[ENH] Refactor VTK and tvtk -based interfaces #973

oesteban · 2014-10-21T18:03:09Z

This PR has ended up as follows:

Improve the way VTK and tvtk are loaded (created nipype.interfaces.vtkbase to encapsulate it).
Improve the use of VTK and tvtk in algorithms.mesh and interfaces.fsl.utils.
Automate outputs/inputs decision depending on VTK version (see AttributeError: 'PolyDataWriter' object has no attribute 'set_input_data' #1218)
Set ETS_TOOLKIT=null (headless operation) before loading tvtk, then leave environment as it was before (close Enthought Tool Suite configuration #972).
Added VTK and tvtk in travis for python 2.7 and in circleCi. AFAIK, VTK wrapping is not quite ready in python 3.x. Before this, both travis and circle skipped tests because VTK was not found (tests had to be run locally).

oesteban · 2014-10-22T08:11:19Z

Hi @satra, I think this is now like the matplotlib backend configuration but it doesn't look like working out... It seems it's not set when pipelines are included in the __main__ of a script.

Conflicts: nipype/pipeline/plugins/base.py

chrisgorgo · 2015-04-09T09:48:54Z

nipype/pipeline/plugins/base.py

 try:
    import matplotlib
    matplotlib.use('%s')
 except ImportError:
    can_import_matplotlib = False
    pass
+except


what's with this lone "except"?

That's ugly :( (deleting...).

Thanks for spotting it :)

chrisgorgo · 2015-04-09T10:07:50Z

Could you add info about this variable to the docs? http://nipy.org/nipype/users/config_file.html

oesteban · 2015-04-09T14:35:17Z

I would not merge this though, I think they are changing this in ETS.

I have to check before merging.

chrisgorgo · 2015-09-09T20:36:36Z

any updates on this?

oesteban · 2015-09-10T09:16:10Z

I think I'm closing this PR. First of all, in ETS this 'null' plugin is changing its place. Second, even with this config, initialization was not working ok.

If somebody else reports problem with ETS, then I will check on this again.

Conflicts: CHANGES nipype/algorithms/mesh.py nipype/algorithms/tests/test_mesh_ops.py

* upstream/master: Correct versions and consistency in install.rst fix:import utils needed one more dot fix: absolute to relative imports add vtk version checking in fsl interfaces update CHANGES Fix nipy#1218 only, not addressing nipy#973 force setting ETS_TOOLKIT before tvtk nipy#972 Created TVTKBaseInterface. Should fix nipy#1218

Conflicts: CHANGES nipype/algorithms/mesh.py

satra · 2016-02-10T17:32:06Z

nipype/interfaces/fsl/utils.py

-                 desc=('Name of file containing initial warp-fields/coefficients (follows premat). This could e.g. be a '
-                       'fnirt-transform from a subjects structural scan to an average of a group '
-                       'of subjects.'))
+                 desc='Name of file containing initial warp-fields/coefficients (follows premat). This could e.g. be a '


are you sure, this works? without the parenthesis? can you check the doc rendering as well?

I think so: https://circle-artifacts.com/gh/nipy/nipype/699/artifacts/0/home/ubuntu/nipype/doc/_build/html/interfaces/generated/nipype.interfaces.fsl.utils.html#convertwarp

I removed the parenthesis because they raised a pylint warning

oesteban · 2016-02-11T16:21:47Z

Hi @satra, I've been fighting with the settings of VTK6 and the mayavi version you suggested. I am reaching to the conclusion that the effort is not worth (yet). Caveats:

VTK6 is not in precise (default release of ubuntu in travis), so I had to update to trusty (which is in testing phase, maybe we don't want to have testing build environments).
Kitware does not support python 3 (see Python 3 support enthought/mayavi#84), therefore we are in the exact same situation as before.

We can move on trusty, and simplify the travis settings, but anyways it has to be on python 2. Should I revert back the code (in the end, it was working before), save the current config to a gist and update it when VTK supports python 3?

oesteban · 2016-02-13T20:18:47Z

@satra, I finally reverted back the travis config file. I think we should wait for support of python 3 in VTK. In the meantime, this is good to check that it works also without VTK

satra · 2016-02-13T20:21:43Z

some conflicts have risen with all the code that has been merged.

@oesteban - do you mean we need to check that it works without VTK? or that you have already checked?

oesteban · 2016-02-13T20:23:49Z

When python is 2 then the vtk is installed and explicit regression tests (no auto tests) are done. If python is 3 vtk is not installed, and we test that this does not cause any problem.

oesteban · 2016-02-22T17:32:12Z

Is this ready to go? I would need to merge this before the inputs/outputs refactoring.

I finally stalled #1240 and continued outside that PR because the changes were huge. If you want to have a sneak peek on how things are, I am working on this branch: https://github.com/oesteban/nipype/tree/enh/DerivationOfInterfacesRefactoring. This branch could mean a jump to v. 1.5 or similar (I would reserve 2.0 for a version including the workflow patterns).

If this branch was merged, then I will withdraw #1240 and #882 since they will not make any sense (for the interfaced workflows, with the new code it will be rather easy to produce the pattern).

[ENH] Refactor VTK and tvtk -based interfaces

satra · 2016-02-22T18:32:28Z

@oesteban - we have merged a bunch of PRs without making any changes to the CHANGES file. can we update it for at least the major ones.

oesteban added 2 commits October 21, 2014 19:48

Added ets.toolkit configuration to initialization

420fa76

remove ets.toolkit config in mesh (nipy#972)

559e698

oesteban added 3 commits February 23, 2015 10:43

Merge branch 'master' into enh/ETSConfigTookit

1f9372f

Conflicts: nipype/pipeline/plugins/base.py

Merge branch 'master' into enh/ETSConfigTookit

545f8c5

add new import under traits as failback for enthougth

1231a5e

chrisgorgo reviewed Apr 9, 2015
View reviewed changes

oesteban added 2 commits April 9, 2015 16:27

Merge branch 'master' into enh/ETSConfigTookit

dda44ba

remove error, add config to docs

a72fd34

oesteban closed this Sep 10, 2015

oesteban mentioned this pull request Sep 16, 2015

nosetest fails when X-server not present #1178

Closed

oesteban reopened this Sep 16, 2015

oesteban added 2 commits September 16, 2015 21:04

setting ETS_TOOLKIT

d53ab22

insert here new TVTKBaseInterface

485c44d

oesteban added a commit to oesteban/nipype that referenced this pull request Sep 18, 2015

Fix nipy#1218 only, not addressing nipy#973

f029d4d

oesteban added 4 commits September 18, 2015 12:02

Merge branch 'fix/TVTKPolyDataWriter' into enh/ETSConfigTookit

bfb0002

ETS_TOOLKIT settings in algorithms.mesh

21b86ac

Merge branch 'fix/TVTKPolyDataWriter' into enh/ETSConfigTookit

e144fd2

search all tvtk imports and fix ETS_TOOLKIT

90f27bd

oesteban changed the title ~~Added ets_toolkit config option~~ [ENH] Prevent crash when tvtk is loaded ETS_TOOLKIT null Sep 24, 2015

Merge branch 'master' into enh/ETSConfigTookit

f8f2bed

Conflicts: CHANGES nipype/algorithms/mesh.py nipype/algorithms/tests/test_mesh_ops.py

oesteban added 4 commits December 14, 2015 07:45

Merge branch 'master' into enh/ETSConfigTookit

f79aaad

Conflicts: CHANGES nipype/algorithms/mesh.py

add autotest file for TVTKBaseInterface

6416e5b

Merge branch 'master' into enh/ETSConfigTookit

befd2db

Merge branch 'master' into enh/ETSConfigTookit

a0f4a7e

satra reviewed Feb 10, 2016
View reviewed changes

Oscar Esteban added 13 commits February 10, 2016 11:15

update travis

94eeea2

remove empty line before docstring

a6ec41e

add multiverse for ubuntu

a17422e

travis set to pin libvtk6-dev from trusty

c9968ae

fix error in travis

807708b

fix error in travis

39b84f7

trying to fix travis

f809b41

add trusty-updates-

76e64cc

still fixing VTK6 installation in travis

bf8192d

fixed command as sudo

5843591

use ubuntu trusty

b9e051d

modify the neurodebian script for travis

62a23e2

remove ubuntu pinning

664a839

Oscar Esteban added 6 commits February 11, 2016 08:26

remove python-vtk from travis

4a778c8

Merge branch 'master' into enh/ETSConfigTookit

3cd40e1

added disable flag in codacy errors

0087bd9

revert back travis

a2e52ee

Merge branch 'master' into enh/ETSConfigTookit

618fb23

add disable flag for codacy

2448821

Merge branch 'master' into enh/ETSConfigTookit

3c75d63

satra added a commit that referenced this pull request Feb 22, 2016

Merge pull request #973 from oesteban/enh/ETSConfigTookit

47587b9

[ENH] Refactor VTK and tvtk -based interfaces

satra merged commit 47587b9 into nipy:master Feb 22, 2016

oesteban deleted the enh/ETSConfigTookit branch September 8, 2016 18:49

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