RFE: EMDB-SFF transform

[pkorir@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.dev202301242251 (2023-01-24 22:51:10 UTC)
Description
To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html#segmentation_transform_list) 
I've tested with two files having the same segmentation but different values for transform 0 and they render the same. 
Could you please implement this feature in ChimeraX? Just to clarify: what are the units of physical space in ChimeraX: Å or nm? 

Log:
UCSF ChimeraX version: 1.6.dev202301242251 (2023-01-24)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i9
      Processor Speed: 2.9 GHz
      Number of Processors: 1
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      L3 Cache: 12 MB
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Software:

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      Time since boot: 1 day, 3 hours, 20 minutes

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      Device ID: 0x67ef
      Revision ID: 0x00c2
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          UI Looks like: 3008 x 1692 @ 60.00Hz
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[pett]

Reported by Paul Korir

[Tom Goddard]

From: Paul Korir <pkorir@ebi.ac.uk>
Subject: Re: [chimerax-users] EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
Date: February 2, 2023 at 5:49:17 AM PST
To: Tom Goddard

Thanks, Tom. Once you have a build ready let me know and I'll test on the data I have.

Hi Paul,

The current ChimeraX EMDB SFF reader tries to apply the correct transformation, but I guess you have a case where it does not work. It would help to have the SFF file and the density map it is supposed to align to that demonstrates the problem. With that it should be very easy to fix.

Tom

[pkorir@…]

Hi Tom,

OK. I can confirm that it works (attached screenshot).

@Martin,

Did you manage to get both image and segmentation to render correctly?

Kind regards,

*Paul K. Korir, PhD*
/3D Visualisation Lead/
CS3DB
*EMBL-EBI*

On 02/02/2023 18:14, ChimeraX wrote:

Screenshot 2023-02-03 at 09.55.25.png​

[pkorir@…]

Added by email2trac

[pkorir@…]

Hi Tom,

While it does work implicitly for segmentations based on label masks 
(lattices), it doesn't seem to work with meshes. Attached is an EMDB-SFF 
with meshes for which the corresponding image is available from: 
https://www.ebi.ac.uk/empiar/EMPIAR-10087/ with name C2_tomo02.mrc

Let me know if you need anything else.

*Paul K. Korir, PhD*
/3D Visualisation Lead/
CS3DB
*EMBL-EBI*

On 03/02/2023 09:57, ChimeraX wrote:

empiar_10087_c2_tomo02.hff.gz​

Screenshot 2023-02-03 at 11.43.19.png​

[pkorir@…]

Added by email2trac

[pkorir@…]

Added by email2trac

[Tom Goddard]

Thanks!  The EMPIAR 10087 example should help me quickly fix this.  Hope to have a fix in today.

[Tom Goddard]

Fixed. In tonight's daily builds dated Feb 4.

The ChimeraX EMDB SFF file reader was not applying any transform to the meshes because the SFFMesh.transform_id in the file was None for all the segmentation meshes. The code expected the transform_id to be 0 if it is intended that transform 0 is supposed to be applied. I've changed the ChimeraX code so it applies transform 0 if the the transform_id is None. It seems like this is a problem with the file, but I do not know the intended meaning of transform_id = None.

[Tom Goddard]

Alignment of empiar 10087 segmentation with fixed code.