[plug-in] Ne pas afficher les images pendant le traitement

**Loy027** · 19/01/2016, 20h35

Bonjour à tous,

Voilà mon problème, dans le cadre d'un projet à la fac j'ai du transformer une macro en plug-in ce que (débutant en java) j'ai plus ou moins réussis à faire :
code de la macro :

Code :

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//////////////////////////////////////////////////////////////////////////////////
//										//
//	Macro for Marion							//
//										//
//////////////////////////////////////////////////////////////////////////////////
///
//////////////////////////////////////////////////////////////////////////////////
//	Open image		//////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
	setBatchMode(true); // Controls whether images are visible or hidden during macro execution. arg is 'true', the interpreter enters batch mode and newly opened images are not displayed.
 
	open(); //open() fonction with no arg : opening of a windows in order to choose a image.
	dir = getInfo("image.directory"); //Returns the directory that the current image was loaded from, or an empty string if the directory is not available.
 
	//print(dir);
	//name=getInfo("image.filename");
	//print(name);
	images = getFileList(dir); //returns the names of the images which are in the folder
	tailleTableau = lengthOf(images);  //lengthOf : return the number of the image in tailleTableau
 
for (i=0; i< images.length/*tailleTableau-1*/; i++) { //de i=0 à 1<tailleTableau-1 with i++. tailleTableau-1 because index 0 at the beginning of the array 
 
	nom = getInfo("image.filename"); //return the file name in "nom"
 
//////////////////////////////////////////////////////////////////////////////////
//	Create Folders		//////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////	
	tmp = dir; //"dir" is put in tempory variable "tmp"
	if (tmp=="") //if tmp correspond to an empty string 
	{
		exit("No temp directory available"); 
	}
	newDir = tmp+"Analyse"+File.separator; //creation of a new folder path : tmp+Analyse+"\"
	File.makeDirectory(newDir); //creation of the folder Analyse
	if (!File.exists(newDir)) //if folder does'nt exist
	{
		exit("Unable to create directory"); //end of the macro
	}
//////////////////////////////////////////////////////////////////////////////////	
	tmpO = dir+"Analyse"+File.separator; //"dir+Analyse+File.separator" is put in tempory variable "tmpO"
	if (tmpO=="") //if tmpO correspond to an empty string 
	{
		exit("No temp directory available");//end of the macro
	}
	newDirE = tmpO+"Images"+File.separator;
	File.makeDirectory(newDirE);//creation of the folder Image in the folder Analyse
	if (!File.exists(newDirE))//if folder does'nt exist
	{
		exit("Unable to create directory");//end of the macro
	}
//////////////////////////////////////////////////////////////////////////////////
	tmpOr = dir+"Analyse"+File.separator;//"dir+Analyse+File.separator" is put in tempory variable "tmpOr"
	if (tmpOr=="")//if tmpOr correspond to an empty string 
	{
		exit("No temp directory available");//end of the macro
	}
	newDirEc = tmpOr+"Results"+File.separator;
	File.makeDirectory(newDirEc);//creation of the folder Result in the folder Analyse
	if (!File.exists(newDirEc))//if folder does'nt exist
	{
		exit("Unable to create directory");//end of the macro
	}
//////////////////////////////////////////////////////////////////////////////////	
	directoryI = dir+"Analyse"+File.separator+"Images"+File.separator; //in directoryI = path of Image folder
	directoryR = dir+"Analyse"+File.separator+"Results"+File.separator; //in directoryR = path of Result folder
 
//////////////////////////////////////////////////////////////////////////////////
//	Split and Close Channels	//////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////	
 
	run("Split Channels"); //spliting of the R G B channels
	colorRed =nom+" (red)"; 
	selectWindow(colorRed);
	close(); //closing the red channel
	colorBlue =nom+" (blue)";
	selectWindow(colorBlue);
	close(); //closing the blue channel
	run("Green"); //just green channel will be used
	indexGreen =" (green).tif";
	saveAs("Tiff", ""+directoryI+""+nom+""+indexGreen+"");	//saving green image in directoryI
 
//////////////////////////////////////////////////////////////////////////////////
//	Calibrate	//////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
 
	run("Properties...", "channels=1 slices=1 frames=1 unit=¬µm pixel_width=0.4857143 pixel_height=0.4857143 voxel_depth=0 frame=[0 sec] origin=0,0");
 
//////////////////////////////////////////////////////////////////////////////////
//	Tubeness	//////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
 
	//tubeness treatment on green channel image
	run("Tubeness", "sigma=5 use");
	indexT ="-01-Tubeness.tif";
	saveAs("Tiff", ""+directoryI+""+nom+""+indexT+""); //creation of transitional image which was treated by tubeness. Saving in directoryI
 
//////////////////////////////////////////////////////////////////////////////////
//	Binary		//////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
 
	//binary treatment on the image which was treated by tubeness
	run("Make Binary");
	indexTB ="-02-TubenessBinarise.tif";
	saveAs("Tiff", ""+directoryI+""+nom+""+indexTB+""); //Creation of transitional image wich was treated by binary. Saving in directoryI
 
//////////////////////////////////////////////////////////////////////////////////
//	Skeletonize	//////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
 
	//Skeletonize treatment on the image which was treated by tubeness and binary previously
	run("Skeletonize (2D/3D)"); 
	indexSkel ="-03-Skeleton.tif";
	saveAs("Tiff", ""+directoryI+""+nom+""+indexSkel+"");//Creation of transitional image wich was treated by binary. Saving in directoryI
 
	///At this stage 4 news images was normaly created
 
//////////////////////////////////////////////////////////////////////////////////
//	Analyze Skeleton	//////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
 
	//binary treatment on the image which was treated by tubeness, binary and skeletonized previously
	run("Analyze Skeleton (2D/3D)", "prune=none calculate show");
	selectWindow("Longest shortest paths");
	indexLSP ="-04-LSP.tif"; 
	saveAs("Tiff", ""+directoryI+""+nom+""+indexLSP+""); //creation of transitional Longest Shortest paths image which was analized by Analyze Skeleton. Saving in directoryI
	close();
	selectWindow("Tagged skeleton");
	indexTS ="-05-TS.tif";
	saveAs("Tiff", ""+directoryI+""+nom+""+indexTS+"");//creation of transitional Tagged skeleton image which was analized by Analyze Skeleton. Saving in directoryI
	close();
	ResultLSP ="-01-ResultLSP.xls";
	saveAs("Results", ""+directoryR+""+nom+""+ResultLSP+""); //creation of result Longest Shortest paths xls which was analized by Analyze Skeleton. Saving in directoryR
	run("Close");
	ResultBI ="-02-ResultBI.xls";
	saveAs("Results", ""+directoryR+""+nom+""+ResultBI+""); //creation of transitional BI xls which was analized by Analyze Skeleton. Saving in directoryR
	run("Clear Results");
	run("Close");
 
//////////////////////////////////////////////////////////////////////////////////
//	Analyze Particles	//////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
	Image =dir+nom;
	open(Image);
	run("Split Channels");
	colorRed =nom+" (red)";
	selectWindow(colorRed);
	close();
	colorBlue =nom+" (blue)";
	selectWindow(colorBlue);
	close();
	run("Green");
	run("Properties...", "channels=1 slices=1 frames=1 unit=¬µm pixel_width=0.4857143 pixel_height=0.4857143 voxel_depth=0 frame=[0 sec] origin=0,0");
	run("Tubeness", "sigma=5 use");
	run("Make Binary");
	run("Set Measurements...", "area mean standard min display redirect=None decimal=3");
	run("Analyze Particles...", "size=0,2359184 circularity=0.00-1.00 show=Outlines display clear record add");
	indexAP ="-06-AP.tif";
	saveAs("Tiff", ""+directoryI+""+nom+""+indexAP+"");
 
	ResultAP ="-03-ResultAP.xls";
	saveAs("Results", ""+directoryR+""+nom+""+ResultAP+"");
	run("Close");
// fin boucle
} 
//////////////////////////////////////////////////////////////////////////////////
//	End of Macro	//////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////

code de mon plug-in :

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

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import ij.*;
/*import ij.process.*;
import ij.gui.*;*/
import ij.plugin.*;
/*import ij.plugin.filter.*;
import ij.plugin.tool.*;
import ij.plugin.frame.*;
import ij.macro.*;
import ij.ImagePlus.*;
//import ij.ImageStack.*;*/
 
/*import java.*;
import java.lang.*;
import java.nio.file.Path;
import java.awt.*;*/
import java.io.*;
/*import java.util.*;
import javax.imageio.spi.ImageReaderSpi;*/
 
import javax.swing.JOptionPane;
 
/**
*
* @author
*/
 
public class CapillaryCaracterization_ implements PlugIn {
 
 
	public void run(String arg) {
 
//////////////////////////////////////////////////////////////////////////////////
///Starting up of the plug-in                                                  ///
//////////////////////////////////////////////////////////////////////////////////
 
 
//Image opening and folder informations recovering
 
		//Open dialog box to choose an image and get the absolute path of the image in order to get the path of the folder
		String path = IJ.getFilePath("image"); 
		System.out.println("path = "+path+"\n"); 
		if ( path == null)
		{
			path = IJ.getFilePath("image");
		}
		//Get in dir the path of the folder of the image 
		String dir = IJ.getDirectory("current"); 
		System.out.println("directory = "+dir+"\n");
 
//In the loop ! It's Go !!
 
		File path_img_list = new File(dir);
		File[] listOfFiles = path_img_list.listFiles();
 
		String[] choices = 
			{ "red", "green", "blue" };
 
        String channel = (String) JOptionPane.showInputDialog
        (null, "Color of your probe ?", "Choose channel", 
        JOptionPane.QUESTION_MESSAGE, null,choices,choices[1]);
 
		String channelUpperCase=channel.substring(0, 1)
		.toUpperCase() + channel.substring(1);
 
		IJ.open(path);
		ImagePlus imp = IJ.getImage();
        Double pixelW = imp.getCalibration().pixelWidth;
		   Double pixelH= imp.getCalibration().pixelHeight;
		   System.out.println("largeur métadata = "+pixelW);
		   System.out.println("longueur métadata = "+pixelH);
 
		String pixel = JOptionPane.showInputDialog("If your image is already calibrated,\nplease enter this value : "+pixelW
				+"\n\nelse enter your own value to calibrate your images");
		//String element = JOptionPane.showInputDialog("Size of structuring element?");
		double pixel_width = Double.parseDouble(pixel);
		double pixel_height = Double.parseDouble(pixel);
		//double struc_element = Double.parseDouble(element);
		IJ.run("Close All");
 
 
 
//////////////////////////////////////////////////////////////////////////////////
///Creation of folders                                                         ///
//////////////////////////////////////////////////////////////////////////////////
 
 
		//Folder Analyze, Images and Results
 
			String newDir_A_I = dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator;
				String newDir_A_R = dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Results"+File.separator;
				new File(newDir_A_I).mkdirs();
				new File(newDir_A_R).mkdirs();
 
 
 
 
///*********************************************************************************************************************************************************************///
///                                                                             Image Processing                                                                        ///
///*********************************************************************************************************************************************************************/// 
 
		for (int i = 0; i < listOfFiles.length; i++) 
	    {	
 
			if (listOfFiles[i].isFile()) 
			{
				@SuppressWarnings("unused")	int index = -1;
				String name = (listOfFiles[i].getName() != null) ? ((index = listOfFiles[i].getName().lastIndexOf(".")) == -1) ? listOfFiles[i].getName() : listOfFiles[i].getName().substring(0,listOfFiles[i].getName().lastIndexOf('.')) : "";
				System.out.println("File n°"+ i +" = " + name);
 
				//Get the name of the image with ".extension"
				String name_ext = listOfFiles[i].getName();
				System.out.println("name.tiff = "+name_ext+"\n");
 
				//Construction of the path of the image which will be treated 
				String tmp_path = dir+name_ext;
				System.out.println("tmp_path = "+tmp_path+"\n");
 
				IJ.open(tmp_path);
 
 
//////////////////////////////////////////////////////////////////////////////////
///Splitting in RGB channel and closing color channels which we don't study    ///
//////////////////////////////////////////////////////////////////////////////////
 
				IJ.run("Split Channels");
 
				for (int j = 0; j < choices.length; j++) 
				{
					if(channel!=choices[j]){
					String Color = name_ext+" ("+choices[j]+")";
					IJ.selectWindow(Color);
					IJ.run("Close");
					}
				else
				{
 
					String Color = name_ext+" ("+channel+")";
					IJ.selectWindow(Color);
					String index_C ="_("+channel+")";
					System.out.println(dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_C);
					IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_C);
 
				}
 
 
 
 
 
				}
				//1st image created
 
//////////////////////////////////////////////////////////////////////////////////
///Calibration                                                                 ///
//////////////////////////////////////////////////////////////////////////////////
 
 
				//Setting up of the properties of the images 
				IJ.run("Properties...", "channels=1 slices=1 frames=1 unit=¬µm pixel_width="+pixel_width+" pixel_height="+pixel_height+" voxel_depth=0 frame=[0 sec] origin=0,0");
//////////////////////////////////////////////////////////////////////////////////
///Tubeness                                                                    ///
//////////////////////////////////////////////////////////////////////////////////
 
				IJ.run("Tubeness", "sigma=5");
				String index_T="-01-Tubeness.tif";
 
				IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_T);
 
				//2nd image created
 
//////////////////////////////////////////////////////////////////////////////////
///Binary                                                                      ///
//////////////////////////////////////////////////////////////////////////////////
 
				IJ.run("Make Binary");
				String index_TB="-02-TubenessBinaries.tif";
 
				IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+""+name+""+index_TB);
				//3th image created
 
//////////////////////////////////////////////////////////////////////////////////
///Skeletonize                                                                 ///
//////////////////////////////////////////////////////////////////////////////////
 
				IJ.run("Skeletonize (2D/3D)", "");
				String index_skel="-03-skeleton.tif";
 
				IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_skel);
 
				//4th image created
 
//////////////////////////////////////////////////////////////////////////////////
///Analyze Skeleton                                                            ///
//////////////////////////////////////////////////////////////////////////////////
 
 
				IJ.run("Analyze Skeleton (2D/3D)", "prune=none calculate show");
				IJ.selectWindow("Longest shortest paths");
				String index_LSP="-04-LSP.tif";
 
				IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_LSP);
 
				//5th image created
 
				IJ.run("Close");
				IJ.selectWindow("Tagged skeleton");
				String index_TS="-05-TS.tif";
 
				IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_TS);
 
 
				IJ.run("Close");
				//6th images created
 
				String Result_LSP ="-01-ResultLSP.xls";
 
				IJ.saveAs("Results",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Results"+File.separator+name+Result_LSP);
 
				IJ.run("Close");
				//1st file of results created
 
				String Result_BI ="-02-ResultBI.xls";
				//IJ.saveAs("Results", ""+Dir_A_R+""+name+""+Result_BI+"");
 
				IJ.saveAs("Results",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Results"+File.separator+name+Result_BI);
 
				IJ.run("Clear Results");
				IJ.run("Close");
				//2nd file of results created
 
//////////////////////////////////////////////////////////////////////////////////
///Analyze Particles                                                           ///	
//////////////////////////////////////////////////////////////////////////////////
 
				/*Re-opening of the image in order to analyze the particles
				 * the image need to be treated a second time with Tubeness, Make Binary.
				 */
 
				IJ.open(tmp_path);
				System.out.println("path 2nde partie = "+tmp_path);
 
				IJ.run("Split Channels");
 
 
				for (int k = 0; k < choices.length; k++) 
				{
					if(channel!=choices[k])
					{
						String Color = name_ext+" ("+choices[k]+")";
						IJ.selectWindow(Color);
						IJ.run("Close");
					}
				else
				{
					String Color = name_ext+" ("+channel+")";
					IJ.selectWindow(Color);
					String index_C="_("+channel+")";
					System.out.println(dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_C);
					IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Images"+File.separator+name+index_C);	
				}
 
 
				}
 
 
 
	            IJ.run("Properties...", "channels=1 slices=1 frames=1 unit=¬µm pixel_width="+pixel_width+" pixel_height="+pixel_height+" voxel_depth=0 frame=[0 sec] origin=0,0");
	            System.out.println("taille pixel = "+pixel_width);
	            IJ.run("Tubeness", "sigma=5 use");
				IJ.run("Make Binary", "");
				IJ.run("Set Measurements...", "area mean standard min display redirect=None decimal=3");
				//////////size of structuring element modification ? 
				IJ.run("Analyze Particles...", "size=0,2359184 circularity=0.00-1.00 show=Outlines display clear record add");
				String index_AP ="-06-AP.tif";
 
				IJ.saveAs("Tiff",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Results"+File.separator+name+index_AP);
 
				String Result_AP ="-03-ResultAP.xls";
 
				IJ.saveAs("Results",dir+"Analyze"+File.separator+channelUpperCase+File.separator+"Results"+File.separator+name+Result_AP);
 
				//3rd file of results created
				IJ.run("Close");
				IJ.run("Close All");
				IJ.selectWindow("ROI Manager");
				IJ.run("Close");
				IJ.selectWindow("Results");
				IJ.run("Close");
 
	      }
      }
 
	}
 
 
}

Sauf que un problème reste et ça m'embête dans la macro il y a un setBatchMode=True, qui permet déjà un traitement de 10 sec/image en moyenne. Avec mon plug-in j'augmente la vitesse de traitement tout en affichant les images d'un facteur 2 ! alors j'imagine qu'en n'affichant pas toutes ces fenêtres ça irait encore plus vite !

Mais je ne trouve pas de solution (j'avais pensais à ImagePlus.hide() mais si c'est ça je ne trouve pas où le mettre)

Pour info il n'y a pas de tricherie quelconque j'ai soutenu aujourd'hui mon rapport de projet tuteuré mais j'ai le goût du travail bien fait =D

Merci d'avance à qui pourra m'aider

Loy0

**Kangourou** · 21/01/2016, 13h16

Bonjour,

je crois que ça va être difficile de faire le traitement sans afficher les fenêtres... Dans la version actuelle de ton plugin, la stratégie consiste à afficher les images, puis à appeler les plugins imageJ qui vont pour la plupart travailler sur l'image courante. Donc, il faudra au moins créer les fenêtre, même si tu les caches.

Une solution alternative, mais qui demande plus de travail, serait de passer par l'API de ImageJ, de charger des objets de type "ImagePlus" ou "ImageProcessor", et de trouver quels sont les méthodes utilisées pour faire le traitement appelé par le plugin. Le problème est que ce n'est pas toujours possible, et qu'il faut parfois passer par des création "à la main" des objets Image manipulés par ImageJ. Par exemple, pour charger une image à partir du nom, plutot que de faire "IJ.open(path);", tu peux utiliser "IJ.openImage(path);" qui te renvoie l'objet ImagePlus mais sans l'afficher. Pour extraire les différents canaux couleurs, tu as une méthdoe "ColorImage.getRGB(...)", mais ça oblige à mouliner les tableaux de bytes correspondant aux différentes images.

A+

**Loy027** · 21/01/2016, 13h36

Salut !
D'accord ! Merci de ta réponse je vais explorer tout ça alors !

Loy0

[plug-in] Ne pas afficher les images pendant le traitement

ImageJ Java

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