FIX: Stateful tractogram examples

[frheault]

After the new merge of PR #1812, most examples were not running.

Considering that before most trk saved and loaded by the tutorials were not valid, this PR is not only updating the function call, but also fixing the resulting TRK files involved.

[pep8speaks]

Hello @frheault, Thank you for updating !

• In the file dipy/workflows/tracking.py:

Line 116:33: E128 continuation line under-indented for visual indent
Line 330:37: E128 continuation line under-indented for visual indent

• In the file doc/examples/afq_tract_profiles.py:

Line 115:75: W291 trailing whitespace

• In the file doc/examples/streamline_tools.py:

Line 227:1: E402 module level import not at top of file

• In the file doc/examples/tracking_introduction_eudx.py:

Line 59:1: E402 module level import not at top of file
Line 201:1: E402 module level import not at top of file

• In the file doc/examples/tracking_pft.py:

Line 33:1: E402 module level import not at top of file

• In the file doc/examples/tracking_probabilistic.py:

Line 26:1: E402 module level import not at top of file
Line 69:1: E402 module level import not at top of file

Comment last updated at 2019-07-29 15:29:35 UTC

[skoudoro]

Thank you for this @frheault! I will try them all because currently, the CI does not run the examples.

[Garyfallidis]

Coool! Thanks @frheault !

[frheault]

I know it is a lot of files, but since it is almost exactly the same lines changed in every examples/workflows I thought that it would be faster for all of us.

Any comments that apply to all, I will fix them similarly everywhere.
Also now I tested them and open the files in MI-Brain & Trackvis and they are valid !

[arokem]

Looks great! A couple of small things.

[arokem]

This comment should now move down, to be adjacent to the line of code it refers to.

[codecov-io]

Codecov Report

Merging #1925 into master will increase coverage by 0.73%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1925      +/-   ##
==========================================
+ Coverage   83.89%   84.62%   +0.73%     
==========================================
  Files         118      118              
  Lines       14679    14682       +3     
  Branches     2326     2326              
==========================================
+ Hits        12315    12425     +110     
+ Misses       1814     1714     -100     
+ Partials      550      543       -7

Impacted Files	Coverage Δ
dipy/workflows/tracking.py	96.55% <100%> (+0.12%)	⬆️
dipy/viz/app.py	52.34% <0%> (+0.39%)	⬆️
dipy/io/vtk.py	56.31% <0%> (+0.97%)	⬆️
dipy/viz/panel.py	83.09% <0%> (+1.4%)	⬆️
dipy/io/utils.py	69.35% <0%> (+2.41%)	⬆️
dipy/testing/__init__.py	78.12% <0%> (+3.12%)	⬆️
dipy/viz/regtools.py	36.79% <0%> (+4.79%)	⬆️
dipy/utils/optpkg.py	78.26% <0%> (+8.69%)	⬆️
dipy/viz/__init__.py	90% <0%> (+10%)	⬆️
dipy/workflows/stats.py	92% <0%> (+30.4%)	⬆️
... and 1 more

[skoudoro]

When I generate the documentation, I got the following error with streamline_tools.py tutorial:

*************************************************************
streamline_tools.py
*************************************************************
Dataset is already in place. If you want to fetch it again please first remove the folder C:\Users\skoudoro\.dipy\stanford_hardi
Dataset is already in place. If you want to fetch it again please first remove the folder C:\Users\skoudoro\.dipy\stanford_hardi
Dataset is already in place. If you want to fetch it again please first remove the folder C:\Users\skoudoro\.dipy\stanford_hardi
Dataset is already in place. If you want to fetch it again please first remove the folder C:\Users\skoudoro\.dipy\stanford_hardi
ERROR:root:Voxel space values higher than dimensions
Traceback (most recent call last):
  File "..\\..\\tools\\make_examples.py", line 166, in <module>
    run_script()
  File "..\\..\\tools\\make_examples.py", line 148, in run_script
    exec(f.read(), namespace)
  File "<string>", line 238, in <module>
  File "c:\users\skoudoro\devel\dipy\dipy\io\streamline.py", line 251, in save_trk
    save_tractogram(sft, filename, bbox_valid_check=bbox_valid_check)
  File "c:\users\skoudoro\devel\dipy\dipy\io\streamline.py", line 39, in save_tractogram
    raise ValueError('Bounding box is not valid in voxel space, cannot ' +
ValueError: Bounding box is not valid in voxel space, cannot save a valid file if some coordinates are invalid

[frheault]

@skoudoro I just fixed it. I guess it me that forgot to save or hit CTRL-Z by accident. The input space was VOX, not RASMM. Perfect catch using the value error, I guess my own code save me !

[skoudoro]

I guess my own code save me!

Nice, Love it! I will try again to generate the doc, check the result and if Travis is Happy, will go ahead and merge it.

Does anyone want to have a look?

[skoudoro]

bundle_extraction.py example stopped to work. I do not think it is related to your PR but can you try to run it quickly and let me know. (Maybe it is my version of fury). Thank you

[frheault]

@skoudoro works fine on my side. I just resetup recently, nothing special that I remember (with vtk/fury)

[skoudoro]

Thank you @frheault, merging