Fiji and Register Virtual Stack Slices plugin

[Jirka]

Good morning,
I found a problem while using the Register Virtual Stack Slices plugin and
calling it as a script in Jyton. I made a script (see attachment) for
registration a image pair stored in input folder. I discussed the script
with Ignacio (one of the authors) and he confirm me that it is fine and on
his Mac it works fine too. But when I launch it on my pc (I am using Gentoo
x64), it randomly shows mi a dialog "Bio-Formats Import Options" and then
it crashs. I even don t understand why ti needs such information. Do you
have any advice where am I doing a mistake or is it a bug in Fiji?

Thanks for any answer
--
Best regards and wishes of a nice day, Jiří Borovec
----------------------------------------------------------------------------------------------------
Jiří Borovec <[e-mail]>
PhD student at CMP CTU, ISC member
http://cmp.felk.cvut.cz/~borovji3


===================================================

import time, sys
from ij import IJ
from register_virtual_stack import Register_Virtual_Stack_MT

# source directory
source_dir = "/home.dokt/borovji3/Desktop/input/"
target_dir = "/home.dokt/borovji3/Desktop/output/"
# transforms directory
transf_dir = "/home.dokt/borovji3/Desktop/output/"
# reference image
reference_name = "29-041-Izd2-w35-He-les1_tif-Fused.jpg"
# shrinkage option (false)
use_shrinking_constraint = 0

p = Register_Virtual_Stack_MT.Param()
# The "maximum image size":
p.sift.maxOctaveSize = 1024
# The "inlier ratio":
p.minInlierRatio = 0.05
# Implemented transformation models for choice
# 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE, 4=ELASTIC,
5=MOVING_LEAST_SQUARES
p.registrationModelIndex = 4
# Implemented transformation models for choice
# 0=TRANSLATION, 1=RIGID, 2=SIMILARITY, 3=AFFINE
p.featuresModelIndex = 3

t = time.time()
Register_Virtual_Stack_MT.exec(source_dir, target_dir, transf_dir,
reference_name, p, use_shrinking_constraint)
t = time.time() - t

f = open(target_dir+"TIME.txt", "w")
f.write(repr(t))
f.close()

IJ.run("Close")
IJ.run("Quit")

===================================================

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

[Stephan Saalfeld]

Could you try to update only jars/loci-common.jar with the Fiji Updater?
It's a blind guess but that was what's been suggested by Johannes
Schindelin to solve just another problem with Bioformats recently.

Best,
Stephan



On Mon, 2013-09-30 at 11:41 +0200, Jiří Borovec wrote:

> Good morning,
> I found a problem while using the Register Virtual Stack Slices plugin and
> calling it as a script in Jyton. I made a script (see attachment) for
> registration a image pair stored in input folder. I discussed the script
> with Ignacio (one of the authors) and he confirm me that it is fine and on
> his Mac it works fine too. But when I launch it on my pc (I am using Gentoo
> x64), it randomly shows mi a dialog "Bio-Formats Import Options" and then
> it crashs. I even don t understand why ti needs such information. Do you
> have any advice where am I doing a mistake or is it a bug in Fiji?
>
> Thanks for any answer

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