Image Browser plugin

[Albert Cardona]

I've created an Image Browser plugin that, when given a folder, finds
all images, stacks and image sequences and places them in a single
window, as sort of virtual stacks. It handles memory automatically so
it can *never* run out of memory. It can create stacks on the fly out
of image sequences, even if composed of images of different dimensions.
I use it to instantly browse 700MB of several image sequences in CDs.
See all details here:

http://www.pensament.net/java/other_plugins.html#image_browser

Albert


--
Albert Cardona
Molecular Cell Developmental Biology
University of California Los Angeles
Tel [phone]
http://www.pensament.net/java/
http://www.mcdb.ucla.edu/Research/Hartenstein/

[Jon Harman]

Hi,

I gave it a try, but even a small (for me) directory of images takes too
long to load.  System (win 2000 with 512M memory)  grinds to a halt,
probably because of memory disk swapping.

I've wanted an imagej image browser for a while, with simple
functionality like irfanview where next and previous buttons send you to
the next or previous image in the current directory.

Jon

Albert Cardona wrote:

> I've created an Image Browser plugin that, when given a folder, finds
> all images, stacks and image sequences and places them in a single
> window, as sort of virtual stacks. It handles memory automatically so
> it can *never* run out of memory. It can create stacks on the fly out
> of image sequences, even if composed of images of different
> dimensions. I use it to instantly browse 700MB of several image
> sequences in CDs. See all details here:
>
> http://www.pensament.net/java/other_plugins.html#image_browser
>
> Albert
>
>
> --
> Albert Cardona
> Molecular Cell Developmental Biology
> University of California Los Angeles
> Tel [phone]
> http://www.pensament.net/java/
> http://www.mcdb.ucla.edu/Research/Hartenstein/
>

[Gabriel Landini]

On Sunday 18 December 2005 21:31, Jon Harman wrote:
> I gave it a try, but even a small (for me) directory of images takes too
> long to load.  System (win 2000 with 512M memory)  grinds to a halt,
> probably because of memory disk swapping.

I really like the browser idea, although I also found very slow loads in
linux.

I wonder if adding some options would reduce the slow load, for example:
option to avoid doing recursive search of directories,
option to load only the first slice of a stack,
option to create a smaller thumbnail rather than the full size collage.

In one computer it gave me this error when compiled for the first time:

java.lang.NullPointerException
 at Image_Browser$IBImage.<init>(Image_Browser.java:748)
 at Image_Browser$IBImage.<init>(Image_Browser.java:740)
 at Image_Browser.extractIBImage(Image_Browser.java:275)
 at Image_Browser.browse(Image_Browser.java:152)
 at Image_Browser.browse(Image_Browser.java:160)
 at Image_Browser.browse(Image_Browser.java:160)
 at Image_Browser.browse(Image_Browser.java:160)
 at Image_Browser.browse(Image_Browser.java:160)
 at Image_Browser.browse(Image_Browser.java:160)
 at Image_Browser.run(Image_Browser.java:74)
 at ij.IJ.runUserPlugIn(IJ.java:271)
 at ij.ImageJ.runUserPlugIn(ImageJ.java:216)
 at ij.plugin.PlugInExecuter.run(Compiler.java:188)
 at java.lang.Thread.run(Thread.java:595)

and the second time it run but then froze IJ after loading 22 images.
(There was a huge frame with 22 images in it, but otherwise empty).
The system monitor showed near 100% CPU load and near 100% cached memory use.
(I had to kill the java process to end IJ).

I eventually run successfully on a directory with 5 or 6 images, but it was
very slow. Not sure what the problem really is.

Albert Cardona wrote:
> I use it to instantly browse 700MB of several image
> sequences in CDs.

But isn't the plugin loading the whole 700MB of images? Can one really browse
"instantly" the whole contents?
What amount of memory do you assign to IJ?

Cheers,

Gabriel

[Kurt De Vos]

Seems to work fine on OSX.
I might take some of the code and try to implement some kind of  
preview function in my ImageViewer plugin.
kurt

On 18 Dec 2005, at 23:00, Gabriel Landini wrote:

> On Sunday 18 December 2005 21:31, Jon Harman wrote:
>> I gave it a try, but even a small (for me) directory of images  
>> takes too
>> long to load.  System (win 2000 with 512M memory)  grinds to a halt,
>> probably because of memory disk swapping.
>
> I really like the browser idea, although I also found very slow  
> loads in
> linux.
>
> I wonder if adding some options would reduce the slow load, for  
> example:
> option to avoid doing recursive search of directories,
> option to load only the first slice of a stack,
> option to create a smaller thumbnail rather than the full size  
> collage.
>
> In one computer it gave me this error when compiled for the first  
> time:
>
> java.lang.NullPointerException
>  at Image_Browser$IBImage.<init>(Image_Browser.java:748)
>  at Image_Browser$IBImage.<init>(Image_Browser.java:740)
>  at Image_Browser.extractIBImage(Image_Browser.java:275)
>  at Image_Browser.browse(Image_Browser.java:152)
>  at Image_Browser.browse(Image_Browser.java:160)
>  at Image_Browser.browse(Image_Browser.java:160)
>  at Image_Browser.browse(Image_Browser.java:160)
>  at Image_Browser.browse(Image_Browser.java:160)
>  at Image_Browser.browse(Image_Browser.java:160)
>  at Image_Browser.run(Image_Browser.java:74)
>  at ij.IJ.runUserPlugIn(IJ.java:271)
>  at ij.ImageJ.runUserPlugIn(ImageJ.java:216)
>  at ij.plugin.PlugInExecuter.run(Compiler.java:188)
>  at java.lang.Thread.run(Thread.java:595)
>
> and the second time it run but then froze IJ after loading 22 images.
> (There was a huge frame with 22 images in it, but otherwise empty).
> The system monitor showed near 100% CPU load and near 100% cached  
> memory use.
> (I had to kill the java process to end IJ).
>
> I eventually run successfully on a directory with 5 or 6 images,  
> but it was
> very slow. Not sure what the problem really is.
>
> Albert Cardona wrote:
>> I use it to instantly browse 700MB of several image
>> sequences in CDs.
>
> But isn't the plugin loading the whole 700MB of images? Can one  
> really browse
> "instantly" the whole contents?
> What amount of memory do you assign to IJ?
>
> Cheers,
>
> Gabriel

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[Albert Cardona]

Jon & Gabriel,

I run the Image Browser plugin both in a macosx 10.3.9 with 512 MB of
RAM (ImageJ uses -Xmx384m), and in a FreeBSD 5.3 with 1GB RAM (ImageJ
uses -Xmx256m). In both machines I have zero problems in loading a CD
with 700 MB of image sequences (23 sequences, between 14 and 32 images
each).

What the plugin does is to read the name of all files, compile a
String[] for each identified sequence, and then open an image
corresponding to the central image in the sequence (for my data, much
more informative than the first). It does NOT load the 700 Mb of
images, only 23 * 1 MB (images are 1024 x 1024). The whole process
takes 13 seconds in the FreeBSD machine, and about 35 in the mac (the
CD reader is 8x only, versus 32x in the FreeBSD).

Then when any of the images is selected by clicking it, the '>' and '<'
keys are used to navigate the sequence it belongs to as a virtual
stack, with the speed of a virtual stack (one can tell the difference,
but not by much). One can open the whole sequence as a stack by
double-clicking it, and then that is a real stack completely loaded in
RAM.

The plugin is setup so that it uses 70% of ImageJ's maximum memory at
most. When it reaches that limit, it will start to release the first
loaded images. If your ImageJ memory -Xmx setting is too low you may be
experiencing slow loads. Otherwise I don't have an explanation for the
slow loads.

Images are loaded in full scale because that's the most convenient for
me. I thought about setting up a dialog to ask for several options, but
I believe it's not worth it. First, the processor is fake: it's a 4x4
pixels ByteProcessor which has been told to use a much larger width and
height, so the ImageCanvas gets the necessary dimensions. But this are
never the super huge "processor" that it would use otherwise. Second,
if the user shift-double-clicks, all resources are released except the
awt images, which in the above CD take up to 22 Mb only. The zomming
and navigating with the hand tool don't affect at all the memory load.
The rest of the memory is free for other tasks.

Jon: the image browser that you want is perfectly doable and for me
quite straight forward. I use a macro in the CLI plugin for that. If
you want a plugin to do it for you, please email me on the side.

Gabriel: the purpose of the Image Browser plugin is to see all the
contents at a glance and to be able to use/process it right away. This
is why I hard-coded the ability to read directories recursively and to
load the images in full size.

About stacks: since they are an image sequence stored as a single file,
the whole stack has to be loaded to show any given slice. Even using
JAI, which the API kind of suggests it can read any slice directly, the
whole stack is loaded (and much slower by the way). So if the user
shift-double-clicks to release all resources, whenever '>' or '<' are
used again the whole stack is loaded, and then stays in memory. But all
other stacks remain unloaded.

Gabriel: the exception you are getting most likely has to do with a
file not being readable. I did not write in any checks for whether the
Opener succeeded in loading a file. I will put them in. Thanks for
reporting on this.

Albert


--
Albert Cardona
Molecular Cell Developmental Biology
University of California Los Angeles
Tel [phone]
http://www.pensament.net/java/
http://www.mcdb.ucla.edu/Research/Hartenstein/

[Gabriel Landini]

Albert,
Thanks for the extensive explanation. Lots of tricks, eh! :-)
On Monday 19 December 2005 16:43, Albert Cardona
 wrote:

> the purpose of the Image Browser plugin is to see all the
> contents at a glance and to be able to use/process it right away. This
> is why I hard-coded the ability to read directories recursively and to
> load the images in full size.

Sure, I understand, it was just a suggestion that may improve use. Sometimes
one may not want to do recursive search. When I browse the IJ directory it
also browses the JDK one :-/ Sure, it would be more sensible to put the JDK
somewhere else.

> Gabriel: the exception you are getting most likely has to do with a
> file not being readable.

I will have a look if I have a non-readable image,
I will try giving more memory to the JVM and see if I get any improvements.

Cheers,

Gabriel

[Albert Cardona]

Gabriel et al,

I've updated the Image Browser plugin:

- introduced failsafe loading, so images which cannot be loaded will not
disrupt anything (will be show as a black canvas, even if within a sequence)
(thanks to Gabriel Landini for reporting on this).
- Added futher memory control when creating awt.Image objects, since it was
not checked that there was enough memory before creating them (only when
loading the files to an ImagePlus object). Yes out of memory errors where
possible because of the double memory representation of any image (the
ImageProcessor and the awt.Image), but hopefully not anymore.
- Increased the minimum amount of memory to be free before loading an image
file or creating an awt.Image to 40%, to ensure proper opening of large files
under low memory conditions. Users may want to fine tune this value for their
specific needs.
- Clicking a panel now makes it be unloaded last in the cache, so most
recently browsed are kept for a longer time.
- Added alt+double-click to open a single slice in a stack or sequence.

Albert