Tiago Ferreira tferr
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| /* | |
| * IJ BAR: https://github.com/tferr/Scripts#scripts | |
| * | |
| * Performs a t-test between two open images (http://thread.gmane.org/gmane.comp.java.imagej/35266) using | |
| * commons-math: | |
| * http://commons.apache.org/proper/commons-math/userguide/stat.html | |
| * http://commons.apache.org/proper/commons-math/apidocs/org/apache/commons/math3/stat/inference/TTest.html | |
| * | |
| */ |
tferr
/ multichannel_profile_plot.ijm
Last active
August 29, 2015 14:09
— forked from mutterer/multichannel_profile_plot.ijm
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| // yet another multichannel profile plotter | |
| // with smart(?) lookuptables | |
| Stack.getDimensions(w, h, c, z, t); | |
| p = getProfile(); | |
| getStatistics(null, null, min, max); | |
| Plot.create("Multi-Channel Profile Plot", "Distance (pixels)", "Value"); | |
| Plot.setLimits(0,p.length,min,max); | |
| for (i=1;i<=c;i++) { | |
| Stack.setChannel(i); |
tferr
/ Mirror_Selection.ijm
Created
December 8, 2014 13:27
ImageJ1 macros that create X/Y mirrors of the active ROI
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| // 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); | |
| } |
tferr
/ ValidateFileExtension.java
Created
January 6, 2015 16:14
Validate file extensions using regex
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| 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
/ Random_String.ijm
Created
January 6, 2015 16:39
ImageJ1 macro function to generate random string
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| 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; |
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| /** | |
| * 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) { |
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| /* 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; |
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
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| 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...") |
tferr
/ Z_Projection.py
Last active
November 14, 2016 18:14
http://imagej.net/ImageJ2_Python_Scripts
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| # @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
/ Default_MacOS_Fiji_Installation_20170221.log
Created
February 21, 2017 13:04
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| 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 |
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