def findRow(md, label, value):
""" Query the metadata for a row with label=value.
Params:
md: metadata to query.
label: label to check value
value: value for equal condition
Returns:
XmippMdRow object of the row found.
None if no row is found with label=value
"""
mdQuery = xmippLib.MetaData() # store result
mdQuery.importObjects(md, xmippLib.MDValueEQ(label, value))
n = mdQuery.size()
if n == 0:
row = None
elif n == 1:
row = XmippMdRow()
row.readFromMd(mdQuery, mdQuery.firstObject())
else:
raise Exception(
"findRow: more than one row found matching the query %s = %s" %
(xmippLib.label2Str(label), value))
return row
def __setXmippImage(label):
attr = '_xmipp_' + xmippLib.label2Str(label)
if not hasattr(particle, attr):
img = Image()
setattr(particle, attr, img)
img.setSamplingRate(particle.getSamplingRate())
else:
img = getattr(particle, attr)
img.setLocation(xmippToLocation(row.getValue(label)))
def calculateDeviationsStep(self, it):
""" Calculate both angles and shifts devitations for all iterations
"""
SL = xmippLib.SymList()
mdIter = xmippLib.MetaData()
#for it in self.allIters():
mdIter.clear()
SL.readSymmetryFile(self._symmetry[it])
md1 = xmippLib.MetaData(self.docFileInputAngles[it])
md2 = xmippLib.MetaData(self.docFileInputAngles[it - 1])
#ignore disabled,
md1.removeDisabled()
md2.removeDisabled()
#first metadata file may not have shiftx and shifty
if not md2.containsLabel(xmippLib.MDL_SHIFT_X):
md2.addLabel(xmippLib.MDL_SHIFT_X)
md2.addLabel(xmippLib.MDL_SHIFT_Y)
md2.fillConstant(xmippLib.MDL_SHIFT_X, 0.)
md2.fillConstant(xmippLib.MDL_SHIFT_Y, 0.)
oldLabels = [
xmippLib.MDL_ANGLE_ROT, xmippLib.MDL_ANGLE_TILT,
xmippLib.MDL_ANGLE_PSI, xmippLib.MDL_SHIFT_X, xmippLib.MDL_SHIFT_Y
]
newLabels = [
xmippLib.MDL_ANGLE_ROT2, xmippLib.MDL_ANGLE_TILT2,
xmippLib.MDL_ANGLE_PSI2, xmippLib.MDL_SHIFT_X2,
xmippLib.MDL_SHIFT_Y2
]
md2.renameColumn(oldLabels, newLabels)
md2.addLabel(xmippLib.MDL_SHIFT_X_DIFF)
md2.addLabel(xmippLib.MDL_SHIFT_Y_DIFF)
md2.addLabel(xmippLib.MDL_SHIFT_DIFF)
mdIter.join1(md1, md2, xmippLib.MDL_IMAGE, xmippLib.INNER_JOIN)
SL.computeDistance(mdIter, False, False, False)
xmippLib.activateMathExtensions()
#operate in sqlite
shiftXLabel = xmippLib.label2Str(xmippLib.MDL_SHIFT_X)
shiftX2Label = xmippLib.label2Str(xmippLib.MDL_SHIFT_X2)
shiftXDiff = xmippLib.label2Str(xmippLib.MDL_SHIFT_X_DIFF)
shiftYLabel = xmippLib.label2Str(xmippLib.MDL_SHIFT_Y)
shiftY2Label = xmippLib.label2Str(xmippLib.MDL_SHIFT_Y2)
shiftYDiff = xmippLib.label2Str(xmippLib.MDL_SHIFT_Y_DIFF)
shiftDiff = xmippLib.label2Str(xmippLib.MDL_SHIFT_DIFF)
#timeStr = str(dtBegin)
operateString = shiftXDiff + "=" + shiftXLabel + "-" + shiftX2Label
operateString += "," + shiftYDiff + "=" + shiftYLabel + "-" + shiftY2Label
mdIter.operate(operateString)
operateString = shiftDiff+"=sqrt(" \
+shiftXDiff+"*"+shiftXDiff+"+" \
+shiftYDiff+"*"+shiftYDiff+");"
mdIter.operate(operateString)
iterFile = self._mdDevitationsFn(it)
mdIter.write(iterFile, xmippLib.MD_APPEND)
self._setLastIter(it)
def test_CTF(self):
""" Test the conversion of a SetOfParticles to Xmipp metadata. """
mdCtf = xmippLib.MetaData(self.dataset.getFile('ctfGold'))
objId = mdCtf.firstObject()
rowCtf = rowFromMd(mdCtf, objId)
ctf = rowToCtfModel(rowCtf)
ALL_CTF_LABELS = [
xmippLib.MDL_CTF_CA,
xmippLib.MDL_CTF_ENERGY_LOSS,
xmippLib.MDL_CTF_LENS_STABILITY,
xmippLib.MDL_CTF_CONVERGENCE_CONE,
xmippLib.MDL_CTF_LONGITUDINAL_DISPLACEMENT,
xmippLib.MDL_CTF_TRANSVERSAL_DISPLACEMENT,
xmippLib.MDL_CTF_K,
xmippLib.MDL_CTF_BG_GAUSSIAN_K,
xmippLib.MDL_CTF_BG_GAUSSIAN_SIGMAU,
xmippLib.MDL_CTF_BG_GAUSSIAN_SIGMAV,
xmippLib.MDL_CTF_BG_GAUSSIAN_CU,
xmippLib.MDL_CTF_BG_GAUSSIAN_CV,
xmippLib.MDL_CTF_BG_SQRT_K,
xmippLib.MDL_CTF_BG_SQRT_U,
xmippLib.MDL_CTF_BG_SQRT_V,
xmippLib.MDL_CTF_BG_SQRT_ANGLE,
xmippLib.MDL_CTF_BG_BASELINE,
xmippLib.MDL_CTF_BG_GAUSSIAN2_K,
xmippLib.MDL_CTF_BG_GAUSSIAN2_SIGMAU,
xmippLib.MDL_CTF_BG_GAUSSIAN2_SIGMAV,
xmippLib.MDL_CTF_BG_GAUSSIAN2_CU,
xmippLib.MDL_CTF_BG_GAUSSIAN2_CV,
xmippLib.MDL_CTF_BG_GAUSSIAN2_ANGLE,
#xmippLib.MDL_CTF_CRIT_FITTINGSCORE,
xmippLib.MDL_CTF_CRIT_FITTINGCORR13,
xmippLib.MDL_CTF_DOWNSAMPLE_PERFORMED,
xmippLib.MDL_CTF_CRIT_PSDVARIANCE,
xmippLib.MDL_CTF_CRIT_PSDPCA1VARIANCE,
xmippLib.MDL_CTF_CRIT_PSDPCARUNSTEST,
xmippLib.MDL_CTF_CRIT_FIRSTZEROAVG,
xmippLib.MDL_CTF_CRIT_DAMPING,
xmippLib.MDL_CTF_CRIT_FIRSTZERORATIO,
xmippLib.MDL_CTF_CRIT_PSDCORRELATION90,
xmippLib.MDL_CTF_CRIT_PSDRADIALINTEGRAL,
xmippLib.MDL_CTF_CRIT_NORMALITY,
]
for label in ALL_CTF_LABELS:
attrName = '_xmipp_%s' % xmippLib.label2Str(label)
self.assertAlmostEquals(mdCtf.getValue(label, objId),
ctf.getAttributeValue(attrName))
def createOutputStep(self):
# PARTICLES
cleanPattern(self._getPath("*.sqlite"))
partSet = self._createSetOfParticles()
readSetOfParticles(self._getPath("particles.xmd"), partSet)
inputSampling = self.inputCoordinates[0].get().getMicrographs(
).getSamplingRate()
partSet.setSamplingRate(self._getDownFactor() * inputSampling)
boxSize = self._getBoxSize()
# COORDINATES
writeSet = False
if self.checkIfPrevRunIsCompatible("coords_"):
writeSet = True
if not "OR" in self.coordinatesDict:
self.loadCoords(self._getExtraPath(
self.CONSENSUS_COOR_PATH_TEMPLATE % 'TRUE'),
'OR',
writeSet=False)
coordSet = SetOfCoordinates(
filename=self._getPath("coordinates.sqlite"))
coordSet.copyInfo(self.coordinatesDict['OR'])
coordSet.setBoxSize(boxSize)
coordSet.setMicrographs(self.coordinatesDict['OR'].getMicrographs())
downFactor = self._getDownFactor()
for part in partSet:
coord = part.getCoordinate().clone()
coord.scale(downFactor)
deepZscoreLabel = '_xmipp_%s' % xmipp.label2Str(
MD.MDL_ZSCORE_DEEPLEARNING1)
setattr(coord, deepZscoreLabel, getattr(part, deepZscoreLabel))
coordSet.append(coord)
coordSet.write()
partSet.write()
self._defineOutputs(outputCoordinates=coordSet)
self._defineOutputs(outputParticles=partSet)
for inSetOfCoords in self.inputCoordinates:
self._defineSourceRelation(inSetOfCoords.get(), coordSet)
self._defineSourceRelation(inSetOfCoords.get(), partSet)
def writeToMd(self, md, objId):
""" Set back row values to a metadata row. """
for label, value in self._labelDict.iteritems():
# TODO: Check how to handle correctly unicode type
# in Xmipp and Scipion
if type(value) is unicode:
value = str(value)
try:
md.setValue(label, value, objId)
except Exception as ex:
import sys
print("XmippMdRow.writeToMd: Error writing value to metadata.",
file=sys.stderr)
print(
" label: %s, value: %s, type(value): %s"
% (label2Str(label), value, type(value)),
file=sys.stderr)
raise ex
def _getMdString(self, filename, block=None):
md = xmippLib.MetaData()
if block:
md.read(block + '@' + filename)
else:
md.read(filename, 1)
labels = md.getActiveLabels()
msg = "Metadata items: *%d*\n" % md.getParsedLines()
msg += "Metadata labels: " + ''.join(
["\n - %s" % xmippLib.label2Str(l) for l in labels])
imgPath = None
for label in labels:
if xmippLib.labelIsImage(label):
imgPath = self._getImgPath(
filename, md.getValue(label, md.firstObject()))
break
if imgPath:
self._imgPreview = self._getImagePreview(imgPath)
self._imgInfo = self._getImageString(imgPath)
return msg
def __str__(self):
s = '{'
for k, v in self._labelDict.iteritems():
s += ' %s = %s\n' % (label2Str(k), v)
return s + '}'
