June 2019 - users - SasView Mailing Lists

Re: [SasView Users] [SasView Help] Error Message when loading 2D data
by Stephen King - UKRI STFC via users 13 Jun '19

13 Jun '19

BSL is just another format. It will output whatever data you give it: raw or reduced. Indeed, it was originally designed as a memory efficient way of storing early 2D SAXS detector data. The SasView File Converter merely converts the data in whatever format it is given and translates – that would be a better word, rather than convert – the input format to NXcanSAS (if the input is 2D). The metadata fields in the Converter are merely for annotation (since BSL saved memory by omitting such information!) and optional. So as Paul notes, Kuo-Chih, you should properly reduce your raw data into Q-space before exporting the 2D. SasView cannot help you with that. If your Bruker software does not do this (though I would hope it did!) you could try looking at some of the data reduction programs in use at synchrotrons. Kind regards, Steve King From: users <users-bounces(a)lists.sasview.org> On Behalf Of Stephen King - UKRI STFC via users Sent: 13 June 2019 09:44 To: users(a)sasview.org Subject: [SasView Users] FW: users post from kuo-chih.shih(a)uconn.edu requires approval From: users <mailman-bounces(a)lists.sasview.org> On Behalf Of Paul Butler Sent: 13 June 2019 00:58 To: users-owner(a)lists.sasview.org; Shih, Kuo-Chih <kuo-chih.shih(a)uconn.edu> Subject: Re: users post from kuo-chih.shih(a)uconn.edu requires approval Excellent! We are part way there ... Sadly it looks like the data is in pixel space rather than Q space (but SasView thinks it is in Q space which is what the NXcanSAS is presumably reporting). As an analysis tool SasView is designed to work in Q space. I am a bit surprised that it converted this way without warning. I guess the BSL output is in pixel space? I will have to think to see if I can come up with a clever solution. We need to wait for someone more familiar with the converter and NXcanSAS reader/writer to see if there is something that can be done at that end. However ... I note that the converter allows you to manually add detector, source, and sample metadata. Assuming you raw data is in fact in pixel space if you fill out those boxed in the converter should do the trick I'm thinking. Have a go and let us know. Paul ---------- Forwarded message ---------- From: "Shih, Kuo-Chih" <kuo-chih.shih(a)uconn.edu<mailto:kuo-chih.shih@uconn.edu>> To: Paul Butler <butlerpd(a)udel.edu<mailto:butlerpd@udel.edu>> Cc: "users(a)sasview.org<mailto:users@sasview.org>" <users(a)sasview.org<mailto:users@sasview.org>>, "help(a)sasview.org<mailto:help@sasview.org>" <help(a)sasview.org<mailto:help@sasview.org>>, "Nieh, Mu-Ping" <mu-ping.nieh(a)uconn.edu<mailto:mu-ping.nieh@uconn.edu>> Bcc: Date: Wed, 12 Jun 2019 23:26:28 +0000 Subject: RE: [SasView Help] Error Message when loading 2D data Dear Paul, Thanks a lot for the information. Yes, you are right. I am able to use Fit2D to export BSL/OTOKO 2D and that file can be directly import into SASView. I will also ask Bruker people whether there is a way for us to output our 2D pattern in the NeXUS NXcanSAS format. Just another question, after I input the 2D pattern, I would like to do a sector average. Is there any way that we can define the beam center manually? The beam center is off as shown in the attached file. Thanks again!! Best regards, Kuo-Chih From: Paul Butler<mailto:butlerpd@udel.edu> Sent: Wednesday, June 12, 2019 6:46 PM To: Shih, Kuo-Chih<mailto:kuo-chih.shih@uconn.edu> Cc: users(a)sasview.org<mailto:users@sasview.org>; help(a)sasview.org<mailto:help@sasview.org>; Nieh, Mu-Ping<mailto:mu-ping.nieh@uconn.edu> Subject: Re: [SasView Help] Error Message when loading 2D data Hi Kuo-Chih, 2D data formats are very specific (unlike 1D which most people default to the same general format). now that the NeXUS NXcanSAS standard reduced data format has been approved, we are trying to encourage its use to avoid exactly this kind of problem. Bruker poeple have attended some of the canSAS meetings where the standard work was discussed and now that it has been approved I encourage you to ask them to output their data in said format. In the meantime, for legacy reasons only, SasView also supports the NIST 2D ASCII format. Further, as you discovered, SasView has a converter which will convert ISIS 2D ASCII format as well as the BSL/OTOKO 2D format. Question: What type of ASCII format are you getting from Fit2D? My guess is that the error is because the format is not a supported input format to the converter? I am assuming this error is being thrown when you try to convert the data? I am well aware of Fit2D but have never used it so not sure what 2D output formats it supports, but looking online I'm not sure that its two ASCII 2D outputs (Spread sheet and MCA) are compatible? It seems like Fit2D will output a BSL 2D? which the SasView converter should be able to handle. It also seems to output a TIFF. If all else fails you can try that and use the image converter to see if it works? There maybe others who know more about the Fit2D output who might have some suggestions. Otherwise please let us know how you get on and if I have misunderstood the problem please don't hesitate to ask again. Cheers Paul . On Wed, Jun 12, 2019 at 4:24 PM Shih, Kuo-Chih via help <help(a)lists.sasview.org<mailto:help@lists.sasview.org>> wrote: Dear SASView Help Team, I am Kuo-Chih Shih from the University of Connecticut. Dr. Mu-Ping Nieh and I are now trying to fit the 2D scattering pattern we got from the Bruker nanostar machine. Since SASView is not able to read the raw data (.gfrm) from Bruker machine, I used Fit2D to convert it to a ASCII data. However, when I try to load the file, SASView shows me the following message. I also try to convert the ASCII file to the NXcanSAS file but it gave me another error message. I also attached the SasView log file. Could you please help me to troubleshoot this? _______________________________________________ help mailing list help(a)lists.sasview.org<mailto:help@lists.sasview.org> http://lists.sasview.org/cgi-bin/mailman/listinfo/help<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.sasv…>

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FW: users post from kuo-chih.shih@uconn.edu requires approval
by Stephen King - UKRI STFC via users 13 Jun '19

13 Jun '19

From: users <mailman-bounces(a)lists.sasview.org> On Behalf Of Paul Butler Sent: 13 June 2019 00:58 To: users-owner(a)lists.sasview.org; Shih, Kuo-Chih <kuo-chih.shih(a)uconn.edu> Subject: Re: users post from kuo-chih.shih(a)uconn.edu requires approval Excellent! We are part way there ... Sadly it looks like the data is in pixel space rather than Q space (but SasView thinks it is in Q space which is what the NXcanSAS is presumably reporting). As an analysis tool SasView is designed to work in Q space. I am a bit surprised that it converted this way without warning. I guess the BSL output is in pixel space? I will have to think to see if I can come up with a clever solution. We need to wait for someone more familiar with the converter and NXcanSAS reader/writer to see if there is something that can be done at that end. However ... I note that the converter allows you to manually add detector, source, and sample metadata. Assuming you raw data is in fact in pixel space if you fill out those boxed in the converter should do the trick I'm thinking. Have a go and let us know. Paul ---------- Forwarded message ---------- From: "Shih, Kuo-Chih" <kuo-chih.shih(a)uconn.edu<mailto:kuo-chih.shih@uconn.edu>> To: Paul Butler <butlerpd(a)udel.edu<mailto:butlerpd@udel.edu>> Cc: "users(a)sasview.org<mailto:users@sasview.org>" <users(a)sasview.org<mailto:users@sasview.org>>, "help(a)sasview.org<mailto:help@sasview.org>" <help(a)sasview.org<mailto:help@sasview.org>>, "Nieh, Mu-Ping" <mu-ping.nieh(a)uconn.edu<mailto:mu-ping.nieh@uconn.edu>> Bcc: Date: Wed, 12 Jun 2019 23:26:28 +0000 Subject: RE: [SasView Help] Error Message when loading 2D data Dear Paul, Thanks a lot for the information. Yes, you are right. I am able to use Fit2D to export BSL/OTOKO 2D and that file can be directly import into SASView. I will also ask Bruker people whether there is a way for us to output our 2D pattern in the NeXUS NXcanSAS format. Just another question, after I input the 2D pattern, I would like to do a sector average. Is there any way that we can define the beam center manually? The beam center is off as shown in the attached file. Thanks again!! Best regards, Kuo-Chih [cid:16b4e157fd6f456b1e53] From: Paul Butler<mailto:butlerpd@udel.edu> Sent: Wednesday, June 12, 2019 6:46 PM To: Shih, Kuo-Chih<mailto:kuo-chih.shih@uconn.edu> Cc: users(a)sasview.org<mailto:users@sasview.org>; help(a)sasview.org<mailto:help@sasview.org>; Nieh, Mu-Ping<mailto:mu-ping.nieh@uconn.edu> Subject: Re: [SasView Help] Error Message when loading 2D data Hi Kuo-Chih, 2D data formats are very specific (unlike 1D which most people default to the same general format). now that the NeXUS NXcanSAS standard reduced data format has been approved, we are trying to encourage its use to avoid exactly this kind of problem. Bruker poeple have attended some of the canSAS meetings where the standard work was discussed and now that it has been approved I encourage you to ask them to output their data in said format. In the meantime, for legacy reasons only, SasView also supports the NIST 2D ASCII format. Further, as you discovered, SasView has a converter which will convert ISIS 2D ASCII format as well as the BSL/OTOKO 2D format. Question: What type of ASCII format are you getting from Fit2D? My guess is that the error is because the format is not a supported input format to the converter? I am assuming this error is being thrown when you try to convert the data? I am well aware of Fit2D but have never used it so not sure what 2D output formats it supports, but looking online I'm not sure that its two ASCII 2D outputs (Spread sheet and MCA) are compatible? It seems like Fit2D will output a BSL 2D? which the SasView converter should be able to handle. It also seems to output a TIFF. If all else fails you can try that and use the image converter to see if it works? There maybe others who know more about the Fit2D output who might have some suggestions. Otherwise please let us know how you get on and if I have misunderstood the problem please don't hesitate to ask again. Cheers Paul . On Wed, Jun 12, 2019 at 4:24 PM Shih, Kuo-Chih via help <help(a)lists.sasview.org<mailto:help@lists.sasview.org>> wrote: Dear SASView Help Team, I am Kuo-Chih Shih from the University of Connecticut. Dr. Mu-Ping Nieh and I are now trying to fit the 2D scattering pattern we got from the Bruker nanostar machine. Since SASView is not able to read the raw data (.gfrm) from Bruker machine, I used Fit2D to convert it to a ASCII data. However, when I try to load the file, SASView shows me the following message. I also try to convert the ASCII file to the NXcanSAS file but it gave me another error message. I also attached the SasView log file. Could you please help me to troubleshoot this? [cid:16b4dbb1d9ff456b1e51] [cid:16b4dbb1d9ff456b1e52] _______________________________________________ help mailing list help(a)lists.sasview.org<mailto:help@lists.sasview.org> http://lists.sasview.org/cgi-bin/mailman/listinfo/help<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.sasv…> ---------- Forwarded message ---------- From: users-request(a)lists.sasview.org<mailto:users-request@lists.sasview.org> To: Cc: Bcc: Date: Wed, 12 Jun 2019 19:26:30 -0400 Subject: confirm 9bfe20656d2f9d2764c7afedd96df15915ab4eb9 If you reply to this message, keeping the Subject: header intact, Mailman will discard the held message. Do this if the message is spam. If you reply to this message and include an Approved: header with the list password in it, the message will be approved for posting to the list. The Approved: header can also appear in the first line of the body of the reply.

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Error Message when loading 2D data
by Shih, Kuo-Chih via users 12 Jun '19

12 Jun '19

Dear SASView Help Team, I am Kuo-Chih Shih from the University of Connecticut. Dr. Mu-Ping Nieh and I are now trying to fit the 2D scattering pattern we got from the Bruker nanostar machine. Since SASView is not able to read the raw data (.gfrm) from Bruker machine, I used Fit2D to convert it to a ASCII data. However, when I try to load the file, SASView shows me the following message. I also try to convert the ASCII file to the NXcanSAS file but it gave me another error message. I also attached the SasView log file. Could you please help me to troubleshoot this? [cid:b505a9c6-94ff-4c90-8c58-2fbdd050503d] [cid:fde63226-c5ac-4997-b80c-8d6ae33ad75e]

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