Skip to content

New interfaces #1460

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 55 commits into from
May 30, 2016
Merged

New interfaces #1460

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
55 commits
Select commit Hold shift + click to select a range
b5a6024
Removed S3 datasink stuff
pintohutch Jan 13, 2016
70ca457
Started adding in logic for num_threads and changed names of real mem…
pintohutch Jan 13, 2016
36e1446
Added cmd-level threads and memory profiling
pintohutch Jan 14, 2016
61b8d0c
Resolved conflicts from re-basing and pulling in nipype master
pintohutch Jan 14, 2016
a3c9be7
Merge branch 'nipy-master' into resource_multiproc
pintohutch Jan 14, 2016
43c0d56
remove MultiProc, MultiprocPlugin is default
carolFrohlich Jan 15, 2016
0bb6d79
change old namespaces
carolFrohlich Jan 19, 2016
a68e0e6
Added initial num_threads monitoring code
pintohutch Jan 19, 2016
5dac574
Merged Carol's changes
pintohutch Jan 19, 2016
e40e305
Merge pull request #8 from nipy/master
sgiavasis Feb 3, 2016
97e7333
Manual merge of s3_datasink and resource_multiproc branch for cpac run
pintohutch Feb 3, 2016
08a485d
Manual merge of s3_datasink and resource_multiproc branch for cpac run
pintohutch Feb 3, 2016
e5945e9
Changed resources fetching to its function and try-blocked it in case…
pintohutch Feb 3, 2016
9cb7a68
Fixed pickling bug of instance method by passing profiling flag inste…
pintohutch Feb 4, 2016
2de8786
Merge pull request #6 from nipy/master
pintohutch Feb 4, 2016
6e3a7b5
Merged resource_multiproc into s3_multiproc
pintohutch Feb 4, 2016
fe0a352
Merged resource_multiproc into s3_multiproc
pintohutch Feb 4, 2016
7cc0731
Merge branch 's3_multiproc' into resource_multiproc
pintohutch Feb 4, 2016
7b3d19f
Re-pulled in changes from github
pintohutch Feb 4, 2016
5733af9
Fixed hsarc related to yrt blocking
pintohutch Feb 4, 2016
544dddf
Removed forcing of runtime_profile to be off:
pintohutch Feb 4, 2016
c074299
Made when result is None that the end stats are N/A
pintohutch Feb 4, 2016
a4e3ae6
Added try-blocks around the runtime profile stats in callback logger
pintohutch Feb 4, 2016
e25ac8c
Cleaned up some code and removed recursion from get_num_threads
pintohutch Feb 5, 2016
d714a03
Added check for runtime having 'get' attribute
pintohutch Feb 9, 2016
27ee192
Removed print statements
pintohutch Feb 12, 2016
c99f834
Removed more print statements and touched up some code to be more lik…
pintohutch Feb 12, 2016
07461cf
Added a fix for the recursive symlink bug (was happening because whil…
pintohutch Feb 12, 2016
116a6a1
Removed node.run level profiling
pintohutch Feb 12, 2016
c1376c4
Updated keyword in result dictionary to runtime instead of cmd-level
pintohutch Feb 17, 2016
2ce2661
Added afni centrality interface
pintohutch Feb 18, 2016
0fe4518
Merge pull request #9 from nipy/master
sgiavasis Feb 23, 2016
05c95b1
Added interface for 3dClipLevel.
sgiavasis Feb 23, 2016
7ec5538
Added an interface for 3dSeg.
sgiavasis Feb 23, 2016
d674756
Added an interface for AFNI's 3dmask_tool.
sgiavasis Feb 26, 2016
c043685
Added small docstring comment
pintohutch Mar 17, 2016
b978529
Merged in commits from @sgiavasis
pintohutch Mar 17, 2016
3f0470e
Merge branch 'sgiavasis-master' into new_interfaces
pintohutch Mar 17, 2016
8e88e09
Added 3dECM interface
pintohutch Mar 23, 2016
a80756c
Merge pull request #12 from nipy/master
pintohutch Mar 25, 2016
cc9918c
Merge pull request #10 from FCP-INDI/new_interfaces
sgiavasis Apr 21, 2016
1db5495
3dAllineate interface out_matrix output file handling fixed.
sgiavasis Apr 21, 2016
3fc3821
Merge pull request #15 from sgiavasis/master
pintohutch Apr 26, 2016
d8119d3
Auto-generated unit tests for new afni interfaces
pintohutch Apr 27, 2016
22677a7
Merge pull request #20 from nipy/master
pintohutch Apr 27, 2016
9f3de6d
Removed resource_multiproc code so only new_interfaces code is left
pintohutch Apr 27, 2016
95d5cc3
Merge branch 'new_interfaces' of https://github.com/fcp-indi/nipype i…
pintohutch Apr 27, 2016
15a7cef
Fixed unit test for s3 datasink override interface input
pintohutch Apr 27, 2016
0a5bb0b
Added new interfaces to __init__ import
pintohutch Apr 27, 2016
df8c65f
Changed doctests to use functional.nii
pintohutch Apr 27, 2016
a28ed37
Fixed commandline strings for centrality doctests
pintohutch Apr 28, 2016
5c89bdf
Minor fix to 3dSeg's aggregate_outputs
sgiavasis May 11, 2016
5ad92bd
Merge pull request #23 from sgiavasis/new_interfaces_seg
pintohutch May 11, 2016
9a8196f
Merge pull request #24 from nipy/master
pintohutch May 11, 2016
bb3a5da
Updated CHANGES to reflect AFNI interfaces
pintohutch May 17, 2016
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGES
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,8 @@ Release 0.12.0-rc1 (April 20, 2016)
* ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
* FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
* ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
* ENH: Added interfaces for AFNI 3dDegreeCentrality, 3dECM, 3dLFCD, 3dClipLevel, 3dmask_tool, and 3dSeg
(https://github.com/nipy/nipype/pull/1460)

Release 0.11.0 (September 15, 2015)
============
Expand Down
7 changes: 4 additions & 3 deletions nipype/interfaces/afni/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,10 @@

from .base import Info
from .preprocess import (To3D, Refit, Resample, TStat, Automask, Volreg, Merge,
ZCutUp, Calc, TShift, Warp, Detrend, Despike, Copy,
Fourier, Allineate, Maskave, SkullStrip, TCat, Fim,
BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
ZCutUp, Calc, TShift, Warp, Detrend, Despike,
DegreeCentrality, ECM, LFCD, Copy, Fourier, Allineate,
Maskave, SkullStrip, TCat, ClipLevel, MaskTool, Seg,
Fim, BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
TCorrelate, TCorr1D, BrickStat, ROIStats, AutoTcorrelate,
AFNItoNIFTI, Eval, Means, Hist, FWHMx, OutlierCount,
QualityIndex)
Expand Down
Loading