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
-
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 inmask
will be copied fromother
-
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 processdataPointNo (int) – datapoint to access
-
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.]
-
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 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
- 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
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 ofDataConstant
- 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
-
promote
((Data)arg1) → None¶
-
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
orlist
-
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
orlist
- 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)¶ 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
andv
are written to “solution.vtu” wheretemp
is named “temperature” andv
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 theData
objects. If not specified, the domain of the givenData
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
withmetadata_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 metadatacycle (
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 ofFunctionSpace
s can be written to a single VTK file. Typically, data on the boundary and on the interior cannot be mixed.