDFql.execute("CREATE DATASET path/test.h5 GeoTiff2 AS OPAQUE(%d) VALUES FROM BINARY FILE filename2.tif" % HDFql.cursor_get_bigint())