OptScan: Change a comment.

* MS-read-parameters-file:
  Implemented "if" to check if settings file exists and put corresponding default values. At end of plugin, the settings file is (re)written with the new parameters.
  Removed temporary file for tests
  Changed if for test
  Added if
  Added hidden file for testing
  Removed stitchedScan line, since this is deprecated.

plugins/Multiscale_Coords.ijm

@@ -4,7 +4,7 @@
 /////////             MULTISCALE TOMOGRAPHY PLUGIN             ///////// 
 /////////                                                      /////////
 /////////      Created by Hector Dejea, hector.dejea@psi.ch    /////////
-/////////                     October, 2019                    /////////
+/////////                       May, 2017                      /////////
 /////////                                                      /////////
 /////////                    Reference paper:                  /////////
 /////////  Dejea, H. et al. Scientific Reports 9, 6996 (2019)  /////////
@@ -28,7 +28,9 @@ The ROI size of the HighRes scan is shown according to the user-
 supplied parameters of LowRes and HighRes scans. The  user can move 
 the ROI interactively to the desired position, and the movements in 
 um are given as the result. Start and end position values for stitched 
-scans are also available. */
+scans are also available. 
+
+Last modified: 10/10/2019*/
 
 //Check if there is a file containing the multiscale settings
 settings_path = getDirectory("home") + "/.multiscale_settings.txt";

plugins/Opt_Scan.ijm

@@ -1,30 +1,67 @@
+////////////////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////
+/////////                                                      ///////// 
+/////////                  OPTIMISED SCAN PLUGIN               ///////// 
+/////////                                                      /////////
+/////////      Created by Hector Dejea, hector.dejea@psi.ch    /////////
+/////////                     February, 2018                   /////////
+/////////                                                      /////////
+////////////////////////////////////////////////////////////////////////
+////////////////////////////////////////////////////////////////////////
+
 /* Optimised Scan
 
-Opt_Scan.ijm is an ImageJ plugin to find the optimal scanning grid for irregular objects. Binary and
-non binary images are accepted. The option to have a constant grid on the whole object or 
-independent grids for each of the different Y layers is given. The plugin generates a .txt file that
-can be used as input for the beamline macro.
+Opt_Scan.ijm is an ImageJ plugin to find the optimal scanning grid for 
+irregular objects. Binary and non binary images are accepted. The option
+to have a constant grid on the whole object or independent grids for 
+each of the different Y layers is given. The plugin generates a .txt file
+that can be used as input for the beamline macro.
 
-*Created by hector.dejea@psi.ch in February 2018* */
+Last modified: 14/10/2019 */ 
 
-//Set default values
-LowResimagePixelSize = 6.5;
-ZZcenterLowRes = 0;
-XXcenterLowRes = 0;
-YposLowRes = 0;
-LowResFOVY = 590;
-cameraFOVX = 2560;
-cameraFOVY = 2160;
-HighResimagePixelSize = 0.65;
-CameraMoveX = 0;
-CameraMoveY = 0;
+//Check if there is a file containing the OptScan settings
+settings_path = getDirectory("home") + "/.optscan_settings.txt";
 
-overlapXZ = cameraFOVX*0.3;
-overlapY = 50;
+if (File.exists(settings_path)){
+
+	//Set default parameters specified in the file
+	parameters_file = File.openAsString(settings_path);
+	lines=split(parameters_file,"\n");
+
+	LowResimagePixelSize = lines[3];
+	ZZcenterLowRes = lines[5];
+	XXcenterLowRes = lines[7];
+	YposLowRes = lines[9];
+	LowResFOVY = lines[11];
+	cameraFOVX = lines[13];
+	cameraFOVY = lines[15];
+	HighResimagePixelSize = lines[17];
+	CameraMoveX = lines[19];
+	CameraMoveY = lines[21];
+	overlapXZ = lines[23];
+	overlapY = lines[25];
+
+} else {
+
+	//Otherwise set these default values
+	LowResimagePixelSize = 6.5;
+	ZZcenterLowRes = 0;
+	XXcenterLowRes = 0;
+	YposLowRes = 0;
+	LowResFOVY = 590;
+	cameraFOVX = 2560;
+	cameraFOVY = 2160;
+	HighResimagePixelSize = 0.65;
+	CameraMoveX = 0;
+	CameraMoveY = 0;
+	overlapXZ = cameraFOVX*0.3;
+	overlapY = 50;
+
+}
 
 repeatFlag = 1;
 while (repeatFlag == 1){
-	print("Welcome to the Scan Optimisation plugin!");
+	print("Welcome to the Scan Optimisation plugin!\n");
 
 	//Ask the user for LowRes and HighRes acquisition parameters
 	Dialog.create("Magnification and Camera Settings");
@@ -41,12 +78,10 @@ while (repeatFlag == 1){
 	Dialog.addNumber("Overlap in X and Z (pixels):", overlapXZ);
 	Dialog.addNumber("Overlap in Y (pixels):", overlapY);
 	Dialog.addChoice("Projection Method:", newArray("MaxIP" ,"MinIP"), "MaxIP");
-	Dialog.addChoice("Grid Mode:", newArray("Constant !!NOT READY!!" ,"Independent"), "Independent");
 
 	Dialog.show();
 
 	LowResimagePixelSize = Dialog.getNumber();
-	//angleLowRes = Dialog.getChoice();
 	XXcenterLowRes = Dialog.getNumber();
 	ZZcenterLowRes = Dialog.getNumber();
 	YposLowRes = Dialog.getNumber();
@@ -59,7 +94,6 @@ while (repeatFlag == 1){
 	overlapXZ = Dialog.getNumber();
 	overlapY = Dialog.getNumber();
 	projMethod = Dialog.getChoice();
-	gridMode = Dialog.getChoice();
 
 	// Real magnification
 	real_magnification = LowResimagePixelSize/HighResimagePixelSize;
@@ -74,13 +108,13 @@ while (repeatFlag == 1){
 
 	//Compute number of acquisition layers in Y and layer size
 	blockSizeY = cameraFOVY-overlapY;
-	print("Complete block Size in Y is " + (cameraFOVY/real_magnification) + " pixels");
+	print("Volume Size in Y is " + (cameraFOVY/real_magnification) + " pixels");
 	print("Block Size in Y is " + (blockSizeY/real_magnification) + " pixels");
 	nLayersY = computeNumberBlocks("Y",blockSizeY,cameraFOVY,StartSlice,EndSlice,real_magnification);
 
 	//Compute blocksize XZ
 	blockSizeXZ = cameraFOVX-overlapXZ;
-	print("Complete block Size in XZ is " + (cameraFOVX/real_magnification) + " pixels");
+	print("Volume Size in XZ is " + (cameraFOVX/real_magnification) + " pixels");
 	print("Block Size in XZ is " + (blockSizeXZ/real_magnification) + " pixels");
 
 	//Check if image is binary
@@ -127,20 +161,10 @@ while (repeatFlag == 1){
 			yEndVals[i] = y + height -1;	
 		}
 
-		//GENERATE Y CONSTANT GRID
-		if (gridMode == "Constant") {
-			centresXXZZY = generateYConstantGrid(blockSizeXZ,blockSizeY,cameraFOVX,cameraFOVY,nLayersY,xVals,
-				yVals,xEndVals,yEndVals,real_magnification,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,
-				HighResimagePixelSize,LowResFOVY,CameraMoveX,CameraMoveY,imagewidth,imageheight,StartSlice);
-		}
-
-		//GENERATE Y INDEPENDENT GRID
-		if (gridMode == "Independent") {
-			centresXXZZY = generateYIndependentGrid(blockSizeXZ,blockSizeY,cameraFOVX,cameraFOVY,nLayersY,xVals,
-				yVals,xEndVals,yEndVals,real_magnification,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,
-				HighResimagePixelSize,LowResFOVY,CameraMoveX,CameraMoveY,imagewidth,imageheight,StartSlice);
-		}
-		
+		//GENERATE GRID
+		centresXXZZY = generateYIndependentGrid(blockSizeXZ,blockSizeY,cameraFOVX,cameraFOVY,nLayersY,xVals,
+			yVals,xEndVals,yEndVals,real_magnification,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,
+			HighResimagePixelSize,LowResFOVY,CameraMoveX,CameraMoveY,imagewidth,imageheight,StartSlice);
 
 		//COMPLETE FOR BINARY IMAGES -> ELIMINATE EMPTY VOLUMES
 
@@ -176,19 +200,11 @@ while (repeatFlag == 1){
 			yEndVals[i] = y + height -1;
 		}
 
-		//GENERATE CONSTANT GRID
-		if (gridMode == "Constant") {
-			centresXXZZY = generateYConstantGrid(blockSizeXZ,blockSizeY,cameraFOVX,cameraFOVY,nLayersY,xVals,
-				yVals,xEndVals,yEndVals,real_magnification,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,
-				HighResimagePixelSize,LowResFOVY,CameraMoveX,CameraMoveY,imagewidth,imageheight,StartSlice);
-		}
+		//GENERATE GRID
+		centresXXZZY = generateYIndependentGrid(blockSizeXZ,blockSizeY,cameraFOVX,cameraFOVY,nLayersY,xVals,
+			yVals,xEndVals,yEndVals,real_magnification,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,
+			HighResimagePixelSize,LowResFOVY,CameraMoveX,CameraMoveY,imagewidth,imageheight,StartSlice);
 
-		//GENERATE INDEPENDENT GRID
-		if (gridMode == "Independent") {
-			centresXXZZY = generateYIndependentGrid(blockSizeXZ,blockSizeY,cameraFOVX,cameraFOVY,nLayersY,xVals,
-				yVals,xEndVals,yEndVals,real_magnification,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,
-				HighResimagePixelSize,LowResFOVY,CameraMoveX,CameraMoveY,imagewidth,imageheight,StartSlice);
-		}
 	}
 
 	//Print .txt file with the generated coordinates
@@ -200,8 +216,26 @@ while (repeatFlag == 1){
 	if (repeatFlag) {
 		closeGeneratedImgs();
 	}
+
+	//Save txt file with the parameters used, so that they are default for next use.
+	settings_file = File.open(settings_path);
+	settings_array = "File containing the last settings used in Opt_Scan.ijm\n" +
+	"\nLowResimagePixelSize\n" + LowResimagePixelSize +
+	"\nZZcenterLowRes\n" + ZZcenterLowRes +
+	"\nXXcenterLowRes\n" + XXcenterLowRes +
+	"\nYposLowRes\n" + YposLowRes +
+	"\nLowResFOVY\n" + LowResFOVY +
+	"\ncameraFOVX\n" + cameraFOVX +
+	"\ncameraFOVY\n" + cameraFOVY +
+	"\nHighResimagePixelSize\n" + HighResimagePixelSize +
+	"\nCameraMoveX\n" + CameraMoveX +
+	"\nCameraMoveY\n" + CameraMoveY +
+	"\noverlapXZ\n" + overlapXZ +
+	"\noverlapY\n" + overlapY;
+	print(settings_file, settings_array);
+	File.close(settings_file);
   
-}
+} //END
 
 
   
@@ -332,8 +366,10 @@ while (repeatFlag == 1){
   	totalBlocksLayer = 0;
   	totalBlocks = 0;
   	for (i = 0; i < nLayersY; i++ ) {
+  		print("\nY layer" + (i+1) + ":");
   		numBlocksXX[i] = computeNumberBlocks("XX",blockSizeXZ,cameraFOVX,yVals[i],yEndVals[i],real_magnification);
 	  	numBlocksZZ[i] = computeNumberBlocks("ZZ",blockSizeXZ,cameraFOVX,xVals[i],xEndVals[i],real_magnification);
+
 	  	//Total number of XX and ZZ blocks
 	  	totalBlocksLayer = numBlocksXX[i]*numBlocksZZ[i];
 	  	totalBlocks = totalBlocks + totalBlocksLayer;
@@ -346,111 +382,6 @@ while (repeatFlag == 1){
   	return centresXXZZY;
   }
 
-  ////////////////////////////////////////
-  
-  function generateYConstantGrid(blockSizeXZ,blockSizeY,cameraFOVX,cameraFOVY,nLayersY,xVals,yVals,xEndVals,
-  	yEndVals,real_magnification,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,HighResimagePixelSize,
-  	LowResFOVY,CameraMoveX,CameraMoveY,imagewidth,imageheight,StartSlice) {
-  	//Function that generates a constant grid for all Y layers.
-
-	  Array.getStatistics(xVals, minx);
-	  Array.getStatistics(yVals, miny);
-	  Array.getStatistics(xEndVals, minw, maxw);
-	  Array.getStatistics(yEndVals, minh, maxh);
-
-	  //Compute number of blocks for most extense rectangle
-	  numBlocksXXmax = computeNumberBlocks("XX",blockSizeXZ,cameraFOVX,miny,maxh,real_magnification);
-	  numBlocksZZmax = computeNumberBlocks("ZZ",blockSizeXZ,cameraFOVX,minx,maxw,real_magnification);
-
-	  //Generate the FIXED GRID (in Low Resolution pixels)
-	  gridXX = newArray(numBlocksXXmax+1);
-	  gridZZ = newArray(numBlocksZZmax+1);
-	  gridXXcentres = newArray(numBlocksXXmax);
-	  gridZZcentres = newArray(numBlocksZZmax);
-
-	  gridXX[0] = miny;
-	  gridZZ[0] = minx;
-
-	  //First block is complete, so the center is computed without overlap taken into account
-	  gridXXcentres[0] = gridXX[0] + cameraFOVX/2/real_magnification;
-
-	  //Compute XX center and XX position for each volume of the grid
-	  for (i=1; i < numBlocksXXmax; i++) {
-	   	gridXXcentres[i] = gridXXcentres[i-1] + blockSizeXZ/real_magnification;
-	  	gridXX[i] = gridXX[i-1] + blockSizeXZ/real_magnification;
-	  }
-
-	  //First block is complete, so the center is computed without overlap taken into account
-	  gridZZcentres[0] = gridZZ[0] + cameraFOVX/2/real_magnification;
-
-	  //Compute ZZ center and ZZ grid position for each volume of the grid
-	  for (i=1; i < numBlocksZZmax; i++) {
-	    gridZZcentres[i] = gridZZcentres[i-1] + blockSizeXZ/real_magnification;
-	  	gridZZ[i] = gridZZ[i-1] + blockSizeXZ/real_magnification;
-	  }
-
-	  //Modify rectangle coordinates to fit the generated grid
-	  //Central position of the corresponding FOV is given (in pixels)
-	  posInZZ = newArray(nLayersY);
-	  posFinZZ = newArray(nLayersY);
-	  posInXX = newArray(nLayersY);
-	  posFinXX = newArray(nLayersY);
-
-	  for (i = 0; i < nLayersY; i++) {
-	  	
-	  	for (j = 1; j < numBlocksZZmax+1; j++) {
-	  		if (xVals[i] < gridZZ[j]){
-	  			posInZZ[i] = gridZZcentres[j-1];
-	  			break;
-	  		}
-	  	}
-
-	  	for (k = j; k < numBlocksZZmax+1; k++) {
-	  		if (xEndVals[i] < gridZZ[k]){
-	  			posFinZZ[i] = gridZZcentres[k-1];
-	  			break;
-	  		}
-	  	}
-
-	  	for (jj = 1; jj < numBlocksXXmax+1; jj++) {
-	  		if (yVals[i] < gridXX[jj]){
-	  			posInXX[i] = gridXXcentres[jj-1];
-	  			break;
-	  		}
-	  	}
-
-	  	for (kk = jj; kk < numBlocksXXmax+1; kk++) {
-	  		if (yEndVals[i] < gridXX[kk]){
-	  			posFinXX[i] = gridXXcentres[kk-1];
-	  			break;
-	  		}
-	  	}
-	  }
-
-	  //Compute Y positions in stage coords
-      centresYreal = computeYCoords(nLayersY,YposLowRes,LowResFOVY,StartSlice,LowResimagePixelSize,CameraMoveY,
-      	cameraFOVY,HighResimagePixelSize,blockSizeY);	
-
-  	  //Compute number of blocks per layer and total number
-  	  numBlocksXX = newArray(nLayersY);
-  	  numBlocksZZ = newArray(nLayersY);
-  	  totalBlocksLayer = 0;
-  	  totalBlocks = 0;
-  	  for (i = 0; i < nLayersY; i++ ) {
-  	  	numBlocksXX[i] = computeNumberBlocks("XX",blockSizeXZ,cameraFOVX,posInXX[i],posFinXX[i],real_magnification);
-	  	numBlocksZZ[i] = computeNumberBlocks("ZZ",blockSizeXZ,cameraFOVX,posInZZ[i],posFinZZ[i],real_magnification);
-	  	//Total number of XX and ZZ blocks
-	  	totalBlocksLayer = numBlocksXX[i]*numBlocksZZ[i];
-	  	totalBlocks = totalBlocks + totalBlocksLayer;
-  	  }
-
-  	  //Grid in stage coords giving (XX,ZZ,Y) for each volume, from top to bottom, left to right and up to down.
-	  centresXXZZY = lowResPx2StageCoords(numBlocksXX,numBlocksZZ,totalBlocks,nLayersY,posInXX,posInZZ,
-	  	cameraFOVX,real_magnification,imagewidth,imageheight,XXcenterLowRes,ZZcenterLowRes,LowResimagePixelSize,
-	  	HighResimagePixelSize,CameraMoveX,blockSizeXZ,centresYreal);
-  	  return centresXXZZY;
-  }
-
   ////////////////////////////////////////
 
   function writeCoordsFile(centresXXZZY) {

plugins/centering_overlay.py

@@ -1,19 +0,0 @@
-from ij import IJ
-from ij.gui import Overlay, Line
-
-imp = IJ.getImage()
-cx = int(imp.width/2.0)
-cy = int(imp.height/2.0)
-
-print cx, cy
-
-overlay = Overlay()
-line_v = Line(cx,0,cx,imp.height)
-line_v.setStrokeWidth(1)
-overlay.add(line_v)
-line_h = Line(0,cy,imp.width,cy)
-line_h.setStrokeWidth(1)
-overlay.add(line_h)
-
-imp.setOverlay(overlay)
-imp.show()