def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-d',
'--dir',
metavar='DIR',
default='.',
help='set working directory [%(default)s]')
arg_parser.add_argument('-l',
'--delay',
metavar='X',
type=float,
default=60.0,
help='set checking interval in min [%(default)s]')
arg_parser.add_argument(
'-r',
'--delay_var',
metavar='DX',
type=float,
default=5,
help='set random variance in the delay as percentage [%(default)s]')
arg_parser.add_argument(
'-m',
'--max_count',
metavar='NUM',
type=int,
default=0,
help='maximum number of actions to be performed [%(default)s]')
arg_parser.add_argument(
'-c',
'--cmd',
metavar='EXECUTABLE',
default=os.path.dirname(__file__) + '/dcm_analyze_dir.py {}',
help='execute when finding a new dir with DICOMs [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Define DEFAULT values
# verbosity
d_verbose = D_VERB_LVL
# default input directory
d_input_dir = '.'
# default output directory
d_output_dir = '.'
# default method
d_method = 'pydicom'
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=d_verbose,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-i',
'--in_dirpath',
metavar='DIR',
default=d_input_dir,
help='set input directory [%(default)s]')
arg_parser.add_argument('-o',
'--out_dirpath',
metavar='DIR',
default=d_output_dir,
help='set output directory [%(default)s]')
arg_parser.add_argument('-m',
'--method',
metavar='METHOD',
default=d_method,
help='set extraction method [%(default)s]')
arg_parser.add_argument('-t',
'--type_ext',
action='store_true',
help='add type extension [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-i',
'--in_dirpath',
metavar='DIR',
default='.',
help='set input directory [%(default)s]')
arg_parser.add_argument('-o',
'--out_dirpath',
metavar='DIR',
default='.',
help='set output directory [%(default)s]')
arg_parser.add_argument('-b',
'--basename',
metavar='NAME',
default='{name}_{date}_{time}_{sys}',
help='set output directory [%(default)s]')
arg_parser.add_argument('-m',
'--method',
metavar='METHOD',
default='pydicom',
help='set extraction method [%(default)s]')
arg_parser.add_argument('-a',
'--file_format',
metavar='METHOD',
default='pdf',
help='set output format [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver', '--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v', '--verbose',
action='count', default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q', '--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument(
'-f', '--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument(
'-i', '--in_dirpath', metavar='DIR',
default='.',
help='set input directory [%(default)s]')
arg_parser.add_argument(
'-o', '--out_dirpath', metavar='DIR',
default='.',
help='set output directory [%(default)s]')
arg_parser.add_argument(
'-n', '--name', metavar='STR',
default='{name}_{date}_{time}_{sys}',
help='set output directory [%(default)s]')
arg_parser.add_argument(
'-m', '--method', metavar='tlz|tgz|tbz2|7z|zip|txz',
default='tlz',
help='set compression method [%(default)s]')
arg_parser.add_argument(
'-k', '--keep',
action='store_true',
help='Keep DICOM sources after do_backup (and test). [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver', '--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v', '--verbose',
action='count', default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
arg_parser.add_argument(
'-q', '--quiet',
action='store_true',
help='override verbosity settings to suppress output [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument(
'-f', '--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument(
'-i', '--in_dirpath', metavar='DIR',
default='.',
help='set input directory [%(default)s]')
arg_parser.add_argument(
'-o', '--out_dirpath', metavar='DIR',
default='.',
help='set output directory [%(default)s]')
arg_parser.add_argument(
'-m', '--method', metavar='copy|move|symlink|link',
default='symlink',
help='Move DICOM sources instead of copying [%(default)s]')
arg_parser.add_argument(
'-s', '--subpath',
default='{study}/{name}_{date}_{time}_{sys}',
help='Append DICOM-generated subpath to output [%(default)s]')
arg_parser.add_argument(
'-e', '--extra_subpath',
default='dcm',
help='Append static subpath to output [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-d',
'--dirpath',
metavar='DIR',
default='.',
help='set working directory [%(default)s]')
arg_parser.add_argument(
'-m',
'--match',
metavar='STR',
default='{"_concat":"and","OperatorsName":"*****@*****.**"}',
help='set a match in the DICOM information [%(default)s]')
arg_parser.add_argument('-a',
'--action',
metavar='STR',
default='email+preprocess',
help='set action to perform [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-d',
'--dirpath',
metavar='DIR',
default='.',
help='set working directory [%(default)s]')
arg_parser.add_argument('-c',
'--dcm_info',
metavar='DIR',
default='{'
'"PatientID": null, '
'"PatientBirthDate": null, '
'"PatientName": null}',
help='set DICOM fields to update [%(default)s]')
arg_parser.add_argument(
'-b',
'--backup_prefix',
default=None,
help='set prefix to be prepended to backup files [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('ui_mode',
nargs='?',
default='tui',
help='set UI mode [%(default)s]')
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument(
'-c',
'--config',
metavar='FILE',
default=CFG_FILENAME,
help='set configuration file name/path [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument(
'-s',
'--summary',
default=utl.D_SUMMARY + '.' + utl.EXT['json'],
help='set expt. summary filepath (empty to skip) [%(default)s]')
arg_parser.add_argument('-d',
'--dirpath',
metavar='DIR',
default='.',
help='set i/o directory path [%(default)s]')
return arg_parser
def handle_arg():
"""
Handle command-line application arguments.
"""
# :: Create Argument Parser
arg_parser = argparse.ArgumentParser(
description=__doc__,
epilog=fmtm('v.{version} - {author}\n{license}', INFO),
formatter_class=argparse.RawDescriptionHelpFormatter)
# :: Add POSIX standard arguments
arg_parser.add_argument(
'--ver',
'--version',
version=fmt(
'%(prog)s - ver. {version}\n{}\n{copyright} {author}\n{notice}',
next(line for line in __doc__.splitlines() if line), **INFO),
action='version')
arg_parser.add_argument(
'-v',
'--verbose',
action='count',
default=D_VERB_LVL,
help='increase the level of verbosity [%(default)s]')
# :: Add additional arguments
arg_parser.add_argument('-f',
'--force',
action='store_true',
help='force new processing [%(default)s]')
arg_parser.add_argument('-i',
'--in_dirpath',
metavar='DIR',
default='.',
help='set input directory [%(default)s]')
arg_parser.add_argument('-o',
'--out_dirpath',
metavar='DIR',
default='.',
help='set output directory [%(default)s]')
arg_parser.add_argument(
'-s',
'--subpath',
default=utl.TPL['acquire'],
help='Append DICOM-generated subpath to output [%(default)s]')
arg_parser.add_argument(
'-n',
'--niz_subpath',
default=utl.ID['niz'],
help='Sub-path for NIfTI extraction. Empty to skip [%(default)s]')
arg_parser.add_argument(
'-m',
'--meta_subpath',
default=utl.ID['meta'],
help='Sub-path for META extraction. Empty to skip [%(default)s]')
arg_parser.add_argument(
'-p',
'--prot_subpath',
default=utl.ID['prot'],
help='Sub-path for PROT extraction. Empty to skip [%(default)s]')
arg_parser.add_argument(
'-t',
'--info_subpath',
default=utl.ID['info'],
help='Sub-path for INFO extraction. Empty to skip [%(default)s]')
arg_parser.add_argument(
'-r',
'--report_subpath',
default=utl.TPL['report'],
help='Template for the report filename. Empty to skip [%(default)s]')
arg_parser.add_argument(
'-b',
'--backup_subpath',
default=utl.TPL['backup'],
help='Template for the backup filename. Empty to skip [%(default)s]')
return arg_parser
def fill_from_dicom(format_str,
filepath,
compression=None,
extra_fields=False,
tmp_path='/tmp'):
"""
Fill a format string with information from a DICOM file.
Parameters
==========
format_str : str
| String used to set a format.
| Field syntax: [FIELD::FORMAT] (::FORMAT part is optional)
| Accepted fields (including accepted formats):
* study : Study Description : 2-int comma-sep. range for slicing.
* date : Study Date. Format : anything accepted by 'strftime'.
* time : Study Time. Format : anything accepted by 'strftime'.
* name : Patient Name. Format : 'mpicbs' to guess ID (only subjects).
* sys : StationName. Format : 'mpicbs' to guess local names.
filepath : str
DICOM file where to get information from.
compression : str or None (optional)
Determine the (de)compression method used to access the data.
extra_fields : bool (optional)
| If True, accept fields directly from pydcm. No format is supported.
| Note that this feature MUST be used with care.
Returns
=======
The formatted string.
"""
fields = {
'study': (
'StudyDescription',
lambda t, f: # slice according to 2-int tuple set in 'f'
t[int(f.split(',')[0]):int(f.split(',')[1])] if f else t,
''),
'date':
('StudyDate', lambda t, f: time.strftime(f, get_date(t)), '%Y-%m-%d'),
'time':
('StudyTime', lambda t, f: time.strftime(f, get_time(t)), '%H-%M'),
'name':
('PatientName', lambda t, f: t[:4]
if f == 'mpicbs' and (t[3] == 'T' or t[3] == 'X') else t, 'mpicbs'),
'sys': ('StationName', lambda t, f: STATION[t]
if f == 'mpicbs' and t in STATION else t, 'mpicbs'),
}
filename = os.path.basename(filepath)
temp_filepath = os.path.join(tmp_path, filename)
shutil.copy(filepath, temp_filepath)
if compression and compression in COMPRESSIONS:
dcm_filepath = os.path.splitext(temp_filepath)[0]
cmd = COMPRESSIONS[compression]['bwd'] + ' {}'.format(temp_filepath)
execute(cmd)
else:
dcm_filepath = temp_filepath
try:
dcm = pydcm.read_file(dcm_filepath)
except Exception as e:
print(e)
print('E: Could not open DICOM file: {}.'.format(dcm_filepath))
out_str = ''
else:
if extra_fields:
for item in dir(dcm):
if item[0].isupper():
fields[item] = (item, None, None)
format_kws = {}
for field_id, field_formatter in sorted(fields.items()):
dcm_id, fmt_func, field_fmt = field_formatter
try:
format_kws[field_id] = \
fmt_func(getattr(dcm, dcm_id), field_fmt) \
if fmt_func else getattr(dcm, dcm_id)
except TypeError:
format_kws[field_id] = getattr(dcm, dcm_id)
out_str = fmtm(format_str, format_kws)
finally:
if os.path.isfile(temp_filepath):
os.remove(temp_filepath)
elif os.path.isfile(dcm_filepath):
os.remove(dcm_filepath)
return out_str
def dcmpi_run(
in_dirpath,
out_dirpath,
subpath=utl.TPL['acquire'],
dcm_subpath=utl.ID['dicom'],
niz_subpath=utl.ID['niz'],
meta_subpath=utl.ID['meta'],
prot_subpath=utl.ID['prot'],
info_subpath=utl.ID['info'],
report_template=utl.TPL['report'],
backup_template=utl.TPL['backup'],
actions=ACTIONS,
force=False,
verbose=D_VERB_LVL):
"""
Standard preprocessing of DICOM files.
Args:
in_dirpath (str): Path to input directory.
out_dirpath (str): Path to output directory.
subpath (str):
dcm_subpath (str):
niz_subpath (str):
meta_subpath (str):
prot_subpath (str):
info_subpath (str):
report_template (str):
backup_template (str):
actions (dict):
force (bool): Force new processing.
verbose (int): Set level of verbosity.
Returns:
None.
"""
from dcmpi.do_acquire_sources import do_acquire_sources
from dcmpi.do_sorting import sorting
# import
dcm_dirpaths = do_acquire_sources(
in_dirpath, out_dirpath, 'copy', subpath, dcm_subpath, force, verbose)
for dcm_dirpath in dcm_dirpaths:
base_dirpath = os.path.dirname(dcm_dirpath)
# sort
sorting(
dcm_dirpath, utl.D_SUMMARY + '.' + utl.EXT['json'],
force, verbose)
# run other actions
dirpath = {
'niz': niz_subpath,
'meta': meta_subpath,
'prot': prot_subpath,
'info': info_subpath, }
dirpath = {
k: os.path.join(base_dirpath, v) for k, v in dirpath.items() if v}
for action, (func, kws) in actions.items():
kws = kws.copy()
for key, val in kws.items():
if isinstance(val, str):
kws[key] = fmtm(val)
kws.update(dict(force=force, verbose=verbose))
try:
func(**kws)
except Exception as e:
warnings.warn(str(e))
msg('Done: {}'.format(dcm_dirpath))