esys.modellib.visualization Package¶

Classes¶

Data
Link
Model
Visualization
WriteVTK

class esys.modellib.visualization.Data¶

Bases: Boost.Python.instance

Represents a collection of datapoints. It is used to store the values of a function. For more details please consult the c++ class documentation.

__init__((object)arg1) → None¶: __init__( (object)arg1, (object)value [, (object)p2 [, (object)p3 [, (object)p4]]]) -> None

conjugate((Data)arg1) → Data¶

copy((Data)arg1, (Data)other) → None :¶

Make this object a copy of other

note: The two objects will act independently from now on. That is, changing other after this call will not change this object and vice versa.

copy( (Data)arg1) -> Data :

note:	In the no argument form, a new object will be returned which is an independent copy of this object.

copyWithMask((Data)arg1, (Data)other, (Data)mask) → None :¶

Selectively copy values from other Data.Datapoints which correspond to positive values in mask will be copied from other

Parameters:	other (`Data`) – source of values mask (Scalar `Data`) –

delay((Data)arg1) → Data :¶: Convert this object into lazy representation

dump((Data)arg1, (str)fileName) → None :¶

Save the data as a netCDF file

Parameters:	fileName (`string`) –

expand((Data)arg1) → None :¶: Convert the data to expanded representation if it is not expanded already.

getDomain((Data)arg1) → Domain :¶

Return type:	`Domain`

getFunctionSpace((Data)arg1) → FunctionSpace :¶

Return type:	`FunctionSpace`

getNumberOfDataPoints((Data)arg1) → int :¶

Return type:	`int`
Returns:	Number of datapoints in the object

getRank((Data)arg1) → int :¶

Returns:	the number of indices required to address a component of a datapoint
Return type:	positive `int`

getShape((Data)arg1) → tuple :¶

Returns the shape of the datapoints in this object as a python tuple. Scalar data has the shape ()

Return type:	`tuple`

getTagNumber((Data)arg1, (int)dpno) → int :¶

Return tag number for the specified datapoint

Return type:	int
Parameters:	dpno (int) – datapoint number

getTupleForDataPoint((Data)arg1, (int)dataPointNo) → object :¶

Returns:	Value of the specified datapoint
Return type:	`tuple`
Parameters:	dataPointNo (`int`) – datapoint to access

getTupleForGlobalDataPoint((Data)arg1, (int)procNo, (int)dataPointNo) → object :¶

Get a specific datapoint from a specific process

Return type:	`tuple`
Parameters:	procNo (positive `int`) – MPI rank of the process dataPointNo (int) – datapoint to access

getX((Data)arg1) → Data :¶: Returns the spatial coordinates of the spatial nodes. :rtype: Data

hasInf((Data)arg1) → bool :¶: Returns return true if data contains +-Inf. [Note that for complex values, hasNaN and hasInf are not mutually exclusive.]

hasNaN((Data)arg1) → bool :¶: Returns return true if data contains NaN. [Note that for complex values, hasNaN and hasInf are not mutually exclusive.]

imag((Data)arg1) → Data¶

internal_maxGlobalDataPoint((Data)arg1) → tuple :¶: Please consider using getSupLocator() from pdetools instead.

internal_minGlobalDataPoint((Data)arg1) → tuple :¶: Please consider using getInfLocator() from pdetools instead.

interpolate((Data)arg1, (FunctionSpace)functionspace) → Data :¶: Interpolate this object’s values into a new functionspace.

interpolateTable((Data)arg1, (object)table, (float)Amin, (float)Astep, (Data)B, (float)Bmin, (float)Bstep[, (float)undef=1e+50[, (bool)check_boundaries=False]]) → Data :¶

Creates a new Data object by interpolating using the source data (which are

looked up in table) A must be the outer dimension on the table

param check_boundaries:
param table:	two dimensional collection of values
param Amin:	The base of locations in table
type Amin:	float
param Astep:	size of gap between each item in the table
type Astep:	float
param undef:	upper bound on interpolated values
type undef:	float
param B:	Scalar representing the second coordinate to be mapped into the table
type B:	`Data`
param Bmin:	The base of locations in table for 2nd dimension
type Bmin:	float
param Bstep:	size of gap between each item in the table for 2nd dimension
type Bstep:	float
	if true, then values outside the boundaries will be rejected. If false, then boundary values will be used.
raise RuntimeError(DataException):
	if the coordinates do not map into the table or if the interpolated value is above `undef`
rtype:	`Data`

interpolateTable( (Data)arg1, (object)table, (float)Amin, (float)Astep [, (float)undef=1e+50 [, (bool)check_boundaries=False]]) -> Data

isComplex((Data)arg1) → bool :¶

Return type:	`bool`
Returns:	True if this `Data` stores complex values.

isConstant((Data)arg1) → bool :¶

Return type:	`bool`
Returns:	True if this `Data` is an instance of `DataConstant`
Note:	This does not mean the data is immutable.

isEmpty((Data)arg1) → bool :¶

Is this object an instance of DataEmpty

Return type:	`bool`
Note:	This is not the same thing as asking if the object contains datapoints.

isExpanded((Data)arg1) → bool :¶

Return type:	`bool`
Returns:	True if this `Data` is expanded.

isLazy((Data)arg1) → bool :¶

Return type:	`bool`
Returns:	True if this `Data` is lazy.

isProtected((Data)arg1) → bool :¶: Can this instance be modified. :rtype: bool

isReady((Data)arg1) → bool :¶

Return type:	`bool`
Returns:	True if this `Data` is not lazy.

isTagged((Data)arg1) → bool :¶

Return type:	`bool`
Returns:	True if this `Data` is expanded.

nonuniformInterpolate((Data)arg1, (object)in, (object)out, (bool)check_boundaries) → Data :¶: 1D interpolation with non equally spaced points

nonuniformSlope((Data)arg1, (object)in, (object)out, (bool)check_boundaries) → Data :¶: 1D interpolation of slope with non equally spaced points

phase((Data)arg1) → Data¶

promote((Data)arg1) → None¶

real((Data)arg1) → Data¶

replaceInf((Data)arg1, (object)value) → None :¶: Replaces +-Inf values with value. [Note, for complex Data, both real and imaginary components are replaced even if only one part is Inf].

replaceNaN((Data)arg1, (object)value) → None :¶: Replaces NaN values with value. [Note, for complex Data, both real and imaginary components are replaced even if only one part is NaN].

resolve((Data)arg1) → None :¶: Convert the data to non-lazy representation.

setProtection((Data)arg1) → None :¶

Disallow modifications to this data object

Note:	This method does not allow you to undo protection.

setTaggedValue((Data)arg1, (int)tagKey, (object)value) → None :¶

Set the value of tagged Data.

param tagKey: tag to update

type tagKey: int

setTaggedValue( (Data)arg1, (str)name, (object)value) -> None :

param name:	tag to update
type name:	`string`
param value:	value to set tagged data to
type value:	`object` which acts like an array, `tuple` or `list`

setToZero((Data)arg1) → None :¶: After this call the object will store values of the same shape as before but all components will be zero.

setValueOfDataPoint((Data)arg1, (int)dataPointNo, (object)value) → None¶

setValueOfDataPoint( (Data)arg1, (int)arg2, (object)arg3) -> None

setValueOfDataPoint( (Data)arg1, (int)arg2, (float)arg3) -> None :

Modify the value of a single datapoint.

param dataPointNo:

type dataPointNo:

int

param value:

type value: float or an object which acts like an array, tuple or list

warning: Use of this operation is discouraged. It prevents some optimisations from operating.

tag((Data)arg1) → None :¶: Convert data to tagged representation if it is not already tagged or expanded

toListOfTuples((Data)arg1[, (bool)scalarastuple=False]) → object :¶

Return the datapoints of this object in a list. Each datapoint is stored as a tuple.

Parameters:	scalarastuple – if True, scalar data will be wrapped as a tuple. True => [(0), (1), (2)]; False => [0, 1, 2]

class esys.modellib.visualization.Link(target, attribute=None)¶

Bases: object

A Link makes an attribute of an object callable:

o.object()
o.a=8
l=Link(o,"a")
assert l()==8

__init__(target, attribute=None)¶: Creates a link to the object target. If attribute is given, the link is established to this attribute of the target. Otherwise the attribute is undefined.

classmethod fromDom(esysxml, node)¶

getAttributeName()¶: Returns the name of the attribute the link is pointing to.

getTarget()¶: Returns the target.

hasDefinedAttributeName()¶: Returns true if an attribute name is set.

setAttributeName(attribute)¶: Sets a new attribute name to be collected from the target object. The target object must have the attribute with name attribute.

toDom(esysxml, node)¶: toDom method of Link. Creates a Link node and appends it to the current XML esysxml.

class esys.modellib.visualization.Model(parameters=[], **kwargs)¶

Bases: esys.escriptcore.modelframe.ParameterSet

A Model object represents a process marching over time until a finalizing condition is fulfilled. At each time step an iterative process can be performed and the time step size can be controlled. A Model has the following work flow:

doInitialization()
while not terminateInitialIteration(): doInitialStep()
doInitialPostprocessing()
while not finalize():
    dt=getSafeTimeStepSize(dt)
    doStepPreprocessing(dt)
    while not terminateIteration(): doStep(dt)
    doStepPostprocessing(dt)
doFinalization()

where doInitialization, finalize, getSafeTimeStepSize, doStepPreprocessing, terminateIteration, doStepPostprocessing, doFinalization are methods of the particular instance of a Model. The default implementations of these methods have to be overwritten by the subclass implementing a Model.

__init__(parameters=[], **kwargs)¶

Creates a model.

Just calls the parent constructor.

UNDEF_DT = 1e+300¶

checkLinkTargets(models, hash)¶: Returns a set of tuples (“<self>(<name>)”, <target model>) if the parameter <name> is linked to model <target model> but <target model> is not in the list of models. If a parameter is linked to another parameter set which is not in the hash list the parameter set is checked for its models. hash gives the call history.

declareParameter(**parameters)¶: Declares one or more new parameters and their initial value.

declareParameters(parameters)¶: Declares a set of parameters. parameters can be a list, a dictionary or a ParameterSet.

doFinalization()¶

Finalizes the time stepping.

This function may be overwritten.

doInitialPostprocessing()¶

Finalises the initialization iteration process. This method is not called in case of a restart.

This function may be overwritten.

doInitialStep()¶

Performs an iteration step in the initialization phase. This method is not called in case of a restart.

This function may be overwritten.

doInitialization()¶

Initializes the time stepping scheme. This method is not called in case of a restart.

This function may be overwritten.

doStep(dt)¶

Executes an iteration step at a time step.

dt is the currently used time step size.

This function may be overwritten.

doStepPostprocessing(dt)¶

Finalises the time step.

dt is the currently used time step size.

This function may be overwritten.

doStepPreprocessing(dt)¶

Sets up a time step of step size dt.

This function may be overwritten.

finalize()¶

Returns False if the time stepping is finalized.

This function may be overwritten.

classmethod fromDom(esysxml, node)¶

getAttributeObject(name)¶: Returns the object stored for attribute name.

getSafeTimeStepSize(dt)¶

Returns a time step size which can be safely used.

dt gives the previously used step size.

This function may be overwritten.

hasAttribute(name)¶: Returns True if self has attribute name.

releaseParameters(name)¶: Removes parameter name from the parameters.

setUp()¶

Sets up the model.

This function may be overwritten.

showParameters()¶: Returns a description of the parameters.

terminateInitialIteration()¶: Returns True if iteration at the inital phase is terminated.

terminateIteration()¶: Returns True if iteration on a time step is terminated.

toDom(esysxml, node)¶: toDom method of Model class.

trace(msg)¶: If debugging is on, prints the message, otherwise does nothing.

writeXML(ostream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)¶: Writes the object as an XML object into an output stream.

class esys.modellib.visualization.Visualization(**kwargs)¶

Bases: esys.escriptcore.modelframe.Model

Generic visualization Model

Variables:	t – current time (in) n – frame counter (in) dt – increment for output (in) filename – name of the output file (in)

__init__(**kwargs)¶

Initialisation of the visualisation model object

Parameters:	debug – Debugging flag

UNDEF_DT = 1e+300¶

checkLinkTargets(models, hash)¶: Returns a set of tuples (“<self>(<name>)”, <target model>) if the parameter <name> is linked to model <target model> but <target model> is not in the list of models. If a parameter is linked to another parameter set which is not in the hash list the parameter set is checked for its models. hash gives the call history.

declareParameter(**parameters)¶: Declares one or more new parameters and their initial value.

declareParameters(parameters)¶: Declares a set of parameters. parameters can be a list, a dictionary or a ParameterSet.

doFinalization()¶

Finalizes the time stepping.

This function may be overwritten.

doInitialPostprocessing()¶

Finalises the initialization iteration process. This method is not called in case of a restart.

This function may be overwritten.

doInitialStep()¶

Performs an iteration step in the initialization phase. This method is not called in case of a restart.

This function may be overwritten.

doInitialization()¶: does some kind of initialisation

doStep(dt)¶

Executes an iteration step at a time step.

dt is the currently used time step size.

This function may be overwritten.

doStepPostprocessing(dt)¶

Finalises the time step.

dt is the currently used time step size.

This function may be overwritten.

doStepPreprocessing(dt)¶

Sets up a time step of step size dt.

This function may be overwritten.

finalize()¶

Returns False if the time stepping is finalized.

This function may be overwritten.

classmethod fromDom(esysxml, node)¶

getAttributeObject(name)¶: Returns the object stored for attribute name.

getFrameCounter()¶: returns a frame counter

getFrameFileName()¶

getSafeTimeStepSize(dt)¶

returns new step size

Parameters:	dt (`float`) – last time step size used
Returns:	time step size that can savely be used
Return type:	`float`

hasAttribute(name)¶: Returns True if self has attribute name.

releaseParameters(name)¶: Removes parameter name from the parameters.

setUp()¶

Sets up the model.

This function may be overwritten.

showParameters()¶: Returns a description of the parameters.

terminateInitialIteration()¶: Returns True if iteration at the inital phase is terminated.

terminateIteration()¶: Returns True if iteration on a time step is terminated.

toDom(esysxml, node)¶: toDom method of Model class.

trace(msg)¶: If debugging is on, prints the message, otherwise does nothing.

writeFrame()¶: returns True if the time stamp for writing frame is reached.

writeXML(ostream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)¶: Writes the object as an XML object into an output stream.

class esys.modellib.visualization.WriteVTK(**kwargs)¶

Bases: esys.modellib.visualization.Visualization

Writes data into a VTK file.

The Model can handel up to 20 data sets that are written into a single file tagged with the given name. If no name is given and the data are defined by a Link the name of the target attribute is used as a tag.

Variables:

data0 – data set 0 to be written
name0 – name tag for data set 0
data1 – data set 1 to be written
name1 – name tag for data set 1
data2 – data set 2 to be written
name2 – name tag for data set 2
data3 – data set 3 to be written
name3 – name tag for data set 3
data4 – data set 4 to be written
name4 – name tag for data set 4
data5 – data set 5 to be written
name5 – name tag for data set 5
data6 – data set 6 to be written
name6 – name tag for data set 6
data7 – data set 7 to be written
name7 – name tag for data set 7
data8 – data set 8 to be written
name8 – name tag for data set 8
data9 – data set 9 to be written
name9 – name tag for data set 9
data10 – data set 10 to be written
name10 – name tag for data set 10
data11 – data set 11 to be written
name11 – name tag for data set 11
data12 – data set 12 to be written
name12 – name tag for data set 12
data13 – data set 13 to be written
name13 – name tag for data set 13
data14 – data set 14 to be written
name14 – name tag for data set 14
data15 – data set 15 to be written
name15 – name tag for data set 15
data16 – data set 16 to be written
name16 – name tag for data set 16
data17 – data set 17 to be written
name17 – name tag for data set 17
data18 – data set 18 to be written
name18 – name tag for data set 18
data19 – data set 19 to be written
name19 – name tag for data set 19

__init__(**kwargs)¶

Initialisation of the WriteVTK object

Parameters:	debug (`bool`) – debugging flag

UNDEF_DT = 1e+300¶

checkLinkTargets(models, hash)¶: Returns a set of tuples (“<self>(<name>)”, <target model>) if the parameter <name> is linked to model <target model> but <target model> is not in the list of models. If a parameter is linked to another parameter set which is not in the hash list the parameter set is checked for its models. hash gives the call history.

collectData()¶

declareParameter(**parameters)¶: Declares one or more new parameters and their initial value.

declareParameters(parameters)¶: Declares a set of parameters. parameters can be a list, a dictionary or a ParameterSet.

doFinalization()¶

Finalizes the time stepping.

This function may be overwritten.

doInitialPostprocessing()¶: writes vtk file at the end of initial iteration

doInitialStep()¶

Performs an iteration step in the initialization phase. This method is not called in case of a restart.

This function may be overwritten.

doInitialization()¶: does some kind of initialisation

doStep(dt)¶

Executes an iteration step at a time step.

dt is the currently used time step size.

This function may be overwritten.

doStepPostprocessing(dt)¶: writes vtk file at the end of time iteration

doStepPreprocessing(dt)¶

Sets up a time step of step size dt.

This function may be overwritten.

finalize()¶

Returns False if the time stepping is finalized.

This function may be overwritten.

classmethod fromDom(esysxml, node)¶

getAttributeObject(name)¶: Returns the object stored for attribute name.

getFrameCounter()¶: returns a frame counter

getFrameFileName()¶

getSafeTimeStepSize(dt)¶

returns new step size

Parameters:	dt (`float`) – last time step size used
Returns:	time step size that can savely be used
Return type:	`float`

hasAttribute(name)¶: Returns True if self has attribute name.

releaseParameters(name)¶: Removes parameter name from the parameters.

setUp()¶

Sets up the model.

This function may be overwritten.

showParameters()¶: Returns a description of the parameters.

terminateInitialIteration()¶: Returns True if iteration at the inital phase is terminated.

terminateIteration()¶: Returns True if iteration on a time step is terminated.

toDom(esysxml, node)¶: toDom method of Model class.

trace(msg)¶: If debugging is on, prints the message, otherwise does nothing.

writeFrame()¶: returns True if the time stamp for writing frame is reached.

writeXML(ostream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)¶: Writes the object as an XML object into an output stream.

Functions¶

esys.modellib.visualization.saveVTK(filename, domain=None, metadata='', metadata_schema=None, write_meshdata=False, time=0.0, cycle=0, **data)¶

Writes Data objects and their mesh to a file using the VTK XML file format.

Example:

temp=Scalar(..)
v=Vector(..)
saveVTK("solution.vtu", temperature=temp, velocity=v)

temp and v are written to “solution.vtu” where temp is named “temperature” and v is named “velocity”.

Meta tags, e.g. a timeStamp, can be added to the file, for instance:

tmp=Scalar(..)
v=Vector(..)
saveVTK("solution.vtu", temperature=tmp, velocity=v,
        metadata="<timeStamp>1.234</timeStamp>",
        metadata_schema={"gml":"http://www.opengis.net/gml"})

The argument metadata_schema allows the definition of name spaces with a schema used in the definition of meta tags.

Parameters:

filename (str) – name of the output file (‘.vtu’ is added if required)
domain (escript.Domain) – domain of the Data objects. If not specified, the domain of the given Data objects is used.
<name> – writes the assigned value to the VTK file using <name> as identifier
metadata (str) – additional XML meta data which are inserted into the VTK file. The meta data are marked by the tag <MetaData>.
metadata_schema (dict with metadata_schema[<namespace>]=<URI> to assign the scheme <URI> to the name space <namespace>.) – assigns schemas to namespaces which have been used to define meta data.
write_meshdata (bool) – whether to save mesh-related data such as element identifiers, ownership etc. This is mainly useful for debugging.
time (float) – the timestamp to save within the file, seperate to metadata
cycle (int) – the cycle (or timestep) of the data

Note:

All data objects have to be defined on the same domain. They may not be in the same FunctionSpace but not all combinations of FunctionSpace s can be written to a single VTK file. Typically, data on the boundary and on the interior cannot be mixed.

esys.modellib.visualization Package¶

Classes¶

Functions¶

Others¶

Packages¶

Table of Contents

param dataPointNo:

type dataPointNo:
	int
param value:
type value:	`float` or an object which acts like an array, `tuple` or `list`
warning:	Use of this operation is discouraged. It prevents some optimisations from operating.