def test_getFiles(self):
# create setofImages
dbFn = self.getOutputPath('multistack_set.sqlite')
# dbFn = ':memory:'
n = 10
m = 3
img = emobj.Particle()
imgSet = emobj.SetOfParticles(filename=dbFn)
imgSet.setSamplingRate(1.0)
goldStacks = set()
for j in range(1, m + 1):
stackName = 'stack%02d.stk' % j
goldStacks.add(stackName)
for i in range(1, n + 1):
img.setLocation(i, stackName)
imgSet.append(img)
img.cleanObjId()
self.assertEquals(goldStacks, imgSet.getFiles())
imgSet.close()
# It should automatically call load
# before accessing items db
imgSet.getFirstItem()
def test_hugeSet(self):
""" Create a set of a big number of particles to measure
creation time with sqlite operations.
"""
# Allow what huge means to be defined with environment var
n = int(os.environ.get('SCIPION_TEST_HUGE', 10000))
print(">>>> Creating a set of %d particles." % n)
print(" (set SCIPION_TEST_HUGE environment var to other value)")
dbFn = self.getOutputPath('huge_set.sqlite')
# dbFn = ':memory:'
img = emobj.Particle()
imgSet = emobj.SetOfParticles(filename=dbFn)
imgSet.setSamplingRate(1.0)
for i in range(1, n + 1):
# Creating object inside the loop significantly
# decrease performance
# img = Particle()
img.setLocation(i, "images.stk")
imgSet.append(img)
img.cleanObjId()
# img.setObjId(None)
imgSet.write()
def test_clone(self):
""" Check that cloning the Transform will
also copy the values of underlying numpy matrix.
"""
t = emobj.Transform()
m = t.getMatrix()
m[0, 3] = 2
m[1, 3] = 4
t2 = t.clone()
m2 = t2.getMatrix()
self.assertTrue(np.allclose(m, m2, rtol=1e-2))
p = emobj.Particle()
p.setTransform(t)
p2 = p.clone()
m3 = p2.getTransform().getMatrix()
self.assertTrue(np.allclose(m, m3, rtol=1e-2))
def test_orderBy(self):
# create setofProjections sorted
imgSet1 = emobj.SetOfParticles(filename=':memory:', prefix='set1')
imgSet2 = emobj.SetOfParticles(filename=':memory:', prefix='set2')
imgSet1.setSamplingRate(1.5)
imgSet2.setSamplingRate(1.5)
img = emobj.Particle()
for i in range(1, 10):
img.setLocation(i, 'mystack.stk')
img.setMicId(10 - i)
img.setClassId(i % 5)
imgSet1.append(img)
img.setMicId(i)
imgSet2.append(img)
img.cleanObjId()
# orderby
for item1, item2 in zip(
imgSet1.iterItems(orderBy='_micId', direction='ASC'),
imgSet2.iterItems(orderBy='_micId', direction='ASC')):
self.assertEquals(item1.getMicId(), item2.getMicId())
def test_mapper(self):
""" test that indexes are created when a
setOfParticles is created """
PARTNUMBER = 10
indexesNames = ['_classId', '_micId']
prot = createDummyProtocol("dummy_protocol")
# create set of particles
partSet = prot._createSetOfParticles()
part = emobj.Particle()
for i in range(PARTNUMBER + 1):
part.setLocation(i, "stack.vol")
partSet.append(part)
part.cleanObjId()
partSet.write()
# check defined indexes
setOfPArticleFileName = prot._getPath("particles.sqlite")
# print os.path.abspath(setOfPArticleFileName)
indexes = sorted(
[index[1] for index in getIndex(setOfPArticleFileName)])
for index, indexName in zip(indexes, indexesNames):
self.assertEqual(index, 'index_' + indexName)
def _checkNewItems(self, objSet):
""" Check for already computed micrograph/movie and
update the output set. """
objDict = {}
newObj = False
for obj in objSet:
objDict[obj.getFileName()] = True
if objDict:
if objSet.getSize():
objSet.enableAppend()
objSet.loadAllProperties()
else:
objSet.setStreamState(objSet.STREAM_OPEN)
acquisition = emobj.Acquisition()
if self.setof == SET_OF_MICROGRAPHS:
acquisition.setMagnification(
self.inputMics.get().getAcquisition().getMagnification())
acquisition.setVoltage(
self.inputMics.get().getAcquisition().getVoltage())
acquisition.setSphericalAberration(
self.inputMics.get().getAcquisition().getSphericalAberration())
acquisition.setAmplitudeContrast(
self.inputMics.get().getAcquisition().getAmplitudeContrast())
objSet.setAcquisition(acquisition)
objSet.setSamplingRate(self.inputMics.get().getSamplingRate())
elif self.setof == SET_OF_MOVIES:
acquisition.setMagnification(
self.inputMovies.get().getAcquisition().getMagnification())
acquisition.setVoltage(
self.inputMovies.get().getAcquisition().getVoltage())
acquisition.setSphericalAberration(
self.inputMovies.get().getAcquisition().getSphericalAberration())
acquisition.setAmplitudeContrast(
self.inputMovies.get().getAcquisition().getAmplitudeContrast())
objSet.setAcquisition(acquisition)
objSet.setSamplingRate(
self.inputMovies.get().getSamplingRate())
else:
acquisition.setMagnification(self._magnification)
acquisition.setVoltage(self._voltage)
acquisition.setSphericalAberration(self._sphericalAberration)
acquisition.setAmplitudeContrast(self._amplitudeContrast)
objSet.setAcquisition(acquisition)
if self.setof == SET_OF_PARTICLES:
objSet.setSamplingRate(
self.inputParticles.get().getSamplingRate())
else:
objSet.setSamplingRate(self.samplingRate.get())
if self.setof == SET_OF_MOVIES:
obj = emobj.Movie()
elif self.setof == SET_OF_MICROGRAPHS:
obj = emobj.Micrograph()
elif self.setof == SET_OF_RANDOM_MICROGRAPHS:
obj = emobj.Micrograph()
elif self.setof == SET_OF_PARTICLES:
obj = emobj.Particle()
else:
raise Exception('Unknown data type')
for k, v in self.dictObj.items():
if k not in objDict:
self.counter += 1
obj.setFileName(k)
if self.setof != SET_OF_PARTICLES:
obj.setMicName(basename(k))
obj.setObjId(self.counter)
objSet.append(obj)
newObj = True
return objSet, newObj # why a dictionary, a boolean may be enough
