Fiji PhotoMonitoringPlugin issue...

[theo....@gmail.com]

Hi

I originally posted this in the Public Lab forum and was helpfully directed here so I hope somebody can offer me a bit of guidance,

I'm trying to process two images in Fiji, one raw infrared, one visible spectrum. When choosing the two image files from which to create a text file the software completes the task but the resulting text file which should contain the path to the two images is blank. The files are independently stored in two different folder as described in the Fiji tutorial. I suspect it may be because I have downloaded these two images from the internet and the metadata has been stripped out. I don't yet have my IR camera up and running which is why I am using downloaded images.

How do I manually create a text file? When I manaully create the MatchedImages file with the paths below, rather than getting a blank file as described above I get an "error reading file pairs" which means the paths are not correctly written I assume.

D:\Users\Theo Wallis\AppData\Fiji\images\NIR
D:\Users\Theo Wallis\AppData\Fiji\images\RGB

Below is the log file that is generated if this is of any help.

Thanks for your resopnse.

PARAMETER SETTINGS:
Use backup registration method if primary fails? true
Select primary registration method: SIFT/Landmark correspondences
Select secondary registration method: SIFT/Landmark correspondences using last valid set of points
Select transformation type if using SIFT: Rigid
Number of tries for SIFT to find correspondence points: 1
Method to improve SIFT point selection: none
Output image type: tiff
Output NRG image? true
Clip images? true
Output clipped visible image? true
Output Color NDVI image? true
Minimum NDVI value for scaling color NDVI image: -1.0
Maximum NDVI value for scaling color NDVI image: 1.0
Output floating point NDVI image? true
Stretch the visible band before creating NDVI? true
Stretch the NIR band before creating NDVI? true
Saturation value for stretch: 2.0
Channel from visible image to use for Red band to create NDVI: 1
Channel from IR image to use for IR band to create NDVI: 3
Select output color table for color NDVI image: 16_colors.lut
PHOTO PAIR PROCESSING SETTINGS:

[Chris Fastie]

Theo,

The text file with the photo pairs should be of the form: 

L:\KAP\2013\Infrablue\leaf\NIR\OaktoberNIR-257-4.JPG, L:\KAP\2013\Infrablue\leaf\VIS\OaktoberVIS-258-5.JPG

L:\KAP\2013\Infrablue\leaf\NIR\OaktoberNIR-257-8.JPG, L:\KAP\2013\Infrablue\leaf\VIS\OaktoberVIS-258-8.JPG

L:\KAP\2013\Infrablue\leaf\NIR\OaktoberNIR-257-13.JPG, L:\KAP\2013\Infrablue\leaf\VIS\OaktoberVIS-258-12.JPG

However, I have made lots of such files manually that do not work in the plugin. There is something about the plugin that is very picky about the format of this file. If the plugin generates the file, it works fine, and sometimes I can edit the file and it still works, but making certain changes to the file breaks it.  I have not figured out exactly why it breaks, or what the critical detail is. But I think the carriage return is suspect.

Chris

[Theo Wallis]

Chris, once again your help is much appreciated! I shall try your suggestion.

Regards

Theo

[Ned Horning]

Hi Theo -

Chris' suggestion should work. Here is the relevant text from the plugin
guide:
If you create your own file you need to ensure the following format is
followed. Each line in the file must have the directory path and file
name for the two images that form a pair with a comma separating the
two. The first image is the near_IR image (the source image that will be
warped) and the second image is the visible image (the target image used
as a reference but not altered). Make sure there is no whitespace
(space, tab, or new line) after the last line of text.
Here is an example of what the text file looks like for two image paris
(4 images):
ned/InputImages/nir/LPV-0001.JPG, ned/InputImages/visible/LPV-1324.JPG
ned/InputImages/nir/LPV-0003.JPG, ned/InputImages/visible/LPV-1325.JPG
--

I'm not sure why the "create dual image list" plugin isn't working for
you but it could be a problem with the images. Did you try the
“Calculate from pair” option?

All the best,

Ned