Tiago Ferreira tferr
tferr
/ SNT_Scripting_Example.groovy
Created
June 8, 2017 19:20
Example on how to script Simple Neurite Tracer (see http://forum.imagej.net/t/macro-able-segmentation-of-filamentous-structures-axons-in-3d/5533/3?u=tferr)
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| //@LogService log | |
| //@UIService ui | |
| import ij.IJ | |
| import ij.gui.Overlay | |
| import features.ComputeCurvatures | |
| import tracing.TracerThread | |
| import tracing.Path | |
tferr
/ GL_Convex_Hull_Plus.groovy
Created
May 18, 2017 17:24
A Groovyfied version of [Gabriel Landini Convex Hull Plus](http://www.mecourse.com/landinig/software/software.html). It is a work in progress
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| //@ImagePlus imp | |
| // Obtains the 2D Convex Hull ROI from a 2D binary image | |
| // TODO: Use imagej.ops / net.imglib2.roi.geometric.Polygon | |
| import ij.process.ImageProcessor; | |
| import ij.gui.PolygonRoi; | |
| def run(ImageProcessor ip) { |
tferr
/ Default_MacOS_Fiji_Installation_20170221.log
Created
February 21, 2017 13:04
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ImageJ 2.0.0-rc-56/1.51j; Java 1.8.0_66 [x86_64] | |
| -- Application: ImageJ -- | |
| Title = ImageJ | |
| Version = 2.0.0-rc-56/1.51j | |
| groupId = net.imagej | |
| artifactId = imagej | |
| Archiver-Version = Plexus Archiver | |
| Build-Jdk = 1.8.0_111 | |
| Built-By = jenkins-maven |
tferr
/ Z_Projection.py
Last active
November 14, 2016 18:14
http://imagej.net/ImageJ2_Python_Scripts
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # @ImageJ ij | |
| # @Dataset data | |
| # @String(label="Projection Type",choices={"Max","Mean","Median","Min", "StdDev", "Sum"}) proj_type | |
| from net.imagej.axis import Axes | |
| from net.imagej.ops import Ops | |
| def proj_method(method): |
tferr
/ Convert_Traces_to_SWC.py
Created
October 27, 2016 17:26
— forked from mhl/Convert_Traces_to_SWC.py
Batch convert Simple Neurite Tracer's .traces files to SWC format
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import os | |
| import re | |
| from tracing import PathAndFillManager | |
| # An example script showing how to convert all the .traces | |
| # files in a directory to SWC files. (The .traces format | |
| # is the native file format of Simple Neurite Tracer.) | |
| def run(): | |
| d = IJ.getDirectory("Choose your directory of .traces files...") |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /* Polar_Plot_Demo.bsh | |
| * IJ BAR: https://github.com/tferr/Scripts#scripts | |
| * | |
| * Beanshell implementation of JFreeChart[1] PolarChartDemo[2] | |
| * | |
| * [1] http://www.jfree.org/jfreechart/api/javadoc/ | |
| * [2] http://www.java2s.com/Code/Java/Chart/JFreeChartPolarChartDemo.htm | |
| */ | |
| import ij.gui.GUI; |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| /** | |
| * Retrieves the Checkbox of a RadioButtonGroup() in an ImageJ1 | |
| * GenericDialog associated with the specified label. | |
| */ | |
| Checkbox getRadioCheckbox(ij.gui.GenericDialog gd, String label) { | |
| Component[] gdComponents = gd.getComponents(); | |
| for (Component c1 : gdComponents) { | |
| if (c1 instanceof Panel) { | |
| Component[] c1Components = ((Panel) c1).getComponents(); | |
| for (Component c2 : c1Components) { |
tferr
/ Random_String.ijm
Created
January 6, 2015 16:39
ImageJ1 macro function to generate random string
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| function randomString(length, spacers) { | |
| template = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"; | |
| nChars = lengthOf(template); | |
| string = ""; | |
| for (i=0; i<length; i++) { | |
| idx = maxOf(0, round(random()*nChars-1)); | |
| string += substring(template, idx, idx+1); | |
| if (spacers && i%5==0) string += "_"; | |
| } | |
| return string; |
tferr
/ ValidateFileExtension.java
Created
January 6, 2015 16:14
Validate file extensions using regex
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import java.util.regex.Matcher; | |
| import java.util.regex.Pattern; | |
| boolean validFile(String filename) { | |
| String FILE_PATTERN = "(.*(\\.(?i)(stk|tif))$)"; | |
| Pattern pattern = Pattern.compile(FILE_PATTERN); | |
| Matcher matcher = pattern.matcher(filename); | |
| return matcher.matches(); | |
| } |
tferr
/ Mirror_Selection.ijm
Created
December 8, 2014 13:27
ImageJ1 macros that create X/Y mirrors of the active ROI
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| // ImageJ1 macros that create X/Y mirrors of the active ROI | |
| // http://thread.gmane.org/gmane.comp.java.imagej/35570 | |
| macro "Contralateral in X [F1]" { | |
| mirrorROI(-1, 1); | |
| } | |
| macro "Contralateral in Y [F2]" { | |
| mirrorROI(1, -1); | |
| } |