1.14.10 - DI - 2D-mapping Total and Ring intensity maps and D-space maps are not showing right.

[rmadhura-iit]

After the total and ring intensity maps are showing just one color, even after adjusting the scale. The intensities of these rings are quite different, in my case, so the heatmap should reflect these. This feature works fine for 1D

[grantnikseresht]

Can you point me to the dataset you're using for this one? Are you manipulating the min and max intensities to adjust the scale?

This feature is working for me on Docker via lethocerus with Muscle X 1.14.11. The colorbar scaling will sometimes show as one color for large absolute numbers since the minimum of the scale is always zero, but this should work at higher minimum intensities. If you are noticing no changes to color at all or unexpected values, let me know.

[rmadhura-iit]

Hi Grant, I am using a local dataset on my workstation and I upgraded to 1.14.11. I still have the same issue. I did modify the minimum on the scale bar. The scale bar gets adjusted but it still shows only one color throughout the map. Rama [image: image.png] -- Rama Sashank Madhurapantula Ph.D. Research Assistant Professor, Biology Center for Molecular Study of Condensed Soft Matter Illinois Institute of Technology Chicago IL

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On Wed, Jul 17, 2019 at 2:31 PM Grant Nikseresht ***@***.***> wrote: Can you point me to the dataset you're using for this one? Are you manipulating the min and max intensities to adjust the scale? This feature is working for me on Docker via lethocerus with Muscle X 1.14.11. The colorbar scaling will sometimes show as one color for large absolute numbers since the minimum of the scale is always zero, but this should work at higher minimum intensities. If you are noticing no changes to color at all or unexpected values, let me know. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#47?email_source=notifications&email_token=AKMIDL3N6ITWMAH3A4GDJVTP75XRJA5CNFSM4IBOZTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2GK6UI#issuecomment-512536401>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKMIDL7B2XJKUI4QLFB56JLP75XRJANCNFSM4IBOZTUQ> .

[grantnikseresht]

Using the Bicuspid data you sent me, I generated a new HDF5 file automatically using Start=0 End=7 and Step Size=1 and the colors are showing normally. When I use the HDF file in calib, I'm getting all one color. I've also noticed that a baseline color is filled in to square off heat maps when they're not perfectly square / rectangular, so perhaps the step size / start / end scales are off.

You could try recreating the HDF5 file you've been using from calib or perhaps generating a new one with the same parameters through DI? I'll look into the differences between your hdf and the DI generated one in the meantime.

[rmadhura-iit]

Hi Grant, This is quite bizzare.. So there is indeed a problem with the HDF files we are collecting at the beamline. This might be something we should bring Tom into the loop about. The step size information is quite important, because for some samples, we will be using this to overlay the heatmap with say a microscopy image. At least that is what the intention is behind writing the HDF files, so we can correspond the exact region of the sample that we are scanning using X-rays. I will try a different data set with generating a new HDF file and see if that works. If it does, may be that is where the problem is. Rama

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-- Rama Sashank Madhurapantula Ph.D. Research Assistant Professor, Biology Center for Molecular Study of Condensed Soft Matter Illinois Institute of Technology Chicago IL

On Fri, Jul 19, 2019 at 3:33 PM Grant Nikseresht ***@***.***> wrote: Using the Bicuspid data you sent me, I generated a new HDF5 file automatically using Start=0 End=7 and Step Size=1 and the colors are showing normally. When I use the HDF file in calib, I'm getting all one color. I've also noticed that a baseline color is filled in to square off heat maps when they're not perfectly square / rectangular, so perhaps the step size / start / end scales are off. You could try recreating the HDF5 file you've been using from calib or perhaps generating a new one with the same parameters through DI? I'll look into the differences between your hdf and the DI generated one in the meantime. [image: Screen Shot 2019-07-19 at 3 24 37 PM] <https://user-images.githubusercontent.com/8533237/61563727-3ffed080-aa3a-11e9-9176-1ea623b040d5.png> [image: Screen Shot 2019-07-19 at 3 25 05 PM] <https://user-images.githubusercontent.com/8533237/61563744-45f4b180-aa3a-11e9-911d-0fa597e1e2d8.png> [image: Screen Shot 2019-07-19 at 3 25 51 PM] <https://user-images.githubusercontent.com/8533237/61563751-49883880-aa3a-11e9-9c03-aa0a7196af80.png> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#47?email_source=notifications&email_token=AKMIDL3NZZ2M33IVQJCRVNTQAIQIPA5CNFSM4IBOZTU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2MWBPQ#issuecomment-513368254>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKMIDL6DFDLKHC643MDBSI3QAIQIPANCNFSM4IBOZTUQ> .

[rmadhura-iit]

Is there any chance we are using a parameter from one of the headers on the HDFs to make this heatmap? Something like beamcurrent? That is usually a very small number (~100). We should check for this.

[grantnikseresht]

I checked the HDF file and it seems like the X initial location and step size are positive but the final location is negative. This case is likely not going to work correctly in current versions of MuscleX.

Is this a detector configuration we need to be able to handle?

[rmadhura-iit]

Well the X and Y motor positions are absolute positions reported from the motors. So the positions are what they are. But we are only using them to generate the grid here though, so I don't know if this needs to be fixed at the beamline?

[rmadhura-iit]

So I put more thought into this. We need a way to make it work with motor positions we collect at the beamline. There is no way around it.

Why can we not use the absolute positions and ignore step size completely, when we are picking up an HDF file? It doesn't matter what the step size is. If we are using X and Y motor positions from the HDF file, step size need not be accounted for.

Does this help?