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[ENH] Retain sub-second resolution in scans files #451

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Merged
merged 9 commits into from
May 28, 2020
Merged

[ENH] Retain sub-second resolution in scans files #451

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0f62a72
Retain sub-second resolution in scans files.
tsalo May 12, 2020
5d1d4c6
Fix tests.
tsalo May 12, 2020
609aa27
Fix test again.
tsalo May 12, 2020
4c25a8b
Move datetime to new util function and add test.
tsalo May 12, 2020
09a9ea2
Fix test.
tsalo May 12, 2020
b95f67b
ENH: Adjust to reflect it is microseconds that are parsed/reported
yarikoptic May 13, 2020
a1e5b33
RF(TST): remove one-time use variables - oneliner is much easier to g…
yarikoptic May 13, 2020
d3e247c
ENH: make get_datetime accept microseconds kwarg to not provide micro…
yarikoptic May 13, 2020
c5fe64f
RF: centralize definition of columns in the _scans files
yarikoptic May 13, 2020
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6 changes: 3 additions & 3 deletions heudiconv/bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -406,9 +406,9 @@ def get_formatted_scans_key_row(dcm_fn):
# parse date and time and get it into isoformat
try:
date = dcm_data.ContentDate
time = dcm_data.ContentTime.split('.')[0]
td = time + date
acq_time = datetime.strptime(td, '%H%M%S%Y%m%d').isoformat()
time = dcm_data.ContentTime
td = time + ':' + date
acq_time = datetime.strptime(td, '%H%M%S.%f:%Y%m%d').isoformat()
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@yarikoptic yarikoptic May 12, 2020

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is .%f guaranteed to be present (above code would work without)? I wonder if there should be a check for '.' to be found in td?
If you could while at it place it into an auxiliary function and give it a dedicated tiny unittest - would be awesome... but if not -- that is ok ;) just feels like worthwhile

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@tsalo tsalo May 12, 2020

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Sounds good. Just added a new function in utils, as well as a test for it.

except (AttributeError, ValueError) as exc:
lgr.warning("Failed to get date/time for the content: %s", str(exc))
acq_time = ''
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2 changes: 1 addition & 1 deletion heudiconv/tests/test_heuristics.py
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Expand Up @@ -116,7 +116,7 @@ def test_scans_keys_reproin(tmpdir, invocation):
if i != 0:
assert(os.path.exists(pjoin(dirname(scans_keys[0]), row[0])))
assert(re.match(
'^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}$',
'^[\d]{4}-[\d]{2}-[\d]{2}T[\d]{2}:[\d]{2}:[\d]{2}.\d]{6}$',
row[1]))


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2 changes: 1 addition & 1 deletion heudiconv/tests/test_main.py
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Expand Up @@ -173,7 +173,7 @@ def test_get_formatted_scans_key_row():

row1 = get_formatted_scans_key_row(dcm_fn)
assert len(row1) == 3
assert row1[0] == '2016-10-14T09:26:36'
assert row1[0] == '2016-10-14T09:26:36.693000'
assert row1[1] == 'n/a'
prandstr1 = row1[2]

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