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--- documents:101029imagej_cui_lifconversion [2010/10/29 15:54] – added macro kota
+++ documents:101029imagej_cui_lifconversion [2020/11/26 09:11] (current) – external edit 127.0.0.1
@@ Line 67: / Line 67: @@
 </sxh>
+===== ImpProps.java =====
+Accessing Image Physical Properties. Compiled class should be copied to the imageJ plugin folder. [[http://rsbweb.nih.gov/ij/plugins/imp-props.html|Original java code]] was modified to access image properties scales and dimensions.
+<sxh java>
+import ij.*;
+import ij.measure.Calibration;
+//import java.lang.Double;
+/**
+ * This simple class can be called from an ImageJ macro via the "call" mechanism to
+ * get and set the (string) properties of the active image (ImagePlus).
+ *
+ * call("ImpProps.setProperty", "<key>", "<value>");
+ *	set property <key> to <value>, returns <value> if successful,
+ *	"" otherwise (no active image)
+ *
+ * call("ImpProps.getProperty", "<key>");
+ *	returns value of property <key> if set, "" otherwise (not found or no active image)
+ *
+ * @see    ij.ImagePlus#setProperty
+ * @see    ij.ImagePlus#getProperty
+ *
+ * @author Joachim Wesner
+ * @author Leica Microsystems CMS GmbH
+ * @author joachim.wesner@leica-microsystems.com
+ * @version 2008-3-15
+ *
+ * @author Kota Miura
+ * cmci, embl
+ * added methods for setting image dimension sizes and pixel scales.
+ * this was done for setting these values in headless mode.
+ * @version 2010-10-28
+ * This class can be compiled with ImageJ's Plugins>Compile and Run command.
+ */
+public class ImpProps {
+	//kota
+	public static String getProperties() {
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return "";
+		Object prop = imp.getProperties();
+		if (prop != null && prop instanceof String)
+			return (String)prop;
+		else
+			return "";
+	}
+	public static String setProperty(String arg1, String arg2) {
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return "";
+		imp.setProperty(arg1, arg2);
+		imp.updateAndDraw();
+		return arg2;
+	}
+	public static String getProperty(String arg1) {
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return "";
+		Object prop = imp.getProperty(arg1);
+		if (prop != null && prop instanceof String)
+			return (String)prop;
+		else
+			return "";
+	}
+	//kota
+	public static int setCalibration(String unit, String spixelWidth, String spixelHeight, String spixelDepth){
+		double pixelWidth = java.lang.Double.parseDouble(spixelWidth);
+		double pixelHeight = java.lang.Double.parseDouble(spixelHeight);
+		double pixelDepth = java.lang.Double.parseDouble(spixelDepth);
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return -1;
+		Calibration cal = imp.getCalibration();
+		cal.setUnit(unit);
+		cal.pixelWidth = pixelWidth;
+		cal.pixelHeight = pixelHeight;
+		cal.pixelDepth = pixelDepth;
+		imp.setCalibration(cal);
+		WindowManager.repaintImageWindows();
+		return 1;
+	}
+	//kota
+	public static int setCalibration(
+		String schannels, String sslices,
+			String sframes, String unit,
+				String spixelWidth, String spixelHeight,
+					String spixelDepth) {
+		int channels = java.lang.Integer.parseInt(schannels);
+		int slices   = java.lang.Integer.parseInt(sslices);
+		int frames   = java.lang.Integer.parseInt(sframes);
+		double pixelWidth  = java.lang.Double.parseDouble(spixelWidth);
+		double pixelHeight = java.lang.Double.parseDouble(spixelHeight);
+		double pixelDepth  = java.lang.Double.parseDouble(spixelDepth);
+		ImagePlus imp = WindowManager.getCurrentImage();
+		if (imp == null)
+			return -1;
+		int stackSize = imp.getImageStackSize();
+		if (channels*slices*frames==stackSize)
+ 			imp.setDimensions(channels, slices, frames);
+ 		else
+ 			IJ.error("Properties", "The product of channels ("+channels+"), slices ("+slices
+ 				+")\n and frames ("+frames+") must equal the stack size ("+stackSize+").");
+		Calibration cal = imp.getCalibration();
+		cal.setUnit(unit);
+		//cal.setTimeUnit(IJ.micronSymbol + "sec");
+		cal.pixelWidth = pixelWidth;
+		cal.pixelHeight = pixelHeight;
+		cal.pixelDepth = pixelDepth;
+		imp.setCalibration(cal);
+		WindowManager.repaintImageWindows();
+		return 1;
+	}
+}
+</sxh>
 ===== bfconvert help =====
-<quote>
+<blockquote>
 To convert a file between formats, run:
   bfconvert [-debug] [-stitch] [-separate] [-merge] [-expand]
@@ Line 113: / Line 234: @@
 Each file would have a single image plane.
-</quote>
+</blockquote>
 ===== LifOpenerCUI.ijm =====
@@ Line 322: / Line 443: @@
 }
 </code>