def write_bids_metadata_file(
scan_dir,
extraction_dicts,
out_file="bids_metadata.json",
task='',
):
"""Create a sidecar JSON file according to the BIDS standard.
Parameters
----------
scan_dir : str
Path to the scan directory containing the acquisition protocol files.
extraction_dicts : str
A list of dictionaries which contain keys including `query_file` (which specifies the file, relative to `scan dir`, which to query), `regex` (which gives a regex expression which will be tested against each rowin the file until a match is found), and `field_name` (which specifies under what field name to record this value in the JSON file).
Additionally, the following keys are also supported: `type` (a python class operator, e.g. `str` to which the value should be converted), and `scale` (a float with which the value is multiplied before recording in JSON).
out_file : str, optional
Path under which to save the resulting JSON.
task_name : str, optional
String value to assign to the "TaskName" field in the BIDS JSON.
If this parameter evaluates to false, no "TaskName" will be recorded.
"""
import json
import re
from os import path
from samri.pipelines.utils import parse_paravision_date
out_file = path.abspath(path.expanduser(out_file))
scan_dir = path.abspath(path.expanduser(scan_dir))
metadata = {}
# Extract nice parameters:
for extraction_dict in extraction_dicts:
query_file = path.abspath(
path.join(scan_dir, extraction_dict['query_file']))
with open(query_file) as search:
for line in search:
if re.match(extraction_dict['regex'], line):
m = re.match(extraction_dict['regex'], line)
value = m.groupdict()['value']
try:
value = extraction_dict['type'](value)
except KeyError:
pass
try:
value = value * extraction_dict['scale']
except KeyError:
pass
metadata[extraction_dict['field_name']] = value
break
# Extract DelayAfterTrigger
try:
query_file = path.abspath(path.join(scan_dir, 'AdjStatePerScan'))
read_line = False
with open(query_file) as search:
for line in search:
if '##$AdjScanStateTime=( 2 )' in line:
read_line = True
continue
if read_line:
m = re.match(r'^<(?P<value>.*?)> <.*?>$', line)
adjustments_start = m.groupdict()['value']
adjustments_start = parse_paravision_date(
adjustments_start)
break
except IOError:
pass
else:
query_file = path.abspath(path.join(scan_dir, 'acqp'))
with open(query_file) as search:
for line in search:
if re.match(r'^##\$ACQ_time=<.*?>$', line):
m = re.match(r'^##\$ACQ_time=<(?P<value>.*?)>$', line)
adjustments_end = m.groupdict()['value']
adjustments_end = parse_paravision_date(adjustments_end)
break
adjustments_duration = adjustments_end - adjustments_start
metadata['DelayAfterTrigger'] = adjustments_duration.total_seconds()
if task:
metadata['TaskName'] = task
with open(out_file, 'w') as out_file_writeable:
json.dump(metadata, out_file_writeable, indent=1)
out_file_writeable.write(
"\n"
) # `json.dump` does not add a newline at the end; we do it here.
return out_file
def write_bids_metadata_file(scan_dir, extraction_dicts,
out_file="bids_metadata.json",
task_name=False,
):
"""Create a sidecar JSON file according to the BIDS standard.
Parameters
----------
scan_dir : str
Path to the scan directory containing the acquisition protocol files.
extraction_dicts : str
A list of dictionaries which contain keys including `query_file` (which specifies the file, relative to `scan dir`, which to query), `regex` (which gives a regex expression which will be tested against each rowin the file until a match is found), and `field_name` (which specifies under what field name to record this value in the JSON file).
Additionally, the following keys are also supported: `type` (a python class operator, e.g. `str` to which the value should be converted), and `scale` (a float with which the value is multiplied before recording in JSON).
out_file : str, optional
Path under which to save the resulting JSON.
task_name : str, optional
String value to assign to the "TaskName" field in the BIDS JSON.
If this parameter evaluates to false, no "TaskName" will be recorded.
"""
import json
import re
from os import path
from samri.pipelines.utils import parse_paravision_date
out_file = path.abspath(path.expanduser(out_file))
scan_dir = path.abspath(path.expanduser(scan_dir))
metadata = {}
# Extract nice parameters:
for extraction_dict in extraction_dicts:
query_file = path.abspath(path.join(scan_dir,extraction_dict['query_file']))
with open(query_file) as search:
for line in search:
if re.match(extraction_dict['regex'], line):
m = re.match(extraction_dict['regex'], line)
value = m.groupdict()['value']
try:
value = extraction_dict['type'](value)
except KeyError:
pass
try:
value = value * extraction_dict['scale']
except KeyError:
pass
metadata[extraction_dict['field_name']] = value
break
# Extract DelayAfterTrigger
try:
query_file = path.abspath(path.join(scan_dir,'AdjStatePerScan'))
read_line = False
with open(query_file) as search:
for line in search:
if '##$AdjScanStateTime=( 2 )' in line:
read_line = True
continue
if read_line:
m = re.match(r'^<(?P<value>.*?)> <.*?>$', line)
adjustments_start = m.groupdict()['value']
adjustments_start = parse_paravision_date(adjustments_start)
break
except IOError:
pass
else:
query_file = path.abspath(path.join(scan_dir,'acqp'))
with open(query_file) as search:
for line in search:
if re.match(r'^##\$ACQ_time=<.*?>$', line):
m = re.match(r'^##\$ACQ_time=<(?P<value>.*?)>$', line)
adjustments_end = m.groupdict()['value']
adjustments_end = parse_paravision_date(adjustments_end)
break
adjustments_duration = adjustments_end - adjustments_start
metadata['DelayAfterTrigger'] = adjustments_duration.total_seconds()
if task_name:
metadata['TaskName'] = task_name
with open(out_file, 'w') as out_file_writeable:
json.dump(metadata, out_file_writeable, indent=1)
out_file_writeable.write("\n") # `json.dump` does not add a newline at the end; we do it here.
return out_file
def write_bids_metadata_file(
scan_dir,
extraction_dicts,
out_file="bids_metadata.json",
):
import json
import re
from os import path
from samri.pipelines.utils import parse_paravision_date
out_file = path.abspath(path.expanduser(out_file))
scan_dir = path.abspath(path.expanduser(scan_dir))
metadata = {}
# Extract nice parameters:
for extraction_dict in extraction_dicts:
query_file = path.abspath(
path.join(scan_dir, extraction_dict['query_file']))
with open(query_file) as search:
for line in search:
if re.match(extraction_dict['regex'], line):
m = re.match(extraction_dict['regex'], line)
value = m.groupdict()['value']
try:
value = extraction_dict['type'](value)
except KeyError:
pass
try:
value = value * extraction_dict['scale']
except KeyError:
pass
metadata[extraction_dict['field_name']] = value
break
# Extract DelayAfterTrigger
try:
query_file = path.abspath(path.join(scan_dir, 'AdjStatePerScan'))
read_line = False
with open(query_file) as search:
for line in search:
if '##$AdjScanStateTime=( 2 )' in line:
read_line = True
continue
if read_line:
m = re.match(r'^<(?P<value>.*?)> <.*?>$', line)
adjustments_start = m.groupdict()['value']
adjustments_start = parse_paravision_date(
adjustments_start)
break
except IOError:
pass
else:
query_file = path.abspath(path.join(scan_dir, 'acqp'))
with open(query_file) as search:
for line in search:
if re.match(r'^##\$ACQ_time=<.*?>$', line):
m = re.match(r'^##\$ACQ_time=<(?P<value>.*?)>$', line)
adjustments_end = m.groupdict()['value']
adjustments_end = parse_paravision_date(adjustments_end)
break
adjustments_duration = adjustments_end - adjustments_start
metadata['DelayAfterTrigger'] = adjustments_duration.total_seconds()
with open(out_file, 'w') as out_file_writeable:
json.dump(metadata, out_file_writeable, indent=1)
out_file_writeable.write(
"\n"
) # `json.dump` does not add a newline at the end; we do it here.
return out_file