The weird thing is if I manually save the cropped image with BF
exporter. It works, OME XML string is correct and the cropped image
can be easly re-opened (and I don't know why but BF exporter image
size is huge (40MB) for and original image of 1.9MB).
--
Hadrien Mary
Ph.D student in Biology
Tour
It appears that I have the same behaviour using 'ij.op().crop()'.
So in short, my script works well for croping but saving the cropped
image on disk totally failed. In appearence it works but if you try to
open the image, axes (other than X and Y) are merged and it seems that
only the first image
I am now using 'ij.op().crop()' which works well.
I also test fix-cell branch with my previous code (using SCIFIOConfig
and ImageRegion) which fix the save issue (both with ImgSaver and
DatasetService). However cropped image histogram is very different
from the original.
This issue appears only w
Hi Hadrien,
>I tried to use another method to save cropped images using DatasetService:
I couldn't reproduce this failure.. it works for me using the
DatasetService. Do you have any local changes? Did you update your Fiji to
the latest version? If you're still having problems, you could also copy
Quick update:
I tried to use another method to save cropped images using DatasetService:
---
# Create dataset
ds = data.create(imp)
# Save cropped image
data.save(ds, crop_fname)
-
And the error is exactly the same as before.
--
Hadrien Mary
Ph.
Hi again,
The script works well for small images (OME Tiff or normal Tiff) with
the recent Fiji update. However when I run it on large movies (13GB),
I have the following error.
--
-- Classpath of ClassLoader --
/home/hadim/local/Fiji.app/pl
I confirm it works !
Thanks again
--
Hadrien Mary
Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088
Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse
On Wed, Jan 14, 2015 at 3:32 PM, Mark Hiner wrote:
> Hi Hadrien,
>
>>Exception in thread "DrawAn
Hi Hadrien,
>Exception in thread "DrawAndDrop" java.lang.NoSuchMethodError:
>io.scif.ImageMetadata.setAxisLength(Lnet/imglib2/meta/AxisType;J)V
Ah sorry - my fault again for responding too quickly. ImageJ.git doesn't
have a dependency on scifio-ome-xml; it's a dependency in Fiji itself[1].
So whe
Ok it makes sense now !
So I did what you told me about cloning imagej repo, building and
install it with maven inside my local Fiji.app/. I don't know if it's
a bug or a missing dependency but I am now unable to open OME Tiff
files (other kind of file works well) wether it is by drag and drop or
Hi Hadrien,
>Sorry if it's off topic but I tried to run my script and I got a python
error
Oh no! This is totally my fault. I had to update your script for the new
dependencies I mentioned and forgot to paste the new version in my response
yesterday:
>from net.imglib2.meta import Axes
This impo
Thank you Mark !
Sorry if it's off topic but I tried to run my script and I got a
python error probably related to type difference between python and
java. It's not the first time I saw this kind of message and I'd like
to know how to resolve it. Note that for python script I mainly use
javadoc as
Hi Hadrien,
Unsurprisingly, cropping and writing OME-TIFFs was quite broken.
It's working for me now, as of the latest SCIFIO[1] and SCIFIO-OME-XML[2].
Note that these libraries have updated dependencies compared to what's
currently on Fiji, so you can't just drop these .jars into your Fiji
ins
Ok. Let me know when you want me to test your changes. I also tested
fix-writing branch and I didn't notice any changes.
--
Hadrien Mary
Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088
Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse
On Fri, Jan
Hi Hadrien,
I've identified at least two bugs that could be affecting you here.
First of all, there was a bug in the OME-TIFF format writing out
multi-dimensional images. That's fixed on a branch but not uploaded to Fiji
yet [1].
Second, it seems like cropping is restricting pixel reads to the c
I also confirm the same behaviour when replacing original file by OME
sample data :
http://www.openmicroscopy.org/Schemas/Samples/2013-06/bioformats-artificial/multi-channel-4D-series.ome.tif.zip.
--
Hadrien Mary
Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088
Université d
After some investigations I think there is a bug with ImgSaver. In the
following script, X, Y crop is fine but axes informations (T and Z)
are lost and all frames appears on the same axes. Now if I replace
"target = "/home/hadim/cropped.tif" by "target =
"/home/hadim/cropped.ome.tif" on line 9. X,
Thanks for the tip (reminder to me: always look for example in tests!).
Unfortunately crop does not work... I will try to do more tests
tomorrow or wait for you or someone else to have a look.
Updated code:
from ij import IJ
from ij import ImagePlus
from io.scif import SCIFIO
from io.scif.confi
Hi Hadrien,
> I would like to be able to crop a region in X and Y while
> keeping any other dimensions which could exist (C, Z, T).
Here's some Java:
int minX = 128, maxX = 255, minY = 128, minY = 255;
AxisType[] axes = { Axes.X, Axes.Y };
String[] ranges = { minX + "-" + maxX, minY
After some investigations, I'm pretty sure I don't instanciate
ImageRegion correctly. Doc and source code didn't help me... I would
like to be able to crop a region in X and Y while keeping any other
dimensions which could exist (C, Z, T).
--
Hadrien Mary
On Thu, Jan 8, 2015 at 10:22 PM, Hadrie
Thank you Curtis for the answer.
I tried to apply what you told me and the code now works without
error. However the saved cropped image is not cropped (same size as
original) and pixel values are modified).
Script:
from io.scif.config import SCIFIOConfig
from io.scif.img import ImageRegion
from
Hi Hadrien,
> I tried to use SCIFIO to write cropped image on disk but it doesn not
> work.
The error you see is because SCIFIO operates on ImgLib2 data structures,
not ImagePlus objects.
> Is there is any “easy” alternative to BF setCropRegion function in
> SCIFIO ?
Yes: you create a SCIFIOCon
I currently use setCropRegion option from BF.openImagePlus but I take
any other option to crop image according to a roi instance. I didn't
find how to do that in python.
--
Hadrien Mary
On Thu, Jan 8, 2015 at 9:18 PM, Hadrien Mary wrote:
> Hi,
>
> I am writing a python macro which iterate over
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