Metadata-Version: 2.1
Name: ridge-detection
Version: 1.1.0
Summary: ridge / line detection algorithm 
Home-page: UNKNOWN
Author: Luca Lusnig
Author-email: luca.lusnig@mpi-dortmund.mpg.de
License: MIT
Description: # ridge_detection
        This package implements and extends the ridge / line detection algorithm described in:
        
        Steger, C., 1998. An unbiased detector of curvilinear structures. IEEE Transactions on Pattern Analysis and Machine Intelligence, 20(2), pp.113–125.  
        
        It is basically the translation from java to python of https://github.com/thorstenwagner/ij-ridgedetection.
        For more informations about the params visit "https://imagej.net/Ridge_Detection".
        
        ## **Please pay attention that we removed some part of the code and some parameters** 
        
        EXAMPLE CONFIG FILE
        -
        I has to be a json format
        
        
            "path_to_file": "../example.tif",
        	"mandatory_parameters": {
                "Sigma": 3.39,
                "Lower_Threshold": 0.34,
                "Upper_Threshold": 1.02,
                "Maximum_Line_Length": 0,
                "Minimum_Line_Length": 0,
                "Darkline": "LIGHT",
                "Overlap_resolution": "NONE"
            },
        
          	"optional_parameters": {
        		"Line_width": 10.0,
                "High_contrast": 200,
                "Low_contrast": 80
        	},
        
        	"further_options": {
        		"Correct_position": true,
        		"Estimate_width": true,
                "doExtendLine": true,
        		"Show_junction_points": true,
                "Show_IDs": false,
        		"Display_results": true,
                "Preview": true,
                "Make_Binary": false,
                "save_on_disk": true
        	}
        
        
        PARAMETER SELECTION
        
        There are three parameters which have to be specified. These are the mandatory parameters. The optional parameters can be used to estimate the mandatory parameters
        
        
        MANDATORY PARAMETERS:
        -
        
        SIGMA  -->  Determines  the sigma for the derivatives. It depends on the line width
        
        LOWER THRESHOLD --> Line points with a response smaller as this threshold are rejected 
        
        UPPER THRESHOLD --> Line points with a response larger as this threshold are accepted. 
        
        DARKLINE (true/false) --> This parameter determines whether dark or bright lines are extracted. 
        
        OVERLAP RESOLUTION (None/Slope) --> You can select a method to attempt automatic overlap resolution. The accuracy of this method will depend on the structure of your data.
         * NONE --> The default behavior: no assumption of overlap is made. Any point of potential intersection will be treated as an end point for the ridges involved.
         * SLOPE --> This method makes the assumption that when two ridges overlap, it is more likely that they will continue on their path than make turns. **This is best suited to datasets with brief periods of overlap!** If two ridges have a significant portion of overlap, the accuracy of this method will rapidly diminish. 
        
        OPTIONAL PARAMETERS: 
        -
        They are used to estimate the mandatory parameters. At version 1.0.0 it is still not implemented
        
        
        LINE WIDTH (w)  --> The line diameter in pixels. It estimates the mandatory parameter 'Sigma' by: <img src="https://latex.codecogs.com/svg.latex?{\color{White} \frac{w}{2\sqrt{3}}+0.5}"/>
        
        HIGH CONTAST (Bupper) -->  Highest grayscale value of the line. It estimates the mandatory parameter 'Upper threshold' by: <img src="https://latex.codecogs.com/svg.latex?{\color{White} 0.17*\frac{2*Bupper*\frac{w}{2}}{\sqrt{2\pi}\sigma^{3}} *   e^{-\frac{(\frac{w}{2})^{2}}{2\sigma ^{2}}} } "/>
        
        LOW CONTAST  (Blow) --> Lowest grayscale value of the line. It estimates the mandatory parameter 'Lower threshold' by: <img src="https://latex.codecogs.com/svg.latex?{\color{White} 0.17*\frac{2*Blow*\frac{w}{2}}{\sqrt{2\pi}\sigma^{3}} *   e^{-\frac{(\frac{w}{2})^{2}}{2\sigma ^{2}}} }"/>
        
        FURTHER OPTIONS (True/False)
        -
        
        CORRECTION POSITION --> Correct the line position if it has different contrast on each side of it
        
        ESTIMATE WIDTH: If this option is selected the width of the line is estimated.
        
        SHOW JUNCTION POINTS: If this option is selected the junctions points will be displayed.
        
        SHOW IDs: The ID of each line will be shown.
        
        DISPLAY RESULTS: If this option is selected, all contours and junctions are filled into a results table.
        
        
        
        
        
         
         
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >3.4.0
Description-Content-Type: text/markdown
