Fixed #550 : Added necessary allignment between glyph creation and ac… #551

Sassafrass6 · 2022-03-04T01:59:51Z

Added necessary alignment between glyph creation and actor mapping. If a vtkSource is not aligned with the X axis, provide 4x4 orientation matrix to repeat_sources to align.

This is necessary for the Cylinder object, which is aligned to the global Y axis in vtk. Without the correct orientation of the glyph, rotation into the z plane is not possible.

Also, the DiskSource is default aligned to the Z axis in vtk.
A similar routine for plotting discs (i.e. another use case for this patch) is included in actor.py.

Cylinder's with same specified direction as Arrows, original:

Trivial implementation of Disks (Non-functional in a similar manner to cylinders):

Correct implementation of Cylinders and Disks:

… and actor mapping. If a vtkSource is not aligned with the X axis, provide 4x4 orientation matrix to repeat_sources to align

pep8speaks · 2022-03-04T01:59:55Z

Hello @Sassafrass6! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2022-04-04 20:08:36 UTC

skoudoro · 2022-03-04T15:36:51Z

Hi @Sassafrass6,

Thank you for this PR. Quite a busy period for me, Not sure I will have time to look at your PR this week or next week.

@guaje, Can you look at this, please?

skoudoro · 2022-03-04T15:37:46Z

Could you also address all pep8 issues as you can see here

codecov · 2022-03-04T15:41:36Z

Codecov Report

Merging #551 (c0c2874) into master (dadbb8e) will decrease coverage by 0.05%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #551      +/-   ##
==========================================
- Coverage   88.61%   88.55%   -0.06%     
==========================================
  Files          55       55              
  Lines       10953    10979      +26     
  Branches     1080     1083       +3     
==========================================
+ Hits         9706     9723      +17     
- Misses        952      959       +7     
- Partials      295      297       +2

Impacted Files	Coverage Δ
fury/fury/data/fetcher.py	`71.03% <0.00%> (-1.38%)`	⬇️
fury/fury/io.py	`81.46% <0.00%> (-0.93%)`	⬇️
fury/fury/actor.py	`88.00% <0.00%> (-0.32%)`	⬇️
fury/fury/tests/test_actors.py	`91.42% <0.00%> (-0.01%)`	⬇️
fury/fury/lib.py	`100.00% <0.00%> (ø)`
fury/fury/tests/test_io.py	`98.51% <0.00%> (+0.01%)`	⬆️
fury/fury/window.py	`83.21% <0.00%> (+0.03%)`	⬆️
fury/fury/utils.py	`91.62% <0.00%> (+0.13%)`	⬆️

Sassafrass6 · 2022-03-04T16:51:25Z

I have addressed all of the PEP8 issues.

EDIT: The latest commit corrects the issue with normals.

FIXED-There is apparently still some issue with the cylinder normals. They are not shaded as one would expect.

…lyphs which must be oriented before mapping to actors

…dicular to the camera

…r to camera's focal point

guaje

Hi @Sassafrass6

Thanks for catching and fixing this. I have added some specific comments and I would like to ask you to add a new function to test the new orientation parameter. You can add it to fury.tests.test_utils.py.

fury/actor.py

fury/tests/test_actors.py

fury/utils.py

guaje

@Sassafrass6 I have added some additional requests based on your latest changes/commits.

fury/actor.py

fury/tests/test_actors.py

guaje · 2022-03-09T21:47:09Z

fury/utils.py

@@ -706,7 +706,7 @@ def get_actor_from_primitive(vertices, triangles, colors=None,


 def repeat_sources(centers, colors, active_scalars=1., directions=None,
-                   source=None, vertices=None, faces=None):
+                   source=None, vertices=None, faces=None, orientation=None):


Testing the orientation argument is not possible without a test on repeat_sources.

Yes, please do add a test in fury.tests.test_utils.py

Your implementation of test_advanced_geometry_actor is nice, thank you. I've committed the change.

repeat_sources is used by several actors. Testing its functionality requires careful thought and definitely some effort.
Because I did not author this routine, and am only trying to submit a bug fix to the code, I respectfully decline.

I understand. You have addressed all my comments. IDK if @skoudoro has anything else to add.

…tion.

Sassafrass6 · 2022-03-22T04:09:05Z

Any update on the acceptance of this PR?

The modification is critical, for the cylinder actor to function.

skoudoro · 2022-03-22T04:53:06Z

Hi @Sassafrass6,

Apologize for not giving news. The core maintainers (including me) are really focused on this workshop that we are organizing: https://dipy.org/workshops/dipy-workshop-2022

That's why we were not so active these past 2 - 3 weeks. The workshop finishes this Friday, so everything will get back to normal, next week (review, update, etc...).

I agree this is an important update which might imply a quick-release also.

skoudoro · 2022-04-04T18:33:04Z

This is necessary for the Cylinder object, which is aligned to the global Y axis in vtk

Should not it be applied to all actors? I am surprised that only the cylinders are oriented along the Y-axis. I suppose this is the case for all vtksource. Which vtksource is aligned along the X-axis?

I need to look deeper at this, when I see this tutorial, they seem to have all the same orientations.

skoudoro

some additional comments. Thank you again @Sassafrass6.

I am currently checking some vtk features and after your update, it should be good to merge

skoudoro · 2022-04-04T18:49:43Z

fury/actor.py

-    src = CylinderSource() if faces is None else None
-
-    if src is not None:


You need to keep this. It allows using your own faces and vertices if you build yourself a cylinder.

it give us flexibility for future change in the API

This appears to be from an early commit, before I addressed Guaje's comments. In the more recent commits, values for src and rotate are appropriately set to None if faces is not None.

Can you point which commit?

I do not find it on master as you can see here

Also, can you revert it? thank you

I’m looking on the glyph_orientation branch of my GitHub’s fury fork, here.

The link you’ve posted is from fury_gl:master, right?
There is no orientation argument, no disk function, etc.

What are you referencing, when you ask me to “revert it”?

Yes, this is fury-gl:master. If I merge your PR as it is, this modification will be applied which we do not want.

So either:

you rebase your PR

you merge master in your branch.

you just change this part of the code yourself and commit it.

Sorry for not being explicit, this is what I meant by reverting it (keep this feature already in master).

Ok, I review the history of this, no need to do any changes, I will go ahead and merge it. Thanks @Sassafrass6

I see what you mean now.
15 commits is a lot to review. Thank you for looking through it all.

skoudoro · 2022-04-04T18:50:18Z

fury/actor.py

+        The orientation vector of the disk.
+    colors : ndarray (N,3) or (N, 4) or tuple (3,) or tuple (4,)
+        RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1]
+    rinner : float


float, optional instead

skoudoro · 2022-04-04T18:50:24Z

fury/actor.py

+        RGB or RGBA (for opacity) R, G, B and A should be at the range [0, 1]
+    rinner : float
+        disk inner radius, default: 0.3
+    router : float


float, optional instead

skoudoro · 2022-04-04T18:50:42Z

fury/actor.py

+        disk inner radius, default: 0.3
+    router : float
+        disk outer radius, default: 0.5
+    cresolution: int, default: 6


int, optional instead

skoudoro · 2022-04-04T18:51:28Z

fury/actor.py

+        disk outer radius, default: 0.5
+    cresolution: int, default: 6
+        Number of facets used to define perimeter of disk.
+    rresolution: int, default: 2


int, optional instead

Sassafrass6 · 2022-04-04T20:00:50Z

This is necessary for the Cylinder object, which is aligned to the global Y axis in vtk

Should not it be applied to all actors? I am surprised that only the cylinders are oriented along the Y-axis. I suppose this is the case for all vtksource. Which vtksource is aligned along the X-axis?

I need to look deeper at this, when I see this tutorial, they seem to have all the same orientations.

In this example that you have linked, the arrow and cone are aligned along x. The cylinder is aligned along y, and the disk is aligned such that the normal is along z.
The camera is oriented the same way as FURY defaults to, with x to the right, y upward, and the z axis out of the monitor.
The other actors implemented within FURY are all correctly aligned on x, as far as I can tell.

I'm making the format changes now.

-Frank

Update: Changes committed

skoudoro · 2022-04-04T21:00:08Z

In this example that you have linked, the arrow and cone are aligned along x. The cylinder is aligned along y, and the disk is aligned such that the normal is along z.

I confirm.

This is ready to go as soon as you address my last comment.

skoudoro · 2022-04-04T21:42:17Z

Thank you for this useful update @Sassafrass6

Fixed fury-gl#550 : Added necessary allignment between glyph creation…

902d50a

… and actor mapping. If a vtkSource is not aligned with the X axis, provide 4x4 orientation matrix to repeat_sources to align

Changed typo in disk description, removed faces argument

f9d2785

Adhere to PEP8 styling.

5df2ff5

Sassafrass6 and others added 7 commits March 4, 2022 10:28

Transform all PolyData, so that normals are preserved on surface of g…

7a19085

…lyphs which must be oriented before mapping to actors

Added tests for advanced geometry actors

077a683

Corrected typo in actor tests

da84d0f

Corrected typo in actor tests

67f0ee2

Corrected typo in actor tests

a089da0

Disks have no thickness, so directions must not be parallel or perpen…

5d256ff

…dicular to the camera

Advanced geometry test failed because disk direction was perpendicula…

d3bacd9

…r to camera's focal point

guaje requested changes Mar 8, 2022

View reviewed changes

Sassafrass6 added 2 commits March 8, 2022 16:52

Updated to Gauje's styling suggestions

7467437

Added optional actor-specific arguments to actor tests

8ddb19a

guaje requested changes Mar 9, 2022

View reviewed changes

Sassafrass6 added 2 commits March 9, 2022 14:08

Cleaned formatting in test_advanced_geometry, thanks to Gaujes sugges…

f18f9cc

…tion.

Forwarded faces

214103e

skoudoro reviewed Apr 4, 2022

View reviewed changes

Disk description format update

c0c2874

skoudoro merged commit 8335555 into fury-gl:master Apr 4, 2022

skoudoro mentioned this pull request Apr 4, 2022

Fixed the rotation matrix in repeat_primitive. #555

Merged

skoudoro added the type:Bug Fix Something isn't working label Apr 4, 2022

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		src = CylinderSource() if faces is None else None

		if src is not None:

Fixed #550 : Added necessary allignment between glyph creation and ac… #551

Fixed #550 : Added necessary allignment between glyph creation and ac… #551

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