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

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

Thank you for your message.
I am out of the office until Monday, August 5th.
I may not be able to reply (quickly) whilst away.

Best wishes,
Julie De Weirdt

Op 11 sep. 2019, om 15:57 heeft PyMca general purpose mailing list. <pym...@li...> het volgende geschreven:

Hi Armando,
Thanks for the reply and apologies for my delayed response. Please find attached an image file showing the structure of our HDF file. There are two datasets in each HDF5 file which they are fitted with the fast XRF stack fitting procedure. I didn't test yet but calling the PyMca module from the command line should work fine for my case. I believe I have to do an iterative procedure in python for instance for this purpose, right?
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


From:
PyMca general purpose mailing list. <pym...@li...>
Sent: Monday, September 9, 2019 11:31 AM
To: pym...@li... <pym...@li...>
Subject: Re: [PyMca] Batch fitting for HDF5 files in PyMca


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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