FW: Trying to rename Results table "Measurements" to a new column.

[Ethan Cohen]

Subject: Trying to rename Results table "Measurements" to new column.


I am trying to make a series of repeated square ROI measurements of the std deviation on a series of stack images of many slices.

I have gotten this code to work, but the problem is each series of StdDev measurements is appended on top of each others in a single column in the Results table in ImageJ. By the end I have THOUSANDS of rows of a single column "StdDev".  

I have devised a copy column kluge around this that works but is computationally slow...it deletes the rows at the end...but there must be a better way.

==>I wonder if there is a better way to create stack column names...like directing the output of "Measure" to an array, rather than always to the "StdDev" column in the Results table. I cannot rename/redirect/cut "StdDev" in "Results"?


getSelectionBounds(x, y, width, height);// get x, y  of selected square and widths
 
  run("Clear Results");
  Stack.getDimensions(dummy, dummy, dummy, Numslices, dummy); //Get # of slices
 
  run("Set Measurements...", "   standard redirect=None decimal=3");// choose std dev output
 setOption("ShowRowNumbers", true);// Row numbers in results table

for (j=1; j<=Numslices; j++){ //selects stack slice number
  Stack.setSlice(j);
        run("Measure");// place sd in column?
        updateResults(); //updates the Results window
}

[Robert Dougherty]

Ethan,
You might want to try Microarray Profile. It gives different results for several ROIs and can now handle square ROIs.
Bob

Robert P. Dougherty
President
OptiNav, Inc.
1414 127th Pl NE #106
Bellevue, WA 98005
[phone]
FAX [phone]
[hidden email]
www.optinav. com

On Apr 22, 2012, at 11:35 AM, "Cohen, Ethan D" <[hidden email]> wrote:

> Subject: Trying to rename Results table "Measurements" to new column.
>
>
> I am trying to make a series of repeated square ROI measurements of the std deviation on a series of stack images of many slices.
>
> I have gotten this code to work, but the problem is each series of StdDev measurements is appended on top of each others in a single column in the Results table in ImageJ. By the end I have THOUSANDS of rows of a single column "StdDev".  
>
> I have devised a copy column kluge around this that works but is computationally slow...it deletes the rows at the end...but there must be a better way.
>
> ==>I wonder if there is a better way to create stack column names...like directing the output of "Measure" to an array, rather than always to the "StdDev" column in the Results table. I cannot rename/redirect/cut "StdDev" in "Results"?
>
>
> getSelectionBounds(x, y, width, height);// get x, y  of selected square and widths
>
>  run("Clear Results");
>  Stack.getDimensions(dummy, dummy, dummy, Numslices, dummy); //Get # of slices
>
>  run("Set Measurements...", "   standard redirect=None decimal=3");// choose std dev output
> setOption("ShowRowNumbers", true);// Row numbers in results table
>
> for (j=1; j<=Numslices; j++){ //selects stack slice number
>      Stack.setSlice(j);
>    run("Measure");// place sd in column?
>    updateResults(); //updates the Results window
> }    

[Ethan Cohen]

Wayne:
Nope.

run("Set Measurements...", "   standard stack redirect=None decimal=3");//choose std dev output

1. Adding stack to SetMeasurements just gives me another single column of the Stack number (in addition to StdDev),

2. I do not have the "StdDev" measurements separated into different columns labeled "Stack#" by stack slice #. I need someway to either rename this column,or cut and copy data.

...as I said I have a kluge solution using getResult, and setResult to transfer the variable in StdDev...but I cannot avoid the long rows.


Ethan

>Ethan Cohen, Ph.D.
>FDA Center for Devices and Radiological Health
>Office: Rm 1204 WO62
>White Oak Federal Res Ctr.
>10903 New Hampshire Ave.
>Silver Spring, MD 20993
>
>Office: 301-796-2485
>Lab:301-796-2762
>Fax: [phone]

Cell: 301-538-7544

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-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Cohen, Ethan D
Sent: Sunday, April 22, 2012 2:36 PM
To: [hidden email]
Subject: FW: Trying to rename Results table "Measurements" to a new column.

Subject: Trying to rename Results table "Measurements" to new column.


I am trying to make a series of repeated square ROI measurements of the std deviation on a series of stack images of many slices.

I have gotten this code to work, but the problem is each series of StdDev measurements is appended on top of each others in a single column in the Results table in ImageJ. By the end I have THOUSANDS of rows of a single column "StdDev".  

I have devised a copy column kluge around this that works but is computationally slow...it deletes the rows at the end...but there must be a better way.

==>I wonder if there is a better way to create stack column names...like directing the output of "Measure" to an array, rather than always to the "StdDev" column in the Results table. I cannot rename/redirect/cut "StdDev" in "Results"?


getSelectionBounds(x, y, width, height);// get x, y  of selected square and widths
 
  run("Clear Results");
  Stack.getDimensions(dummy, dummy, dummy, Numslices, dummy); //Get # of slices
 
  run("Set Measurements...", "   standard redirect=None decimal=3");// choose std dev output
 setOption("ShowRowNumbers", true);// Row numbers in results table

for (j=1; j<=Numslices; j++){ //selects stack slice number
  Stack.setSlice(j);
        run("Measure");// place sd in column?
        updateResults(); //updates the Results window
}

[Michael Schmid]

Hi Ethan,

maybe the getStatistics macro call should do it?
  http://rsb.info.nih.gov/ij/developer/macro/functions.html#getStatistics

Then you could store the results in an array and print it to the Results Table or a file in whatever form you like.

Michael
________________________________________________________________
On Apr 22, 2012, at 20:35, Cohen, Ethan D wrote:

> Subject: Trying to rename Results table "Measurements" to new column.
>
>
> I am trying to make a series of repeated square ROI measurements of the std deviation on a series of stack images of many slices.
>
> I have gotten this code to work, but the problem is each series of StdDev measurements is appended on top of each others in a single column in the Results table in ImageJ. By the end I have THOUSANDS of rows of a single column "StdDev".  
>
> I have devised a copy column kluge around this that works but is computationally slow...it deletes the rows at the end...but there must be a better way.
>
> ==>I wonder if there is a better way to create stack column names...like directing the output of "Measure" to an array, rather than always to the "StdDev" column in the Results table. I cannot rename/redirect/cut "StdDev" in "Results"?
>
>
> getSelectionBounds(x, y, width, height);// get x, y  of selected square and widths
>
>  run("Clear Results");
>  Stack.getDimensions(dummy, dummy, dummy, Numslices, dummy); //Get # of slices
>
>  run("Set Measurements...", "   standard redirect=None decimal=3");// choose std dev output
> setOption("ShowRowNumbers", true);// Row numbers in results table
>
> for (j=1; j<=Numslices; j++){ //selects stack slice number
>   Stack.setSlice(j);
> run("Measure");// place sd in column?
> updateResults(); //updates the Results window
> }