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saving multiple measurements to the same spreadsheet or text file

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patrick coffey

saving multiple measurements to the same spreadsheet or text file

Hi, I'm trying to determine if there is a straightforward way using a macro with imageJ to save multiple measurements to a spreadsheet file (or tab delimited txt file) in the form of a measurement for each column. Currently I can save a single measurement at a time where the relevant code is as follows

... looping through images (image1, image2, image3 ... and so on)
Plot.create("Profile", "X", "Value", profile); // Plot profile
Plot.show();
waitForUser("","review Plot");
saveAs("Measurements");

I'd like the columns to be image1, image2, etc ...

Any sample code is greatly appreciated. Many thanks,
Patrick

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Jim Passmore-2

Re: saving multiple measurements to the same spreadsheet or text file

Patrick,
Based on your brief description, I think there may be what you need in the
standard Results Table. For example, if you measure a series of lines, you
can get a result table with the length and angle orientation (2 columns) of
each line, one line per row in the table. It can easily be saved to a text
file to import into a spreadsheet.

There are probably multiple ways to use it that will accomplish what you
need. First off, bookmark the "developer resources" page, as it will come
in handy. http://imagej.net/developer/index.html

Second, from that page there is a list of macro language functions at
http://imagej.net/developer/macro/functions.html
I would search through that page for commands that operate on the result
table. In particular, the setResult and updateResults commands might
help. Use ctrl-F in the browser window and search for "result" to find a
few more useful commands.

Another option would be to save your measurements in an array, then use the
Array.show command to display them in a result window, which again can be
saved to a file. Array commands are on the same web page.

Note that there are numerous examples linked to from the list of macro
functions, and there are other resources on the developer page, including a
couple of "manuals" on macro programming and many more examples. You may
find better ideas there. Happy programming!

On Wed, Mar 18, 2015 at 3:02 PM, Patrick Coffey <[hidden email]>
wrote:

> Hi, I'm trying to determine if there is a straightforward way using a
> macro with imageJ to save multiple measurements to a spreadsheet file (or
> tab delimited txt file) in the form of a measurement for each column.
> Currently I can save a single measurement at a time where the relevant code
> is as follows
>
> ... looping through images (image1, image2, image3 ... and so on)
> Plot.create("Profile", "X", "Value", profile); // Plot profile
> Plot.show();
> waitForUser("","review Plot");
> saveAs("Measurements");
>
> I'd like the columns to be image1, image2, etc ...
>
> Any sample code is greatly appreciated. Many thanks,
> Patrick
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

*-- Jim Passmore*
Research Associate
Sealed Air Corporation

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

patrick coffey

Re: saving multiple measurements to the same spreadsheet or text file

Dear Jim,
Thank you for your response. (I have spent countless hours on the
resources that you mentioned). Unfortunately there is not a single example
of saving data from columns of multiple measurements to a spreadsheet or txt
file (one can build up a multi-column table one row at a time). Just to
re-cap - I want to measure multiple profiles and save them to the "same"
file as columns. Saving the profiles to individual files is easy to do.

So the output would look something like this

Profile1 Profile2 Profile3
130 240 255
77 212 170
And so on ....

I believe the problem is that imagej does not support 2D arrays,
hence it is impossible to build up a 2D array in nested loops in the typical
fashion. My guess is that I will have to resort to a 1D array that has the
same number of positions as the 2D array. Then I will have to literally
build up the results table one line at a time where the intended columns are
separated by "\t". Once the results table is built, I will be able to save
that as a spreadsheet file.

Please let me know if you have a workaround and thanks for the help.
Patrick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jim
Passmore
Sent: Thursday, March 19, 2015 6:20 AM
To: [hidden email]
Subject: Re: saving multiple measurements to the same spreadsheet or text
file

Patrick,
Based on your brief description, I think there may be what you need in the
standard Results Table. For example, if you measure a series of lines, you
can get a result table with the length and angle orientation (2 columns) of
each line, one line per row in the table. It can easily be saved to a text
file to import into a spreadsheet.

There are probably multiple ways to use it that will accomplish what you
need. First off, bookmark the "developer resources" page, as it will come
in handy. http://imagej.net/developer/index.html

Second, from that page there is a list of macro language functions at
http://imagej.net/developer/macro/functions.html
I would search through that page for commands that operate on the result
table. In particular, the setResult and updateResults commands might help.
Use ctrl-F in the browser window and search for "result" to find a few more
useful commands.

Another option would be to save your measurements in an array, then use the
Array.show command to display them in a result window, which again can be
saved to a file. Array commands are on the same web page.

Note that there are numerous examples linked to from the list of macro
functions, and there are other resources on the developer page, including a
couple of "manuals" on macro programming and many more examples. You may
find better ideas there. Happy programming!

On Wed, Mar 18, 2015 at 3:02 PM, Patrick Coffey <[hidden email]>
wrote:

> Hi, I'm trying to determine if there is a straightforward way using a
> macro with imageJ to save multiple measurements to a spreadsheet file
> (or tab delimited txt file) in the form of a measurement for each column.
> Currently I can save a single measurement at a time where the relevant
> code is as follows
>
> ... looping through images (image1, image2, image3 ... and so on)
> Plot.create("Profile", "X", "Value", profile); // Plot profile
> Plot.show();
> waitForUser("","review Plot");
> saveAs("Measurements");
>
> I'd like the columns to be image1, image2, etc ...
>
> Any sample code is greatly appreciated. Many thanks, Patrick
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

*-- Jim Passmore*
Research Associate
Sealed Air Corporation

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Cammer, Michael

Re: saving multiple measurements to the same spreadsheet or text file

Here is a macro we wrote quickly on Thursday to output the mean intensity of a bunch of ROIs in 3 channels. It's not fully realized-- for instance ratios aren't calculated, it doesn't read all files from a folder and match them with the ROI files, and it prints to the Log window instead of out to files, but I'm putting it here because of the trick we often use for generating columns of data. It's not my idea; I found it a few years ago in someone else's macro.

Simply define an output string and set it null. Then in each iteration of a loop append new text or numbers to the string followed by a tab. At the end of the loop, print it. Usually we use two print statements, one to send to the Log window and one to a text file with the same name as the image being analyzed or one big text file for all images with the same root name. It's a flexible method because columns can be added/subtracted without dealing with arrays and it is easy to read in text files generated this way and split them back into numbers. And maybe the d2s command isn't really needed.

Relevant code in boldface (may or may not survive the repost).

var tab = " \t ";
var bg = newArray(104, 175, 124); // bg of each channel

macro "measure all cells [F4]" {
run("Set Measurements...", "mean redirect=None decimal=4");
print(getTitle());
print("cell# \t YFP \t FRET \t CFP");
means = newArray(3);
for (i=0; i<roiManager("count"); i++){
roiManager("select", i);
outputstring = "" + d2s((i+1),0) + tab;
for (s=1; s<=3; s++) {
setSlice(s);
run("Measure");
means[s-1] = getResult("Mean", nResults-1) - bg[s-1];
outputstring = outputstring + d2s(means[s-1],0) + tab;
}
print(outputstring);
} // end for i
} // end macro

_________________________________________
Michael Cammer, Optical Microscopy Specialist
http://ocs.med.nyu.edu/microscopy
Lab: (212) 263-3208 Cell: (914) 309-3270

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of Patrick Coffey [[hidden email]]
Sent: Sunday, March 29, 2015 12:25 PM
To: [hidden email]
Subject: Re: saving multiple measurements to the same spreadsheet or text file

Dear Jim,
Thank you for your response. (I have spent countless hours on the
resources that you mentioned). Unfortunately there is not a single example
of saving data from columns of multiple measurements to a spreadsheet or txt
file (one can build up a multi-column table one row at a time). Just to
re-cap - I want to measure multiple profiles and save them to the "same"
file as columns. Saving the profiles to individual files is easy to do.

So the output would look something like this

Profile1 Profile2 Profile3
130 240 255
77 212 170
And so on ....

I believe the problem is that imagej does not support 2D arrays,
hence it is impossible to build up a 2D array in nested loops in the typical
fashion. My guess is that I will have to resort to a 1D array that has the
same number of positions as the 2D array. Then I will have to literally
build up the results table one line at a time where the intended columns are
separated by "\t". Once the results table is built, I will be able to save
that as a spreadsheet file.

Please let me know if you have a workaround and thanks for the help.
Patrick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jim
Passmore
Sent: Thursday, March 19, 2015 6:20 AM
To: [hidden email]
Subject: Re: saving multiple measurements to the same spreadsheet or text
file

Patrick,
Based on your brief description, I think there may be what you need in the
standard Results Table. For example, if you measure a series of lines, you
can get a result table with the length and angle orientation (2 columns) of
each line, one line per row in the table. It can easily be saved to a text
file to import into a spreadsheet.

There are probably multiple ways to use it that will accomplish what you
need. First off, bookmark the "developer resources" page, as it will come
in handy. http://imagej.net/developer/index.html

Second, from that page there is a list of macro language functions at
http://imagej.net/developer/macro/functions.html
I would search through that page for commands that operate on the result
table. In particular, the setResult and updateResults commands might help.
Use ctrl-F in the browser window and search for "result" to find a few more
useful commands.

Another option would be to save your measurements in an array, then use the
Array.show command to display them in a result window, which again can be
saved to a file. Array commands are on the same web page.

Note that there are numerous examples linked to from the list of macro
functions, and there are other resources on the developer page, including a
couple of "manuals" on macro programming and many more examples. You may
find better ideas there. Happy programming!

On Wed, Mar 18, 2015 at 3:02 PM, Patrick Coffey <[hidden email]>
wrote:

*-- Jim Passmore*
Research Associate
Sealed Air Corporation

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Jim Passmore-2

Re: saving multiple measurements to the same spreadsheet or text file

In reply to this post by patrick coffey

Hi Patrick,
I'm not using a computer with ImageJ at the moment, so I can't test the
following, but I had in mind something like this snippet. Watch out for
extra line breaks via email.

// ****************************************
// Adapted from http://imagej.net/macros/GetProfileExample.txt
loop through files { // I belive you already know how to do this
column_label = filename;
makeline(0,0,10,10); // or however you want to set selection
profile = getProfile();
for (i=0; i<profile.length; i++) {
setResult(column_label, i, profile(i));
}
updateResults();
} // return to get next file

// Save as spreadsheet compatible text file
saveAs("results");
//*****************************************

It is, of course, incomplete, but it sounds like you already know how to
loop through your images. Also note that I normally do my scripting in
jython rather than the ImageJ macro language, so this could be buggy.

Hope this helps.

On Sun, Mar 29, 2015 at 12:25 PM, Patrick Coffey <[hidden email]>
wrote:

> Dear Jim,
> Thank you for your response. (I have spent countless hours on the
> resources that you mentioned). Unfortunately there is not a single example
> of saving data from columns of multiple measurements to a spreadsheet or
> txt
> file (one can build up a multi-column table one row at a time). Just to
> re-cap - I want to measure multiple profiles and save them to the "same"
> file as columns. Saving the profiles to individual files is easy to do.
>
> So the output would look something like this
>
> Profile1 Profile2 Profile3
> 130 240 255
> 77 212 170
> And so on ....
>
> I believe the problem is that imagej does not support 2D arrays,
> hence it is impossible to build up a 2D array in nested loops in the
> typical
> fashion. My guess is that I will have to resort to a 1D array that has the
> same number of positions as the 2D array. Then I will have to literally
> build up the results table one line at a time where the intended columns
> are
> separated by "\t". Once the results table is built, I will be able to save
> that as a spreadsheet file.
>
> Please let me know if you have a workaround and thanks for the
> help.
> Patrick
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jim
> Passmore
> Sent: Thursday, March 19, 2015 6:20 AM
> To: [hidden email]
> Subject: Re: saving multiple measurements to the same spreadsheet or text
> file
>
> Patrick,
> Based on your brief description, I think there may be what you need in the
> standard Results Table. For example, if you measure a series of lines, you
> can get a result table with the length and angle orientation (2 columns) of
> each line, one line per row in the table. It can easily be saved to a text
> file to import into a spreadsheet.
>
> There are probably multiple ways to use it that will accomplish what you
> need. First off, bookmark the "developer resources" page, as it will come
> in handy. http://imagej.net/developer/index.html
>
> Second, from that page there is a list of macro language functions at
> http://imagej.net/developer/macro/functions.html
> I would search through that page for commands that operate on the result
> table. In particular, the setResult and updateResults commands might help.
> Use ctrl-F in the browser window and search for "result" to find a few more
> useful commands.
>
> Another option would be to save your measurements in an array, then use the
> Array.show command to display them in a result window, which again can be
> saved to a file. Array commands are on the same web page.
>
> Note that there are numerous examples linked to from the list of macro
> functions, and there are other resources on the developer page, including a
> couple of "manuals" on macro programming and many more examples. You may
> find better ideas there. Happy programming!
>
>
>
> On Wed, Mar 18, 2015 at 3:02 PM, Patrick Coffey <[hidden email]>
> wrote:
>
> > Hi, I'm trying to determine if there is a straightforward way using a
> > macro with imageJ to save multiple measurements to a spreadsheet file
> > (or tab delimited txt file) in the form of a measurement for each column.
> > Currently I can save a single measurement at a time where the relevant
> > code is as follows
> >
> > ... looping through images (image1, image2, image3 ... and so on)
> > Plot.create("Profile", "X", "Value", profile); // Plot profile
> > Plot.show();
> > waitForUser("","review Plot");
> > saveAs("Measurements");
> >
> > I'd like the columns to be image1, image2, etc ...
> >
> > Any sample code is greatly appreciated. Many thanks, Patrick
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
>
> *-- Jim Passmore*
> Research Associate
> Sealed Air Corporation
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

*-- Jim Passmore*
Research Associate
Sealed Air Corporation

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Rasband, Wayne (NIH/NIMH) [E]

Re: saving multiple measurements to the same spreadsheet or text file

In reply to this post by patrick coffey

On Mar 29, 2015, at 12:25 PM, Patrick Coffey <[hidden email]> wrote:
>
> Dear Jim,
> Thank you for your response. (I have spent countless hours on the
> resources that you mentioned). Unfortunately there is not a single example
> of saving data from columns of multiple measurements to a spreadsheet or txt
> file (one can build up a multi-column table one row at a time). Just to
> re-cap - I want to measure multiple profiles and save them to the "same"
> file as columns. Saving the profiles to individual files is easy to do.

This example macro generates 10 profiles and saves them in a file as columns.

-wayne

run("Blobs (25K)");
run("Clear Results");
setOption("ShowRowNumbers", false);
for (y=10; y<=200; y+=20) {
makeLine(30, y, 120, y);
profile = getProfile();
for (i=0; i<profile.length; i++) {
if (y==10)
setResult("X", i, i);
setResult("Y"+y, i, profile[i]);
}
}
updateResults;
saveAs("Results", "");

> So the output would look something like this
>
> Profile1 Profile2 Profile3
> 130 240 255
> 77 212 170
> And so on ....
>
> I believe the problem is that imagej does not support 2D arrays,
> hence it is impossible to build up a 2D array in nested loops in the typical
> fashion. My guess is that I will have to resort to a 1D array that has the
> same number of positions as the 2D array. Then I will have to literally
> build up the results table one line at a time where the intended columns are
> separated by "\t". Once the results table is built, I will be able to save
> that as a spreadsheet file.
>
> Please let me know if you have a workaround and thanks for the help.
> Patrick
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jim
> Passmore
> Sent: Thursday, March 19, 2015 6:20 AM
> To: [hidden email]
> Subject: Re: saving multiple measurements to the same spreadsheet or text
> file
>
> Patrick,
> Based on your brief description, I think there may be what you need in the
> standard Results Table. For example, if you measure a series of lines, you
> can get a result table with the length and angle orientation (2 columns) of
> each line, one line per row in the table. It can easily be saved to a text
> file to import into a spreadsheet.
>
> There are probably multiple ways to use it that will accomplish what you
> need. First off, bookmark the "developer resources" page, as it will come
> in handy. http://imagej.net/developer/index.html
>
> Second, from that page there is a list of macro language functions at
> http://imagej.net/developer/macro/functions.html
> I would search through that page for commands that operate on the result
> table. In particular, the setResult and updateResults commands might help.
> Use ctrl-F in the browser window and search for "result" to find a few more
> useful commands.
>
> Another option would be to save your measurements in an array, then use the
> Array.show command to display them in a result window, which again can be
> saved to a file. Array commands are on the same web page.
>
> Note that there are numerous examples linked to from the list of macro
> functions, and there are other resources on the developer page, including a
> couple of "manuals" on macro programming and many more examples. You may
> find better ideas there. Happy programming!
>
>
>
> On Wed, Mar 18, 2015 at 3:02 PM, Patrick Coffey <[hidden email]>
> wrote:
>
>> Hi, I'm trying to determine if there is a straightforward way using a
>> macro with imageJ to save multiple measurements to a spreadsheet file
>> (or tab delimited txt file) in the form of a measurement for each column.
>> Currently I can save a single measurement at a time where the relevant
>> code is as follows
>>
>> ... looping through images (image1, image2, image3 ... and so on)
>> Plot.create("Profile", "X", "Value", profile); // Plot profile
>> Plot.show();
>> waitForUser("","review Plot");
>> saveAs("Measurements");
>>
>> I'd like the columns to be image1, image2, etc ...
>>
>> Any sample code is greatly appreciated. Many thanks, Patrick
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
>
> *-- Jim Passmore*
> Research Associate
> Sealed Air Corporation
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

patrick coffey

Re: saving multiple measurements to the same spreadsheet or text file

Wayne et al. - thanks so much for your help. This solved the issue!
Patrick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Rasband, Wayne (NIH/NIMH) [E]
Sent: Sunday, March 29, 2015 7:33 PM
To: [hidden email]
Subject: Re: saving multiple measurements to the same spreadsheet or text
file

On Mar 29, 2015, at 12:25 PM, Patrick Coffey <[hidden email]> wrote:
>
> Dear Jim,
> Thank you for your response. (I have spent countless hours on the
> resources that you mentioned). Unfortunately there is not a single
> example of saving data from columns of multiple measurements to a
> spreadsheet or txt file (one can build up a multi-column table one row
> at a time). Just to re-cap - I want to measure multiple profiles and save
them to the "same"
> file as columns. Saving the profiles to individual files is easy to do.

This example macro generates 10 profiles and saves them in a file as
columns.

-wayne

run("Blobs (25K)");
run("Clear Results");
setOption("ShowRowNumbers", false);
for (y=10; y<=200; y+=20) {
makeLine(30, y, 120, y);
profile = getProfile();
for (i=0; i<profile.length; i++) {
if (y==10)
setResult("X", i, i);
setResult("Y"+y, i, profile[i]);
}
}
updateResults;
saveAs("Results", "");

might help.

> Use ctrl-F in the browser window and search for "result" to find a few
> more useful commands.
>
> Another option would be to save your measurements in an array, then
> use the Array.show command to display them in a result window, which
> again can be saved to a file. Array commands are on the same web page.
>
> Note that there are numerous examples linked to from the list of macro
> functions, and there are other resources on the developer page,
> including a couple of "manuals" on macro programming and many more
> examples. You may find better ideas there. Happy programming!
>
>
>
> On Wed, Mar 18, 2015 at 3:02 PM, Patrick Coffey
> <[hidden email]>
> wrote:
>
>> Hi, I'm trying to determine if there is a straightforward way using a
>> macro with imageJ to save multiple measurements to a spreadsheet file
>> (or tab delimited txt file) in the form of a measurement for each column.
>> Currently I can save a single measurement at a time where the
>> relevant code is as follows
>>
>> ... looping through images (image1, image2, image3 ... and so on)
>> Plot.create("Profile", "X", "Value", profile); // Plot profile
>> Plot.show();
>> waitForUser("","review Plot");
>> saveAs("Measurements");
>>
>> I'd like the columns to be image1, image2, etc ...
>>
>> Any sample code is greatly appreciated. Many thanks, Patrick
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>
>
> *-- Jim Passmore*
> Research Associate
> Sealed Air Corporation
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html