Posted by
Wayne Rasband on
Mar 20, 2009; 2:47pm
URL: http://imagej.273.s1.nabble.com/Images-to-stack-in-batch-mode-tp3693222p3693226.html
This bug is fixed in the ImageJ 1.42l daily build. The
Image>Stacks>Plot Z-axis profile command was not working correctly in
batch mode macros.
-wayne
On Mar 20, 2009, at 5:39 AM, Remi wrote:
> Gabriel Landini wrote:
>> On Friday 20 March 2009 01:25:15 David Webster wrote:
>>
>>> setBatchMode(true);
>>> newImage("1", "8-bit Black", 100, 100, 1);
>>> newImage("2", "8-bit Black", 100, 100, 1);
>>> newImage("3", "8-bit Black", 100, 100, 1);
>>> // Point 1
>>> //setBatchMode(false);
>>> // Point 2
>>> run("Images to Stack");
>>> //setBatchMode(false);
>>>
>>> If I uncomment the first "setBatchMode(false)" then images 1 and 2
>>> aren't
>>> seen and I get the error message "There must be two images open"
>>> (image 3
>>> is open).
>>>
>>
>> But that is correct. The documentation states that when you exit
>> batch mode with "false", only the last selected image is shown, the
>> others are closed.
>>
>>
>>>> I am currently trying to do some image analysis with an imageJ
>>>> macro that
>>>> I launch in batch mode from the command line (-batch option and
>>>> setBatch(true)). After generating 68 images I would like to run the
>>>> 'Images to Stack' command, to 'compile' them. Unfortunately, the
>>>> stack is
>>>> never generated.
>>>>
>>
>> Does it run without the batchmode?
>> Do you by any chance have different types of images, or different
>> sizes?
>>
>> cheers,
>> G.
>>
>
> This code, with a Z-axis plot doesn't work
>
> setBatchMode(true);
>
> //Setting the autoclose options
> run("Profile Plot Options...", "width=450 height=200 minimum=0
> maximum=0 do auto-close interpolate draw")
>
> //Creating three pictures
> newImage("1", "8-bit White", 500, 500, 1);
> newImage("2", "8-bit White", 500, 500, 1);
> newImage("3", "8-bit White", 500, 500, 1);
>
> //Making a stack
> run("Images to Stack");
>
> print("nImages: "+nImages);
> print("title: "+getTitle);
> print("stack size: "+nSlices);
>
> //Doing some analysis
> run("Plot Z-axis Profile");
> close(); //On ferme le plot généré par le Z-axis Profile-A
>
> //Closing the stack
> selectWindow("Stack");
> close();
>
> print("nImages: "+nImages);
> print("title: "+getTitle);
> print("stack size: "+nSlices);
>
>
> //Creating three pictures
> newImage("1", "8-bit White", 500, 500, 1);
> newImage("2", "8-bit White", 500, 500, 1);
> newImage("3", "8-bit White", 500, 500, 1);
>
> // ---> Impossible to make this stack <---
> run("Images to Stack"); // <--
>