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Re: Comparison of three ImageJ-tools for global orientation analysis

Posted by Herbie on Sep 11, 2019; 12:11pm
URL: http://imagej.273.s1.nabble.com/Comparison-of-three-ImageJ-tools-for-global-orientation-analysis-tp5022438p5022439.html

Attached please find the missing ZIP-archive with the histogram-results.
Histograms.zip
<http://imagej.1557.x6.nabble.com/file/t380516/Histograms.zip>  


Herbie wrote

> Dear ImageJ-listers and experts!
>
> To my knowledge, there are three currently maintained ImageJ-tools
> (plugins
> or macros) that can perform *global* orientation analyses of images:
>
> 1. OrientationJ v2.0.4 and v16.01.2018  (macro-recordable ImageJ-plugin)
> &lt;http://bigwww.epfl.ch/demo/orientation/#soft&gt;
>
> 2. Directionality v2.3.0  (macro-recordable ImageJ-plugin)
> &lt;https://imagej.net/Directionality&gt;
>
> 3. Easy Orientation v2.0.0  (macro-wrapper of ImageJ-plugins)
> &lt;https://www.gluender.de/Miscellanea/MiscTexts/UtilitiesText.html#Gl-2019-2&gt;
>
> Since 2013 I've received quite some requests and seen quite some posts on
> the list and the forum, dealing with the question
> "What ImageJ-tools are best suited for *global* orientation analyses?"
> I've tried to answer and I've commented on this question in numerous
> contributions but they are scattered over several places. So here is the
> missing compilation...
>
> Before I start with quantitative comparisons, I should like to sketch the
> approaches (source code has not been inspected for this purpose):
>
> -----------------------------------------------------------------------
> General:
> --------
>
> 1. OrientationJ approach (tool: "Orientation Distribution")____________
> -- In the first place, this plugin is meant for local orientation analyses
> based on "Structure Tensors". Global results (orientation histograms) are
> obtained by combining (weighted) results of the local analyses which is
> performed by the tool "Orientation Distribution".
> -- OrientationJ lets one choose from six kinds of "Structure Tensors".
> Their
> Gaussian windowed area of local operation can be specified (sigma). In the
> present context of global analyses, the "Fourier"-scheme and a Gaussian of
> sigma=1 lead to relative good results.
> -- The weighting of the locally obtained orientations during the process
> of
> their combination mainly depends on the parameter "Minimum Coherence". In
> the present context, 70% was found to be reasonable and is suggested by
> the
> authors as well. ("Min. Energy" = 10%)
> -- The angular range of analysis is always 180deg (-90 to +89; -89.5 to
> 89.5) with fixed angular resolution of 1deg.
> -- The scaling of the histogram values remains unexplained.
> -- In the histograms 0deg stands for the horizontal and the angle
> increases
> counter-clockwise.
> -- "Orientation Distribution" accepts images of rectangular support.
> -- "OrientationJ" is easily installed on ImageJ and Fiji.
>
> 2. Directionality approaches (both methods)____________________________
> (a) Method: "Local Gradient Orientation"
> -- In this mode the plugin computes global orientation histograms from
> results of local analyses, in a similar fashion as the tool "Orientation
> Distribution" described above.
> -- Only a single local operator of fixed size is available.
> (b) Method: "Fourier components"
> -- In this mode the plugin computes global orientation histograms from
> results of (regional?) Fourier power-spectral analyses.
> -- The image or regions appear to be windowed and each power spectrum is
> summed in several blurred double-sectors centered on the spectral origin.
> Sums of rotated double-sectors give the histogram values, with the
> rotation
> angles plus 90deg as the histogram abscissa.
> -- The radial shape of the double-sectors realize a highpass of fixed
> transfer function.
> (a) & (b)
> -- The angular range of analysis and the angular resolution can be set by
> the user. The latter is done by specifying the desired number of histogram
> values.
> -- The scaling of the histogram values is as usual: The summed values add
> to
> one.
> -- In the histograms 0deg stands for the horizontal and the angle
> increases
> counter-clockwise.
> -- "Directionality" accepts images of rectangular support.
> -- "Directionality" comes with Fiji and is difficult to install on ImageJ.
>
> 3. Easy Orientation approach (tool: "Easy Orientation Analysis")_______
> -- The approach is related to that of "Directionality (b)". It works
> purely
> global and is mathematically well-founded.*
> -- The image is windowed by a defined function and its DC-component is
> suppressed.
> -- The Fourier power-spectrum is summed along straight lines through its
> origin. The number of rotated lines depends on the image size and is
> individually determined according to the angular sampling theorem.**
> -- The power-spectral analysis is not restricted by any additional
> filters,
> although a highpass of a user-set cutoff frequency can optionally be
> applied.
> -- The angular range of analysis is always 180deg (0 to 180-delta) with
> image size-specific best angular resolution according to the angular
> sampling theorem.
> -- The scaling of the histogram values is as usual: The summed values add
> to
> one.
> -- In the histograms 0deg stands for the horizontal and the angle
> increases
> counter-clockwise.
> -- "Easy Orientation Analysis" always analyzes the largest square-sized
> and
> central area of an image.
> -- "Easy Orientation" is easily installed on ImageJ and Fiji.
> -- About verification and validation of this tool, please read:
> &lt;http://imagej.1557.x6.nabble.com/info-on-directionality-plugin-tp5022022p5022074.html&gt;
>
>   *&lt;www.gluender.de/Writings/WritingsTexts/HardText.html#Gl-1986-2&gt;
> **&lt;http://www.gluender.de/Writings/WritingsTexts/HardText.html#Gl-2013-1&gt;
> -----------------------------------------------------------------------
>
> Again:
> "What ImageJ-tools are best suited for global orientation analyses?"
>
> This question isn't easy to answer but what can be done, is to apply the
> above ImageJ-tools to the same test image,
> -- judge the quality of the result,
> -- estimate the relative speed of execution, and
> -- take into account individual features (see above).
>
> It appears obvious that there isn't a single test image that is suited for
> this task, i.e. that can represent all kinds of images *and* leads to
> results that can be judged objectively.
>
> Images for which the latter is possible, are those with (concentric)
> circular structures. Ideally, such images should show independence of
> orientation, i.e. a "flat" histogram.
>
> I've decided to use a radial chirp, i.e. a gray-level zone-plate having an
> 256x256 support (canvas). The maximum fundamental spatial frequency of
> this
> zone-plate is 2/3 of the Nyquist-frequency. For this image support the
> best
> angular resolution is obtained for 402 angles per 180deg or 403 angles per
> 181deg.
>
> -- Attached please find a ZIP-archive that contains the zone-plate image
> and
> six result plots (histograms).
> -- The relative deviation of the histogram values from their mean is
> denoted
> as "Coefficient of Variation" (CV) in percent. Ideally it should be zero.
> -- Execution times (T) in seconds are measured for a 1024x1024 zone-plate
> with the display of the histogram plot and the table of histogram values.
> Of
> course the times are machine-dependent, i.e. only the relations are of
> importance.
>
> Configuration for 1. and 3.:
> ImageJ 1.52p; Java 1.8.0_172; dedicated RAM 5 GB, 8 threads
> Configuration for 2.:
> Fiji 2.0.0-rc-69/1.52p; Java 1.8.0_202; dedicated RAM 5 GB, 8 threads
>
>
> -----------------------------------------------------------------------
> Results:
> --------
>
> 1. tool: "Orientation Distribution"____________________________________
> I've considered two versions of this tool that, with the same parameter
> settings (see screen-shots), resulted in fairly different histograms:
> (a) OrientationJ-v204_OJ-Histogram.png
> (b) OrientationJ-v16012018_S-Distribution.png
>
> (a) CV =  5.13 % (180 values;   T ≈  1.060 s (180 values);
> (b) CV =  1.58 % (180 values;   T ≈  0.950 s (180 values);
>
> Comments:
> -- Reasons for the different results of the two versions are unclear.
> -- Regarding the execution times one should bear in mind that they are for
> computations of 180 values *only*.
> -- It is by no means clear which parameter setting gives optimum global
> results and why.
>
>
> 2. tool: "Directionality"______________________________________________
> I've set the angular range of analysis to the default (-90 to 90) and the
> number of histogram values to 403 and for (b) additionally to 181. The
> resulting histograms are:
> (a) Directionality-230_LocalGradientOrient-Histogram_403.png
> (b) Directionality-230_FourierComponents-Histogram_403.png
>     Directionality-230_FourierComponents-Histogram_181.png
>
> (a) CV = 40.16 % (403 values);  T ≈  0.275 s (1609 values);
> (b) CV = 27.97 % (403 values);  T ≈ 64.5   s (1609 values);*
>     CV = 12.19 % (181 values);  T ≈  7.1   s (181 values);
>
> *needs more than 5 GB of dedicated RAM (runs with 9 GB)
>
> Comments:
> -- Reasons for the poor CVs are unclear.
> -- Reasons for the enormous processing time and memory consumption of
> approach (b) are unclear but may be caused by sub-optimum source code.
> -- The appearance of the original histograms (not shown here) is
> questionable. Every bin appears to have a distracting gray shadow and it
> is
> difficult to obtain a display size that provides a regular (gap-less)
> bin-arrangement. The fitted curve makes little sense.
>
>
> 3. tool: "Easy Orientation Analysis"___________________________________
> The number of histogram values is automatically set according to the
> angular
> sampling theorem. No highpass is applied. The resulting histograms is:
>     EasyOrientation-200_Orientation Salience.png
>
>     CV =  0.068 % (402 values); T ≈  1.020 s (1608 values);
>
> Comment:
> -- For many natural images the cutoff frequency of an optional highpass is
> crucial. "Easy Orientation Analysis" provides this option and the
> companion
> tool "Orientation Highpass Test" facilitates the choice of an adequate
> cutoff.
> -----------------------------------------------------------------------
>
> As always, please perform your own tests and form your own opinion about
> the
> tools.
>
> Regards
>
> Herbie
>
>
>
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html





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