add batch processing macro and script examples

Author: ekatrukha

script_examples/BT_batch_IJ_macro.ijm

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+
+
+//define file suffix here, can be different, czi, lif, xml, etc
+suffix = ".tif";
+//define autotrace min intensity start 
+dMinIntStart = 30000.;
+//minimum lenght for autotrace
+nMinLength = 100;
+
+// Choose input directory
+input = getDirectory("Input directory");
+
+//clear the log window
+print("\\Clear");
+
+// Create timestamp to save log later
+timestamp = getTimeStamp_sec();
+
+// Get file list
+list = getFileList(input);
+
+nCount = 0;
+bFirst = true;
+
+for (nFile = 0; nFile < list.length; nFile++) 
+{
+	if(endsWith(list[nFile], suffix))	
+	{		
+		basecurr = input + list[nFile];
+		//in case you need only filename without extension somewhere later
+		noExtFilename = substring(list[nFile], 0, lengthOf(list[nFile])-lengthOf(suffix));
+		nCount++;
+		if(bFirst)
+		{
+			run("Open 3D image", "open=[" + basecurr + "]"); 
+			bFirst = false;
+		}
+		else 
+		{
+			Ext.btOpenNext(basecurr); 
+		}
+
+		//make a folder to store things
+		saveDir = input + toString(nCount) + "/";		
+		File.makeDirectory(saveDir); 
+		
+		//process image in BigTrace
+		///set active channel for tracing (if multichannel)
+		Ext.btSetActiveChannel(1);
+		//maybe set other parameters, otherwise current stored (last used) will be used
+		//....
+		
+		//run auto-trace (all frames)
+		Ext.btRunFullAutoTrace(dMinIntStart, nMinLength);
+		//save ROIs in CSV
+		Ext.btSaveROIs(saveDir + "rois.csv", "CSV");
+		//obtain and save measurements
+		Ext.btMeasureAndSave (saveDir + "Results.csv");
+		//save straightened versions of ROIs
+		//Ext.btStraighten(0, saveDir, "Round");
+		//can save log file here too, after each volume, in case something goes wrong
+	}
+
+}
+Ext.btClose(); 
+selectWindow("Log");
+saveAs("Text", input + "BigTrace_IJmacro_" + timestamp + ".txt");
+	
+function getTimeStamp_sec() 
+{ 
+	// returns timestamp: yearmonthdayhourminutesecond
+	getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
+	
+	TimeStamp = toString(year) + "-" + IJ.pad(month+1,2) + "-" + IJ.pad(dayOfMonth,2) + "-";
+	TimeStamp = TimeStamp + IJ.pad(hour,2) + "-" + IJ.pad(minute,2) + "-" + IJ.pad(second,2);
+	return TimeStamp;
+}

script_examples/BT_batch_script.groovy

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+import ij.IJ
+import ij.io.DirectoryChooser
+import ij.text.TextWindow
+import ij.WindowManager
+import java.text.SimpleDateFormat
+import java.util.Date
+import java.io.File
+import bigtrace.BigTrace
+
+//define file suffix here, can be different, czi, lif, xml, etc
+def suffix = ".tif"
+//define autotrace min intensity start 
+def dMinIntStart = 30000 as double
+//minimum lenght for autotrace
+def nMinLength = 100 as int
+
+// Choose input directory
+def dc = new DirectoryChooser("Input directory")
+def input = dc.getDirectory()
+
+//clear the log window
+def logWindow = WindowManager.getWindow("Log")
+if (logWindow != null) {
+    def textPanel = logWindow.getTextPanel()
+    textPanel.clear()
+}
+// Create timestamp to save log later
+def sdf = new SimpleDateFormat("yyyy-MM-dd_HH-mm-ss")
+def timestamp = sdf.format(new Date())
+
+// Get file list
+def dir = new File(input)
+def list = dir.list()
+
+int nCount = 0
+boolean bFirst = true
+
+BT = new BigTrace(); 
+list.each { filename ->
+
+    if (filename.endsWith(suffix)) {
+
+        def basecurr = input + filename
+
+        // filename without extension
+        def noExtFilename = filename[0..-(suffix.length()+1)]
+
+        nCount++
+
+        if (bFirst) {
+            BT.run( basecurr )
+            bFirst = false
+        } else {
+            BT.btMacro.macroOpenNext(basecurr)
+        }
+		//make a folder to store things
+        def saveDir = input + nCount + File.separator
+        new File(saveDir).mkdirs()
+        
+        //process image in BigTrace
+
+		//set active channel for tracing (if multichannel)
+        BT.btMacro.macroSetActiveChannel(1)
+        //maybe set other parameters, otherwise current stored (last used) will be used
+		//....
+		
+		//run auto-trace (all frames)
+        BT.btMacro.macroRunFullAutoTrace(dMinIntStart, nMinLength)
+        //save ROIs in CSV
+        BT.btMacro.macroSaveROIs(saveDir + "rois.csv", "CSV")
+        //obtain and save measurements
+        BT.btMacro.macroMeasureAndSave(saveDir + "Results.csv")
+        //save straightened versions of ROIs
+        //BT.btMacro.macroStraighten(0, saveDir, "Round")
+        //can save log file here too, after each volume, in case something goes wrong
+    }
+}
+BT.btMacro.macroClose()
+
+//save log
+// Create filename
+def filePath = input + "BigTrace_groovy_Log_" + timestamp + ".txt"
+
+// Save log to file
+new File(filePath).text = IJ.getLog()