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Start of sampling time is now the same for all frequencies #283

Merged
merged 11 commits into from
Aug 19, 2020
Merged

Start of sampling time is now the same for all frequencies #283

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2f33442
add time channel to all the freq outputs
vinferrer Aug 11, 2020
2070ee7
correct lintin
vinferrer Aug 11, 2020
f465c9c
eliminate unused import
vinferrer Aug 11, 2020
abc5a34
change sampling start at in the 40hz output
vinferrer Aug 11, 2020
0ee73ae
change intregration test checks so the test passes
vinferrer Aug 11, 2020
190586b
Merge branch 'master' of https://github.com/physiopy/phys2bids into s…
vinferrer Aug 12, 2020
f814aa1
Merge branch 'master' of https://github.com/physiopy/phys2bids into s…
vinferrer Aug 18, 2020
a950def
blank commit
vinferrer Aug 18, 2020
cf201d1
Merge branch 'master' of github.com:vinferrer/phys2bids into start_time
vinferrer Aug 18, 2020
7ada730
change sampling start time in the test
vinferrer Aug 18, 2020
df3c05e
Update phys2bids/phys2bids.py
vinferrer Aug 18, 2020
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7 changes: 7 additions & 0 deletions phys2bids/phys2bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -373,6 +373,13 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
# Also create a BlueprintOutput object for each unique frequency found.
# Populate it with the corresponding blueprint input and replace it
# in the dictionary.
# Add time channel in the proper frequency.
if uniq_freq != phys_in[run].freq[0]:
phys_out[key].ch_name.insert(0, phys_in[run].ch_name[0])
phys_out[key].units.insert(0, phys_in[run].units[0])
phys_out[key].timeseries.insert(0, np.linspace(phys_in[run].timeseries[0][0],
phys_in[run].timeseries[0][-1],
num=phys_out[key].timeseries[0].shape[0]))
phys_out[key] = BlueprintOutput.init_from_blueprint(phys_out[key])

# Preparing output parameters: name and folder.
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12 changes: 6 additions & 6 deletions phys2bids/tests/test_integration.py
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Expand Up @@ -156,7 +156,7 @@ def test_integration_heuristic(skip_integration, multifreq_lab_file):
# Check sampling frequency
assert check_string(log_info, 'Sampling Frequency', '40.0')
# Check sampling started
assert check_string(log_info, 'Sampling started', '-157.8535')
assert check_string(log_info, 'Sampling started', '3.6960')
# Check first trigger
assert check_string(log_info, 'first trigger', 'Time 0', is_num=False)

Expand All @@ -167,8 +167,8 @@ def test_integration_heuristic(skip_integration, multifreq_lab_file):

# Compares values in json file with ground truth
assert math.isclose(json_data['SamplingFrequency'], 40.0,)
assert math.isclose(json_data['StartTime'], -157.8535,)
assert json_data['Columns'] == ['O2']
assert math.isclose(json_data['StartTime'], 3.6960,)
assert json_data['Columns'] == ['time', 'O2']

# ##### Checks for 100 Hz files
# Read log file (note that this file is not the logger file)
Expand All @@ -183,7 +183,7 @@ def test_integration_heuristic(skip_integration, multifreq_lab_file):
# Check sampling frequency
assert check_string(log_info, 'Sampling Frequency', '100.0')
# Check sampling started
assert check_string(log_info, 'Sampling started', '-0.3057')
assert check_string(log_info, 'Sampling started', '3.6960')
# Check first trigger
assert check_string(log_info, 'first trigger', 'Time 0', is_num=False)

Expand All @@ -194,8 +194,8 @@ def test_integration_heuristic(skip_integration, multifreq_lab_file):

# Compares values in json file with ground truth
assert math.isclose(json_data['SamplingFrequency'], 100.0,)
assert math.isclose(json_data['StartTime'], -0.3057,)
assert json_data['Columns'] == ['CO2']
assert math.isclose(json_data['StartTime'], 3.6960,)
assert json_data['Columns'] == ['time', 'CO2']

# Remove generated files
shutil.rmtree(test_path_output)
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