Note
Click here to download the full example code
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.
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)
We instantiate our CSA model with spherical harmonic order of 4
csamodel = CsaOdfModel(gtab, 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.
sphere = get_sphere('repulsion724')
start_time = time.time()
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.
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")
peaks_from_model using 2 processes ran in : 164.9475257396698 seconds
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:
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")
peaks_from_model ran in : 122.12185287475586 seconds
peaks_from_model ran in : 196.872478008 seconds
print("Speedup factor : " + str(time_single / time_parallel))
Speedup factor : 0.7403678977731135
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 main function and use:
if __name__ == '__main__':
import multiprocessing
multiprocessing.freeze_support()
main()
Total running time of the script: ( 4 minutes 50.025 seconds)