help='angle (in degrees) for y rotation',
dest='yangle', default=0.0)
parser.add_argument('-z', type=float,
help='angle (in degrees) for z rotation',
dest='zangle', default=0.0)
parser.add_argument('-f', '--frames', type=int,
help='number of frames per degree',
dest='fpd', default=100)
parser.add_argument('-r', '--rate', type=int,
help='frame rate',
dest='framerate', default=25)
parser.add_argument('-o', '--output', type=str,
help='output filename', dest='outfile',
required=True)
args = parser.parse_args()
infile = args.infile
outfile = args.outfile
fpd = args.fpd
framerate = args.framerate
print(args.xangle, args.yangle, args.zangle, fpd, framerate)
graph = ng.tograph(infile)
dump_movie(outfile, graph, xrot=args.xrot, yrot=args.yrot, zrot=args.zrot,
xangle=args.xangle, yangle=args.yangle, zangle=args.zangle,
frames_per_degree=fpd, framerate=framerate)
print('Saved movie in', outfile)
#
# vtk_dump_movie.py ends here
try:
colormap = ng.colormaps[args.colormap]
except KeyError:
print('Colormap must be one of', ng.colormaps.keys())
sys.exit(0)
background = [0, 0, 0]
for ii, fstr in enumerate(args.bg.split()):
background[ii] = float(fstr)
if ii >= 3:
break
cell_graphs = {}
cell_pos = {}
cell_rot = {}
label_nodes = defaultdict(list)
for ii, fname in enumerate(args.filenames):
cg = ng.tograph(fname)
cell_graphs[fname] = cg
if ii < len(args.mirror):
maxes = args.mirror[ii].split()
for ax in maxes:
for n in cg.nodes():
cg.node[n][ax] = -cg.node[n][ax]
if ii < len(args.translate):
cell_pos[fname] = [int(x) for x in args.translate[ii].split()]
else:
cell_pos[fname] = [0, 0, 0]
if ii < len(args.rotate):
rot = args.rotate[ii].split()
for jj in range(0, len(rot), 2):
rot[jj + 1] = float(rot[jj + 1])
cell_rot[fname] = zip(rot[0::2], rot[1::2])
sys.exit(0)
if args.bg:
background = (0, 0, 0)
else:
background = (1, 1, 1)
if module == 'vispy':
from morph3d_vispy import neuron3d
elif module == 'vpython':
from morph3d_vpython import neuron3d
else:
from morph3d_vtk import neuron3d
# Build the graph
combined_cellgraph = nx.DiGraph()
for ii, fname in enumerate(args.filenames):
print('Opening', fname)
cellgraph = ng.tograph(fname)
xshift, yshift, zshift = (0, 0, 0)
print('##', args.translate)
if len(args.translate) > ii:
xshift, yshift, zshift = args.translate[ii]
xrot, yrot, zrot = (0, 0, 0)
if len(args.rotate) > ii:
xrot, yrot, zrot = args.rotate[ii]
tmatrix = make_tmatrix(xshift, yshift, zshift, xrot, yrot, zrot)
print('Transformation matrix for', fname)
print(tmatrix)
rigid_transform_graph(cellgraph, tmatrix)
if ii > 0:
maxnode = max(combined_cellgraph.nodes())
for node in cellgraph.nodes():
cellgraph.node[node]['p'] += maxnode