def plot_all(conn_matrix, conn_model, atlas_select, dir_path, ID, network, label_names, mask, coords, edge_threshold, plot_switch):
from nilearn import plotting as niplot
pruning=True
dpi_resolution=1000
if plot_switch == True:
import pkg_resources
import networkx as nx
from pynets import plotting
import matplotlib.pyplot as plt
from pynets.netstats import most_important
G_pre=nx.from_numpy_matrix(conn_matrix)
if pruning == True:
[G, pruned_nodes, pruned_edges] = most_important(G_pre)
else:
G = G_pre
conn_matrix = nx.to_numpy_array(G)
pruned_nodes.sort(reverse = True)
for j in pruned_nodes:
del label_names[label_names.index(label_names[j])]
del coords[coords.index(coords[j])]
pruned_edges.sort(reverse = True)
for j in pruned_edges:
del label_names[label_names.index(label_names[j])]
del coords[coords.index(coords[j])]
##Plot connectogram
if len(conn_matrix) > 20:
try:
plotting.plot_connectogram(conn_matrix, conn_model, atlas_select, dir_path, ID, network, label_names)
except RuntimeError:
print('\n\n\nError: Connectogram plotting failed!')
else:
print('Error: Cannot plot connectogram for graphs smaller than 20 x 20!')
##Plot adj. matrix based on determined inputs
plotting.plot_conn_mat(conn_matrix, conn_model, atlas_select, dir_path, ID, network, label_names, mask)
##Plot connectome
if mask != None:
if network != 'None':
out_path_fig=dir_path + '/' + ID + '_' + atlas_select + '_' + str(conn_model) + '_' + str(os.path.basename(mask).split('.')[0]) + '_' + str(network) + '_connectome_viz.png'
else:
out_path_fig=dir_path + '/' + ID + '_' + atlas_select + '_' + str(conn_model) + '_' + str(os.path.basename(mask).split('.')[0]) + '_connectome_viz.png'
else:
if network != 'None':
out_path_fig=dir_path + '/' + ID + '_' + atlas_select + '_' + str(conn_model) + '_' + str(network) + '_connectome_viz.png'
else:
out_path_fig=dir_path + '/' + ID + '_' + atlas_select + '_' + str(conn_model) + '_connectome_viz.png'
#niplot.plot_connectome(conn_matrix, coords, edge_threshold=edge_threshold, node_size=20, colorbar=True, output_file=out_path_fig)
ch2better_loc = pkg_resources.resource_filename("pynets", "templates/ch2better.nii.gz")
connectome = niplot.plot_connectome(np.zeros(shape=(1,1)), [(0,0,0)], black_bg=True, node_size=0.0001)
connectome.add_overlay(ch2better_loc, alpha=0.4, cmap=plt.cm.gray)
[z_min, z_max] = -np.abs(conn_matrix).max(), np.abs(conn_matrix).max()
connectome.add_graph(conn_matrix, coords, edge_threshold = edge_threshold, edge_cmap = 'Blues', edge_vmax=z_max, edge_vmin=z_min, node_size=4)
connectome.savefig(out_path_fig, dpi=dpi_resolution)
else:
pass
return
def test_plot_connectogram():
##Set example inputs##
base_dir = str(Path(__file__).parent/"examples")
#base_dir = '/Users/PSYC-dap3463/Applications/PyNets/tests/examples'
dir_path= base_dir + '/997'
network=None
ID = '997'
conn_model = 'sps'
atlas_select = 'whole_brain_cluster_labels_PCA200'
conn_matrix = np.genfromtxt(dir_path + '/whole_brain_cluster_labels_PCA200/997_est_sps_0.94.txt')
labels_file_path = dir_path + '/whole_brain_cluster_labels_PCA200/WB_func_labelnames_wb.pkl'
labels_file = open(labels_file_path,'rb')
label_names = pickle.load(labels_file)
plotting.plot_connectogram(conn_matrix, conn_model, atlas_select, dir_path, ID, network, label_names)
def test_plot_connectogram():
# Set example inputs
base_dir = str(Path(__file__).parent / "examples")
#base_dir = '/Users/rxh180012/PyNets-development/tests/examples'
dir_path = base_dir + '/997'
network = None
ID = '997'
conn_model = 'sps'
atlas_select = 'whole_brain_cluster_labels_PCA200'
conn_matrix = np.genfromtxt(
dir_path +
'/whole_brain_cluster_labels_PCA200/997_Default_est_sps_0.94.txt')
labels_file_path = dir_path + '/whole_brain_cluster_labels_PCA200/Default_func_labelnames_wb.pkl'
labels_file = open(labels_file_path, 'rb')
label_names = pickle.load(labels_file)
start_time = time.time()
plotting.plot_connectogram(conn_matrix, conn_model, atlas_select, dir_path,
ID, network, label_names)
print("%s%s%s" % ('plot_connectogram --> finished: ',
str(np.round(time.time() - start_time, 1)), 's'))
def plot_all(conn_matrix, conn_model, atlas_select, dir_path, ID, network,
label_names, mask, coords, thr, node_size, edge_threshold, smooth,
prune, uatlas_select):
import matplotlib
matplotlib.use('agg')
from matplotlib import pyplot as plt
from nilearn import plotting as niplot
import pkg_resources
import networkx as nx
from pynets import plotting, thresholding
from pynets.netstats import most_important, prune_disconnected
try:
import cPickle as pickle
except ImportError:
import _pickle as pickle
coords = list(coords)
label_names = list(label_names)
dpi_resolution = 500
if '\'b' in atlas_select:
atlas_select = atlas_select.decode('utf-8')
if (prune == 1 or prune == 2) and len(coords) == conn_matrix.shape[0]:
G_pre = nx.from_numpy_matrix(conn_matrix)
if prune == 1:
[G, pruned_nodes] = prune_disconnected(G_pre)
elif prune == 2:
[G, pruned_nodes] = most_important(G_pre)
else:
G = G_pre
pruned_nodes = []
pruned_nodes.sort(reverse=True)
print('(Display)')
coords_pre = list(coords)
label_names_pre = list(label_names)
if len(pruned_nodes) > 0:
for j in pruned_nodes:
label_names_pre.pop(j)
coords_pre.pop(j)
conn_matrix = nx.to_numpy_array(G)
label_names = label_names_pre
coords = coords_pre
else:
print('No nodes to prune for plot...')
coords = list(tuple(x) for x in coords)
# Plot connectogram
if len(conn_matrix) > 20:
try:
plotting.plot_connectogram(conn_matrix, conn_model, atlas_select,
dir_path, ID, network, label_names)
except:
print('\n\n\nWarning: Connectogram plotting failed!')
else:
print(
'Warning: Cannot plot connectogram for graphs smaller than 20 x 20!'
)
# Plot adj. matrix based on determined inputs
if not node_size or node_size == 'None':
node_size = 'parc'
plotting.plot_conn_mat_func(conn_matrix, conn_model, atlas_select,
dir_path, ID, network, label_names, mask, thr,
node_size, smooth)
# Plot connectome
if mask:
out_path_fig = "%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s" % (
dir_path, '/', ID, '_', str(atlas_select), '_', str(conn_model),
'_', str(os.path.basename(mask).split('.')[0]), "%s" %
("%s%s%s" % ('_', network, '_') if network else "_"), str(thr),
'_', str(node_size), '%s' %
("mm_" if node_size != 'parc' else "_"), "%s" %
("%s%s" % (smooth, 'fwhm_') if float(smooth) > 0 else 'nosm_'),
'func_glass_viz.png')
# Save coords to pickle
coord_path = "%s%s%s%s" % (dir_path, '/coords_',
os.path.basename(mask).split('.')[0],
'_plotting.pkl')
with open(coord_path, 'wb') as f:
pickle.dump(coords, f, protocol=2)
# Save labels to pickle
labels_path = "%s%s%s%s" % (dir_path, '/labelnames_',
os.path.basename(mask).split('.')[0],
'_plotting.pkl')
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f, protocol=2)
else:
out_path_fig = "%s%s%s%s%s%s%s%s%s%s%s%s%s%s" % (
dir_path, '/', ID, '_', str(atlas_select), '_', str(conn_model),
"%s" % ("%s%s%s" % ('_', network, '_') if network else "_"),
str(thr), '_', str(node_size), '%s' %
("mm_" if node_size != 'parc' else "_"), "%s" %
("%s%s" % (smooth, 'fwhm_') if float(smooth) > 0 else 'nosm_'),
'func_glass_viz.png')
# Save coords to pickle
coord_path = "%s%s" % (dir_path, '/coords_plotting.pkl')
with open(coord_path, 'wb') as f:
pickle.dump(coords, f, protocol=2)
# Save labels to pickle
labels_path = "%s%s" % (dir_path, '/labelnames_plotting.pkl')
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f, protocol=2)
ch2better_loc = pkg_resources.resource_filename(
"pynets", "templates/ch2better.nii.gz")
connectome = niplot.plot_connectome(np.zeros(shape=(1, 1)), [(0, 0, 0)],
node_size=0.0001,
black_bg=True)
connectome.add_overlay(ch2better_loc, alpha=0.35, cmap=plt.cm.gray)
conn_matrix = np.array(np.array(thresholding.autofix(conn_matrix)))
[z_min, z_max] = -np.abs(conn_matrix).max(), np.abs(conn_matrix).max()
if node_size == 'parc':
node_size_plot = int(2)
if uatlas_select:
connectome.add_contours(uatlas_select,
filled=False,
alpha=0.3,
colors='black')
else:
node_size_plot = int(node_size)
if len(coords) != conn_matrix.shape[0]:
raise RuntimeWarning(
'WARNING: Number of coordinates does not match conn_matrix dimensions. If you are using disparity filtering, try relaxing the α threshold.'
)
else:
connectome.add_graph(conn_matrix,
coords,
edge_threshold=edge_threshold,
edge_cmap='Blues',
edge_vmax=float(z_max),
edge_vmin=float(z_min),
node_size=node_size_plot,
node_color='auto')
connectome.savefig(out_path_fig, dpi=dpi_resolution)
return
def run_struct_mapping(FSLDIR, ID, bedpostx_dir, dir_path, NETWORK, coords_MNI,
node_size, atlas_select, atlas_name, label_names,
plot_switch):
edge_threshold = 0.90
connectome_fdt_thresh = 1000
####Auto-set INPUTS####
nodif_brain_mask_path = bedpostx_dir + '/nodif_brain_mask.nii.gz'
merged_th_samples_path = bedpostx_dir + '/merged_th1samples.nii.gz'
merged_f_samples_path = bedpostx_dir + '/merged_f1samples.nii.gz'
merged_ph_samples_path = bedpostx_dir + '/merged_ph1samples.nii.gz'
input_MNI = FSLDIR + '/data/standard/MNI152_T1_2mm_brain.nii.gz'
probtrackx_output_dir_path = bedpostx_dir + '/probtrackx_' + NETWORK
####Auto-set INPUTS####
##Delete any existing roi spheres
del_files_spheres = glob.glob(bedpostx_dir + '/roi_sphere*diff.nii.gz')
try:
for i in del_files_spheres:
os.remove(i)
except:
pass
##Create transform matrix between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = merged_f_samples_path
flirt.inputs.in_file = input_MNI
flirt.inputs.out_matrix_file = bedpostx_dir + '/xfms/MNI2diff.mat'
flirt.run()
##Apply transform between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = merged_f_samples_path
flirt.inputs.in_file = input_MNI
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/MNI2diff.mat'
flirt.inputs.out_file = bedpostx_dir + '/xfms/MNI2diff_affine.nii.gz'
flirt.run()
x_vox = np.diagonal(
masking._load_mask_img(nodif_brain_mask_path)[1][:3, 0:3])[0]
y_vox = np.diagonal(
masking._load_mask_img(nodif_brain_mask_path)[1][:3, 0:3])[1]
z_vox = np.diagonal(
masking._load_mask_img(nodif_brain_mask_path)[1][:3, 0:3])[2]
def mmToVox(mmcoords):
voxcoords = ['', '', '']
voxcoords[0] = int((round(int(mmcoords[0]) / x_vox)) + 45)
voxcoords[1] = int((round(int(mmcoords[1]) / y_vox)) + 63)
voxcoords[2] = int((round(int(mmcoords[2]) / z_vox)) + 36)
return voxcoords
##Convert coords back to voxels
coords_vox = []
for coord in coords_MNI:
coords_vox.append(mmToVox(coord))
coords = list(tuple(x) for x in coords_vox)
j = 0
for i in coords:
##Grow spheres at ROI
X = coords[j][0]
Y = coords[j][1]
Z = coords[j][2]
out_file1 = bedpostx_dir + '/roi_point_' + str(j) + '.nii.gz'
args = '-mul 0 -add 1 -roi ' + str(X) + ' 1 ' + str(Y) + ' 1 ' + str(
Z) + ' 1 0 1'
maths = fsl.ImageMaths(in_file=input_MNI,
op_string=args,
out_file=out_file1)
os.system(maths.cmdline + ' -odt float')
out_file2 = bedpostx_dir + '/roi_sphere_' + str(j) + '.nii.gz'
args = '-kernel sphere ' + str(node_size) + ' -fmean -bin'
maths = fsl.ImageMaths(in_file=out_file1,
op_string=args,
out_file=out_file2)
os.system(maths.cmdline + ' -odt float')
##Map ROIs from Standard Space to diffusion Space:
##Applying xfm and input matrix to transform ROI's between diff and MNI using FLIRT,
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = nodif_brain_mask_path
flirt.inputs.in_file = out_file2
out_file_diff = out_file2.split('.nii')[0] + '_diff.nii.gz'
flirt.inputs.out_file = out_file_diff
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/MNI2diff.mat'
flirt.run()
j = j + 1
if not os.path.exists(probtrackx_output_dir_path):
os.makedirs(probtrackx_output_dir_path)
seed_files = glob.glob(bedpostx_dir + '/*diff.nii.gz')
seeds_text = probtrackx_output_dir_path + '/masks.txt'
try:
os.remove(seeds_text)
except OSError:
pass
seeds_file_list = []
for seed_file in seed_files:
seeds_file_list.append(seed_file)
f = open(seeds_text, 'w')
l1 = map(lambda x: x + '\n', seeds_file_list)
f.writelines(l1)
f.close()
del_files_points = glob.glob(bedpostx_dir + '/roi_point*.nii.gz')
for i in del_files_points:
os.remove(i)
del_files_spheres = glob.glob(bedpostx_dir + '/roi_sphere*[!diff].nii.gz')
for i in del_files_spheres:
os.remove(i)
mx_path = dir_path + '/' + str(ID) + '_' + NETWORK + '_structural_mx.txt'
probtrackx2 = pe.Node(interface=fsl.ProbTrackX2(), name='probtrackx2')
probtrackx2.inputs.network = True
probtrackx2.inputs.seed = seeds_text
probtrackx2.inputs.onewaycondition = True
probtrackx2.inputs.c_thresh = 0.2
probtrackx2.inputs.n_steps = 2000
probtrackx2.inputs.step_length = 0.5
probtrackx2.inputs.n_samples = 5000
probtrackx2.inputs.dist_thresh = 0.0
probtrackx2.inputs.opd = True
probtrackx2.inputs.loop_check = True
probtrackx2.inputs.omatrix1 = True
probtrackx2.overwrite = True
probtrackx2.inputs.verbose = True
probtrackx2.inputs.mask = nodif_brain_mask_path
probtrackx2.inputs.out_dir = probtrackx_output_dir_path
probtrackx2.inputs.thsamples = merged_th_samples_path
probtrackx2.inputs.fsamples = merged_f_samples_path
probtrackx2.inputs.phsamples = merged_ph_samples_path
probtrackx2.iterables = ("seed", seed_files)
try:
probtrackx2.inputs.avoid_mp = vetricular_CSF_mask_path
except:
pass
probtrackx2.run()
del (probtrackx2)
if os.path.exists(probtrackx_output_dir_path + '/fdt_network_matrix'):
mx = np.genfromtxt(probtrackx_output_dir_path + '/fdt_network_matrix')
waytotal = np.genfromtxt(probtrackx_output_dir_path + '/waytotal')
np.seterr(divide='ignore', invalid='ignore')
conn_matrix = np.divide(mx, waytotal)
conn_matrix[np.isnan(conn_matrix)] = 0
conn_matrix = np.nan_to_num(conn_matrix)
conn_matrix = normalize(conn_matrix)
##Save matrix
out_path_mx = dir_path + '/' + str(
ID) + '_' + NETWORK + '_structural_mx.txt'
np.savetxt(out_path_mx, conn_matrix, delimiter='\t')
if plot_switch == True:
rois_num = conn_matrix.shape[0]
print("Creating plot of dimensions:\n" + str(rois_num) + ' x ' +
str(rois_num))
plt.figure(figsize=(10, 10))
plt.imshow(conn_matrix,
interpolation="nearest",
vmax=1,
vmin=-1,
cmap=plt.cm.RdBu_r)
##And display the labels
plt.colorbar()
plt.title(atlas_select.upper() + ' ' + NETWORK +
' Structural Connectivity')
out_path_fig = dir_path + '/' + str(
ID) + '_' + NETWORK + '_structural_adj_mat.png'
plt.savefig(out_path_fig)
plt.close()
conn_matrix_symm = np.maximum(conn_matrix, conn_matrix.transpose())
fdt_paths_loc = probtrackx_output_dir_path + '/fdt_paths.nii.gz'
##Plotting with glass brain
##Create transform matrix between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = input_MNI
flirt.inputs.in_file = nodif_brain_mask_path
flirt.inputs.out_matrix_file = bedpostx_dir + '/xfms/diff2MNI.mat'
flirt.run()
##Apply transform between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = input_MNI
flirt.inputs.in_file = nodif_brain_mask_path
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/diff2MNI.mat'
flirt.inputs.out_file = bedpostx_dir + '/xfms/diff2MNI_affine.nii.gz'
flirt.run()
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),
name='coregister')
flirt.inputs.reference = input_MNI
flirt.inputs.in_file = fdt_paths_loc
out_file_MNI = fdt_paths_loc.split('.nii')[0] + '_MNI.nii.gz'
flirt.inputs.out_file = out_file_MNI
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/diff2MNI.mat'
flirt.run()
fdt_paths_MNI_loc = probtrackx_output_dir_path + '/fdt_paths_MNI.nii.gz'
if plot_switch == True:
norm = colors.Normalize(vmin=-1, vmax=1)
clust_pal = sns.color_palette("Blues_r", 4)
clust_colors = colors.to_rgba_array(clust_pal)
connectome = plotting.plot_connectome(
conn_matrix_symm,
coords_MNI,
edge_threshold=edge_threshold,
node_color=clust_colors,
edge_cmap=plotting.cm.black_blue_r)
connectome.add_overlay(img=fdt_paths_MNI_loc,
threshold=connectome_fdt_thresh,
cmap=plotting.cm.cyan_copper_r)
out_file_path = dir_path + '/structural_connectome_fig_' + NETWORK + '_' + str(
ID) + '.png'
plt.savefig(out_file_path)
plt.close()
from pynets import plotting as pynplot
NETWORK = NETWORK + '_structural'
pynplot.plot_connectogram(conn_matrix, conn_model, atlas_name,
dir_path, ID, NETWORK, label_names)
if NETWORK != None:
est_path = dir_path + '/' + ID + '_' + NETWORK + '_structural_est.txt'
else:
est_path = dir_path + '/' + ID + '_structural_est.txt'
try:
np.savetxt(est_path, conn_matrix_symm, delimiter='\t')
except RuntimeError:
print('Diffusion network connectome failed!')
return (est_path)
def structural_plotting(conn_matrix, conn_matrix_symm, label_names, atlas_select, ID, bedpostx_dir, network, parc, plot_switch, coords):
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe
import matplotlib.pyplot as plt
import seaborn as sns
from pynets import plotting as pynplot
from matplotlib import colors
from nilearn import plotting as niplot
edge_threshold = 0.90
connectome_fdt_thresh = 1000
####Auto-set INPUTS####
try:
FSLDIR = os.environ['FSLDIR']
except NameError:
print('FSLDIR environment variable not set!')
nodif_brain_mask_path = bedpostx_dir + '/nodif_brain_mask.nii.gz'
input_MNI = FSLDIR + '/data/standard/MNI152_T1_1mm_brain.nii.gz'
if network:
probtrackx_output_dir_path = bedpostx_dir + '/probtrackx_' + network
else:
probtrackx_output_dir_path = bedpostx_dir + '/probtrackx_Whole_brain'
dir_path = os.path.dirname(bedpostx_dir)
####Auto-set INPUTS####
if plot_switch == True:
plt.figure(figsize=(8, 8))
plt.imshow(conn_matrix, interpolation="nearest", vmax=1, vmin=-1, cmap=plt.cm.RdBu_r)
plt.xticks(range(len(label_names)), label_names, size='xx-small', rotation=90)
plt.yticks(range(len(label_names)), label_names, size='xx-small')
plt_title = atlas_select + ' Structural Connectivity of: ' + str(ID)
plt.title(plt_title)
plt.grid(False)
plt.gcf().subplots_adjust(left=0.8)
out_path_fig=dir_path + '/structural_adj_mat_' + str(ID) + '.png'
plt.savefig(out_path_fig)
plt.close()
##Prepare glass brain figure
fdt_paths_loc = probtrackx_output_dir_path + '/fdt_paths.nii.gz'
##Create transform matrix between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),name='coregister')
flirt.inputs.reference = input_MNI
flirt.inputs.in_file = nodif_brain_mask_path
flirt.inputs.out_matrix_file = bedpostx_dir + '/xfms/diff2MNI.mat'
flirt.run()
##Apply transform between diff and MNI using FLIRT
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),name='coregister')
flirt.inputs.reference = input_MNI
flirt.inputs.in_file = nodif_brain_mask_path
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/diff2MNI.mat'
flirt.inputs.out_file = bedpostx_dir + '/xfms/diff2MNI_affine.nii.gz'
flirt.run()
flirt = pe.Node(interface=fsl.FLIRT(cost_func='mutualinfo'),name='coregister')
flirt.inputs.reference = input_MNI
flirt.inputs.in_file = fdt_paths_loc
out_file_MNI = fdt_paths_loc.split('.nii')[0] + '_MNI.nii.gz'
flirt.inputs.out_file = out_file_MNI
flirt.inputs.apply_xfm = True
flirt.inputs.in_matrix_file = bedpostx_dir + '/xfms/diff2MNI.mat'
flirt.run()
fdt_paths_MNI_loc = probtrackx_output_dir_path + '/fdt_paths_MNI.nii.gz'
colors.Normalize(vmin=-1, vmax=1)
clust_pal = sns.color_palette("Blues_r", 4)
clust_colors = colors.to_rgba_array(clust_pal)
##Plotting with glass brain
connectome = niplot.plot_connectome(conn_matrix_symm, coords, edge_threshold=edge_threshold, node_color=clust_colors, edge_cmap=niplot.cm.black_blue_r)
connectome.add_overlay(img=fdt_paths_MNI_loc, threshold=connectome_fdt_thresh, cmap=niplot.cm.cyan_copper_r)
out_file_path = dir_path + '/structural_connectome_fig_' + network + '_' + str(ID) + '.png'
plt.savefig(out_file_path)
plt.close()
network = network + '_structural'
conn_model = 'struct'
pynplot.plot_connectogram(conn_matrix, conn_model, atlas_select, dir_path, ID, network, label_names)
else:
pass
return
def wb_connectome_with_us_atlas_coords(input_file, ID, atlas_select, NETWORK,
node_size, mask, thr, parlistfile,
all_nets, conn_model, dens_thresh, conf,
adapt_thresh, plot_switch,
bedpostx_dir):
nilearn_atlases = [
'atlas_aal', 'atlas_craddock_2012', 'atlas_destrieux_2009'
]
##Input is nifti file
func_file = input_file
##Test if atlas_select is a nilearn atlas
if atlas_select in nilearn_atlases:
try:
parlistfile = getattr(datasets, 'fetch_%s' % atlas_select)().maps
try:
label_names = getattr(datasets,
'fetch_%s' % atlas_select)().labels
except:
label_names = None
try:
networks_list = getattr(datasets,
'fetch_%s' % atlas_select)().networks
except:
networks_list = None
except:
print(
'PyNets is not ready for multi-scale atlases like BASC just yet!'
)
sys.exit()
##Fetch user-specified atlas coords
[coords, atlas_name,
par_max] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
atlas_select = atlas_name
try:
label_names
except:
label_names = np.arange(len(coords) +
1)[np.arange(len(coords) + 1) != 0].tolist()
##Get subject directory path
dir_path = os.path.dirname(
os.path.realpath(func_file)) + '/' + atlas_select
if not os.path.exists(dir_path):
os.makedirs(dir_path)
##Get coord membership dictionary if all_nets option triggered
if all_nets != None:
try:
networks_list
except:
networks_list = None
[membership,
membership_plotting] = nodemaker.get_mem_dict(func_file, coords,
networks_list)
##Describe user atlas coords
print('\n' + atlas_name + ' comes with {0} '.format(par_max) + 'parcels' +
'\n')
print('\n' + 'Stacked atlas coordinates in array of shape {0}.'.format(
coords.shape) + '\n')
##Mask coordinates
if mask is not None:
[coords, label_names] = nodemaker.coord_masker(mask, coords,
label_names)
##Save coords and label_names to pickles
coord_path = dir_path + '/coords_wb_' + str(thr) + '.pkl'
with open(coord_path, 'wb') as f:
pickle.dump(coords, f)
labels_path = dir_path + '/labelnames_wb_' + str(thr) + '.pkl'
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f)
if bedpostx_dir is not None:
from pynets.diffconnectometry import run_struct_mapping
FSLDIR = os.environ['FSLDIR']
try:
FSLDIR
except NameError:
print('FSLDIR environment variable not set!')
est_path2 = run_struct_mapping(FSLDIR, ID, bedpostx_dir, dir_path,
NETWORK, coords, node_size)
##extract time series from whole brain parcellaions:
parcellation = nib.load(parlistfile)
parcel_masker = input_data.NiftiLabelsMasker(labels_img=parcellation,
background_label=0,
memory='nilearn_cache',
memory_level=5,
standardize=True)
ts_within_parcels = parcel_masker.fit_transform(func_file, confounds=conf)
print('\n' +
'Time series has {0} samples'.format(ts_within_parcels.shape[0]) +
'\n')
##Save time series as txt file
out_path_ts = dir_path + '/' + ID + '_whole_brain_ts_within_parcels.txt'
np.savetxt(out_path_ts, ts_within_parcels)
##Fit connectivity model
if adapt_thresh is not False:
if os.path.isfile(est_path2) == True:
[conn_matrix, est_path, edge_threshold,
thr] = thresholding.adaptive_thresholding(ts_within_parcels,
conn_model, NETWORK, ID,
est_path2, dir_path)
else:
print('No structural mx found! Exiting...')
sys.exit(0)
elif dens_thresh is None:
edge_threshold = str(float(thr) * 100) + '%'
[conn_matrix,
est_path] = graphestimation.get_conn_matrix(ts_within_parcels,
conn_model, NETWORK, ID,
dir_path, thr)
conn_matrix = thresholding.threshold_proportional(
conn_matrix, float(thr), dir_path)
conn_matrix = thresholding.normalize(conn_matrix)
elif dens_thresh is not None:
[conn_matrix, est_path, edge_threshold,
thr] = thresholding.density_thresholding(ts_within_parcels,
conn_model, NETWORK, ID,
dens_thresh, dir_path)
if plot_switch == True:
##Plot connectogram
plotting.plot_connectogram(conn_matrix, conn_model, atlas_name,
dir_path, ID, NETWORK, label_names)
##Plot adj. matrix based on determined inputs
atlast_graph_title = plotting.plot_conn_mat(conn_matrix, conn_model,
atlas_name, dir_path, ID,
NETWORK, label_names, mask)
##Plot connectome viz for all Yeo networks
if all_nets != False:
plotting.plot_membership(membership_plotting, conn_matrix,
conn_model, coords, edge_threshold,
atlas_name, dir_path)
else:
out_path_fig = dir_path + '/' + ID + '_connectome_viz.png'
niplot.plot_connectome(conn_matrix,
coords,
title=atlast_graph_title,
edge_threshold=edge_threshold,
node_size=20,
colorbar=True,
output_file=out_path_fig)
return est_path, thr
def network_connectome(input_file, ID, atlas_select, NETWORK, node_size, mask,
thr, parlistfile, all_nets, conn_model, dens_thresh,
conf, adapt_thresh, plot_switch, bedpostx_dir):
nilearn_atlases = [
'atlas_aal', 'atlas_craddock_2012', 'atlas_destrieux_2009'
]
##Input is nifti file
func_file = input_file
##Test if atlas_select is a nilearn atlas
if atlas_select in nilearn_atlases:
atlas = getattr(datasets, 'fetch_%s' % atlas_select)()
try:
parlistfile = atlas.maps
try:
label_names = atlas.labels
except:
label_names = None
try:
networks_list = atlas.networks
except:
networks_list = None
except RuntimeError:
print('Error, atlas fetching failed.')
sys.exit()
if parlistfile == None and atlas_select not in nilearn_atlases:
##Fetch nilearn atlas coords
[coords, atlas_name, networks_list,
label_names] = nodemaker.fetch_nilearn_atlas_coords(atlas_select)
if atlas_name == 'Power 2011 atlas':
##Reference RSN list
import pkgutil
import io
network_coords_ref = NETWORK + '_coords.csv'
atlas_coords = pkgutil.get_data("pynets",
"rsnrefs/" + network_coords_ref)
df = pd.read_csv(io.BytesIO(atlas_coords)).ix[:, 0:4]
i = 1
net_coords = []
ix_labels = []
for i in range(len(df)):
#print("ROI Reference #: " + str(i))
x = int(df.ix[i, 1])
y = int(df.ix[i, 2])
z = int(df.ix[i, 3])
#print("X:" + str(x) + " Y:" + str(y) + " Z:" + str(z))
net_coords.append((x, y, z))
ix_labels.append(i)
i = i + 1
#print(net_coords)
label_names = ix_labels
elif atlas_name == 'Dosenbach 2010 atlas':
coords = list(tuple(x) for x in coords)
##Get coord membership dictionary
[membership, membership_plotting
] = nodemaker.get_mem_dict(func_file, coords, networks_list)
##Convert to membership dataframe
mem_df = membership.to_frame().reset_index()
nets_avail = list(set(list(mem_df['index'])))
##Get network name equivalents
if NETWORK == 'DMN':
NETWORK = 'default'
elif NETWORK == 'FPTC':
NETWORK = 'fronto-parietal'
elif NETWORK == 'CON':
NETWORK = 'cingulo-opercular'
elif NETWORK not in nets_avail:
print('Error: ' + NETWORK + ' not available with this atlas!')
sys.exit()
##Get coords for network-of-interest
mem_df.loc[mem_df['index'] == NETWORK]
net_coords = mem_df.loc[mem_df['index'] == NETWORK][[0]].values[:,
0]
net_coords = list(tuple(x) for x in net_coords)
ix_labels = mem_df.loc[mem_df['index'] == NETWORK].index.values
####Add code for any special RSN reference lists for the nilearn atlases here#####
##If labels_names are not indices and NETWORK is specified, sub-list label names
if label_names != ix_labels:
try:
label_names = label_names.tolist()
except:
pass
label_names = [label_names[i] for i in ix_labels]
##Get subject directory path
dir_path = os.path.dirname(
os.path.realpath(func_file)) + '/' + atlas_select
if not os.path.exists(dir_path):
os.makedirs(dir_path)
##If masking, remove those coords that fall outside of the mask
if mask != None:
[net_coords,
label_names] = nodemaker.coord_masker(mask, net_coords,
label_names)
##Save coords and label_names to pickles
coord_path = dir_path + '/coords_' + NETWORK + '_' + str(thr) + '.pkl'
with open(coord_path, 'wb') as f:
pickle.dump(net_coords, f)
labels_path = dir_path + '/labelnames_' + NETWORK + '_' + str(
thr) + '.pkl'
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f)
if bedpostx_dir is not None:
from pynets.diffconnectometry import run_struct_mapping
FSLDIR = os.environ['FSLDIR']
try:
FSLDIR
except NameError:
print('FSLDIR environment variable not set!')
est_path2 = run_struct_mapping(FSLDIR, ID, bedpostx_dir, dir_path,
NETWORK, net_coords, node_size)
else:
##Fetch user-specified atlas coords
[coords_all, atlas_name,
par_max] = nodemaker.get_names_and_coords_of_parcels(parlistfile)
coords = list(tuple(x) for x in coords_all)
##Get subject directory path
dir_path = os.path.dirname(
os.path.realpath(func_file)) + '/' + atlas_name
if not os.path.exists(dir_path):
os.makedirs(dir_path)
##Get coord membership dictionary
try:
networks_list
except:
networks_list = None
[membership,
membership_plotting] = nodemaker.get_mem_dict(func_file, coords,
networks_list)
##Convert to membership dataframe
mem_df = membership.to_frame().reset_index()
##Get coords for network-of-interest
mem_df.loc[mem_df['index'] == NETWORK]
net_coords = mem_df.loc[mem_df['index'] == NETWORK][[0]].values[:, 0]
net_coords = list(tuple(x) for x in net_coords)
ix_labels = mem_df.loc[mem_df['index'] == NETWORK].index.values
try:
label_names = [label_names[i] for i in ix_labels]
except:
label_names = ix_labels
if mask != None:
[net_coords,
label_names] = nodemaker.coord_masker(mask, net_coords,
label_names)
##Save coords and label_names to pickles
coord_path = dir_path + '/coords_' + NETWORK + '_' + str(thr) + '.pkl'
with open(coord_path, 'wb') as f:
pickle.dump(net_coords, f)
labels_path = dir_path + '/labelnames_' + NETWORK + '_' + str(
thr) + '.pkl'
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f)
if bedpostx_dir is not None:
from pynets.diffconnectometry import run_struct_mapping
est_path2 = run_struct_mapping(FSLDIR, ID, bedpostx_dir, dir_path,
NETWORK, net_coords, node_size)
##Generate network parcels image (through refinement, this could be used
##in place of the 3 lines above)
#net_parcels_img_path = gen_network_parcels(parlistfile, NETWORK, labels)
#parcellation = nib.load(net_parcels_img_path)
#parcel_masker = input_data.NiftiLabelsMasker(labels_img=parcellation, background_label=0, memory='nilearn_cache', memory_level=5, standardize=True)
#ts_within_parcels = parcel_masker.fit_transform(func_file)
#net_ts = ts_within_parcels
##Grow ROIs
masker = input_data.NiftiSpheresMasker(seeds=net_coords,
radius=float(node_size),
allow_overlap=True,
memory_level=5,
memory='nilearn_cache',
verbose=2,
standardize=True)
ts_within_spheres = masker.fit_transform(func_file, confounds=conf)
net_ts = ts_within_spheres
##Save time series as txt file
out_path_ts = dir_path + '/' + ID + '_' + NETWORK + '_net_ts.txt'
np.savetxt(out_path_ts, net_ts)
##Fit connectivity model
if adapt_thresh is not False:
if os.path.isfile(est_path2) == True:
[conn_matrix, est_path, edge_threshold,
thr] = thresholding.adaptive_thresholding(ts_within_spheres,
conn_model, NETWORK, ID,
est_path2, dir_path)
else:
print('No structural mx found! Exiting...')
sys.exit(0)
elif dens_thresh is None:
edge_threshold = str(float(thr) * 100) + '%'
[conn_matrix,
est_path] = graphestimation.get_conn_matrix(ts_within_spheres,
conn_model, NETWORK, ID,
dir_path, thr)
conn_matrix = thresholding.threshold_proportional(
conn_matrix, float(thr), dir_path)
conn_matrix = thresholding.normalize(conn_matrix)
elif dens_thresh is not None:
[conn_matrix, est_path, edge_threshold,
thr] = thresholding.density_thresholding(ts_within_spheres,
conn_model, NETWORK, ID,
dens_thresh, dir_path)
if plot_switch == True:
##Plot connectogram
plotting.plot_connectogram(conn_matrix, conn_model, atlas_name,
dir_path, ID, NETWORK, label_names)
##Plot adj. matrix based on determined inputs
plotting.plot_conn_mat(conn_matrix, conn_model, atlas_name, dir_path,
ID, NETWORK, label_names, mask)
##Plot network time-series
plotting.plot_timeseries(net_ts, NETWORK, ID, dir_path, atlas_name,
label_names)
##Plot connectome viz for specific Yeo networks
title = "Connectivity Projected on the " + NETWORK
out_path_fig = dir_path + '/' + ID + '_' + NETWORK + '_connectome_plot.png'
niplot.plot_connectome(conn_matrix,
net_coords,
edge_threshold=edge_threshold,
title=title,
display_mode='lyrz',
output_file=out_path_fig)
return est_path, thr
def wb_connectome_with_nl_atlas_coords(input_file, ID, atlas_select, NETWORK,
node_size, mask, thr, all_nets,
conn_model, dens_thresh, conf,
adapt_thresh, plot_switch,
bedpostx_dir):
nilearn_atlases = [
'atlas_aal', 'atlas_craddock_2012', 'atlas_destrieux_2009'
]
##Input is nifti file
func_file = input_file
##Fetch nilearn atlas coords
[coords, atlas_name, networks_list,
label_names] = nodemaker.fetch_nilearn_atlas_coords(atlas_select)
##Get subject directory path
dir_path = os.path.dirname(
os.path.realpath(func_file)) + '/' + atlas_select
if not os.path.exists(dir_path):
os.makedirs(dir_path)
##Get coord membership dictionary if all_nets option triggered
if all_nets != False:
try:
networks_list
except:
networks_list = None
[membership,
membership_plotting] = nodemaker.get_mem_dict(func_file, coords,
networks_list)
##Mask coordinates
if mask is not None:
[coords, label_names] = nodemaker.coord_masker(mask, coords,
label_names)
##Save coords and label_names to pickles
coord_path = dir_path + '/coords_wb_' + str(thr) + '.pkl'
with open(coord_path, 'wb') as f:
pickle.dump(coords, f)
labels_path = dir_path + '/labelnames_wb_' + str(thr) + '.pkl'
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f)
if bedpostx_dir is not None:
from pynets.diffconnectometry import run_struct_mapping
FSLDIR = os.environ['FSLDIR']
try:
FSLDIR
except NameError:
print('FSLDIR environment variable not set!')
est_path2 = run_struct_mapping(FSLDIR, ID, bedpostx_dir, dir_path,
NETWORK, coords, node_size)
##Extract within-spheres time-series from funct file
spheres_masker = input_data.NiftiSpheresMasker(seeds=coords,
radius=float(node_size),
memory='nilearn_cache',
memory_level=5,
verbose=2,
standardize=True)
ts_within_spheres = spheres_masker.fit_transform(func_file, confounds=conf)
print('\n' +
'Time series has {0} samples'.format(ts_within_spheres.shape[0]) +
'\n')
##Save time series as txt file
out_path_ts = dir_path + '/' + ID + '_whole_brain_ts_within_spheres.txt'
np.savetxt(out_path_ts, ts_within_spheres)
##Fit connectivity model
if adapt_thresh is not False:
if os.path.isfile(est_path2) == True:
[conn_matrix, est_path, edge_threshold,
thr] = thresholding.adaptive_thresholding(ts_within_spheres,
conn_model, NETWORK, ID,
est_path2, dir_path)
else:
print('No structural mx found! Exiting...')
sys.exit(0)
elif dens_thresh is None:
edge_threshold = str(float(thr) * 100) + '%'
[conn_matrix,
est_path] = graphestimation.get_conn_matrix(ts_within_spheres,
conn_model, NETWORK, ID,
dir_path, thr)
conn_matrix = thresholding.threshold_proportional(
conn_matrix, float(thr), dir_path)
conn_matrix = thresholding.normalize(conn_matrix)
elif dens_thresh is not None:
[conn_matrix, est_path, edge_threshold,
thr] = thresholding.density_thresholding(ts_within_spheres,
conn_model, NETWORK, ID,
dens_thresh, dir_path)
if plot_switch == True:
##Plot connectogram
plotting.plot_connectogram(conn_matrix, conn_model, atlas_name,
dir_path, ID, NETWORK, label_names)
##Plot adj. matrix based on determined inputs
plotting.plot_conn_mat(conn_matrix, conn_model, atlas_name, dir_path,
ID, NETWORK, label_names, mask)
##Plot connectome viz for all Yeo networks
if all_nets != False:
plotting.plot_membership(membership_plotting, conn_matrix,
conn_model, coords, edge_threshold,
atlas_name, dir_path)
else:
out_path_fig = dir_path + '/' + ID + '_' + atlas_name + '_connectome_viz.png'
niplot.plot_connectome(conn_matrix,
coords,
title=atlas_name,
edge_threshold=edge_threshold,
node_size=20,
colorbar=True,
output_file=out_path_fig)
return est_path, thr
def plot_all(conn_matrix, conn_model, atlas_select, dir_path, ID, network,
label_names, mask, coords, thr, node_size, edge_threshold):
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot as plt
from nilearn import plotting as niplot
import pkg_resources
import networkx as nx
from pynets import plotting
from pynets.netstats import most_important
try:
import cPickle as pickle
except ImportError:
import _pickle as pickle
pruning = True
dpi_resolution = 500
G_pre = nx.from_numpy_matrix(conn_matrix)
if pruning == True:
[G, pruned_nodes, pruned_edges] = most_important(G_pre)
else:
G = G_pre
conn_matrix = nx.to_numpy_array(G)
pruned_nodes.sort(reverse=True)
for j in pruned_nodes:
del label_names[label_names.index(label_names[j])]
del coords[coords.index(coords[j])]
pruned_edges.sort(reverse=True)
for j in pruned_edges:
del label_names[label_names.index(label_names[j])]
del coords[coords.index(coords[j])]
# Plot connectogram
if len(conn_matrix) > 20:
try:
plotting.plot_connectogram(conn_matrix, conn_model, atlas_select,
dir_path, ID, network, label_names)
except RuntimeError:
print('\n\n\nError: Connectogram plotting failed!')
else:
print(
'Error: Cannot plot connectogram for graphs smaller than 20 x 20!')
# Plot adj. matrix based on determined inputs
plotting.plot_conn_mat_func(conn_matrix, conn_model, atlas_select,
dir_path, ID, network, label_names, mask, thr,
node_size)
# Plot connectome
if mask:
if network:
out_path_fig = "%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s" % (
dir_path, '/', ID, '_', str(atlas_select), '_',
str(conn_model), '_', str(
os.path.basename(mask).split('.')[0]), '_', str(network),
'_', str(thr), '_', str(node_size), '_func_glass_viz.png')
else:
out_path_fig = "%s%s%s%s%s%s%s%s%s%s%s%s%s%s" % (
dir_path, '/', ID, '_', str(atlas_select), '_',
str(conn_model), '_', str(
os.path.basename(mask).split('.')[0]), '_', str(thr), '_',
str(node_size), '_func_glass_viz.png')
# Save coords to pickle
coord_path = "%s%s%s%s" % (dir_path, '/coords_',
os.path.basename(mask).split('.')[0],
'_plotting.pkl')
with open(coord_path, 'wb') as f:
pickle.dump(coords, f, protocol=2)
net_parcels_map_nifti = None
# Save labels to pickle
labels_path = "%s%s%s%s" % (dir_path, '/labelnames_',
os.path.basename(mask).split('.')[0],
'_plotting.pkl')
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f, protocol=2)
else:
if network:
out_path_fig = "%s%s%s%s%s%s%s%s%s%s%s%s%s%s" % (
dir_path, '/', ID, '_', str(atlas_select), '_',
str(conn_model), '_', str(network), '_', str(thr), '_',
str(node_size), '_func_glass_viz.png')
else:
out_path_fig = "%s%s%s%s%s%s%s%s%s%s%s%s" % (
dir_path, '/', ID, '_',
str(atlas_select), '_', str(conn_model), '_', str(thr), '_',
str(node_size), '_func_glass_viz.png')
# Save coords to pickle
coord_path = "%s%s" % (dir_path, '/coords_plotting.pkl')
with open(coord_path, 'wb') as f:
pickle.dump(coords, f, protocol=2)
# Save labels to pickle
labels_path = "%s%s" % (dir_path, '/labelnames_plotting.pkl')
with open(labels_path, 'wb') as f:
pickle.dump(label_names, f, protocol=2)
#niplot.plot_connectome(conn_matrix, coords, edge_threshold=edge_threshold, node_size=20, colorbar=True, output_file=out_path_fig)
ch2better_loc = pkg_resources.resource_filename(
"pynets", "templates/ch2better.nii.gz")
connectome = niplot.plot_connectome(np.zeros(shape=(1, 1)), [(0, 0, 0)],
node_size=0.0001)
connectome.add_overlay(ch2better_loc, alpha=0.4, cmap=plt.cm.gray)
[z_min, z_max] = -np.abs(conn_matrix).max(), np.abs(conn_matrix).max()
connectome.add_graph(conn_matrix,
coords,
edge_threshold=edge_threshold,
edge_cmap='Greens',
edge_vmax=z_max,
edge_vmin=z_min,
node_size=4)
connectome.savefig(out_path_fig, dpi=dpi_resolution)
#connectome.savefig(out_path_fig, dpi=dpi_resolution, facecolor ='k', edgecolor ='k')
return