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DICOM_Sorter |
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package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.util.*;
/* Sorts a DICOM stack by image number. */
public class DICOM_Sorter implements PlugIn {
static final int MAX_DIGITS = 5;
public void run(String arg) {
ImagePlus imp = IJ.getImage();
if (!isDicomStack(imp)) {
IJ.showMessage("DICOM Sorter", "This command requires a DICOM stack");
return;
}
int stackSize = imp.getStackSize();
ImageStack stack = imp.getStack();
String[] strings = getSortStrings(stack, "0020,0013");
StringSorter.sort(strings);
ImageStack stack2 = sortStack(stack, strings);
if (stack2!=null)
imp.setStack(null, stack2);
}
public ImageStack sort(ImageStack stack) {
if (IJ.debugMode) IJ.log("DICOM_Sorter: sorting by image number");
if (stack.getSize()==1) return stack;
String[] strings = getSortStrings(stack, "0020,0013");
if (strings==null) return stack;
StringSorter.sort(strings);
ImageStack stack2 = sortStack(stack, strings);
return stack2!=null?stack2:stack;
}
ImageStack sortStack(ImageStack stack, String[] strings) {
ImageProcessor ip = stack.getProcessor(1);
ImageStack stack2 = new ImageStack(ip.getWidth(), ip.getHeight(), ip.getColorModel());
for (int i=0; i<stack.getSize(); i++) {
int slice = (int)Tools.parseDouble(strings[i].substring(strings[i].length()-MAX_DIGITS), 0.0);
if (slice==0) return null;
stack2.addSlice(stack.getSliceLabel(slice), stack.getPixels(slice));
}
stack2.update(stack.getProcessor(1));
return stack2;
}
String[] getSortStrings(ImageStack stack, String tag) {
double series = getSeries(stack.getSliceLabel(1));
int n = stack.getSize();
String[] values = new String[n];
for (int i=1; i<=n; i++) {
String tags = stack.getSliceLabel(i);
if (tags==null) return null;
double value = getNumericTag(tags, tag);
if (Double.isNaN(value)) {
if (IJ.debugMode) IJ.log(" "+tag+" tag missing in slice "+i);
return null;
}
if (getSeries(tags)!=series) {
if (IJ.debugMode) IJ.log(" all slices must be part of the same series");
return null;
}
values[i-1] = toString(value, MAX_DIGITS) + toString(i, MAX_DIGITS);
}
return values;
}
String toString(double value, int width) {
String s = " " + IJ.d2s(value,0);
return s.substring(s.length()-MAX_DIGITS);
}
boolean isDicomStack(ImagePlus imp) {
if (imp.getStackSize()==1)
return false;
ImageStack stack = imp.getStack();
String label = stack.getSliceLabel(1);
return label!=null && label.lastIndexOf("7FE0,0010")>0;
}
double getSeries(String tags) {
double series = getNumericTag(tags, "0020,0011");
if (Double.isNaN(series)) series = 0;
return series;
}
double getNumericTag(String hdr, String tag) {
String value = getTag(hdr, tag);
if (value.equals("")) return Double.NaN;
int index3 = value.indexOf("\\");
if (index3>0)
value = value.substring(0, index3);
return Tools.parseDouble(value);
}
String getTag(String hdr, String tag) {
if (hdr==null) return "";
int index1 = hdr.indexOf(tag);
if (index1==-1) return "";
//IJ.log(hdr.charAt(index1+11)+" "+hdr.substring(index1,index1+20));
if (hdr.charAt(index1+11)=='>') {
// ignore tags in sequences
index1 = hdr.indexOf(tag, index1+10);
if (index1==-1) return "";
}
index1 = hdr.indexOf(":", index1);
if (index1==-1) return "";
int index2 = hdr.indexOf("\n", index1);
String value = hdr.substring(index1+1, index2);
return value;
}
}
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DICOM_Sorter |
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