[Paraview-developers] [EXTERNAL] Re: Time-varying data reader
Sebastien Jourdain
sebastien.jourdain at kitware.com
Fri Sep 7 19:55:43 EDT 2012
You are missing that part in RequestData
// Create an ITK reader and connect it to a Connector to get VTK output
// ------------------------------------------------------------
--------
this->reader->SetFileName(FileName);
this->connector->SetInput(reader->GetOutput());
this->connector->Update();
vtkImageData *imageData = this->connector->GetOutput();
// ------------------------------------------------------------
--------
On Fri, Sep 7, 2012 at 4:31 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>wrote:
> I am not sure how to check the first file's name.
> My reader code is not very long, so I paste it below:
>
> BioFormatsReader::BioFormatsReader()
> {
> this->FileName = NULL;
> this->SetNumberOfInputPorts(0);
> this->SetNumberOfOutputPorts(1);
>
> this->reader = ReaderType::New();
> this->connector = ConnectorType::New();
>
> }
>
> BioFormatsReader::~BioFormatsReader()
> {
> if( this->reader )
> this->reader = NULL;
>
> if( this->connector )
> this->connector = NULL;
> }
>
> int BioFormatsReader::RequestInformation(
> vtkInformation *vtkNotUsed(request),
> vtkInformationVector **vtkNotUsed(inputVector),
> vtkInformationVector *outputVector)
> {
> if (!this->FileName)
> {
> vtkErrorMacro(<< "A FileName must be specified.");
> return 0;
> }
>
> // Create an ITK reader and connect it to a Connector to get VTK
> output
> //
> --------------------------------------------------------------------
> this->reader->SetFileName(FileName);
>
> this->connector->SetInput(reader->GetOutput());
> this->connector->Update();
>
> vtkImageData *imageData = this->connector->GetOutput();
> //
> --------------------------------------------------------------------
>
> double spacing[3], origin[3];
> int extent[6];
>
> imageData->GetExtent(extent);
> imageData->GetOrigin(origin);
> imageData->GetSpacing(spacing);
>
> // get the info object
> vtkInformation *outInfo = outputVector->GetInformationObject(0);
>
> outInfo->Set(vtkDataObject::ORIGIN(),origin,3);
> outInfo->Set(vtkDataObject::SPACING(),spacing,3);
>
> outInfo->Set(vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT(),extent,6);
>
> this->GetOutput()->SetNumberOfScalarComponents(1);
> this->GetOutput()->SetScalarType(VTK_FLOAT);
>
> return 1;
> }
> int BioFormatsReader::RequestData(
> vtkInformation *vtkNotUsed(request),
> vtkInformationVector **vtkNotUsed(inputVector),
> vtkInformationVector *outputVector)
> {
>
> vtkInformation *outInfo = outputVector->GetInformationObject(0);
> vtkImageData *output = vtkImageData::SafeDownCast(
> (outInfo->Get(vtkDataObject::DATA_OBJECT())));
>
> if (!output)
> {
> vtkErrorMacro("Output is not of type vtkImageData");
> return 0;
> }
>
> /*
> if (output->GetScalarType() != VTK_FLOAT)
> {
> vtkErrorMacro("Execute: This source only outputs floats.");
> return 1;
> }
> */
>
> output->ShallowCopy(this->connector->GetOutput());
>
> return 1;
> }
>
> void BioFormatsReader::PrintSelf(ostream& os, vtkIndent indent)
> {
> this->Superclass::PrintSelf(os,indent);
>
> os << indent << "File Name: "
> << (this->FileName ? this->FileName : "(none)") << "\n";
> }
>
> On Fri, Sep 7, 2012 at 1:19 PM, Sebastien Jourdain
> <sebastien.jourdain at kitware.com> wrote:
> > Did you check in your reader that you get properly the file name of the
> > first file ? When you switch back to the first time ?
> >
> > Seb
> >
> > On Fri, Sep 7, 2012 at 1:04 PM, Joe Ping-Lin Hsiao <phsiao at cs.unc.edu>
> > wrote:
> >>
> >> Besides the capital letters, another error is my gui xml has a
> >> mismatched source name. (Later I figure out that I don't need a gui
> >> xml for the reader to run.) Now I can load data without crash.
> >>
> >> But the problem remains. The animation plays fine at the first time.
> >> After it plays to the end, I click the 'Go back to the first frame'
> >> button, but the rendering still stays at the last frame even though in
> >> the information tab it says it's at frame 0. Am I missing something?
> >>
> >> Joe
> >>
> >> On Mon, Sep 3, 2012 at 10:12 AM, Sebastien Jourdain
> >> <sebastien.jourdain at kitware.com> wrote:
> >> > I've just fixed the wiki example to match the current ParaView
> version.
> >> >
> >> > The issue in your XML is due to the usage of capital letters in
> >> > attributes
> >> > here:
> >> >
> >> > <SubProxy>
> >> > <Proxy name="Reader"
> >> > ProxyGroup="internal_sources"
> >> > ProxyName="bioformatsreadercore">
> >> > </Proxy>
> >> > </SubProxy>
> >> >
> >> > === Should be ===
> >> >
> >> > <SubProxy>
> >> > <Proxy name="Reader"
> >> > proxygroup="internal_sources"
> >> > proxyname="bioformatsreadercore">
> >> > </Proxy>
> >> > </SubProxy>
> >> >
> >> > Seb
> >> >
> >> > On Fri, Aug 31, 2012 at 12:58 PM, Joe Ping-Lin Hsiao <
> phsiao at cs.unc.edu>
> >> > wrote:
> >> >>
> >> >> It's me again.
> >> >>
> >> >> Turns out that my animation plugin is buggy. The symptom is after I
> >> >> play the animation once, it doesn't go back to the first animation
> >> >> position even I click rewind in ParaView. The frame number in the
> >> >> Information tab doesn't match what is currently rendered.
> >> >>
> >> >> When I go back to check my xml, I found I was overwriting the .vtk
> >> >> file series reader cause I just copied the whole SourceProxy section
> >> >> over and didn't change the name field. (I confirm this because
> >> >> ParaView doesn't recognize .vtk files anymore in the open file dialog
> >> >> if I load my reader.)
> >> >>
> >> >> But after I assign this file series reader proxy a new name, ParaView
> >> >> would just crash after I load files in and click 'Apply'. Also, the
> >> >> messages in my core reader are not printed out. It looks like
> ParaView
> >> >> is not using my core reader at all.
> >> >>
> >> >> I have attached my xml code below.
> >> >>
> >> >> <ServerManagerConfiguration>
> >> >> <ProxyGroup name="internal_sources">
> >> >> <SourceProxy name="bioformatsreadercore"
> >> >> class="BioFormatsReader"
> >> >> label="BioFormats Reader">
> >> >> <Documentation
> >> >> long_help="Read Bio-Formats files."
> >> >> short_help="Read Bio-Formats files.">
> >> >> </Documentation>
> >> >> <StringVectorProperty
> >> >> name="FileName"
> >> >> animateable="0"
> >> >> command="SetFileName"
> >> >> number_of_elements="1">
> >> >> <FileListDomain name="files"/>
> >> >> <Documentation>
> >> >> This property specifies the input file name.
> >> >> </Documentation>
> >> >> </StringVectorProperty>
> >> >>
> >> >> </SourceProxy>
> >> >> </ProxyGroup>
> >> >>
> >> >> <ProxyGroup name="sources">
> >> >> <SourceProxy name="BioFormatsFileReader"
> >> >> class="vtkFileSeriesReader"
> >> >> label="Legacy VTK Reader"
> >> >> si_class="vtkSIFileSeriesReaderProxy"
> >> >> file_name_method="SetFileName">
> >> >> <Documentation
> >> >> short_help="Read legacy VTK files."
> >> >> long_help="Reads files stored in VTK's legacy file format.">
> >> >> The Legacy VTK reader loads files stored in VTK's legacy file
> >> >> format (before VTK 4.2, although still supported). The expected file
> >> >> extension is .vtk. The type of the dataset may be structured grid,
> >> >> uniform rectilinear grid (image/volume), non-uniform rectiinear grid,
> >> >> unstructured grid, or polygonal. This reader also supports file
> >> >> series.
> >> >> </Documentation>
> >> >> <SubProxy>
> >> >> <Proxy name="Reader"
> >> >> ProxyGroup="internal_sources"
> >> >> ProxyName="bioformatsreadercore">
> >> >> </Proxy>
> >> >> </SubProxy>
> >> >>
> >> >> <StringVectorProperty name="FileNameInfo"
> >> >> command="GetCurrentFileName"
> >> >> information_only="1" >
> >> >> <SimpleStringInformationHelper />
> >> >> </StringVectorProperty>
> >> >>
> >> >> <StringVectorProperty
> >> >> name="FileNames"
> >> >> clean_command="RemoveAllFileNames"
> >> >> command="AddFileName"
> >> >> animateable="0"
> >> >> number_of_elements="1"
> >> >> repeat_command="1"
> >> >> information_property="FileNameInfo" >
> >> >> <FileListDomain name="files"/>
> >> >> <Documentation>
> >> >> The list of files to be read by the reader. If more than one
> >> >> file is specified, the reader will switch to file series mode in
> which
> >> >> it will pretend that it can support time and provide one file per
> time
> >> >> step.
> >> >> </Documentation>
> >> >> </StringVectorProperty>
> >> >>
> >> >> <DoubleVectorProperty
> >> >> name="TimestepValues"
> >> >> repeatable="1"
> >> >> information_only="1">
> >> >> <TimeStepsInformationHelper/>
> >> >> <Documentation>
> >> >> Available timestep values.
> >> >> </Documentation>
> >> >> </DoubleVectorProperty>
> >> >>
> >> >> <Hints>
> >> >> <ReaderFactory extensions="tif"
> >> >> file_description="Legacy VTK files" />
> >> >> </Hints>
> >> >> <!-- End LegacyVTKFileReader -->
> >> >> </SourceProxy>
> >> >> </ProxyGroup>
> >> >>
> >> >> </ServerManagerConfiguration>
> >> >>
> >> >>
> >> >> On Fri, Aug 24, 2012 at 3:15 PM, Moreland, Kenneth <
> kmorel at sandia.gov>
> >> >> wrote:
> >> >> > In that case, someone should definitely update the wiki page.
> >> >> >
> >> >> > I see a note added by Jourdain on another page
> >> >> > (
> http://paraview.org/Wiki/ServerManager_XML_Hints#TimeSeries_readers)
> >> >> > that
> >> >> > suggests a change in 3.12. Perhaps he can update the example.
> >> >> >
> >> >> > -Ken
> >> >> >
> >> >> > Sent from my iPad so blame autocorrect.
> >> >> >
> >> >> > On Aug 24, 2012, at 11:27 AM, "Joe Ping-Lin Hsiao"
> >> >> > <phsiao at cs.unc.edu>
> >> >> > wrote:
> >> >> >
> >> >> >> It's working!
> >> >> >> I just followed the VTK reader code in readers.xml at
> >> >> >> ParaView3.14.1\ParaViewCore\ServerImplementation\Resources.
> >> >> >>
> >> >> >> Ken,
> >> >> >> I first tried the xml code from the wiki, but I couldn't even
> read
> >> >> >> a
> >> >> >> file. I guess the xml scheme had changed in ParaView 3.14, and
> >> >> >> what's
> >> >> >> on the wiki is for older versions of ParaView.
> >> >> >>
> >> >> >> Thanks,
> >> >> >> Joe
> >> >> >>
> >> >> >> On Thu, Aug 23, 2012 at 6:43 PM, Moreland, Kenneth
> >> >> >> <kmorel at sandia.gov>
> >> >> >> wrote:
> >> >> >>> It looks like there is a Wiki page describing how to use the
> >> >> >>> vtkFileSeriesReader to convert a reader to understand file
> series.
> >> >> >>>
> >> >> >>> http://www.paraview.org/Wiki/Animating_legacy_VTK_file_series
> >> >> >>>
> >> >> >>> -Ken
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>> On 8/23/12 3:35 PM, "David E DeMarle" <dave.demarle at kitware.com>
> >> >> >>> wrote:
> >> >> >>>
> >> >> >>>> To make uniformly increasing time denoted in numbered file
> >> >> >>>> sequences,
> >> >> >>>> encapsulate your reader in a sub proxy of a vtkFileSeriesReader.
> >> >> >>>> See
> >> >> >>>> readers.xml for numerous examples of that.
> >> >> >>>>
> >> >> >>>> If you need nonuniform temporal spacing or need to improve upon
> >> >> >>>> the
> >> >> >>>> file series reader's IO performance, make your reader supply
> >> >> >>>> temporal
> >> >> >>>> information and respond to time requests appropriately in
> >> >> >>>> RequestInformation and RequestData respectively. See
> >> >> >>>> vtkTimeSourceExample for an example of that.
> >> >> >>>>
> >> >> >>>> David E DeMarle
> >> >> >>>> Kitware, Inc.
> >> >> >>>> R&D Engineer
> >> >> >>>> 21 Corporate Drive
> >> >> >>>> Clifton Park, NY 12065-8662
> >> >> >>>> Phone: 518-881-4909
> >> >> >>>>
> >> >> >>>>
> >> >> >>>> On Thu, Aug 23, 2012 at 5:22 PM, Joe Ping-Lin Hsiao
> >> >> >>>> <phsiao at cs.unc.edu>
> >> >> >>>> wrote:
> >> >> >>>>> Hi,
> >> >> >>>>>
> >> >> >>>>> I have written a customized reader in ParaView which reads 3D
> >> >> >>>>> stacks.
> >> >> >>>>> Now I'd like to add the function of reading time-varying data
> to
> >> >> >>>>> it,
> >> >> >>>>> so I can create animations from stacks.
> >> >> >>>>>
> >> >> >>>>> ParaView has this function already. If I convert time-varying
> >> >> >>>>> stacks
> >> >> >>>>> and name them stack001.vtk, stack002.vtk, and etc, ParaView
> would
> >> >> >>>>> recognize the sequence and load them in at once, and I'd be
> able
> >> >> >>>>> to
> >> >> >>>>> play the animation just by clicking the 'Play' icon.
> >> >> >>>>>
> >> >> >>>>> I wonder is there any example of how to do that to a reader?
> >> >> >>>>>
> >> >> >>>>> Thanks,
> >> >> >>>>> Joe
> >> >> >>>>> _______________________________________________
> >> >> >>>>> Paraview-developers mailing list
> >> >> >>>>> Paraview-developers at paraview.org
> >> >> >>>>> http://public.kitware.com/mailman/listinfo/paraview-developers
> >> >> >>>> _______________________________________________
> >> >> >>>> Paraview-developers mailing list
> >> >> >>>> Paraview-developers at paraview.org
> >> >> >>>> http://public.kitware.com/mailman/listinfo/paraview-developers
> >> >> >>>>
> >> >> >>>
> >> >> >>>
> >> >> >>
> >> >> >
> >> >> _______________________________________________
> >> >> Paraview-developers mailing list
> >> >> Paraview-developers at paraview.org
> >> >> http://public.kitware.com/mailman/listinfo/paraview-developers
> >> >
> >> >
> >
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/paraview-developers/attachments/20120907/e29480f1/attachment-0001.htm>
More information about the Paraview-developers
mailing list