[ome-users] Batch image export script (Bug fixed)

[Will Moore]

Hi Martin,

  Thanks for your feedback.

I have fixed the "ALL Z PLANES" bug. Fixed script is attached, so you  
can replace the existing one.

I wasn't able to reproduce the "EXPORT INDIVIDUAL CHANNELS" bug. Could  
you try reproducing this and send me both the "Error" and "Info" logs  
from this?

Strange that Java update should fix a Python scripting problem - but  
maybe the bug was in Insight's display of results?


I originally was going to add a MAX PROJECTION option to this script,  
but was advised not to, because of the potential processing hit on the  
server of batch projecting a large number of images.

However, I'll discuss this a bit more and maybe experiment with that  
option.
If we decide to go ahead, it would be nice to hear your experiences  
with setting the rendering levels. I think our standard projection  
uses the existing rendering levels, leading to a lot of saturated  
pixels if you have the auto-set levels.

Options are
  - Set levels to the min and max pixels for each image (each image  
different)
  - For a batch of images, find the min and max pixel value for all  
the images (all the images would have to be 'compatible' - same number  
of channels, same pixel-type)
  - Use the existing rendering settings, and rely on the user to set  
the levels they want in Insight before running the script. This is  
easiest from the script point of view, and actually gives the user  
most flexibility without complicating the script UI. However, you may  
not want to overwrite existing levels and it requires more instruction  
on running the script.

   Cheers,

   Will




On 18 Jul 2011, at 21:38, Martin Spitaler wrote:

> Hi Will,
>
>  I have now been trying your Batch Image Export script, it's really  
> useful, but I've come a few questions:
> first a bug: it works fine as long as I keep the default settings,  
> but it doesn't like when I change them, e.g. if I untick the box  
> EXPORT INDIVIDUAL CHANNELS and only want to export the MERGE it  
> comes up with the attached error message "File_29683.txt", or when I  
> switch the stacks to ALL Z PLANES with error message
> second, just for your information: on one computer, it seemed to do  
> the export, but didn't create an attachment or offer the DOWNLOAD  
> option; updating Java solved the problem
> third: would you be able to build in a MAXIMUM PROJECTION option for  
> stacks? That would solve our problem (Mark's conversation about the  
> script he has been working on)
> Best,
>
> Martin
> <File_29683.txt><File_29689.txt>

William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org





-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20110719/5cf37a1a/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Batch_Image_Export.py
Type: text/x-python-script
Size: 17494 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20110719/5cf37a1a/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20110719/5cf37a1a/attachment-0001.html>