Skip to content

Feature/shell_as_G-Delta-delta-TE #76

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
davidrs06 wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Feature/shell_as_G-Delta-delta-TE #76

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
4a947fa
Define shells as unique combinations of G, Delta, delta and TE
davidrs06 Dec 19, 2018
b0e8e32
Bug: extract idx from list returned by np.where
davidrs06 Dec 19, 2018
b8ce417
Added latin1 encoding
davidrs06 Mar 25, 2021
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
2 changes: 1 addition & 1 deletion amico/lut.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ def load_precomputed_rotation_matrices( lmax = 12 ) :
filename = pjoin( dipy_home, 'AMICO_aux_matrices_lmax=%d.pickle'%lmax )
if not isfile( filename ) :
raise RuntimeError( 'Auxiliary matrices not found; call "lut.precompute_rotation_matrices()" first.' )
return pickle.load( open(filename,'rb') )
return pickle.load( open(filename,'rb'),encoding='latin1' )


def aux_structures_generate( scheme, lmax = 12 ) :
Expand Down
33 changes: 15 additions & 18 deletions amico/scheme.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,30 +95,27 @@ def load_from_table( self, data, b0_thr = 0 ) :

# store information about each shell in a dictionary
self.shells = []

tmp = np.ascontiguousarray( self.raw[:,3:] )
schemeUnique, schemeUniqueInd = np.unique( tmp.view([('', tmp.dtype)]*tmp.shape[1]), return_index=True )
schemeUnique = schemeUnique.view(tmp.dtype).reshape((schemeUnique.shape[0], tmp.shape[1]))
schemeUnique = [tmp[index] for index in sorted(schemeUniqueInd)]
bUnique = [self.b[index] for index in sorted(schemeUniqueInd)]
for i in xrange(len(schemeUnique)) :
if bUnique[i] <= b0_thr :
continue

tmp1,tmp2 = np.unique(self.raw[:,3:],axis=0,return_index=True) # Find unique b-values or combinations of G, Delta, delta and TE (and the 1st index of each of those shells)
tmp1 = tmp1[self.b[tmp2] > 0,:] # Remove b0
tmp2 = tmp2[self.b[tmp2] > 0] # Remove b0
# For each shell, find its indexes, grad, b-value and shell parameters
for tmp3 in np.argsort(tmp2):
shell_features = tmp1[tmp3,:]
shell = {}
shell['b'] = bUnique[i]
if self.version == 0 :
shell['idx'] = np.where((self.raw[:,3:] == shell_features).all(axis=1))[0]
shell['grad'] = self.raw[shell['idx'],:3]
shell['b'] = np.unique(self.b[shell['idx']])[0]
if self.version == 0:
shell['G'] = None
shell['Delta'] = None
shell['delta'] = None
shell['TE'] = None
else :
shell['G'] = schemeUnique[i][0]
shell['Delta'] = schemeUnique[i][1]
shell['delta'] = schemeUnique[i][2]
shell['TE'] = schemeUnique[i][3]

shell['idx'] = np.where((tmp == schemeUnique[i]).all(axis=1))[0]
shell['grad'] = self.raw[shell['idx'],0:3]
shell['G'] = shell_features[0]
shell['Delta'] = shell_features[1]
shell['delta'] = shell_features[2]
shell['TE'] = shell_features[3]
self.shells.append( shell )


Expand Down