import os
from dmipy.signal_models import g_from_b
from scipy.stats import gamma
gradient_folder = '/user/rfick/home/microstruktur/microstruktur/gradient_tables/'

bvals_hcp = np.loadtxt(gradient_folder + 'bvals_hcp_wu_minn.txt')  # in s/mm^2, shape (N)
bvecs_hcp = np.loadtxt(gradient_folder + 'bvecs_hcp_wu_minn.txt').T  # Cartesian unit vectors, shape(N x 3)
delta, Delta = np.loadtxt(gradient_folder + 'delta_Delta_hcp_wu_minn.txt', skiprows=1)  # in seconds
G = g_from_b(bvals_hcp * 1e6, delta, Delta)  # gradient strength in T/m. bvals input as s/m^2 so x10^6
G[G == 5.] = 0.  # set b0 measurements to 0 explicitly
TE = 2 * delta + Delta + 0.001
Camino schemefiles are formed as:

VERSION: STEJSKALTANNER
x_1, y_1, z_1, |G_1|, DELTA_1, delta_1, TE_1
x_2 ...
...

where x, y, z are the orientations of the b-vectors, |G| is the gradient strength, DELTA is the pulse separation, delta is the pulse length and TE is the Echo Time. Everything is in SI units, so a Connectom gradient strength of 300 mT/m is put in as 0.3 T/m for example.

Reference: http://camino.cs.ucl.ac.uk/index.php?n=Docs.SchemeFiles
N = len(bvals_hcp)  # length of acquisition
scheme = np.concatenate([bvecs_hcp, G[:, None].T,
                         np.tile(Delta, (1, N)),
                         np.tile(delta, (1, N)),
                         np.tile(TE, (1, N))], axis=0).T  # camino schemefile of size (N x 7)
header = np.array([['VERSION: STEJSKALTANNER' ,'','','','','','']])  # clumsy way to make an array with text
scheme_with_header = np.concatenate([header, scheme], axis=0)  # the to-be-saved schemefile
np.savetxt(gradient_folder + 'schemefile_hcp_wu_minn.scheme1', scheme_with_header, fmt="%s")

lattices, alpha, beta = np.loadtxt(gradient_folder + 'camino_substrate_parameters_alexander2010.txt',
                                  skiprows=1, usecols=(0, 1, 2)).T
x = np.linspace(0, 4e-6, 200)
for alpha_, beta_ in zip(alpha[::2], beta[::2]):
    gamma_dist = gamma(alpha_, scale=beta_)
    plt.plot(x * 2e6, gamma_dist.pdf(x))
xlabel('Axon Diameter ($\mu$m)', fontsize=15)
ylabel('Probability Density', fontsize=15)
title('Simulated Gamma Distributions', fontsize=17)

plt.hist(alpha[::2] * beta[::2] * 2e6, bins=15)
xlabel('Mean Axon Diameter ($\mu$m)', fontsize=15)
ylabel('Frequency', fontsize=15)
The latices were selected by alexander et al (2010) to maximize the packing of the cylinders for the given gamma distribrution to an intra-axonal volume fraction of around (0.7).
latices_onesize = lattices[::2]
latice_surfaces = latices_onesize ** 2
original_surface_intra = latice_surfaces * 0.7  # volume fraction of maximum packing
largest_latice_surface = original_surface_intra * 5  # to make the intra-axonal surface fraction 0.2

latice_steps = 10
output = []
fnames = []
for i in np.arange(latices_onesize.shape[0]):
    latices_ = np.sqrt(np.linspace(latice_surfaces[i], largest_latice_surface[i], latice_steps))
    alphas_ = np.tile(alpha[::2][i], latice_steps)
    betas_ = np.tile(beta[::2][i], latice_steps)
    for latnum_ in np.arange(10):
        fnames.append('gamma'+str(i)+'lat'+str(latnum_)+'.Bfloat') 
    output.append(np.c_[latices_, alphas_, betas_])

parameter_list = np.c_[np.concatenate(output), np.array(fnames)]
savetxt(gradient_folder + 'camino_substrate_parameters_review_fick2017.txt', parameter_list, fmt="%s")
The Camino command to run one simulation:

SCHEMEFILES="schemefile_hcp_wu_minn"

WALKERS=80000
TIMESTEPS=5000

DIFF=1.7E-9;

BASEDIR=/home/rfick/simulations/journal_review
OUTPUTDIR=$BASEDIR/data
mkdir ${OUTPUTDIR}

for scheme in $SCHEMEFILES
do
    mkdir ${OUTPUTDIR}/${scheme}   
    while read -r LATSIZE GAMA GAMB FNAME; do
    datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -geometry inflammation -numcylinders 100 -p 0.0 -initial uniform -voxels 1 -increments 1 -separateruns -latticesize ${LATSIZE} -schemefile $BASEDIR/schemes/$scheme.scheme1 -gamma ${GAMA} ${GAMB} -diffusivity ${DIFF} 1> ${OUTPUTDIR}/${scheme}/${FNAME} 2> ${OUTPUTDIR}/${scheme}/${FNAME}_log.txt && cat ${OUTPUTDIR}/${scheme}/${FNAME}_log.txt | grep fraction | awk '{print $5}' > ${OUTPUTDIR}/${scheme}/${FNAME}_fraction.txt"
    done <camino_substrate_parameters_review_fick2017.txt
done