sys.exit()
# parse the arguments
if not iter:
iter = 10
else:
iter = int(iter)
if metafile and os.path.exists(metafile):
metadata = loadstar(metafile, dtype=datatype)
tiltAngles = metadata['TiltAngle']
else:
tiltAngles = []
# start reconstruction
from pytom.tompy.io import read, write
from nufft.reconstruction import fourier_2d1d_iter_reconstruct
from pytom.reconstruction.reconstructionStructures import ProjectionList
projections = ProjectionList()
projections.loadDirectory(proj_dir, tiltAngles=tiltAngles)
projections.sort()
projs = []
tilt_angles = []
for p in projections:
print(p.getTiltAngle(), p.getFilename())
projs.append(read(p.getFilename()))
tilt_angles.append(p.getTiltAngle())
v = fourier_2d1d_iter_reconstruct(projs, tilt_angles, iter)
write(output_filename, v)
if not aw:
aw = 0
else:
aw = float(aw)
if recOffset:
recOffset = [int(i) for i in recOffset.split(",")]
else:
recOffset = [0., 0., 0.]
try:
numProcesses = int(numProcesses)
except:
numProcesses = 0
projections = ProjectionList()
if checkFileExists(projectionList):
projections.fromXMLFile(projectionList)
elif checkDirExists(projectionDirectory):
projections.loadDirectory(projectionDirectory, metafile=metafile)
else:
raise RuntimeError(
'Neither projectionList existed nor the projectionDirectory you specified! Abort'
)
import os
if os.path.exists(os.path.join(projectionDirectory,
'alignmentResults.txt')):
alignResultFile = os.path.join(projectionDirectory,
'alignmentResults.txt')
raise ValueError("The particle size has to be an even number.")
peak_border = vol_size // 2 - max_shift
if peak_border < 0:
raise ValueError(
"The given shiftStandardDeviation and peakBorderSize result in a maximal shift "
"bigger than the given volume. Please use a bigger volume or a smaller maximal shift."
)
# Split particlelist based on filename
# Map filename to right projection directory
mpi = MPI()
mpi.begin()
projections = ProjectionList()
projections.loadDirectory(proj_dir)
projections.sort()
# create the list of projectionfilenames and tiltangles
proj = []
tilt_angles = []
for p in projections:
proj.append(p.getFilename())
tilt_angles.append(p.getTiltAngle())
polish_particles(particleList,
proj_dir,
template,
coordinateBinning,
else:
projBinning = 1
if coordinateBinning:
coordinateBinning = float(coordinateBinning)
else:
coordinateBinning = 1
if not aw:
aw = False
if recOffset:
recOffset = [int(i) for i in recOffset.split(",")]
else:
recOffset = [0., 0., 0.]
projections = ProjectionList()
if checkFileExists(projectionList):
projections.fromXMLFile(projectionList)
elif checkDirExists(projectionDirectory):
projections.loadDirectory(projectionDirectory)
else:
raise RuntimeError(
'Neither projectionList existed nor the projectionDirectory you specified! Abort'
)
if tomogram:
vol = projections.reconstructVolume(dims=size,
reconstructionPosition=recOffset,
binning=projBinning,
applyWeighting=aw)
vol.write(tomogram)