Comments (1)
Hi @meliamne. This is happening because the msfm package isn't being compiled properly for some reason.
The most immediate fix is to remove the import msfm
call at the top of the module, and only be imported if using quality=True
for R2Tracer.
So this:
def _fast_marching(self):
speed = self._make_speed()
# # Fast Marching
if self._quality:
# if not self._silent: print('--MSFM...')
self._t = msfm.run(speed, self._bimg.copy().astype(
'int64'), self._soma.centroid, True, True)
else:
# if not self._silent: print('--FM...')
marchmap = np.ones(self._bimg.shape)
marchmap[self._soma.centroid[0],
self._soma.centroid[1], self._soma.centroid[2]] = -1
self._t = skfmm.travel_time(marchmap, speed, dx=5e-3)
should be changed to this:
def _fast_marching(self):
speed = self._make_speed()
# # Fast Marching
if self._quality:
# only import msfm if quality = True
import msfm
# if not self._silent: print('--MSFM...')
self._t = msfm.run(speed, self._bimg.copy().astype(
'int64'), self._soma.centroid, True, True)
else:
# if not self._silent: print('--FM...')
marchmap = np.ones(self._bimg.shape)
marchmap[self._soma.centroid[0],
self._soma.centroid[1], self._soma.centroid[2]] = -1
self._t = skfmm.travel_time(marchmap, speed, dx=5e-3)
from rivuletpy.
Related Issues (19)
- Implement MSFM
- Missing module simpleitk Suggestion: edit instalation instructions HOT 2
- swc.shape and soma.save, soma.pad don't exist HOT 8
- scikit-image<0.14.2 will raise an ImportError with numpy HOT 1
- Setup incompatible with pip3 HOT 2
- Installation documentation error HOT 1
- soma object has no attribute 'pad' HOT 7
- Get Voxel array HOT 1
- Cannot read .swc file result in NeuroM HOT 2
- Example usage
- Failed to find TIFF header file
- Add V3DRAW support for IO
- Can not Download test file
- Implement new performance metric
- See if dt can be reused from soma detection
- msfm segmentation fault sometimes for Bigneuron first2000 images
- Failed to find TIFF library HOT 16
- setup.py not compatible with pip>10.0.0
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from rivuletpy.