[GSAS-II] GSAS-II Digest, Vol 399, Issue 1: Bug in BRML file import

Fri Dec 13 09:11:49 CST 2024

Hi,
GSAS-II has no means of reading Bruker raw4 files - they never made the format documentation available (I suspect they don't know what it is anymore). PowDLL (Windows only) can read raw4 files & make a gsas format data file readable by GSAS-II but all metadata (e.g. temperature) is lost. It is not clear this includes multiscan raw4 files. The brml file is potentially far more digestible.
A Bruker brml file is in fact a zip file of a collection of xml files. GSAS-II does not have currently an importer for that, but one could be written based on the Panalytical importers for powder and reflectometry data (.xrdml) and some of the other importers know how to use zip files. The powder patterns in the Bruker brml file are all "RawDatan.xml" (n = integer 0,1,2... for as many scans that are in the file); some appear to be setups & others have the actual scan - these are much larger.  There are also various "nameContainer.xml" files within the brml (aka zip) file that may contain useful information about the data set. To access all this, change the brml extension to zip, unzip the result, and then use an xml reader to examine the xml file contents (MS Edge  or Chrome will read it just fine - one can see the file layout directly - it's all text). From that an importer can be written in python that will process a multiscan brml file & recover the desired metadata as well.
To whoever takes this on; it will be much appreciated by the GSAS-II user community and we'd very much like to include this importer in GSAS-II.
Best,
Bob
________________________________
From: GSAS-II <gsas-ii-bounces at aps.anl.gov> on behalf of SUCHOMEL Matthew via GSAS-II <gsas-ii at aps.anl.gov>
Sent: Friday, December 13, 2024 2:08 AM
To: gsas-ii at aps.anl.gov <gsas-ii at aps.anl.gov>; matthew.brown at ubc.ca <matthew.brown at ubc.ca>
Subject: Re: [GSAS-II] GSAS-II Digest, Vol 399, Issue 1: Bug in BRML file import

Dear Matthew I’m not familer with all the details of the GSAS-II Module for Bruker .raw & .brml imports: you see the docs and source here (section 20. 3. 5): https: //urldefense. us/v3/__https: //gsas-ii. readthedocs. io/en/latest/imports. html__;!!G_uCfscf7eWS!bR02qPdZlmP9aYfS8uRGMxA7yLoDeyWSzsg6KY91wzjxwMwtMXmPgPxzbKhz9gCWy3oseCWGqQgrVhg2CwP6pkVSscqqtX3v-Xg$
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Dear Matthew

I’m not familer with all the details of the GSAS-II Module for Bruker .raw & .brml imports: you see the docs and source here (section 20.3.5):
https://urldefense.us/v3/__https://gsas-ii.readthedocs.io/en/latest/imports.html__;!!G_uCfscf7eWS!bR02qPdZlmP9aYfS8uRGMxA7yLoDeyWSzsg6KY91wzjxwMwtMXmPgPxzbKhz9gCWy3oseCWGqQgrVhg2CwP6pkVSscqqtX3v-Xg$

There might be a bug, but I’d also be surprised if the module was designed to handle the case of brml files which contain many distinct datasets or scans in the single zip file (like your VT case).  Moreover, the details of the .brml files seem to sometimes vary depending of the exact types of scans in the .brml zip (continuous scan, static scans, etc).  Even Bruker's own DIFFRAC.FileExchange program doesn’t always work.

In situation like this, I typically use DIFFRAC.EVA to just export all the datasets from a multi-scan brml as separate RAW or XY files.  I believe you can select all files in the data-tree within EVA and export with a single click.  Then, it is rather more simple to plot and / or analysis the data using non-Bruker software.

best regards
Matthew

Matthew SUCHOMEL
Chargé de recherche
ICMCB - CNRS
87 avenue du Dr Schweitzer
33608 Pessac Cedex
matthew.suchomel at icmcb.cnrs.fr

> On 12 Dec 2024, at 22:35, gsas-ii-request at aps.anl.gov wrote:
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>   1. Bug in BRML file importer (Brown, Matthew)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Thu, 12 Dec 2024 21:34:58 +0000
> From: "Brown, Matthew" <matthew.brown at ubc.ca>
> To: "gsas-ii at aps.anl.gov" <gsas-ii at aps.anl.gov>
> Subject: [GSAS-II] Bug in BRML file importer
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> [https://urldefense.us/v3/__https://res-1.cdn.office.net/assets/mail/file-icon/png/generic_16x16.png*MgO-UncalibratedChamber__;XQ!!G_uCfscf7eWS!bNY0qQlIoNHaEq63fO0o2xzWaD5MrQhac_EIkT1kGLbz-i5qL3-iouaB9gzD87G9e6roHiNrzLK4sX3ziff9Yw2lug$ 1.brml<https://urldefense.us/v3/__https://ubcca-my.sharepoint.com/:u:/g/personal/matthew_brown_ubc_ca/ETFyDK_sFwpDsUDg9__nFpABgHHJzniJRO9J5nYYqHVFOA__;!!G_uCfscf7eWS!bNY0qQlIoNHaEq63fO0o2xzWaD5MrQhac_EIkT1kGLbz-i5qL3-iouaB9gzD87G9e6roHiNrzLK4sX3zifdfPyqgxg$>
> [https://urldefense.us/v3/__https://res-1.cdn.office.net/assets/mail/file-icon/png/generic_16x16.png*MgO-UncalibratedChamber__;XQ!!G_uCfscf7eWS!bNY0qQlIoNHaEq63fO0o2xzWaD5MrQhac_EIkT1kGLbz-i5qL3-iouaB9gzD87G9e6roHiNrzLK4sX3ziff9Yw2lug$ 1.raw<https://urldefense.us/v3/__https://ubcca-my.sharepoint.com/:i:/g/personal/matthew_brown_ubc_ca/EakiDvxk031GrH-Kxu26wuEBFa9YNOjoUGffypXoBnC-8w__;!!G_uCfscf7eWS!bNY0qQlIoNHaEq63fO0o2xzWaD5MrQhac_EIkT1kGLbz-i5qL3-iouaB9gzD87G9e6roHiNrzLK4sX3zifeRLFL5nA$>
>
> Salutations
>
> I'm trying to do a temperature calibration for my MTC-Furnace based on the Bruker manual. So I used the automation system to get an MgO measurement at each relevant temperature, and then I was going to use GSAS-II to do Ritveld on it to get the temperature. However, when I try and open any *.brml file with more then one data set in it, I get the following error:
>
> The Bruker .brml file reader was not able to read file C:\Users\BrukerAXS\Documents\Data\ImportantData\HighTemp\MgO-UncalibratedChamber.brml
>
> Error message(s):
>
> Bruker .brml file read error:
>  Unhandled read exception: list index out of range
>  Traceback info:
> Traceback (most recent call last):
>  File "C:\Users\BrukerAXS\gsas2full\GSAS-II\GSASII\GSASIIdataGUI.py", line 1007, in OnImportGeneric
>    flag = rd.Reader(filename,self,buffer=rdbuffer,
>           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>  File "C:\Users\BrukerAXS\gsas2full\GSAS-II\GSASII\imports\G2pwd_BrukerRAW.py", line 287, in Reader
>    x[i] = float(entry[2])
>                 ~~~~~^^^
> IndexError: list index out of range
>
> (I got the exact same error when trying to import the LaB6 data; I took one of those at each temperature I got MgO data for, as I wasn't sure if the instrument parameters would change with temperature, and I figured it was better to have the data and not need it, then find I needed it later.)
>
> Thank you all
>
> --Dr Matthew L. Brown
>
> P.S. If anyone has advice on high temperature PXRD, or how to calibrate an ambient high temperature chamber, or working with Bruker's Diffrac.Commander software at high temperature, I'd love to talk as some of this is rather non-intuitive and I'm way behind schedule on these experiments.
>
> ---

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