Re: ImagePlus into postgresql

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Re: ImagePlus into postgresql

Albert-5
Hi all,

Finally it's working: I can save and read any ImagePlus as a Tiff file
into a PostgreSQL database using the JDBC driver. For stacks only the
first slice is read, but it could easily be adapted to save stacks in
full.
I gave up on using piped streams as these could not guarantee that the
stream was completely written when the database was attempting to use
it for saving the image (there the truncated images).

Find it here: http://www.pensament.net/java/other_plugins.html at the
very bottom.

Albert



Albert Cardona
Institute of Neuroinformatics     Tel : +41 1 635 3052
University/ETH Zurich             Fax : +41 1 635 3053
Winterthurerstrasse 190           acardona (at) ini phys ethz ch
Zurich 8057, Switzerland          www.ini.unizh.ch
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Re: ImagePlus into postgresql

Prodanov, D. (FYS)
Hi albert,

Good job! Although, I wonder how useful it will be to store entire
images in database.
I chose alternative approch to my work. I store
the images on a local disc in a folder tree, but store
their  various measurements in a (remote) MySQL database
with thumbnails kept in the database. This is beacuse the database
connections break somwehow easily in my experience.

best regards

Dimiter Prodanov
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Saving 32 bit tiff with IJ 1.34s

H. Gluender
Dear experts,

saving 32bit tiff-images with ImageJ 1.34s under MacOS9.1 (MRJ_2.2.5)
repeatedly fails with:

---------------------------------------------------------------
results in java.lang.NoSuchMethodError: java.lang.Float: method
floatToRawIntBits(F)I not found
  at ij.io.ImageWriter.writeFloatImage(Compiled Code)
  at ij.io.ImageWriter.write(ImageWriter.java:188)
  at ij.io.TiffEncoder.write(Compiled Code)
  at ij.io.FileSaver.saveAsTiff(FileSaver.java:82)
  at ij.io.FileSaver.saveAsTiff(FileSaver.java:70)
  at ij.io.FileSaver.save(FileSaver.java:45)
  at ij.Executer.runImageCommand(Executer.java:148)
  at ij.Executer.runCommand(Executer.java:133)
  at ij.Executer.run(Executer.java:63)
  at java.lang.Thread.run(Thread.java)
---------------------------------------------------------------

(A file is created but the image has zero values only.)


Is this a general problem?
(If not what can I do to make it disappear?)

Best
--


                   Herbie

          ------------------------

          <http://www.gluender.de>
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Re: ImagePlus into postgresql

Albert-5
In reply to this post by Albert-5
Hi Dimitri,

Well this draft program is just to see how easy and fast it is to save
entire images into a database. It turns out it is both easy and quite
fast, even in the slow hard drive of the laptop from which I'm coding.
The target is a modelling program that will require very little RAM but
will be capable of enabling the assembling several z-levels of a 30x30
grid of 1MB images, for the ultimate purpose of outlining structures
and generating 3D models for them. So the trick is to dynamically load
and unload images in order to show just the ones within view, or their
scaled-down versions when looking at the whole thing zoomed out.
The reasons why we choose the database approach is in the first place
to make the whole thing independent of the underlying operating system,
the same way ImageJ itself is, and second, to make it really easy to
copy the user "file", in this case a file containing data exported from
the database, and use it in any other computer setup directly. Whish me
luck, the project is quite challenging even though all the pieces are
quite working, but separately at the moment.
If any of the code you have for managing the MySQL database is GPLed, I
would love to have a look at it for study, basically to save me trouble
with known-to-work solutions.

Also: do you have any experience with the java document object (JDO)
model and databases? Is it really as bad as it looks, with all the
required xml files for each class and the numerous dependencies each
implementation I've seen needs? (one would think the JDO guys never
looked at reflection or something, same with serialization).

All the best,

Albert



Albert Cardona
Institute of Neuroinformatics     Tel : +41 1 635 3052
University/ETH Zurich             Fax : +41 1 635 3053
Winterthurerstrasse 190           acardona (at) ini phys ethz ch
Zurich 8057, Switzerland          www.ini.unizh.ch
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