documents:101029imagej_cui_lifconversion
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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 | ||
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</ | </ | ||
+ | ===== ImpProps.java ===== | ||
+ | |||
+ | Accessing Image Physical Properties. Compiled class should be copied to the imageJ plugin folder. [[http:// | ||
+ | |||
+ | <sxh java> | ||
+ | import ij.*; | ||
+ | import ij.measure.Calibration; | ||
+ | //import java.lang.Double; | ||
+ | /** | ||
+ | * This simple class can be called from an ImageJ macro via the " | ||
+ | * get and set the (string) properties of the active image (ImagePlus). | ||
+ | * | ||
+ | * call(" | ||
+ | * set property <key> to < | ||
+ | | ||
+ | * | ||
+ | * call(" | ||
+ | | ||
+ | * | ||
+ | * @see ij.ImagePlus# | ||
+ | * @see ij.ImagePlus# | ||
+ | * | ||
+ | * @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' | ||
+ | */ | ||
+ | |||
+ | 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, | ||
+ | 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, | ||
+ | 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 spixelDepth) { | ||
+ | int channels = java.lang.Integer.parseInt(schannels); | ||
+ | int slices | ||
+ | int frames | ||
+ | double pixelWidth | ||
+ | double pixelHeight = java.lang.Double.parseDouble(spixelHeight); | ||
+ | double pixelDepth | ||
+ | |||
+ | ImagePlus imp = WindowManager.getCurrentImage(); | ||
+ | if (imp == null) | ||
+ | return -1; | ||
+ | int stackSize = imp.getImageStackSize(); | ||
+ | if (channels*slices*frames==stackSize) | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | Calibration cal = imp.getCalibration(); | ||
+ | cal.setUnit(unit); | ||
+ | // | ||
+ | cal.pixelWidth = pixelWidth; | ||
+ | cal.pixelHeight = pixelHeight; | ||
+ | cal.pixelDepth = pixelDepth; | ||
+ | imp.setCalibration(cal); | ||
+ | WindowManager.repaintImageWindows(); | ||
+ | return 1; | ||
+ | } | ||
+ | } | ||
+ | </ | ||
===== bfconvert help ===== | ===== bfconvert help ===== | ||
- | <quote> | + | <blockquote> |
To convert a file between formats, run: | To convert a file between formats, run: | ||
bfconvert [-debug] [-stitch] [-separate] [-merge] [-expand] | bfconvert [-debug] [-stitch] [-separate] [-merge] [-expand] | ||
Line 113: | Line 234: | ||
Each file would have a single image plane. | Each file would have a single image plane. | ||
- | </quote> | + | </blockquote> |
===== LifOpenerCUI.ijm ===== | ===== LifOpenerCUI.ijm ===== | ||
Line 322: | Line 443: | ||
} | } | ||
</ | </ | ||
+ | |||
+ |
documents/101029imagej_cui_lifconversion.txt · Last modified: 2020/11/26 09:11 by 127.0.0.1