enh: calcmedian interface #2167
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Codecov Report
@@ Coverage Diff @@
## master #2167 +/- ##
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+ Coverage 72.25% 72.26% +<.01%
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Files 1168 1168
Lines 58405 58438 +33
Branches 8400 8402 +2
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+ Hits 42203 42232 +29
- Misses 14868 14871 +3
- Partials 1334 1335 +1
Continue to review full report at Codecov.
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Codecov Report
@@ Coverage Diff @@
## master #2167 +/- ##
==========================================
- Coverage 72.25% 72.25% -0.01%
==========================================
Files 1168 1169 +1
Lines 58405 58486 +81
Branches 8400 8416 +16
==========================================
+ Hits 42203 42261 +58
- Misses 14868 14879 +11
- Partials 1334 1346 +12
Continue to review full report at Codecov.
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nipype/algorithms/misc.py
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| @@ -1380,6 +1380,51 @@ def merge_rois(in_files, in_idxs, in_ref, | |||
| return out_file | |||
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| class CalculateMedianInputSpec(BaseInterfaceInputSpec): | |||
| in_file = InputMultiPath(File(exists=True, mandatory=True, | |||
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in_files since multiple files are acceptable.
nipype/algorithms/misc.py
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| in_file = InputMultiPath(File(exists=True, mandatory=True, | ||
| desc="One or more realigned Nifti 4D timeseries")) | ||
| median_file = traits.Str('median.nii.gz', usedefault=True, | ||
| desc="Filename to store median image") |
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perhaps add a boolean flag to indicate whether the median should be computed individually or across files. and generate the appropriate outputs based on the flag.
nipype/algorithms/misc.py
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| class CalculateMedianInputSpec(BaseInterfaceInputSpec): | ||
| in_file = InputMultiPath(File(exists=True, mandatory=True, | ||
| desc="One or more realigned Nifti 4D timeseries")) | ||
| median_file = traits.Str('median.nii.gz', usedefault=True, |
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I defined a _gen_fname instead that should handle multiple in_files accordingly
Changes proposed in this pull request
CalculateMedianinterface that takes one or more 4D realigned timeseries and returns the average across each timeseries' medians.