probleme script enregistrement de valeurs dans un fichier csv

Bonjour,

j'ai un problème avec mon script imagej:

Script:

Code:

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// Ouverture du dossier contenant les images à traiter et ou les enregistrer
input = getDirectory("Dossier à traiter?"); 
list = getFileList(input); 
output = getDirectory("Ou enregistrer?");
 
  Dialog.create("operating system");
  Dialog.addChoice("Type:", newArray("Linux", "Windows"));
  Dialog.show();
  type = Dialog.getChoice();
 
  if (type=="Linux") os="\/";
 
  if (type=="Windows") os="\\";
 
 
// Liste des images
for (i=0; i<list.length; i++)
{
    image = list[i];
    path = input + image;
 
// Utilisation de Bio-Formats macro avec recuperation des données 
    run("Bio-Formats Macro Extensions");
    Ext.setId(path);
    Ext.getCurrentFile(file);
    Ext.getSeriesCount(seriesCount);
 
 
 
// Importation de Bio-Formats (chemin du stack d'image, mode couleur,hyperstack, serie d'images)
    run("Bio-Formats Importer", "open=&path  color_mode=Colorized view=Hyperstack stack_order=XYCZT series_");
 
// Titre de l'image
    t=getTitle();
 
// Creation d'un sous repertoire pour y stocker les images finales
    sub_output = output +t+" Bacteria";
    File.makeDirectory(sub_output);                                                 
    close();
 
//Creation tableau csv
    table1=*"Results of "+t*;
    Table.create(table1)*;
 
// Creation Array pour %Bacteria et %Area
 
 
 
// Importation des differentes series du numero 4 au maximum
    	for (s=4; s<=seriesCount; s++)
	{
 
		run("Bio-Formats Importer", "open=&path color_mode=Colorized split_channels view=Hyperstack stack_order=XYCZT series_"+s);  
 
		run("Close");
 
// Titre de l'image
        	subtitle=getTitle();
 
		run("Duplicate...","title=["+ subtitle+" -Bacteria]");
		run("32-bit");
		run("Maximum...");//"radius=2"
		waitForUser;
 
		imageCalculator("Subtract create 32-bit", subtitle,subtitle+" -Bacteria");
		selectWindow("Result of "+subtitle);
		setOption("BlackBackground", false);
		run("Make Binary");
		run("Close-");
		waitForUser;
 
		run("Set Measurements...", "area mean min centroid center perimeter fit median display redirect=None decimal=3");
		run("Analyze Particles...", "size=0-Infinity circularity=0.0-1.0 display clear summarize add in_situ");
		waitForUser;
 
// Recuperation de la valeur %Area 
    selectWindow("Summary")*;
    IJ.renameResults("Summary","Results");
 
    pArea=getResult("%Area",0)*;
    pBacteria=pArea*;
 
 
    waitForUser;
 
// Selection du tableau et insertion des valeurs (nom de l'image, %Area, % bacteria)
    selectWindow(*"Results of "+t)*;
 
    Table.set("Slice", s-4,subtitle)*;
    Table.set("% Area",s-4,pArea)*;
    Table.set("% Bacteria",s-4,pBacteria)*;
 
    Table.update;
 
 
waitForUser;
// Enregistrement du fichier csv
    Table.save(sub_output + os + t + " bacteria Summary.csv");
 
// Enregistrement de l'image et region d'interet
    selectWindow(subtitle);
    saveAs("Tiff",  sub_output + os+ subtitle+ "+bacteria");
    roiManager("Save", sub_output + os + subtitle+ " Bacteria Roi.zip");
    waitForUser;
	}
 
open(sub_output + os + t + " bacteria Summary.csv");
//selectWindow(t + " bacteria Summary.csv");
 
ValTab=Table.size();
ArrAr=newArray(ValTab);
ArrBact=newArray(ValTab);
 
for(i=0;i<=(ValTab-1);i++)
{
selectWindow( t + " bacteria Summary.csv");
print("tableau: ",  t + " bacteria Summary.csv");
print("valeur :",i);
ArrAr[i]=getResult("% Area",i);
ArrBact[i]=getResult("% Bacteria",i);
print("Area :",ArrAr[i]);
print("Bacteria :",ArrBact[i]);
}
waitForUser;
 
Array.sort(ArrAr);
Array.sort(ArrBact);
 
LAr=ArrAr.length;
LBa=ArrBact.length;
 
 
// calcul de la mediane
 
if ((LAr % 2)==0){
 
print("Pair");
MAr1=ArrAr[((LAr/2)-1)];
MAr2=ArrAr[(LAr/2)];
MedArea=((MAr1+MAr2)/2);
print(MAr1);
print(MAr2);
print(MedArea);
 
}
 
if ((LAr % 2)==1){
 
print("Impair");
MedArea=ArrAr[(LAr/2)];
print(MedArea);
 
}
 
waitForUser;
 
 
if ((LBa % 2)==0){
 
print("Pair");
LBa1=ArrBact[((LBa/2)-1)];
LBa2=ArrBact[(LBa/2)];
MedBact=((LBa1+LBa2)/2);
print(LBa1);
print(LBa2);
print(MedBact);
 
}
 
if ((LBa % 2)==1){
 
print("Impair");
MedBact=ArrBact[(LBa/2)];
print(MedBact);
 
}
waitForUser;
selectWindow( t + " bacteria Summary.csv");
Array.getStatistics(ArrAr, minA, maxA, meanA, stdA);
 
Table.set("Slice", ValTab,"Mean");
Table.set("% Area",ValTab, meanA);
Table.set("Slice", ValTab+1,"Median");
Table.set("% Area",ValTab+1, MedArea);
Table.set("Slice", ValTab+2,"Min");
Table.set("% Area",ValTab+2, minA);
Table.set("Slice", ValTab+3,"Max");
Table.set("% Area",ValTab+3, maxA);
Table.set("Slice", ValTab+4,"SD");
Table.set("% Area",ValTab+4, stdA);
Table.update;
 
Array.getStatistics(ArrBact, minB, maxB, meanB, stdB);
 
Table.set("Slice",ValTab,"Mean");
Table.set("% Bacteria",ValTab, meanB);
Table.set("Slice", ValTab+1,"Median");
Table.set("% Bacteria",ValTab+1, MedBact);
Table.set("Slice", ValTab+2,"Min");
Table.set("% Bacteria",ValTab+2, minB);
Table.set("Slice", ValTab+3,"Max");
Table.set("% Bacteria",ValTab+3, maxB);
Table.set("Slice", ValTab+4,"SD");
Table.set("% Bacteria",ValTab+4, stdB);
Table.update;
 
 
 Table.save(sub_output + os + t + " bacteria Summary.csv");
 
 
 
}

voici la fenetre Debug:

Code:

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Memory	*	185MB of 1820MB (10%)
nImages()	*	18
getTitle()	*	"image.lif - Image009 - C=0+bacteria.tif"
input	*	"/home/user/Bureau/images/"
list	*	array[1]
output	*	"/home/user/Bureau/images/"
type	*	"Linux"
os	*	"/"
i	*	1
image	*	"image.lif"
path	*	"/home/user/Bureau/images/image.lif"
file	*	"/home/user/Bureau/images/image.lif"
seriesCount	*	9
t	*	"image.lif - Series001"
sub_output	*	"/home/user/Bureau/images/image.lif - Series001 Bacteria"
table1	*	"Results of image.lif - Series001"
s	*	10
subtitle	*	"image.lif - Image009 - C=0"
pArea	*	28.7523
pBacteria	*	28.7523
ValTab	*	6
ArrAr	*	array[6]
ArrBact	*	array[6]
 
---		---
Error:		Row (1) out of range in line 119:
		ArrAr [ i ] = getResult ( "% Area" , i <)> ;

voici ce que retourne la fenetre log:

Code:

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image:  image.lif - Series001 bacteria Summary.csv
valeur : 0
Area : NaN
Bacteria : NaN
image:  image.lif - Series001 bacteria Summary.csv
valeur : 1

voici ce que retourne mon tableau de valeurs:

Code:

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Slice                                         % Area      %Bacteria
image.lif - Image004 - C=0	31.155	31.155
image.lif - Image005 - C=0	33.537	33.537
image.lif - Image006 - C=0	32.691	32.691
image.lif - Image007 - C=0	29.726	29.726
image.lif - Image008 - C=0	30.546	30.546
image.lif - Image009 - C=0	28.752	28.752

Je ne sais pas à quoi cela est du.

Car si j'utilise ce script:

Code:

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// Ouverture du dossier contenant les images � traiter et ou les enregistrer
input = getDirectory("Dossier � traiter?"); 
list = getFileList(input); 
output = getDirectory("O� enregistrer?");
 
  Dialog.create("operating system");
  Dialog.addChoice("Type:", newArray("Linux", "Windows"));
  Dialog.show();
  type = Dialog.getChoice();
 
  if (type=="Linux") os="\/";
 
  if (type=="Windows") os="\\";
 
 
// Liste des images
for (i=0; i<list.length; i++)
{
    image = list[i];
    path = input + image;
 
// Utilisation de Bio-Formats macro avec recuperation des donn�es 
    run("Bio-Formats Macro Extensions");
    Ext.setId(path);
    Ext.getCurrentFile(file);
    Ext.getSeriesCount(seriesCount);
 
 
 
// Importation de Bio-Formats (chemin du stack d'image, mode couleur,hyperstack, serie d'images)
    run("Bio-Formats Importer", "open=&path  color_mode=Colorized view=Hyperstack stack_order=XYCZT series_");
 
// Titre de l'image
    t=getTitle();
 
// Creation d'un sous repertoire pour y stocker les images finales
    sub_output = output +t+" Bacteria";
    File.makeDirectory(sub_output);                                                 
    close();
 
//Creation tableau csv
    table1=*"Results of "+t*;
    Table.create(table1)*;
 
// Creation Array pour %Bacteria et %Area
 
 
 
// Importation des differentes series du numero 4 au maximum
    	for (s=4; s<=seriesCount; s++)
	{
 
		run("Bio-Formats Importer", "open=&path color_mode=Colorized split_channels view=Hyperstack stack_order=XYCZT series_"+s);  
 
		run("Close");
 
// Titre de l'image
        	subtitle=getTitle();
 
print("Inserer ici le script");
 
    waitForUser;
	}
 
open(sub_output + os + t + " bacteria Summary.csv");
//selectWindow(t + " bacteria Summary.csv");
 
ValTab=Table.size();
ArrAr=newArray(ValTab);
ArrBact=newArray(ValTab);
 
for(i=0;i<=(ValTab-1);i++)
{
selectWindow( t + " bacteria Summary.csv");
print("image: ",  t + " bacteria Summary.csv");
print("valeur :",i);
ArrAr[i]=getResult("% Area",i);
ArrBact[i]=getResult("% Bacteria",i);
print("Area :",ArrAr[i]);
print("Bacteria :",ArrBact[i]);
}
waitForUser;
 
Array.sort(ArrAr);
Array.sort(ArrBact);
 
LAr=ArrAr.length;
LBa=ArrBact.length;
 
 
// calcul de la mediane
 
if ((LAr % 2)==0){
 
print("Pair");
MAr1=ArrAr[((LAr/2)-1)];
MAr2=ArrAr[(LAr/2)];
MedArea=((MAr1+MAr2)/2);
print(MAr1);
print(MAr2);
print(MedArea);
 
}
 
if ((LAr % 2)==1){
 
print("Impair");
MedArea=ArrAr[(LAr/2)];
print(MedArea);
 
}
 
waitForUser;
 
 
if ((LBa % 2)==0){
 
print("Pair");
LBa1=ArrBact[((LBa/2)-1)];
LBa2=ArrBact[(LBa/2)];
MedBact=((LBa1+LBa2)/2);
print(LBa1);
print(LBa2);
print(MedBact);
 
}
 
if ((LBa % 2)==1){
 
print("Impair");
MedBact=ArrBact[(LBa/2)];
print(MedBact);
 
}
waitForUser;
selectWindow( t + " bacteria Summary.csv");
Array.getStatistics(ArrAr, minA, maxA, meanA, stdA);
 
Table.set("Slice", ValTab,"Mean");
Table.set("% Area",ValTab, meanA);
Table.set("Slice", ValTab+1,"Median");
Table.set("% Area",ValTab+1, MedArea);
Table.set("Slice", ValTab+2,"Min");
Table.set("% Area",ValTab+2, minA);
Table.set("Slice", ValTab+3,"Max");
Table.set("% Area",ValTab+3, maxA);
Table.set("Slice", ValTab+4,"SD");
Table.set("% Area",ValTab+4, stdA);
Table.update;
 
Array.getStatistics(ArrBact, minB, maxB, meanB, stdB);
 
Table.set("Slice",ValTab,"Mean");
Table.set("% Bacteria",ValTab, meanB);
Table.set("Slice", ValTab+1,"Median");
Table.set("% Bacteria",ValTab+1, MedBact);
Table.set("Slice", ValTab+2,"Min");
Table.set("% Bacteria",ValTab+2, minB);
Table.set("Slice", ValTab+3,"Max");
Table.set("% Bacteria",ValTab+3, maxB);
Table.set("Slice", ValTab+4,"SD");
Table.set("% Bacteria",ValTab+4, stdB);
Table.update;
}

et voici ce que retourne mon tableau:

Code:

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Slice                                         % Area      %Bacteria
image.lif - Image004 - C=0	31.155	31.155
image.lif - Image005 - C=0	33.537	33.537
image.lif - Image006 - C=0	32.691	32.691
image.lif - Image007 - C=0	29.726	29.726
image.lif - Image008 - C=0	30.546	30.546
image.lif - Image009 - C=0	28.752	28.752
Mean	31.068	31.068
Median	30.851	30.851
Min	28.752	28.752
Max	33.537	33.537
SD	1.799	1.799
 
C'est ce que je doit obtenir a la fin

Merci pour votre aide.