def main(args):
# ----- Load and validate file ---------------------------------------------
if (args.config_local):
if not os.path.exists(args.config_local):
logging.error("Could not find local config file %s",
args.config_local)
return
dset = h5py.File(args.filename, 'r')
if not dset:
logging.error("Not a valid dataset: %s" % args.filename)
return
dsetNames = dset.keys()
logging.info("File %s contains %d groups:", args.filename,
len(dset.keys()))
print(" ", "\n ".join(dsetNames))
if not args.in_group:
if len(dset.keys()) is 1:
args.in_group = list(dset.keys())[0]
else:
logging.error(
"Input group not specified and multiple groups are present")
return
if args.in_group not in dset:
logging.error("Could not find group %s", args.in_group)
return
group = dset.get(args.in_group)
logging.info("Reading data from group '%s' in file '%s'", args.in_group,
args.filename)
# ----- Determine type of data stored --------------------------------------
# Raw data is stored as:
# /group/config text of recon config parameters (optional)
# /group/xml text of ISMRMRD flexible data header
# /group/data array of IsmsmrdAcquisition data + header
# /group/waveforms array of waveform (e.g. PMU) data
# Image data is stored as:
# /group/config text of recon config parameters (optional)
# /group/xml text of ISMRMRD flexible data header (optional)
# /group/image_0/data array of IsmrmrdImage data
# /group/image_0/header array of ImageHeader
# /group/image_0/attributes text of image MetaAttributes
isRaw = False
isImage = False
if (('data' in group) and ('xml' in group)):
isRaw = True
else:
isImage = True
imageNames = group.keys()
logging.info("Found %d image sub-groups: %s", len(imageNames),
", ".join(imageNames))
# print(" ", "\n ".join(imageNames))
for imageName in imageNames:
image = group[imageName]
if not (('data' in image) and ('header' in image) and
('attributes' in image)):
isImage = False
dset.close()
if ((isRaw is False) and (isImage is False)):
logging.error(
"File does not contain properly formatted MRD raw or image data")
return
# ----- Open connection to server ------------------------------------------
# Spawn a thread to connect and handle incoming data
logging.info("Connecting to MRD server at %s:%d" %
(args.address, args.port))
sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
sock.connect((args.address, args.port))
process = multiprocessing.Process(
target=connection_receive_loop,
args=[sock, args.outfile, args.out_group])
process.daemon = True
process.start()
# This connection is only used for outgoing data. It should not be used for
# writing to the HDF5 file as multi-threading issues can occur
connection = Connection(sock, False)
if (args.config_local):
fid = open(args.config_local, "r")
config_text = fid.read()
fid.close()
logging.info("Sending local config file '%s' with text:",
args.config_local)
logging.info(config_text)
connection.send_config_text(config_text)
else:
logging.info("Sending remote config file name '%s'", args.config)
connection.send_config_file(args.config)
# --------------- Send raw data ----------------------
if isRaw:
logging.info("Starting raw data session")
dset = ismrmrd.Dataset(args.filename, args.in_group, False)
xml_header = dset.read_xml_header()
connection.send_metadata(xml_header)
logging.info("Found %d raw data readouts",
dset.number_of_acquisitions())
for idx in range(dset.number_of_acquisitions()):
acq = dset.read_acquisition(idx)
try:
connection.send_acquisition(acq)
except:
logging.error('Failed to send acquisition %d' % idx)
dset.close()
# --------------- Send image data ----------------------
else:
logging.info("Starting image data session")
dset = ismrmrd.Dataset(args.filename, args.in_group, False)
groups = dset.list()
if ('xml' in groups):
xml_header = dset.read_xml_header()
else:
xml_header = "Dummy XML header"
connection.send_metadata(xml_header)
for group in groups:
if ((group is 'config') or (group is 'xml')):
logging.info("Skipping group %s", group)
logging.info("Reading images from '/" + args.in_group + "/" +
group + "'")
for imgNum in range(0, dset.number_of_images(group)):
image = dset.read_image(group, imgNum)
image.attribute_string = image.attribute_string.decode('utf-8')
logging.debug("Sending image %d of %d", imgNum,
dset.number_of_images(group) - 1)
connection.send_image(image)
dset.close()
connection.send_close()
# Wait for incoming data and cleanup
logging.debug("Waiting for threads to finish")
process.join()
logging.info("Session complete")
return
# coding: utf-8
import os
import ismrmrd
import ismrmrd.xsd
import numpy as np
from ismrmrdtools import show, transform
# Load file
filename = '/media/george/storge/DeepMRI_data/knee1.h5'
if not os.path.isfile(filename):
print("%s is not a valid file" % filename)
raise SystemExit
dset = ismrmrd.Dataset(filename, 'dataset', create_if_needed=False)
header = ismrmrd.xsd.CreateFromDocument(dset.read_xml_header())
enc = header.encoding[0]
# Matrix size
eNx = enc.encodedSpace.matrixSize.x
eNy = enc.encodedSpace.matrixSize.y
eNz = enc.encodedSpace.matrixSize.z
# rNx = enc.reconSpace.matrixSize.x
# rNy = enc.reconSpace.matrixSize.y
# rNz = enc.reconSpace.matrixSize.z
# Field of View
eFOVx = enc.encodedSpace.fieldOfView_mm.x
eFOVy = enc.encodedSpace.fieldOfView_mm.y
eFOVz = enc.encodedSpace.fieldOfView_mm.z
dwell=1e-6 * dwelltime_us,
delay=gx.rise_time,
system=system)
# RF spoiling
rf_spoiling_inc = 117
rf_phase = 0
rf_inc = 0
#%% Set up metadata
meta_folder = '../../dependency/metadata/'
meta_filename = meta_folder + seq_name + '.h5'
if os.path.isfile(meta_filename):
os.remove(meta_filename)
meta_file = ismrmrd.Dataset(meta_filename)
hdr = ismrmrd.xsd.ismrmrdHeader()
params_hdr = {
"trajtype": "cartesian",
"fov": fov * 1e3,
"res": res * 1e3,
"slices": slices,
"slice_res": slice_res,
"nintl": Ny,
"ncontrast": len(TE)
}
create_hdr(hdr, params_hdr)
#%% Set up sequence
seq.set_definition(