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crop_40x_to_63x_cam.ijm
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crop_40x_to_63x_cam.ijm
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//setBatchMode(true)
// From OpenSeriesUsingFilter.txt
// Recursive file listing.
count = 1;
function listFiles(dir, rootDir, search, array) {
fileList = getFileList(dir);
for (i=0; i<fileList.length; i++) {
if (endsWith(fileList[i], "/")) {
array = listFiles(""+dir+fileList[i], rootDir, search, array);
} else {
if (filter(i, fileList[i], search)) {
pathToString = dir + fileList[i];
array = addToArray(pathToString, array, array.length);
//testing
print((count++) + ": " + array[array.length-1]);
}
}
}
return array;
}
// From OpenSeriesUsingFilter.txt
// Filter files in chosen directory and sub-directories to use for analysis,
// by conditions set below.
function filter(i, name, search) {
// is directory?
if (endsWith(name, File.separator)) return false;
// does name match regex search?
if (matches(name, search) != true) return false;
// open only first 10 images
// if (i >= 10) return false;
return true;
}
// From Array_Tools.ijm.
// Adds the value to the array at the specified position,
// expanding if necessary. Returns the modified array.
function addToArray(value, array, position) {
if (position<lengthOf(array)) {
array[position]=value;
} else {
temparray=newArray(position+1);
for (i=0; i<lengthOf(array); i++) {
temparray[i]=array[i];
}
temparray[position]=value;
array=temparray;
}
return array;
}
// Set path to image directory.
dirChosen = getDirectory("Choose a Directory ");
topDir = dirChosen;
fileArray = newArray();
fileArray = listFiles(dirChosen, topDir, ".+E01.+\\.tif$", fileArray);
// Write existing coordinate file contents to new file.
if (File.exists(topDir+"63x_coords.csv") == true) {
fileString = File.openAsString(topDir+"63x_coords.csv");
} else {
fileString = "fov,dxM,dyM,dxPx,dyPx";
}
success = File.delete(topDir+"63x_coords.csv");
// Open file to write output to.
output = File.open(topDir+"63x_coords.csv");
print(output, fileString);
// For-loop ends at the bottom of the code, as most of it is done on each image.
for (j = 0; j < fileArray.length; j++) {
//Open image.
open(fileArray[j]);
//Get image name.
name = getTitle();
//Image size (pixels)
width = getWidth;
//Close the image if it does not have the correct image size in pixels.
if (width < 512) {
print("Not correct size of image!");
close();
} else {
//Well, field and channel
xWellIndex = indexOf(name, "U");
yWellIndex = indexOf(name, "--V");
xWell = substring(name, xWellIndex+1, xWellIndex+3);
yWell = substring(name, yWellIndex+3, yWellIndex+5);
wellNumber = (8 * (parseInt(xWell)) + (parseInt(yWell)))+1;
xFieldIndex = indexOf(name, "--X");
yFieldIndex = indexOf(name, "--Y");
xField = substring(name, xFieldIndex+3, xFieldIndex+5);
yField = substring(name, yFieldIndex+3, yFieldIndex+5);
cIndex = indexOf(name, "--C");
channel = substring(name, cIndex+3, cIndex+5);
jobOrderIndex = indexOf(name, "--E");
jobOrder = substring(name, jobOrderIndex+3, jobOrderIndex+5);
jobNumberIndex = indexOf(name, "--J");
jobNumber = substring(name, jobNumberIndex+3, jobNumberIndex+5);
redPath = replace(replace(fileArray[j], "--E"+jobOrder, "--E03"), "--J"+jobNumber, "--J"+toString(parseInt(jobNumber)+2)+"");
open(redPath);
redName = getTitle();
if (xWell == "00" && yWell == "00" && xField == "00" && yField == "00") {
makeRectangle(0, 0, width/2, width/2);
run("Draw");
makeRectangle(width/2, width/2, width/2, width/2);
run("Draw");
saveAs("PNG", topDir+"start_position.png");
close;
open(redPath);
}
run("Merge Channels...", "c1="+redName+" c2="+name+"");
// Make selection rectangle
makeRectangle(width/2, width/2, round(width*164/387.5), round(width*164/387.5));
// waitForUser(title, message)
waitForUser("Well: "+wellNumber+" Fieldx: "+xField+" Fieldy: "+yField+"",
"Please select the area to be cropped. When you are done, click ok.");
// Get selection coordinates
getSelectionCoordinates(roiX, roiY);
if(!getBoolean("Do you want to save the position of the cropped image for 63x imaging? Cancel will quit the macro.")) {
close;
err=File.rename(fileArray[j], fileArray[j]+".bak");
} else {
//Testing
for (k=0; k<roiX.length; k++) {
print(k+" "+roiX[k]+" "+roiY[k]);
}
for (k = 1; k < 4; k++) {
//imageChannel = replace(fileArray[j], "--C"+channel, "--C0"+k+"");
imageChannel = replace(replace(fileArray[j], "--E"+jobOrder, "--E0"+k+""), "--J"+jobNumber, "--J"+toString(parseInt(jobNumber)+k-1)+"");
open(imageChannel);
makeRectangle(roiX[0], roiY[0], round(width*164/387.5), round(width*164/387.5));
run("Crop");
saveAs("Tiff", ""+replace(imageChannel, ".tif", "_cropped.tif"));
close();
err=File.rename(replace(imageChannel, ".tif", "_cropped.tif"), replace(imageChannel, ".tif", "_cropped.tif")+".bak");
if (k == 2) {
imageChannel = replace(imageChannel, "--C"+channel, "--C01");
open(imageChannel);
makeRectangle(roiX[0], roiY[0], round(width*164/387.5), round(width*164/387.5));
run("Crop");
saveAs("Tiff", ""+replace(imageChannel, ".tif", "_cropped.tif"));
close();
err=File.rename(replace(imageChannel, ".tif", "_cropped.tif"), replace(imageChannel, ".tif", "_cropped.tif")+".bak");
}
//err=File.rename(replace(imageChannel, ".ome.tif", "_cropped.ome.tif"), replace(replace(imageChannel, ".ome.tif", "_cropped.ome.tif"), "image--.+", "/cropped/"+replace(replace(imageChannel, ".ome.tif", "_cropped.ome.tif"), ".+image--", "image--")));
}
// A half 63x zoom 1.5 image is ~433 px on a 40x zoom 1 image.
// 0.1892 um/px for 40x zoom 1. 6.05 um/px for 10x zoom 1, 1550 um/256 px image,
// which is the selected dummy job settings.
// Difference in XY after changing from 40x to 63x oil objective
// in Y is +17.0 um (90 px for 40x zoom 1) on the image, or -17.0 um
// on the table. Don't need to correct for that if start coordinates are
// synced instead. Using image rotation -90 degrees, flips X and Y axes.
//pixels in a 63x zoom 1.5 image
dxPx = round((1024 - roiX[0] - 433) * (0.1892/6.05));
dyPx = round((1024 - roiY[0] - 433) * (0.1892/6.05));
//m
dxM = (dxPx * 6.05)/1000000;
dyM = (dyPx * 6.05)/1000000;
//Testing
print("xWell: "+xWell);
print("yWell: "+yWell);
print(output, "U"+xWell+"--V"+yWell+"--X"+xField+"--Y"+yField+","+dxM+","+dyM+","+dxPx+","+dyPx);
//Close the image.
close();
err=File.rename(fileArray[j], fileArray[j]+".bak");
}
}
}
File.close(output);
print("Analysis finished!");