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Minor mods
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@daducci
daducci committed Jan 31, 2022
1 parent 1d8e62a commit 3882d27
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103 changes: 55 additions & 48 deletions commit/core.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -119,15 +119,16 @@ cdef class Evaluation :
return self.CONFIG.get( key )


def load_data( self, dwi_filename='DWI.nii', scheme_filename='DWI.scheme', b0_thr=0, b0_min_signal=0 ) :
def load_data( self, dwi_filename, scheme_filename, b0_thr=0, b0_min_signal=0 ) :
"""Load the diffusion signal and its corresponding acquisition scheme.
Parameters
----------
dwi_filename : string
The file name of the DWI data, relative to the subject folder (default : 'DWI.nii')
The filename of the DWI data, relative to the subject folder.
scheme_filename : string
The file name of the corresponding acquisition scheme (default : 'DWI.scheme')
The file name of the corresponding acquisition scheme.
If None, assumes the data is scalar, i.e. 1 value per voxel.
b0_thr : float
The threshold below which a b-value is considered a b0 (default : 0)
b0_min_signal : float
Expand All @@ -138,7 +139,7 @@ cdef class Evaluation :
tic = time.time()
LOG( '\n-> Loading data:' )

print( '\t* DWI signal:' )
print( '\t* Input signal:' )
self.set_config('dwi_filename', dwi_filename)
self.niiDWI = nibabel.load( pjoin( self.get_config('DATA_path'), dwi_filename) )
self.niiDWI_img = np.asanyarray( self.niiDWI.dataobj ).astype(np.float32)
Expand All @@ -152,61 +153,67 @@ cdef class Evaluation :
print( '\t\t- values : min=%.2f, max=%.2f, mean=%.2f' % ( self.niiDWI_img.min(), self.niiDWI_img.max(), self.niiDWI_img.mean() ) )

print( '\t* Acquisition scheme:' )
self.set_config('scheme_filename', scheme_filename)
self.set_config('b0_thr', b0_thr)
self.scheme = amico.scheme.Scheme( pjoin( self.get_config('DATA_path'), scheme_filename), b0_thr )
print( '\t\t- %d samples, %d shells' % ( self.scheme.nS, len(self.scheme.shells) ) )
print( '\t\t- %d @ b=0' % ( self.scheme.b0_count ), end='' )
for i in xrange(len(self.scheme.shells)) :
print( ', %d @ b=%.1f' % ( len(self.scheme.shells[i]['idx']), self.scheme.shells[i]['b'] ), end='' )
print()
if scheme_filename is not None:
self.scheme = amico.scheme.Scheme( pjoin( self.get_config('DATA_path'), scheme_filename), b0_thr )
print( '\t\t- %d samples, %d shells' % ( self.scheme.nS, len(self.scheme.shells) ) )
print( '\t\t- %d @ b=0' % ( self.scheme.b0_count ), end='' )
for i in xrange(len(self.scheme.shells)) :
print( ', %d @ b=%.1f' % ( len(self.scheme.shells[i]['idx']), self.scheme.shells[i]['b'] ), end='' )
print()
else:
# if no scheme is passed, assume data is scalar
self.scheme = amico.scheme.Scheme( np.array( [[0,0,0,1000]] ), 0 )
print( '\t\t- scalar data' )

if self.scheme.nS != self.niiDWI_img.shape[3] :
ERROR( 'Scheme does not match with DWI data' )

ERROR( 'Scheme does not match with input data' )
if self.scheme.dwi_count == 0 :
ERROR( 'There are no DWI volumes in the data' )

self.set_config('b0_thr', b0_thr)
self.set_config('scheme_filename', scheme_filename)

LOG( ' [ %.1f seconds ]' % ( time.time() - tic ) )

# Preprocessing
tic = time.time()
LOG( '\n-> Preprocessing:' )

if self.get_config('doNormalizeSignal') :
if self.scheme.b0_count > 0 :
print( '\t* Normalizing to b0... ', end='' )
if self.get_config('scheme_filename') is not None:
tic = time.time()
LOG( '\n-> Preprocessing:' )

if self.get_config('doNormalizeSignal') :
if self.scheme.b0_count > 0:
print( '\t* Normalizing to b0... ', end='' )
sys.stdout.flush()
b0 = np.mean( self.niiDWI_img[:,:,:,self.scheme.b0_idx], axis=3 )
idx = b0 <= b0_min_signal * b0[b0>0].mean()
b0[ idx ] = 1
b0 = 1.0 / b0
b0[ idx ] = 0
for i in xrange(self.scheme.nS) :
self.niiDWI_img[:,:,:,i] *= b0
print( '[ min=%.2f, max=%.2f, mean=%.2f ]' % ( self.niiDWI_img.min(), self.niiDWI_img.max(), self.niiDWI_img.mean() ) )
del idx, b0
else :
WARNING( 'There are no b0 volumes for normalization' )

if self.scheme.b0_count > 1:
if self.get_config('doMergeB0') :
print( '\t* Merging multiple b0 volume(s)... ', end='' )
mean = np.expand_dims( np.mean( self.niiDWI_img[:,:,:,self.scheme.b0_idx], axis=3 ), axis=3 )
self.niiDWI_img = np.concatenate( (mean, self.niiDWI_img[:,:,:,self.scheme.dwi_idx]), axis=3 )
del mean
else :
print( '\t* Keeping all b0 volume(s)... ', end='' )
print( '[ %d x %d x %d x %d ]' % self.niiDWI_img.shape )

if self.get_config('doDemean'):
print( '\t* Demeaning signal... ', end='' )
sys.stdout.flush()
b0 = np.mean( self.niiDWI_img[:,:,:,self.scheme.b0_idx], axis=3 )
idx = b0 <= b0_min_signal * b0[b0>0].mean()
b0[ idx ] = 1
b0 = 1.0 / b0
b0[ idx ] = 0
for i in xrange(self.scheme.nS) :
self.niiDWI_img[:,:,:,i] *= b0
mean = np.repeat( np.expand_dims(np.mean(self.niiDWI_img,axis=3),axis=3), self.niiDWI_img.shape[3], axis=3 )
self.niiDWI_img = self.niiDWI_img - mean
print( '[ min=%.2f, max=%.2f, mean=%.2f ]' % ( self.niiDWI_img.min(), self.niiDWI_img.max(), self.niiDWI_img.mean() ) )
del idx, b0
else :
WARNING( 'There are no b0 volumes for normalization' )

if self.scheme.b0_count > 1 :
if self.get_config('doMergeB0') :
print( '\t* Merging multiple b0 volume(s)... ', end='' )
mean = np.expand_dims( np.mean( self.niiDWI_img[:,:,:,self.scheme.b0_idx], axis=3 ), axis=3 )
self.niiDWI_img = np.concatenate( (mean, self.niiDWI_img[:,:,:,self.scheme.dwi_idx]), axis=3 )
del mean
else :
print( '\t* Keeping all b0 volume(s)... ', end='' )
print( '[ %d x %d x %d x %d ]' % self.niiDWI_img.shape )

if self.get_config('doDemean') :
print( '\t* Demeaning signal... ', end='' )
sys.stdout.flush()
mean = np.repeat( np.expand_dims(np.mean(self.niiDWI_img,axis=3),axis=3), self.niiDWI_img.shape[3], axis=3 )
self.niiDWI_img = self.niiDWI_img - mean
print( '[ min=%.2f, max=%.2f, mean=%.2f ]' % ( self.niiDWI_img.min(), self.niiDWI_img.max(), self.niiDWI_img.mean() ) )

LOG( ' [ %.1f seconds ]' % ( time.time() - tic ) )
LOG( ' [ %.1f seconds ]' % ( time.time() - tic ) )


def set_model( self, model_name ) :
Expand Down
2 changes: 1 addition & 1 deletion commit/info.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
# Format version as expected by setup.py (string of form "X.Y.Z")
_version_major = 1
_version_minor = 6
_version_micro = 0
_version_micro = 1
_version_extra = '' #'.dev'
__version__ = "%s.%s.%s%s" % (_version_major,_version_minor,_version_micro,_version_extra)

Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,6 @@ def run(self):
cmdclass={'build_ext': CustomBuildExtCommand},
ext_modules=get_extensions(),
setup_requires=['Cython>=0.29', 'numpy>=1.12'],
install_requires=['wheel', 'setuptools>=46.1', 'Cython>=0.29', 'numpy>=1.12', 'scipy>=1.0', 'dipy>=1.0', 'dmri-amico>=1.4.0'],
install_requires=['wheel', 'setuptools>=46.1', 'Cython>=0.29', 'numpy>=1.12', 'scipy>=1.0', 'dipy>=1.0', 'dmri-amico>=1.3.2'],
package_data={'commit.operator': ["*.*"]}
)

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