Philipp Rieger
2012-06-07 07:52:00 UTC
Hallo,
I am trying to analyse multi-channel (visual and infrared) images with
Fiji and Weka.
In detail I have to do a segmentation of forest crown pictures into
three classes (crown, sky and trunk) and analysing the percentage of
each class for the entire picture.
My approach is to do segmentation with the ‘Advanced Weka
Segmentation’ Plugin. Therefore I import a NEF file from a digital
camera, split the 3 channels and isolate one of the infrared channels.
Then I import another NEF with 3 ‘normal’ visual channels and stitch
them to a 4 channel composite. I save this composite as a TIFF for
further processing.
In a next step I open the ‘Advanced Weka Segmentation’ Plugin and
create the 3 mentioned classes. I set the settings to: Training
features – Mean, Variance, Minimum and Maximum (I use those for
setting up the process. Which feature will be used at the end is
another topic); Classifier option - RandomForest with –I 10 –K 0 –S 1
and set Homogenize classes to TRUE.
Then I mark training areas for each class (subjective to cover as much
as possible colour values) and press ‘train classifier’.
My question now is how to go on?
As I have 4 channel pictures, do I have to train each channel by hand
or is there a method the segmentation plugin uses the same trainings
areas for each of the 4 channels?
After the ‘train classifier’ is done I get a nice 3 colour image with
(depending on the training areas) a more or less perfect matching
segmentation.
How do I go on if I want to use this segmentation for several more
images? Saving as a *.MODEL and going on with the ‘Apply classifier’
function does create results but those are not always as useful. I am
not sure if the segmentation is done with all channels or just the
first one.
I Save the result as a TIFF and create a Histogram on it so that I get
the total amount of pixels for each colour. Is there a better way to
do it? Because it is kind of uncomfortable to save, open, create, show
list, save the list and open it in Excel to perform further
statistics.
That is why I wanted to use Weka but after hours of reading
documentations, books and wikis I still do not understand how to
analyse the results of my segmentation in Weka.
I tried the Explorer and opened the data.arff file I created after I
performed the ‘train classifier’ function. But when I do a
classification with these data and a RandomForest classifier, aren’t I
am doing the same thing again that I have done in the segmentation
plugin before I saved the data.arff?
You see I get more and more confused about the different functions and
how to put them into the right order. Maybe I am doing something
completely wrong and just don’t getting it?
Any help is welcome! And if further information are needed feel free
to contact me.
Tanks
I am trying to analyse multi-channel (visual and infrared) images with
Fiji and Weka.
In detail I have to do a segmentation of forest crown pictures into
three classes (crown, sky and trunk) and analysing the percentage of
each class for the entire picture.
My approach is to do segmentation with the ‘Advanced Weka
Segmentation’ Plugin. Therefore I import a NEF file from a digital
camera, split the 3 channels and isolate one of the infrared channels.
Then I import another NEF with 3 ‘normal’ visual channels and stitch
them to a 4 channel composite. I save this composite as a TIFF for
further processing.
In a next step I open the ‘Advanced Weka Segmentation’ Plugin and
create the 3 mentioned classes. I set the settings to: Training
features – Mean, Variance, Minimum and Maximum (I use those for
setting up the process. Which feature will be used at the end is
another topic); Classifier option - RandomForest with –I 10 –K 0 –S 1
and set Homogenize classes to TRUE.
Then I mark training areas for each class (subjective to cover as much
as possible colour values) and press ‘train classifier’.
My question now is how to go on?
As I have 4 channel pictures, do I have to train each channel by hand
or is there a method the segmentation plugin uses the same trainings
areas for each of the 4 channels?
After the ‘train classifier’ is done I get a nice 3 colour image with
(depending on the training areas) a more or less perfect matching
segmentation.
How do I go on if I want to use this segmentation for several more
images? Saving as a *.MODEL and going on with the ‘Apply classifier’
function does create results but those are not always as useful. I am
not sure if the segmentation is done with all channels or just the
first one.
I Save the result as a TIFF and create a Histogram on it so that I get
the total amount of pixels for each colour. Is there a better way to
do it? Because it is kind of uncomfortable to save, open, create, show
list, save the list and open it in Excel to perform further
statistics.
That is why I wanted to use Weka but after hours of reading
documentations, books and wikis I still do not understand how to
analyse the results of my segmentation in Weka.
I tried the Explorer and opened the data.arff file I created after I
performed the ‘train classifier’ function. But when I do a
classification with these data and a RandomForest classifier, aren’t I
am doing the same thing again that I have done in the segmentation
plugin before I saved the data.arff?
You see I get more and more confused about the different functions and
how to put them into the right order. Maybe I am doing something
completely wrong and just don’t getting it?
Any help is welcome! And if further information are needed feel free
to contact me.
Tanks
--
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Please avoid top-posting, and please make sure to reply-to-all!
Mailing list web interface: http://groups.google.com/group/fiji-users