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IDE@L version 1.0
“Image DEndrochronology @ Liama”
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Joseph Morlier1*, Thierry Fourcaud2
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LRBB,UMR 5103, CNRS/INRA/Université Bordeaux 1, domaine de l’Hermitage, 69 route d’Arcachon, 33612
Cestas cedex, France
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LIAMA-CASIA, Institute of Automation Chinese Academy of Sciences, PB 2728, Beijing 100080, P.R. CHINA
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Abstract: IDE@L is a toolbox for Matlab dealing with Tree rings detection by image
processing. This is a Graphical User Interface (GUI) which can help wood scientists in
extracting tree rings coordinates. Version 1.0 runs under Matlab 65 (R13) and needs
image processing toolbox for “Canny” edge detection. The outputs are detected rings
coordinates (.xls) which can be used by FEM software.
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Keywords: Tree rings, image processing, morphological segmentation, pixel labelling,
finite element reconstruction.
Aknowledgements:
The MATLAB Central File Exchange, http://www.mathworks.com/matlabcentral/fileexchange,
which contains thousands of files contributed by users and developers of MATLAB, Simulink and
related products. Some of these toolboxes files are a compilation of MATLAB Central files.
MATLAB and Octave Functions for Computer Vision and Image Processing,
http://www.csse.uwa.edu.au/~pk/research/matlabfns/ by Peter Kovesi (School of Computer
Science & Software Engineering, The University of Western Australia,Crawley, Western Autralia.
6009). Chapter Edge linking and line segment fitting.
Henri D. Grissino-Mayer's Ultimate Tree-Ring Web Pages,
http://web.utk.edu/~grissino/gallery.htm for original tree rings images support.
IDE@L Matlab Toolbox
• Description
• Requirements
• FAQ
• Functions List
• Tutorial #1
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*contact: jmorlier@lrbb.u-bordeaux.fr
Description
Matlab is a commercial software package for numeric
computation, graphics, visualization, and high-level
programming. Matlab is available from The MathWorks,
Inc. The basic Matlab package has many functions
generally useful for tree-ring studies. Matlab "toolboxes"
with specialized functions can also purchased from The
MathWorks, Inc. Toolboxes are available for signal
processing, mapping, image processing, neural networks,
statistics, and many other topics. Many additional userwritten functions are available over the Web. One excellent
source is http://www.mathtools.net.
The "IDE@L" is not a commercially available Matlab
toolbox
Requirements
To use the IDE@L Toolbox, you must have Matlab
(version 5.3 or later) installed on your computer or
network. Depending on which functions you intend to use,
you may also need to have one or more "Matlab toolboxes"
(e.g. image for edge detection) installed.
Note: The code for canny's edge detector is from
Matlab 6.5's image processing toolbox.
To use the IDE@L Toolbox, you must also have its
toolbox functions in a directory on your Matlab path.
FAQ:
Why the analysis is very long sometimes ?
For high resolution image (1.jpg ~100 ko or 535x545
pixels) the analysis will take several minutes and few
seconds for low resolution (mini1.jpg~20 ko or 267x272
pixels) but less ring can be detected ...
Why using Canny method for edge detection?
The Canny method finds edges by looking for local
maxima of the gradient of I. The gradient is calculated
using the derivative of a Gaussian filter. The method uses
two thresholds, to detect strong and weak edges, and
includes the weak edges in the output only if they are
connected to strong edges. This method is therefore less
likely than the others to be "fooled" by noise, and more
likely to detect true weak edges.
Default threshold is: [0.1 0.2]
For more details try [0.1 0.15]
For high details [0.05 0.1]
Figure 1: Maxima above value 25 of rings indicator are
detected
How works partial reconstruction of Rings ?
Just pick interested points of a the ring and finished with
‘e’ on the keyboard. Then an excel sheet appears with your
data. Copy and paste ...or save.
...
left-click : Mark a point
'e' : End
No wavelets ?? Curvelets ?? for edge detection
Not at this time ...
List of Functions
IDEAL/
File: IDE@L.doc
Directory: IMAGES
File: Ring_label2.m
File: Ring_label_save.m
File: ait_imneg.m
File: loadfile.m
File: IDEAL_gui.m
File: edge_parameter.m
File: edgelink.m
File: maxlinedev.m
File: mergeseg.m
File: perimeter_parameter.m
File: xlswrite.m
File: Ring_Reconstruction.m
How classified rings from curvature of labelled region?
Each extracted labelled region  are threshold by an
indicator of ring curvature  (second derivative)
Rings Indicators 
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length(  )
a “circular like” ring.
to see if this region is really
Empirical value for “circle like” ring indicator is 25
(Figure 1)
Try 10 or less to detect more rings!
*contact: jmorlier@lrbb.u-bordeaux.fr
List of Functions not yet implemented
Processing Menu:
'Del False Ring ', ...
'Del Double Ring ', ...
47 KB
760KB
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Tutorial #1
The best way of describing this code is by way of example.
To find out what's in the IDE@L Matlab Toolbox, check
out the list of functions.
From the processing menu, you can pick manually the
interested ring, an excel sheet open with the extracted data.
Type on matlab prompt >> IDEAL_gui
From the File menu, load an image, for example mini3.jpg
in the image directory (CTRL+F).
From the Analysis menu, Ring, Ring Detection (CTRL+R
analysis with default parameters). You obtain 9 detected
rings (Figure 2, R1 to R9), that you can save with the menu
export data to excel (CTRL+S). If the you know the real
size of the image, enter in the expected zone.
Figure 4: In red picked points with the mouse
Don’t forget to add the partial ring reconstruction data in
the saved file !
Problems
#1
For saving the data in case of 2 steps detection (change in
parameters between 2 analysis) a problem occurs:
??? Improper assignment with rectangular empty matrix.
Figure 2: detected rings with default parameters
Now you can clear the interface (CTRL+A) and setup the
analysis with better threshold for edge detection:
Setup edge detection (CTRL+D): [0.05 0.1]
The new detected rings are numbered from R10 to R28
(Figure 3). See problem #1 for saving data.
Error in ==> e:\matlab\work\IDEAL\Ring_export.m
On line 16 ==> mp(j)=max(find(m1(:,1)~=0));
Relaunch the GUI, setup the good parameters, launch the
analysis (only one step) and then the data will be saved
with no problems.
#2
The exported data are completed with zero in last rings
detected. In excel you could do
Selected the rows
Data > Filter > Automatic
Personnalised
Different to : select 0
***
Future works will be to correct bugs, improve detection
(curvelets...) and to develop IDE@L for Scilab and Matlab.
***
Figure 3: More detected rings with high details for edge
detection
*contact: jmorlier@lrbb.u-bordeaux.fr