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Ok sorry for the delay. I have uploaded all the examples to my home folder so you can run them to see the examples.
Hope this helps.

For a good example of how the data is supposed to look (in black and white), load the the following (Load Dataset from File)
/home/sci/crottman/korenberg/results/data_veq2.tif
This tif stack works as expected. This is good, but I want to be able to do the same thing in color.

For color images, try loading (Load Dataset from File)
/home/sci/crottman/korenberg/results/img_stack_color.tif
This is the same data except in color. This is where I get the error and it won't even load the data.

As for loading a directory of color tifs, try loading the following (Load Dataset from Directory)
/home/sci/crottman/korenberg/results/aligned_numbered2_color/
Here, the data is loaded in some non-sequential order (note the difference in how this looks compared to the good example).
(This is the directory that has images 001, 002, ... 00N).
I have the same problem when i load a directory of black-and-white images. See:
/home/sci/crottman/korenberg/results/aligned_numbered2_bw/

Let me know if you have any questions with these examples. Hopefully this clarifies things.

Caleb


On 05/09/2013 06:38 AM, tom fogal wrote:

Hi Caleb!  Sorry IV3D isn't working out of the box for you :-(

Caleb Rottman writes:

I am trying to load a stack of color tifs into ImageVis3D.  When I
load using "Load Dataset from Directory", it loads the individual tif
images in random order (even though my data is ordered '0001.tif',
'0002.tif', ...).

This is definitely the way you want to go.  I am a bit perplexed that
the ordering is broken, though.  Could you send 3 or 4 images from the
sequence so that I could take a look at what's going on myself?

Since you're at SCI, you could just put them somewhere on the SCI
filesystem.

When i convert these images to a tiff stack, (using "Load Dataset
from file") i get an error ("ERROR (DetermineNumberOfTimesteps): UVF
Block combinations do not match;...").

It sounds like you're trying to use the 'file'-based load, but
selecting multiple files.  IV3D assumes each file is then a new
*time*step!  Hence this confusing error message.

I am disheartened to learn this operation gives an error---it
isn't designed to work in the way you'd like, but it shouldn't be
*broken*---but I am not surprised as we haven't tested time-dependent
data in some time. Something else to add to our list.

I am able to load the dataset from a tif stack of just black and
white images - it loads fine - , but I would like to do this for
color images.  Anybody have any suggestions?

So, to make sure I understand this: B&W data named "0001.tif",
"0002.tif", ..., "000N.tif" work perfectly correctly, and color data
named similarly load fine (and in color) but are ordered in correctly?

Thanks,

-tom

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• [IV3D-USERS] Trouble trying to load RGB tifs, Caleb Rottman, 05/07/2013
  • [IV3D-USERS] Re: Trouble trying to load RGB tifs, tom fogal, 05/09/2013
    • [IV3D-USERS] Re: Trouble trying to load RGB tifs, Caleb Rottman, 05/13/2013

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