Siliceous and Delicious

Well. Another somewhat slow day, but not without progress. Managed to hash out the remainder of the ImageJ portion of the measurement interface. It seems to be quite reliably making measurements, with the intervening calculations of area, and writing them successfully to the “pipe” file—all the while keeping track of the measurement number to facilitate easy reference to the image displayed by the R portion of the interface. Huzzah!

Here the product of the last two days’ work—embarrassing though it may be that it took so long, I’m proud that it seems to work. Many may have been able to do it faster, but far more would not have been able to do it at all…

//Macros to collect radiolarian morphometric measurements for acquisition

//to the RadData database, via its R interface.

//Written by Ben Kotrc, Mar 1st, 2011

//Declare global variables

//Measurement number (in reference to R interface image)

var counter = 0;

//Microscope magnification (e.g. 16x, 40x, etc)

var objective = “??x.”;

//Macro to write all measurements of type “Length” taken since the last

//file write operation, with the current image file name, to the pipe file

macro “Save linear measurements to file [1]” {

//Get name of currently open image file

curfname=getInfo(“image.filename”);

//Loop through each row in the Results table

for (i=counter; i<nResults; i++){

//Extract the ith row from the “Length” column of the Results table

measurement = getResult(“Length”, i);

//Concatenate row of data to be appended to pipe file (data + filename)

insertion = d2s(measurement,2) + “\t” + curfname;

//Append the ith measurement to the Results table

File.append(insertion, “/Users/Ben/Dropbox/Harvard/By-Lineage\ Rads/RadData\ Database/pipefilename.txt”);

//Increment the measurement counter

counter++;

}

//Display in log window how many measurements have been written to file

print(“\\Clear”);

print(“Scale set to ” + objective + “.”);

print(d2s(counter,0) + ” measurements recorded to file.”);

}

//Macro to calculate the pore area proportion from the measurements added

//to the results table since the last file write operation, then write the

//number to file with the current image file name

macro “Save area measurement to file [2]” {

//Get name of currently open image file

curfname=getInfo(“image.filename”);

//Find the sum of all but the first row in the Results table

sum=0;

for (i=counter+1; i<nResults; i++){

sum = sum + getResult(“Area”,i);

}

//Find the pore area proportion

measurement = sum/getResult(“Area”,counter);

//Concatenate row of data to be appended to pipe file (data + filename)

insertion = d2s(measurement,4) + “\t” + curfname;

//Append the result to file

File.append(insertion, “/Users/Ben/Dropbox/Harvard/By-Lineage\ Rads/RadData\ Database/pipefilename.txt”);

//Increment the measurement counter

counter++;

//Display in log window how many measurements have been written to file

print(“\\Clear”);

print(“Scale set to ” + objective + “.”);

print(d2s(counter,0) + ” measurements recorded to file.”);

//Tidy up the Results table

IJ.deleteRows(counter,nResults-1);

setResult(“Area”,counter-1,measurement);

}

//Macro to insert a zero-valued measurement to the pipe file, and update

//the ImageJ results table accordingly

macro “Add zero measurement to file [3]” {

measurement = 0;

curfname = “No file”;

//Concatenate row of data to be appended to pipe file (data + filename)

insertion = d2s(measurement,4) + “\t” + curfname;

//Append the result to file

File.append(insertion, “/Users/Ben/Dropbox/Harvard/By-Lineage\ Rads/RadData\ Database/pipefilename.txt”);

//Update Results table to reflect added zero “measurement”

setResult(“Area”, counter, 0);

//Increment the measurement counter

counter++;

//Display in log window how many measurements have been written to file

print(“\\Clear”);

print(“Scale set to ” + objective + “.”);

print(d2s(counter,0) + ” measurements recorded to file.”);

}

//Macro to reset the tally of the number of measurements written to file,

//as displayed in the log window, to zero (use each time a new individual

//is started)

macro “Reset measurement counter [4]” {

//Clear the Results table

selectWindow(“Results”);

run(“Close”);

//Reset counter

counter = 0;

//Display in log window

print(“\\Clear”);

print(“Scale set to ” + objective + “.”);

print(d2s(counter,0) + ” measurements recorded to file.”);

}

\\Macro to set the appropriate scale for different microscope objectives

macro “Set magnification… [5]” {

Dialog.create(“Set magnification”);

Dialog.addChoice(“Objective:”, newArray(“16x”, “40x”, “80x”, “100x”));

Dialog.show();

objective = Dialog.getChoice();

if (objective == “16x”) {

run(“Set Scale…”, “distance=1190 known=26.3 pixel=1 unit=µm”);

} else if (objective == “40x”){

run(“Set Scale…”, “distance=1190 known=26.3 pixel=1 unit=µm”);

} else if (objective == “80x”){

run(“Set Scale…”, “distance=1190 known=26.3 pixel=1 unit=µm”);

} else if (objective == “1000x”){

run(“Set Scale…”, “distance=1190 known=26.3 pixel=1 unit=µm”);

}

//Print new magnification in log window, along with # of measurements taken

print(“\\Clear”);

print(“Scale set to ” + objective + “.”);

print(d2s(counter,0) + ” measurements recorded to file.”);

}