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.

Sarim Sikander · Accepted Answer · 2022-02-03 20:11:45Z

0

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.

answered Feb 3, 2022 at 20:11

Sarim Sikander

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1 Comment

Niklas1009 Over a year ago

Hey, thanks for the suggestion. When I implement that I get the follow error: AttributeError: 'DatasetReader' object has no attribute 'dtype' Which I think has something to do with the rasterio.open(). Any suggestions?

SOG · Accepted Answer · 2023-09-06 07:03:44Z

0

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

import HDFql

HDFql.execute("CREATE DATASET path/test.h5 GeoTiff1 VALUES FROM BINARY FILE filename.tif")

HDFql.execute("CREATE DATASET path/test.h5 GeoTiff2 VALUES FROM BINARY FILE filename2.tif")

edited Sep 6, 2023 at 7:03

answered Feb 3, 2022 at 20:26

SOG

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Comments

kcw78 · Accepted Answer · 2024-05-10 14:06:15Z

0

Quite old question, but the issue is that you're trying to save the file reference and not the actual data.

import h5py
import rasterio

with rasterio.open("filename.tif") as f:
    r1 = f.read()
with rasterio.open("filename2.tif") as f:
    r2 = f.read()

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

edited May 10, 2024 at 14:06

kcw78

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answered May 10, 2024 at 7:48

hyit

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