Using the BAR tool in a macro...writing

[Ethan Cohen]

Using Fiji, I can run the BAR tool find Peaks tool from the macro recorder, and find 1-D peaks.
This executes fine in ImageJ macro language..

However, the macro recorder does not pick up pressing the "List" or "Save" buttons. So I cannot see the arguments passed.

Q1: Could somebody provide an example of ImageJ macro code with BAR find Peaks that some how accesses these SAVE/LIST buttons?

Thanks,

Ethan.

Ethan Cohen, Ph.D.
Div of Biomedical Physics,
Office of Science and Engineering Labs,
FDA Center for Devices and Radiological Health
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[Emanuele Martini]

Hi Ethan,
I used "Find Peaks" once in a plugin writed in jython.
I used this workaround to retrieve the peaks values:
I get the Result table created by "Find Peaks"
in jython is:

1)retrieve the window of peak plot
MAX_plot=WindowManager.getWindow("Peaks in "+tit)
where tit is the title of the curve analyzed by "Find Peaks"


2) retrieve the *Results Table* of your find plot
MAX_rt_temp=MAX_plot.getResultsTable()

3) now you can access the peaks and any values like that
a=MAX_rt_temp.getValueAsDouble(column_index,row_index)


4) and/or if you want show the peaks like that
MAX_rt_temp.show("res peaks")
and then if you want save as you save resulttable

I use python/jython and I really don't know how to "translate" in Imagej Macro Language, since i use the macro language very few.

hoping to be in someway useful,
have a nice day
Emanuele

[Tiago Ferreira-2]

Dear Ethan,

Cohen, Ethan D <Ethan.Cohen@...> writes:

> Using Fiji, I can run the BAR tool find Peaks tool from the macro recorder,
> and find 1-D peaks. This executes fine in ImageJ macro language..
>
> However, the macro recorder does not pick up pressing the "List" or "Save"
> buttons. So I cannot see the arguments passed.
>
> Q1: Could somebody provide an example of ImageJ macro code with BAR Find Peaks
> that some how accesses these SAVE/LIST buttons?
>
>

[Re-posting to the list: For whatever reason previous message went astray]

I just pushed an updated version that includes a "List values" option, that will
display the  Plot's table[1]. To save it programmatically, you can append the
following to your macro:

    selectWindow("Plot Values");
    saveAs("Results", "Path/to/Output/Directory/Plot Values.csv");
    run("Close");

In case you need to access tables from other Plot Windows:
The option to display the data table for _ALL_ IJ plots is set in 'Edit>Options>
Profile Plot Options' ("List values" checkbox). So, it can be set using the Macro
recorder. Here is an example:

// Set the "PlotWindow.listValues" option using Edit>Options>Profile Plot Options
run("Profile Plot Options...",
    "width=450 height=200 minimum=0 maximum=0 list interpolate");

// Generate your plot. The plot table will be displayed
run("Find Peaks",
    "min._peak_amplitude=20 min._peak_distance=0 min._value=NaN max._value=NaN");

// Save the plot's data table
selectWindow("Plot Values");
saveAs("Results", "/Path/to/Output/Directory/Plot Values.csv");

// Unset the "PlotWindow.listValues" option so it won't affect future plots.
// Note the omission of the keyword "list"
run("Profile Plot Options...",
    "width=450 height=200 minimum=0 maximum=0 interpolate");


Again, this should work for IJ generated plot.
-tiago

[1] https://github.com/tferr/Scripts/commit/ca5fe4a

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