[Paraview-developers] [EXTERNAL] Re: Time-varying data reader
Joe Ping-Lin Hsiao
phsiao at cs.unc.edu
Mon Sep 10 13:03:57 EDT 2012
Thank you! That fixes the problem!
On Fri, Sep 7, 2012 at 7:55 PM, Sebastien Jourdain
<sebastien.jourdain at kitware.com> wrote:
> 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
>> >> >
>> >> >
>> >
>> >
>
>
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