def __init__(self, **kwargs):
MockSet.__init__(self, **kwargs)
self._samplingRate = pwobj.Float()
self._hasCtf = pwobj.Boolean(kwargs.get('ctf', False))
self._isPhaseFlipped = pwobj.Boolean(False)
self._isAmplitudeCorrected = pwobj.Boolean(False)
self._acquisition = MockAcquisition()
self._firstDim = MockImageDim() # Dimensions of the first image
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 createOutputStep(self):
set1 = self.inputSets[0].get() # 1st set (we use it many times)
# Read ClassName and create the corresponding EMSet (SetOfParticles...)
try:
outputSetFunction = getattr(self, "_create%s" % set1.getClassName())
outputSet = outputSetFunction()
except Exception:
outputSet = set1.create(self._getPath())
# Copy info from input sets (sampling rate, etc).
outputSet.copyInfo(set1) # all sets must have the same info as set1!
# Renumber from the beginning if either the renumber option is selected
# or we find duplicated ids in the sets
cleanIds = not self.ignoreDuplicates.get() and self.duplicatedIds()
# TODO ROB remove ignoreExtraAttributes condition
# or implement it. But this will be for Scipion 1.2
self.ignoreExtraAttributes = pwobj.Boolean(True)
if self.ignoreExtraAttributes:
_, commonAttrs = self.commonAttributes()
# Get the 1st level attributes to be used for the copyAttributes
copyAttrs = list()
for attr in commonAttrs:
if "." not in attr:
copyAttrs.append(attr)
idsList = []
setNum = 0
for itemSet in self.inputSets:
setNum += 1
for obj in itemSet.get():
objId = obj.getObjId()
if self.ignoreDuplicates.get():
if objId in idsList:
continue
idsList.append(objId)
if self.ignoreExtraAttributes:
newObj = itemSet.get().ITEM_TYPE()
newObj.copyAttributes(obj, *copyAttrs)
self.cleanExtraAttributes(newObj, commonAttrs)
if not cleanIds or setNum == 1:
newObj.setObjId(objId)
else:
newObj = obj
if (cleanIds and setNum > 1) or self.renumber.get():
newObj.cleanObjId()
outputSet.append(newObj)
self._defineOutputs(outputSet=outputSet)
for itemSet in self.inputSets:
self._defineSourceRelation(itemSet, outputSet)
def __init__(self, location=None, **kwargs):
"""
Params:
:param location: Could be a valid location: (index, filename)
or filename
"""
EdBaseObject.__init__(self, **kwargs)
# Image location is composed by an index and a filename
self._index = pwobj.Integer(0)
self._filename = pwobj.String()
# Detector distance of this image
self._distance = pwobj.Float()
# Where oscillation starts and its range
self._oscStart = pwobj.Float()
self._oscRange = pwobj.Float()
# Beam center (in pixels)
self._beamCenterX = pwobj.Float()
self._beamCenterY = pwobj.Float()
# Exposure time (in seconds)
self._exposureTime = pwobj.Float()
# TwoTheta
self._twoTheta = pwobj.Float()
# Pixel size of the image (in millimeters)
self._pixelSizeX = pwobj.Float()
self._pixelSizeY = pwobj.Float()
# Dimensions of images in this set (number of pixels)
self._dimX = pwobj.Integer()
self._dimY = pwobj.Integer()
# Wavelength
self._wavelength = pwobj.Float()
# Detector type
self._detector = Detector()
# Experiment time
self._collectionTime = pwobj.String()
# Add parameter to state if the image should be ignored in processing
self._ignore = pwobj.Boolean()
# Add information about goniometer rotation axis relative to image
self._rotX = pwobj.Float()
self._rotY = pwobj.Float()
self._rotZ = pwobj.Float()
if location:
self.setLocation(location)
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 __init__(self, text=None, value=None, icon=None, tag=None, **kwargs):
"""Constructor for the Menu config item.
Arguments:
text: text to be displayed
value: internal value associated with the item.
icon: display an icon with the item
tag: put some tags to items
**args: pass other options to base class.
"""
self.text = pwobj.String(text)
self.value = pwobj.String(value)
self.icon = pwobj.String(icon)
self.tag = pwobj.String(tag)
self.childs = pwobj.List()
self.openItem = pwobj.Boolean(kwargs.get('openItem', False))
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):
EMProtocol.__init__(self, **kwargs)
self.stepsExecutionMode = pwcts.STEPS_PARALLEL
self.isFirstTime = pwobj.Boolean(False)
