ENH: Support for BIDS event files #2845
Conversation
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Just a heads up that we're working on putting all of this functionality into pybids and FitLins (see That said, this is a pretty light-weight addition that will make adapting existing pipelines to handle BIDS-formatted inputs easy, especially in the absence of BIDS stats models, which is still a draft spec. Can you merge |
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Mostly style issues, but it would also be good to add a test with the expected outputs for a simple file. Perhaps try durations and repetition times that have the potential to hit Python 2/3 differences.
$ python2.7 -c 'print(round(2.5, 0))'
3.0
$ python3.6 -c 'print(round(2.5, 0))'
2.0np.round is consistent across versions, and consistent with Python 3, evenly rounding.
nipype/algorithms/modelgen.py
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| @@ -144,6 +144,61 @@ def scale_timings(timelist, input_units, output_units, time_repetition): | |||
| timelist = [np.max([0., _scalefactor * t]) for t in timelist] | |||
| return timelist | |||
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| def bids_gen_info(bids_event_files, | |||
| condition_column='trial_type', | |||
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The space before each parameter should align with the open paren:
| condition_column='trial_type', | |
| condition_column='trial_type', |
nipype/algorithms/modelgen.py
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| @@ -144,6 +144,61 @@ def scale_timings(timelist, input_units, output_units, time_repetition): | |||
| timelist = [np.max([0., _scalefactor * t]) for t in timelist] | |||
| return timelist | |||
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| def bids_gen_info(bids_event_files, | |||
| condition_column='trial_type', | |||
| amplitude_column=None, | |||
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| amplitude_column=None, | |
| amplitude_column=None, |
nipype/algorithms/modelgen.py
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| condition_column='trial_type', | ||
| amplitude_column=None, | ||
| time_repetition=False, | ||
| ): |
nipype/algorithms/modelgen.py
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| with open(bids_event_file) as f: | ||
| f_events = csv.DictReader(f, skipinitialspace=True, delimiter='\t') | ||
| events = [{k: v for k, v in row.items()} for row in f_events] | ||
| conditions = list(set([i[condition_column] for i in events])) |
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You can release the file handle as soon as it has been fully read.
| conditions = list(set([i[condition_column] for i in events])) | |
| conditions = list(set([i[condition_column] for i in events])) |
nipype/algorithms/modelgen.py
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| amplitudes = [float(i[amplitude_column]) for i in selected_events] | ||
| runinfo.amplitudes.append(amplitudes) | ||
| except KeyError: | ||
| runinfo.amplitudes.append([1]*len(onsets)) |
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| runinfo.amplitudes.append([1]*len(onsets)) | |
| runinfo.amplitudes.append([1] * len(onsets)) |
Codecov Report
@@ Coverage Diff @@
## master #2845 +/- ##
==========================================
- Coverage 67.44% 67.41% -0.04%
==========================================
Files 341 341
Lines 43393 43427 +34
Branches 5382 5396 +14
==========================================
+ Hits 29268 29277 +9
- Misses 13427 13453 +26
+ Partials 698 697 -1
Continue to review full report at Codecov.
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@TheChymera Can you merge/rebase current master? |
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@effigies ok :) |
1.1.8 (January 28, 2019) * FIX: ANTS LaplacianThickness cmdline opts fixed up (nipy#2846) * FIX: Resolve LinAlgError during SVD (nipy#2838) * ENH: Add interfaces wrapping DIPY worflows (nipy#2830) * ENH: Update BIDSDataGrabber for pybids 0.7 (nipy#2737) * ENH: Add FSL `eddy_quad` interface (nipy#2825) * ENH: Support tckgen -select in MRtrix3 v3+ (nipy#2823) * ENH: Support for BIDS event files (nipy#2845) * ENH: CompositeTransformUtil, new ANTs interface (nipy#2785) * RF: Move pytest and pytest-xdist from general requirement into tests_required (nipy#2850) * DOC: Add S3DataGrabber example (nipy#2849) * DOC: Skip conftest module in API generation (nipy#2852) * DOC: Hyperlink DOIs to preferred resolver (nipy#2833) * MAINT: Install numpy!=1.16.0 from conda in Docker (nipy#2862) * MAINT: Drop pytest-xdist requirement, minimum pytest version (nipy#2856) * MAINT: Disable numpy 1.16.0 for Py2.7 (nipy#2855) * tag '1.1.8': (79 commits) MNT: Add @feilong to .zenodo, update ordering MNT: Update .mailmap MNT: Update .zenodo ordering Accept invitation as Zenodo release co-author (see nipy#2864) MAINT: Update .mailmap BF: allowing bids_event_file as alternate input MNT: Update .zenodo ordering MNT: Version 1.1.8 DOC: 1.1.8 changelog Update nipype/interfaces/dipy/tracks.py Update nipype/interfaces/dipy/reconstruction.py MNT: Install numpy!=1.16.0 from conda in Docker Add FSL auto test remake specs Update nipype/interfaces/io.py Remove return type named tuple Update nipype/info.py STY: Whitespace, line length Remove out_ prefix from EddyQuad outputs Apply minor edits from code review ...
SpecifyModel now supports BIDS event files as inputs.
Acknowledgment