esys.modellib.visualization Package

Classes

class esys.modellib.visualization.Data

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, (object)dpno) int :

Return tag number for the specified datapoint

Return type

int

Parameters

dpno (int) – datapoint number

getTupleForDataPoint((Data)arg1, (object)dataPointNo) object :
Returns

Value of the specified datapoint

Return type

tuple

Parameters

dataPointNo (int) – datapoint to access

getTupleForGlobalDataPoint((Data)arg1, (object)procNo, (object)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, (object)Amin, (object)Astep, (Data)B, (object)Bmin, (object)Bstep[, (object)undef=1e+50[, (object)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 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

param check_boundaries

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, (object)Amin, (object)Astep [, (object)undef=1e+50 [, (object)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, (object)check_boundaries) Data :

1D interpolation with non equally spaced points

nonuniformSlope((Data)arg1, (object)in, (object)out, (object)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, (object)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, (object)dataPointNo, (object)value) None

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

setValueOfDataPoint( (Data)arg1, (object)arg2, (object)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[, (object)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]

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)

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
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.

getSafeTimeStepSize(dt)

Returns a time step size which can be safely used.

dt gives the previously used step size.

This function may be overwritten.

setUp()

Sets up the model.

This function may be overwritten.

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.

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

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

doInitialization()

does some kind of initialisation

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

writeFrame()

returns True if the time stamp for writing frame is reached.

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

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

collectData()
doInitialPostprocessing()

writes vtk file at the end of initial iteration

doStepPostprocessing(dt)

writes vtk file at the end of time iteration

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.

Others

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