Sorry, there was an error in the exception handling part of the python
script I posted previously. The script below should work:
# Enabling/disabling IJ1 macro mode
from ij.macro import Interpreter as IJ1
from java.lang import Exception
from ij import IJ
# activate batchmode
IJ1.batchMode = True
try:
imp = IJ.getImage()
IJ.run(imp, "FFTs", "")
IJ.log("Done")
except Exception as err:
IJ1.batchMode = False;
IJ.log("!Error with do process...")
IJ.log(err.toString())
# de-activate batchmode
IJ1.batchMode = False
On <a href="tel:01904%20201%20714" value="+911904201714" target="_blank">19.04.2017 14:08, Jan Eglinger wrote:--
> Dear GP,
>
> usually, there's no need to have a batch mode with the full-featured
> scripting languages, since they can work with images in variables.
>
> For example, the IJ.run() method would always work on the image given as
> first parameter:
>
> IJ.run(imp, "Gaussian Blur...", "sigma=2")
>
>
> ----
>
> However, there are cases where using IJ.run() _will_ create a new image;
> in these cases you can use more low-level commands directly calling the
> respective Java classes. The Macro Recorder [2] will record these when
> you switch to e.g. Javascript or Beanshell mode:
>
> imp2 = new Duplicator().run(imp, 1, 10);
>
>
> ----
>
> In addition, the whole ImageJ-Ops framework [1] was created to simplify
> calling commands from scripts or other commands, by clearly defining
> possible inputs and outputs for each command.
>
> ----
>
> Nevertheless, if you really _want_ to use batch mode, it is possible as
> you suggested by modifying the javascript from
> http://wiki.cmci.info/documents/110822jsip_cooking/ javascript_imagej_cookbook# activatingdeactivating_ batchmode
>
>
> Here's a Python version that worked for me:
>
> ********* Python script ************
> # Enabling/disabling IJ1 macro mode
>
> from ij.macro import Interpreter as IJ1
> from ij import IJ
>
> # activate batchmode
> IJ1.batchMode = True
>
> try:
> imp = IJ.getImage()
> IJ.run(imp, "FFT", "")
> IJ.log("Done")
> except(err):
> IJ1.batchMode = False;
> IJ.log("!Error with do process...")
> IJ.log(err.rhinoException.toString())
> IJ.log(err.javaException.toString())
>
> # de-activate batchmode
> IJ1.batchMode = False
> ************************************
>
> Cheers,
> Jan
>
>
> [1]: http://imagej.net/ImageJ_Ops
> [2]: http://imagej.net/Macro_recorder
>
>
> On <a href="tel:01904%20201%20702" value="+911904201702" target="_blank">19.04.2017 02:31, GP wrote:
>> Hie!
>>
>> I have been converting my script from ".ijm" to ".py".
>> The problem is that the output images generated from plugins pop open. I
>> couldn't find any setBatchMode(true) option for python script.
>> I found the discussion
>> (http://forum.imagej.net/t/jython-equivalent-for- )setbatchmode-true/1197/3
>>
>> but was not able to apply to all the plugins used in this script:
>>
>> Following are the tasks performed over all sub-folders in the directory:
>>
>> 1) Get Images
>> 2) Find Focussed Slice
>> 3) Make Substack around it
>> 4) Duplicate Substack
>> 4) Process Duplicate Substack
>> 5) Restore Selection on Substack
>> 6) Process Original Substack
>> 7) Save Final Image
>>
>> Script as follows:
>>
>> imp = IJ.openImage(images)
>> title = imp.getTitle()
>> IJ.run(imp, "Find focused slices", "select=100 variance=0.000") #All
>> image
>> windows start opening from this
>>
>> #step onwards
>> IJ.run(imp, "Make Substack...", " slices=" "")
>> #makes 'Substack' around focussed slice
>> Substack = IJ.getImage()
>> IJ.run("Duplicate...", "duplicate")
>> IJ.run("Remove Outliers...", "radius=1 threshold=50 which=Bright stack")
>> IJ.run("Auto Threshold", "method=Otsu ignore_black ignore_white white")
>> IJ.run("Z Project...", "projection=[Max Intensity]")
>> IJ.run("Shen-Castan Edge Detector", "coefficient=0.55")
>> IJ.run("Find Connected Regions", "allow_diagonal display_one_image
>> display_results regions_for_values_over=100 minimum_number_of_points=1
>> stop_after=-1")
>> IJ.run("Ridge Detection", "line_width=3.5 high_contrast=230
>> low_contrast=87
>> correct_position extend_line show_junction_points show_ids verbose
>> displayresults add_to_manager make_binary
>> method_for_overlap_resolution=NONE
>> sigma=1.51 lower_threshold=1.06 upper_threshold=4.99")
>> IJ.run("Find Maxima...", "noise=255 output=[Point Selection]")
>> h = ImagePlus.getRoi(k)
>> r = h.getBounds()
>> IJ.makeRectangle(x-300, y-300, x-300, y-300)
>> IJ.run(Substack, "Restore Selection", "")
>> IJ.run(Substack, "Crop", "")
>> IJ.run(Substack, "Z Project...", "projection=[Max Intensity]")
>> IJ.saveAs("Tiff" , os.path.join(output_path, title))
>>
>> In Java API I found out batch mode possibility
>> (http://wiki.cmci.info/documents/110822jsip_cooking/ ).javascript_imagej_cookbook
>>
>> Can this be translated to python as well?
>> Please let me know if there's a way to do all the steps without having
>> image
>> windows opening.
>>
>>
>> Thank you so much.
>> Best Regards,
>>
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