John Bogovic bogovicj
bogovicj
/ OptionalMapAbuse.java
Last active
May 10, 2024 21:24
Use the map method to cause a side-effect if the optional is not-empty.
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| public T getValidateDefault(String parameter, Predicate<T> validator, T defaultValue) { | |
| return getOptional(parameter).filter(validator) | |
| .map(x -> { | |
| allDefault = false; | |
| return x; | |
| }).orElse(defaultValue); | |
| } |
bogovicj
/ n5vMetadataCorrection.groovy
Created
April 16, 2024 19:49
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| #@ File(styles="both") root | |
| #@ String(value="/") datasetPath | |
| /* | |
| * If you used Fiji to export a multi-scale image with N5Viewer metadata using average downsampling | |
| * between approximately March 13 and April 15 2024, the translation metadata may be incorrect. | |
| * | |
| * Running this script will correct the metadata. | |
| * | |
| * John Bogovic |
bogovicj
/ cosemMetadataCorrection.groovy
Created
April 16, 2024 15:57
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| #@ File(styles="both") root | |
| #@ String(value="/") datasetPath | |
| /* | |
| * If you used Fiji to export a multi-scale an image with COSEM metadata using average downsampling | |
| * between approximately March 13 and April 15 2024, the translation metadata may be incorrect. | |
| * | |
| * Running this script will correct the metadata. | |
| * | |
| * John Bogovic |
bogovicj
/ omeZarrMetadataCorrection.groovy
Created
April 16, 2024 01:53
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| #@ File(styles="both") root | |
| #@ String(value="/") datasetPath | |
| /* | |
| * If you used Fiji to export a multi-scale OME-Zarr image using average downsampling | |
| * between approximately March 13 and April 15 2024, the translation metadata may be incorrect. | |
| * | |
| * Running this script will correct the metadata. | |
| * | |
| * John Bogovic |
bogovicj
/ shapeDemo.groovy
Created
April 2, 2024 14:12
ImageJ2 script that displays a Diamond or Hypersphere neighborhood for a given radius
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| #@ DatasetService ds | |
| #@ UIService ui | |
| #@ Long radius = 13 | |
| #@ String (choices={"Diamond", "Hypersphere"}, style="listBox") shapeType | |
| /* | |
| * Displays a Diamond or Hypersphere neighborhood for a given radius | |
| */ | |
| if( shapeType.equals("Diamond")) | |
| shp = new DiamondShape(radius); |
bogovicj
/ skimage_affine.ipynb
Created
March 20, 2024 14:06
Apply an affine or scaling transform with scikit-image
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bogovicj
/ CompressionExamples.java
Created
December 8, 2023 18:16
Create example n5 array datasets for a variety of compression methods.
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| package org.janelia.saalfeldlab.n5.generateExamples; | |
| import org.janelia.saalfeldlab.n5.Bzip2Compression; | |
| import org.janelia.saalfeldlab.n5.Compression; | |
| import org.janelia.saalfeldlab.n5.GzipCompression; | |
| import org.janelia.saalfeldlab.n5.Lz4Compression; | |
| import org.janelia.saalfeldlab.n5.N5Writer; | |
| import org.janelia.saalfeldlab.n5.RawCompression; | |
| import org.janelia.saalfeldlab.n5.XzCompression; | |
| import org.janelia.saalfeldlab.n5.blosc.BloscCompression; |
bogovicj
/ image_geometry.ipynb
Last active
March 7, 2024 15:37
Image geometry and indexing in python
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| import com.amazonaws.auth.AWSCredentials; | |
| import com.amazonaws.auth.AWSStaticCredentialsProvider; | |
| import com.amazonaws.auth.AnonymousAWSCredentials; | |
| import com.amazonaws.auth.DefaultAWSCredentialsProviderChain; | |
| import com.amazonaws.client.builder.AwsClientBuilder.EndpointConfiguration; | |
| import com.amazonaws.services.s3.AmazonS3; | |
| import com.amazonaws.services.s3.AmazonS3ClientBuilder; | |
| import com.amazonaws.services.s3.model.ListObjectsV2Request; | |
bogovicj
/ iterateRows.groovy
Created
June 22, 2023 20:57
ImageJ2 script to perform an operation over the rows of a dataset
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| #@ Dataset img | |
| /** | |
| * Perform an operation on every row of the input image. | |
| * | |
| * This sets every pixel in the first row to have value zero, | |
| * the second row will have value one, etc. | |
| * | |
| * https://forum.image.sc/t/best-way-to-iterate-over-columns-rows/82472 | |
| */ |
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