def __init__(self, confs={}, **kwargs):
pwobj.OrderedObject.__init__(self, **kwargs)
self.config = ProjectConfig()
# Store the current view selected by the user
self.currentProtocolsView = pwobj.String()
# Store the color mode: 0= Status, 1=Labels, ...
self.colorMode = pwobj.Integer(ProjectSettings.COLOR_MODE_STATUS)
self.nodeList = NodeConfigList(
) # Store graph nodes positions and other info
self.labelsList = LabelsList() # Label list
self.mapper = None # This should be set when load, or write
self.runsView = pwobj.Integer(1) # by default the graph view
self.readOnly = pwobj.Boolean(False)
self.runSelection = pwobj.CsvList(int) # Store selected runs
self.dataSelection = pwobj.CsvList(int) # Store selected runs
# Some extra settings stored, now mainly used
# from the webtools
# Time when the project was created
self.creationTime = pwobj.String(dt.datetime.now())
# Number of days that this project is active
# if None, the project will not expire
# This is used in webtools where a limited time
# is allowed for each project
self.lifeTime = pwobj.Integer()
# Set a disk quota for the project (in Gb)
# if None, quota is unlimited
self.diskQuota = pwobj.Integer()
def __init__(self, **kwargs):
EdBaseObject.__init__(self, **kwargs)
self._spotId = pwobj.Integer()
self._bbox = pwobj.CsvList()
self._flag = pwobj.Integer()
self._intensitySumValue = pwobj.Float()
self._intensitySumVariance = pwobj.Float()
self._nSignal = pwobj.Integer()
self._panel = pwobj.Integer()
self._shoebox = None
self._xyzobsPxValue = pwobj.CsvList()
self._xyzobsPxVariance = pwobj.CsvList()
def _setAlignmentInfo(self, movie, obj):
""" Set alignment info such as plot and psd filename, and
the cumulative shifts values.
Params:
movie: Pass the reference movie
obj: should pass either the created micrograph or movie
"""
obj.plotCart = Image()
obj.plotCart.setFileName(self._getPlotCart(movie))
if self.doComputePSD:
obj.psdCorr = Image()
obj.psdCorr.setFileName(self._getPsdCorr(movie))
meanX, meanY = self._loadMeanShifts(movie)
obj._xmipp_OFMeanX = pwobj.CsvList()
obj._xmipp_OFMeanX.set(meanX)
obj._xmipp_OFMeanY = pwobj.CsvList()
obj._xmipp_OFMeanY.set(meanY)
def test_Object(self):
value = 2
i = pwobj.Integer(value)
self.assertEqual(value, i.get())
# compare objects
i2 = pwobj.Integer(value)
self.assertEqual(i, i2)
value = 2.
f = pwobj.Float(value)
self.assertAlmostEqual(value, f.get())
f.multiply(5)
self.assertAlmostEqual(value*5, f.get())
a = pwobj.Integer()
self.assertEqual(a.hasValue(), False)
c = Complex.createComplex()
# Check values are correct
self.assertEqual(c.imag.get(), Complex.cGold.imag)
self.assertEqual(c.real.get(), Complex.cGold.real)
# Test Boolean logic
b = pwobj.Boolean(False)
self.assertTrue(not b.get())
b.set('True')
self.assertTrue(b.get())
b = pwobj.Boolean()
b.set(False)
self.assertTrue(not b.get())
# CsvList should be empty if set to ''
l = pwobj.CsvList()
l.set('')
self.assertEqual(len(l), 0)
# Test emptiness
self.assertIsNotEmpty(b)
def test_SqliteMapper(self):
fn = self.getOutputPath("basic.sqlite")
mapper = pwmapper.SqliteMapper(fn)
# Insert a Float
f = pwobj.Float(5.4)
mapper.insert(f)
# Insert an pwobj.Integer
i = pwobj.Integer(1)
mapper.insert(i)
# Insert two pwobj.Boolean
b = pwobj.Boolean(False)
b2 = pwobj.Boolean(True)
mapper.insert(b)
mapper.insert(b2)
# Test storing pointers
p = pwobj.Pointer(b)
mapper.insert(p)
# Store csv list
strList = ['1', '2', '3']
csv = pwobj.CsvList()
csv += strList
mapper.insert(csv)
# Test normal List
iList = pwobj.List()
mapper.insert(iList) # Insert the list when empty
i1 = pwobj.Integer(4)
i2 = pwobj.Integer(3)
iList.append(i1)
iList.append(i2)
mapper.update(iList) # now update with some items inside
pList = pwobj.PointerList()
p1 = pwobj.Pointer(b)
# p1.set(b)
p2 = pwobj.Pointer(b2)
# p2.set(b2)
pList.append(p1)
pList.append(p2)
mapper.store(pList)
# Test to add relations
relName = 'testRelation'
creator = f
mapper.insertRelation(relName, creator, i, b)
mapper.insertRelation(relName, creator, i, b2)
mapper.insertRelation(relName, creator, b, p)
mapper.insertRelation(relName, creator, b2, p)
# Save changes to file
mapper.commit()
self.assertEqual(1, mapper.db.getVersion())
mapper.close()
# TODO: Maybe some mapper test for backward compatibility can be
# include in scipion-em, where we already have defined datasets
# and reference old sqlite files
# Test using SqliteDb class
db = pwmapper.SqliteDb()
db._createConnection(fn, timeout=1000)
tables = ['Objects', 'Relations']
self.assertEqual(tables, db.getTables())
# Test getting the version, for the gold file it should be 0
self.assertEqual(1, db.getVersion())
db.close()
# Reading test
mapper2 = pwmapper.SqliteMapper(fn, pw.Config.getDomain().getMapperDict())
print("Checking that Relations table is updated and version to 1")
self.assertEqual(1, mapper2.db.getVersion())
# Check that the new column is properly added after updated to version 1
colNamesGold = [u'id', u'parent_id', u'name', u'classname',
u'value', u'label', u'comment', u'object_parent_id',
u'object_child_id', u'creation',
u'object_parent_extended', u'object_child_extended']
colNames = [col[1] for col in mapper2.db.getTableColumns('Relations')]
self.assertEqual(colNamesGold, colNames)
l = mapper2.selectByClass('Integer')[0]
self.assertEqual(l.get(), 1)
f2 = mapper2.selectByClass('Float')[0]
self.assertEqual(f, f2.get())
b = mapper2.selectByClass('Boolean')[0]
self.assertTrue(not b.get())
p = mapper2.selectByClass('Pointer')[0]
self.assertEqual(b.get(), p.get())
csv2 = mapper2.selectByClass('CsvList')[0]
self.assertTrue(list.__eq__(csv2, strList))
# Iterate over all objects
allObj = mapper2.selectAll()
iterAllObj = mapper2.selectAll(iterate=True)
for a1, a2 in zip(allObj, iterAllObj):
# Note compare the scalar objects, which have a well-defined comparison
if isinstance(a1, pwobj.Scalar):
self.assertEqual(a1, a2)
# Test select all batch approach
allBatch = mapper2.selectAllBatch()
# Test relations
childs = mapper2.getRelationChilds(relName, i)
parents = mapper2.getRelationParents(relName, p)
# In this case both childs and parent should be the same
for c, p in zip(childs, parents):
self.assertEqual(c, p,
"Childs of object i, should be the parents of object p")
relations = mapper2.getRelationsByCreator(creator)
for row in relations:
print(dict(row))
def __init__(self, **kwargs):
ProtMonitor.__init__(self, **kwargs)
self._runIds = pwobj.CsvList(pType=int)
def rotateAstimatism(self, tsObjId):
getTMTS = self.getTMSetOfTiltSeries.get()[tsObjId]
tsId = getTMTS.getTsId()
# inputCtfTomoSeries = self.inputSetOfCtfTomoSeries.get()[tsObjId]
match = False
for inputCtfTomoSeries in self.inputSetOfCtfTomoSeries.get():
if tsId == inputCtfTomoSeries.getTsId():
match = True
self.getOutputSetOfCTFTomoSeries()
newCTFTomoSeries = tomoObj.CTFTomoSeries()
newCTFTomoSeries.copyInfo(inputCtfTomoSeries)
newCTFTomoSeries.setTiltSeries(getTMTS)
newCTFTomoSeries.setTsId(tsId)
newCTFTomoSeries.setObjId(tsObjId)
newCTFTomoSeries.setIMODDefocusFileFlag(inputCtfTomoSeries.getIMODDefocusFileFlag())
newCTFTomoSeries.setNumberOfEstimationsInRange(inputCtfTomoSeries.getNumberOfEstimationsInRange())
self.outputSetOfCTFTomoSeries.append(newCTFTomoSeries)
for index, (tiltImageGetTM, inputCtfTomo) in enumerate(zip(getTMTS, inputCtfTomoSeries)):
newCTFTomo = tomoObj.CTFTomo()
newCTFTomo.copyInfo(inputCtfTomo)
rotationAngle = utils.calculateRotationAngleFromTM(tiltImageGetTM)
if newCTFTomo.hasAstigmatismInfoAsList():
defocusAngleList = pwobj.CsvList(pType=float)
for angle in inputCtfTomo.getDefocusAngleList().split(','):
defocusAngleList.append(pwobj.Float(round(float(angle)+rotationAngle,2)))
newCTFTomo.setDefocusAngleList(defocusAngleList)
newCTFTomo.completeInfoFromList()
else:
newCTFTomo.setDefocusAngle(pwobj.Float(inputCtfTomo.getDefocusAngle() + rotationAngle))
newCTFTomo.standardize()
newCTFTomoSeries.append(newCTFTomo)
newCTFTomoSeries.setNumberOfEstimationsInRangeFromDefocusList()
newCTFTomoSeries.setIsDefocusUDeviationInRange(inputCtfTomoSeries.getIsDefocusUDeviationInRange())
newCTFTomoSeries.setIsDefocusVDeviationInRange(inputCtfTomoSeries.getIsDefocusVDeviationInRange())
if not (newCTFTomoSeries.getIsDefocusUDeviationInRange() and
newCTFTomoSeries.getIsDefocusVDeviationInRange()):
newCTFTomoSeries.setEnabled(False)
newCTFTomoSeries.write(properties=False)
self.outputSetOfCTFTomoSeries.update(newCTFTomoSeries)
self.outputSetOfCTFTomoSeries.write()
self._store()
if not match:
raise Exception("There is no matching CtfTomoSeries for a tilt-series %s"
% (tsId))
def __init__(self, **kwargs):
EMProtocol.__init__(self, **kwargs)
self._runIds = pwobj.CsvList(pType=int)
self.childs = []
def _floatList(key):
fl = pwobj.CsvList(pType=float)
fl.set(kwargs.get(key, []))
return fl
def importSetOfCtfTomoSeries(self):
inputSetOfTiltSeries = self.inputSetOfTiltSeries.get()
self.getOutputSetOfCTFTomoSeries()
for ts in inputSetOfTiltSeries:
tsId = ts.getTsId()
tsFileName = ts.getFirstItem().parseFileName(extension='')
for ctfFile, _ in self.iterFiles():
defocusFilePath = ctfFile
defocusFileName = os.path.basename(
os.path.splitext(ctfFile)[0])
if tsFileName == defocusFileName:
print("Parsing file: " + defocusFilePath)
defocusFileFlag = utils.getDefocusFileFlag(defocusFilePath)
newCTFTomoSeries = tomoObj.CTFTomoSeries()
newCTFTomoSeries.copyInfo(ts)
newCTFTomoSeries.setTiltSeries(ts)
newCTFTomoSeries.setTsId(tsId)
newCTFTomoSeries.setIMODDefocusFileFlag(defocusFileFlag)
# We need to create now all the attributes of this object in order to append it to the set and be
# able to update it posteriorly.
newCTFTomoSeries.setNumberOfEstimationsInRange(None)
self.outputSetOfCTFTomoSeries.append(newCTFTomoSeries)
if defocusFileFlag == 0:
" Plain estimation "
defocusUDict = utils.readCTFEstimationInfoFile(
defocusFilePath, flag=defocusFileFlag)
elif defocusFileFlag == 1:
" Astigmatism estimation "
defocusUDict, defocusVDict, defocusAngleDict = utils.readCTFEstimationInfoFile(
defocusFilePath, flag=defocusFileFlag)
elif defocusFileFlag == 4:
" Phase-shift information "
defocusUDict, phaseShiftDict = utils.readCTFEstimationInfoFile(
defocusFilePath, flag=defocusFileFlag)
elif defocusFileFlag == 5:
" Astigmatism and phase shift estimation "
defocusUDict, defocusVDict, defocusAngleDict, phaseShiftDict = \
utils.readCTFEstimationInfoFile(defocusFilePath,
flag=defocusFileFlag)
elif defocusFileFlag == 37:
" Astigmatism, phase shift and cut-on frequency estimation "
defocusUDict, defocusVDict, defocusAngleDict, phaseShiftDict, cutOnFreqDict = \
utils.readCTFEstimationInfoFile(defocusFilePath,
flag=defocusFileFlag)
else:
raise Exception(
"Defocus file flag do not supported. Only supported formats corresponding to flags 0, "
"1, 4, 5, and 37.")
for index, _ in enumerate(ts):
newCTFTomo = tomoObj.CTFTomo()
newCTFTomo.setIndex(pwobj.Integer(index + 1))
if defocusFileFlag == 0:
" Plain estimation "
newCTFTomo._defocusUList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
elif defocusFileFlag == 1:
" Astigmatism estimation "
newCTFTomo._defocusUList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._defocusVList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusVList(defocusVDict[index + 1])
newCTFTomo._defocusAngleList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusAngleList(
defocusAngleDict[index + 1])
elif defocusFileFlag == 4:
" Phase-shift information "
newCTFTomo._defocusUList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._phaseShiftList = pwobj.CsvList(
pType=float)
newCTFTomo.setPhaseShiftList(phaseShiftDict[index +
1])
elif defocusFileFlag == 5:
" Astigmatism and phase shift estimation "
newCTFTomo._defocusUList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._defocusVList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusVList(defocusVDict[index + 1])
newCTFTomo._defocusAngleList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusAngleList(
defocusAngleDict[index + 1])
newCTFTomo._phaseShiftList = pwobj.CsvList(
pType=float)
newCTFTomo.setPhaseShiftList(phaseShiftDict[index +
1])
elif defocusFileFlag == 37:
" Astigmatism, phase shift and cut-on frequency estimation "
newCTFTomo._defocusUList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._defocusVList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusVList(defocusVDict[index + 1])
newCTFTomo._defocusAngleList = pwobj.CsvList(
pType=float)
newCTFTomo.setDefocusAngleList(
defocusAngleDict[index + 1])
newCTFTomo._phaseShiftList = pwobj.CsvList(
pType=float)
newCTFTomo.setPhaseShiftList(phaseShiftDict[index +
1])
newCTFTomo._cutOnFreqList = pwobj.CsvList(
pType=float)
newCTFTomo.setCutOnFreqList(cutOnFreqDict[index +
1])
defocusUDict, defocusVDict, defocusAngleDict, phaseShiftDict, cutOnFreqDict = \
utils.readCTFEstimationInfoFile(defocusFilePath,
flag=defocusFileFlag)
newCTFTomo.completeInfoFromList()
newCTFTomoSeries.append(newCTFTomo)
newCTFTomoSeries.setNumberOfEstimationsInRangeFromDefocusList(
)
newCTFTomoSeries.write(properties=False)
self.outputSetOfCTFTomoSeries.update(newCTFTomoSeries)
self.outputSetOfCTFTomoSeries.write()
self._store()
def createOutputStep(self, tsObjId, outputSetName):
ts = self._getTiltSeries(tsObjId)
tsId = ts.getTsId()
objId = ts.getObjId()
self.outputSetName = outputSetName
extraPrefix = self._getExtraPath(tsId)
defocusFilePath = os.path.join(
extraPrefix,
ts.getFirstItem().parseFileName(extension=".defocus"))
if os.path.exists(defocusFilePath):
self.getOutputSetOfCTFTomoSeries(self.outputSetName)
defocusFileFlag = utils.getDefocusFileFlag(defocusFilePath)
newCTFTomoSeries = tomoObj.CTFTomoSeries()
newCTFTomoSeries.copyInfo(ts)
newCTFTomoSeries.setTiltSeries(ts)
newCTFTomoSeries.setTsId(tsId)
newCTFTomoSeries.setObjId(objId)
newCTFTomoSeries.setIMODDefocusFileFlag(defocusFileFlag)
# We need to create now all the attributes of this object in order
# to append it to the set and be able to update it posteriorly. "
newCTFTomoSeries.setNumberOfEstimationsInRange(None)
output = getattr(self, self.outputSetName)
output.append(newCTFTomoSeries)
if defocusFileFlag == 0:
" Plain estimation "
defocusUDict = utils.readCTFEstimationInfoFile(
defocusFilePath, flag=defocusFileFlag)
elif defocusFileFlag == 1:
" Astigmatism estimation "
defocusUDict, defocusVDict, defocusAngleDict = utils.readCTFEstimationInfoFile(
defocusFilePath, flag=defocusFileFlag)
elif defocusFileFlag == 4:
" Phase-shift information "
defocusUDict, phaseShiftDict = utils.readCTFEstimationInfoFile(
defocusFilePath, flag=defocusFileFlag)
elif defocusFileFlag == 5:
" Astigmatism and phase shift estimation "
defocusUDict, defocusVDict, defocusAngleDict, phaseShiftDict = \
utils.readCTFEstimationInfoFile(defocusFilePath,
flag=defocusFileFlag)
elif defocusFileFlag == 37:
" Astigmatism, phase shift and cut-on frequency estimation "
defocusUDict, defocusVDict, defocusAngleDict, phaseShiftDict, cutOnFreqDict = \
utils.readCTFEstimationInfoFile(defocusFilePath,
flag=defocusFileFlag)
else:
raise Exception(
"Defocus file flag do not supported. Only supported formats corresponding to flags 0, "
"1, 4, 5, and 37.")
for index, _ in enumerate(ts):
newCTFTomo = tomoObj.CTFTomo()
newCTFTomo.setIndex(pwobj.Integer(index + 1))
if defocusFileFlag == 0:
" Plain estimation "
newCTFTomo._defocusUList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
elif defocusFileFlag == 1:
" Astigmatism estimation "
newCTFTomo._defocusUList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._defocusVList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusVList(defocusVDict[index + 1])
newCTFTomo._defocusAngleList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusAngleList(defocusAngleDict[index + 1])
elif defocusFileFlag == 4:
" Phase-shift information "
newCTFTomo._defocusUList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._phaseShiftList = pwobj.CsvList(pType=float)
newCTFTomo.setPhaseShiftList(phaseShiftDict[index + 1])
elif defocusFileFlag == 5:
" Astigmatism and phase shift estimation "
newCTFTomo._defocusUList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._defocusVList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusVList(defocusVDict[index + 1])
newCTFTomo._defocusAngleList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusAngleList(defocusAngleDict[index + 1])
newCTFTomo._phaseShiftList = pwobj.CsvList(pType=float)
newCTFTomo.setPhaseShiftList(phaseShiftDict[index + 1])
elif defocusFileFlag == 37:
" Astigmatism, phase shift and cut-on frequency estimation "
newCTFTomo._defocusUList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusUList(defocusUDict[index + 1])
newCTFTomo._defocusVList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusVList(defocusVDict[index + 1])
newCTFTomo._defocusAngleList = pwobj.CsvList(pType=float)
newCTFTomo.setDefocusAngleList(defocusAngleDict[index + 1])
newCTFTomo._phaseShiftList = pwobj.CsvList(pType=float)
newCTFTomo.setPhaseShiftList(phaseShiftDict[index + 1])
newCTFTomo._cutOnFreqList = pwobj.CsvList(pType=float)
newCTFTomo.setCutOnFreqList(cutOnFreqDict[index + 1])
defocusUDict, defocusVDict, defocusAngleDict, phaseShiftDict, cutOnFreqDict = \
utils.readCTFEstimationInfoFile(defocusFilePath,
flag=defocusFileFlag)
newCTFTomo.completeInfoFromList()
newCTFTomoSeries.append(newCTFTomo)
newCTFTomoSeries.setNumberOfEstimationsInRangeFromDefocusList()
newCTFTomoSeries.calculateDefocusUDeviation(
defocusUTolerance=self.defocusUTolerance)
newCTFTomoSeries.calculateDefocusVDeviation(
defocusVTolerance=self.defocusVTolerance)
if not (newCTFTomoSeries.getIsDefocusUDeviationInRange()
and newCTFTomoSeries.getIsDefocusVDeviationInRange()):
newCTFTomoSeries.setEnabled(False)
newCTFTomoSeries.write(properties=False)
output.update(newCTFTomoSeries)
output.write()
self._store()
def __init__(self, **args):
pwobj.Object.__init__(self, **args)
self.csv = pwobj.CsvList()
