Adding 3dQwarpPlusMinus Interface #1974

chrisgorgo · 2017-04-27T01:31:35Z

No description provided.

codecov-io · 2017-04-27T03:30:13Z

Codecov Report

Merging #1974 into master will increase coverage by <.01%.
The diff coverage is 76.92%.

@@            Coverage Diff             @@
##           master    #1974      +/-   ##
==========================================
+ Coverage   72.63%   72.63%   +<.01%     
==========================================
  Files        1070     1070              
  Lines       54407    54433      +26     
  Branches     7857     7857              
==========================================
+ Hits        39517    39537      +20     
- Misses      13659    13665       +6     
  Partials     1231     1231

Flag	Coverage Δ
#smoketests	`72.63% <76.92%> (ø)`	⬆️
#unittests	`70.19% <76.92%> (ø)`	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/afni/__init__.py	`100% <ø> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`85.66% <76.92%> (-0.4%)`	⬇️

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codecov-io · 2017-04-27T03:30:14Z

Codecov Report

Merging #1974 into master will increase coverage by <.01%.
The diff coverage is 76.92%.

@@            Coverage Diff             @@
##           master    #1974      +/-   ##
==========================================
+ Coverage   72.63%   72.63%   +<.01%     
==========================================
  Files        1070     1070              
  Lines       54407    54433      +26     
  Branches     7857     7857              
==========================================
+ Hits        39517    39537      +20     
- Misses      13659    13665       +6     
  Partials     1231     1231

Flag	Coverage Δ
#smoketests	`72.63% <76.92%> (ø)`	⬆️
#unittests	`70.19% <76.92%> (ø)`	⬆️

Impacted Files	Coverage Δ
nipype/interfaces/afni/__init__.py	`100% <ø> (ø)`	⬆️
nipype/interfaces/afni/preprocess.py	`85.66% <76.92%> (-0.4%)`	⬇️

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 ccd0527...a64071b. Read the comment docs.

codecov-io · 2017-04-27T03:30:28Z

Codecov Report

❗ No coverage uploaded for pull request base (master@048413e). Click here to learn what that means.
The diff coverage is 75%.

@@            Coverage Diff            @@
##             master    #1974   +/-   ##
=========================================
  Coverage          ?   72.26%           
=========================================
  Files             ?     1087           
  Lines             ?    55483           
  Branches          ?     7987           
=========================================
  Hits              ?    40096           
  Misses            ?    14122           
  Partials          ?     1265

Flag	Coverage Δ
#smoketests	`72.26% <75%> (?)`
#unittests	`69.86% <75%> (?)`

Impacted Files	Coverage Δ
nipype/interfaces/afni/__init__.py	`100% <ø> (ø)`
nipype/interfaces/afni/preprocess.py	`85.61% <75%> (ø)`

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 048413e...b823356. Read the comment docs.

satra · 2017-04-27T15:01:50Z

nipype/interfaces/afni/preprocess.py

+
+
+class Qwarp(CommandLine):
+    _cmd = '3dQwarp -prefix Qwarp.nii.gz'


description, example

satra · 2017-04-27T15:01:58Z

nipype/interfaces/afni/preprocess.py

+    _cmd = '3dQwarp -prefix Qwarp.nii.gz'
+    input_spec = QwarpInputSpec
+    output_spec = QwarpOutputSpec
+


satra · 2017-04-27T15:02:30Z

nipype/interfaces/afni/preprocess.py

+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['warped_source'] = os.path.abspath("Qwarp_PLUS.nii.gz")


could these be listed with name_template in outputs

satra · 2017-04-27T15:02:54Z

nipype/interfaces/afni/preprocess.py

+
+class QwarpInputSpec(CommandLineInputSpec):
+    source_file = File(
+        desc='',


missing descriptions

satra · 2017-04-28T00:25:12Z

nipype/interfaces/afni/preprocess.py

+    """
+    _cmd = '3dQwarp -prefix Qwarp.nii.gz -plusminus'
+    input_spec = QwarpPlusMinusInputSpec
+    output_spec = QwarpPlusMinusOutputSpec


add references

done (see above)

effigies

Looks reasonable. Possible text fix.

effigies · 2017-04-28T14:43:37Z

nipype/interfaces/afni/preprocess.py

+        desc='Undistorted source file.',
+        exists=True)
+    warped_base = File(
+        desc='Undistorted source file.',


Undistored base file?

oesteban

Very useful!

chrisgorgo added 2 commits April 26, 2017 18:28

add qwarp

4032ee1

Merge branch 'master' of github.com:nipy/nipype into enh/qwarp

a64071b

chrisgorgo added 3 commits April 27, 2017 15:27

Added documentation and doctests.

9b9c3db

naming fixes

f95ce0d

fixing expected output string

01747aa

chrisgorgo added enhancement needs-review labels Apr 27, 2017

chrisgorgo changed the title ~~[WIP] adding 3dQwarp Interface~~ Adding 3dQwarpPlusMinus Interface Apr 27, 2017

fixing arg strings

3f47b2e

satra reviewed Apr 28, 2017

View reviewed changes

Merge branch 'master' of github.com:nipy/nipype into enh/qwarp

a30b2e6

effigies reviewed Apr 28, 2017

View reviewed changes

Fixed description.

5dee2f0

effigies approved these changes Apr 29, 2017

View reviewed changes

Merge branch 'master' of github.com:nipy/nipype into enh/qwarp

b823356

oesteban approved these changes Apr 29, 2017

View reviewed changes

chrisgorgo merged commit c26b3de into nipy:master Apr 29, 2017

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Adding 3dQwarpPlusMinus Interface #1974

Adding 3dQwarpPlusMinus Interface #1974

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		class Qwarp(CommandLine):
		_cmd = '3dQwarp -prefix Qwarp.nii.gz'

Adding 3dQwarpPlusMinus Interface #1974

Adding 3dQwarpPlusMinus Interface #1974

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chrisgorgo commented Apr 27, 2017

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codecov-io commented Apr 27, 2017 •

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