def test_insertObjects(self):
dbName = self.getOutputPath("images.sqlite")
print ">>> test_insertObjects: dbName = '%s'" % dbName
mapper = SqliteFlatMapper(dbName, globals())
n = 10
for i in range(n):
img = Image()
img.setLocation(i + 1, "images.stk")
mapper.store(img)
mapper.setProperty("samplingRate", "3.0")
mapper.setProperty("defocusU", 1000)
mapper.setProperty("defocusV", 1000)
mapper.setProperty("defocusU", 2000) # Test update a property value
mapper.deleteProperty("defocusV") # Test delete a property
mapper.commit()
mapper.close()
# Test that values where stored properly
mapper2 = SqliteFlatMapper(dbName, globals())
self.assertTrue(mapper2.hasProperty("samplingRate"))
self.assertTrue(mapper2.hasProperty("defocusU"))
self.assertFalse(mapper2.hasProperty("defocusV"))
self.assertEqual(mapper2.getProperty("samplingRate"), "3.0")
self.assertEqual(mapper2.getProperty("defocusU"), "2000")
def test_insertObjects(self):
dbName = self.getOutputPath('images.sqlite')
print ">>> test_insertObjects: dbName = '%s'" % dbName
mapper = SqliteFlatMapper(dbName, globals())
n = 10
for i in range(n):
img = Image()
img.setLocation(i+1, 'images.stk')
mapper.store(img)
mapper.setProperty('samplingRate', '3.0')
mapper.setProperty('defocusU', 1000)
mapper.setProperty('defocusV', 1000)
mapper.setProperty('defocusU', 2000) # Test update a property value
mapper.deleteProperty('defocusV') # Test delete a property
mapper.commit()
self.assertEqual(1, mapper.db.getVersion())
mapper.close()
# Test that values where stored properly
mapper2 = SqliteFlatMapper(dbName, globals())
self.assertTrue(mapper2.hasProperty('samplingRate'))
self.assertTrue(mapper2.hasProperty('defocusU'))
self.assertFalse(mapper2.hasProperty('defocusV'))
self.assertEqual(mapper2.getProperty('samplingRate'), '3.0')
self.assertEqual(mapper2.getProperty('defocusU'), '2000')
def test_insertObjects(self):
dbName = self.getOutputPath('images.sqlite')
print ">>> test_insertObjects: dbName = '%s'" % dbName
mapper = SqliteFlatMapper(dbName, globals())
n = 10
for i in range(n):
img = Image()
img.setLocation(i + 1, 'images.stk')
mapper.store(img)
mapper.setProperty('samplingRate', '3.0')
mapper.setProperty('defocusU', 1000)
mapper.setProperty('defocusV', 1000)
mapper.setProperty('defocusU', 2000) # Test update a property value
mapper.deleteProperty('defocusV') # Test delete a property
mapper.commit()
self.assertEqual(1, mapper.db.getVersion())
mapper.close()
# Test that values where stored properly
mapper2 = SqliteFlatMapper(dbName, globals())
self.assertTrue(mapper2.hasProperty('samplingRate'))
self.assertTrue(mapper2.hasProperty('defocusU'))
self.assertFalse(mapper2.hasProperty('defocusV'))
self.assertEqual(mapper2.getProperty('samplingRate'), '3.0')
self.assertEqual(mapper2.getProperty('defocusU'), '2000')
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 _updateClass(self, item):
classId = item.getObjId()
classRow = findRow(self.mdClasses, xmipp.MDL_REF2, classId)
representative = item.getRepresentative()
representative.setTransform(rowToAlignment(classRow, ALIGN_PROJ))
representative.setLocation(xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE)))
setXmippAttributes(representative, classRow, xmipp.MDL_ANGLE_ROT)
setXmippAttributes(representative, classRow, xmipp.MDL_ANGLE_TILT)
setXmippAttributes(representative, classRow, xmipp.MDL_CLASS_COUNT)
self.averageSet.append(representative)
reprojection = Image()
reprojection.setLocation(xmippToLocation(classRow.getValue(xmipp.MDL_IMAGE1)))
item.reprojection = reprojection
def _updateClass(self, item):
classId = item.getObjId()
classRow = findRow(self.mdClasses, xmippLib.MDL_REF2, classId)
representative = item.getRepresentative()
representative.setTransform(rowToAlignment(classRow, ALIGN_PROJ))
representative.setLocation(xmippToLocation(classRow.getValue(xmippLib.MDL_IMAGE)))
setXmippAttributes(representative, classRow, xmippLib.MDL_ANGLE_ROT)
setXmippAttributes(representative, classRow, xmippLib.MDL_ANGLE_TILT)
setXmippAttributes(representative, classRow, xmippLib.MDL_CLASS_COUNT)
self.averageSet.append(representative)
reprojection = Image()
reprojection.setLocation(xmippToLocation(classRow.getValue(xmippLib.MDL_IMAGE1)))
item.reprojection = reprojection
def createOutputStep(self):
inputMics = self.inputMicrographs.get()
outputMics = self._createSetOfMicrographs()
outputMics.copyInfo(inputMics)
for mic in inputMics:
# Set the thumbnail image
mic.thumbnail = Image(self._getOutputMicThumbnail(mic.getObjId()))
outputMics.append(mic)
self._defineOutputs(outputMicrographs=outputMics)
self._defineTransformRelation(self.inputMicrographs, outputMics)
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 createOutputStep(self):
# Really load the input, since in the streaming case we can not
# use the self.inputMovies directly
allFramesSum = self._getPath('all_frames_sum.mrc')
allFramesAvg = self._getPath('all_frames_avg.mrc')
self._loadInputList()
n = len(self.listOfMovies)
ih = ImageHandler()
sumImg = ih.read(allFramesSum)
sumImg.inplaceDivide(float(n))
sumImg.write(allFramesAvg)
outputAvg = Image()
outputAvg.setFileName(allFramesAvg)
outputAvg.setSamplingRate(self.listOfMovies[0].getSamplingRate())
self._defineOutputs(outputAverage=outputAvg)
self._defineSourceRelation(self.inputMovies, outputAvg)
def test_insertObjects(self):
dbName = self.getOutputPath('images.sqlite')
print ">>> test_insertObjects: dbName = '%s'" % dbName
mapper = SqliteFlatMapper(dbName, globals())
self.assertEqual(0, mapper.count())
self.assertEqual(0, mapper.maxId())
n = 10
for i in range(n):
img = Image()
img.setLocation(i + 1, 'images.stk')
mapper.insert(img)
self.assertEqual(n, mapper.count())
self.assertEqual(n, mapper.maxId())
# Store one more image with bigger id
img = Image()
bigId = 1000
img.setLocation(bigId, 'images.stk')
img.setObjId(bigId)
mapper.insert(img)
self.assertEqual(bigId, mapper.maxId())
# Insert another image with None as id, it should take bigId + 1
img.setLocation(bigId + 1, 'images.stk')
img.setObjId(None)
mapper.insert(img)
self.assertEqual(bigId + 1, mapper.maxId())
mapper.setProperty('samplingRate', '3.0')
mapper.setProperty('defocusU', 1000)
mapper.setProperty('defocusV', 1000)
mapper.setProperty('defocusU', 2000) # Test update a property value
mapper.deleteProperty('defocusV') # Test delete a property
mapper.commit()
self.assertEqual(1, mapper.db.getVersion())
mapper.close()
# Test that values where stored properly
mapper2 = SqliteFlatMapper(dbName, globals())
self.assertTrue(mapper2.hasProperty('samplingRate'))
self.assertTrue(mapper2.hasProperty('defocusU'))
self.assertFalse(mapper2.hasProperty('defocusV'))
self.assertEqual(mapper2.getProperty('samplingRate'), '3.0')
self.assertEqual(mapper2.getProperty('defocusU'), '2000')
# Make sure that maxId() returns the proper value after loading db
self.assertEqual(bigId + 1, mapper2.maxId())
