def openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path) else os.path.join(
os.getcwd(), path))
subprocess.Popen([pw.getScipionScript(), 'view', dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
import xmipp
fn = xmipp.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.viewer import DataView
DataView(path).show()
else:
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def runCreateOutputStep(self):
''' Create standard output results_images, result_classes'''
#creating results files
imgSet = self.inputParticles.get()
lastIter = self.numberOfIterations.get()
if self.numberOfReferences != 1:
inDocfile = self._getFileName('docfileInputAnglesIters', iter=lastIter)
ClassFnTemplate = '%(rootDir)s/reconstruction_Ref3D_%(ref)03d.vol'
allExpImagesinDocfile = xmipp.FileName()
all_exp_images="all_exp_images"
allExpImagesinDocfile.compose(all_exp_images, inDocfile)
dataClasses = self._getFileName('sqliteClasses')
createClassesFromImages(imgSet, str(allExpImagesinDocfile), dataClasses,
SetOfClasses3D, xmipp.MDL_REF3D, ClassFnTemplate, lastIter)
classes = self._createSetOfClasses3D(imgSet)
clsSet = SetOfClasses3D(dataClasses)
classes.appendFromClasses(clsSet)
volumes = self._createSetOfVolumes()
volumes.setSamplingRate(imgSet.getSamplingRate())
for refN in self.allRefs():
volFn = self._getFileName('reconstructedFileNamesIters', iter=lastIter, ref=refN)
vol = Volume()
vol.setFileName(volFn)
volumes.append(vol)
self._defineOutputs(outputVolumes=volumes)
self._defineOutputs(outputClasses=classes)
self._defineSourceRelation(self.inputParticles, volumes)
self._defineSourceRelation(self.inputParticles, classes)
self._defineSourceRelation(self.input3DReferences, volumes)
self._defineSourceRelation(self.input3DReferences, classes)
else:
volFn = self._getFileName('reconstructedFileNamesIters',
iter=lastIter, ref=1)
halfMap1 = self._getFileName('reconstructedFileNamesItersSplit1',
iter=lastIter, ref=1)
halfMap2 = self._getFileName('reconstructedFileNamesItersSplit2',
iter=lastIter, ref=1)
vol = Volume()
vol.setFileName(volFn)
vol.setSamplingRate(imgSet.getSamplingRate())
vol.setHalfMaps([halfMap1, halfMap2])
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
self._defineSourceRelation(self.input3DReferences, vol)
#create set of images
imgSetOut = self._createSetOfParticles("_iter_%03d" %lastIter)
self._fillParticlesFromIter(imgSetOut, lastIter)
self._defineOutputs(outputParticles=imgSetOut)
self._defineSourceRelation(self.inputParticles, imgSetOut)
self._defineSourceRelation(self.input3DReferences, imgSetOut)
def _checkOutputs(self, outputs, random=False, errorthreshold=0.001):
""" Check that all output files are produced
and are equivalent to the ones in goldStandard folder.
"""
for out in outputs:
outFile = os.path.join(self._testDir, self.outputDir, out)
fileGoldStd = os.path.join(self.goldDir, out)
# Check the expect output file was produced
msg = "Missing expected output file:\n output: %s" % outFile
self.assertTrue(os.path.exists(outFile), msg)
if random:
print "WARNING: %s was created using a random seed, check skipped\n " % outFile
else:
fnGoldStd = xmipp.FileName(fileGoldStd)
if fnGoldStd.isImage():
im1 = xmipp.Image(fileGoldStd)
im2 = xmipp.Image(outFile)
msg = "Images are not equal (+-%f):\n output: %s\n gold: %s" % \
(errorthreshold, outFile, fileGoldStd)
self.assertTrue(im1.equal(im2, errorthreshold), msg)
elif fnGoldStd.isMetaData():
msg = "MetaDatas are not equal:\n output: %s\n gold: %s" % (
outFile, fileGoldStd)
self.assertTrue(
xmipp.compareTwoMetadataFiles(outFile, fileGoldStd),
msg)
else:
msg = "Files are not equal:\n output: %s\n gold: %s" % (
outFile, fileGoldStd)
self.assertTrue(
xmipp.compareTwoFiles(outFile, fileGoldStd, 0), msg)
def createMetaDataFromPattern(pattern, isStack=False, label="image"):
''' Create a metadata from files matching pattern'''
import glob
files = glob.glob(pattern)
files.sort()
label = xmipp.str2Label(label) #Check for label value
mD = xmipp.MetaData()
inFile = xmipp.FileName()
nSize = 1
for file in files:
fileAux = file
if isStack:
if file.endswith(".mrc"):
fileAux = file + ":mrcs"
x, x, x, nSize = xmipp.getImageSize(fileAux)
if nSize != 1:
counter = 1
for jj in range(nSize):
inFile.compose(counter, fileAux)
objId = mD.addObject()
mD.setValue(label, inFile, objId)
mD.setValue(xmipp.MDL_ENABLED, 1, objId)
counter += 1
else:
objId = mD.addObject()
mD.setValue(label, fileAux, objId)
mD.setValue(xmipp.MDL_ENABLED, 1, objId)
return mD
def xmippToLocation(xmippFilename):
""" Return a location (index, filename) given
a Xmipp filename with the index@filename structure. """
if '@' in xmippFilename:
return xmipp.FileName(xmippFilename).decompose()
else:
return NO_INDEX, str(xmippFilename)
def _showProjMatchLibAndClasses(self, paramName=None):
#map stack position with ref number
list = []
mdIn = xmipp.MetaData()
mdOut = xmipp.MetaData()
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
if exists(file_name):
mdReferences = xmipp.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(
xmipp.MDL_NEIGHBOR, id)] = id
file_nameAverages = self.protocol._getFileName(
'outClassesXmd', iter=it, ref=ref3d)
file_references = self.protocol._getFileName(
'projectLibraryStk', iter=it, ref=ref3d)
if exists(file_nameAverages):
mdIn.read(file_nameAverages)
mdOut.clear()
for i in mdIn:
ref2D = mdIn.getValue(xmipp.MDL_REF, i)
file_reference = xmipp.FileName()
file_reference.compose(
convert_refno_to_stack_position[ref2D],
file_references)
id1 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE,
mdIn.getValue(xmipp.MDL_IMAGE, i),
id1)
mdOut.setValue(xmipp.MDL_IMAGE2, file_reference,
id1)
if mdOut.size() == 0:
print "Empty metadata: ", file_nameReferences
else:
file_nameReferences = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.merge(mdIn)
mdOut.write(file_nameReferences)
# ToDo: show the metadata in "metadata" form.
list.append(
self.createDataView(file_nameReferences))
else:
print "File %s does not exist" % file_name
return list
def _getImgPath(self, mdFn, imgFn):
""" Get ups and ups until finding the relative location to images. """
path = dirname(mdFn)
index, fn = xmipp.FileName(imgFn).decompose()
while path and path != '/':
newFn = os.path.join(path, fn)
if os.path.exists(newFn):
if index:
newFn = '%d@%s' % (index, newFn)
return newFn
path = dirname(path)
return None
def isImageFile(self, imgFn):
""" Check if imgFn has an image extension. The function
is implemented in the Xmipp binding.
"""
return xmipp.FileName(imgFn).isImage()
def xmippExists(path):
return xmipp.FileName(path).exists()
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 _showProjMatchLibAndImages(self, paramName=None):
from numpy import array, dot
#map stack position with ref number
imgAndClasses = []
mdIn = xmipp.MetaData()
mdOut = xmipp.MetaData()
mdTmp = xmipp.MetaData()
for ref3d in self._refsList:
for it in self._iterations:
convert_refno_to_stack_position = {}
file_name = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
file_nameReferences = 'projectionDirections@' + file_name
if exists(file_name):
#last reference name
mdReferences = xmipp.MetaData(file_nameReferences)
mdReferencesSize = mdReferences.size()
for id in mdReferences:
convert_refno_to_stack_position[mdReferences.getValue(
xmipp.MDL_NEIGHBOR, id)] = id
file_nameImages = "ctfGroup[0-9][0-9][0-9][0-9][0-9][0-9]@" + self.protocol._getFileName(
'docfileInputAnglesIters', iter=it)
mdTmp.read(file_nameImages) #query with ref3D
mdIn.importObjects(mdTmp,
xmipp.MDValueEQ(xmipp.MDL_REF3D, ref3d))
mdOut.clear()
for i in mdIn:
id1 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE,
mdIn.getValue(xmipp.MDL_IMAGE, i), id1)
psi = -1. * mdIn.getValue(xmipp.MDL_ANGLE_PSI, i)
flip = mdIn.getValue(xmipp.MDL_FLIP, i)
if (flip):
psi = -psi
eulerMatrix = xmipp.Euler_angles2matrix(0., 0., psi)
x = mdIn.getValue(xmipp.MDL_SHIFT_X, i)
y = mdIn.getValue(xmipp.MDL_SHIFT_Y, i)
shift = array([x, y, 0])
shiftOut = dot(eulerMatrix, shift)
[x, y, z] = shiftOut
if flip:
x = -x
mdOut.setValue(xmipp.MDL_ANGLE_PSI, psi, id1)
mdOut.setValue(xmipp.MDL_SHIFT_X, x, id1)
mdOut.setValue(xmipp.MDL_SHIFT_Y, y, id1)
mdOut.setValue(xmipp.MDL_FLIP, flip, id1)
ref2D = mdIn.getValue(xmipp.MDL_REF, i)
file_references = self.protocol._getFileName(
'projectLibraryStk', iter=it, ref=ref3d)
file_reference = xmipp.FileName()
file_reference.compose(
convert_refno_to_stack_position[ref2D],
file_references)
id2 = mdOut.addObject()
mdOut.setValue(xmipp.MDL_IMAGE, file_reference, id2)
mdOut.setValue(xmipp.MDL_ANGLE_PSI, 0., id2)
if mdOut.size() == 0:
print "Empty metadata"
else:
file_nameReferences = self.protocol._getFileName(
'projectLibrarySampling', iter=it, ref=ref3d)
sfn = createUniqueFileName(file_nameReferences)
file_nameReferences = 'projectionDirections@' + sfn
mdOut.write(file_nameReferences)
imgAndClasses.append(
self.createDataView(file_nameReferences))
else:
print "File %s does not exist" % file_name
return imgAndClasses
