def aaatest_particlesToStar(self):
""" Write a SetOfParticles to Relion star input file. """
imgSet = SetOfParticles(
filename=self.getOutputPath("particles.sqlite"))
n = 10
fn = self.particles
ctfs = [
CTFModel(defocusU=10000, defocusV=15000, defocusAngle=15),
CTFModel(defocusU=20000, defocusV=25000, defocusAngle=25)
]
acquisition = Acquisition(magnification=60000,
voltage=300,
sphericalAberration=2.,
amplitudeContrast=0.07)
imgSet.setAcquisition(acquisition)
coord = Coordinate()
coord.setMicId(1)
for i in range(n):
p = Particle()
p.setLocation(i + 1, fn)
ctf = ctfs[i % 2]
p.setCTF(ctf)
p.setAcquisition(acquisition)
p._xmipp_zScore = Float(i)
coord.setX(i * 10)
coord.setY(i * 10)
p.setCoordinate(coord)
imgSet.append(p)
fnStar = self.getOutputPath('particles.star')
fnStk = self.getOutputPath('particles.stk')
print ">>> Writing to file: %s" % fnStar
relion.writeSetOfParticles(imgSet, fnStar, fnStk)
mdAll = md.MetaData(fnStar)
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_X))
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_Y))
self.assertFalse(mdAll.containsLabel(md.RLN_SELECT_PARTICLES_ZSCORE))
def test_particlesWithPhaseShiftToStar(self):
""" Write a SetOfParticles to Relion star input file. """
imgSet = SetOfParticles(filename=self.getOutputPath("particles_ph_sh.sqlite"))
n = 10
fn = self.getFile('particles_binary')
ctfs = [CTFModel(defocusU=10000, defocusV=15000,
defocusAngle=15, phaseShift=90),
CTFModel(defocusU=20000, defocusV=25000,
defocusAngle=25, phaseShift=60)
]
acquisition = Acquisition(magnification=60000, voltage=300,
sphericalAberration=2.,
amplitudeContrast=0.07)
imgSet.setAcquisition(acquisition)
coord = Coordinate()
coord.setMicId(1)
for i in range(n):
p = Particle()
p.setLocation(i + 1, fn)
ctf = ctfs[i % 2]
p.setCTF(ctf)
p.setAcquisition(acquisition)
p._xmipp_zScore = Float(i)
coord.setX(i * 10)
coord.setY(i * 10)
p.setCoordinate(coord)
imgSet.append(p)
fnStar = self.getOutputPath('particles_ph_sh.star')
fnStk = self.getOutputPath('particles.stk')
print (">>> Writing to file: %s" % fnStar)
relion.writeSetOfParticles(imgSet, fnStar, fnStk)
mdAll = md.MetaData(fnStar)
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_X))
self.assertTrue(mdAll.containsLabel(md.RLN_IMAGE_COORD_Y))
self.assertFalse(mdAll.containsLabel(md.RLN_SELECT_PARTICLES_ZSCORE))
self.assertTrue(mdAll.containsLabel(md.RLN_CTF_PHASESHIFT))
def launchTest(self, fileKey, mList, alignType=None, **kwargs):
""" Helper function to launch similar alignment tests
give the EMX transformation matrix.
Params:
fileKey: the file where to grab the input stack images.
mList: the matrix list of transformations
(should be the same length of the stack of images)
"""
print "\n"
print "*" * 80
print "* Launching test: ", fileKey
print "*" * 80
is2D = alignType == ALIGN_2D
stackFn = self.dataset.getFile(fileKey)
partFn1 = self.getOutputPath(fileKey + "_particles1.sqlite")
mdFn = self.getOutputPath(fileKey + "_particles.star")
partFn2 = self.getOutputPath(fileKey + "_particles2.sqlite")
if self.IS_ALIGNMENT:
outputFn = self.getOutputPath(fileKey + "_output.mrcs")
outputFnRelion = self.getOutputPath(fileKey + "_output")
goldFn = self.dataset.getFile(fileKey + '_Gold_output_relion.mrcs')
else:
outputFn = self.getOutputPath(fileKey + "_output.vol")
goldFn = self.dataset.getFile(fileKey + '_Gold_output.vol')
if PRINT_FILES:
print "BINARY DATA: ", stackFn
print "SET1: ", partFn1
print " MD: ", mdFn
print "SET2: ", partFn2
print "OUTPUT: ", outputFn
print "GOLD: ", goldFn
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
partSet = SetOfParticles(filename=partFn1)
else:
partSet = SetOfVolumes(filename=partFn1)
partSet.setAlignment(alignType)
partSet.setAcquisition(
Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
# Populate the SetOfParticles with images
# taken from images.mrc file
# and setting the previous alignment parameters
aList = [numpy.array(m) for m in mList]
for i, a in enumerate(aList):
p = Particle()
p.setLocation(i + 1, stackFn)
p.setTransform(Transform(a))
partSet.append(p)
# Write out the .sqlite file and check that are correctly aligned
print "Parset", partFn1
partSet.printAll()
partSet.write()
# Convert to a Xmipp metadata and also check that the images are
# aligned correctly
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.writeSetOfParticles(partSet,
mdFn,
"/tmp",
alignType=alignType)
partSet2 = SetOfParticles(filename=partFn2)
else:
relion.writeSetOfVolumes(partSet, mdFn, alignType=alignType)
partSet2 = SetOfVolumes(filename=partFn2)
# Let's create now another SetOfImages reading back the written
# Xmipp metadata and check one more time.
partSet2.copyInfo(partSet)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.readSetOfParticles(mdFn, partSet2, alignType=alignType)
else:
relion.readSetOfVolumes(mdFn, partSet2, alignType=alignType)
partSet2.write()
if PRINT_MATRIX:
for i, img in enumerate(partSet2):
m1 = aList[i]
m2 = img.getTransform().getMatrix()
print "-" * 5
print img.getFileName(), img.getIndex()
print 'm1:\n', m1, relion.geometryFromMatrix(m1, False)
print 'm2:\n', m2, relion.geometryFromMatrix(m2, False)
# self.assertTrue(numpy.allclose(m1, m2, rtol=1e-2))
# Launch apply transformation and check result images
runRelionProgram(self.CMD % locals())
if SHOW_IMAGES:
runRelionProgram('scipion show %(outputFn)s' % locals())
if os.path.exists(goldFn):
self.assertTrue(
ImageHandler().compareData(goldFn, outputFn, tolerance=0.001),
"Different data files:\n>%s\n<%s" % (goldFn, outputFn))
def launchTest(self, fileKey, mList, alignType=None, **kwargs):
""" Helper function to launch similar alignment tests
give the EMX transformation matrix.
Params:
fileKey: the file where to grab the input stack images.
mList: the matrix list of transformations
(should be the same length of the stack of images)
"""
print ("\n")
print ("*" * 80)
print ("* Launching test: ", fileKey)
print ("*" * 80)
is2D = alignType == ALIGN_2D
stackFn = self.dataset.getFile(fileKey)
partFn1 = self.getOutputPath(fileKey + "_particles1.sqlite")
mdFn = self.getOutputPath(fileKey + "_particles.star")
partFn2 = self.getOutputPath(fileKey + "_particles2.sqlite")
if self.IS_ALIGNMENT:
outputFn = self.getOutputPath(fileKey + "_output.mrcs")
outputFnRelion = self.getOutputPath(fileKey + "_output")
goldFn = self.dataset.getFile(fileKey + '_Gold_output_relion.mrcs')
else:
outputFn = self.getOutputPath(fileKey + "_output.vol")
goldFn = self.dataset.getFile(fileKey + '_Gold_output.vol')
if PRINT_FILES:
print("BINARY DATA: ", stackFn)
print("SET1: ", partFn1)
print(" MD: ", mdFn)
print("SET2: ", partFn2)
print("OUTPUT: ", outputFn)
print("GOLD: ", goldFn)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
partSet = SetOfParticles(filename=partFn1)
else:
partSet = SetOfVolumes(filename=partFn1)
partSet.setAlignment(alignType)
partSet.setAcquisition(Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
# Populate the SetOfParticles with images
# taken from images.mrc file
# and setting the previous alignment parameters
aList = [numpy.array(m) for m in mList]
for i, a in enumerate(aList):
p = Particle()
p.setLocation(i + 1, stackFn)
p.setTransform(Transform(a))
partSet.append(p)
# Write out the .sqlite file and check that are correctly aligned
print ("Parset", partFn1)
partSet.printAll()
partSet.write()
# Convert to a Xmipp metadata and also check that the images are
# aligned correctly
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.writeSetOfParticles(partSet, mdFn,"/tmp", alignType=alignType)
partSet2 = SetOfParticles(filename=partFn2)
else:
relion.writeSetOfVolumes(partSet, mdFn, alignType=alignType)
partSet2 = SetOfVolumes(filename=partFn2)
# Let's create now another SetOfImages reading back the written
# Xmipp metadata and check one more time.
partSet2.copyInfo(partSet)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.readSetOfParticles(mdFn, partSet2, alignType=alignType)
else:
relion.readSetOfVolumes(mdFn, partSet2, alignType=alignType)
partSet2.write()
if PRINT_MATRIX:
for i, img in enumerate(partSet2):
m1 = aList[i]
m2 = img.getTransform().getMatrix()
print ("-" * 5)
print (img.getFileName(), img.getIndex())
print ('m1:\n', m1, relion.geometryFromMatrix(m1, False))
print ('m2:\n', m2, relion.geometryFromMatrix(m2, False))
# self.assertTrue(numpy.allclose(m1, m2, rtol=1e-2))
# Launch apply transformation and check result images
runRelionProgram(self.CMD % locals())
if SHOW_IMAGES:
runRelionProgram('scipion show %(outputFn)s' % locals())
if os.path.exists(goldFn):
self.assertTrue(
ImageHandler().compareData(goldFn, outputFn, tolerance=0.001),
"Different data files:\n>%s\n<%s" % (goldFn, outputFn))