[Insight-users] Overlay a path on the image

[Shady Shidfar]

Hi Dan
 
Thanks so much for your help. I used your piece of code with an analyze file and it solved the problem, thanks. Now the problem is:
 
1- I need to draw the path on the input image. Right now the created image only includes the path not the image itself. how can I fix that? 
2- I need to use orientImageFilter to make sure the read images are in common orientation. I can't find any  
SetDesiredCoordinateOrientation method to set the orientation to RPI, PIR, and RIP so I get the error Analyze 7.5 File Format Only Allows RPI, PIR, and RIP Orientation
 
Thanks verymuch for all your help
 
Shaady
 
Here's my code:
 
usingSystem;usingSystem.Collections.Generic;usingSystem.ComponentModel;usingSystem.Data;usingSystem.Drawing;usingSystem.Linq;usingSystem.Text;usingSystem.Windows.Forms;usingvtk;usingitk;namespace
{InteractiveHierarchicalSegmentationDotNetpublicpartialclassTestForm: Form{
{
InitializeComponent();publicTestForm()try{// Read imageitkImage_UC3input = itkImage_UC3.New();itkImage_UC3output = itkImage_UC3.New();input.Read(
// Create pathpoint[0] = 0.0;
point[1] = 0.0;
point[2] = 0.0;
input.TransformPhysicalPointToContinuousIndex(point, 
path.AddVertex(vertex);
point[0] = 180.0;
point[1] = 180.0;
point[2] = 0.0;
input.TransformPhysicalPointToContinuousIndex(point, 
path.AddVertex(vertex);
// Convert path to imagepathToImage.Size = input.Size;
pathToImage.Spacing = input.Spacing;
pathToImage.Origin = input.Origin;
pathToImage.SetInput(path);
pathToImage.PathValue = 255;itkPathToImageFilter_PLPP3IUC3pathToImage =itkPathToImageFilter_PLPP3IUC3.New();//pathToImage.BackgroundValue = 0;pathToImage.UpdateLargestPossibleRegion();
pathToImage.GetOutput(output);//set orientation of the imageorientFilter.UseImageDirection = itkOrientImageFilter_IUC3IUC3orientFilter = itkOrientImageFilter_IUC3IUC3.New();true;// orientFilter.SetDesiredCoordinateOrientationToAxial();//orientFilter.SetDesiredCoordinateOrientationToCoronal();//orientFilter.SetDesiredCoordinateOrientationToSagittal();orientFilter.SetInput(output);
orientFilter.GetOutput(outputO);
output.Write("D:/PHD/images/BI02_PSMR_copy.hdr"); //I actually need to write outputO to output not output}
{
}
}
}
}catch(Exceptionex)Console.WriteLine(ex);
 itkPolyLineParametricPath_3path =itkPolyLineParametricPath_3.New();itkPointpoint = newitkPoint(3U);itkContinuousIndexvertex = newitkContinuousIndex(3U);outvertex);outvertex); itkImage_UC3outputO = itkImage_UC3.New();"D:/PHD/images/BI02_PSMR.hdr"); 


----- Forwarded Message ----
From: Dan Mueller <dan.muel at gmail.com>
To: Shady Shidfar <shady_shidfar at yahoo.com>
Cc: Insight Users <insight-users at itk.org>
Sent: Wednesday, 23 July, 2008 8:28:43 AM
Subject: Re: [Insight-users] using spatialObjects in ManagedITK

Hi Shady,

Please find attached the following code which I have tested and
verifies works correctly.

The differences are the following:
  1. When you create a new itkPoint or itkContinuousIndex be careful
to use itkPoint.New(3U) in the constructor. This creates a
three-dimensional empty object, rather than itkPoint.New(3) which
(may) create a 1 dimensional object with value "3".
  2. The input image must be three-dimensional (I don't think
"brain.tif" is 3-D).
  3. Ensure all vertices added to the path are inside the largest
possible region of the image. If not, you can receive the error
message you reported. (Without further investigation, I'm not sure if
this is a problem with the wrappings or with ITK itself...)

Hope this helps.

Regards, Dan

using System;
using itk;

namespace ItkPathTest
{
    class Program
    {
        static void Main(string[] args)
        {
            // Read image
            itkImage_UC3 input = itkImage_UC3.New();
            itkImage_UC3 output = itkImage_UC3.New();
            input.Read("D:/Temp/engine.mhd");

            // Create path
            itkPolyLineParametricPath_3 path =
                itkPolyLineParametricPath_3.New();
            itkPoint point = new itkPoint(3U);
            itkContinuousIndex vertex = new itkContinuousIndex(3U);
            point[0] = 50.0;
            point[1] = 50.0;
            point[2] = 50.0;
            input.TransformPhysicalPointToContinuousIndex(point, out vertex);
            path.AddVertex(vertex);
            point[0] = 200.0;
            point[1] = 200.0;
            point[2] = 100.0;
            input.TransformPhysicalPointToContinuousIndex(point, out vertex);
            path.AddVertex(vertex);

            // Convert path to image
            itkPathToImageFilter_PLPP3IUC3 pathToImage =
                itkPathToImageFilter_PLPP3IUC3.New();
            pathToImage.Size = input.Size;
            pathToImage.Spacing = input.Spacing;
            pathToImage.Origin = input.Origin;
            pathToImage.SetInput(path);
            pathToImage.PathValue = 255;
            pathToImage.BackgroundValue = 0;
            pathToImage.UpdateLargestPossibleRegion();
            pathToImage.GetOutput(output);
            output.Write("D:/Temp/Path01.mhd");
        }
    }
}


2008/7/22 Shady Shidfar <shady_shidfar at yahoo.com>:
> Hi Dan,
>
> Thanks for the file, I guess I'll wait for you to solve the problem :-). Now
> instead of using SpatialObjects I'm trying to
> use itkPolyLineParametricPath  to draw contours on my image, then use
> itkPathToImageFilter to display them on the image. The problem is that I get
> a weird message. Could you please have a look at the following code and see
> what the problem is.
>
>
>
> the error is: Attempted to read or write protected memory. This is often an
> indication that other memory is corrupt.
>
>
>
> using
>
> System;
>
> using
>
> System.Collections.Generic;
>
> using
>
> System.Linq;
>
> using
>
> System.Windows.Forms;
>
> namespace
>
> InteractiveHierarchicalSegmentationDotNet
>
> {
>
> static class Program
>
> {
>
> /// <summary>
>
> /// The main entry point for the application.
>
> /// </summary>
>
> [
>
> STAThread]
>
> static void Main()
>
> {
>
> //Application.EnableVisualStyles();
>
> //Application.SetCompatibleTextRenderingDefault(false);
>
> //Application.Run(new Form1());
>
> Application.Run(new TestForm());
>
> }
>
> }
>
> }
>
>
>
>
>
>
>
>
>
> using
>
> System;
>
> using
>
> System.Collections.Generic;
>
> using
>
> System.ComponentModel;
>
> using
>
> System.Data;
>
> using
>
> System.Drawing;
>
> using
>
> System.Linq;
>
> using
>
> System.Text;
>
> using
>
> System.Windows.Forms;
>
> using
>
> vtk;
>
> using
>
> itk;
>
> namespace
>
> InteractiveHierarchicalSegmentationDotNet
>
> {
>
> public partial class TestForm : Form
>
> {
>
> public TestForm()
>
> {
>
> InitializeComponent();
>
> try
>
> {
>
> // Read ITK image
>
> itkImage_UC3 inputImage = itkImage_UC3.New();
>
> inputImage.Read(
>
> "C:/brain.tif");
>
> inputImage.DisconnectPipeline();
>
> // Import ITK image to VTK
>
> itkImageToVTKImageFilter itk2vtk =
>
> itkImageToVTKImageFilter.New(inputImage);
>
> itk2vtk.SetInput(inputImage);
>
> itk2vtk.Update();
>
> vtkImageData data = itk2vtk.GetOutput();
>
> vtkImageActor actor = new vtkImageActor();
>
> actor.SetInput(data);
>
> Console.WriteLine(actor.ToString());
>
> vtkRenderer vtkRenderer1 = new vtkRenderer();
>
> this.vtkFormsWindowControl1.GetRenderWindow().AddRenderer(vtkRenderer1);
>
> vtkRenderer1.AddActor(actor);
>
>
>
> // define and display a path
>
> itkPoint origin = inputImage.Origin;
>
> itkSpacing spacing = inputImage.Spacing;
>
> itkSize size = inputImage.Size;
>
> itkPoint point = new itkPoint(3);
>
> itkPolyLineParametricPath_3 path = itkPolyLineParametricPath_3.New();
>
> point[0] = origin[0] + spacing[0] * size[0];
>
> point[1] = origin[1] + spacing[1] * size[1];
>
> //point[3] = origin[2] + spacing[2] * size[2];
>
> itkContinuousIndex cindex = new itkContinuousIndex(3);
>
> inputImage.TransformPhysicalPointToContinuousIndex(origin,
>
> out cindex);
>
> path.AddVertex(cindex);
>
> inputImage.TransformPhysicalPointToContinuousIndex(point,
>
> out cindex);
>
> path.AddVertex(cindex);
>
> itkPathToImageFilter_PLPP3IUC3 path2ImageFilter =
> itkPathToImageFilter_PLPP3IUC3.New();
>
> path2ImageFilter.SetInput(path);
>
> path2ImageFilter.PathValue = 200;
>
> path2ImageFilter.GetOutput(inputImage);
>
> }
>
> catch (Exception ex)
>
> {
>
> Console.WriteLine(ex);
>
> }
>
> }
>
> }
>
> }
>
>
>
>
>
> I can send you the whole project if it helps.
>
>
>
> Cheers, Shaady



      __________________________________________________________
Not happy with your email address?.
Get the one you really want - millions of new email addresses available now at Yahoo! http://uk.docs.yahoo.com/ymail/new.html
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.itk.org/pipermail/insight-users/attachments/20080729/37775a16/attachment-0001.htm>