Re: [PyMca] Batch fitting for HDF5 files in PyMca

[PyMca g. p. m. list. <pym...@li...>]

Hi Carlos,

I am not sure to have understood where is the difficulty.


If you have many files with each of them containing a stack and your
problem is to avoid to use the ROI imaging GUI, you just need to call
the appropriate PyMca module from the command line:


python -m PyMca5.PyMcaPhysics.xrf.FastXRFLinearFit
--cfg=configuration_file --weight=0 --tif=1 --concentrations=0 --refit=0
filename::dataset_path


What is the structure of your HDF5 files?


Armando


On 03/09/2019 22:33, PyMca general purpose mailing list. wrote:
> Hi pymca users,
> I have been using (for a quite long time) HDF5 files to store the
> micro-XRF dataset got from measurements collected in 2D scanning mode
> and I also use the "Fast XRF stack fitting" plugin to fit all XRF
> spectra since it is quite fast.
> As we are now saving many HDF5 files from one experiment and also in
> each of these files a new dataset is being stored related to a second
> detector, I am wondering if there is any possibility to have a batch
> fitting mode for HDF5 files but using the "Fast XRF stack fitting
> mode" option. Currently, If I use the PyMca batch fitting with many
> HDF5 files, the procedure is extremely slow, creating the *.dat file
> instead of creating the *.csv file.  
> Is there any kind of solution to this problem or another way to face it?.
> Thanks in advance,
> Sincerely,
> Carlos
>
>
>
> Carlos A. Pérez, Ph.D.
> Researcher - XRF Beamline Coordinator
> CARNAÚBA Group
> LNLS -Brazilian Synchrotron Light Source Laboratory
> http://www.lnls.br
> Phone: +55 (19) 3517-5081
> Mail address:
> Caixa Postal 6192
> CEP 13083-970
> Campinas-SP, Brazil
>
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