John Bogovic bogovicj
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| #!/bin/bash | |
| isMac12 () { | |
| hasSwVers=$(command -v sw_vers) | |
| if [ ! -z $hasSwVers ] | |
| then | |
| ver=$(sw_vers | grep -Eo '[0-9]+\.[0-9]+\.[0-9]+') | |
| if [[ $ver =~ ^12\..* ]] | |
| then |
bogovicj
/ padCropToTarget.groovy
Last active
August 19, 2021 23:12
Pads/crops the source image such that its field of view matches that target image.
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| #@ Dataset source | |
| #@ Dataset target | |
| /** | |
| * Pads/crops the source image such that its field of view matches that target image, | |
| * respecting the target image origin. | |
| * | |
| * Currently only supports pixel-length shifts, and ignores source origin. | |
| * | |
| * see: |
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| #@File lut | |
| lut = ij.plugin.LutLoader.openLut( lut.getCanonicalPath() ); | |
| for( i in 0..<lut.getMapSize() ) | |
| { | |
| println( [lut.getRed( i ), lut.getGreen(i), lut.getBlue(i)].join(" ") ) | |
| } |
bogovicj
/ N5GenericSingleScaleMetadataParser.java
Created
May 19, 2021 14:26
Tmp n5 parser for caleb
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| package org.janelia.saalfeldlab.n5.metadata; | |
| import org.janelia.saalfeldlab.n5.DatasetAttributes; | |
| import org.janelia.saalfeldlab.n5.N5Reader; | |
| import org.janelia.saalfeldlab.n5.N5TreeNode; | |
| import java.io.IOException; | |
| import java.util.Map; | |
| import java.util.Optional; |
bogovicj
/ ResaveCosemMultiscaleSubset.java
Created
April 27, 2021 21:12
Resave a subset of a multiscale cosem dataset locally
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| package cosem; | |
| import java.io.IOException; | |
| import java.util.Arrays; | |
| import org.janelia.saalfeldlab.n5.DatasetAttributes; | |
| import org.janelia.saalfeldlab.n5.N5Reader; | |
| import org.janelia.saalfeldlab.n5.N5Writer; | |
| import org.janelia.saalfeldlab.n5.ij.N5Factory; | |
| import org.janelia.saalfeldlab.n5.imglib2.N5Utils; |
bogovicj
/ voronoiFiji.groovy
Created
April 8, 2021 22:52
Voronoi diagram / "Natural interpolation"with imglib2-KDTree
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| #@ Dataset img | |
| /** | |
| * Voronoi diagram / "Natural interpolation"with imglib2-KDTree | |
| * see | |
| * https://forum.image.sc/t/natural-neighbor-interpolation-in-3d/51243 | |
| * | |
| * John Bogovic | |
| */ | |
bogovicj
/ zarrBdv.groovy
Created
March 19, 2021 21:48
Read a zarr volume and display with bigdataviewer
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| import net.imglib2.*; | |
| import bdv.util.*; | |
| import org.janelia.saalfeldlab.n5.zarr.*; | |
| import org.janelia.saalfeldlab.n5.imglib2.*; | |
| /* | |
| * A groovy script for Fiji that reads a zarr volume and displays it using BigDataViewer | |
| * | |
| * John Bogovic | |
| */ |
bogovicj
/ RemoveAffineExample.java
Created
November 24, 2020 15:22
example "removing" an affine from a Realtransform with n5-imglib2
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| package demos; | |
| import java.io.IOException; | |
| import java.util.concurrent.ExecutorService; | |
| import java.util.concurrent.Executors; | |
| import org.janelia.saalfeldlab.n5.GzipCompression; | |
| import org.janelia.saalfeldlab.n5.N5FSReader; | |
| import org.janelia.saalfeldlab.n5.N5FSWriter; | |
| import org.janelia.saalfeldlab.n5.N5Reader; |
bogovicj
/ fijiUnicodeTest.groovy
Last active
October 27, 2020 17:33
Testing how unicode is rendered in swing using fiji
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| import java.awt.Dimension; | |
| import java.awt.Font; | |
| import javax.swing.JFrame; | |
| import javax.swing.JLabel; | |
| import javax.swing.JPanel; | |
| String arrow = "→ "; | |
| String ts = " "; | |
| String times = "✕"; |
bogovicj
/ fijiCauseAwsError.groovy
Last active
September 23, 2020 21:25
a groovy script that reproduces some aws errors in sept 2020
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| import org.janelia.saalfeldlab.n5.N5Reader; | |
| import org.janelia.saalfeldlab.n5.N5TreeNode; | |
| import org.janelia.saalfeldlab.n5.imglib2.N5Utils; | |
| import org.janelia.saalfeldlab.n5.metadata.*; | |
| import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader; | |
| import net.imglib2.util.Intervals; | |
| import com.amazonaws.services.s3.*; | |
| import com.amazonaws.regions.Regions; | |
| import com.amazonaws.auth.profile.ProfileCredentialsProvider; |