def execution(self, context):
command = ['AimsFileConvert', '-i', self.read, '-o', self.write]
if self.ascii:
command += ['-a']
if self.voxelType is not None:
command += ['-t', self.voxelType]
if self.rescaleDynamic:
command += ['-r']
if self.useInputTypeLimits:
command += ['--itypelimits']
if self.inputDynamicMin != None:
command += ['--imin', self.inputDynamicMin]
if self.inputDynamicMax != None:
command += ['--imax', self.inputDynamicMax]
if self.outputDynamicMin != None:
command += ['--omin', self.outputDynamicMin]
if self.outputDynamicMax != None:
command += ['--omax', self.outputDynamicMax]
if context.system(*command):
raise RuntimeError(_t_(
'Error while converting <em>%s</em> to <em>%s</em>')
% (command[2], command[4]))
if self.removeSource:
for f in self.read.fullPaths():
shelltools.rm(f)
def execution(self, context):
from soma import aims
graph = aims.read(self.read.fullPath())
aims.GraphManip.buckets2Volume(graph)
if self.extract_volume:
vol = graph[self.extract_volume]
else:
atts = [
x for x in graph.keys()
if isinstance(graph[x], aims.rc_ptr_Volume_S16)
]
if len(atts) == 0:
raise RuntimeError(_t_('the ROI graph contains no voxel data'))
elif len(atts) > 1:
raise RuntimeError(
_t_('the ROI graph contains several volumes. '
'Select the extract_volume parameter as one in ') + '( ' +
', '.join(atts) + ' )')
vol = graph[atts[0]]
# handle bounding box which may have cropped the data
bmin = graph['boundingbox_min']
bmax = graph['boundingbox_max']
context.write('vol:', vol)
context.write('bmin:', bmin, ', bmax:', bmax, ', size:', vol.getSize())
if bmin[:3] != [0, 0, 0] \
or bmax[:3] != [x+1 for x in vol.getSize()[:3]]:
context.write('enlarging')
# needs expanding in a bigger volume
vol2 = aims.Volume_S16(bmax[0] + 1, bmax[1] + 1, bmax[2] + 1)
vol2.fill(0)
ar = vol2.np
ar[bmin[0]:bmax[0] + 1, bmin[1]:bmax[1] + 1, bmin[2]:bmax[2] + 1, :] \
= vol.np
if self.extract_contours == 'Yes':
ar_copy = ar.copy()
for label in [v['roi_label'] for v in graph.vertices()]:
ind = list(zip(*np.where(ar_copy == label)))
for i in ind:
erase = True
for neigh in neighbors(*i):
if ar_copy[neigh] != label:
erase = False
if erase:
ar[i] = 0
vol2.copyHeaderFrom(vol.header())
aims.write(vol2, self.write.fullPath())
else:
# bounding box OK
aims.write(vol.get(), self.write.fullPath())
registration.getTransformationManager().copyReferential(
self.read, self.write)
if self.removeSource:
for f in self.read.fullPaths():
shelltools.rm(f)
def execution(self, context):
command = ['AimsFileConvert', '-i', self.read, '-o', self.write]
if self.ascii:
command += ['-a']
if context.system(*command):
raise RuntimeError(
_t_('Error while converting <em>%s</em> to <em>%s</em>') %
(command[2], command[4]))
if self.removeSource:
for f in self.read.fullPaths():
shelltools.rm(f)
def execution(self, context):
self.read = None
if self.input_file:
self.read = self.input_file
elif self.input_directory:
self.read = self.input_directory
else:
context.error(
"You must give a valid value for input_file or input_directory.")
if self.read:
context.system(
'AimsFileConvert', '-i', self.read, '-o', self.write)
registration.getTransformationManager().copyReferential(self.read,
self.write)
if self.removeSource:
for f in self.read.fullPaths():
shelltools.rm(f)