def _getMdString(self, filename, block=None):
md = emlib.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" % emlib.label2Str(l) for l in labels])
imgPath = None
for label in labels:
if emlib.labelIsImage(label):
imgPath = self._getImgPath(
filename, md.getValue(label, md.firstObject()))
if imgPath is None or not os.path.exists(imgPath):
imgPath = None
break
# If there is an image and is not too big
if imgPath and pwutils.getFileSize(imgPath) < (
pwem.Config.MAX_PREVIEW_FILE_SIZE * 1024 * 1024):
self._imgPreview = self._getImagePreview(imgPath)
self._imgInfo = self._getImageString(imgPath)
return msg
def __setXmippImage(label):
attr = '_xmipp_' + emlib.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 = emlib.SymList()
mdIter = emlib.MetaData()
#for it in self.allIters():
mdIter.clear()
SL.readSymmetryFile(self._symmetry[it])
md1 = emlib.MetaData(self.docFileInputAngles[it])
md2 = emlib.MetaData(self.docFileInputAngles[it - 1])
#ignore disabled,
md1.removeDisabled()
md2.removeDisabled()
#first metadata file may not have shiftx and shifty
if not md2.containsLabel(emlib.MDL_SHIFT_X):
md2.addLabel(emlib.MDL_SHIFT_X)
md2.addLabel(emlib.MDL_SHIFT_Y)
md2.fillConstant(emlib.MDL_SHIFT_X, 0.)
md2.fillConstant(emlib.MDL_SHIFT_Y, 0.)
oldLabels = [
emlib.MDL_ANGLE_ROT, emlib.MDL_ANGLE_TILT, emlib.MDL_ANGLE_PSI,
emlib.MDL_SHIFT_X, emlib.MDL_SHIFT_Y
]
newLabels = [
emlib.MDL_ANGLE_ROT2, emlib.MDL_ANGLE_TILT2, emlib.MDL_ANGLE_PSI2,
emlib.MDL_SHIFT_X2, emlib.MDL_SHIFT_Y2
]
md2.renameColumn(oldLabels, newLabels)
md2.addLabel(emlib.MDL_SHIFT_X_DIFF)
md2.addLabel(emlib.MDL_SHIFT_Y_DIFF)
md2.addLabel(emlib.MDL_SHIFT_DIFF)
mdIter.join1(md1, md2, emlib.MDL_IMAGE, emlib.INNER_JOIN)
SL.computeDistance(mdIter, False, False, False)
emlib.activateMathExtensions()
#operate in sqlite
shiftXLabel = emlib.label2Str(emlib.MDL_SHIFT_X)
shiftX2Label = emlib.label2Str(emlib.MDL_SHIFT_X2)
shiftXDiff = emlib.label2Str(emlib.MDL_SHIFT_X_DIFF)
shiftYLabel = emlib.label2Str(emlib.MDL_SHIFT_Y)
shiftY2Label = emlib.label2Str(emlib.MDL_SHIFT_Y2)
shiftYDiff = emlib.label2Str(emlib.MDL_SHIFT_Y_DIFF)
shiftDiff = emlib.label2Str(emlib.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, emlib.MD_APPEND)
self._setLastIter(it)
def test_CTF(self):
""" Test the conversion of a SetOfParticles to Xmipp metadata. """
mdCtf = emlib.MetaData(self.dataset.getFile('ctfGold'))
objId = mdCtf.firstObject()
rowCtf = rowFromMd(mdCtf, objId)
ctf = rowToCtfModel(rowCtf)
ALL_CTF_LABELS = [
emlib.MDL_CTF_CA,
emlib.MDL_CTF_ENERGY_LOSS,
emlib.MDL_CTF_LENS_STABILITY,
emlib.MDL_CTF_CONVERGENCE_CONE,
emlib.MDL_CTF_LONGITUDINAL_DISPLACEMENT,
emlib.MDL_CTF_TRANSVERSAL_DISPLACEMENT,
emlib.MDL_CTF_K,
emlib.MDL_CTF_BG_GAUSSIAN_K,
emlib.MDL_CTF_BG_GAUSSIAN_SIGMAU,
emlib.MDL_CTF_BG_GAUSSIAN_SIGMAV,
emlib.MDL_CTF_BG_GAUSSIAN_CU,
emlib.MDL_CTF_BG_GAUSSIAN_CV,
emlib.MDL_CTF_BG_SQRT_K,
emlib.MDL_CTF_BG_SQRT_U,
emlib.MDL_CTF_BG_SQRT_V,
emlib.MDL_CTF_BG_SQRT_ANGLE,
emlib.MDL_CTF_BG_BASELINE,
emlib.MDL_CTF_BG_GAUSSIAN2_K,
emlib.MDL_CTF_BG_GAUSSIAN2_SIGMAU,
emlib.MDL_CTF_BG_GAUSSIAN2_SIGMAV,
emlib.MDL_CTF_BG_GAUSSIAN2_CU,
emlib.MDL_CTF_BG_GAUSSIAN2_CV,
emlib.MDL_CTF_BG_GAUSSIAN2_ANGLE,
#emlib.MDL_CTF_CRIT_FITTINGSCORE,
emlib.MDL_CTF_CRIT_FITTINGCORR13,
emlib.MDL_CTF_DOWNSAMPLE_PERFORMED,
emlib.MDL_CTF_CRIT_PSDVARIANCE,
emlib.MDL_CTF_CRIT_PSDPCA1VARIANCE,
emlib.MDL_CTF_CRIT_PSDPCARUNSTEST,
emlib.MDL_CTF_CRIT_FIRSTZEROAVG,
emlib.MDL_CTF_CRIT_DAMPING,
emlib.MDL_CTF_CRIT_FIRSTZERORATIO,
emlib.MDL_CTF_CRIT_PSDCORRELATION90,
emlib.MDL_CTF_CRIT_PSDRADIALINTEGRAL,
emlib.MDL_CTF_CRIT_NORMALITY,
]
for label in ALL_CTF_LABELS:
attrName = '_xmipp_%s' % emlib.label2Str(label)
self.assertAlmostEquals(mdCtf.getValue(label, objId),
ctf.getAttributeValue(attrName))
def _getMdString(self, filename, block=None):
md = emlib.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" % emlib.label2Str(l) for l in labels])
imgPath = None
for label in labels:
if emlib.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 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:
Row object of the row found.
None if no row is found with label=value
"""
mdQuery = emlib.MetaData() # store result
mdQuery.importObjects(md, emlib.MDValueEQ(label, value))
n = mdQuery.size()
if n == 0:
row = None
elif n == 1:
row = emlib.metadata.Row()
row.readFromMd(mdQuery, mdQuery.firstObject())
else:
raise Exception("findRow: more than one row found matching the query "
"%s = %s" % (emlib.label2Str(label), value))
return row