hanslovsky

hanslovsky

@file:Repository("https://maven.scijava.org/content/groups/public")
@file:DependsOn("org.janelia.saalfeldlab:n5-zarr:0.0.8")

import kotlin.math.ceil

import org.janelia.saalfeldlab.n5.zarr.N5ZarrWriter
import org.janelia.saalfeldlab.n5.zarr.ZArrayAttributes
import org.janelia.saalfeldlab.n5.zarr.ZarrCompressor

require(args.size == 2) { "Two arguments required, zarr group and dataset"}

hanslovsky

[packages]
numba = "~=0.55"
matplotlib = "~=3.5"

[requires]
python_version = "3.9"

hanslovsky

package me.hanslovsky.konkorde

import com.sun.jna.Library
import com.sun.jna.Memory
import com.sun.jna.Native
import com.sun.jna.Pointer
import com.sun.jna.Structure

interface ConcordeLib  : Library {

hanslovsky

interface Base<T: Base<T>>
interface Derived<T: Derived<T>> : Base<T>
class Impl: Derived<Impl>
data class Container<T>(val t: T)

@JvmName("f1")
fun <T: Base<T>> Container<T>.someFunc(c: Container<T>) =
    println("generic: $c")
@JvmName("f2")
fun Container<out Derived<*>>.someFunc(c: Container<out Derived<*>>) =

hanslovsky

[[source]]
url = "https://pypi.org/simple"
verify_ssl = true
name = "pypi"

[packages]
imglyb = "~=2.0"
jupyter = "~=1.0"
matplotlib = "~=3.4"
pillow = "~=8.4"

hanslovsky

#!/usr/bin/env kscript

// requires kscript: https://github.com/holgerbrandl/kscript
// install jep native libraries with
//     python -m pip install jep
// When using Python interpreter in a a non-standard location, set PYTHONHOME appropriately.

@file:MavenRepository("scijava", "https://maven.scijava.org/content/groups/public")
@file:DependsOn("net.imglib2:imglib2-cache:1.0.0-beta-16")
@file:DependsOn("net.imglib2:imglib2:5.12.0")

hanslovsky

import java.lang.Class
import java.lang.Thread
import java.util.concurrent.Callable
import java.util.concurrent.ExecutorService
import java.util.concurrent.Executors
import jep.Interpreter
import jep.SharedInterpreter


class ThreadsafeInterpreter2(

hanslovsky

#!/usr/bin/env python3.9

from functools import reduce
from pathlib import Path
from subprocess import check_output

import re

m2_repo = Path.home() / '.m2' / 'repository'

hanslovsky

import net.imglib2.imklib.*
import net.imglib2.type.volatiles.*
import net.imglib2.type.numeric.integer.*

// pick any data here
val rawData = imklib.io.n5.openUntypedHDF5("/home/zottel/Downloads/sample_A_20160501.hdf", "volumes/raw").asUnsignedBytes()
val rawDataExtended = rawData.extendBorder().asInts()
val gradientMagnitudeData = (0..2)
    .map { d -> LongArray(3) { if (it == d) 1 else 0 } }
    .map { rawDataExtended[rawData + it].zeroMin - rawDataExtended[rawData - it].zeroMin }