def testTableIncludingNanAndErrors(self):
X,LAMB = numpy.meshgrid(numpy.linspace(-1.5,1.5,self.n),
numpy.linspace(-1.0,1.0,self.m))
self.lambDim = LAMB[:,0]
self.xDim = numpy.linspace(-1.5,1.5,self.n)
lambField = DC.FieldContainer(self.lambDim,
unit = '1 V / m**3',
longname='parameter',
shortname=r'\lambda')
xField = DC.FieldContainer(self.xDim,
unit = '1 m',
longname = 'position',
shortname = 'x')
x0,curv,mask = Helpers.fixedPoints(lambField.data,kappa1=self.kappa1)
fixedPoints = DC.FieldContainer(numpy.array(x0).transpose(),
unit = xField.unit,
dimensions=[DC.generateIndex(0,3), lambField],
longname = 'position of the local extrema of electric potential',
shortname = 'x_0',
attributes={'title':'testTableIncludingNanAndErrors'})
fixedPoints.error = 0.1 * fixedPoints.data
fixedPoints.seal()
visualizer = self.visualizer(fixedPoints,show=False)
filename = os.path.join(self.tmpdir,'pyphant-'+DC.parseId(fixedPoints.id)[0]+'%s.%s' % (visualizer.name,outputFormat))
visualizer.figure.savefig(filename.replace(' ',''))
def testVisualization(self):
X,LAMB = numpy.meshgrid(numpy.linspace(-1.5,1.5,self.n),
numpy.linspace(-1.0,1.0,self.m))
self.lambDim = numpy.linspace(-1.0,1.0,self.m)
self.xDim = numpy.linspace(-1.5,1.5,self.n)
lambField = DC.FieldContainer(self.lambDim,
unit = '1 V / m**3',
longname='parameter',
shortname='\lambda')
xField = DC.FieldContainer(self.xDim,
unit = '1 m',
longname = 'position',
shortname = 'x')
#Prepare potential
V = []
for i in xrange(len(lambField.data)):
u = X[i]
V.append(-lambField.data[i]/2* u**2 + u**4/4-u*self.kappa1)
self.V = DC.FieldContainer(numpy.array(V),unit='1 V',dimensions=[lambField,xField],
longname = 'electric potential',
shortname=r'\varphi')
self.V.seal()
#Visualise result
visualizer = ImageVisualizer(self.V,show=False)
filename = os.path.join(self.tmpdir,'pyphant-'+DC.parseId(self.V.id)[0]+'.pdf')
visualizer.figure.savefig(filename)
def saveDataContainer(self, result):
"""
Saves a given DataContainer instance to the HDF5 file.
The DataContainer has to be sealed or at least provide a valid
emd5 in its '.id' attribute.
A HDF5 group path that points to the location the DC was stored at
is returned.
result -- sealed DC instance
"""
dcHash, uriType = DataContainer.parseId(result.id)
resId = u"result_" + dcHash
try:
resultGroup = self.handle.getNode("/results/" + resId)
except tables.NoSuchNodeError:
try:
resultGroup = self.handle.createGroup(
"/results", resId, result.id.encode("utf-8")
)
except tables.NoSuchNodeError:
self.handle.createGroup('/', 'results')
resultGroup = self.handle.createGroup(
"/results", resId, result.id.encode("utf-8")
)
if uriType == 'field':
self.saveField(resultGroup, result)
elif uriType == 'sample':
self.saveSample(resultGroup, result)
else:
raise KeyError(
"Unknown UriType %s in saving result %s." % (
uriType, result.id
)
)
return resId
def loadSample(h5, resNode):
result = DataContainer.SampleContainer.__new__(
DataContainer.SampleContainer
)
result.longname = unicode(h5.getNodeAttr(resNode, "longname"), 'utf-8')
result.shortname = unicode(h5.getNodeAttr(resNode, "shortname"), 'utf-8')
result.creator = unicode(h5.getNodeAttr(resNode, "creator"), 'utf-8')
result.machine = unicode(h5.getNodeAttr(resNode, "machine"), 'utf-8')
result.attributes = {}
for key in resNode._v_attrs._v_attrnamesuser:
if key not in _reservedAttributes:
result.attributes[key] = h5.getNodeAttr(resNode, key)
columns = []
for resId in h5.getNodeAttr(resNode, "columns"):
nodename = "/results/" + resId
hash, uriType = DataContainer.parseId(
h5.getNodeAttr(nodename, "TITLE")
)
if uriType == 'sample':
loader = loadSample
elif uriType == 'field':
loader = loadField
else:
raise KeyError(
"Unknown UriType %s in saving result %s." % (
uriType, result.id
)
)
columns.append(loader(h5, h5.getNode(nodename)))
result.columns = columns
result.seal(resNode._v_title)
return result
def testIntersectionXVector(self):
X, LAMB = numpy.meshgrid(numpy.linspace(-1.5, 1.5, self.n),
numpy.linspace(-1.0, 1.0, self.m))
self.lambDim = LAMB[:, 0]
self.xDim = numpy.linspace(-1.5, 1.5, self.n)
lambField = DC.FieldContainer(self.lambDim,
unit='1 V / m**3',
longname='parameter',
shortname=r'\lambda')
xField = DC.FieldContainer(self.xDim,
unit='1 m',
longname='position',
shortname='x')
#Prepare potential
V = []
for i in xrange(len(lambField.data)):
u = X[i]
V.append(-lambField.data[i] / 2 * u**2 + u**4 / 4 -
u * self.kappa1)
self.V = DC.FieldContainer(
numpy.array(V),
unit='1 V',
dimensions=[lambField, xField],
longname='electric potential',
shortname=r'\varphi',
attributes={'title': 'testIntersectionXVector'})
self.V.seal()
visualizer = self.visualizer(self.V, show=False)
filename = os.path.join(
self.tmpdir, 'pyphant-' + DC.parseId(self.V.id)[0] + '%s.%s' %
(visualizer.name, outputFormat))
visualizer.figure.savefig(filename.replace(' ', ''))
def saveDataContainer(self, result):
"""
Saves a given DataContainer instance to the HDF5 file.
The DataContainer has to be sealed or at least provide a valid
emd5 in its '.id' attribute.
A HDF5 group path that points to the location the DC was stored at
is returned.
result -- sealed DC instance
"""
dcHash, uriType = DataContainer.parseId(result.id)
resId = u"result_" + dcHash
try:
resultGroup = self.handle.getNode("/results/" + resId)
except tables.NoSuchNodeError:
try:
resultGroup = self.handle.createGroup(
"/results", resId, result.id.encode("utf-8"))
except tables.NoSuchNodeError:
self.handle.createGroup('/', 'results')
resultGroup = self.handle.createGroup(
"/results", resId, result.id.encode("utf-8"))
if uriType == 'field':
self.saveField(resultGroup, result)
elif uriType == 'sample':
self.saveSample(resultGroup, result)
else:
raise KeyError, "Unknown UriType %s in saving result %s."\
% (uriType, result.id)
return resId
def loadSample(h5, resNode):
result = DataContainer.SampleContainer.__new__(
DataContainer.SampleContainer)
result.longname = unicode(h5.getNodeAttr(resNode, "longname"), 'utf-8')
result.shortname = unicode(h5.getNodeAttr(resNode, "shortname"), 'utf-8')
result.creator = unicode(h5.getNodeAttr(resNode, "creator"), 'utf-8')
result.machine = unicode(h5.getNodeAttr(resNode, "machine"), 'utf-8')
result.attributes = {}
for key in resNode._v_attrs._v_attrnamesuser:
if key not in _reservedAttributes:
result.attributes[key] = h5.getNodeAttr(resNode, key)
columns = []
for resId in h5.getNodeAttr(resNode, "columns"):
nodename = "/results/" + resId
hash, uriType = DataContainer.parseId(h5.getNodeAttr(
nodename, "TITLE"))
if uriType == 'sample':
loader = loadSample
elif uriType == 'field':
loader = loadField
else:
raise KeyError, "Unknown UriType %s in saving result %s." % (
uriType, result.id)
columns.append(loader(h5, h5.getNode(nodename)))
result.columns = columns
result.seal(resNode._v_title)
return result
def testVisualization(self):
X, LAMB = numpy.meshgrid(numpy.linspace(-1.5, 1.5, self.n),
numpy.linspace(-1.0, 1.0, self.m))
self.lambDim = numpy.linspace(-1.0, 1.0, self.m)
self.xDim = numpy.linspace(-1.5, 1.5, self.n)
lambField = DC.FieldContainer(self.lambDim,
unit='1 V / m**3',
longname='parameter',
shortname='\lambda')
xField = DC.FieldContainer(self.xDim,
unit='1 m',
longname='position',
shortname='x')
#Prepare potential
V = []
for i in xrange(len(lambField.data)):
u = X[i]
V.append(-lambField.data[i] / 2 * u**2 + u**4 / 4 -
u * self.kappa1)
self.V = DC.FieldContainer(numpy.array(V),
unit='1 V',
dimensions=[lambField, xField],
longname='electric potential',
shortname=r'\varphi')
self.V.seal()
#Visualise result
visualizer = ImageVisualizer(self.V, show=False)
filename = os.path.join(self.tmpdir,
'pyphant-' + DC.parseId(self.V.id)[0] + '.pdf')
visualizer.figure.savefig(filename)
def testTableIncludingNanAndErrors(self):
X, LAMB = numpy.meshgrid(numpy.linspace(-1.5, 1.5, self.n),
numpy.linspace(-1.0, 1.0, self.m))
self.lambDim = LAMB[:, 0]
self.xDim = numpy.linspace(-1.5, 1.5, self.n)
lambField = DC.FieldContainer(self.lambDim,
unit='1 V / m**3',
longname='parameter',
shortname=r'\lambda')
xField = DC.FieldContainer(self.xDim,
unit='1 m',
longname='position',
shortname='x')
x0, curv, mask = Helpers.fixedPoints(lambField.data,
kappa1=self.kappa1)
fixedPoints = DC.FieldContainer(
numpy.array(x0).transpose(),
unit=xField.unit,
dimensions=[DC.generateIndex(0, 3), lambField],
longname='position of the local extrema of electric potential',
shortname='x_0',
attributes={'title': 'testTableIncludingNanAndErrors'})
fixedPoints.error = 0.1 * fixedPoints.data
fixedPoints.seal()
visualizer = self.visualizer(fixedPoints, show=False)
filename = os.path.join(
self.tmpdir, 'pyphant-' + DC.parseId(fixedPoints.id)[0] + '%s.%s' %
(visualizer.name, outputFormat))
visualizer.figure.savefig(filename.replace(' ', ''))
def testIntersectionXVector(self):
X,LAMB = numpy.meshgrid(numpy.linspace(-1.5,1.5,self.n),
numpy.linspace(-1.0,1.0,self.m))
self.lambDim = LAMB[:,0]
self.xDim = numpy.linspace(-1.5,1.5,self.n)
lambField = DC.FieldContainer(self.lambDim,
unit = '1 V / m**3',
longname='parameter',
shortname=r'\lambda')
xField = DC.FieldContainer(self.xDim,
unit = '1 m',
longname = 'position',
shortname = 'x')
#Prepare potential
V = []
for i in xrange(len(lambField.data)):
u = X[i]
V.append(-lambField.data[i]/2* u**2 + u**4/4-u*self.kappa1)
self.V = DC.FieldContainer(numpy.array(V),unit='1 V',dimensions=[lambField, xField],
longname = 'electric potential',
shortname=r'\varphi',
attributes={'title':'testIntersectionXVector'})
self.V.seal()
visualizer = self.visualizer(self.V,show=False)
filename = os.path.join(self.tmpdir,'pyphant-'+DC.parseId(self.V.id)[0]+'%s.%s' % (visualizer.name,outputFormat))
visualizer.figure.savefig(filename.replace(' ',''))
def loadField(h5, resNode):
longname = unicode(h5.getNodeAttr(resNode, "longname"), 'utf-8')
shortname = unicode(h5.getNodeAttr(resNode, "shortname"), 'utf-8')
try:
creator = unicode(h5.getNodeAttr(resNode, "creator"), 'utf-8')
machine = unicode(h5.getNodeAttr(resNode, "machine"), 'utf-8')
except:
from pyphant.core.Helpers import emd52dict
emd5dict = emd52dict(resNode._v_title)
creator = emd5dict['creator']
machine = emd5dict['machine']
data = scipy.array(resNode.data.read())
def loads(inputList):
if type(inputList) == type([]):
try:
return map(lambda s: eval(s), inputList)
except:
return map(lambda s: unicode(s, 'utf-8'), inputList)
else:
return map(loads, inputList)
if data.dtype.char == 'S':
data = scipy.array(loads(data.tolist()))
attributes = {}
for key in resNode.data._v_attrs._v_attrnamesuser:
attributes[key] = h5.getNodeAttr(resNode.data, key)
try:
error = scipy.array(resNode.error.read())
except tables.NoSuchNodeError:
error = None
try:
mask = scipy.array(resNode.mask.read())
except tables.NoSuchNodeError:
mask = None
unit = eval(unicode(h5.getNodeAttr(resNode, "unit"), 'utf-8'))
try:
dimTable = resNode.dimensions
dimensions = [
loadField(
h5,
h5.getNode(
"/results/result_" + DataContainer.parseId(row['id'])[0]
)
)
for row in dimTable.iterrows()
]
except tables.NoSuchNodeError:
dimensions = DataContainer.INDEX
result = DataContainer.FieldContainer(data, unit, error, mask,
dimensions, longname, shortname,
attributes)
result.creator = creator
result.machine = machine
result.seal(resNode._v_title)
return result
def saveResult(result, h5):
hash, uriType = DataContainer.parseId(result.id)
resId = u"result_"+hash
try:
resultGroup = h5.getNode("/results/"+resId)
except tables.NoSuchNodeError, e:
resultGroup = h5.createGroup("/results", resId, result.id.encode("utf-8"))
if uriType=='field':
saveField(h5, resultGroup, result)
elif uriType=='sample':
saveSample(h5, resultGroup, result)
else:
raise KeyError, "Unknown UriType %s in saving result %s." % (uriType, result.id)
def getNodeAndTypeFromId(self, dcId):
"""
Returns a tuple (HDF5 node, uriType) for the given
DataContainer emd5.
dcId -- emd5 of the DataContainer
"""
dcHash, uriType = DataContainer.parseId(dcId)
try:
resNode = self.handle.getNode("/results/result_" + dcHash)
except (AttributeError, tables.NoSuchNodeError):
raise AttributeError("Container %s not found in file %s."
% (dcId, self.filename))
if isinstance(uriType, unicode):
uriType = uriType.encode('utf-8')
return (resNode, uriType)
def execute(self):
dialog = wx.FileDialog(None,message='Choose file for saving the data', defaultDir=os.getcwd(),
style=wx.SAVE | wx.OVERWRITE_PROMPT,
wildcard = "Comma separated values (*.csv)|*.csv|Plain text (*.dat)|*.dat")
if dialog.ShowModal() == wx.ID_OK:
path = dialog.GetPath()
print "Selected:",path
else:
print "Nothing was selected."
dialog.Destroy()
hash, uriType = DataContainer.parseId(self.dataContainer.id)
if uriType == u"field":
self.saveField(path)
elif uriType == u"sample":
self.saveSample(path)
def getNodeAndTypeFromId(self, dcId):
"""
Returns a tuple (HDF5 node, uriType) for the given
DataContainer emd5.
dcId -- emd5 of the DataContainer
"""
dcHash, uriType = DataContainer.parseId(dcId)
try:
resNode = self.handle.getNode("/results/result_" + dcHash)
except (AttributeError, tables.NoSuchNodeError):
raise AttributeError("Container %s not found in file %s." %
(dcId, self.filename))
if isinstance(uriType, unicode):
uriType = uriType.encode('utf-8')
return (resNode, uriType)
def saveResult(result, h5):
hash, uriType = DataContainer.parseId(result.id)
resId = u"result_" + hash
try:
resultGroup = h5.getNode("/results/" + resId)
except tables.NoSuchNodeError, e:
resultGroup = h5.createGroup("/results", resId,
result.id.encode("utf-8"))
if uriType == 'field':
saveField(h5, resultGroup, result)
elif uriType == 'sample':
saveSample(h5, resultGroup, result)
else:
raise KeyError, "Unknown UriType %s in saving result %s." % (
uriType, result.id)
def testVisualization(self):
X = numpy.linspace(-1.5,1.5,self.n)
self.lambDim = 1.0
xField = DC.FieldContainer(X,
unit = '1 m',
longname = 'position',
shortname = 'x')
self.V = DC.FieldContainer(-self.lambDim/2* X**2 + X**4/4-X*self.kappa1,
unit='1 V',dimensions=[xField],
longname = 'electric potential',
shortname=r'\varphi',
attributes={'title':'testVisualization'})
self.V.seal()
visualizer = self.visualizer(self.V,show=False)
filename = os.path.join(self.tmpdir,'pyphant-'+DC.parseId(self.V.id)[0]+'%s.%s' % (visualizer.name,outputFormat))
visualizer.figure.savefig(filename.replace(' ',''))
def execute(self):
dialog = wx.FileDialog(
None,
message='Choose file for saving the data',
defaultDir=os.getcwd(),
style=wx.SAVE | wx.OVERWRITE_PROMPT,
wildcard=("Comma separated values "
"(*.csv)|*.csv|Plain text (*.dat)|*.dat"))
if dialog.ShowModal() == wx.ID_OK:
path = dialog.GetPath()
print "Selected:", path
else:
print "Nothing was selected."
dialog.Destroy()
hash, uriType = DataContainer.parseId(self.dataContainer.id)
if uriType == u"field":
self.saveField(path)
elif uriType == u"sample":
self.saveSample(path)
def restoreResultsToWorkers(recipeGroup, workers, h5):
for workerGroup in recipeGroup:
for plugGroup in workerGroup.plugs:
plug = workers[workerGroup._v_name].getPlug(plugGroup._v_name)
try:
resId = plugGroup._v_attrs.result
resNode = h5.getNode("/results/" + resId)
hash, uriType = DataContainer.parseId(resNode._v_title)
if uriType == u'field':
result = loadField(h5, resNode)
elif uriType == u'sample':
_logger.info("Trying to load sample data...")
result = loadSample(h5, resNode)
_logger.info("...successfully loaded.")
else:
raise TypeError, "Unknown result uriType in <%s>" % resNode._v_title
plug._result = result
except (AttributeError, tables.NoSuchNodeError), e:
_logger.info("Exception: " + str(e))
def restoreResultsToWorkers(recipeGroup, workers, h5):
for workerGroup in recipeGroup:
for plugGroup in workerGroup.plugs:
plug=workers[workerGroup._v_name].getPlug(plugGroup._v_name)
try:
resId = plugGroup._v_attrs.result
resNode = h5.getNode("/results/"+resId)
hash, uriType = DataContainer.parseId(resNode._v_title)
if uriType==u'field':
result=loadField(h5, resNode)
elif uriType==u'sample':
_logger.info("Trying to load sample data...")
result=loadSample(h5, resNode)
_logger.info("...successfully loaded.")
else:
raise TypeError, "Unknown result uriType in <%s>"%resNode._v_title
plug._result = result
except (AttributeError, tables.NoSuchNodeError), e:
_logger.info( "Exception: "+str(e) )
def testVisualization(self):
X = numpy.linspace(-1.5, 1.5, self.n)
self.lambDim = 1.0
xField = DC.FieldContainer(X,
unit='1 m',
longname='position',
shortname='x')
self.V = DC.FieldContainer(-self.lambDim / 2 * X**2 + X**4 / 4 -
X * self.kappa1,
unit='1 V',
dimensions=[xField],
longname='electric potential',
shortname=r'\varphi',
attributes={'title': 'testVisualization'})
self.V.seal()
visualizer = self.visualizer(self.V, show=False)
filename = os.path.join(
self.tmpdir, 'pyphant-' + DC.parseId(self.V.id)[0] + '%s.%s' %
(visualizer.name, outputFormat))
visualizer.figure.savefig(filename.replace(' ', ''))
data = scipy.array(loads(data.tolist()))
attributes = {}
for key in resNode.data._v_attrs._v_attrnamesuser:
attributes[key]=h5.getNodeAttr(resNode.data,key)
try:
error = scipy.array(resNode.error.read())
except tables.NoSuchNodeError, e:
error = None
try:
mask = scipy.array(resNode.mask.read())
except tables.NoSuchNodeError, e:
mask = None
unit = eval(unicode(h5.getNodeAttr(resNode, "unit"), 'utf-8'))
try:
dimTable = resNode.dimensions
dimensions = [loadField(h5, h5.getNode("/results/result_"+DataContainer.parseId(row['id'])[0]))
for row in dimTable.iterrows()]
except tables.NoSuchNodeError, e:
dimensions = DataContainer.INDEX
result = DataContainer.FieldContainer(data, unit, error, mask,
dimensions, longname, shortname,
attributes)
result.creator = creator
result.machine = machine
result.seal(resNode._v_title)
return result
def loadSample(h5, resNode):
result = DataContainer.SampleContainer.__new__(DataContainer.SampleContainer)
result.longname = unicode(h5.getNodeAttr(resNode, "longname"), 'utf-8')
result.shortname = unicode(h5.getNodeAttr(resNode, "shortname"), 'utf-8')
try:
error = scipy.array(resNode.error.read())
except tables.NoSuchNodeError, e:
error = None
try:
mask = scipy.array(resNode.mask.read())
except tables.NoSuchNodeError, e:
mask = None
unit = eval(unicode(h5.getNodeAttr(resNode, "unit"), 'utf-8'))
try:
dimTable = resNode.dimensions
dimensions = [
loadField(
h5,
h5.getNode("/results/result_" +
DataContainer.parseId(row['id'])[0]))
for row in dimTable.iterrows()
]
except tables.NoSuchNodeError, e:
dimensions = DataContainer.INDEX
result = DataContainer.FieldContainer(data, unit, error, mask, dimensions,
longname, shortname, attributes)
result.creator = creator
result.machine = machine
result.seal(resNode._v_title)
return result
def loadSample(h5, resNode):
result = DataContainer.SampleContainer.__new__(
DataContainer.SampleContainer)