def refineMarkerPositions(tiltSeriesName,
markerFileName,
firstProj,
lastProj,
finealigfile,
ireftilt=0,
irefmark=1,
cent=[1025, 1025],
dimBox=32,
verbose=False):
"""
refine coordinates of markers
@param tiltSeriesName: name of tilt series (<Name>_index.em or <Name>_index.mrc)
@type tiltSeriesName: L{str}
@param markerFileName: name of marker file
@type markerFileName: L{str}
@param firstProj: index of first projection
@type firstProj: L{int}
@param lastProj: index of last projection
@type lastProj: L{int}
@param finealigfile: output file with refined marker coordinates
@type finealigfile: L{str}
@param dimBox: dimension of box for markers
@type dimBox: L{int}
@param verbose: verbose for debugging
@type verbose: L{bool}
@author: FF
"""
from pytom.reconstruction.TiltAlignmentStructures import TiltAlignmentParameters, TiltSeries, TiltAlignment
#read data
MyTiltAlignmentParas = TiltAlignmentParameters(dmag=False,
drot=False,
dbeam=False,
finealig=True,
finealigfile=finealigfile,
grad=False,
irefmark=irefmark,
ireftilt=ireftilt,
r=None,
cent=cent,
handflip=False,
optimizer='leastsq',
maxIter=0)
MyTiltSeries = TiltSeries(tiltSeriesName=tiltSeriesName,
TiltAlignmentParas=MyTiltAlignmentParas,
alignedTiltSeriesName='dummy',
markerFileName=markerFileName,
firstProj=firstProj,
lastProj=lastProj)
MyTiltAlignment = TiltAlignment(MyTiltSeries)
#MyTiltAlignment.computeCarseAlignment( MyTiltSeries, mute=True)
MyTiltAlignment.refineMarkerPositions(TiltSeries_=MyTiltSeries,
dimBox=dimBox,
finealigfile=finealigfile,
verbose=False)
def refineMarkerPositions( tiltSeriesName, markerFileName, firstProj,
lastProj, finealigfile, dimBox=32, projIndices=None, tiltSeriesFormat='em',ret=False,write=True,ireftilt=21,size=30000):
"""
refine coordinates of markers
"""
mask = None
#read data
MyTiltAlignmentParas=TiltAlignmentParameters(
dmag=False, drot=False, dbeam=False,
finealig=True, finealigfile=finealigfile,
grad=False,
irefmark=1, ireftilt=ireftilt, r=None, cent= [1025,1025],
handflip=False,
optimizer='leastsq', maxIter=0)
MyTiltSeries= TiltSeries(tiltSeriesName=tiltSeriesName,
TiltAlignmentParas=MyTiltAlignmentParas,
alignedTiltSeriesName='dummy',
markerFileName=markerFileName,
firstProj=firstProj, lastProj=lastProj,projIndices=projIndices,tiltSeriesFormat=tiltSeriesFormat)
MyTiltAlignment = TiltAlignment(MyTiltSeries)
MyTiltAlignment.computeCoarseAlignment( MyTiltSeries)
#MyTiltAlignment.alignFromFiducials()
dxdy_markers = numpy.zeros((len(projIndices),len(MyTiltSeries._Markers),2),dtype=float)
missing = []
for (imark, marker) in enumerate(MyTiltSeries._Markers):
markerImageStack = ImageStack(verbose=False)
len_stack = 0
for itilt in range(0,len(marker._projIndices)):
x = round(marker.get_xProj(itilt))
y = round(marker.get_yProj(itilt))
if (x-dimBox//2 -2 > 0.01) and ( y -dimBox//2 -2 > 0.01) and size-x > dimBox//2+1 and size-y > dimBox//2+1:
proj = MyTiltSeries._ProjectionList[itilt]
filename = proj.getFilename()
#copy data to ImageStack
xmin, ymin = x-dimBox//2-2, y-dimBox//2-2
xend, yend= min(xmin+dimBox, size), min(ymin+dimBox,size)
xoff, yoff = dimBox-(xend-xmin), dimBox-(yend-ymin)
markerImageStack.addImageFromFile(filename=filename, boxCoords=[max(0,xmin), max(0,ymin), 0],
dims=[dimBox, dimBox, 1], shiftX=0, shiftY=0, rotation=0,
appliedShiftX=0, appliedShiftY=0, index=itilt)
len_stack +=1
else:
proj = MyTiltSeries._ProjectionList[itilt]
print("marker not clicked in "+proj.getFilename())
#markerImageStack.normalize( normtype="StdMeanInMask", mask=mask)
if len_stack == 0:
continue
markerImageStack.bandpass( lowfreq=dimBox/32., hifreq=6.*dimBox/32., smooth=2.*dimBox/32., bpf=None)
markerImageStack.normalize( normtype="StdMean")
# smoothen edges
markerImageStack.taper_edges( width=dimBox/8.)
markerImageStack.exMaxAlign( niter=10, mask=mask)
if write:
dirname = os.path.dirname(tiltSeriesName)
markerImageStack.writeWorkingCopies( filename="{}/Marker_{:02d}.em".format(dirname,imark) )
markerImageStack.writeAverage( filename='{}/av_{:02d}.em'.format(dirname,imark) )
# set new coordinates
irun = 0
for itilt in range(0,len(marker._projIndices)):
x = round(marker.get_xProj(itilt))
y = round(marker.get_yProj(itilt))
if ( x > -1 ) and ( y > -1 ):
try:
dx = x+markerImageStack.images[irun].shiftX
dy = y+markerImageStack.images[irun].shiftY
except: continue
dxdy_markers[itilt][imark][0] = dy
dxdy_markers[itilt][imark][1] = dx
marker.set_xProj(itilt, x+ markerImageStack.images[irun].shiftX)
marker.set_yProj(itilt, y+ markerImageStack.images[irun].shiftY)
irun = irun + 1
#(psiindeg, shiftX, shiftY, x, y, z, distLine, diffX, diffY,
# shiftVarX, shiftVarY) = MyTiltAlignment.computeCoarseAlignment( MyTiltSeries)
#for i in range(len(MyTiltSeries._Markers)):
errors = MyTiltAlignment.alignmentResidual()
transX = MyTiltAlignment._alignmentTransY - MyTiltAlignment.TiltSeries_._TiltAlignmentParas.cent[0]
transY = MyTiltAlignment._alignmentTransX - MyTiltAlignment.TiltSeries_._TiltAlignmentParas.cent[1]
if ret:
return dxdy_markers, errors, transX, transY
def alignWeightReconstructOld(tiltSeriesName,
markerFileName,
lastProj,
tltfile=None,
prexgfile=None,
preBin=None,
volumeName=None,
volumeFileType='em',
alignResultFile='',
voldims=None,
recCent=[0, 0, 0],
tiltSeriesFormat='st',
firstProj=1,
irefmark=1,
ireftilt=1,
handflip=False,
alignedTiltSeriesName='align/myTilt',
weightingType=-1,
lowpassFilter=1.,
projBinning=1,
outMarkerFileName=None,
verbose=False,
outfile='',
write_images=True):
"""
@param tiltSeriesName: Name of tilt series (set of image files in .em or .mrc format) or stack file (ending '.st').\
Note: the actual file ending should NOT be provided.
@type tiltSeriesName: str
@param markerFileName: name of EM markerfile or IMOD wimp File containing marker coordinates
@type markerFileName: str
@param lastProj: index of last projection
@param tltfile: ascii file containing the tilt angles
@type tltfile: str
@type lastProj: int
@param prexgfile: file containing pre-shifts (IMOD way of doing things)
@type prexgfile: str
@param preBin: pre-binning in IMOD used for marker determination
@type preBin: int
@param volumeName: Filename of volume
@type volumeName: str
@param volumeFileType: type of output volume - em or mrc
@type volumeFileType: str
@param voldims: dimensions of reconstruction volume, e.g. [512,512,128] - if None chosen only aligned projs are \
written
@type voldims: list
@param recCent: offset from center of volume - for example choose z!=0 to shift in z (post-binning coordinates) - \
default (0,0,0)
@type recCent: list
@param tiltSeriesFormat: file format of tilt series: 'em', 'mrc' or 'st'
@type tiltSeriesFormat: str
@param firstProj: index of first projection - default 1
@type firstProj: int
@param irefmark: index of reference marker for alignment
@type irefmark: int
@param ireftilt: index of reference tilt
@type ireftilt: int
@param handflip: add 180 deg to default tilt axis resulting in change of handedness?
@type handflip: bool
@param alignedTiltSeriesName: name of ailgned tilt series
@type alignedTiltSeriesName: str
@param weightingType: type of weighting - -1 is analytical 'ramp' weighting and 0 is no weighting
@type weightingType: int
@param lowpassFilter: lowpass filter in Nyquist
@type lowpassFilter: float
@param projBinning: binning of projection (factor rather than power of two!)
@type projBinning: int or float
@param outMarkerFileName: filename of output marker file
@type outMarkerFileName: str
@param verbose: verbose?
@type verbose: bool
@author: FF
"""
from pytom.reconstruction.TiltAlignmentStructures import TiltSeries, TiltAlignment, TiltAlignmentParameters
if not alignResultFile:
if verbose:
print("Function alignWeightReconstruct started")
mute = False
else:
mute = True
from pytom.reconstruction.TiltAlignmentStructures import TiltSeries, TiltAlignment, TiltAlignmentParameters
tiltParas = TiltAlignmentParameters(dmag=True,
drot=True,
dbeam=False,
finealig=True,
finealigfile='xxx.txt',
grad=False,
irefmark=irefmark,
ireftilt=ireftilt,
r=None,
cent=[2049, 2049],
handflip=handflip,
optimizer='leastsq',
maxIter=1000)
markerFileType = markerFileName.split('.')[-1]
# align with wimpfile
if not preBin:
preBin = 1
if markerFileType == 'wimp':
if verbose:
print(" WIMP file used for alignment")
tiltSeries = TiltSeries(
tiltSeriesName=tiltSeriesName,
TiltAlignmentParas=tiltParas,
alignedTiltSeriesName=alignedTiltSeriesName,
markerFileName=None,
firstProj=firstProj,
lastProj=lastProj,
tiltSeriesFormat=tiltSeriesFormat)
tiltSeries.readIMODwimp(markerFileName=markerFileName,
prexgfile=prexgfile,
tltfile=tltfile,
preBin=preBin,
verbose=False)
else:
if verbose:
print(" EM markerfile file used for alignment")
tiltSeries = TiltSeries(
tiltSeriesName=tiltSeriesName,
TiltAlignmentParas=tiltParas,
alignedTiltSeriesName=alignedTiltSeriesName,
markerFileName=markerFileName,
firstProj=firstProj,
lastProj=lastProj,
tiltSeriesFormat=tiltSeriesFormat)
if tltfile:
tiltSeries.getTiltAnglesFromIMODfile(tltfile=tltfile)
tiltAlignment = TiltAlignment(TiltSeries_=tiltSeries)
if outMarkerFileName:
tiltSeries.writeMarkerFile(markerFileName=outMarkerFileName)
tiltSeries._markerFileName = outMarkerFileName
tiltAlignment.resetAlignmentCenter() # overrule cent in Paras
print(outfile)
tiltAlignment.computeCoarseAlignment(tiltSeries,
mute=mute,
outfile=outfile)
tiltAlignment.alignFromFiducials(mute=mute)
# creating dir for aligned tilt series if default filename
if alignedTiltSeriesName == 'align/myTilt':
from os import mkdir
try:
mkdir('align')
except OSError:
print(
" dir 'align' already exists - writing aligned files into existing dir"
)
tiltSeries.write_aligned_projs(weighting=weightingType,
lowpassFilter=lowpassFilter,
binning=projBinning,
verbose=verbose,
write_images=write_images)
if voldims:
# overrule tiltSeriesFormat - aligned tiltseries is always a series of em files
#tiltSeries._tiltSeriesFormat = 'em'
vol_bp = tiltSeries.reconstructVolume(
dims=voldims, reconstructionPosition=recCent, binning=1)
vol_bp.write(volumeName, volumeFileType)
else:
print('new code')
tiltSeries = TiltSeries(tiltSeriesName=tiltSeriesName)
vol_bp = tiltSeries.reconstructVolume(dims=voldims,
reconstructionPosition=recCent,
binning=projBinning,
alignResultFile=alignResultFile)
vol_bp.write(volumeName, volumeFileType)
def alignWeightReconstruct(tiltSeriesName,
markerFileName,
lastProj,
tltfile=None,
prexgfile=None,
preBin=None,
volumeName=None,
volumeFileType='em',
alignResultFile='',
voldims=None,
recCent=[0, 0, 0],
tiltSeriesFormat='st',
firstProj=0,
irefmark=1,
ireftilt=1,
handflip=False,
alignedTiltSeriesName='align/myTilt',
weightingType=-1,
lowpassFilter=1.,
projBinning=1,
outMarkerFileName=None,
verbose=False,
outfile='',
write_images=True,
shift_markers=True,
logfile_residual='',
refMarkTomo=''):
"""
@param tiltSeriesName: Name of tilt series (set of image files in .em or .mrc format) or stack file (ending '.st').\
Note: the actual file ending should NOT be provided.
@type tiltSeriesName: str
@param markerFileName: name of EM markerfile or IMOD wimp File containing marker coordinates
@type markerFileName: str
@param lastProj: index of last projection
@param tltfile: ascii file containing the tilt angles
@type tltfile: str
@type lastProj: int
@param prexgfile: file containing pre-shifts (IMOD way of doing things)
@type prexgfile: str
@param preBin: pre-binning in IMOD used for marker determination
@type preBin: int
@param volumeName: Filename of volume
@type volumeName: str
@param volumeFileType: type of output volume - em or mrc
@type volumeFileType: str
@param voldims: dimensions of reconstruction volume, e.g. [512,512,128] - if None chosen only aligned projs are \
written
@type voldims: list
@param recCent: offset from center of volume - for example choose z!=0 to shift in z (post-binning coordinates) - \
default (0,0,0)
@type recCent: list
@param tiltSeriesFormat: file format of tilt series: 'em', 'mrc' or 'st'
@type tiltSeriesFormat: str
@param firstProj: index of first projection - default 1
@type firstProj: int
@param irefmark: index of reference marker for alignment
@type irefmark: int
@param ireftilt: index of reference tilt
@type ireftilt: int
@param handflip: add 180 deg to default tilt axis resulting in change of handedness?
@type handflip: bool
@param alignedTiltSeriesName: name of ailgned tilt series
@type alignedTiltSeriesName: str
@param weightingType: type of weighting - -1 is analytical 'ramp' weighting and 0 is no weighting
@type weightingType: int
@param lowpassFilter: lowpass filter in Nyquist
@type lowpassFilter: float
@param projBinning: binning of projection (factor rather than power of two!)
@type projBinning: int or float
@param outMarkerFileName: filename of output marker file
@type outMarkerFileName: str
@param verbose: verbose?
@type verbose: bool
@author: FF
"""
from pytom.reconstruction.TiltAlignmentStructures import TiltSeries, TiltAlignment, TiltAlignmentParameters
from pytom.gui.guiFunctions import savestar, headerMarkerResults, fmtMR
import numpy
if not alignResultFile:
if verbose:
print("Function alignWeightReconstruct started")
mute = False
else:
mute = True
from pytom.reconstruction.TiltAlignmentStructures import TiltSeries, TiltAlignment, TiltAlignmentParameters
if not shift_markers:
irefmarkInit = irefmark
irefmark = refMarkTomo if refMarkTomo else 0
tiltParas = TiltAlignmentParameters(dmag=True,
drot=True,
dbeam=False,
finealig=True,
finealigfile='xxx.txt',
grad=False,
irefmark=irefmark,
ireftilt=ireftilt,
r=None,
cent=[2049, 2049],
handflip=handflip,
optimizer='leastsq',
maxIter=1000)
markerFileType = markerFileName.split('.')[-1]
# align with wimpfile
if not preBin:
preBin = 1
if markerFileType == 'wimp':
if verbose:
print(" WIMP file used for alignment")
tiltSeries = TiltSeries(
tiltSeriesName=tiltSeriesName,
TiltAlignmentParas=tiltParas,
alignedTiltSeriesName=alignedTiltSeriesName,
markerFileName=None,
firstProj=firstProj,
lastProj=lastProj,
tiltSeriesFormat=tiltSeriesFormat)
tiltSeries.readIMODwimp(markerFileName=markerFileName,
prexgfile=prexgfile,
tltfile=tltfile,
preBin=preBin,
verbose=False)
else:
if verbose:
format = markerFileName.split('.')[-1].upper()
print(f"{format} markerfile file used for alignment")
tiltSeries = TiltSeries(
tiltSeriesName=tiltSeriesName,
TiltAlignmentParas=tiltParas,
alignedTiltSeriesName=alignedTiltSeriesName,
markerFileName=markerFileName,
firstProj=firstProj,
lastProj=lastProj,
tiltSeriesFormat=tiltSeriesFormat)
if tltfile:
tiltSeries.getTiltAnglesFromIMODfile(tltfile=tltfile)
tiltAlignment = TiltAlignment(TiltSeries_=tiltSeries)
if outMarkerFileName:
tiltSeries.writeMarkerFile(markerFileName=outMarkerFileName)
tiltSeries._markerFileName = outMarkerFileName
tiltAlignment.resetAlignmentCenter() # overrule cent in Paras
tiltAlignment.computeCoarseAlignment(tiltSeries,
mute=mute,
optimizeShift=shift_markers)
ireftilt = int(
numpy.argwhere(
tiltAlignment._projIndices.astype(int) ==
tiltSeries._TiltAlignmentParas.ireftilt)[0][0])
tiltAlignment.alignFromFiducials(mute=mute,
shift_markers=True,
logfile_residual=logfile_residual)
if not shift_markers:
tiltSeries._TiltAlignmentParas.irefmark = irefmarkInit
tiltParas.irefmark = irefmarkInit
for (imark, Marker) in enumerate(tiltAlignment._Markers):
r = Marker.get_r()
# Marker.set_r(numpy.array([r[0] - tiltSeries._ProjectionList[ireftilt]._alignmentTransX,
# r[1] - tiltSeries._ProjectionList[ireftilt]._alignmentTransY, r[2]]))
tiltAlignment.alignFromFiducials(mute=mute,
shift_markers=False,
logfile_residual=logfile_residual)
values = []
if outfile:
# Retrieve the index of reference image
ireftilt = int(
numpy.argwhere(
tiltAlignment._projIndices.astype(int) ==
tiltSeries._TiltAlignmentParas.ireftilt)[0][0])
# for n, i in enumerate(tiltAlignment._projIndices.astype(int)):
#
#
# print("{:3.0f} {:6.0f} {:6.0f} {:6.0f} {:6.0f}".format(tiltAlignment._tiltAngles[n],
# tiltAlignment._Markers[tiltSeries._TiltAlignmentParas.irefmark].xProj[n],
# tiltAlignment._Markers[tiltSeries._TiltAlignmentParas.irefmark].yProj[n],
# tiltSeries._ProjectionList[int(n)]._alignmentTransX,
# tiltSeries._ProjectionList[int(n)]._alignmentTransY))
# Create center point (3D)
cent = tiltAlignment.TiltSeries_._TiltAlignmentParas.cent
cent.append(float(tiltSeries._imdim // 2 + 1))
# Create shift
shift = [
tiltSeries._ProjectionList[ireftilt]._alignmentTransX,
tiltSeries._ProjectionList[ireftilt]._alignmentTransY, 0
]
# Retrieve the two relevant angles
inPlaneAng = tiltAlignment._alignmentRotations[ireftilt]
tiltAng = tiltAlignment._tiltAngles[ireftilt]
# Retrieve the original pick position
xx = tiltAlignment._Markers[
tiltSeries._TiltAlignmentParas.irefmark].xProj[ireftilt]
yy = tiltAlignment._Markers[
tiltSeries._TiltAlignmentParas.irefmark].yProj[ireftilt]
dx, dy = float(tiltSeries._imdimX // 2 +
1), float(tiltSeries._imdimY // 2 + 1)
dz = min(dx, dy)
# Create ref marker point
ref = tiltAlignment._Markers[
tiltSeries._TiltAlignmentParas.irefmark].get_r()
ref = rotate_vector3D(ref, [0, 0, 0], shift, inPlaneAng, tiltAng)
for (imark, Marker) in enumerate(tiltAlignment._Markers):
# reference marker irefmark is fixed to standard value
r = rotate_vector3D(Marker.get_r(), [0, 0, 0], shift,
inPlaneAng, tiltAng)
values.append([
imark, r[0] - ref[0], r[1] - ref[1], r[2] - ref[2],
r[0] + dx, r[1] + dy, r[2] + dz
])
savestar(outfile,
numpy.array(values),
header=headerMarkerResults,
fmt=fmtMR)
# creating dir for aligned tilt series if default filename
if alignedTiltSeriesName == 'align/myTilt':
from os import mkdir
try:
mkdir('align')
except OSError:
print(
" dir 'align' already exists - writing aligned files into existing dir"
)
tiltSeries.write_aligned_projs(weighting=weightingType,
lowpassFilter=lowpassFilter,
binning=projBinning,
verbose=verbose,
write_images=write_images)
if voldims:
# overrule tiltSeriesFormat - aligned tiltseries is always a series of em files
#tiltSeries._tiltSeriesFormat = 'em'
vol_bp = tiltSeries.reconstructVolume(
dims=voldims, reconstructionPosition=recCent, binning=1)
vol_bp.write(volumeName, volumeFileType)
else:
print('new code')
tiltSeries = TiltSeries(tiltSeriesName=tiltSeriesName)
vol_bp = tiltSeries.reconstructVolume(dims=voldims,
reconstructionPosition=recCent,
binning=projBinning,
alignResultFile=alignResultFile)
vol_bp.write(volumeName, volumeFileType)
reconstructionPosition=[0,0,0] # offset from center of volume - for example choose z!=0 to shift in z (post-binning coordinates)
volumeName="./testvol.em" # final tomogram
filetype='em' # filetype of final tomogram - can be 'em' or 'mrc'
####################################################################
######## do not edit unless you know what your are doing ###########
####################################################################
MyTiltAlignmentParas=TiltAlignmentParameters(
dmag=True, drot=True, dbeam=False,
finealig=True, finealigfile='xxx.dat',
grad=False,
irefmark=irefmark, ireftilt=ireftilt, r=None, cent= [1025,1025],
handflip=handflip,
optimizer='leastsq', maxIter=0)
MyTiltSeries= TiltSeries(tiltSeriesName=tiltSeriesName,
TiltAlignmentParas=MyTiltAlignmentParas,
alignedTiltSeriesName=alignedTiltSeriesName,
markerFileName=markerFileName,
firstProj=firstProj, lastProj=lastProj)
MyTiltAlignment = TiltAlignment(MyTiltSeries)
MyTiltAlignment.computeCoarseAlignment( MyTiltSeries)
MyTiltAlignment.alignFromFiducials()
MyTiltSeries.write_aligned_projs( weighting=-1, lowpassFilter=lowpassFilter,
binning=projBinning)
if not onlyWeightedProjections:
vol_bp = MyTiltSeries.reconstructVolume( dims=voldims,
reconstructionPosition=reconstructionPosition, binning=1)
vol_bp.write(volumeName, filetype)