pymca-users

[PyMca] Batch fitting with BCF

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

Hello (Hola), Armando:
I am a recent user of PyMCA and I am still trying to get the most out of my spectra...
I've managed to adjust the spectra well, but now I need to obtain good quality images, preferably in TIFF format. Unfortunately, I can't get the batch adjustment tool to work and I don't know why. What I get are empty files. My input data is .BCF (Bruker's native format for MA-XRF): do I need to transform my data in some way beforehand?
Thank you so much in advance!
Maite Jover de Celis
Laboratorio de Análisis (Área de Restauración)
Museo Nacional del Prado
Ruiz de Alarcón 23, 28014 Madrid
Tfno +34 913302389, interno 289245

Re: [PyMca] Batch fitting with BCF

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

Dear Maite,

Please, can you specify what version of PyMca you are using, what 
operating system and from where you obtained the program?

I do not exclude errors at the PyMca side, but the support of BCF files 
is relatively recent and it is not available by default on source 
installations.

Best regards,

Armando

On 03/12/2025 15:06, PyMca general purpose mailing list. via PyMca-users 
wrote:
>
> Hello (Hola), Armando:
>
> I am a recent user of PyMCA and I am still trying to get the most out 
> of my spectra...
>
> I've managed to adjust the spectra well, but now I need to obtain good 
> quality images, preferably in TIFF format. Unfortunately, I can't get 
> the batch adjustment tool to work and I don't know why. What I get are 
> empty files. My input data is .BCF (Bruker's native format for 
> MA-XRF): do I need to transform my data in some way beforehand?
>
> Thank you so much in advance!
>
> Maite Jover de Celis
>
>
>
>
> _______________________________________________
> PyMca-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymca-users

Re: [PyMca] Batch fitting with BCF

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

Dear Armando,
I am using PyMCA 5.9.4  version for windows 11. I downloaded it from Sourceforge.net about one month ago.
As far as I know, other tools seem to work properly, although I have had some other issues with images (for instance, elements with low count rates show very poor definition with Fast fitting linear fit, in TIFF format images, but this can be my inexperience’s fault. In the case of Batch fitting, it just does not work with my data.
Thank you again,
Maite

De: PyMca general purpose mailing list. <pym...@li...>
Enviado el: miércoles, 3 de diciembre de 2025 15:44
Para: pym...@li...
Asunto: Re: [PyMca] Batch fitting with BCF


Dear Maite,

Please, can you specify what version of PyMca you are using, what operating system and from where you obtained the program?

I do not exclude errors at the PyMca side, but the support of BCF files is relatively recent and it is not available by default on source installations.

Best regards,

Armando
On 03/12/2025 15:06, PyMca general purpose mailing list. via PyMca-users wrote:
Hello (Hola), Armando:
I am a recent user of PyMCA and I am still trying to get the most out of my spectra...
I've managed to adjust the spectra well, but now I need to obtain good quality images, preferably in TIFF format. Unfortunately, I can't get the batch adjustment tool to work and I don't know why. What I get are empty files. My input data is .BCF (Bruker's native format for MA-XRF): do I need to transform my data in some way beforehand?
Thank you so much in advance!
Maite Jover de Celis






_______________________________________________

PyMca-users mailing list

PyM...@li...<mailto:PyM...@li...>

https://lists.sourceforge.net/lists/listinfo/pymca-users

Re: [PyMca] Batch fitting with BCF

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

Dear Maite,

Please replace the McaAdvancedFitBatch.py file in your installation with 
the attached one.

If you used the default installation path it should be located into the 
directory:

C:\Program Files\PyMca 5.9.4\lib\PyMca5\PyMcaPhysics\xrf

Please, let us know if that solves the issue.

Best regards,

Armando

On 03/12/2025 17:31, PyMca general purpose mailing list. via PyMca-users 
wrote:
>
> Dear Armando,
>
> I am using PyMCA 5.9.4  version for windows 11. I downloaded it from 
> Sourceforge.net about one month ago.
>
> As far as I know, other tools seem to work properly, although I have 
> had some other issues with images (for instance, elements with low 
> count rates show very poor definition with Fast fitting linear fit, in 
> TIFF format images, but this can be my inexperience’s fault. In the 
> case of Batch fitting, it just does not work with my data.
>
> Thank you again,
>
> Maite
>
> *De:*PyMca general purpose mailing list. 
> <pym...@li...>
> *Enviado el:* miércoles, 3 de diciembre de 2025 15:44
> *Para:* pym...@li...
> *Asunto:* Re: [PyMca] Batch fitting with BCF
>
> Dear Maite,
>
> Please, can you specify what version of PyMca you are using, what 
> operating system and from where you obtained the program?
>
> I do not exclude errors at the PyMca side, but the support of BCF 
> files is relatively recent and it is not available by default on 
> source installations.
>
> Best regards,
>
> Armando
>
> On 03/12/2025 15:06, PyMca general purpose mailing list. via 
> PyMca-users wrote:
>
>     Hello (Hola), Armando:
>
>     I am a recent user of PyMCA and I am still trying to get the most
>     out of my spectra...
>
>     I've managed to adjust the spectra well, but now I need to obtain
>     good quality images, preferably in TIFF format. Unfortunately, I
>     can't get the batch adjustment tool to work and I don't know why.
>     What I get are empty files. My input data is .BCF (Bruker's native
>     format for MA-XRF): do I need to transform my data in some way
>     beforehand?
>
>     Thank you so much in advance!
>
>     Maite Jover de Celis
>
>
>
>
>     _______________________________________________
>
>     PyMca-users mailing list
>
>     PyM...@li...
>
>     https://lists.sourceforge.net/lists/listinfo/pymca-users
>
>
>
> _______________________________________________
> PyMca-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymca-users

Re: [PyMca] Batch fitting with BCF

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

Thank you Armando, but my firewall blocked the file so I cannot download it. May you please contact me directly to my mail so I can send you an alternative mail address?
(My apologies about that!)
Thank you again
Maite

De: PyMca general purpose mailing list. <pym...@li...>
Enviado el: miércoles, 3 de diciembre de 2025 18:11
Para: pym...@li...
Asunto: Re: [PyMca] Batch fitting with BCF


Dear Maite,

Please replace the McaAdvancedFitBatch.py file in your installation with the attached one.

If you used the default installation path it should be located into the directory:

C:\Program Files\PyMca 5.9.4\lib\PyMca5\PyMcaPhysics\xrf

Please, let us know if that solves the issue.

Best regards,

Armando
On 03/12/2025 17:31, PyMca general purpose mailing list. via PyMca-users wrote:
Dear Armando,
I am using PyMCA 5.9.4  version for windows 11. I downloaded it from Sourceforge.net about one month ago.
As far as I know, other tools seem to work properly, although I have had some other issues with images (for instance, elements with low count rates show very poor definition with Fast fitting linear fit, in TIFF format images, but this can be my inexperience’s fault. In the case of Batch fitting, it just does not work with my data.
Thank you again,
Maite

De: PyMca general purpose mailing list. <pym...@li...><mailto:pym...@li...>
Enviado el: miércoles, 3 de diciembre de 2025 15:44
Para: pym...@li...<mailto:pym...@li...>
Asunto: Re: [PyMca] Batch fitting with BCF


Dear Maite,

Please, can you specify what version of PyMca you are using, what operating system and from where you obtained the program?

I do not exclude errors at the PyMca side, but the support of BCF files is relatively recent and it is not available by default on source installations.

Best regards,

Armando
On 03/12/2025 15:06, PyMca general purpose mailing list. via PyMca-users wrote:
Hello (Hola), Armando:
I am a recent user of PyMCA and I am still trying to get the most out of my spectra...
I've managed to adjust the spectra well, but now I need to obtain good quality images, preferably in TIFF format. Unfortunately, I can't get the batch adjustment tool to work and I don't know why. What I get are empty files. My input data is .BCF (Bruker's native format for MA-XRF): do I need to transform my data in some way beforehand?
Thank you so much in advance!
Maite Jover de Celis







_______________________________________________

PyMca-users mailing list

PyM...@li...<mailto:PyM...@li...>

https://lists.sourceforge.net/lists/listinfo/pymca-users




_______________________________________________

PyMca-users mailing list

PyM...@li...<mailto:PyM...@li...>

https://lists.sourceforge.net/lists/listinfo/pymca-users

Re: [PyMca] Batch fitting with BCF

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

Please try to download it directly from the mailing list to see if it works:

https://sourceforge.net/p/pymca/mailman/message/59268275/

Just click on the file name:

On 03/12/2025 18:20, PyMca general purpose mailing list. via PyMca-users 
wrote:
>
> Thank you Armando, but my firewall blocked the file so I cannot 
> download it. May you please contact me directly to my mail so I can 
> send you an alternative mail address?
>
> (My apologies about that!)
>
> Thank you again
>
> Maite
>
> *De:*PyMca general purpose mailing list. 
> <pym...@li...>
> *Enviado el:* miércoles, 3 de diciembre de 2025 18:11
> *Para:* pym...@li...
> *Asunto:* Re: [PyMca] Batch fitting with BCF
>
> Dear Maite,
>
> Please replace the McaAdvancedFitBatch.py file in your installation 
> with the attached one.
>
> If you used the default installation path it should be located into 
> the directory:
>
> C:\Program Files\PyMca 5.9.4\lib\PyMca5\PyMcaPhysics\xrf
>
> Please, let us know if that solves the issue.
>
> Best regards,
>
> Armando
>
> On 03/12/2025 17:31, PyMca general purpose mailing list. via 
> PyMca-users wrote:
>
>     Dear Armando,
>
>     I am using PyMCA 5.9.4  version for windows 11. I downloaded it
>     from Sourceforge.net about one month ago.
>
>     As far as I know, other tools seem to work properly, although I
>     have had some other issues with images (for instance, elements
>     with low count rates show very poor definition with Fast fitting
>     linear fit, in TIFF format images, but this can be my
>     inexperience’s fault. In the case of Batch fitting, it just does
>     not work with my data.
>
>     Thank you again,
>
>     Maite
>
>     *De:*PyMca general purpose mailing list.
>     <pym...@li...>
>     <mailto:pym...@li...>
>     *Enviado el:* miércoles, 3 de diciembre de 2025 15:44
>     *Para:* pym...@li...
>     *Asunto:* Re: [PyMca] Batch fitting with BCF
>
>     Dear Maite,
>
>     Please, can you specify what version of PyMca you are using, what
>     operating system and from where you obtained the program?
>
>     I do not exclude errors at the PyMca side, but the support of BCF
>     files is relatively recent and it is not available by default on
>     source installations.
>
>     Best regards,
>
>     Armando
>
>     On 03/12/2025 15:06, PyMca general purpose mailing list. via
>     PyMca-users wrote:
>
>         Hello (Hola), Armando:
>
>         I am a recent user of PyMCA and I am still trying to get the
>         most out of my spectra...
>
>         I've managed to adjust the spectra well, but now I need to
>         obtain good quality images, preferably in TIFF format.
>         Unfortunately, I can't get the batch adjustment tool to work
>         and I don't know why. What I get are empty files. My input
>         data is .BCF (Bruker's native format for MA-XRF): do I need to
>         transform my data in some way beforehand?
>
>         Thank you so much in advance!
>
>         Maite Jover de Celis
>
>
>
>
>
>         _______________________________________________
>
>         PyMca-users mailing list
>
>         PyM...@li...
>
>         https://lists.sourceforge.net/lists/listinfo/pymca-users
>
>
>
>
>     _______________________________________________
>
>     PyMca-users mailing list
>
>     PyM...@li...
>
>     https://lists.sourceforge.net/lists/listinfo/pymca-users
>
>
>
> _______________________________________________
> PyMca-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymca-users

Re: [PyMca] Batch fitting with BCF

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

Thank you Armando, I followed your instructions and now I can perform Batch fitting perfectly!

De: PyMca general purpose mailing list. <pym...@li...>
Enviado el: miércoles, 3 de diciembre de 2025 19:09
Para: pym...@li...
Asunto: Re: [PyMca] Batch fitting with BCF


Please try to download it directly from the mailing list to see if it works:

https://sourceforge.net/p/pymca/mailman/message/59268275/

Just click on the file name:

[cid:image001.png@01DC65D3.9EF4F230]
On 03/12/2025 18:20, PyMca general purpose mailing list. via PyMca-users wrote:
Thank you Armando, but my firewall blocked the file so I cannot download it. May you please contact me directly to my mail so I can send you an alternative mail address?
(My apologies about that!)
Thank you again
Maite

De: PyMca general purpose mailing list. <pym...@li...><mailto:pym...@li...>
Enviado el: miércoles, 3 de diciembre de 2025 18:11
Para: pym...@li...<mailto:pym...@li...>
Asunto: Re: [PyMca] Batch fitting with BCF


Dear Maite,

Please replace the McaAdvancedFitBatch.py file in your installation with the attached one.

If you used the default installation path it should be located into the directory:

C:\Program Files\PyMca 5.9.4\lib\PyMca5\PyMcaPhysics\xrf

Please, let us know if that solves the issue.

Best regards,

Armando
On 03/12/2025 17:31, PyMca general purpose mailing list. via PyMca-users wrote:
Dear Armando,
I am using PyMCA 5.9.4  version for windows 11. I downloaded it from Sourceforge.net about one month ago.
As far as I know, other tools seem to work properly, although I have had some other issues with images (for instance, elements with low count rates show very poor definition with Fast fitting linear fit, in TIFF format images, but this can be my inexperience’s fault. In the case of Batch fitting, it just does not work with my data.
Thank you again,
Maite

De: PyMca general purpose mailing list. <pym...@li...><mailto:pym...@li...>
Enviado el: miércoles, 3 de diciembre de 2025 15:44
Para: pym...@li...<mailto:pym...@li...>
Asunto: Re: [PyMca] Batch fitting with BCF


Dear Maite,

Please, can you specify what version of PyMca you are using, what operating system and from where you obtained the program?

I do not exclude errors at the PyMca side, but the support of BCF files is relatively recent and it is not available by default on source installations.

Best regards,

Armando
On 03/12/2025 15:06, PyMca general purpose mailing list. via PyMca-users wrote:
Hello (Hola), Armando:
I am a recent user of PyMCA and I am still trying to get the most out of my spectra...
I've managed to adjust the spectra well, but now I need to obtain good quality images, preferably in TIFF format. Unfortunately, I can't get the batch adjustment tool to work and I don't know why. What I get are empty files. My input data is .BCF (Bruker's native format for MA-XRF): do I need to transform my data in some way beforehand?
Thank you so much in advance!
Maite Jover de Celis








_______________________________________________

PyMca-users mailing list

PyM...@li...<mailto:PyM...@li...>

https://lists.sourceforge.net/lists/listinfo/pymca-users





_______________________________________________

PyMca-users mailing list

PyM...@li...<mailto:PyM...@li...>

https://lists.sourceforge.net/lists/listinfo/pymca-users




_______________________________________________

PyMca-users mailing list

PyM...@li...<mailto:PyM...@li...>

https://lists.sourceforge.net/lists/listinfo/pymca-users

[PyMca] spectral contamination

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

Hello Armando, hope you are doing well.
XRF spectra from several detectors, including Ketek detectors, are 
contaminated by fluorescece lines produced by the interaction of the 
incoming radiation with the detector materials. Despite being weak, 
these lines affect background and detection limits
Spectra from my Ketek AXAS-D, for example, are contaminated by Ni and Sn 
K-lines. A similar behaviour can be observed in Bruker Tracer 5.
My question is: is it possible to model such contaminations by either 
the "Matrix Spectrum" or the "MC Matrix Spectrum" option?
Thank you in advance for your help,
Marco



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Re: [PyMca] spectral contamination

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

Dear Marco,

The quick answer is no. With a generic Monte Carlo code you can 
certainly model anything provided you know everything but I do not think 
we are in that case.

In some cases you might estimate the contamination contribution from the 
measured scatter peak, but I think the safest approach is to use 
standards representative of your samples and deduce the upper limit of 
the contamination contribution from their measurements.

Best regards,

Armando

On 06/12/2025 11:10, PyMca general purpose mailing list. wrote:
> Hello Armando, hope you are doing well.
> XRF spectra from several detectors, including Ketek detectors, are 
> contaminated by fluorescece lines produced by the interaction of the 
> incoming radiation with the detector materials. Despite being weak, 
> these lines affect background and detection limits
> Spectra from my Ketek AXAS-D, for example, are contaminated by Ni and 
> Sn K-lines. A similar behaviour can be observed in Bruker Tracer 5.
> My question is: is it possible to model such contaminations by either 
> the "Matrix Spectrum" or the "MC Matrix Spectrum" option?
> Thank you in advance for your help,
> Marco
>
>
>