brief introduction to paraview dev - insa lyondavila/bbtk/software/new/doc/vtk... · load a le:...

Brief introduction to Paraview dev

Anna Puig Puig and Jordi Campos i Miralles

July 16, 2007

Anna Puig Puig and Jordi Campos i Miralles Brief introduction to Paraview dev

Contents I

Paraview

1 Introduction

2 Using the GUI

3 Using scripts

Internals

4 Architecture

5 Plugins


Contents II

Appendixes

6 Building

7 From VTK to Paraview

8 PV-Dump.py

9 References


IntroductionUsing the GUIUsing scripts

Part I

Overview



Overview

1 Introduction

2 Using the GUI

3 Using scripts



Paraview ApplicationExecution modesArchitecture overview

Introduction

1 IntroductionParaview ApplicationExecution modesArchitecture overview




Paraview

ParaView License - BSD style - source redistribution nomandatory

single-processor, multi-processor shared-memory and clusters.

structured and unstructured, time varying and static.




Paraview




Modes

Single-User: everything local.

Client-Server: remote server (rendering local or remote).

Client-Distributed Server: multiple remote servers MPI(rendering locally or in parallel).

Client-Distributed Data-Distributed Render: data serverscluster / multiple graphicsHW cluster

RenderWall: display can be tiled for a RenderWall or CAVE.




Architecture

Client

Server Manager

Data Srv. Render Srv.

Client: user interface → Server Manager.

Server Manager: layer between data/render servers and user interface. Runs ona single processor.

PVBatchScripts: access to Server Manager without GUI.



Using the GUI

2 Using the GUI



Using the GUI

Follow the paraview-head-example-english.pdf tutorial:

Load a �le: head.vtk

Skull extraction: isosurface density=1200

Changing the visual parameters

Clip the volume (obtain half volume)

Skin extraction: isosurface density=700

Get an slice

Create an animation (moving the slice position)



Python scriptingArchitecture - the Server ManagerPV Python ShellStand-alone scriptsSaving GUI status

Using scripts

3 Using scriptsPython scriptingArchitecture - the Server ManagerPV Python ShellStand-alone scriptsSaving GUI status




Python scripting

Python scripting: http://www.paraview.org/Wiki/ParaView:pvpython

Execution environments: import paraview

PV Python Shell: inside ParaView application.Stand-alone scripts: using pvpython interpreter (includes aserver manager initialization)

Server connection: connect to an existing data/render server(it may be local).

Proxies: creation/registration; to wrap VTK objects.

Render modules: choose render (or let automatic process).

Displays: choose how to display each object.


http://www.paraview.org/Wiki/ParaView:pvpython



Server Manager

vtkSMProxyManager = singleton to create/manage proxies.

Proxies(vtkSMProxy): placeholders of vtkObjects on theserver (SSObjs)

create SSObjsmantain references to SSObjs (vtkClientServerIDs).mantain a copy of the state of SSObjs. using properties.

Properties(vtkSMProperty): interface to SSobjs.

Domains(vtkSMDomain): possible values Properties can have.

XML is parsed from a �le or string to indicate proxies andproperties creation/con�guration (see Servers/ServerManager/Resources/*.xml).




Python Shell

Menu - Tools - Python Shell:

Environment: automatically imported "paraview" pythonmodule.

Connection to PV: paraview.ActiveConnection

Proxy Manager: paraview.pyProxyManager()

Introspection:

Print: useful object information.Iterators: ex. groups in a proxy collection. . .ListProperties: list proxy available properties.dir(): all symbols associated.




Example: List all proxies I

(press back arrow after pasting code into the PV-Python-Shell before pushing Enter)

# PV -XX -PVshell -ListProxies.pyproxies = paraview.pyProxyManager (). GetProxiesOnConnection(

paraview.ActiveConnection )

# Iteratorfor group in proxies: # - groups

print "* ", group

for name in proxies[group ]: # -- proxiesprint " - ", name , " ( ", proxies[group ][name]. SMProxy.GetXMLGroup (), " )"

print




Example: Properties I

(First: start PV, load some data, and create a �rst Contour �lter; Nest: execute line by line and

interpret output)

# PV -XX -PVshell -ListProxies.pyproxies = paraview.pyProxyManager (). GetProxiesOnConnection(

paraview.ActiveConnection )

contour = proxies["sources"]["Contour1"] # Get contour

print contour.ListProperties () # Get propertiesprint contour.GetContourValues ()

contour.SetContourValues( 700. ) # Set propertiescontour.UpdateVTKObjects ()

print dir( contour ) # Internalsprint dir( contour.SMProxy )print contour.SMProxy.GetVTKClassName ()print contour.SMProxy.GetClassName ()




Stand-alone scripts

Interpreter: pvpython

Imports: import paraview

Connection: paraview.ActiveConnection = paraview.Connect()

Sources: always register in "sources", updateVTKObjreader = paraview.CreateProxy("sources", "legacyreader", "sources")reader.SetFileName("ironProt.vtk") ; reader.UpdateVTKObjects()

thresh = paraview.CreateProxy("filters", "Threshold", "sources")thresh.SetInput( reader ) ; thresh.SetThresholdBetween(80, 255)thresh.UpdateVTKObjects()

Window: renderW = paraview.CreateRenderWindow()

How to display: create one display per "actor"disp = paraview.CreateDisplay(trifil, renderW)disp.SetOpacity( 0.5 )disp.SetRepresentation( 1 ) # 0=Points, 1=Wireframe, 2=Surface, 3=Outline, 4=Voldisp.UpdateVTKObjects()

Non-interactive rendering:renderW.ResetCamera() ; renderW.StillRender() ; raw_input("Push Enter to finish")renderM.WriteImage("screenshot.png", "vtkPNGWriter")




Example: Sphere - screenshot




Example:Sphere - Stand-alone script I

# (use pvpython to execute) PV -01- Sphere.pyimport paraview

paraview.ActiveConnection = paraview.Connect () # Create a built -in server

source = paraview.CreateProxy("sources", # Create & register a sphere"SphereSource", "sources")

renderW = paraview.CreateRenderWindow () # Create a renderWin module

display = paraview.CreateDisplay(source ,renderW) # Create a display

renderW.ResetCamera ()renderW.StillRender () # Renders at full resolutionraw_input("Enter to finish")




Example: Displays - screenshot




Example: Displays I

# (use pvpython to execute) PV -04- Displays.pyimport paraviewparaview.ActiveConnection = paraview.Connect () # Create a built -in server

renderW = paraview.CreateRenderWindow () # RenderWindow

source1 = paraview.CreateProxy("sources", # Sphere: source"SphereSource", "sources")

disp1 = paraview.CreateDisplay(source1 , renderW) # Sphere: displaydisp1.SetRepresentation( 1 ) ; disp1.SetOpacity( 0.5 )disp1.SetScale( 0.8, 1.2, 1. ) ; disp1.UpdateVTKObjects ()

source2 = paraview.CreateProxy("sources", # Cone: source"ConeSource", "sources")

disp2 = paraview.CreateDisplay(source2 , renderW) # Cone: displaydisp2.SetRepresentation( 2 ) ; disp2.SetColor( 1, 1, 0 )disp2.SetPosition( -0.25, 0, 0 ) ; disp2.SetOrientation( 0, 0, 20 )disp2.UpdateVTKObjects ()

renderW.ResetCamera () ; renderW.StillRender ()raw_input("Enter to finish")




Generating XML status

Menu - File - Save state(use a text editor to check the XML created �le)

Easy to understand / update.

Useful to create unit-tests.

BUT: you can't create a batch script.




Generating scripts

PV 2.x: was able to generate Tcl scripts

PV 3.0: is not able to generate scripts by defaultPV-Dump.py: self-created script to generate python codeusing introspection (the code is listed in Appendixes):

Menu - Tools - Python Shell - Run script

locate and choose PV-Dump.py

help(Dump): help about Dump tools

Dump.proxyList(): list current proxies

Dump.allToPython("script.py"): create script




Example: Apply masks to an original dataset

1 Load teddy-64.bin (643)

2 Load teddy-64-seg1-mascara.bin with ScalarArrayName="Mask"

3 Filter: Append Attributes (having both data sets selected)

4 Filter: Calculator with formula "ImageFile*Mask/255"

5 Menu - Tools - Python Shell - Run script: PV-Dump.py

6 Generate the script with Dump.allToPython("script.py")7 Test the generated script:

as a stand-alone script: pvpython script.py

inside PV-GUI: start PV and Run script from the Python

Shell

8 Modify the generated script:to allow to apply all the masks to the original data set.to save only the volume of interest of each mask.




Example: Apply masks to an original dataset I

# (use pvpython to execute) PV -XX -TeddyMasks.pyimport sysimport paraviewif paraview.ActiveConnection == None : CONSOLE = Trueelse : CONSOLE = False

def main ():if CONSOLE: # INI: Conn. and RenderM

paraview.ActiveConnection = paraview.Connect ()renderM = paraview.CreateRenderWindow ()

else:renders = paraview.pyProxyManager (). GetProxiesInGroup("multirendermodule",

paraview.ActiveConnection)renderM = renders.values ()[0]. GetRenderModules ()[0]

for i in [ 1, 4, 6, 8, 10, 12 ]: # Extract ROIsextractROI( i, ".", "teddy -64. bin", "teddy -64-seg"+str(i)+"-mascara.bin",

"teddy -64-seg"+str(i)+"-extracted.vti", renderM )

if CONSOLE: # END: renderrenderM.ResetCamera ()renderM.StillRender ()import time ; time.sleep (2)




Example: Apply masks to an original dataset II

def extractROI(idx , workingDir , dataFile , maskFile , outFile , renderM ):data = paraview.CreateProxy("sources", # Data

"ImageReader", "sources", dataFile )data.SetFilePrefix ( workingDir + "/" + dataFile )data.SetDataScalarType (3) ; data.SetScalarArrayName ("ImageFile")data.SetFileDimensionality (3) ; data.SetNumberOfScalarComponents (1)data.SetDataOrigin (0, 0, 0) ; data.SetDataSpacing (1, 1, 1)data.SetDataExtent (0, 63, 0, 63, 0, 63)data.UpdateVTKObjects ()

mask = paraview.CreateProxy("sources", # Mask"ImageReader", "sources", maskFile)

mask.SetFilePrefix ( workingDir + "/" + maskFile )mask.SetDataScalarType (3) ; mask.SetScalarArrayName ("Mask")mask.SetFileDimensionality (3) ; mask.SetNumberOfScalarComponents (1)mask.SetDataOrigin (0, 0, 0) ; mask.SetDataSpacing (1, 1, 1)mask.SetDataExtent (0, 63, 0, 63, 0, 63)mask.UpdateVTKObjects ()

append = paraview.CreateProxy("filters", # Append"AppendAttributes", "sources", "append"+dataFile)

append.AddToInput( data ) ; append.AddToInput( mask )append.UpdateVTKObjects ()

calc = paraview.CreateProxy("filters", # Apply mask"Calculator", "sources", "calc"+dataFile)




Example: Apply masks to an original dataset III

calc.SetInput( append )calc.SetAddScalarVariable( "ImageFile", "ImageFile", "0", "Mask", "Mask", "0" )if idx != 6: calc.SetFunction( "ImageFile *(Mask /255)" ) # normalelse: calc.SetFunction( "ImageFile *( abs(Mask -255) / 255)" ) # inversecalc.SetAttributeMode( 1 ) ; calc.SetCoordinateResults( 0 )calc.SetReplaceInvalidValues( 1 ) ; calc.SetReplacementValue( 0 )calc.SetResultArrayName( "Result" )calc.UpdateVTKObjects ()

thresh = paraview.CreateProxy("filters", # ROI"Threshold", "sources", "thresh"+dataFile)

thresh.SetInput( calc ) ; thresh.SetAllScalars( 1 )thresh.SetSelectInputScalars( "Result" ) ; thresh.SetThresholdBetween( 1, 42 )thresh.UpdateVTKObjects ()

extract = paraview.CreateProxy("filters", # ROIextraction"ExtractGrid", "sources", "extract"+dataFile)

extract.SetInput( calc )b = thresh.SMProxy.GetDataInformation (). GetBounds () # - get ROI boundsextract.SetVOI( int(b[0]),int(b[1]),int(b[2]),int(b[3]),int(b[4]),int(b[5]) )extract.SetSampleRateI (1); extract.SetSampleRateJ (1); extract.SetSampleRateK (1)extract.SetIncludeBoundary( 1 )extract.UpdateVTKObjects ()

writer = paraview.CreateProxy("writers", # Writer"XMLImageDataWriter", "sources", "writer"+dataFile)




Example: Apply masks to an original dataset IV

writer.SetInput( extract )writer.SetFileName( workingDir + "/" + outFile )writer.SetDataMode( 1 ) # 0=Ascii 1= Binary 2= Appendwriter.UpdateVTKObjects () ; writer.SMProxy.UpdatePipeline ()

main()


ArchitecturePlugins

Part II

Internals


ArchitecturePlugins

Internals

4 Architecture

5 Plugins


ArchitecturePlugins

Proxies, Properties and DomainsDisplays and Render ModulesOther proxies

Architecture

4 ArchitectureProxies, Properties and DomainsDisplays and Render ModulesOther proxies


ArchitecturePlugins


Proxies

Proxy = wrapper of VTK Objects

Example:<ServerManagerConfiguration>

<ProxyGroup name="filters"><SourceProxy name="MyFilter" class="vtkMyFilter" label="MyFilter"></SourceProxy>

</ProxyGroup></ServerManagerConfiguration>

Creation: vtkSMProxyManager::NewProxy(group, name)

Storage: map< string, map<string, vtkSmartPointer< vtkPVXMLElement > > >

RegisterProxy/UnRegisterProxy: to pass the proxymanagement from user code to the Proxy Manager.


ArchitecturePlugins


Properties

Property = (method + arguments) of a VTK Object

Types: vtkSMProperty (no args),vtkSMIntVectorProperty (vector of ints),vtkSMStringVectorProperty (vector of strings, ints anddoubles) . . .

Example:<SourceProxy name="SphereSource" class="vtkSphereSource" label="Sphere">

<DoubleVectorProperty name="Radius" command="SetRadius" number_of_elements="1"animateable="1" default_values="0.5" >

<DoubleRangeDomain name="range" min="0"/></DoubleVectorProperty>...

</SourceProxy>

AddProperty/GetProperty: accessors.

UpdateVTKObjects: apply all modi�ed properties.


ArchitecturePlugins


Domains

Domain = domain of a property (possible values)

Literals:<DoubleVectorProperty name="Radius" ...>

<DoubleRangeDomain name="range" min="0"/></DoubleVectorProperty>

From other properties:<IntVectorProperty name="TimeStepRangeInfo" ...>...</IntVectorProperty><IntVectorProperty name="TimeStep" ...>

<IntRangeDomain name="range"><RequiredProperties>

<Property name="TimeStepRangeInfo" function="Range"/></RequiredProperties>

</IntRangeDomain></IntVectorProperty>

AddProperty/GetProperty: accessors.

UpdateVTKObjects: apply all modi�ed properties.


ArchitecturePlugins


Example: Proxies I

#!/usr/local/bin/pvpython# PV -02- Proxies.pyimport paraview


manager = paraview.pyProxyManager () # Access to Proxy Manager

for defin in manager.definition_iter("sources"): # Get all available proxiesprint "%s : %s" % (defin["group"], defin["key"])

print manager.ListProperties("sources", # Get property names"SphereSource") # w/o creating proxy

proxy = paraview.CreateProxy("sources", # Create a proxy"SphereSource", "sources")

proxy.SetThetaResolution (20) # Calling accessorsproxy.UpdateVTKObjects () # Apply changes

print proxy.ListProperties () # Get property names

for property in proxy: print property # List all Properties

print proxy.GetDocumentation (). GetShortHelp () # Obtain documentation


ArchitecturePlugins


Example: Proxies II

print manager.GetProxiesInGroup("sources") # Get current proxies/cnnction

for prxy in manager: print prxy.GetXMLName () # Iterate on current prxyies


ArchitecturePlugins


Displays and Render Modules

vtkSMProxy

...

vtkSMDisplayProxy

...

vtkSMRenderModuleProxy


ArchitecturePlugins


Displays

Display = everyting required to render an object.

Consumer

...

Axes

DataObj LOD Comp Multi IceT


ArchitecturePlugins


Example: Displays I

# (use pvpython to execute) PV -04- Displays.pyimport paraviewparaview.ActiveConnection = paraview.Connect () # Create a built -in server

renderW = paraview.CreateRenderWindow () # RenderWindow

source1 = paraview.CreateProxy("sources", # Sphere: source"SphereSource", "sources")

disp1 = paraview.CreateDisplay(source1 , renderW) # Sphere: displaydisp1.SetRepresentation( 1 ) ; disp1.SetOpacity( 0.5 )disp1.SetScale( 0.8, 1.2, 1. ) ; disp1.UpdateVTKObjects ()

source2 = paraview.CreateProxy("sources", # Cone: source"ConeSource", "sources")

disp2 = paraview.CreateDisplay(source2 , renderW) # Cone: displaydisp2.SetRepresentation( 2 ) ; disp2.SetColor( 1, 1, 0 )disp2.SetPosition( -0.25, 0, 0 ) ; disp2.SetOrientation( 0, 0, 20 )disp2.UpdateVTKObjects ()

renderW.ResetCamera () ; renderW.StillRender ()raw_input("Enter to finish")


ArchitecturePlugins


Render Modules

Render Module = all required to display and render a dataset. PVmay automatically choose one of them.

Simple LOD Compos.

MPI

IceTDesk IceT

Cave

LOD (local), IceTDesk (cli/srv), IceT (tiled)[IceT: tiled distributed rendering librfary] MPI HAS DISAPEARED?


ArchitecturePlugins


Example: Render Modules I

TODO

#!/usr/local/bin/pvpython# PV -03- RenderM.pyimport paraview


source1 = paraview.CreateProxy("sources", # Sources"SphereSource", "sources")

renderW = paraview.CreateRenderWindow () # RenderWindows

disp1 = paraview.CreateDisplay(source1 , renderW) # Displays

# TODO: play with camera parameters

renderW.ResetCamera ()renderW.StillRender ()#renderW.WriteImage ("PV -03- RenderM.png", "vtkPNGWriter ")raw_input("Enter to finish")

# I'M INTERESTED IN CONNECTING TO A RUNNING PARAVIEW (LOCAL IN MY MACHINE),# CREATE THE SCENE AND AFTERWARDS LET THE USER INTERACT , IS IT POSSIBLE ???


ArchitecturePlugins


Other proxies

There are proxies for the other VTK objects:http://www.paraview.org/Wiki/ProxyXMLName

sources, �lters, readers/writers

mappers, renderers, interactors

axes, piecewise_functions, 3d_widgets...


http://www.paraview.org/Wiki/ProxyXMLName

ArchitecturePlugins


Example: Other proxies I

#!/usr/local/bin/pvpython# PV -05- OtherProxies.pyimport paraview


reader = paraview.CreateProxy("sources", # Reader"XMLImageDataReader", "sources")

reader.SetFileName("head.vti") ; reader.UpdateVTKObjects ()

filter = paraview.CreateProxy("filters", # Filter"Contour", "filters")

filter.SetInput( reader )filter.SetContourValues( 1500. ) ; filter.UpdateVTKObjects ()

axes = paraview.CreateProxy("sources", # Axes"Axes", "sources")

axes.SetOrigin( 100, 100, 100 ) ; axes.SetScaleFactor( 100 )axes.SetSymmetric( 0 ) ; axes.UpdateVTKObjects ()

light = paraview.CreateProxy("lights", # Lights"Light", "lights")

light.SetLightAmbientColor( 0, 1, 0 )light.SetLightIntensity( 1. )light.SetLightType( 2 ) # HOW USING VTK_LIGHT_TYPE_CAMERA_LIGHT CONSTANT ???


ArchitecturePlugins


Example: Other proxies II

light.SetLightSwitch( 1 )#light.SetFocalPoint( 0, 0, 0) # FAILS , HOW SHOULD IT BE DONE ???#light.SetPosition( 1000, 0, 1000 ) # FAILS , HOW SHOULD IT BE DONE ???light.UpdateVTKObjects ()

renderW = paraview.CreateRenderWindow () # Render Windowprint renderW.ListProperties ()# HOW CAN I ADD LIGHT ???

display = paraview.CreateDisplay(filter , renderW) # Displaysdisplay = paraview.CreateDisplay(axes , renderW)

renderW.ResetCamera ()renderW.StillRender ()raw_input("Enter to finish")

writer = paraview.CreateProxy("writers", # Writer"XMLImageDataWriter", "writers")

writer.SetInput( filter )writer.SetFileName("skull.vti")writer.UpdateVTKObjects ()writer.InvokeCommand("Write")# IT DOES NOT WORK , WHY ??? (I also try with XMLPolyDataWriter)


ArchitecturePlugins

VTK objectsQt widgetsToolbarsViews

Plugins

5 PluginsVTK objectsQt widgetsToolbarsViews


ArchitecturePlugins


Plugins

Plugins: http://www.paraview.org/Wiki/Plugin_HowTo

Extending:

VTK objects: readers, writers, �lters. . .Qt widgets:Toolbars:Views: in addition to the existing render view, line chart andbar chart.

May contain both client and server extensions and work if theappropriate client side libraries are on the server.

Use:

Manually: Menu Tools/Plugin Manager.At startup: PV_PLUGIN_PATH = list of semi-colon separateddirectories where plugins exists.


http://www.paraview.org/Wiki/Plugin_HowTo

ArchitecturePlugins


VTK objects

CMakeLists.txt:FIND_PACKAGE(ParaView REQUIRED)INCLUDE($PARAVIEW_USE_FILE) # $ADD_PARAVIEW_PLUGIN(SMMyPluginFilter "1.0"

SERVER_MANAGER_XML MyPluginFilter.xmlSERVER_MANAGER_SOURCES vtkMyPluginFilter.cxx)

xml: Proxy declaration.<ServerManagerConfiguration>

<ProxyGroup name="filters"><SourceProxy name="MyPluginFilter" class="vtkMyPluginFilter" label="MyFilter">

<Documentation long_help="Long" short_help="Short"> Doc</Documentation><InputProperty name="Input" command="SetInputConnection">...

</SourceProxy></ProxyGroup>

</ServerManagerConfiguration>

sources: normal vtk *.h and *.cxxbuild:ccmake .

ParaView_DIR /opt/local/fonts/ParaView3-bin (dir with ParaViewConfig.cmake)EXECUTABLE_OUTPUT_PATH (your local output dir)LIBRARY_OUTPUT_PATH (your local output dir)

make install

(see cpp/PV-01-PluginFilter)


ArchitecturePlugins


GUI development

XML: TODO

Qt: TODOQtDesigner: can be used to view/update UIaptitude install qt4-designer # and use QtDesignerdesigner-qt4 Qt/Components/Resources/UI/pqAnimationPanel.ui


ArchitecturePlugins


Toolbars

TODO


ArchitecturePlugins


Views

TODO


BuildingFrom VTK to Paraview

PV-Dump.pyReferences

Part III

Appendixes




Appendixes

6 Building


8 PV-Dump.py

9 References




Building

6 Building




PV Build I

cvs -d :pserver:[email protected]:/cvsroot/ParaView3 login # Empty passwordcvs -d :pserver:[email protected]:/cvsroot/ParaView3 co -r ParaView-3-0 ParaView3

mkdir ParaView3-bin ; cd ParaView3-bin # Out-source built

aptitude install libqt4-dev python2.5-dev

ccmake ../Paraview3BUILD_SHARED_LIBS ONCMAKE_BUILD_TYPE DebugPARAVIEW_ENABLE_PYTHON ONVTK_USE_RPATH ON

makemake install

paraview # Installation finished

cmake -GKDevelop3 ../ParaView3 # You can create a KDevelop projectkdevelop ParaView.kdevelop

aptitude install qt4-designer # and use QtDesignerdesigner-qt4 Qt/Components/Resources/UI/pqAnimationPanel.ui

aptitude install tk8.4-dev # To build vtkpython




PV Build II

cd VTK # (to run 'VTK only' examples)ccmake ../../Paraview3/VTK # (not required for PVpython ex)

BUILD_SHARED_LIBS ONVTK_WRAP_PYTHON ON

makemake install

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib/:/usr/local/lib/paraview-3.0/export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python2.4/site-packages/

vtkpython <any *.py using vtk> # Installation finished




From VTK to Paraview





From VTK to Paraview

VTK Paraview

readers, writers, �lters use "sources"

mappers, actors use "displays"

camera, lights use "render module"(When a source is created using the GUI, its corresponding displayis directly created also. Thus, not only the last pipeline step isrendered, but all the intermmediate steps can be rendered.)




PV-Dump.py

8 PV-Dump.py




PV-Dump.py

PV-Dump.py = self-created script to generate python code.How to dump a PV session to a script:

1 Start Paraview (PV)2 Use the GUI to build the desired pipeline3 Load PV-Dump.py: Menu - Tools - Python Shell - Run script4 Dump session to a script: Dump.allToPython("script.py")

You can use the resulting script:

to learn how PV builds the pipeline.

as an stand-alone script (pvpython script.py)

to restore the session (it works also from inside PV-GUI).

to build "batch" scripts: add loops, get data from onepipeline step to modify another step, access your own �les. . .

(see an example in the Overview part)Anna Puig Puig and Jordi Campos i Miralles Brief introduction to Paraview dev



PV-Dump.py I

# PV -Dump.py# Script to be run inside Paraview:# Menu Tools -> Python Shell , Run Script# Afterwards try using "help(Dump)", "Dump.proxyList ()" ...import re

class Dump:"""Collection of 'static methods ' useful to inspect a running Paraviewpipeline (dumping information to screen or Python code)."""

@staticmethoddef proxyList ():

"""Prints current proxies groups and names"""proxies = Dump.__getProxies ()for group in proxies:

print "* ", groupfor name in proxies[group ]:

print " - ", name , " ( ", proxies[group ][name]. SMProxy.GetXMLGroup (), " )"print

@staticmethoddef allToPython( fileName=None ):

"""Prints the python code necessary to recreate the current PV session.If a file name is provided , it is save into the file."""import sys




PV-Dump.py II

if fileName:stdoutOrig = sys.stdoutfile = open( fileName , 'w')sys.stdout = file

Dump.__scriptStart ()Dump.proxiesToPython ()Dump.__scriptEnd ()

if fileName:sys.stdout = stdoutOrigfile.close ()

@staticmethoddef proxiesToPython( includeAll=False ):

"""Prints python code to create the current proxies.By default some PV infrastructure proxies are not printed ,but if includeAll is True all of them are printed."""proxies = Dump.__getProxies ()

order = Dump.__orderProxies( proxies ) # Get proxies# ordered by dependencies among them

for level in order:for item in level:




PV-Dump.py III

(group , name) = item.split(':') # Iterate on them

wrapName = proxies[group ][name]. SMProxy.GetXMLName ()

if includeAll or wrapName not in Dump.__HIDDENPROXIES: # Avoid defaultsDump.proxyToPython( group , name , Dump.__niceLabel(name)) # Dump code

print

@staticmethoddef proxyToPython(group , name , varName='proxy '):

"""Prints the python code necessary to create and setup the given proxy ,using varName as the variable identifier"""proxies = Dump.__getProxies ()proxy = proxies[group ][name]wrapGroup = proxy.SMProxy.GetXMLGroup ()wrapName = proxy.SMProxy.GetXMLName ()

print ' '*54, "# ", varName # Code: createif wrapName == "LODDisplay": # - display proxy

dispInput = Dump.__niceLabel( Dump.__proxyIdLabel( proxy.GetInput ()[0] ) )print varName +' = paraview.CreateDisplay(' \

+ dispInput +', renderM)'elif wrapName == "LODRenderModule": # - render proxy

varName = "renderM"else: # - other proxies




PV-Dump.py IV

print varName +' = paraview.CreateProxy ("' \+ wrapGroup +'", "'+ wrapName +'", "' \+ group +'", "'+ name +'")'

patternName = re.compile(' *XMLName: *(.*) ')patternValues = re.compile(' *Values: *(.*) ')patternNum = re.compile('^[ -+]?[0 -9.]+$')patternHex = re.compile('^0x[0-9a-f]+$')patternBadProp= re.compile('LightK \:| Displays|InteractorStyle ')for prop in proxy: # For each property

match = patternName.search( str(prop) )propName = match.groups ()[0]

match = patternValues.search( str(prop) ) # Get property.Valuesif match:

values = match.groups ()[0]valuesArray = values.strip (). split(' ')

if patternNum.match( valuesArray [0] ): # If numeric: no quotevaluesList = ', '.join( valuesArray )

elif patternHex.match( valuesArray [0] ): # If hex: fetch objectvaluesArray = proxy.__getattr__("Get"+propName )()valuesList = ', '.join( Dump.__niceLabel( Dump.__proxyIdLabel(p) )

for p in valuesArray)




PV-Dump.py V

else: # If alpha: quotevaluesList = ', '.join('"' + p + '"' for p in valuesArray)

# Code: set valueif not patternBadProp.search( propName ) and \

valuesList != "none" and \valuesList != '""':

print varName +'.Set'+ propName +'( '+ valuesList +' )'else: # Code: comment

print '# '+ varName +'.Set'+ propName +'( '+ valuesList +' )'#else:# print '# '+ varName +'.'+ propName +': no match for Values '

print varName +'.UpdateVTKObjects ()'print

@staticmethoddef getProxy( group , name ):

"""Return the proxy group:name"""proxies = Dump.__getProxies ()return proxies[group ][name]

# Private -----------------------------------------------




PV-Dump.py VI

__HIDDENPROXIES = [ "Manipulators", "InteractorStyle", "TrackballZoom","PVAnimationScene", "TimeKeeper", "ElementInspectorView","MultiViewRenderModule" ]

@staticmethoddef __getProxies ():

"""Returns the list of proxies in the current connection"""proxies = paraview.pyProxyManager (). GetProxiesOnConnection( \

paraview.ActiveConnection )return proxies

@staticmethoddef __orderProxies( proxies ):

"""Returns an array , where each entry contains the names of the proxies thatdepend on the previous array entry."""patternName = re.compile(' *XMLName: *(.*) ')patternValues = re.compile(' *Values: *(.*) ')patternHex = re.compile('^0x[0-9a-f]+$')pmanager = paraview.pyProxyManager ()

dependencies = {} # COLLECT DEPSfor group in proxies: # For each proxy

for name in proxies[group ]:dependencies[group+':'+name] = {} # Init its depend.proxy = proxies[group ][name]




PV-Dump.py VII

for prop in proxy:match = patternName.search( str(prop) )propName = match.groups ()[0]match = patternValues.search( str(prop) ) # Check prop. valuesif match:

values = match.groups ()[0]valuesArray = values.strip (). split(' ')

if patternHex.match( valuesArray [0] ): # If memory addressvaluesArray = proxy.__getattr__("Get"+propName )()for mother in valuesArray:

motherProxyVTK = mother.SMProxy

for motherGroup in proxies: # Find proxy by addrmotherName= pmanager.IsProxyInGroup( motherProxyVTK , motherGroup )if motherName:

dependencies[group+':'+name][ motherGroup+':'+motherName ]=1

order = [] ; currentLevel = [] ; previousLevel = [] # ORDER DEPS

for proxy in pmanager.GetProxiesInGroup('view_modules ', # Start by Viewsparaview.ActiveConnection ):

previousLevel.append( 'view_modules:'+ proxy )




PV-Dump.py VIII

renders = pmanager.GetProxiesInGroup("multirendermodule", # add Renderersparaview.ActiveConnection)

for renderM in renders.keys ():previousLevel.append( 'multirendermodule:'+renderM )

order.append( previousLevel )

while len( previousLevel ) > 0: # Follow depend.

for item in previousLevel:currentLevel.extend( dependencies[ item ].keys() )

if len(currentLevel) > 0 :order.append( currentLevel )

previousLevel = [] ; previousLevel.extend( currentLevel )currentLevel = []

order.reverse () # First pxs w/o deps

uniqueOrder = [] ; alreadyDeclared = {} # Remove duplicatesfor level in order:

newLevel = []for item in level:

if not alreadyDeclared.get( item ):alreadyDeclared[ item ] = True




PV-Dump.py IX

newLevel.append( item )

uniqueOrder.append( newLevel )

return uniqueOrder

@staticmethoddef __niceLabel( label ):

"""Returns a string that can be used as var name(starting by a letter , without .-_, ...)"""if not label: return "none"

label = label.replace('.', '') # drop .-_label = label.replace('-', '')label = label.replace('_', '')

if re.compile('[A-z]1').match( label [-2:] ):label = label [0: -1] # drop suffix '1'

if re.compile('^[0 -9]').match( label ):label = 'v' + label # add preffix when starts by number

label = label [0]. lower () + label [1:] # lower 1st char

return label




PV-Dump.py X

@staticmethoddef __proxyIdLabel( proxy ):

"""Returns the given proxy 's PV displayed name"""proxyVTK = proxy.SMProxypmanager = paraview.pyProxyManager ()proxies = Dump.__getProxies ()for group in proxies:

idLabel = pmanager.IsProxyInGroup( proxyVTK , group )if idLabel:

return idLabelreturn None

@staticmethoddef __scriptStart ():

print '#!/ usr/local/bin/pvpython 'print '# <script >.py'print 'import paraview 'print 'if paraview.ActiveConnection == None : CONSOLE = True'print 'else : CONSOLE = False 'print 'if CONSOLE: # init Conn and RenderM 'print ' paraview.ActiveConnection = paraview.Connect ()'print ' renderM = paraview.CreateRenderWindow ()'print 'else:'print ' renders = paraview.pyProxyManager (). GetProxiesInGroup (" multirendermodule",'




PV-Dump.py XI

print ' paraview.ActiveConnection)'print ' renderM = renders.values ()[0]. GetRenderModules ()[0] 'print

@staticmethoddef __scriptEnd ():

printprint 'if CONSOLE:'print ' renderM.ResetCamera ()'print ' renderM.StillRender ()'print ' raw_input ("Enter to finish ")'print ' #import time ; time.sleep (2)'printprint '#renderM.WriteImage (" screenshot.png", "vtkPNGWriter ")'




Example: script generated by PV-Dump.py I

# (use pvpython to execute) PV -06- FrogContourScreenshot.pyimport paraviewif paraview.ActiveConnection == None : CONSOLE = Trueelse : CONSOLE = Falseif CONSOLE: # init Conn and RenderM

paraview.ActiveConnection = paraview.Connect ()renderM = paraview.CreateRenderWindow ()

else:renders = paraview.pyProxyManager (). GetProxiesInGroup("multirendermodule",

paraview.ActiveConnection)renderM = renders.values ()[0]. GetRenderModules ()[0]

# sourcesource = paraview.CreateProxy("sources", "legacyreader", "sources", "frog.vtk")source.SetFileName( "frog.vtk" )source.UpdateVTKObjects ()

# scalarOpacityFunctionscalarOpacityFunction = paraview.CreateProxy("piecewise_functions",

"PiecewiseFunction", "pq_helper_proxies .77", "ScalarOpacityFunction")scalarOpacityFunction.SetPoints( 0, 0, 1, 1 )scalarOpacityFunction.UpdateVTKObjects ()

# contourcontour = paraview.CreateProxy("filters", "Contour", "sources", "Contour1")contour.SetInput( source )contour.SetComputeGradients( 0 )contour.SetComputeNormals( 1 )




Example: script generated by PV-Dump.py II

contour.SetComputeScalars( 0 )contour.SetContourValues( 107 )contour.SetSelectInputScalars( "ImageFile" )contour.UpdateVTKObjects ()

# dispdisp = paraview.CreateDisplay(contour , renderM)disp.SetInput( contour )disp.SetVisibility( 1 )disp.SetOpacity( 1 )disp.SetColorMode( 1 )disp.SetColor( 1, 1, 1 )disp.SetDiffuseColor( 1, 1, 1 )disp.SetAmbientColor( 1, 1, 1 )disp.SetMapScalars( 1 )disp.UpdateVTKObjects ()

# RenderrenderM.SetBackground( 0.329412 , 0.34902 , 0.427451 )renderM.SetCameraFocalPoint( 130.57 , 115.332 , 36.0827 )renderM.SetCameraFocalPointInfo( 130.57 , 115.332 , 36.0827 )renderM.SetCameraParallelProjection( 0 )renderM.SetCameraPosition( 386.84 , 502.75 , -398.694 )renderM.SetCameraPositionInfo( 386.84 , 502.75 , -398.694 )renderM.SetCameraViewAngle( 30 )renderM.SetCameraViewUp( -0.285638 , -0.625687 , -0.725897 )renderM.SetCameraViewUpInfo( -0.285638 , -0.625687 , -0.725897 )renderM.UpdateVTKObjects ()




Example: script generated by PV-Dump.py III

if CONSOLE:renderM.ResetCamera ()renderM.StillRender ()raw_input("Enter to finish")#import time ; time.sleep (2)

renderM.WriteImage("screenshot.png", "vtkPNGWriter")




References

9 References




References I

Paraview

Paraview Guide:http://www.kitware.com/products/paraviewguide.html

KW Newsletter:http://www.kitware.com/products/newsletter.html

PV Doc:

User: ParaView3/Documentation/GUIOverview.htmlDeveloper: cd Utilities/Doxygen/ ; make ; source

doc_makeall.sh ; firefox

Utilities/Doxygen/doc/html IS THERE A BETTER WAYTO CREATE PV-Doxygen?

PVpython:http://www.paraview.org/Wiki/ParaView:pvpython


http://www.kitware.com/products/paraviewguide.html

http://www.kitware.com/products/newsletter.html

http://www.paraview.org/Wiki/ParaView:pvpython



References II

VTK

VTK User's Guide:http://www.kitware.com/products/vtkguide.html

VTKbook: http://www.bioimagesuite.org/vtkbook/

KW Newsletter:http://www.kitware.com/products/newsletter.html


http://www.kitware.com/products/vtkguide.html

http://www.bioimagesuite.org/vtkbook/

http://www.kitware.com/products/newsletter.html

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