Getting started
Important: You have to work alone on your project work. No team partners allowed anymore 😔!
CT reconstruction treats the problem of recovering a three-dimensional volume from a set of X-ray images. So we will need two classes that represent our volume and our stack of X-ray projections. It turns out that we can interpret our projections and our volume just as a list of 2-d images.
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| A volume: very much just multiple images stacked one over another |
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Create a class mt.Volume
// Your name <your idm>
// No team partner... So sad 😢!
package mt;
import java.util.Arrays;
import java.util.stream.IntStream;
public class Volume {
// Here we store our images
protected mt.Image[] slices;
// Dimensions of our volume
protected int width, height, depth;
// Spacing and origin like for mt.Image
protected float spacing = 1.f; // spacing is now our voxel size
protected float[] origin = new float[]{0, 0, 0}; // position of the top-left-bottom corner
// A name for the volume
protected String name;
}
Create a constructor. Remember: width, height, depth, name must be set and slices must be created as an array.
We need depth images of size width $\times$ height for the slices.
public Volume(int width, int height, int depth, String name)
Getters/setters...
public int width()
public int height()
public int depth()
public float physicalWidth() // width * spacing()
public float physicalHeight() // height * spacing()
public float physicalDepth() // depth * spacing()
public mt.Image getSlice(int z)
public void setSlice(int z, mt.Image slice)
public float spacing()
public void setSpacing(float spacing) // should also set spacing also for all slices!
public String name()
public float[] origin()
// should set origin to (-0.5 physicalWidth, -0.5 physicalHeight, -0.5 physicalDepth) and call centerOrigin on each slice
public void centerOrigin()
Now comes the interesting part: visualize the volume!
You will need to update src/main/java/lme/DisplayUtils.java file and use the following command to visualize the volume.
public void show() {
lme.DisplayUtils.showVolume(this);
}
You can download a volume from the Cancer Imaging Archive. Use one of the following links (it does not matter which CT volume you use).
Unzip the folder and drag the whole folder onto a running ImageJ, e.g. by the following code snippet in a file src/main/java/project/Playground.java.
(if you have problems unzipping the files you might try the official downloader from the website. You need their downloader to open the *.tcia files).
// This file is only for you to experiment. We will not correct it.
package project;
import mt.Volume;
class Playground {
public static void main(String[] args) {
// Starts ImageJ
(new ij.ImageJ()).exitWhenQuitting(true);
// You can now use drag & drop to convert the downloaded folder into a *.tif file
}
}
Save it the opened DICOM as a *.tif file (File > Save As > Tiff...).
There are more smaller test volumes on studOn.
Open the saved tiff file in the main of a file src/main/java/project/Playground.java:
// This file is only for you to experiment. We will not correct it.
package project;
import mt.Volume;
class Playground {
public static void main(String[] args) {
(new ij.ImageJ()).exitWhenQuitting(true);
Volume groundTruth = DisplayUtils.openVolume("path/to/file.tif");
groundTruth.show();
}
}
You can now scroll through the different slices.
Here a short summary of handy functions of ImageJ when working with CT images.
- Ctrl+Shift+C: Brightness and Contrast
- Ctrl+Shift+H: Orthogonal Views (view volume from three sides)
- After selecting a line: Ctrl+K Line Plot
- Ctrl+I: Get patient information of a DICOM
- Look at a 3-d rendering with ClearVolume