#https://askubuntu.com/a/138010
xprop _NET_WM_PID | sed 's/_NET_WM_PID(CARDINAL) = //' | ps `cat`
- Install rjava on ubuntu 18.10: this was essential: https://stackoverflow.com/a/52110207
Tiago Ferreira tferr
tferr
/ Autotrace_DemoTree.py
Created
June 18, 2019 17:12
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| # @LogService log | |
| # @SNTService snt | |
| # @UIService ui | |
| """ | |
| file: Autotrace_OP_1.py | |
| """ | |
| import time | |
| from sc.fiji.snt import (Path, SNT, Tree) |
tferr
/ Autotrace_OP_1.py
Created
June 18, 2019 16:06
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| # @LogService log | |
| # @SNTService snt | |
| # @UIService ui | |
| """ | |
| file: Autotrace_OP_1.py | |
| """ | |
| import time | |
| from sc.fiji.snt import (Path, SNT, Tree) |
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| { | |
| "background-color": "#343D46", | |
| "border-color": "#2A3138", | |
| "page-width": 630, | |
| "page-height": 790, | |
| "text-color": "#F7F7F7", | |
| "text-font-family": "Ubuntu", | |
| "text-font-size": 11, | |
| "margin-left": 90, | |
| "margin-right": 30, |
tferr
/ DiekProblematicCells.groovy
Created
March 19, 2019 15:45
SNT script that checks for the presence of an unknown ARA ID detected on manually downloaded MouseLight reconstructions.
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| /* | |
| * SNT script that checks for the presence of a misterious ARA ID that | |
| * somehow was detected on manually downloaded MouseLight reconstructions. | |
| */ | |
| import tracing.io.MouseLightLoader; | |
| import org.json.* | |
| ids = ["AA0189", "AA0360", "AA0362"] | |
| unknowCompartmentID = 484682464 |
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| ferreirat@ferreirat-ws1:~/code/n5-utils$ _JAVA_OPTIONS=-Djdk.net.URLClassPath.disableClassPathURLCheck=true ./install $HOME/bin | |
| Installing into /groups/mousebrainmicro/home/ferreirat/bin | |
| Assuming operating system linux | |
| Picked up _JAVA_OPTIONS: -Djdk.net.URLClassPath.disableClassPathURLCheck=true | |
| [INFO] Scanning for projects... | |
| Downloading from saalfeld-lab-maven-repo: https://saalfeldlab.github.io/maven/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom | |
| Downloading from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom | |
| Downloaded from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom (129 kB at 239 kB/s) | |
| Downloading from saalfeld-lab-maven-repo: https://saalfeldlab.github.io/maven/org/scijava/pom-scijava-base/3.5.2/pom-scijava-base-3.5.2.pom | |
| Downloading from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava-base/3.5.2/pom-scijava-base-3.5.2. |
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| /* Subfield Tool.ijm | |
| * IJ BAR: https://github.com/tferr/Scripts | |
| * | |
| * Creates a square ROI sized from on the length of a straight line | |
| */ | |
| var sizeRatio = 1/3; | |
| macro "SubField Tool - C037 L0ff0 R3399" { | |
| getCursorLoc(x, y, z, flags); |
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)
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| //@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
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| //@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
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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 |