def relionLabelString():
""" create an string that can be used for XMIPP_EXTRA_ALIASES
for adding the labels of Relion.
"""
from xmipp import label2Str
pairs = []
for k, v in XMIPP_RELION_LABELS.iteritems():
pairs.append('%s=%s' % (label2Str(k), v))
for k, v in XMIPP_RELION_LABELS_EXTRA.iteritems():
pairs.append('%s=%s' % (label2Str(k), v))
return ';'.join(pairs)
def objectToRow(obj, row, attrDict, extraLabels={}):
""" This function will convert an EMObject into a XmippMdRow.
Params:
obj: the EMObject instance (input)
row: the XmippMdRow instance (output)
attrDict: dictionary with the map between obj attributes(keys) and
row MDLabels in Xmipp (values).
extraLabels: a list with extra labels that could be included
as _xmipp_labelName
"""
if obj.isEnabled():
enabled = 1
else:
enabled = -1
row.setValue(xmipp.MDL_ENABLED, enabled)
for attr, label in attrDict.iteritems():
if hasattr(obj, attr):
valueType = getLabelPythonType(label)
row.setValue(label, valueType(getattr(obj, attr).get()))
attrLabels = attrDict.values()
for label in extraLabels:
attrName = '_xmipp_%s' % xmipp.label2Str(label)
if label not in attrLabels and hasattr(obj, attrName):
value = obj.getAttributeValue(attrName)
row.setValue(label, value)
def objectToRow(obj, row, attrDict, extraLabels={}):
""" This function will convert an EMObject into a XmippMdRow.
Params:
obj: the EMObject instance (input)
row: the XmippMdRow instance (output)
attrDict: dictionary with the map between obj attributes(keys) and
row MDLabels in Xmipp (values).
extraLabels: a list with extra labels that could be included
as _xmipp_labelName
"""
if obj.isEnabled():
enabled = 1
else:
enabled = -1
row.setValue(xmipp.MDL_ENABLED, enabled)
for attr, label in attrDict.iteritems():
if hasattr(obj, attr):
valueType = getLabelPythonType(label)
row.setValue(label, valueType(getattr(obj, attr).get()))
attrLabels = attrDict.values()
for label in extraLabels:
attrName = '_xmipp_%s' % xmipp.label2Str(label)
if label not in attrLabels and hasattr(obj, attrName):
value = obj.getAttributeValue(attrName)
row.setValue(label, value)
def rowToObject(row, obj, attrDict, extraLabels={}):
""" This function will convert from a XmippMdRow to an EMObject.
Params:
row: the XmippMdRow instance (input)
obj: the EMObject instance (output)
attrDict: dictionary with the map between obj attributes(keys) and
row MDLabels in Xmipp (values).
extraLabels: a list with extra labels that could be included
as _xmipp_labelName
"""
obj.setEnabled(row.getValue(xmipp.MDL_ENABLED, 1) > 0)
for attr, label in attrDict.iteritems():
value = row.getValue(label)
if not hasattr(obj, attr):
setattr(obj, attr, ObjectWrap(value))
else:
getattr(obj, attr).set(value)
attrLabels = attrDict.values()
for label in extraLabels:
if label not in attrLabels and row.hasLabel(label):
labelStr = xmipp.label2Str(label)
setattr(obj, '_xmipp_%s' % labelStr, row.getValueAsObject(label))
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 = xmipp.MetaData() # store result
mdQuery.importObjects(md, xmipp.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" %
(xmipp.label2Str(label), value))
return row
def convertCtfparam(oldCtf):
'''Convert the old format (Xmipp2.4) of the CTF
and return a new MetaData'''
f = open(oldCtf)
md = MetaData()
md.setColumnFormat(False)
objId = md.addObject()
for line in f:
line = line.strip()
if len(line) and not line.startswith('#'):
parts = line.split('=')
old_key = parts[0].strip()
if old_key in OLD_CTF_BASIC_DICT:
value = float(parts[1].strip())
label = OLD_CTF_BASIC_DICT[old_key]
md.setValue(label, value, objId)
else:
print "WARNING: Ignoring old ctfparam key:", old_key
f.close()
#Change sign of defocusU, defocusV and Q0
labels = [label2Str(l) for l in [MDL_CTF_DEFOCUSU, MDL_CTF_DEFOCUSV, MDL_CTF_Q0]]
exps = ["%s=%s*-1" % (l, l) for l in labels]
expression = ','.join(exps)
md.operate(expression)
return md
def rowToObject(row, obj, attrDict, extraLabels={}):
""" This function will convert from a XmippMdRow to an EMObject.
Params:
row: the XmippMdRow instance (input)
obj: the EMObject instance (output)
attrDict: dictionary with the map between obj attributes(keys) and
row MDLabels in Xmipp (values).
extraLabels: a list with extra labels that could be included
as _xmipp_labelName
"""
obj.setEnabled(row.getValue(xmipp.MDL_ENABLED, 1) > 0)
for attr, label in attrDict.iteritems():
value = row.getValue(label)
if not hasattr(obj, attr):
setattr(obj, attr, ObjectWrap(value))
else:
getattr(obj, attr).set(value)
attrLabels = attrDict.values()
for label in extraLabels:
if label not in attrLabels and row.hasLabel(label):
labelStr = xmipp.label2Str(label)
setattr(obj, '_xmipp_%s' % labelStr, row.getValueAsObject(label))
def setXmippAttributes(obj, objRow, *labels):
""" Set an attribute to obj from a label that is not
basic ones. The new attribute will be named _xmipp_LabelName
and the datatype will be set correctly.
"""
for label in labels:
setattr(obj, '_xmipp_%s' % xmipp.label2Str(label),
objRow.getValueAsObject(label))
def __setXmippImage(label):
attr = '_xmipp_' + xmipp.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 __setXmippImage(label):
attr = '_xmipp_' + xmipp.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 = xmipp.SymList()
mdIter = xmipp.MetaData()
#for it in self.allIters():
mdIter.clear()
SL.readSymmetryFile(self._symmetry[it])
md1 = xmipp.MetaData(self.docFileInputAngles[it])
md2 = xmipp.MetaData(self.docFileInputAngles[it-1])
#ignore disabled,
md1.removeDisabled()
md2.removeDisabled()
#first metadata file may not have shiftx and shifty
if not md2.containsLabel(xmipp.MDL_SHIFT_X):
md2.addLabel(xmipp.MDL_SHIFT_X)
md2.addLabel(xmipp.MDL_SHIFT_Y)
md2.fillConstant(xmipp.MDL_SHIFT_X,0.)
md2.fillConstant(xmipp.MDL_SHIFT_Y,0.)
oldLabels=[xmipp.MDL_ANGLE_ROT,
xmipp.MDL_ANGLE_TILT,
xmipp.MDL_ANGLE_PSI,
xmipp.MDL_SHIFT_X,
xmipp.MDL_SHIFT_Y]
newLabels=[xmipp.MDL_ANGLE_ROT2,
xmipp.MDL_ANGLE_TILT2,
xmipp.MDL_ANGLE_PSI2,
xmipp.MDL_SHIFT_X2,
xmipp.MDL_SHIFT_Y2]
md2.renameColumn(oldLabels,newLabels)
md2.addLabel(xmipp.MDL_SHIFT_X_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_Y_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_DIFF)
mdIter.join1(md1, md2, xmipp.MDL_IMAGE, xmipp.INNER_JOIN)
SL.computeDistance(mdIter,False,False,False)
xmipp.activateMathExtensions()
#operate in sqlite
shiftXLabel = xmipp.label2Str(xmipp.MDL_SHIFT_X)
shiftX2Label = xmipp.label2Str(xmipp.MDL_SHIFT_X2)
shiftXDiff = xmipp.label2Str(xmipp.MDL_SHIFT_X_DIFF)
shiftYLabel = xmipp.label2Str(xmipp.MDL_SHIFT_Y)
shiftY2Label = xmipp.label2Str(xmipp.MDL_SHIFT_Y2)
shiftYDiff = xmipp.label2Str(xmipp.MDL_SHIFT_Y_DIFF)
shiftDiff = xmipp.label2Str(xmipp.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,xmipp.MD_APPEND)
self._setLastIter(it)
def calculateDeviationsStep(self, it):
""" Calculate both angles and shifts devitations for all iterations
"""
SL = xmipp.SymList()
mdIter = xmipp.MetaData()
#for it in self.allIters():
mdIter.clear()
SL.readSymmetryFile(self._symmetry[it])
md1 = xmipp.MetaData(self.docFileInputAngles[it])
md2 = xmipp.MetaData(self.docFileInputAngles[it-1])
#ignore disabled,
md1.removeDisabled()
md2.removeDisabled()
#first metadata file may not have shiftx and shifty
if not md2.containsLabel(xmipp.MDL_SHIFT_X):
md2.addLabel(xmipp.MDL_SHIFT_X)
md2.addLabel(xmipp.MDL_SHIFT_Y)
md2.fillConstant(xmipp.MDL_SHIFT_X,0.)
md2.fillConstant(xmipp.MDL_SHIFT_Y,0.)
oldLabels=[xmipp.MDL_ANGLE_ROT,
xmipp.MDL_ANGLE_TILT,
xmipp.MDL_ANGLE_PSI,
xmipp.MDL_SHIFT_X,
xmipp.MDL_SHIFT_Y]
newLabels=[xmipp.MDL_ANGLE_ROT2,
xmipp.MDL_ANGLE_TILT2,
xmipp.MDL_ANGLE_PSI2,
xmipp.MDL_SHIFT_X2,
xmipp.MDL_SHIFT_Y2]
md2.renameColumn(oldLabels,newLabels)
md2.addLabel(xmipp.MDL_SHIFT_X_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_Y_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_DIFF)
mdIter.join1(md1, md2, xmipp.MDL_IMAGE, xmipp.INNER_JOIN)
SL.computeDistance(mdIter,False,False,False)
xmipp.activateMathExtensions()
#operate in sqlite
shiftXLabel = xmipp.label2Str(xmipp.MDL_SHIFT_X)
shiftX2Label = xmipp.label2Str(xmipp.MDL_SHIFT_X2)
shiftXDiff = xmipp.label2Str(xmipp.MDL_SHIFT_X_DIFF)
shiftYLabel = xmipp.label2Str(xmipp.MDL_SHIFT_Y)
shiftY2Label = xmipp.label2Str(xmipp.MDL_SHIFT_Y2)
shiftYDiff = xmipp.label2Str(xmipp.MDL_SHIFT_Y_DIFF)
shiftDiff = xmipp.label2Str(xmipp.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,xmipp.MD_APPEND)
self._setLastIter(it)
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, ex:
print >> sys.stderr, "XmippMdRow.writeToMd: Error writting value to metadata."
print >> sys.stderr, " label: %s, value: %s, type(value): %s" % (
label2Str(label), value, type(value))
raise ex
def test_CTF(self):
""" Test the conversion of a SetOfParticles to Xmipp metadata. """
mdCtf = xmipp.MetaData(self.dataset.getFile('ctfGold'))
objId = mdCtf.firstObject()
rowCtf = rowFromMd(mdCtf, objId)
ctf = rowToCtfModel(rowCtf)
ALL_CTF_LABELS = [
xmipp.MDL_CTF_CA,
xmipp.MDL_CTF_ENERGY_LOSS,
xmipp.MDL_CTF_LENS_STABILITY,
xmipp.MDL_CTF_CONVERGENCE_CONE,
xmipp.MDL_CTF_LONGITUDINAL_DISPLACEMENT,
xmipp.MDL_CTF_TRANSVERSAL_DISPLACEMENT,
xmipp.MDL_CTF_K,
xmipp.MDL_CTF_BG_GAUSSIAN_K,
xmipp.MDL_CTF_BG_GAUSSIAN_SIGMAU,
xmipp.MDL_CTF_BG_GAUSSIAN_SIGMAV,
xmipp.MDL_CTF_BG_GAUSSIAN_CU,
xmipp.MDL_CTF_BG_GAUSSIAN_CV,
xmipp.MDL_CTF_BG_SQRT_K,
xmipp.MDL_CTF_BG_SQRT_U,
xmipp.MDL_CTF_BG_SQRT_V,
xmipp.MDL_CTF_BG_SQRT_ANGLE,
xmipp.MDL_CTF_BG_BASELINE,
xmipp.MDL_CTF_BG_GAUSSIAN2_K,
xmipp.MDL_CTF_BG_GAUSSIAN2_SIGMAU,
xmipp.MDL_CTF_BG_GAUSSIAN2_SIGMAV,
xmipp.MDL_CTF_BG_GAUSSIAN2_CU,
xmipp.MDL_CTF_BG_GAUSSIAN2_CV,
xmipp.MDL_CTF_BG_GAUSSIAN2_ANGLE,
xmipp.MDL_CTF_CRIT_FITTINGSCORE,
xmipp.MDL_CTF_CRIT_FITTINGCORR13,
xmipp.MDL_CTF_DOWNSAMPLE_PERFORMED,
xmipp.MDL_CTF_CRIT_PSDVARIANCE,
xmipp.MDL_CTF_CRIT_PSDPCA1VARIANCE,
xmipp.MDL_CTF_CRIT_PSDPCARUNSTEST,
xmipp.MDL_CTF_CRIT_FIRSTZEROAVG,
xmipp.MDL_CTF_CRIT_DAMPING,
xmipp.MDL_CTF_CRIT_FIRSTZERORATIO,
xmipp.MDL_CTF_CRIT_PSDCORRELATION90,
xmipp.MDL_CTF_CRIT_PSDRADIALINTEGRAL,
xmipp.MDL_CTF_CRIT_NORMALITY,
]
for label in ALL_CTF_LABELS:
attrName = '_xmipp_%s' % xmipp.label2Str(label)
self.assertAlmostEquals(mdCtf.getValue(label, objId),
ctf.getAttributeValue(attrName))
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 test_CTF(self):
""" Test the convertion of a SetOfParticles to Xmipp metadata. """
mdCtf = xmipp.MetaData(self.dataset.getFile('ctfGold'))
objId = mdCtf.firstObject()
rowCtf = rowFromMd(mdCtf, objId)
ctf = rowToCtfModel(rowCtf)
ALL_CTF_LABELS = [
xmipp.MDL_CTF_CA,
xmipp.MDL_CTF_ENERGY_LOSS,
xmipp.MDL_CTF_LENS_STABILITY,
xmipp.MDL_CTF_CONVERGENCE_CONE,
xmipp.MDL_CTF_LONGITUDINAL_DISPLACEMENT,
xmipp.MDL_CTF_TRANSVERSAL_DISPLACEMENT,
xmipp.MDL_CTF_K,
xmipp.MDL_CTF_BG_GAUSSIAN_K,
xmipp.MDL_CTF_BG_GAUSSIAN_SIGMAU,
xmipp.MDL_CTF_BG_GAUSSIAN_SIGMAV,
xmipp.MDL_CTF_BG_GAUSSIAN_CU,
xmipp.MDL_CTF_BG_GAUSSIAN_CV,
xmipp.MDL_CTF_BG_SQRT_K,
xmipp.MDL_CTF_BG_SQRT_U,
xmipp.MDL_CTF_BG_SQRT_V,
xmipp.MDL_CTF_BG_SQRT_ANGLE,
xmipp.MDL_CTF_BG_BASELINE,
xmipp.MDL_CTF_BG_GAUSSIAN2_K,
xmipp.MDL_CTF_BG_GAUSSIAN2_SIGMAU,
xmipp.MDL_CTF_BG_GAUSSIAN2_SIGMAV,
xmipp.MDL_CTF_BG_GAUSSIAN2_CU,
xmipp.MDL_CTF_BG_GAUSSIAN2_CV,
xmipp.MDL_CTF_BG_GAUSSIAN2_ANGLE,
xmipp.MDL_CTF_CRIT_FITTINGSCORE,
xmipp.MDL_CTF_CRIT_FITTINGCORR13,
xmipp.MDL_CTF_DOWNSAMPLE_PERFORMED,
xmipp.MDL_CTF_CRIT_PSDVARIANCE,
xmipp.MDL_CTF_CRIT_PSDPCA1VARIANCE,
xmipp.MDL_CTF_CRIT_PSDPCARUNSTEST,
xmipp.MDL_CTF_CRIT_FIRSTZEROAVG,
xmipp.MDL_CTF_CRIT_DAMPING,
xmipp.MDL_CTF_CRIT_FIRSTZERORATIO,
xmipp.MDL_CTF_CRIT_PSDCORRELATION90,
xmipp.MDL_CTF_CRIT_PSDRADIALINTEGRAL,
xmipp.MDL_CTF_CRIT_NORMALITY,
]
for label in ALL_CTF_LABELS:
attrName = '_xmipp_%s' % xmipp.label2Str(label)
self.assertAlmostEquals(mdCtf.getValue(label, objId), ctf.getAttributeValue(attrName))
def _getMdString(self, filename, block=None):
md = xmipp.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" % xmipp.label2Str(l) for l in labels])
imgPath = None
for label in labels:
if xmipp.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 _getMdString(self, filename, block=None):
md = xmipp.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" % xmipp.label2Str(l) for l in labels])
imgPath = None
for label in labels:
if xmipp.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 exportMdToRelion(md, outputRelion):
""" This function will receive a Xmipp metadata and will
convert to the one expected by Relion.
All labels not recognized by Relion will be dropped.
Params:
md: input xmipp metadata.
outputRelion: output filename to store the Relion star file.
"""
for label in md.getActiveLabels():
if not label in XMIPP_RELION_LABELS:
md.removeLabel(label)
tmpFile = outputRelion + '.tmp'
md.write(tmpFile)
# Create a dict with the names
d = {}
for k, v in XMIPP_RELION_LABELS.iteritems():
d[label2Str(k)] = v
#print "dict: ", d
renameMdLabels(tmpFile, outputRelion, d)
from protlib_filesystem import deleteFile
deleteFile(None, tmpFile)
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
t = type(value)
if t is unicode:
value = str(value)
if t is int and xmipp.labelType(label) == xmipp.LABEL_SIZET:
value = long(value)
try:
md.setValue(label, value, objId)
except Exception as ex:
print(
"XmippMdRow.writeToMd: Error writting 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 __str__(self):
s = "{"
for k, v in self._labelDict.iteritems():
s += " %s = %s\n" % (xmipp.label2Str(k), v)
return s + "}"
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
t = type(value)
if t is unicode:
value = str(value)
if t is int and xmipp.labelType(label) == xmipp.LABEL_SIZET:
value = long(value)
try:
md.setValue(label, value, objId)
except Exception, ex:
print >> sys.stderr, "XmippMdRow.writeToMd: Error writting value to metadata."
print >> sys.stderr, " label: %s, value: %s, type(value): %s" % (label2Str(label), value, type(value))
raise ex
def _convertLabelToColumn(self, label, md):
""" From an Xmipp label, create the corresponding column. """
return ds.Column(xmipp.label2Str(label),
getLabelPythonType(label),
renderType=self._getLabelRenderType(label, md))
def __str__(self):
s = '{'
for k, v in self._labelDict.iteritems():
s += ' %s = %s\n' % (xmipp.label2Str(k), v)
return s + '}'
def __str__(self):
s = '{'
for k, v in self._labelDict.iteritems():
s += ' %s = %s\n' % (label2Str(k), v)
return s + '}'
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 = xmipp.MetaData() # store result
mdQuery.importObjects(md, xmipp.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" % (xmipp.label2Str(label), value))
return row
def _convertLabelToColumn(self, label):
""" From an Xmipp label, create the corresponding column. """
return ds.Column(xmipp.label2Str(label),
getLabelPythonType(label),
renderType=self._getLabelRenderType(label))
def _plotHistogramAngularMovement(self, paramName=None):
from numpy import arange
from matplotlib.ticker import FormatStrFormatter
plots = []
colors = ['g', 'b', 'r', 'y', 'c', 'm', 'k']
lenColors = len(colors)
numberOfBins = self.numberOfBins.get()
md = xmipp.MetaData()
for it in self._iterations:
mdFn = self.protocol._mdDevitationsFn(it)
if xmipp.existsBlockInMetaDataFile(mdFn):
md.read(mdFn)
if not self.usePsi:
md.fillConstant(xmipp.MDL_ANGLE_PSI, 0.)
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
xplotterShift = XmippPlotter(*gridsize,
mainTitle='Iteration_%d\n' % it,
windowTitle="ShiftDistribution")
xplotter = XmippPlotter(*gridsize,
mainTitle='Iteration_%d' % it,
windowTitle="AngularDistribution")
for ref3d in self._refsList:
mDoutRef3D = xmipp.MetaData()
mDoutRef3D.importObjects(
md, xmipp.MDValueEQ(xmipp.MDL_REF3D, ref3d))
_frequency = "Frequency (%d)" % mDoutRef3D.size()
xplotterShift.createSubPlot(
"%s_ref3D_%d" %
(xmipp.label2Str(xmipp.MDL_SHIFT_DIFF), ref3d),
"pixels", _frequency)
xplotter.createSubPlot(
"%s_ref3D_%d" %
(xmipp.label2Str(xmipp.MDL_ANGLE_DIFF), ref3d),
"degrees", _frequency)
#mDoutRef3D.write("*****@*****.**",MD_APPEND)
xplotter.plotMd(
mDoutRef3D,
xmipp.MDL_ANGLE_DIFF,
xmipp.MDL_ANGLE_DIFF,
color=colors[ref3d % lenColors],
#nbins=50
nbins=int(numberOfBins)
) #if nbins is present do an histogram
xplotterShift.plotMd(
mDoutRef3D,
xmipp.MDL_SHIFT_DIFF,
xmipp.MDL_SHIFT_DIFF,
color=colors[ref3d % lenColors],
nbins=int(numberOfBins
)) #if nbins is present do an histogram
if self.angleSort:
mDoutRef3D.sort(xmipp.MDL_ANGLE_DIFF)
fn = xmipp.FileName()
baseFileName = self.protocol._getTmpPath(
"angle_sort.xmd")
fn = self.protocol._getRefBlockFileName(
"angle_iter", it, "ref3D", ref3d, baseFileName)
mDoutRef3D.write(fn, xmipp.MD_APPEND)
print "File with sorted angles saved in:", fn
if self.shiftSort:
mDoutRef3D.sort(xmipp.MDL_SHIFT_DIFF)
fn = xmipp.FileName()
baseFileName = self.protocol._getTmpPath(
"angle_sort.xmd")
fn = self.protocol._getRefBlockFileName(
"shift_iter", it, "ref3D", ref3d, baseFileName)
mDoutRef3D.write(fn, xmipp.MD_APPEND)
print "File with sorted shifts saved in:", fn
plots.append(xplotterShift)
plots.append(xplotter)
else:
print "File %s does not exist" % mdFn
return plots
def _plotHistogramAngularMovement(self, paramName=None):
from numpy import arange
from matplotlib.ticker import FormatStrFormatter
plots = []
colors = ['g', 'b', 'r', 'y', 'c', 'm', 'k']
lenColors=len(colors)
numberOfBins = self.numberOfBins.get()
md = xmipp.MetaData()
for it in self._iterations:
mdFn = self.protocol._mdDevitationsFn(it)
if xmipp.existsBlockInMetaDataFile(mdFn):
md.read(mdFn)
if not self.usePsi:
md.fillConstant(xmipp.MDL_ANGLE_PSI,0.)
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
xplotterShift = XmippPlotter(*gridsize, mainTitle='Iteration_%d\n' % it, windowTitle="ShiftDistribution")
xplotter = XmippPlotter(*gridsize, mainTitle='Iteration_%d' % it, windowTitle="AngularDistribution")
for ref3d in self._refsList:
mDoutRef3D = xmipp.MetaData()
mDoutRef3D.importObjects(md, xmipp.MDValueEQ(xmipp.MDL_REF3D, ref3d))
_frequency = "Frequency (%d)" % mDoutRef3D.size()
xplotterShift.createSubPlot("%s_ref3D_%d"%(xmipp.label2Str(xmipp.MDL_SHIFT_DIFF),ref3d), "pixels", _frequency)
xplotter.createSubPlot("%s_ref3D_%d"%(xmipp.label2Str(xmipp.MDL_ANGLE_DIFF),ref3d), "degrees", _frequency)
#mDoutRef3D.write("*****@*****.**",MD_APPEND)
xplotter.plotMd(mDoutRef3D,
xmipp.MDL_ANGLE_DIFF,
xmipp.MDL_ANGLE_DIFF,
color=colors[ref3d%lenColors],
#nbins=50
nbins=int(numberOfBins)
)#if nbins is present do an histogram
xplotterShift.plotMd(mDoutRef3D,
xmipp.MDL_SHIFT_DIFF,
xmipp.MDL_SHIFT_DIFF,
color=colors[ref3d%lenColors],
nbins=int(numberOfBins)
)#if nbins is present do an histogram
if self.angleSort:
mDoutRef3D.sort(xmipp.MDL_ANGLE_DIFF)
fn = xmipp.FileName()
baseFileName = self.protocol._getTmpPath("angle_sort.xmd")
fn = self.protocol._getRefBlockFileName("angle_iter", it, "ref3D", ref3d, baseFileName)
mDoutRef3D.write(fn, xmipp.MD_APPEND)
print "File with sorted angles saved in:", fn
if self.shiftSort:
mDoutRef3D.sort(xmipp.MDL_SHIFT_DIFF)
fn = xmipp.FileName()
baseFileName = self.protocol._getTmpPath("angle_sort.xmd")
fn = self.protocol._getRefBlockFileName("shift_iter", it, "ref3D", ref3d, baseFileName)
mDoutRef3D.write(fn, xmipp.MD_APPEND)
print "File with sorted shifts saved in:", fn
plots.append(xplotterShift)
plots.append(xplotter)
else:
print "File %s does not exist" % mdFn
return plots
