John Bogovic bogovicj
bogovicj
/ bsplineInterpolationDemo.groovy
Created
March 4, 2020 16:19
Demonstration cubic bspline interpolation with imglib2
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| #@ Dataset img | |
| #@ Boolean(value=true) precompute | |
| /** | |
| * Prerequisite: | |
| * Get the bspline branch of bogovicj's (my) fork of imglib2: | |
| * git clone -b bspline [email protected]:bogovicj/imglib2.git | |
| * | |
| * Install it: | |
| * mvn -Dscijava.app.directory=<your_Fiji_directory> install |
bogovicj
/ FCWB-to-JRC2018F_bwlandmarks.csv
Created
September 3, 2019 18:58
Rough bigwarp landmarks for FCWB template to JRC2018F template.
We can make this file beautiful and searchable if this error is corrected: It looks like row 8 should actually have 8 columns, instead of 6 in line 7.
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| "Pt-0","true","281.716910229645","95.80208768267224","48.70146137787056","313.5204418371608","97.00407557411268","86.78014572025053" | |
| "Pt-1","true","221.96116910229637","30.159081419624187","60.77035490605427","253.6870980375783","25.727196075156513","96.26193244258873" | |
| "Pt-2","true","341.4726513569937","31.63089770354904","60.77035490605427","372.04595298538624","24.74632158663877","96.26193244258873" | |
| "Pt-3","true","281.42254697286006","209.72066805845515","20.442588726513552","312.8665255114823","202.9385203340292","35.447714154488516" | |
| "Pt-4","true","147.78162839248424","82.8501043841336","59.887265135699366","178.48672058455114","79.34833478079327","104.43588651356994" | |
| "Pt-5","true","412.41419624217116","80.20083507306887","61.94780793319415","444.9576232985387","76.40571131524001","106.07067732776619" | |
| "Pt-6","true","282.01127348643","104.33862212943632","77.84342379958247","313.19348367432156","88.83012150313147","145.305656868476" | |
| "Pt-7","true","129.9088624076395","145.08624526854425","90.75408368394483", |
bogovicj
/ bigwarpSimilarityPart.groovy
Last active
June 7, 2022 12:31
Extract the scale parameter for a set of bigwarp landmark points defining a similarity model.
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| #@ File (label="Landmark file") landmarksPath | |
| #@ Integer (label="Number of dimensions", value=3) nd | |
| #@ String (label="Direction", choices={"Forward", "Inverse" }, value="Forward") direction | |
| import mpicbg.models.*; | |
| import bigwarp.landmarks.LandmarkTableModel; | |
| import net.imglib2.util.*; |
bogovicj
/ Align_Image_Roi_Parameters.groovy
Created
August 8, 2019 13:19
copy of https://github.com/fiji/VIB/blob/master/src/main/java/Align_Image.java that prints out parameters
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| import ij.IJ; | |
| import ij.ImagePlus; | |
| import ij.WindowManager; | |
| import ij.gui.GenericDialog; | |
| import ij.gui.Line; | |
| import ij.gui.Roi; | |
| import ij.plugin.PlugIn; | |
| import ij.process.ByteProcessor; | |
| import ij.process.ColorProcessor; | |
| import ij.process.FloatProcessor; |
bogovicj
/ bigwarpDemo.groovy
Created
July 25, 2019 18:16
An imagej2 example script for running bigwarp and getting at its landmark pairs
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| #@ Dataset (label="moving image") mvgImg | |
| #@ Dataset (label="target image") tgtImg | |
| #@ File (label="landmarks file csv", required=false ) landmarksFile | |
| import bdv.util.*; | |
| import bdv.viewer.*; | |
| import net.imagej.*; | |
| import bigwarp.*; |
bogovicj
/ morphOpenGeneral.groovy
Last active
June 14, 2019 12:15
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| #@ OpService ops | |
| #@ UIService ui | |
| #@ Dataset(label="Binary image") image | |
| #@ Integer(label="Width of the structuring element", min=1, value=1) width | |
| /* | |
| * A Fiji script for applying a morphological opening using imageJ ops, | |
| */ | |
| import net.imglib2.type.numeric.integer.*; | |
| import net.imglib2.algorithm.neighborhood.*; |
bogovicj
/ merge_images.groovy
Last active
April 5, 2019 14:11
An ImageJ2 script for combining binary images with specified physical bounding boxes
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| // @UIService ui | |
| // @LogService log | |
| // @Dataset base | |
| // @String baseMinArg | |
| // @String baseMaxArg | |
| // @Dataset add | |
| // @String addMinArg | |
| // @String addMaxArg | |
| // @Integer value |
bogovicj
/ scale_mask_centered.groovy
Last active
February 18, 2019 12:30
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| #@Dataset(label="Image to transform") img | |
| #@Double(label="scale") scaling_factor | |
| #@UIService ui | |
| import net.imglib2.*; | |
| import net.imglib2.realtransform.*; | |
| import net.imglib2.view.*; | |
| import net.imglib2.interpolation.*; | |
| import net.imglib2.interpolation.randomaccess.*; |
bogovicj
/ parse_and_transform.groovy
Last active
April 2, 2019 17:27
ImageJ / Fiji: Parses a string representing an affine transormation, applies it to an image, and displays it.
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| #@Dataset(label="Image to transform") img | |
| #@String(label="affine transform string") affineString | |
| #@UIService ui | |
| import net.imglib2.realtransform.*; | |
| import net.imglib2.view.*; | |
| import net.imglib2.interpolation.*; | |
| import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory; | |
| nd = 3 |
bogovicj
/ trakem2_exportAreaLists-asMasks_limitZ.bsh
Created
March 8, 2018 22:37
trakem2_exportAreaLists-asMasks_limitZ.bsh
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| import java.awt.Color; | |
| import java.awt.Graphics2D; | |
| import java.awt.Rectangle; | |
| import java.awt.geom.AffineTransform; | |
| import java.awt.geom.Area; | |
| import java.awt.image.BufferedImage; | |
| import java.awt.image.DataBufferByte; | |
| import java.io.File; | |
| import java.util.ArrayList; | |
| import java.util.Collections; |