FIX: Viz test correction #1374

skoudoro · 2017-11-02T15:41:24Z

The goal of this PR is to update some tests for VTK 7.1.x. This PR:

Resolve tests recording on windows (Permission Error)
Update disk_slider_2d recorded_events
Replacing vtkVolumeTextureMapper2D by vtkSmartVolumeMapper

it should resolve #1282.

Can you have a look and test it @ranveeraggarwal @MarcCote @dmreagan?

Fix typos and formatting in .rst files and Python examples' documentations: - Fix typos in files. - Replace tabs for two white spaces. - Fix errors in citation and DIPY internal cross-refs. - Add missing cross-refs (e.g. Aganj MRM 2010). - Add links where necessary (ISBI HARDI Contest 2013 and FreeSurfer). - Fix LaTeX math formatting errors. - Make the example/DIPY code object markdown consistent (inverted commas). - Capitalize the acronym long names' first/corresponding letters (e.g. Constrained Spherical Deconvolution). - Capitalize acronyms (e.g. FA). - Make the writing of terms consistent in terms of uppercase/lowercase (e.g. b0 vs. B0; cospus callosum vs. Corpus Callosum, etc.). - Use the [NameYear] convention for citations. - Place all citations under a 'References' section, and use the subsection markdown for the section. - Use inverted commas consistently to reference code objects. - Make the b-value units consistent across files (s/mm^2). - Create and include missing figures for 'reconst_fwdti.py'. - Write DIPY instead of any of its variants in the documentation. - Link the first appearance of dipy in every file (use dipy_).

Use the reST syntax to highlight code blocks in README.rst when describing the DIPY installation commands.

…void "Permission Error: [WinError 32]" on windows

…vtkSmartVolumeMapper

skoudoro · 2017-11-02T20:49:16Z

Because of this line, I get this error on python 2.7 :

SyntaxError: cannot delete variable 'recorder' referenced in nested scope

This syntax is authorized in python 3.6. I do not see how I can manage that. Indeed, the recorder files need to be closed before the end of this with InTemporaryDirectory() directive. Any idea for this python problem @arokem @Garyfallidis @MarcCote @ranveeraggarwal ?

ranveeraggarwal · 2017-11-03T09:11:36Z

recorder is being referenced in the function _stop_recording_and_close. If you delete it outside its scope, it'll cause an error if the function is called after deletion.
I did a little research on this topic, and it seems that Python 2.7.x is safer when it comes to this. Python 3.2+ tells you to take care of it yourself.
Solution: we'll need to change the way this is done.

MarcCote · 2017-11-03T11:55:11Z

While at it, can you describe what you've recorded for test_ui_disk_slider. You can put it in a comment like I did for UI ListBox (see https://github.com/nipy/dipy/pull/1355/files#diff-cbb804b6eece2deed9da8e763c2a7e76R359).

MarcCote · 2017-11-03T12:11:43Z

While testing your patch, I realized that using protocol=-1 in pickle.save (in test_ui.py) causes some backward compatibility issues. Protocol 4 is not available in Python 2.7. I think we should use protocol=2 instead. Could you make the modification in this PR and re-save your .pkl using protocol 2? Thanks.

MarcCote · 2017-11-03T12:17:58Z

Regarding the del recorder issue. Why do we need the file to be close at that specific point? Is it a Windows issue?

skoudoro · 2017-11-03T13:01:40Z

Because with InTemporaryDirectory(): delete the entire directory tree at the end of this function. Unfortunately, recorder does not close the file before this deletion and it raises the following error:

Permission Error: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\Users\\koudoro\\AppData\\Local\\Temp\\tmpm1x9w6uj\\recorded_events.log'

Otherwise, ok for pickle and comment on test @MarcCote

codecov-io · 2017-11-03T13:48:49Z

Codecov Report

Merging #1374 into master will decrease coverage by 0.03%.
The diff coverage is 25%.

@@            Coverage Diff             @@
##           master    #1374      +/-   ##
==========================================
- Coverage   87.04%   87.01%   -0.04%     
==========================================
  Files         228      228              
  Lines       29077    29086       +9     
  Branches     3129     3131       +2     
==========================================
- Hits        25311    25310       -1     
- Misses       3059     3068       +9     
- Partials      707      708       +1

Impacted Files	Coverage Δ
dipy/viz/tests/test_ui.py	`83.53% <0%> (ø)`	⬆️
dipy/viz/window.py	`64.22% <0%> (-0.64%)`	⬇️
dipy/viz/tests/test_window.py	`93.6% <100%> (+0.05%)`	⬆️
dipy/viz/tests/test_fvtk.py	`91.46% <100%> (+0.1%)`	⬆️
dipy/viz/fvtk.py	`61.36% <50%> (-0.29%)`	⬇️
dipy/viz/ui.py	`89.86% <0%> (-0.48%)`	⬇️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 26413a2...0e80bc3. Read the comment docs.

MarcCote · 2017-11-03T21:38:56Z

LGTM

ranveeraggarwal · 2017-11-04T11:28:10Z

dipy/viz/window.py

@@ -514,7 +514,7 @@ def _stop_recording_and_close(obj, evt):
            self.iren.Start()
            # Deleting this object is the unique way
            # to close the file.
-            del recorder
+            recorder = None


In the _stop_recording_and_close shouldn't we have something like:

if (recorder): recorder.stop()

to prevent crash because of nullref?
Or is it that that scenario won't happen?

From what I understand self.iren.Start() is blocking until the user closes the window at which point the ExitEvents are handled before releasing the block. So, it should happen that recorder is None inside _stop_recording_and_close.

But, yeah, we could add the check to be on the safe side because something VTK still surprises me :P.

ahaha :-) , @dmreagan told me to do that and I gave the same answer as @MarcCote.

No problem, I will add this test when I will get access to my computer.

FIX: Viz test correction

Jon Haitz Legarreta Gorroño and others added 14 commits October 9, 2017 10:32

DOC: Format README.rst file code blocks.

742a74c

Use the reST syntax to highlight code blocks in README.rst when describing the DIPY installation commands.

Merge branch 'master' of https://github.com/skoudoro/dipy

20fdb6f

Merge branch 'master' of https://github.com/nipy/dipy

69a3b70

Merge branch 'master' of https://github.com/nipy/dipy

92f9a98

Merge branch 'master' of https://github.com/nipy/dipy

c5dc2e5

Merge branch 'master' of https://github.com/nipy/dipy

f9d9fc0

Merge branch 'master' of https://github.com/nipy/dipy

40478af

Merge branch 'master' of https://github.com/nipy/dipy

0553583

Merge branch 'master' of https://github.com/nipy/dipy

91a0938

Merge branch 'master' of https://github.com/nipy/dipy

b4e1895

improve open / close management of "recorded_events.log" file. This a…

343d48f

…void "Permission Error: [WinError 32]" on windows

vtkVolumeTextureMapper does not exist on vtk 7.1 so we replace it by …

77ec0f8

…vtkSmartVolumeMapper

update disk_slider_2d recording

52e1df3

skoudoro mentioned this pull request Nov 2, 2017

Tests fail on viz module #1282

Closed

re-save .pkl using protocol 2

4ff3aa9

workaround for deleting recorder object

c150783

MarcCote approved these changes Nov 3, 2017

View reviewed changes

ranveeraggarwal reviewed Nov 4, 2017

View reviewed changes

skoudoro added 2 commits November 7, 2017 09:24

prevent crash because of nullref

d4e4c1c

adding a small cosmetic test to make happy travis

0e80bc3

Garyfallidis merged commit 991b279 into dipy:master Nov 9, 2017

skoudoro deleted the fix-viz-1282 branch November 16, 2017 22:41

ShreyasFadnavis pushed a commit to ShreyasFadnavis/dipy that referenced this pull request Sep 20, 2018

Merge pull request dipy#1374 from skoudoro/fix-viz-1282

a7e32f7

FIX: Viz test correction

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

FIX: Viz test correction #1374

FIX: Viz test correction #1374

skoudoro commented Nov 2, 2017

skoudoro commented Nov 2, 2017

ranveeraggarwal commented Nov 3, 2017

MarcCote commented Nov 3, 2017

MarcCote commented Nov 3, 2017 •

edited

Loading

MarcCote commented Nov 3, 2017

skoudoro commented Nov 3, 2017

codecov-io commented Nov 3, 2017 •

edited

Loading

MarcCote commented Nov 3, 2017

ranveeraggarwal Nov 4, 2017

MarcCote Nov 4, 2017

skoudoro Nov 4, 2017

FIX: Viz test correction #1374

FIX: Viz test correction #1374

Conversation

skoudoro commented Nov 2, 2017

skoudoro commented Nov 2, 2017

ranveeraggarwal commented Nov 3, 2017

MarcCote commented Nov 3, 2017

MarcCote commented Nov 3, 2017 • edited Loading

MarcCote commented Nov 3, 2017

skoudoro commented Nov 3, 2017

codecov-io commented Nov 3, 2017 • edited Loading

Codecov Report

MarcCote commented Nov 3, 2017

ranveeraggarwal Nov 4, 2017

Choose a reason for hiding this comment

MarcCote Nov 4, 2017

Choose a reason for hiding this comment

skoudoro Nov 4, 2017

Choose a reason for hiding this comment

MarcCote commented Nov 3, 2017 •

edited

Loading

codecov-io commented Nov 3, 2017 •

edited

Loading