We show an example of parallel reconstruction using a Q-Ball Constant Solid
Angle model (see Aganj et al. (MRM 2010)) and peaks_from_model. Import modules, fetch and read data, and compute the mask. We instantiate our CSA model with spherical harmonic order of 4 Peaks_from_model is used to calculate properties of the ODFs (Orientation
Distribution Function) and return for
example the peaks and their indices, or GFA which is similar to FA but for ODF
based models. This function mainly needs a reconstruction model, the data and a
sphere as input. The sphere is an object that represents the spherical discrete
grid where the ODF values will be evaluated. We will first run peaks_from_model using parallelism with 2 processes. If
num_processes is None (default option) then this function will find the total
number of processors from the operating system and use this number as
num_processes. Sometimes it makes sense to use only a few of the processes in
order to allow resources for other applications. However, most of the times
using the default option will be sufficient. peaks_from_model using 2 process ran in : 114.333221912 seconds, using 2
process If we don’t use parallelism then we need to set parallel=False: peaks_from_model ran in : 196.872478008 seconds Speedup factor : 1.72191839533 In Windows if you get a runtime error about frozen executable please start
your script by adding your code above in a Example source code You can download Parallel reconstruction using Q-Ball
import time
from dipy.core.gradients import gradient_table
from dipy.data import get_fnames, get_sphere
from dipy.io.gradients import read_bvals_bvecs
from dipy.io.image import load_nifti
from dipy.reconst.shm import CsaOdfModel
from dipy.direction import peaks_from_model
from dipy.segment.mask import median_otsu
hardi_fname, hardi_bval_fname, hardi_bvec_fname = get_fnames('stanford_hardi')
data, affine = load_nifti(hardi_fname)
bvals, bvecs = read_bvals_bvecs(hardi_bval_fname, hardi_bvec_fname)
gtab = gradient_table(bvals, bvecs)
maskdata, mask = median_otsu(data, vol_idx=range(10, 50), median_radius=3,
numpass=1, autocrop=True, dilate=2)
csamodel = CsaOdfModel(gtab, 4)
sphere = get_sphere('repulsion724')
start_time = time.time()
csapeaks_parallel = peaks_from_model(model=csamodel,
data=maskdata,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False,
normalize_peaks=True,
npeaks=5,
parallel=True,
num_processes=2)
time_parallel = time.time() - start_time
print("peaks_from_model using 2 processes ran in : " +
str(time_parallel) + " seconds")
start_time = time.time()
csapeaks = peaks_from_model(model=csamodel,
data=maskdata,
sphere=sphere,
relative_peak_threshold=.5,
min_separation_angle=25,
mask=mask,
return_odf=False,
normalize_peaks=True,
npeaks=5,
parallel=False,
num_processes=None)
time_single = time.time() - start_time
print("peaks_from_model ran in : " + str(time_single) + " seconds")
print("Speedup factor : " + str(time_single / time_parallel))
main
function and use:if __name__ == '__main__':
import multiprocessing
multiprocessing.freeze_support()
main()
the full source code of this example
. This same script is also included in the dipy source distribution under the doc/examples/
directory.