def push_zero_projections(resolution, host="localhost", port=5558):
m = resolution
proj_count, rows, cols = m, m, m
scene_id = 0
pub = tomop.publisher(host, port)
# We let the server know we will send one dark field, and one flat field
num_darks, num_flats = 1, 1
packet_scan_settings = tomop.scan_settings_packet(scene_id, num_darks,
num_flats, False)
pub.send(packet_scan_settings)
# Initialize volume and acquisition geometry
packet_vol_geom = tomop.geometry_specification_packet(
scene_id, [0, 0, 0], [1, 1, 1])
pub.send(packet_vol_geom)
angles = np.linspace(0, np.pi, proj_count, endpoint=False)
packet_geometry = tomop.parallel_beam_geometry_packet(
scene_id, rows, cols, proj_count, angles)
pub.send(packet_geometry)
# Send dark(s) and flat(s)
dark = np.zeros((rows, cols), dtype=np.float32).ravel()
packet_dark = tomop.projection_packet(0, 0, [rows, cols], dark)
pub.send(packet_dark)
flat = np.ones((rows, cols), dtype=np.float32).ravel()
packet_flat = tomop.projection_packet(1, 0, [rows, cols], flat)
pub.send(packet_flat)
# Create and send projection data consisting of zeros
proj_data = np.zeros((proj_count, rows, cols))
for i in np.arange(0, proj_count):
packet_proj = tomop.projection_packet(2, i, [rows, cols],
proj_data[i, :, :].ravel())
pub.send(packet_proj)
pub = tomop.publisher(args.host, args.port)
path = args.path
# PACKET 1: object volume specification
print("Sending object volume")
geom_spec = tomop.geometry_specification_packet(0, [-n / 2, -n / 2, -n / 2],
[n / 2, n / 2, n / 2])
pub.send(geom_spec)
# PACKET 2: acquisition geometry
print("Sending acquisition geometry")
par_beam = tomop.parallel_beam_geometry_packet(0, m, n, count, angles)
pub.send(par_beam)
# PACKET 3: scan settings
print("Sending scan data (linear: ", not args.linearize, ")")
pub.send(tomop.scan_settings_packet(0, 0, 0, not args.linearize))
# PACKET 4..: Projections
while not os.path.isfile(files[0][1]):
time.sleep(0.01)
time.sleep(1.0)
shape, first_proj = ser_parser.parser(files[0][1])
prev = np.reshape(first_proj, [m, n])
prev = np.transpose(prev, axes=[1, 0])
def center(xs):
val = ski.filters.threshold_otsu(xs)
ys = xs.copy()
print(proj_geom)
print('proj geom vector count', len(proj_geom['Vectors']))
print(vol_geom)
packet_vol_geom = tomop.geometry_specification_packet(0, [
vol_geom['option']['WindowMinX'], vol_geom['option']['WindowMinY'],
vol_geom['option']['WindowMinZ']
], [
vol_geom['option']['WindowMaxX'], vol_geom['option']['WindowMaxY'],
vol_geom['option']['WindowMaxZ']
])
if not args.skipgeometry:
pub.send(packet_vol_geom)
print("flat dark", flat.shape, dark.shape)
packet_scan_settings = tomop.scan_settings_packet(0, dark.shape[1],
flat.shape[1], False)
if not args.skipgeometry:
pub.send(packet_scan_settings)
packet_geometry = tomop.cone_vec_geometry_packet(
0, rows, cols, proj_count, proj_geom['Vectors'].flatten())
if not args.skipgeometry:
pub.send(packet_geometry)
# send darks (0), lights (1), projs (2)
for i in np.arange(0, dark.shape[1]):
packet_dark = tomop.projection_packet(
0, i, [rows, cols], np.ascontiguousarray(dark[:, i, :].flatten()))
pub.send(packet_dark)
print(proj_geom)
print('proj geom vector count', len(proj_geom['Vectors']))
print(vol_geom)
packet_vol_geom = tomop.geometry_specification_packet(0, [
vol_geom['option']['WindowMinX'], vol_geom['option']['WindowMinY'],
vol_geom['option']['WindowMinZ']
], [
vol_geom['option']['WindowMaxX'], vol_geom['option']['WindowMaxY'],
vol_geom['option']['WindowMaxZ']
])
if not args.skipgeometry:
pub.send(packet_vol_geom)
packet_scan_settings = tomop.scan_settings_packet(0, dark.shape[0],
flat.shape[0])
if not args.skipgeometry:
pub.send(packet_scan_settings)
packet_geometry = tomop.cone_vec_geometry_packet(
0, rows, cols, proj_count, proj_geom['Vectors'].flatten())
if not args.skipgeometry:
pub.send(packet_geometry)
# send darks (0), lights (1), projs (2)
for i in np.arange(0, dark.shape[0]):
packet_dark = tomop.projection_packet(
0, i, [rows, cols], np.ascontiguousarray(dark[i, :, :].flatten()))
pub.send(packet_dark)
parser.add_argument('--time',
type=float,
default=0.0,
help='time interval')
parser.add_argument('--projs', type=int, help='proj count')
args = parser.parse_args()
hdf5Reader = Hdf5ReaderClass(args.path)
proj = hdf5Reader.getRawImage(0)
rows, cols = proj.shape
pub = tp.publisher(args.host, args.port)
pub.send(
tp.scan_settings_packet(0, hdf5Reader.numberOfDarks,
hdf5Reader.totalNumberOfFlats // 2, False))
r = max(rows, cols)
window_min_point = [-cols // 2, -cols // 2, -rows // 2]
window_max_point = [cols // 2, cols // 2, rows // 2]
pub.send(
tp.geometry_specification_packet(0, window_min_point,
window_max_point))
angles = np.linspace(0, np.pi, args.projs, endpoint=False)
pub.send(
tp.parallel_beam_geometry_packet(0, rows, cols, args.projs, angles))
for i in range(hdf5Reader.numberOfDarks):
packet_dark = tp.projection_packet(
0, i, [rows, cols],