Skip to content

Fixed ismrmrd.xsd referfences and array indexing #24

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
seogier wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Fixed ismrmrd.xsd referfences and array indexing #24

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 7 additions & 7 deletions generate_cartesian_shepp_logan_dataset.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,24 +43,24 @@ def create(filename='testdata.h5', matrix_size=256, coils=8, oversampling=2, rep
header.acquisitionSystemInformation = sys

# Encoding
encoding = ismrmrd.xsd.encoding()
encoding.trajectory = ismrmrd.xsd.trajectoryType.cartesian
encoding = ismrmrd.xsd.encodingType()
encoding.trajectory = ismrmrd.xsd.trajectoryType.CARTESIAN

# encoded and recon spaces
efov = ismrmrd.xsd.fieldOfView_mm()
efov = ismrmrd.xsd.fieldOfViewMm()
efov.x = oversampling*256
efov.y = 256
efov.z = 5
rfov = ismrmrd.xsd.fieldOfView_mm()
rfov = ismrmrd.xsd.fieldOfViewMm()
rfov.x = 256
rfov.y = 256
rfov.z = 5

ematrix = ismrmrd.xsd.matrixSize()
ematrix = ismrmrd.xsd.matrixSizeType()
ematrix.x = nkx
ematrix.y = nky
ematrix.z = 1
rmatrix = ismrmrd.xsd.matrixSize()
rmatrix = ismrmrd.xsd.matrixSizeType()
rmatrix.x = nx
rmatrix.y = ny
rmatrix.z = 1
Expand Down Expand Up @@ -107,7 +107,7 @@ def create(filename='testdata.h5', matrix_size=256, coils=8, oversampling=2, rep
encoding.encodingLimits = limits
header.encoding.append(encoding)

dset.write_xml_header(header.toxml('utf-8'))
dset.write_xml_header(header.toXML('utf-8'))

# Synthesize the k-space data
Ktrue = transform.transform_image_to_kspace(coil_images,(1,2))
Expand Down
8 changes: 4 additions & 4 deletions recon_ismrmrd_dataset.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
from ismrmrdtools import show, transform

# Load file
filename = '/tmp/testdata.h5'
filename = 'testdata.h5'
if not os.path.isfile(filename):
print("%s is not a valid file" % filename)
raise SystemExit
Expand Down Expand Up @@ -77,11 +77,11 @@
# Remove oversampling if needed
if eNx != rNx:
xline = transform.transform_kspace_to_image(acq.data, [1])
x0 = (eNx - rNx) / 2
x1 = (eNx - rNx) / 2 + rNx
x0 = int((eNx - rNx) / 2)
x1 = int((eNx - rNx) / 2 + rNx)
xline = xline[:,x0:x1]
acq.resize(rNx,acq.active_channels,acq.trajectory_dimensions)
acq.center_sample = rNx/2
acq.center_sample = int(rNx/2)
# need to use the [:] notation here to fill the data
acq.data[:] = transform.transform_image_to_kspace(xline, [1])

Expand Down