Empty acq_time results in empty cell not 'n/a' #390
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BIDS validator gives me this error for acq_time: `[ERR] Empty cell in TSV file detected: The proper way of labeling missing values is "n/a"` This is because `str(None)` in Python gives 'None' which has True boolean value. Fortunately, the fix is simple.
for cases where the field exists but is empty
ok...
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Coverage 74.56% 74.56%
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Files 35 35
Lines 2744 2744
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Misses 698 698
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yarikoptic
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Dec 16, 2019
This is largely a bug fix. Metadata and order of `_key-value` fields in BIDS could change from the result of converting using previous versions, thus minor version boost. 14 people contributed to this release -- thanks [everyone](https://github.com/nipy/heudiconv/graphs/contributors)! Enhancement - Use [etelemetry](https://pypi.org/project/etelemetry) to inform about most recent available version of heudiconv. Please set `NO_ET` environment variable if you want to disable it ([#369][]) - BIDS: - `--bids` flag became an option. It can (optionally) accept `notop` value to avoid creation of top level files (`CHANGES`, `dataset_description.json`, etc) as a workaround during parallel execution to avoid race conditions etc. ([#344][]) - Generate basic `.json` files with descriptions of the fields for `participants.tsv` and `_scans.tsv` files ([#376][]) - Use `filelock` while writing top level files. Use `HEUDICONV_FILELOCK_TIMEOUT` environment to change the default timeout value ([#348][]) - `_PDT2` was added as a suffix for multi-echo (really "multi-modal") sequences ([#345][]) - Calls to `dcm2niix` would include full output path to make it easier to discern in the logs what file it is working on ([#351][]) - With recent [datalad]() (>= 0.10), created DataLad dataset will use `--fake-dates` functionality of DataLad to not leak data conversion dates, which might be close to actual data acquisition/patient visit ([#352][]) - Support multi-echo EPI `_phase` data ([#373][] fixes [#368][]) - Log location of a bad .json file to ease troubleshooting ([#379][]) - Add basic pypi classifiers for the package ([#380][]) Fixed - Sorting `_scans.tsv` files lacking valid dates field should not cause a crash ([#337][]) - Multi-echo files detection based number of echos ([#339][]) - BIDS - Use `EchoTimes` from the associated multi-echo files if `EchoNumber` tag is missing ([#366][] fixes [#347][]) - Tolerate empty ContentTime and/or ContentDate in DICOMs ([#372][]) and place "n/a" if value is missing ([#390][]) - Do not crash and store original .json file is "JSON pretification" fails ([#342][]) - ReproIn heuristic - tollerate WIP prefix on Philips scanners ([#343][]) - allow for use of `(...)` instead of `{...}` since `{}` are not allowed ([#343][]) - Support pipolar fieldmaps by providing them with `_epi` not `_magnitude`. "Loose" BIDS `_key-value` pairs might come now after `_dir-` even if they came first before ([#358][] fixes [#357][]) - All heuristics saved under `.heudiconv/` under `heuristic.py` name, to avoid discrepancy during reconversion ([#354][] fixes [#353][]) - Do not crash (with TypeError) while trying to sort absent file list ([#360][]) - heudiconv requires nipype >= 1.0.0 ([#364][]) and blacklists `1.2.[12]` ([#375][]) * tag 'v0.6.0': (60 commits) Version boost to 0.6.0 DOC: populate detailed changelog for 0.6.0 and tune up formatting in previous one Fix miscellaneous typos in ReproIn heuristic file. BF: fix check for the sbatch (SLURM) not being available ENH: make test-compare-two-versions take any two worktrees, and just show diff if results already known Update heudiconv/convert.py apply @mgxd 's suggestions, adding a warning and a timeout environment variable need str typecast Use empty string not None Empty acq_time results in empty cell not 'n/a' DOC: Clarify tarball session handling remove repetitive import statement respond to review - add explicit py2 check - change file saving strategy - use logger instead of print fix remaning py2 errors MNT: Add Python support metadata to package fix some python2/3 incompatibilities add return data (accidently removed return) make content unicode test that load_json provides filename if invalid explicitly name invalid json ...
yarikoptic
added a commit
that referenced
this pull request
Dec 16, 2019
[0.6.0] - 2019-12-16 This is largely a bug fix. Metadata and order of `_key-value` fields in BIDS could change from the result of converting using previous versions, thus minor version boost. 14 people contributed to this release -- thanks [everyone](https://github.com/nipy/heudiconv/graphs/contributors)! Enhancement - Use [etelemetry](https://pypi.org/project/etelemetry) to inform about most recent available version of heudiconv. Please set `NO_ET` environment variable if you want to disable it ([#369][]) - BIDS: - `--bids` flag became an option. It can (optionally) accept `notop` value to avoid creation of top level files (`CHANGES`, `dataset_description.json`, etc) as a workaround during parallel execution to avoid race conditions etc. ([#344][]) - Generate basic `.json` files with descriptions of the fields for `participants.tsv` and `_scans.tsv` files ([#376][]) - Use `filelock` while writing top level files. Use `HEUDICONV_FILELOCK_TIMEOUT` environment to change the default timeout value ([#348][]) - `_PDT2` was added as a suffix for multi-echo (really "multi-modal") sequences ([#345][]) - Calls to `dcm2niix` would include full output path to make it easier to discern in the logs what file it is working on ([#351][]) - With recent [datalad]() (>= 0.10), created DataLad dataset will use `--fake-dates` functionality of DataLad to not leak data conversion dates, which might be close to actual data acquisition/patient visit ([#352][]) - Support multi-echo EPI `_phase` data ([#373][] fixes [#368][]) - Log location of a bad .json file to ease troubleshooting ([#379][]) - Add basic pypi classifiers for the package ([#380][]) Fixed - Sorting `_scans.tsv` files lacking valid dates field should not cause a crash ([#337][]) - Multi-echo files detection based number of echos ([#339][]) - BIDS - Use `EchoTimes` from the associated multi-echo files if `EchoNumber` tag is missing ([#366][] fixes [#347][]) - Tolerate empty ContentTime and/or ContentDate in DICOMs ([#372][]) and place "n/a" if value is missing ([#390][]) - Do not crash and store original .json file is "JSON pretification" fails ([#342][]) - ReproIn heuristic - tolerate WIP prefix on Philips scanners ([#343][]) - allow for use of `(...)` instead of `{...}` since `{}` are not allowed ([#343][]) - Support pipolar fieldmaps by providing them with `_epi` not `_magnitude`. "Loose" BIDS `_key-value` pairs might come now after `_dir-` even if they came first before ([#358][] fixes [#357][]) - All heuristics saved under `.heudiconv/` under `heuristic.py` name, to avoid discrepancy during reconversion ([#354][] fixes [#353][]) - Do not crash (with TypeError) while trying to sort absent file list ([#360][]) - heudiconv requires nipype >= 1.0.0 ([#364][]) and blacklists `1.2.[12]` ([#375][]) * tag 'v0.6.0': Boost perspective release date in changelog to today ENH(TST): Fix version to older pytest to ease backward compatibility testing RF: use tmpdir not tmp_path fixture FIX: minor typo in CHANGELOG.md
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BIDS validator gives me this error for acq_time:
[ERR] Empty cell in TSV file detected: The proper way of labeling missing values is "n/a"This is because
str(None)in Python gives 'None' which has True boolean value. Fortunately, the fix is simple.