Skip to content
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

read obj bug fix and implement write_gifti with Julia's nibabel comma… #10

Merged
merged 3 commits into from
Mar 7, 2017
Merged

read obj bug fix and implement write_gifti with Julia's nibabel comma… #10

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
c2d1d44
read obj bug fix and implement write_gifti with Julia's nibabel comma…
Feb 28, 2017
67562f4
Merge branch 'master' of https://github.com/kwagstyl/laminar_python
Feb 28, 2017
5d1529d
updated read gifti to read multidimensional/multisubject gifti
Mar 1, 2017
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
29 changes: 23 additions & 6 deletions io_mesh.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,15 @@ def load_mesh_data(surf_data, gii_darray=0):
data = nb.freesurfer.io.read_label(surf_data)
# check if this works with multiple indices (if dim(data)>1)
elif surf_data.endswith('gii'):
data = nb.gifti.giftiio.read(surf_data).darrays[gii_darray].data
fulldata = nb.gifti.giftiio.read(surf_data)
n_vectors = len(fulldata.darrays)
if n_vectors == 1:
data = fulldata.darrays[gii_darray].data
else:
print "Multiple data files found, output will be matrix"
data = np.zeros([len(fulldata.darrays[gii_darray].data), n_vectors])
for gii_darray in range(n_vectors):
data[:,gii_darray] = fulldata.darrays[gii_darray].data
elif surf_data.endswith('vtk'):
_, _, data = read_vtk(surf_data)
elif surf_data.endswith('txt'):
Expand Down Expand Up @@ -159,7 +167,7 @@ def read_ply(file):

return vertex_array, face_array


#function to read MNI obj mesh format
def read_obj(file):
def chunks(l,n):
"""Yield n-sized chunks from l"""
Expand Down Expand Up @@ -188,8 +196,6 @@ def indices(lst,element):
XYZ=np.zeros([n_vert,3])
elif i<=n_vert:
XYZ[i-1]=map(float,line.split())
elif i==2*n_vert+3:
n_poly=int(line)
elif i>2*n_vert+5:
if not line.strip():
k=1
Expand All @@ -212,7 +218,6 @@ def save_mesh_geometry(fname,surf_dict):
nb.freesurfer.io.write_geometry(fname,surf_dict['coords'],surf_dict['faces'])
# save_freesurfer(fname,surf_dict['coords'],surf_dict['faces'])
elif fname.endswith('gii'):
print('please implement a lovely save_gifti command')
write_gifti(fname,surf_dict['coords'],surf_dict['faces'])
elif fname.endswith('vtk'):
if 'data' in surf_dict.keys():
Expand All @@ -223,12 +228,24 @@ def save_mesh_geometry(fname,surf_dict):
write_ply(fname,surf_dict['coords'],surf_dict['faces'])
elif fname.endswith('obj'):
save_obj(fname,surf_dict['coords'],surf_dict['faces'])
print('to view mesh in brainview,\n first use average_objects on the .obj to generate surface normals,\n otherwise mesh is invisible')
print('to view mesh in brainview, run the command:\n')
print('average_objects ' + fname + ' ' + fname)
else:
raise ValueError('fname must be a filename and surf_dict must be a dictionary')

def write_gifti(surf_mesh, coords, faces):
coord_array = nb.gifti.GiftiDataArray(data=coords,
intent=nb.nifti1.intent_codes[
'NIFTI_INTENT_POINTSET'])
face_array = nb.gifti.GiftiDataArray(data=faces,
intent=nb.nifti1.intent_codes[
'NIFTI_INTENT_TRIANGLE'])
gii = nb.gifti.GiftiImage(darrays=[coord_array, face_array])
nb.gifti.write(gii, surf_mesh)


def save_obj(surf_mesh,coords,faces):
#write out MNI - obj format
n_vert=len(coords)
XYZ=coords.tolist()
Tri=faces.tolist()
Expand Down