; expected in line

[flettster]

Dear all

I have just combined 2 of my macros which work fine by themselves.

Since joining them when i run it it says ; expected in line 324. There is clearly a ; present however.

Would very much appreciate some help if you can figure out whats going on!

Thanks

Andy

[flettster]

Here is the txt.

run("Set Measurements...", "area mean standard min display redirect=None decimal=6");
run("Colors...", "foreground=black background=black selection=yellow");
dir = getDirectory("image");
calw = getWidth();
calh = getHeight();
name = getTitle;
dotIndex = indexOf(name, ".");
underscoreindex = indexOf(name, "_")
Dim = substring(name, 2, dotIndex);
x = substring(name, 0, underscoreindex)
run("Scale...", "x=3 y=3 interpolate create title=preimage.raw");
preimage = getImageID()
wait(40)
ID = getImageID();
run("Window/Level...");
run("Enhance Contrast", "saturated=0.5");
run("Enhance Contrast", "saturated=0.5");
run("Enhance Contrast", "saturated=0.5");
setTool(0);
makeRectangle(160, 210, 150, 150);
waitForUser("Draw LV region");
run("Crop");
scwidth = 0.005 * screenWidth
scheight = 0.25 * screenHeight
setLocation(scwidth, scheight)
run("In");
run("In");

run("Duplicate...", "title=Working.TIF");
working = getImageID()
run("8-bit")
wscwidth = 0.5 * screenWidth
wscheight = 0.25 * screenHeight
setLocation (wscwidth, wscheight)
run("In");
run("In");
run("Window/Level...");
run("Enhance Contrast", "saturated=0.5");
height = 0.45 * getHeight()
width = 0.5 * getWidth()
setTool(3);
setAutoThreshold("Percentile dark");

waitForUser("Refine threshold");
setTool(8);
doWand(height,width);
resetThreshold();
setTool(10);
run("Enhance Contrast", "saturated=0.5");
waitForUser("Correct endocardium");
run("Clear");
run("Add to Manager ");
roiManager("Select", 0);
roiManager("Rename", "Endo");
setTool(3);
run("Enhance Contrast", "saturated=0.5");
waitForUser("Draw epicardium");

wait(60)
run("Clear Outside");
run("Add to Manager ");
roiManager("Select", 1);
roiManager("Rename", "Epi");

setOption("Show All",true);
roiManager("Select", 1);
setTool(10);
run("ROI Manager...");
selectImage(ID)
setOption("Show All",true);
selectWindow("Working.TIF")
setTool(10);
setOption("Show All",true);
setAutoThreshold();
waitForUser("Correct endo, epicardium");
roiManager("update");

selectWindow("Working.TIF")
roiManager("Select", 0);
wait(60)
run("Clear");
roiManager("Select", 1);
wait(60)
run("Clear Outside");

setTool(3);
resetThreshold();
roiManager("Deselect");
run("Enhance Contrast", "saturated=0.5");

Dialog.create("T2?");
Dialog.addMessage("Do you wish to run T2 analysis?");
Dialog. addCheckbox("Yes", true);
Dialog.show();
LGEpos = Dialog.getCheckbox();

if (LGEpos==1) {
waitForUser("Please carefully draw T2 enhanced area manually");
run("Add to Manager ");
roiManager("select",2);
roiManager("Rename", "man");
roiManager("Measure");
max1 = getResult("Max");
selectImage(ID);
setOption("Show All",true);
setTool(3);
selectWindow("Working.TIF");
FWHM1 = 0.5 * max1;
setThreshold(FWHM1,1000000);
wait(30);
run("Threshold...");
run("Create Selection");
waitForUser("Remove artifact (FWHM 1st pass)");
selectWindow("Working.TIF");
run("Measure");
max2 = getResult("Max");
FWHM2 = 0.5 * max2;
setThreshold(FWHM2,1000000);
wait(30);
run("Threshold...");
run("Create Selection");
waitForUser("Remove artifact (FWHM final)");
run("Add to Manager ");
wait(30);
roiManager("Select", 3);
roiManager("Rename", "FWHM");

roiManager("Deselect");

run("Create Selection");
directory = getDirectory("temp");
roiManager("Save", directory+"Temp.zip");
roiManager("Select", 2);
roiManager("Delete");
roiManager("Select", 2);
roiManager("Delete");

roiManager("Deselect");
roiManager("XOR");

setAutoThreshold("Otsu dark");
run("Create Selection");
waitForUser("Remove artifact (OTSU)");
roiManager("Deselect");
roiManager("Delete");
roiManager("Open", directory+"Temp.zip");
run("Add to Manager ");
roiManager("Select", 4);
roiManager("Rename", "OTSU");

roiManager("Save", directory+"Temp.zip");
roiManager("Select", 2);
roiManager("Delete");
roiManager("Select", 2);
roiManager("Delete");
roiManager("Select", 2);
roiManager("Delete");

roiManager("Deselect");
roiManager("XOR");

setAutoThreshold("Huang dark");
run("Create Selection");
waitForUser("Remove artifact (Huang)");
roiManager("Deselect")
roiManager("Delete")
roiManager("Open", directory+"Temp.zip");
run("Add to Manager ");
roiManager("Select", 5);
roiManager("Rename", "Huang");

resetThreshold();
roiManager("Deselect");
roiManager("Show None");
run("Select None");
setTool(3);
waitForUser("please draw remote myocardium");
run("Add to Manager ");
roiManager("Select", 6);
roiManager("Rename", "Remote");

run("Measure");
SD = getResult("StdDev");
Mean = getResult("Mean");
max = getResult("Max");

t2=100000;
t5= 3*SD + Mean;
setThreshold(t5,t2);
run("Threshold...");
run("Create Selection");
setTool(10);
waitForUser("Remove artifacts (3SD)");
run("Add to Manager ");
run("ROI Manager...");
setOption("Show All",true);
resetThreshold();
roiManager("Select", 7);
roiManager("Rename", "3SD");

t6= 2*SD + Mean;
setThreshold(t6,t2);
run("Threshold...");
run("Create Selection");
setTool(10);
waitForUser("Remove artifacts (2SD)");
run("Add to Manager ");
run("ROI Manager...");
setOption("Show All",true);
resetThreshold();
roiManager("Select", 8);
roiManager("Rename", "2SD");


setOption("Show All",true);
roiManager("Select", 0);
roiManager("Measure");
roiManager("Select", 1);
roiManager("Measure");
roiManager("Select", 2);
roiManager("Measure");
roiManager("Select", 3);
roiManager("Measure");
roiManager("Select", 4);
roiManager("Measure");
roiManager("Select", 5);
roiManager("Measure");
roiManager("Select", 6);
roiManager("Measure");
roiManager("Select", 7);
roiManager("Measure");
roiManager("Select", 8);
roiManager("Measure");
roiManager("Deselect");
updateResults();
String.copyResults();

waitForUser("Finished with thresholds?");
selectWindow("ROI Manager");
roiManager("Save", dir+"RoiSet"+x+"TH"+".zip");
selectWindow("preimage.raw");
saveAs("tiff", dir+"preimage"+x);
selectWindow("Working.TIF");
saveAs("tiff", dir+"Working"+x);


roiManager("Select", 3);
roiManager("Delete");
roiManager("Select", 3);
roiManager("Delete");
roiManager("Select", 3);
roiManager("Delete");
roiManager("Select", 3);
roiManager("Delete");
roiManager("Select", 3);
roiManager("Delete");
roiManager("Select", 3);
roiManager("Delete");

roiManager("Select", 0);
getSelectionBounds(xini1,yini1,rubbish,rubbish2);
roiManager("Show All");
roiManager("Show None");
roiManager("Show All");
roiManager("UseNames", "true");
setTool("point");
waitForUser("Please identify superior RV insertion point");
getSelectionBounds(xini,yini,rubbish,rubbish2);

roiManager("select", newArray(0,1));
roiManager("XOR");
run("Add to Manager ");
roiManager("Select", 3);
roiManager("Rename", "Epi-Endo");

roiManager("Select", 1);
getSelectionBounds(xini2,yini2,rubbish,rubbish2);
x1=xini-xini2;
y1=yini-yini2;
x3=xini1-xini2;
y3=yini1-yini2;
run("Duplicate...", "title=working.raw");
run("In");
run("In");
run("In");
run("In");

roiManager("Select", 3);
setSelectionLocation(0, 0);
roiManager("Update");
roiManager("Select", 0);
setSelectionLocation(x3, y3);
roiManager("Update");
roiManager("Select", 1);
setSelectionLocation(0, 0);
roiManager("Update");
getSelectionBounds(x,y,width,height);

x2=0.5*width;
y2=0.5*height;
theta2=asin((y2-y1)/y2);
theta=acos(((x2-x1)/x2));


pi=3.14159265358932384626;


makePolygon(x2-(2*(cos(theta)*x2)),y2-(2*(sin(theta)*y2)),x2,y2,x2-(2*(cos(theta+(pi/3))*x2)),y2-(2*(sin(theta+(pi/3)))*y2));
roiManager("Add");
roiManager("Select", 4);
roiManager("Rename", "1");

makePolygon(x2-(2*(cos(theta)*x2)),y2-(2*(sin(theta)*y2)),x2,y2,x2-(2*(cos(theta-(pi/3))*x2)),y2-(2*(sin(theta-(pi/3)))*y2));
roiManager("Add");
roiManager("Select", 5);
roiManager("Rename", "2");

makePolygon(x2-(2*(cos(theta-(pi/3))*x2)),y2-(2*(sin(theta-(pi/3)))*y2),x2,y2,x2-(2*(cos(theta-(2*pi/3))*x2)),y2-(2*(sin(theta-(2*pi/3)))*y2));
roiManager("Add");
roiManager("Select", 6);
roiManager("Rename", "3");

makePolygon(x2,y2,x2-(2*(cos(theta-(2*pi/3))*x2)),y2-(2*(sin(theta-(2*pi/3)))*y2),x2-(2*(cos(theta-(3*pi/3))*x2)),y2-(2*(sin(theta-(3*pi/3)))*y2);
roiManager("Add");
roiManager("Select", 7);
roiManager("Rename", "4");

makePolygon(x2,y2,x2-(2*(cos(theta-(4*pi/3))*x2)),y2-(2*(sin(theta-(4*pi/3)))*y2),x2-(2*(cos(theta-(3*pi/3))*x2)),y2-(2*(sin(theta-(3*pi/3)))*y2);
roiManager("Add");
roiManager("Select", 8);
roiManager("Rename", "5");

makePolygon(x2,y2,x2-(2*(cos(theta-(4*pi/3))*x2)),y2-(2*(sin(theta-(4*pi/3)))*y2),x2-(2*(cos(theta-(5*pi/3))*x2)),y2-(2*(sin(theta-(5*pi/3)))*y2);
roiManager("Add");
roiManager("Select", 9);
roiManager("Rename", "6");


roiManager("select", newArray(3,4));
roiManager("AND");
roiManager("Add");
roiManager("Deselect");
roiManager("Select", 4);
roiManager("Delete");
roiManager("Deselect");
roiManager("Select", 9);
roiManager("Rename", "1");
wait(10);

roiManager("select", newArray(3,4));
roiManager("AND");
roiManager("Add");
roiManager("Deselect");
roiManager("Select", 4);
roiManager("Delete");
roiManager("Deselect");
roiManager("Select", 9);
roiManager("Rename", "2");
wait(10);

roiManager("select", newArray(3,4));
roiManager("AND");
roiManager("Add");
roiManager("Deselect");
roiManager("Select", 4);
roiManager("Delete");
roiManager("Deselect");
roiManager("Select", 9)
roiManager("Rename", "3");
wait(10);

roiManager("select", newArray(3,4));
roiManager("AND")
roiManager("Add");
roiManager("Deselect");
roiManager("Select", 4);
roiManager("Delete");
roiManager("Deselect");
roiManager("Select", 9)
roiManager("Rename", "4");
wait(10);

roiManager("select", newArray(3,4));
roiManager("AND");
roiManager("Add");
roiManager("Deselect");
roiManager("Select", 4);
roiManager("Delete");
roiManager("Deselect");
roiManager("Select", 9);
roiManager("Rename", "5");
wait(10);

roiManager("select", newArray(3,4));
roiManager("AND");
roiManager("Add");
roiManager("Deselect");
roiManager("Select", 4)
roiManager("Delete");
roiManager("Deselect");
roiManager("Select", 9);
roiManager("Rename", "6");
wait(10);

roiManager("Select", 3);
roiManager("Measure");
mean1 = getResult("Mean");
SD = getResult("StdDev")
t1c= 3*SD + mean1
setThreshold(t1c,1000)
run("Threshold...");

roiManager("Show All");
roiManager("Show None");
roiManager("Show All");
roiManager("Select", 3);
setAutoThreshold("Triangle dark");
waitForUser("Edit segments and update in Roi Manager");

roiManager("Deselect");
roiManager("Select", 0);
getSelectionBounds(x4,y4,widthendo,heightendo)
widthblood=widthendo*0.5
heightblood=heightendo*0.5
xblood=x4*2
yblood=y4*2
makeOval(xblood, yblood, widthblood, heightblood)
setTool("oval");
waitForUser("Edit Blood");
run("Add to Manager ");
roiManager("Select", 10);
roiManager("Rename", "Blood");

roiManager("Deselect");
roiManager("Select", 0);
roiManager("Measure");
roiManager("Select", 4);
roiManager("Measure");
roiManager("Select", 5);
roiManager("Measure");
roiManager("Select", 6);
roiManager("Measure");
roiManager("Select", 7);
roiManager("Measure");
roiManager("Select", 7);
roiManager("Measure");
roiManager("Select", 8);
roiManager("Measure");
roiManager("Select", 9);
roiManager("Measure");

roiManager("Show All");
roiManager("Show None");
roiManager("Show All");
roiManager("select",2);
roiManager("Rename", "Manual Roi");
roiManager("Measure");



selectWindow("Results");
run("Close");

}

else {
setOption("Show All",true);
roiManager("Select", 0);
roiManager("Measure");
roiManager("Measure");
roiManager("Measure");
roiManager("Select", 1);
roiManager("Measure");
roiManager("Deselect");
setResult("calibration", 4, 0);
setResult("calibration", 5, 0);
setResult("calibration", 6, Dim);
setResult("calibration", 7, calw);
setResult("calibration", 8, calh);
updateResults();
String.copyResults();

waitForUser("Paste to Excel NOW - Finished?");
selectWindow("preimage.raw");
saveAs("tiff", dir+"preimage"+x);
close();
selectWindow("Working.TIF");
saveAs("tiff", dir+"Working"+x);
close();
selectWindow("Results");
run("Close");
selectWindow("ROI Manager");
roiManager("Save", dir+"RoiSet"+x+".zip");
run("Close");
}

[dscho]

Hi,

since it said "line 324", that should have been enough. Your lines are too
long, so they were wrapped and I did not want to spend time to unwrap
them, so I guess this here is the culprit:

On Mon, 9 Jan 2012, flettster wrote:

> SD = getResult("StdDev")
> t1c= 3*SD + mean1
> setThreshold(t1c,1000)

These three lines all lack a semicolon at the end, as the error message
suggests.

Ciao,
Johannes

P.S.: Even if ImageJ's default editor lacks line numbers (if you want a
nicer editor, try Fiji's Script Editor), it still has the Edit>Goto
Line... menu entry.

[BenTupper]

Hi,

On Jan 9, 2012, at 7:51 PM, Johannes Schindelin wrote:

> Hi,
>
> since it said "line 324", that should have been enough. Your lines are too
> long, so they were wrapped and I did not want to spend time to unwrap
> them, so I guess this here is the culprit:
>
> On Mon, 9 Jan 2012, flettster wrote:
>
>> SD = getResult("StdDev")
>> t1c= 3*SD + mean1
>> setThreshold(t1c,1000)
>
> These three lines all lack a semicolon at the end, as the error message
> suggests.
>

In addition, it appears that some of the lines that start with makePolygon (one of which is on line 324!) have unmatched parentheses.

Cheers,
Ben




> Ciao,
> Johannes
>
> P.S.: Even if ImageJ's default editor lacks line numbers (if you want a
> nicer editor, try Fiji's Script Editor), it still has the Edit>Goto
> Line... menu entry.

[mikeadams709]

Hi Andy,

May I suggest using Notepad++ as your editor
It has all the major features necessary to help you avoid these frustrating
errors.
I find it very useful for writing plugins and it is completely free!

http://notepad-plus-plus.org/


Best,

Mike

On Tue, Jan 10, 2012 at 10:11 AM, Ben Tupper <[hidden email]> wrote:

> Hi,
>
> On Jan 9, 2012, at 7:51 PM, Johannes Schindelin wrote:
>
> > Hi,
> >
> > since it said "line 324", that should have been enough. Your lines are
> too
> > long, so they were wrapped and I did not want to spend time to unwrap
> > them, so I guess this here is the culprit:
> >
> > On Mon, 9 Jan 2012, flettster wrote:
> >
> >> SD = getResult("StdDev")
> >> t1c= 3*SD + mean1
> >> setThreshold(t1c,1000)
> >
> > These three lines all lack a semicolon at the end, as the error message
> > suggests.
> >
>
> In addition, it appears that some of the lines that start with makePolygon
> (one of which is on line 324!) have unmatched parentheses.
>
> Cheers,
> Ben
>
>
>
>
> > Ciao,
> > Johannes
> >
> > P.S.: Even if ImageJ's default editor lacks line numbers (if you want a
> > nicer editor, try Fiji's Script Editor), it still has the Edit>Goto
> > Line... menu entry.
>