def run_fuse(self):
"""
Run fusion.
"""
assert os.path.exists(self.options.depth_dir)
common.makedir(self.options.out_dir)
files = self.read_directory(self.options.depth_dir)
timer = common.WallTimer()
Rs = self.get_views()
for filepath in files:
# As rendering might be slower, we wait for rendering to finish.
# This allows to run rendering and fusing in parallel (more or less).
depths = common.read_hdf5(filepath)
timer.reset()
tsdf = self.fusion(depths, Rs)
tsdf = tsdf[0]
vertices, triangles = libmcubes.marching_cubes(-tsdf, 0)
vertices /= self.options.resolution
vertices -= 0.5
off_file = os.path.join(self.options.out_dir, ntpath.basename(filepath)[:-3])
exporter.export_off(vertices, triangles, off_file)
print('[Data] wrote %s (%f seconds)' % (off_file, timer.elapsed()))
def run_sample(self, filepath):
"""
Run sampling.
"""
timer = common.Timer()
Rs = self.get_views()
# As rendering might be slower, we wait for rendering to finish.
# This allows to run rendering and fusing in parallel (more or less).
depths = common.read_hdf5(filepath)
timer.reset()
tsdf = self.fusion(depths, Rs)
xs = np.linspace(-0.5, 0.5, tsdf.shape[0])
ys = np.linspace(-0.5, 0.5, tsdf.shape[1])
zs = np.linspace(-0.5, 0.5, tsdf.shape[2])
tsdf_func = rgi((xs, ys, zs), tsdf)
modelname = os.path.splitext(os.path.splitext(os.path.basename(filepath))[0])[0]
points = self.get_random_points(tsdf)
values = tsdf_func(points)
t_loc, t_scale = self.get_transform(modelname)
occupancy = (values <= 0.)
out_file = self.get_outpath(filepath)
np.savez(out_file, points=points, occupancy=occupancy, loc=t_loc, scale=t_scale)
print('[Data] wrote %s (%f seconds)' % (out_file, timer.elapsed()))
def run_fuse(self, filepath):
"""
Run fusion.
"""
timer = common.Timer()
Rs = self.get_views()
# As rendering might be slower, we wait for rendering to finish.
# This allows to run rendering and fusing in parallel (more or less).
depths = common.read_hdf5(filepath)
timer.reset()
tsdf = self.fusion(depths, Rs)
# To ensure that the final mesh is indeed watertight
tsdf = np.pad(tsdf, 1, 'constant', constant_values=1e6)
vertices, triangles = libmcubes.marching_cubes(-tsdf, 0)
# Remove padding offset
vertices -= 1
# Normalize to [-0.5, 0.5]^3 cube
vertices /= self.options.resolution
vertices -= 0.5
modelname = os.path.splitext(os.path.splitext(os.path.basename(filepath))[0])[0]
t_loc, t_scale = self.get_transform(modelname)
vertices = t_loc + t_scale * vertices
off_file = self.get_outpath(filepath)
libmcubes.export_off(vertices, triangles, off_file)
print('[Data] wrote %s (%f seconds)' % (off_file, timer.elapsed()))
def __call__(self):
self.treatment = read_hdf5(self.treatment_file)
self.control = read_hdf5(self.control_file)
name_counts = np.unique(np.concatenate(
[self.treatment['name'], self.control['name']]),
return_counts=True)
common_names = name_counts[0][name_counts[1] == 2]
if self.names is None:
self.names = common_names[:self.max_plots]
from matplotlib.backends.backend_pdf import PdfPages
self.logger.info('open pdf file: {}'.format(self.outfile))
make_dir(os.path.dirname(self.outfile))
with PdfPages(self.outfile) as pdf:
for seqname in self.names:
self.logger.info('plot track: {}'.format(seqname))
pdf.savefig(self.plot_tracks(seqname))
def analyze(self):
self.icshape = read_hdf5(self.icshape_file)
self.background = read_hdf5(self.background_file)
self.target = read_hdf5(self.target_file)
name_counts = np.unique(np.concatenate([
self.icshape['name'], self.background['name'], self.target['name']
]),
return_counts=True)
common_names = name_counts[0][name_counts[1] == 3]
if self.names is None:
self.names = common_names[:self.max_plots]
from matplotlib.backends.backend_pdf import PdfPages
self.logger.info('open pdf file: {}'.format(self.outfile))
make_dir(os.path.dirname(self.outfile))
with PdfPages(self.outfile) as pdf:
for seqname in self.names:
self.logger.info('plot track: {}'.format(seqname))
pdf.savefig(self.plot_tracks(seqname))
"""
timer.reset()
mesh = common.Mesh.from_off(scaled_off_path)
depths = fusion_tools.render(mesh, Rs)
depth_file_path = os.path.join(options.depth_dir,
os.path.basename(filepath) + '.h5')
common.write_hdf5(depth_file_path, np.array(depths))
print('----- [Depth] wrote %s (%f seconds)' %
(depth_file_path, timer.elapsed()))
"""
Performs TSDF fusion.
As rendering might be slower, we wait for rendering to finish.
This allows to run rendering and fusing in parallel (more or less).
"""
depths = common.read_hdf5(depth_file_path)
timer.reset()
tsdf = fusion_tools.fusion(depths, Rs)
tsdf = tsdf[0]
vertices, triangles = libmcubes.marching_cubes(-tsdf, 0)
vertices /= options.resolution
vertices -= 0.5
# vertices = vertices[:, [2, 1, 0]]
# print(vertices.shape)
off_file = os.path.join(options.out_dir,
'0_scaled_' + ntpath.basename(filepath))
libmcubes.export_off(vertices, triangles, off_file)
def run_fuse(self):
"""
Run fusion.
"""
assert os.path.exists(self.options.depth_dir)
common.makedir(self.options.out_dir)
common.makedir('4_tsdf')
files = self.read_directory(self.options.depth_dir)
timer = common.Timer()
Rs = self.get_views()
for filepath in files:
# As rendering might be slower, we wait for rendering to finish.
# This allows to run rendering and fusing in parallel (more or less).
depths = common.read_hdf5(filepath)
timer.reset()
tsdf = self.fusion(depths, Rs)
tsdf = tsdf[0]
vertices, triangles = libmcubes.marching_cubes(-tsdf, 0)
# vertices, triangles, _, _ = measure.marching_cubes_lewiner(-tsdf, 0)
print tsdf.shape
np.save(os.path.join('4_tsdf', ntpath.basename(filepath)[:-3]).replace('.off', ''), -tsdf)
vertices /= self.options.resolution
vertices -= 0.5
off_file = os.path.join(self.options.out_dir, ntpath.basename(filepath)[:-3])
libmcubes.export_off(vertices, triangles, off_file)
print('[Data] wrote %s (%f seconds)' % (off_file, timer.elapsed()))
mesh = common.Mesh.from_off(off_file)
s_t = scipy.io.loadmat(off_file.replace('2_watertight', '1_s_t').replace('.off', '.mat'))
# scales_ori = (1./s_t['scales'][0][0], 1./s_t['scales'][0][1], 1./s_t['scales'][0][2])
# translation_ori = (-s_t['translation'][0][0], -s_t['translation'][0][1], -s_t['translation'][0][2])
sizes_ori = (s_t['sizes'][0][0], s_t['sizes'][0][1], s_t['sizes'][0][2])
# print scales, translation
min, max = mesh.extents()
total_min = np.min(np.array(min))
total_max = np.max(np.array(max))
# Set the center (although this should usually be the origin already).
centers = (
(min[0] + max[0]) / 2,
(min[1] + max[1]) / 2,
(min[2] + max[2]) / 2
)
# Scales all dimensions equally.
sizes = (
total_max - total_min,
total_max - total_min,
total_max - total_min
)
translation = (
-centers[0],
-centers[1],
-centers[2]
)
mesh.translate(translation)
mesh.scale((sizes_ori[0]/sizes[0], sizes_ori[1]/sizes[1], sizes_ori[2]/sizes[2]))
mesh.to_off(off_file)