def ecg_to_dcm(src, dest, extra_ds=dicom.dataset.Dataset(), format_ch='d', callback=None):
"""Convert 12-Lead Electrocardiogram data into DICOM-ECG standard compliant format."""
# Data values are encoded interleaved. That is:
# Lead I, II, III, aVR, aVL, aVF, V1, V2, V3, V4, V5, V6, I, II, III, ...
# The unit of signals collected by the cardiac conduction is: 0.4V/(2^15).
if not dest:
dest = fileutil.replace_ext(src, '.dcm')
data_set = ECGDataset(src, '<{}'.format(format_ch * 12), 500,
('I', 'II', 'III', 'aVR', 'aVL', 'aVF', 'V1', 'V2', 'V3', 'V4', 'V5', 'V6'),
adjust_callback=callback)
data_set.update(extra_ds)
data_set.save_as(dest)
def main():
args = _parse_args()
_load_config(args)
logger = _get_logger(args)
if not args.source or not os.path.isfile(args.source):
logger.error('Invalid source file: {}'.format(args.source))
_report_error(_ErrorCode.source_file_not_found)
if not args.target:
args.target = fileutil.replace_ext(args.source, '.dcm')
import tempfile
if args.host:
fd, dest_dcm = tempfile.mkstemp()
os.close(fd)
else:
dest_dcm = args.target
import dat2dcm_v2
from PatientInfoProvider import fetch_patient_info
try:
extra_ds = {}
if args.info:
extra_ds = fetch_patient_info(args.info,
criteria_arg=args.criteria)
dat2dcm_v2.ecg_to_dcm(args.source, dest_dcm, extra_ds, args.format)
logger.info('{} -> {}'.format(args.source, dest_dcm))
except Exception as exc:
logger.info('Failed to complete this operation: {} -> {}. {!r}'.format(
args.source, dest_dcm, exc))
raise
if args.host:
import ftplib
try:
with ftplib.FTP() as ftp:
ftp.connect(args.host, int(args.port, 0) if args.port else 0)
ftp.login(args.user, args.passwd)
args.target = os.path.basename(args.target)
with open(dest_dcm, 'rb') as fp:
ftp.storbinary('STOR {}'.format(args.target), fp)
logger.info('The target file is saved as: {}'.format(
args.target))
except (ftplib.Error, OSError) as e:
logger.error('{!r}'.format(e))
_report_error(_ErrorCode.ftp_error)
finally:
os.unlink(dest_dcm)
def fecg_to_dcm(src, dest=None):
'''Convert Foetus Electrocardiogram data into DICOM-ECG standard compliant format.'''
# Data values are encoded interleaved. That is:
# lead 1, 2, 3, 4, 5, 1, 2, ...
if not dest:
dest = fileutil.replace_ext(src, '.dcm')
data_set = DCMECGDataset(src,
'<{}'.format('d' * 5),
1000,
5, ('', '', '', '', ''),
adjust_callback=lambda v: int(v * 100),
is_12_lead_ecg=False)
data_set.save_as(dest)
def ecg_to_dcm(src, dest=None):
'''Convert 12-Lead Electrocardiogram data into DICOM-ECG standard compliant format.'''
# Data values are encoded interleaved. That is:
# Lead I, II, III, aVR, aVL, aVF, V1, V2, V3, V4, V5, V6, I, II, III, ...
# The unit of signals collected by the cardiac conduction is: 0.4V/(2^15).
if not dest:
dest = fileutil.replace_ext(src, '.dcm')
data_set = DCMECGDataset(src,
'<{}'.format('d' * 12),
500,
12, ('I', 'II', 'III', 'aVR', 'aVL', 'aVF', 'V1',
'V2', 'V3', 'V4', 'V5', 'V6'),
adjust_callback=lambda v: int(v * 1000 / 6))
data_set.save_as(dest)
def main():
args = _parse_args()
_load_config(args)
logger = _get_logger(args)
if not args.source or not os.path.isfile(args.source):
logger.error('Invalid source file: {}'.format(args.source))
_report_error(_ErrorCode.source_file_not_found)
if not args.target:
args.target = fileutil.replace_ext(args.source, '.dcm')
import tempfile
if args.host:
fd, dest_dcm = tempfile.mkstemp(); os.close(fd)
else:
dest_dcm = args.target
import dat2dcm_v2
from PatientInfoProvider import fetch_patient_info
try:
extra_ds = {}
if args.info:
extra_ds = fetch_patient_info(args.info, criteria_arg=args.criteria)
dat2dcm_v2.ecg_to_dcm(args.source, dest_dcm, extra_ds, args.format)
logger.info('{} -> {}'.format(args.source, dest_dcm))
except Exception as exc:
logger.info('Failed to complete this operation: {} -> {}. {!r}'.format(args.source, dest_dcm, exc))
raise
if args.host:
import ftplib
try:
with ftplib.FTP() as ftp:
ftp.connect(args.host, int(args.port, 0) if args.port else 0)
ftp.login(args.user, args.passwd)
args.target = os.path.basename(args.target)
with open(dest_dcm, 'rb') as fp:
ftp.storbinary('STOR {}'.format(args.target), fp)
logger.info('The target file is saved as: {}'.format(args.target))
except (ftplib.Error, OSError) as e:
logger.error('{!r}'.format(e))
_report_error(_ErrorCode.ftp_error)
finally:
os.unlink(dest_dcm)
def ecg_to_dcm(src, dest=None):
"""Convert 12-Lead Electrocardiogram data into DICOM-ECG standard compliant format."""
# Data values are encoded interleaved. That is:
# Lead I, II, III, aVR, aVL, aVF, V1, V2, V3, V4, V5, V6, I, II, III, ...
# The unit of signals collected by the cardiac conduction is: 0.4V/(2^15).
if not dest:
dest = fileutil.replace_ext(src, ".dcm")
data_set = DCMECGDataset(
src,
"<{}".format("d" * 12),
500,
12,
("I", "II", "III", "aVR", "aVL", "aVF", "V1", "V2", "V3", "V4", "V5", "V6"),
adjust_callback=lambda v: int(v * 1000 / 6),
)
data_set.save_as(dest)
def fecg_to_dcm(src, dest=None):
"""Convert Foetus Electrocardiogram data into DICOM-ECG standard compliant format."""
# Data values are encoded interleaved. That is:
# lead 1, 2, 3, 4, 5, 1, 2, ...
if not dest:
dest = fileutil.replace_ext(src, ".dcm")
data_set = DCMECGDataset(
src,
"<{}".format("d" * 5),
1000,
5,
("", "", "", "", ""),
adjust_callback=lambda v: int(v * 100),
is_12_lead_ecg=False,
)
data_set.save_as(dest)
import dicom # [pydicom](http://www.pydicom.org/)
import fileutil
import unpacker
_frozen = hasattr(sys, "frozen") or hasattr(sys, "importers")
if _frozen:
__file__ = sys.executable # Fix issue #6
else:
import warnings # Fix issue #7
# Fix issue #5
# Don't use os.environ['HOME'], use os.path.expanduser('~') instead.
logger_filename = os.path.join(os.path.expanduser("~"), fileutil.replace_ext(os.path.basename(__file__), ".log"))
logging.basicConfig(level=logging.NOTSET, filename=logger_filename, format="%(asctime)s [%(levelname)s]: %(message)s")
# logging.captureWarnings(True)
logger = logging.getLogger(__name__)
# PS3.16 CID 3001 ECG Leads
CID_3001_for_12_Lead_ECG = {
"I": ("2:1", "Lead I"),
"II": ("2:2", "Lead II"),
"III": ("2:61", "Lead III"),
"aVR": ("2:62", "aVR, augmented voltage, right"),
"aVL": ("2:63", "aVL, augmented voltage, left"),
"aVF": ("2:64", "aVF, augmented voltage, foot"),
"V1": ("2:3", "Lead V1"),
"V2": ("2:4", "Lead V2"),
import fileutil
import unpacker
_frozen = hasattr(sys, 'frozen') or hasattr(sys, 'importers')
if _frozen:
__file__ = sys.executable # Fix issue #6
else:
import warnings # Fix issue #7
# Fix issue #5
# Don't use os.environ['HOME'], use os.path.expanduser('~') instead.
logger_filename = os.path.join(
os.path.expanduser('~'),
fileutil.replace_ext(os.path.basename(__file__), '.log'))
logging.basicConfig(level=logging.NOTSET,
filename=logger_filename,
format='%(asctime)s [%(levelname)s]: %(message)s')
#logging.captureWarnings(True)
logger = logging.getLogger(__name__)
# PS3.16 CID 3001 ECG Leads
CID_3001_for_12_Lead_ECG = {
'I': ('2:1', 'Lead I'),
'II': ('2:2', 'Lead II'),
'III': ('2:61', 'Lead III'),
'aVR': ('2:62', 'aVR, augmented voltage, right'),
'aVL': ('2:63', 'aVL, augmented voltage, left'),
'aVF': ('2:64', 'aVF, augmented voltage, foot'),
'V1': ('2:3', 'Lead V1'),
from flask import Flask, abort, flash, g, redirect, \
render_template, request, session, url_for
import fileutil
module_path = os.path.dirname(__file__)
path_of = lambda resource: os.path.join(module_path, resource)
# configuration
DATABASE = path_of('data/db/seveny.db')
DEBUG = True
SECRET_KEY = 'haha'
config_envvar = 'FLASK_SETTINGS'
if config_envvar not in os.environ:
os.environ[config_envvar] = fileutil.replace_ext(__file__, '.cfg')
app = Flask(__name__)
#app.config.from_envvar(config_envvar, slient=True)
app.config.from_object(__name__)
def init_db():
import contextlib
with contextlib.closing(connect_db()) as db:
with app.open_resource(path_of('schema.sql'), mode='r') as fp:
db.cursor().executescript(fp.read())
db.commit()
render_template, request, session, url_for
import fileutil
module_path = os.path.dirname(__file__)
path_of = lambda resource: os.path.join(module_path, resource)
# configuration
DATABASE = path_of('data/db/seveny.db')
DEBUG = True
SECRET_KEY = 'haha'
config_envvar = 'FLASK_SETTINGS'
if config_envvar not in os.environ:
os.environ[config_envvar] = fileutil.replace_ext(__file__, '.cfg')
app = Flask(__name__)
#app.config.from_envvar(config_envvar, slient=True)
app.config.from_object(__name__)
def init_db():
import contextlib
with contextlib.closing(connect_db()) as db:
with app.open_resource(path_of('schema.sql'), mode='r') as fp:
db.cursor().executescript(fp.read())
db.commit()
