def addAlignmentU(md, micNo, imgNo, nx, ny, psi, flip):
T=translation_matrix([nx,ny,0])
if flip:
psi=-psi
angle=-float(psi)-AlphaUList[micNo-1]
psi+=AlphaUList[micNo-1]
R=em_euler_matrix(0,0,psi,'rzyz')
M=T.dot(R)
Rinv=inv(R)
newT=translation_from_matrix(Rinv.dot(M))
if flip:
newT[0]=-newT[0]
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dU.stk" % (imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_SHIFT_X, float(newT[0]), objId)
md.setValue(MDL_SHIFT_Y, float(newT[1]), objId)
md.setValue(MDL_ANGLE_PSI, angle, objId)
md.setValue(MDL_FLIP, flip, objId)
def addAlignmentU(md, micNo, imgNo, nx, ny, psi, flip):
T = translation_matrix([nx, ny, 0])
if flip:
psi = -psi
angle = -float(psi) - AlphaUList[micNo - 1]
psi += AlphaUList[micNo - 1]
R = em_euler_matrix(0, 0, psi, 'rzyz')
M = T.dot(R)
Rinv = inv(R)
newT = translation_from_matrix(Rinv.dot(M))
if flip:
newT[0] = -newT[0]
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dU.stk" % (
imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_SHIFT_X, float(newT[0]), objId)
md.setValue(MDL_SHIFT_Y, float(newT[1]), objId)
md.setValue(MDL_ANGLE_PSI, angle, objId)
md.setValue(MDL_FLIP, flip, objId)
def createPhantomMicrograph(log, WorkingDir, ORoot, micNo):
'''Function to create micrographs and particles metadata'''
md = MetaData("block1@" + InputMotif)
half = MicrographSize / 2
v_half = array([half, half, 0, 0])
MU = em_euler_matrix(0,0, AlphaUList[micNo-1], 'rzyz')
M = em_euler_matrix(AlphaTList[micNo-1], TiltAngle, 0, 'rzyz')
# Used later for projection
dims = [float(MicrographSize) for i in range(3)]
md.setValue(MDL_DIMENSIONS_3D, dims, md.firstObject())
mdAll = MetaData()
mdPos = MetaData() # Metadata with the coordinates of each particle
mdPosT = MetaData() # same for tilted coordinates
mdPos_geo = MetaData() # Metadata with the coordinates of each particle
mdPosT_geo = MetaData() # same for tilted coordinates
mdAlignedU = MetaData() # 2D alignment file untilted
mdAlignedT = MetaData() # 2D alignment file tilted
fnAlignedU = os.path.join(WorkingDir,"untilted.xmd")
fnAlignedT = os.path.join(WorkingDir,"tilted.xmd")
if os.path.exists(fnAlignedU):
mdAlignedU.read(fnAlignedU)
if os.path.exists(fnAlignedT):
mdAlignedT.read(fnAlignedT)
program = ""
if DoRotate:
# rotations = random.random_integers(0, 360, NumberOfElements)
rotations = []
step=360.0/(NumberOfElements-1)
for i in range(NumberOfElements):
rotations.append(i*step)
else:
rotations = zeros(NumberOfElements)
if Coordinates == "random":
xcoords, ycoords = generateRandomPositions(MicrographSize, NumberOfElements)
elif Coordinates == "from_file":
xcoords, ycoords = readPositionFromFile(CoordinatesFile)
def runProgram(args):
runJob(log, program, args)
def addPos(md, x, y, nx, ny):
xy=dot(MU,array([x,y,0,1]))
xy[0]+=nx
xy[1]+=ny
objId = md.addObject()
md.setValue(MDL_XCOOR, int(round(half + xy[0])), objId)
md.setValue(MDL_YCOOR, int(round(half + xy[1])), objId)
return objId
def addPosT(md, x, y, nx, ny):
xy = dot(M, array([x, y, 0, 1]))
xy[0]+=nx
xy[1]+=ny
objId = md.addObject()
md.setValue(MDL_XCOOR, int(round(half + xy[0])), objId)
md.setValue(MDL_YCOOR, int(round(half + xy[1])), objId)
def addGeo(md, micNo, imgNo, newx, newy, x, y, nx, ny, rot=0, flip=False):
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dU.stk" % (imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_XCOOR, half + int(x), objId)
md.setValue(MDL_YCOOR, half + int(y), objId)
md.setValue(MDL_XCOOR_TILT, half + int(x), objId)
md.setValue(MDL_YCOOR_TILT, half + int(y), objId)
if flip:
rot=-rot
r = float(rot)
rr = deg2rad(-r)
cr = cos(rr)
sr = sin(rr)
shiftX = nx * cr + ny * sr
shiftY = ny * cr - nx * sr
if flip:
shiftX=-shiftX
md.setValue(MDL_SHIFT_X, shiftX, objId)
md.setValue(MDL_SHIFT_Y, shiftY, objId)
md.setValue(MDL_ANGLE_PSI, -r, objId)
md.setValue(MDL_FLIP, flip, objId)
return objId
def addAlignmentU(md, micNo, imgNo, nx, ny, psi, flip):
T=translation_matrix([nx,ny,0])
if flip:
psi=-psi
angle=-float(psi)-AlphaUList[micNo-1]
psi+=AlphaUList[micNo-1]
R=em_euler_matrix(0,0,psi,'rzyz')
M=T.dot(R)
Rinv=inv(R)
newT=translation_from_matrix(Rinv.dot(M))
if flip:
newT[0]=-newT[0]
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dU.stk" % (imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_SHIFT_X, float(newT[0]), objId)
md.setValue(MDL_SHIFT_Y, float(newT[1]), objId)
md.setValue(MDL_ANGLE_PSI, angle, objId)
md.setValue(MDL_FLIP, flip, objId)
def addAlignmentT(md, micNo, imgNo, nx, ny, psi, flip):
#T=translation_matrix([nx,ny,0])
#R=em_euler_matrix(AlphaT,0,0,'rzyz')
#M=T.dot(R)
#Rinv=inv(R)
#newT=translation_from_matrix(Rinv.dot(M))
newT=[nx,ny]
#print("nx,ny="+str(nx)+","+str(ny)+" newT="+str(newT[0])+","+str(newT[1]))
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dT.stk" % (imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_SHIFT_X, float(newT[0]), objId)
md.setValue(MDL_SHIFT_Y, float(newT[1]), objId)
md.setValue(MDL_ANGLE_ROT, float(psi), objId)
angle=TiltAngle
if flip:
angle+=180
md.setValue(MDL_ANGLE_TILT, float(angle), objId)
md.setValue(MDL_ANGLE_PSI, float(AlphaTList[micNo-1]), objId)
def addGeoT(md, x, y, nx, ny):
posT = dot(M, array([x, y, 0, 1]))
PosT = dot(M, array([nx, ny, 0, 1]))
addGeo(md, posT[0], posT[1], nPosT[0], nPosT[1])
tmpDescr = ORoot + '_tmp.descr'
program = "xmipp_phantom_transform"
imgNo = 0
for x, y, rot in zip(xcoords, ycoords, rotations):
# Make a copy of the phantom file
copyFile(log, InputMotif, tmpDescr)
# Rotate the phantom
runProgram(" -i %(tmpDescr)s --operation rotate_axis 0 0 1 %(rot)d" % locals())
# Flip particles if neccesary
flip = DoFlip and random.rand() <= FlipRate
if flip:
runProgram(" -i %(tmpDescr)s --operation rotate_axis 0 1 0 180" % locals())
# Apply shift to motif phantom
runProgram(" -i %(tmpDescr)s --operation shift %(x)d %(y)d 0" % locals())
# Read the metadata with features to group all
md2 = MetaData('block2@' + tmpDescr)
mdAll.unionAll(md2)
nx, ny = (0, 0)
if AddNoiseU: # Add some noise to exact coordinates
nx, ny = random.normal(0., NoiseSigma, 2).round()
nx, ny = (2., 4.)
addPos(mdPos, x, y, nx, ny)
imgNo = imgNo + 1
addGeo(mdPos_geo, micNo, imgNo, x+nx, y+ny, x, y, nx, ny, rot, flip)
addAlignmentU(mdAlignedU, micNo, imgNo, nx, ny, rot, flip)
nx, ny = (0, 0)
if AddNoiseT: # Add some noise to exact coordinates
nx, ny = random.normal(0., NoiseSigma, 2).round()
addPosT(mdPosT, x, y, nx, ny)
#addGeoT(mdPosT_geo, x, y, nx, ny)
addAlignmentT(mdAlignedT, micNo, imgNo, nx, ny, rot, flip)
# Write phantom .descr file
outDescr = ORoot + '.descr'
# Write the phantom metadata with all phantom particles
md.write('block1@' + outDescr)
mdAll.write('block2@' + outDescr, MD_APPEND)
mdAlignedU.write("images@"+fnAlignedU)
mdAlignedT.write("images@"+fnAlignedT)
# Write .pos with coordinates
def writePos(mdPos, outPos):
family = "DefaultFamily"
# mdFamily = MetaData()
# objId = mdFamily.addObject()
# mdFamily.setValue(MDL_PICKING_FAMILY, family, objId)
# mdFamily.setValue(MDL_PICKING_MICROGRAPH_FAMILY_STATE, 'Manual', objId)
# mdFamily.write('families@%(outPos)s' % locals())
mdPos.write("%(family)s@%(outPos)s" % locals())
writePos(mdPos, ORoot + 'U.pos')
#print mdPos
writePos(mdPosT, ORoot + 'T.pos')
mdPos_geo.write(ORoot + 'U_geo.xmd')
mdPosT_geo.write(ORoot + 'T_geo.xmd')
program = "xmipp_phantom_project"
outMicU = ORoot + "U.mrc"
alpha= AlphaUList[micNo-1]
runProgram(" -i %(outDescr)s -o %(outMicU)s --angles %(alpha)d 0 0" % locals())
outMicT = ORoot + "T.mrc"
tilt = TiltAngle # Register in locals() dictionary
alpha = AlphaTList[micNo-1]
runProgram(" -i %(outDescr)s -o %(outMicT)s --angles 0 %(tilt)d %(alpha)d" % locals())
def createPhantomMicrograph(log, WorkingDir, ORoot, micNo):
'''Function to create micrographs and particles metadata'''
md = MetaData("block1@" + InputMotif)
half = MicrographSize / 2
v_half = array([half, half, 0, 0])
MU = em_euler_matrix(0, 0, AlphaUList[micNo - 1], 'rzyz')
M = em_euler_matrix(AlphaTList[micNo - 1], TiltAngle, 0, 'rzyz')
# Used later for projection
dims = [float(MicrographSize) for i in range(3)]
md.setValue(MDL_DIMENSIONS_3D, dims, md.firstObject())
mdAll = MetaData()
mdPos = MetaData() # Metadata with the coordinates of each particle
mdPosT = MetaData() # same for tilted coordinates
mdPos_geo = MetaData() # Metadata with the coordinates of each particle
mdPosT_geo = MetaData() # same for tilted coordinates
mdAlignedU = MetaData() # 2D alignment file untilted
mdAlignedT = MetaData() # 2D alignment file tilted
fnAlignedU = os.path.join(WorkingDir, "untilted.xmd")
fnAlignedT = os.path.join(WorkingDir, "tilted.xmd")
if os.path.exists(fnAlignedU):
mdAlignedU.read(fnAlignedU)
if os.path.exists(fnAlignedT):
mdAlignedT.read(fnAlignedT)
program = ""
if DoRotate:
# rotations = random.random_integers(0, 360, NumberOfElements)
rotations = []
step = 360.0 / (NumberOfElements - 1)
for i in range(NumberOfElements):
rotations.append(i * step)
else:
rotations = zeros(NumberOfElements)
if Coordinates == "random":
xcoords, ycoords = generateRandomPositions(MicrographSize,
NumberOfElements)
elif Coordinates == "from_file":
xcoords, ycoords = readPositionFromFile(CoordinatesFile)
def runProgram(args):
runJob(log, program, args)
def addPos(md, x, y, nx, ny):
xy = dot(MU, array([x, y, 0, 1]))
xy[0] += nx
xy[1] += ny
objId = md.addObject()
md.setValue(MDL_XCOOR, int(round(half + xy[0])), objId)
md.setValue(MDL_YCOOR, int(round(half + xy[1])), objId)
return objId
def addPosT(md, x, y, nx, ny):
xy = dot(M, array([x, y, 0, 1]))
xy[0] += nx
xy[1] += ny
objId = md.addObject()
md.setValue(MDL_XCOOR, int(round(half + xy[0])), objId)
md.setValue(MDL_YCOOR, int(round(half + xy[1])), objId)
def addGeo(md, micNo, imgNo, newx, newy, x, y, nx, ny, rot=0, flip=False):
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dU.stk" % (
imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_XCOOR, half + int(x), objId)
md.setValue(MDL_YCOOR, half + int(y), objId)
md.setValue(MDL_XCOOR_TILT, half + int(x), objId)
md.setValue(MDL_YCOOR_TILT, half + int(y), objId)
if flip:
rot = -rot
r = float(rot)
rr = deg2rad(-r)
cr = cos(rr)
sr = sin(rr)
shiftX = nx * cr + ny * sr
shiftY = ny * cr - nx * sr
if flip:
shiftX = -shiftX
md.setValue(MDL_SHIFT_X, shiftX, objId)
md.setValue(MDL_SHIFT_Y, shiftY, objId)
md.setValue(MDL_ANGLE_PSI, -r, objId)
md.setValue(MDL_FLIP, flip, objId)
return objId
def addAlignmentU(md, micNo, imgNo, nx, ny, psi, flip):
T = translation_matrix([nx, ny, 0])
if flip:
psi = -psi
angle = -float(psi) - AlphaUList[micNo - 1]
psi += AlphaUList[micNo - 1]
R = em_euler_matrix(0, 0, psi, 'rzyz')
M = T.dot(R)
Rinv = inv(R)
newT = translation_from_matrix(Rinv.dot(M))
if flip:
newT[0] = -newT[0]
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dU.stk" % (
imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_SHIFT_X, float(newT[0]), objId)
md.setValue(MDL_SHIFT_Y, float(newT[1]), objId)
md.setValue(MDL_ANGLE_PSI, angle, objId)
md.setValue(MDL_FLIP, flip, objId)
def addAlignmentT(md, micNo, imgNo, nx, ny, psi, flip):
#T=translation_matrix([nx,ny,0])
#R=em_euler_matrix(AlphaT,0,0,'rzyz')
#M=T.dot(R)
#Rinv=inv(R)
#newT=translation_from_matrix(Rinv.dot(M))
newT = [nx, ny]
#print("nx,ny="+str(nx)+","+str(ny)+" newT="+str(newT[0])+","+str(newT[1]))
objId = md.addObject()
imgFn = "%06d@Images/Extracted/run_001/extra/micrograph%03dT.stk" % (
imgNo, micNo)
md.setValue(MDL_IMAGE, imgFn, objId)
md.setValue(MDL_SHIFT_X, float(newT[0]), objId)
md.setValue(MDL_SHIFT_Y, float(newT[1]), objId)
md.setValue(MDL_ANGLE_ROT, float(psi), objId)
angle = TiltAngle
if flip:
angle += 180
md.setValue(MDL_ANGLE_TILT, float(angle), objId)
md.setValue(MDL_ANGLE_PSI, float(AlphaTList[micNo - 1]), objId)
def addGeoT(md, x, y, nx, ny):
posT = dot(M, array([x, y, 0, 1]))
PosT = dot(M, array([nx, ny, 0, 1]))
addGeo(md, posT[0], posT[1], nPosT[0], nPosT[1])
tmpDescr = ORoot + '_tmp.descr'
program = "xmipp_phantom_transform"
imgNo = 0
for x, y, rot in zip(xcoords, ycoords, rotations):
# Make a copy of the phantom file
copyFile(log, InputMotif, tmpDescr)
# Rotate the phantom
runProgram(" -i %(tmpDescr)s --operation rotate_axis 0 0 1 %(rot)d" %
locals())
# Flip particles if necessary
flip = DoFlip and random.rand() <= FlipRate
if flip:
runProgram(" -i %(tmpDescr)s --operation rotate_axis 0 1 0 180" %
locals())
# Apply shift to motif phantom
runProgram(" -i %(tmpDescr)s --operation shift %(x)d %(y)d 0" %
locals())
# Read the metadata with features to group all
md2 = MetaData('block2@' + tmpDescr)
mdAll.unionAll(md2)
nx, ny = (0, 0)
if AddNoiseU: # Add some noise to exact coordinates
nx, ny = random.normal(0., NoiseSigma, 2).round()
nx, ny = (2., 4.)
addPos(mdPos, x, y, nx, ny)
imgNo = imgNo + 1
addGeo(mdPos_geo, micNo, imgNo, x + nx, y + ny, x, y, nx, ny, rot,
flip)
addAlignmentU(mdAlignedU, micNo, imgNo, nx, ny, rot, flip)
nx, ny = (0, 0)
if AddNoiseT: # Add some noise to exact coordinates
nx, ny = random.normal(0., NoiseSigma, 2).round()
addPosT(mdPosT, x, y, nx, ny)
#addGeoT(mdPosT_geo, x, y, nx, ny)
addAlignmentT(mdAlignedT, micNo, imgNo, nx, ny, rot, flip)
# Write phantom .descr file
outDescr = ORoot + '.descr'
# Write the phantom metadata with all phantom particles
md.write('block1@' + outDescr)
mdAll.write('block2@' + outDescr, MD_APPEND)
mdAlignedU.write("images@" + fnAlignedU)
mdAlignedT.write("images@" + fnAlignedT)
# Write .pos with coordinates
def writePos(mdPos, outPos):
family = "DefaultFamily"
# mdFamily = MetaData()
# objId = mdFamily.addObject()
# mdFamily.setValue(MDL_PICKING_FAMILY, family, objId)
# mdFamily.setValue(MDL_PICKING_MICROGRAPH_FAMILY_STATE, 'Manual', objId)
# mdFamily.write('families@%(outPos)s' % locals())
mdPos.write("%(family)s@%(outPos)s" % locals())
writePos(mdPos, ORoot + 'U.pos')
#print mdPos
writePos(mdPosT, ORoot + 'T.pos')
mdPos_geo.write(ORoot + 'U_geo.xmd')
mdPosT_geo.write(ORoot + 'T_geo.xmd')
program = "xmipp_phantom_project"
outMicU = ORoot + "U.mrc"
alpha = AlphaUList[micNo - 1]
runProgram(" -i %(outDescr)s -o %(outMicU)s --angles %(alpha)d 0 0" %
locals())
outMicT = ORoot + "T.mrc"
tilt = TiltAngle # Register in locals() dictionary
alpha = AlphaTList[micNo - 1]
runProgram(
" -i %(outDescr)s -o %(outMicT)s --angles 0 %(tilt)d %(alpha)d" %
locals())
