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Error in conversion of certain euler angles when loading star file #366

Closed
jojoelfe opened this issue Nov 30, 2023 · 6 comments
Closed

Error in conversion of certain euler angles when loading star file #366

jojoelfe opened this issue Nov 30, 2023 · 6 comments
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bug Something isn't working

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@jojoelfe
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Describe the bug
Some eulerangles are not converting correctly into blender coordinate system. It might be related to this bug, alisterburt/eulerangles#8, in the eulerangles package used for the conversion.

This can be fixed when falling back to the previous conversion code from

target_metadata = ConversionMeta(name='output', 
                                   axes='xyz', 
                                    intrinsic=False,
                                    right_handed_rotation=True,
                                    active=True)
eulers = np.deg2rad(convert_eulers(euler_angles, 
                               source_meta='relion', 
                               target_meta=target_metadata))

to

eulers = R.from_euler(
        seq='ZYZ', angles=euler_angles, degrees=True
    ).inv().as_euler('xyz')

Happy to submit a PR, but noticed you are currently making the 4.0 transistion and refactoring a bit, so I can wait until this is more or less finished.

Thanks,

Johannes

To Reproduce
I pasted a diagnostic starfile below

Expected behavior
Currently this loads like this (notice incosnisten behaviour in central cross):

image

while it should look like this

image

Error Codes
Please include associated error codes that are shown in the python console when the error occurs.

To view the python console on Windows, Window -> Toggle System Console, on Mac you must start Blender from the terminal.

# paste error codes from python console here

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

  • OS: [e.g. Windows / MacOS / Linux]
  • Hardware: [e.g. Intel Mac, M1 Mac, x86 PC]
  • Blender Version:
  • MolecularNodes Version:

Additional context

# Created by the starfile Python package (version 0.5.1) at 10:44:33 on 30/11/2023


data_particles

loop_
_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnCoordinateZ #3
_rlnOriginXAngst #4
_rlnOriginYAngst #5
_rlnOriginZAngst #6
_rlnAngleRot #7
_rlnAngleTilt #8
_rlnAnglePsi #9
_rlnImagePixelSize #10
_rlnMicrographName #11
_rlnOpticsGroup #12
_faVectorX #13
_faVectorY #14
_faVectorZ #15
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0	800	1200	0	0	0	80	120	0	1.000000	micrograph.mrc	1	0	0	0
0	800	1300	0	0	0	80	130	0	1.000000	micrograph.mrc	1	0	0	0
0	800	1400	0	0	0	80	140	0	1.000000	micrograph.mrc	1	0	0	0
0	800	1500	0	0	0	80	150	0	1.000000	micrograph.mrc	1	0	0	0
0	800	1600	0	0	0	80	160	0	1.000000	micrograph.mrc	1	0	0	0
0	800	1700	0	0	0	80	170	0	1.000000	micrograph.mrc	1	0	0	0
0	800	1800	0	0	0	80	180	0	1.000000	micrograph.mrc	1	0	0	0
0	800	1900	0	0	0	80	190	0	1.000000	micrograph.mrc	1	0	0	0
0	900	0	0	0	0	90	0	0	1.000000	micrograph.mrc	1	0	0	0
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0	900	200	0	0	0	90	20	0	1.000000	micrograph.mrc	1	0	0	0
0	900	300	0	0	0	90	30	0	1.000000	micrograph.mrc	1	0	0	0
0	900	400	0	0	0	90	40	0	1.000000	micrograph.mrc	1	0	0	0
0	900	500	0	0	0	90	50	0	1.000000	micrograph.mrc	1	0	0	0
0	900	600	0	0	0	90	60	0	1.000000	micrograph.mrc	1	0	0	0
0	900	700	0	0	0	90	70	0	1.000000	micrograph.mrc	1	0	0	0
0	900	800	0	0	0	90	80	0	1.000000	micrograph.mrc	1	0	0	0
0	900	900	0	0	0	90	90	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1000	0	0	0	90	100	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1100	0	0	0	90	110	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1200	0	0	0	90	120	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1300	0	0	0	90	130	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1400	0	0	0	90	140	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1500	0	0	0	90	150	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1600	0	0	0	90	160	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1700	0	0	0	90	170	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1800	0	0	0	90	180	0	1.000000	micrograph.mrc	1	0	0	0
0	900	1900	0	0	0	90	190	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	0	0	0	0	100	0	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	100	0	0	0	100	10	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	200	0	0	0	100	20	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	300	0	0	0	100	30	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	400	0	0	0	100	40	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	500	0	0	0	100	50	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	600	0	0	0	100	60	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	700	0	0	0	100	70	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	800	0	0	0	100	80	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	900	0	0	0	100	90	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1000	0	0	0	100	100	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1100	0	0	0	100	110	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1200	0	0	0	100	120	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1300	0	0	0	100	130	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1400	0	0	0	100	140	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1500	0	0	0	100	150	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1600	0	0	0	100	160	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1700	0	0	0	100	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1800	0	0	0	100	180	0	1.000000	micrograph.mrc	1	0	0	0
0	1000	1900	0	0	0	100	190	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	0	0	0	0	110	0	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	100	0	0	0	110	10	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	200	0	0	0	110	20	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	300	0	0	0	110	30	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	400	0	0	0	110	40	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	500	0	0	0	110	50	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	600	0	0	0	110	60	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	700	0	0	0	110	70	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	800	0	0	0	110	80	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	900	0	0	0	110	90	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1000	0	0	0	110	100	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1100	0	0	0	110	110	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1200	0	0	0	110	120	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1300	0	0	0	110	130	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1400	0	0	0	110	140	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1500	0	0	0	110	150	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1600	0	0	0	110	160	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1700	0	0	0	110	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1800	0	0	0	110	180	0	1.000000	micrograph.mrc	1	0	0	0
0	1100	1900	0	0	0	110	190	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	0	0	0	0	120	0	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	100	0	0	0	120	10	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	200	0	0	0	120	20	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	300	0	0	0	120	30	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	400	0	0	0	120	40	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	500	0	0	0	120	50	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	600	0	0	0	120	60	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	700	0	0	0	120	70	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	800	0	0	0	120	80	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	900	0	0	0	120	90	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1000	0	0	0	120	100	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1100	0	0	0	120	110	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1200	0	0	0	120	120	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1300	0	0	0	120	130	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1400	0	0	0	120	140	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1500	0	0	0	120	150	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1600	0	0	0	120	160	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1700	0	0	0	120	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1800	0	0	0	120	180	0	1.000000	micrograph.mrc	1	0	0	0
0	1200	1900	0	0	0	120	190	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	0	0	0	0	130	0	0	1.000000	micrograph.mrc	1	0	0	0
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0	1300	200	0	0	0	130	20	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	300	0	0	0	130	30	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	400	0	0	0	130	40	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	500	0	0	0	130	50	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	600	0	0	0	130	60	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	700	0	0	0	130	70	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	800	0	0	0	130	80	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	900	0	0	0	130	90	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	1000	0	0	0	130	100	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	1100	0	0	0	130	110	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	1200	0	0	0	130	120	0	1.000000	micrograph.mrc	1	0	0	0
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0	1300	1600	0	0	0	130	160	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	1700	0	0	0	130	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	1800	0	0	0	130	180	0	1.000000	micrograph.mrc	1	0	0	0
0	1300	1900	0	0	0	130	190	0	1.000000	micrograph.mrc	1	0	0	0
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0	1400	200	0	0	0	140	20	0	1.000000	micrograph.mrc	1	0	0	0
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0	1400	600	0	0	0	140	60	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	700	0	0	0	140	70	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	800	0	0	0	140	80	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	900	0	0	0	140	90	0	1.000000	micrograph.mrc	1	0	0	0
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0	1400	1100	0	0	0	140	110	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	1200	0	0	0	140	120	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	1300	0	0	0	140	130	0	1.000000	micrograph.mrc	1	0	0	0
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0	1400	1600	0	0	0	140	160	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	1700	0	0	0	140	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	1800	0	0	0	140	180	0	1.000000	micrograph.mrc	1	0	0	0
0	1400	1900	0	0	0	140	190	0	1.000000	micrograph.mrc	1	0	0	0
0	1500	0	0	0	0	150	0	0	1.000000	micrograph.mrc	1	0	0	0
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0	1500	700	0	0	0	150	70	0	1.000000	micrograph.mrc	1	0	0	0
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0	1500	1200	0	0	0	150	120	0	1.000000	micrograph.mrc	1	0	0	0
0	1500	1300	0	0	0	150	130	0	1.000000	micrograph.mrc	1	0	0	0
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0	1500	1600	0	0	0	150	160	0	1.000000	micrograph.mrc	1	0	0	0
0	1500	1700	0	0	0	150	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1500	1800	0	0	0	150	180	0	1.000000	micrograph.mrc	1	0	0	0
0	1500	1900	0	0	0	150	190	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	0	0	0	0	160	0	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	100	0	0	0	160	10	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	200	0	0	0	160	20	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	300	0	0	0	160	30	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	400	0	0	0	160	40	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	500	0	0	0	160	50	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	600	0	0	0	160	60	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	700	0	0	0	160	70	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	800	0	0	0	160	80	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	900	0	0	0	160	90	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	1000	0	0	0	160	100	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	1100	0	0	0	160	110	0	1.000000	micrograph.mrc	1	0	0	0
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0	1600	1700	0	0	0	160	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1600	1800	0	0	0	160	180	0	1.000000	micrograph.mrc	1	0	0	0
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0	1700	1100	0	0	0	170	110	0	1.000000	micrograph.mrc	1	0	0	0
0	1700	1200	0	0	0	170	120	0	1.000000	micrograph.mrc	1	0	0	0
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0	1800	700	0	0	0	180	70	0	1.000000	micrograph.mrc	1	0	0	0
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0	1800	900	0	0	0	180	90	0	1.000000	micrograph.mrc	1	0	0	0
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0	1800	1100	0	0	0	180	110	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1200	0	0	0	180	120	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1300	0	0	0	180	130	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1400	0	0	0	180	140	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1500	0	0	0	180	150	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1600	0	0	0	180	160	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1700	0	0	0	180	170	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1800	0	0	0	180	180	0	1.000000	micrograph.mrc	1	0	0	0
0	1800	1900	0	0	0	180	190	0	1.000000	micrograph.mrc	1	0	0	0
0	1900	0	0	0	0	190	0	0	1.000000	micrograph.mrc	1	0	0	0
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0	1900	200	0	0	0	190	20	0	1.000000	micrograph.mrc	1	0	0	0
0	1900	300	0	0	0	190	30	0	1.000000	micrograph.mrc	1	0	0	0
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0	1900	500	0	0	0	190	50	0	1.000000	micrograph.mrc	1	0	0	0
0	1900	600	0	0	0	190	60	0	1.000000	micrograph.mrc	1	0	0	0
0	1900	700	0	0	0	190	70	0	1.000000	micrograph.mrc	1	0	0	0
0	1900	800	0	0	0	190	80	0	1.000000	micrograph.mrc	1	0	0	0
0	1900	900	0	0	0	190	90	0	1.000000	micrograph.mrc	1	0	0	0
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0	1900	1900	0	0	0	190	190	0	1.000000	micrograph.mrc	1	0	0	0


data_optics

loop_
_rlnOpticsGroup #1
1
@jojoelfe jojoelfe added the bug Something isn't working label Nov 30, 2023
@jojoelfe jojoelfe mentioned this issue Nov 30, 2023
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@alisterburt
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+1 on pushing this over to scipy - I'm not sure of the best way to handle these floating point errors in a general way within eulerangles and am no longer really using the package myself

@BradyAJohnston
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BradyAJohnston commented Nov 30, 2023 •
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Oooh this is a funky one. We are in luck though, as of Blender 4.0, Geometry Nodes now explicitly supports quaternions. They were actually always using quaternions under the hood, and just exposing eulers to the user. Which means we should be able to use the QUATERNION attribute type, and then use the Quaternion to Rotation node for the Instance on Points. In Blender 4.1 they will be supporting direct Quaternion input into the rotation sockert of the IoP node.

CleanShot 2023-12-01 at 06 00 26@2x

This is actually a refactoring across all of MN that can be done, for the biological assembly and CellPack instancing as well can be changed to in theory, remove the necessity for scipy altogether.

The major refactoring I am now done with (I think), so hopefully it is clear how the package still works. If you'd like to open a PR for the starfile stuff, then I can add in the CellPack / biological assembly stuff as well (unless you wanted to have a crack at them as well).

@BradyAJohnston
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Actually looking in to the Blender mathutils submodule, there is a Matrix class which has .decompose() which we could be using instead of adding the scipy dependency.

@jojoelfe
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jojoelfe commented Dec 1, 2023

Using quaternions is probably the way to go, especially when thinking about animations, but the problem then becomes converting the relion/frealign euler angle conventions into blenders quaternion convention.

Thinking about it a bit, probably the neatest approach would be to do this conversion inside Geometry Nodes using "Rotate around axis" nodes. This way this is completely exposed in the node tree and could be easily tinkered with. So in this scenario:

  • The Rot,Tilt,Psi values are being saved as attributed
  • There is a Nodegroup that called "Relion euler to quaternion" that converts these values to a quaternion
  • The quaternion goes into a "quaternion to rotation node" (which can go away in blender 4.1)
  • The rotation goes into the IoP node

I will look into this and create a PR for the starfile code first and we can go from there to assembly/cellpack (my impression was that assembly use a transformation matrix, right?)

@BradyAJohnston
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Yeah that's a good idea to just keep the raw ZYZ rotations from Relion, and then create a node group which converts it to a quaternion. You can store it as a vector or separate float attributes, up to you as to which would make more sense.

The assembly / cellpack uses rotation matrices, which is where I can replace the currently scipy usage with just storing the actual quaternions and using them inside of GN.

@BradyAJohnston BradyAJohnston mentioned this issue Dec 1, 2023
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BradyAJohnston commented Dec 5, 2023 •
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This should now be fixed in the latest release after #374 .

@BradyAJohnston BradyAJohnston mentioned this issue Dec 8, 2023
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