def __init__(self, filename=None):
self._md = MetaData()
self._md.setColumnFormat(False)
self._id = self._md.addObject()
if filename:
self.read(filename)
def _plotFSC(self, ab, fnFSC):
md = MetaData(fnFSC)
resolution_inv = [md.getValue(MDL_RESOLUTION_FREQ, f) for f in md]
frc = [md.getValue(MDL_RESOLUTION_FRC, f) for f in md]
# self.maxFrc = max(frc)
self.minInv.append(min(resolution_inv))
self.maxInv.append(max(resolution_inv))
ab.plot(resolution_inv, frc)
ab.xaxis.set_major_formatter(self._plotFormatter)
ab.set_ylim([-0.1, 1.1])
def getAngles(self, fnAngles=""):
if fnAngles == "":
if self.searchMode.get() == self.GLOBAL_SEARCH:
fnAngles = self._getExtraPath("coarse.xmd")
else:
fnAngles = self._getExtraPath("fine.xmd")
md = MetaData(fnAngles)
objId = md.firstObject()
rot0 = md.getValue(MDL_ANGLE_ROT, objId)
tilt0 = md.getValue(MDL_ANGLE_TILT, objId)
return (rot0, tilt0)
def createOutput(self):
volume = Volume()
volume.setFileName(self._getPath('volume_symmetrized.vol'))
#volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
volume.copyInfo(self.inputVolume.get())
self._defineOutputs(outputVolume=volume)
self._defineTransformRelation(self.inputVolume, self.outputVolume)
md = MetaData(self._getExtraPath('fineParams.xmd'))
objId = md.firstObject()
self._defineOutputs(deltaRot=pwobj.Float(
md.getValue(MDL_ANGLE_ROT, objId)),
deltaZ=pwobj.Float(md.getValue(MDL_SHIFT_Z,
objId)))
def plotMdFile(self, mdFilename, mdLabelX, mdLabelY, color='g', **args):
""" plot metadataFile columns mdLabelX and mdLabelY
if nbins is in args then and histogram over y data is made
"""
from xmippLib import MetaData
md = MetaData(mdFilename)
self.plotMd(md, mdLabelX, mdLabelY, color=color, **args)
def runFineSearch(self, fnVol, dihedral, fnCoarse, fnFine, heightFraction,
z0, zF, rot0, rotF, cylinderInnerRadius,
cylinderOuterRadius, height, Ts):
md = MetaData(fnCoarse)
objId = md.firstObject()
rotInit = md.getValue(MDL_ANGLE_ROT, objId)
zInit = md.getValue(MDL_SHIFT_Z, objId)
args = "-i %s --sym %s --heightFraction %f --localHelical %f %f -o %s -z %f %f 1 --rotHelical %f %f 1 --sampling %f" % (
fnVol, self.getSymmetry(dihedral), heightFraction, zInit, rotInit,
fnFine, z0, zF, rot0, rotF, Ts)
if cylinderOuterRadius > 0 and cylinderInnerRadius < 0:
args += " --mask cylinder %d %d" % (-cylinderOuterRadius, -height)
elif cylinderOuterRadius > 0 and cylinderInnerRadius > 0:
args += " --mask tube %d %d %d" % (-cylinderInnerRadius,
-cylinderOuterRadius, -height)
self.runJob('xmipp_volume_find_symmetry', args, numberOfMpi=1)
def projMatchStep(self, volume, angularSampling, symmetryGroup, images,
fnAngles, Xdim):
from pyworkflow.utils.path import cleanPath
# Generate gallery of projections
fnGallery = self._getExtraPath('gallery.stk')
if volume.endswith('.mrc'):
volume += ":mrc"
self.runJob("xmipp_angular_project_library", "-i %s -o %s --sampling_rate %f --sym %s --method fourier 1 0.25 bspline --compute_neighbors --angular_distance -1 --experimental_images %s"\
% (volume, fnGallery, angularSampling, symmetryGroup, images))
# Assign angles
self.runJob("xmipp_angular_projection_matching", "-i %s -o %s --ref %s --Ri 0 --Ro %s --max_shift 1000 --search5d_shift %s --search5d_step %s --append"\
% (images, fnAngles, fnGallery, str(Xdim/2), str(int(Xdim/10)), str(int(Xdim/25))))
cleanPath(self._getExtraPath('gallery_sampling.xmd'))
cleanPath(self._getExtraPath('gallery_angles.doc'))
cleanPath(self._getExtraPath('gallery.doc'))
# Write angles in the original file and sort
MD = MetaData(fnAngles)
for id in MD:
galleryReference = MD.getValue(xmippLib.MDL_REF, id)
MD.setValue(xmippLib.MDL_IMAGE_REF,
"%05d@%s" % (galleryReference + 1, fnGallery), id)
MD.write(fnAngles)
def runSymmetrize(self, fnVol, dihedral, fnParams, fnOut, heightFraction,
cylinderInnerRadius, cylinderOuterRadius, height, Ts):
md = MetaData(fnParams)
objId = md.firstObject()
rot0 = md.getValue(MDL_ANGLE_ROT, objId)
z0 = md.getValue(MDL_SHIFT_Z, objId)
args = "-i %s --sym %s --helixParams %f %f --heightFraction %f -o %s --sampling %f" % (
fnVol, self.getSymmetry(dihedral), z0, rot0, heightFraction, fnOut,
Ts)
self.runJob('xmipp_transform_symmetrize', args, numberOfMpi=1)
doMask = False
if cylinderOuterRadius > 0 and cylinderInnerRadius < 0:
args = "-i %s --mask cylinder %d %d" % (
fnVol, -cylinderOuterRadius, -height)
doMask = True
elif cylinderOuterRadius > 0 and cylinderInnerRadius > 0:
args = "-i %s --mask tube %d %d %d" % (
fnVol, -cylinderInnerRadius, -cylinderOuterRadius, -height)
doMask = True
if doMask:
self.runJob('xmipp_transform_mask', args, numberOfMpi=1)
class RowMetaData():
""" This class is a wrapper for MetaData in row mode.
Where only one object is used.
"""
def __init__(self, filename=None):
self._md = MetaData()
self._md.setColumnFormat(False)
self._id = self._md.addObject()
if filename:
self.read(filename)
def setValue(self, label, value):
self._md.setValue(label, value, self._id)
def getValue(self, label):
return self._md.getValue(label, self._id)
def write(self, filename, mode=MD_APPEND):
self._md.write(filename, mode)
def read(self, filename):
self._md.read(filename)
self._md.setColumnFormat(False)
self._id = self._md.firstObject()
def containsLabel(self, label):
return self._md.containsLabel(label)
def __str__(self):
return str(self._md)
def writeToFile(self, fn):
md = MetaData()
self.writeToMd(md, md.addObject())
md.write(fn)
def readFromFile(self, fn):
md = MetaData(fn)
self.readFromMd(md, md.firstObject())
def _iterAngles(self, fnAngles):
md = MetaData(fnAngles)
for objId in md:
rot = md.getValue(MDL_ANGLE_ROT, objId)
tilt = md.getValue(MDL_ANGLE_TILT, objId)
yield rot, tilt
def evaluateDeformationsStep(self):
N = self.inputStructures.get().getSize()
import numpy
distances = numpy.zeros([N, N])
for volCounter in range(1, N + 1):
pdb1 = open(
self._getPath('pseudoatoms_%02d.pdb' % volCounter)).readlines()
for volCounter2 in range(1, N + 1):
if volCounter != volCounter2:
davg = 0.
Navg = 0.
pdb2 = open(self._getExtraPath('alignment_%02d_%02d.pdb' % (
volCounter, volCounter2))).readlines()
for i in range(len(pdb1)):
line1 = pdb1[i]
if line1.startswith("ATOM"):
line2 = pdb2[i]
x1 = float(line1[30:37])
y1 = float(line1[38:45])
z1 = float(line1[46:53])
x2 = float(line2[30:37])
y2 = float(line2[38:45])
z2 = float(line2[46:53])
dx = x1 - x2
dy = y1 - y2
dz = z1 - z2
d = math.sqrt(dx * dx + dy * dy + dz * dz)
davg += d
Navg += 1
if Navg > 0:
davg /= Navg
distances[volCounter - 1, volCounter2 - 1] = davg
distances = 0.5 * (distances + numpy.transpose(distances))
numpy.savetxt(self._getPath('distances.txt'), distances)
distances1D = numpy.mean(distances, axis=0)
print("Average distance to rest of volumes=", distances1D)
imin = numpy.argmin(distances1D)
print("The volume in the middle is pseudoatoms_%02d.pdb" % (imin + 1))
createLink(self._getPath("pseudoatoms_%02d.pdb" % (imin + 1)),
self._getPath("pseudoatoms.pdb"))
createLink(self._getPath("modes_%02d.xmd" % (imin + 1)),
self._getPath("modes.xmd"))
createLink(
self._getExtraPath("pseudoatoms_%02d_distance.hist" % (imin + 1)),
self._getExtraPath("pseudoatoms_distance.hist"))
# Measure range
minDisplacement = 1e38 * numpy.ones([self.numberOfModes.get(), 1])
maxDisplacement = -1e38 * numpy.ones([self.numberOfModes.get(), 1])
mdNMA = MetaData(self._getPath("modes.xmd"))
for volCounter in range(1, N + 1):
if volCounter != imin + 1:
md = MetaData(self._getExtraPath(
"alignment_%02d_%02d.xmd" % (imin + 1, volCounter)))
displacements = md.getValue(MDL_NMA, md.firstObject())
idx1 = 0
idx2 = 0
for idRow in mdNMA:
if mdNMA.getValue(MDL_ENABLED, idRow) == 1:
minDisplacement[idx2] = min(minDisplacement[idx2],
displacements[idx1])
maxDisplacement[idx2] = max(maxDisplacement[idx2],
displacements[idx1])
idx1 += 1
else:
minDisplacement[idx2] = 0
maxDisplacement[idx2] = 0
idx2 += 1
idx2 = 0
for idRow in mdNMA:
mdNMA.setValue(MDL_NMA_MINRANGE, float(minDisplacement[idx2]),
idRow)
mdNMA.setValue(MDL_NMA_MAXRANGE, float(maxDisplacement[idx2]),
idRow)
idx2 += 1
mdNMA.write(self._getPath("modes.xmd"))
# Create output
volCounter = 0
for inputStructure in self.inputStructures.get():
if volCounter == imin:
print("The corresponding volume is %s" % (
getImageLocation(inputStructure)))
finalStructure = inputStructure
break
volCounter += 1
pdb = AtomStruct(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
self._defineOutputs(outputPdb=pdb)
modes = NormalModes(filename=self._getPath('modes.xmd'))
self._defineOutputs(outputModes=modes)
self._defineSourceRelation(self.inputStructures, self.outputPdb)
def produceAlignedImagesStep(self, volumeIsCTFCorrected, fn, images):
from numpy import array, dot
fnOut = 'classes_aligned@' + fn
MDin = MetaData(images)
MDout = MetaData()
n = 1
hasCTF = MDin.containsLabel(xmippLib.MDL_CTF_MODEL)
for i in MDin:
fnImg = MDin.getValue(xmippLib.MDL_IMAGE, i)
fnImgRef = MDin.getValue(xmippLib.MDL_IMAGE_REF, i)
maxCC = MDin.getValue(xmippLib.MDL_MAXCC, i)
rot = MDin.getValue(xmippLib.MDL_ANGLE_ROT, i)
tilt = MDin.getValue(xmippLib.MDL_ANGLE_TILT, i)
psi = -1. * MDin.getValue(xmippLib.MDL_ANGLE_PSI, i)
flip = MDin.getValue(xmippLib.MDL_FLIP, i)
if flip:
psi = -psi
eulerMatrix = Euler_angles2matrix(0., 0., psi)
x = MDin.getValue(xmippLib.MDL_SHIFT_X, i)
y = MDin.getValue(xmippLib.MDL_SHIFT_Y, i)
shift = array([x, y, 0])
shiftOut = dot(eulerMatrix, shift)
[x, y, z] = shiftOut
if flip:
x = -x
id = MDout.addObject()
MDout.setValue(xmippLib.MDL_IMAGE, fnImg, id)
MDout.setValue(xmippLib.MDL_IMAGE_REF, fnImgRef, id)
MDout.setValue(xmippLib.MDL_IMAGE1,
"%05d@%s" % (n, self._getExtraPath("diff.stk")), id)
if hasCTF:
fnCTF = MDin.getValue(xmippLib.MDL_CTF_MODEL, i)
MDout.setValue(xmippLib.MDL_CTF_MODEL, fnCTF, id)
MDout.setValue(xmippLib.MDL_MAXCC, maxCC, id)
MDout.setValue(xmippLib.MDL_ANGLE_ROT, rot, id)
MDout.setValue(xmippLib.MDL_ANGLE_TILT, tilt, id)
MDout.setValue(xmippLib.MDL_ANGLE_PSI, psi, id)
MDout.setValue(xmippLib.MDL_SHIFT_X, x, id)
MDout.setValue(xmippLib.MDL_SHIFT_Y, y, id)
MDout.setValue(xmippLib.MDL_FLIP, flip, id)
MDout.setValue(xmippLib.MDL_ENABLED, 1, id)
n += 1
MDout.write(fnOut, xmippLib.MD_APPEND)
# Actually create the differences
img = Image()
imgRef = Image()
if hasCTF and volumeIsCTFCorrected:
Ts = MDin.getValue(xmippLib.MDL_SAMPLINGRATE, MDin.firstObject())
for i in MDout:
img.readApplyGeo(MDout, i)
imgRef.read(MDout.getValue(xmippLib.MDL_IMAGE_REF, i))
if hasCTF and volumeIsCTFCorrected:
fnCTF = MDout.getValue(xmippLib.MDL_CTF_MODEL, i)
applyCTF(imgRef, fnCTF, Ts)
img.convert2DataType(DT_DOUBLE)
imgDiff = img - imgRef
imgDiff.write(MDout.getValue(xmippLib.MDL_IMAGE1, i))
