Using fabio to read detector H5 files other than Eiger (e.g. Lambda, etc)

[lorcat]

Hi!
I have tried recently to use fabio for an HDF5/NEXUS from an X-spectrum Lambda multi-module system.

Python 3.12.3
fabio 2024.4.0 py312ha90f08f_0 conda-forge

fabio.openimage.openimage("l1_test02_00002_master.nxs")
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\glazyrin.conda\envs\latest_fabio\Lib\site-packages\fabio\openimage.py", line 210, in openimage
obj = obj.read(obj.filename, frame)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\glazyrin.conda\envs\latest_fabio\Lib\site-packages\fabio\eigerimage.py", line 156, in read
raise NotGoodReader("HDF5 file does not contain an Eiger-like structure.")
fabio.fabioutils.NotGoodReader: HDF5 file does not contain an Eiger-like structure.

I am interested in using fabio in own code and as a part of DIOPTAS, including HDF5 VDS capability. Do you think it will be possible to add this detector structure to fabio?

The appended files are as follows:
l1_test02_00002_m0[1-3].nxs - correspond to individual modules
l1_test02_00002_master.nxs - The master file with VDS (Virtual Datasets)

lambda_detector.zip

[kif]

This should be possible if there are some headers which allow to distinguish those files from the one generated by lima or dectris.

[lorcat]

The structure of these NEXUS files is fairly simple and one can also check it via silx or else viewer.

Here are the pictures illustrating it for the individual module and the master file.

Hopefully there will be more multimodule lambdas around, I know about 9M with 12 modules under commissioning now. Having the capability with fabio would be great!

[kif]

There is the /entry/instrument/detector/description, but it will be fragile at best ...

[lorcat]

yes, it has the "Lambda" string. The master file and the modules files are different by absence of the ../module[0-9]+ branch

[kif]

@lorcat : Can you have a look the associated PR to check if it meets your needs ?

[lorcat]

Hi! PR=pull request. Sure, what should I do?

[kif]

Can you retrieve the PR and install it locally to validate the reading on your files

wget https://github.com/kif/fabio/archive/refs/heads/565_lambda.zip
unzip 565_lambda.zip
cd fabio-565_lambda
pip install .

and then check it is working for your files...

[lorcat]

Hi!

I have tried the master file and the individual module. So far works, thank you!

import fabio
fh = fabio.openimage.openimage("l1_test02_00002_master.nxs")
fh.data
array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]], dtype=int16)
fh.data.shape
(1813, 1555)

fh = fabio.openimage.openimage("l1_test02_00002_m01.nxs")
fh.data.shape
(516, 1554)
fh.data
array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]], dtype=int16)

[kif]

Well, those data are part of the non regression test ... I would expect them to work.
Maybe you can test on some other data with actual beam and sample to validate.

[lorcat]

Right, we will have a 2M lambda in 1 week. I will let you know then.
Many thanks!

[lorcat]

One thing to mention is that the master file and modules contain 5 frames.

The following code reports only one:

import fabio
fh = fabio.openimage.openimage("l1_test02_00002_master.nxs")
fh.data
array([[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
...,
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0],
[0, 0, 0, ..., 0, 0, 0]], dtype=int16)
fh.data.shape
(1813, 1555)

[kif]

That's the normal behaviour of fabio ... you can access to all frames: * either using the FabioImage as an iterator, * or using the getframe method to get access to the frame of your choice. This all comes from a time when there was no reason to put more then a single frame per file ... FabIO was started around 2006 !

[lorcat]

Hi! I have tested the library and it seem to work ok for now.
FABIO version: 15/03/2024

with fabio.openimage.openimage(filename) as data:
    for frame in (100,200,300):
        print(data.getframe(frame).shape, np.sum(data.getframe(frame).data))

[kif]

Thanks for the feed-back. The code has been merged.