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" Multi-scan files seem to have way more RawData files than there are actual scans. " Having been the one to generate the sample files I can explain this, or at least take a guess. Bruker's automation software is both rather inflexible, and tries</div>
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<meta charset="utf-8"></head><body><pre style="font-family: sans-serif; font-size: 100%; white-space: pre-wrap; word-wrap: break-word">" Multi-scan files seem to have way more RawData files than there are actual scans."
Having been the one to generate the sample files I can explain this, or at least take a guess. Bruker's automation software is both rather inflexible, and tries to be very generic, which leads to some odd situations. Measurements have to be *part* of another item, for example. (Why oh why could they not just do it like APEX and have a table of what you want to do?)
Anyway, this means my experiment was:
-Ramp to target temperature.
-Hold at temperature for 3600 seconds (To allow the sample to hit thermal equilibrium)
-Hold at temperature for the length of the experiment
-Measure sample (which is counted as a part of the previous hold)
So if I had to take a guess, I would say it generates a line for each stage of the experiment, with measurements just being a thing that happens during one of the stages. This would match every 3rd file having a valid dataset in it, and file 39 being the last with a valid datset, and 40 being the last file: After I got the 776 C dataset, I ordered it to ramp down to 25 C.
I don't know if that that is helpful to anyone, and if someone wants to really get into how the files are arranged, I can construct and run some arbitrary measurement patterns for them to confirm this.
(Now I need to actually expand my own PXRDreport.py program ( <a href="https://urldefense.us/v3/__https://bitbucket.org/pxrd-report/pxrd-report/src__;!!G_uCfscf7eWS!ZtRZJK4X6CL7vE0RysYEA3pmKES1MHcVBdLEEi04Xv-wLVNUgYt9Akw0tgEjNKj2Oeld5lV9-uRweAqYmz0ela7OOQ$">https://urldefense.us/v3/__https://bitbucket.org/pxrd-report/pxrd-report/src__;!!G_uCfscf7eWS!ZtRZJK4X6CL7vE0RysYEA3pmKES1MHcVBdLEEi04Xv-wLVNUgYt9Akw0tgEjNKj2Oeld5lV9-uRweAqYmz0ela7OOQ$</a> ) to actually extract the data directly from the BRML files instead of using the RAW4-as-text export as a shortcut and to work on multi-dataset BRML files). Nice project for when I'm sitting there assisting with labs with nothing to do next semester.
Storm (née Matthew) (they/them)
Lab Technician V (Chemistry, Crystallography)
Office: 250-807-8365
UBC School of Engineering
1540 Innovation Dr.
Kelowna, BC
V1V 1V7
On 13 December 2024 18:44:30 CET, "Toby, Brian H. via GSAS-II" <gsas-ii@aps.anl.gov> wrote:
>Indeed, the BRML importer was designed only to handle single-scan
>files. Multi-scan files seem to have way more RawData files than there
>are actual scans. The importer choked on the first entry in a
>multi-scan .brml file because it did not contain a valid scan. I’m not
>sure I’d call this a bug, since the importer was only designed to read
>single-scan .brml files (all that we had seen.)
>
>Anyway, yesterday and today, I updated the BRML importer and it now it will read all the files with valid diffraction scans from a multi-scan file and will pass quietly over the ones that don’t. The importer also ignores all the other information in the zip archive, as I have no idea what is there; but I’m not sure I want to write code read it either, but I could be convinced.
>
>For that matter we also can’t read Bruker Raw version 4 (versions 1-3 are OK) because we can’t get any information on how the version 4 file is structured (and Bruker does not seem to have any records). Information on that would be helpful and would be acted upon if anyone seeing that can help.
>
>Brian
>
>P.S. Merci Matt!
>
>From: GSAS-II <gsas-ii-bounces@aps.anl.gov> on behalf of SUCHOMEL
>Matthew via GSAS-II <gsas-ii@aps.anl.gov>
>Date: Friday, December 13, 2024 at 2:08 AM ZjQcmQRYFpfptBannerEnd
>
>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)
>
>
>
>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@icmcb.cnrs.fr
>
>
>
>
>
>> Today's Topics:
>
>>
>
>> 1. Bug in BRML file importer (Brown, Matthew)
>
>>
>
>>
>
>> ---------------------------------------------------------------------
>> -
>
>>
>
>> Message: 1
>
>> Date: Thu, 12 Dec 2024 21:34:58 +0000
>
>> From: "Brown, Matthew" <matthew.brown@ubc.ca>
>
>> To: "gsas-ii@aps.anl.gov" <gsas-ii@aps.anl.gov>
>
>> Subject: [GSAS-II] Bug in BRML file importer
>
>> Message-ID:
>
>>
>> <QB1PR01MB348903E674AA3D04935D0E3E9C3F2@QB1PR01MB3489.CANPRD01.PROD.O
>> UTLOOK.COM>
>
>>
>
>> Content-Type: text/plain; charset="iso-8859-1"
>
>>
>
>>
>
>> 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-Uncalibr
>> atedChamber.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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