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Mark Hiner hinerm

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hinerm / BFITKTest.cxxitkLSMBioFormatsImageIOTest.cxx
Created October 16, 2012 17:55
bf-itk-pipe time splitting example
/*
* #%L
* Bio-Formats plugin for the Insight Toolkit.
* %%
* Copyright (C) 2010 - 2012 Insight Software Consortium, and Open Microscopy
* Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
@hinerm
hinerm / hcheck.sh
Last active December 15, 2015 04:59
Script for finding valid commits on a git branch.
#!/bin/bash
#
# History checking script
#
# This script checks out each commit that
# exists on a dev_branch but not a base_branch.
# "ant clean tools" is run on that branch,
# and a log file is written with the results
# of the build to
# <log_dir>/<PASSED/FAILED><commit hash><commit message>.log
@hinerm
hinerm / FollowedClasses
Last active December 15, 2015 11:49
FollowedClasses - a list of classes that have SCIFIO equivalents. git log --follow should work for these. NewClasses - a parallel list of the modern classes follow.sh - a script that will compare the log --follow results of FollowedClasses and NewClasses and log the results.
components/loci-legacy/src/loci/common/AbstractNIOHandle.java
components/loci-legacy/src/loci/common/BZip2Handle.java
components/loci-legacy/src/loci/common/ByteArrayHandle.java
components/loci-legacy/src/loci/common/CBZip2InputStream.java
components/loci-legacy/src/loci/common/CRC.java
components/loci-legacy/src/loci/common/CaseInsensitiveLocation.java
components/loci-legacy/src/loci/common/Constants.java
components/loci-legacy/src/loci/common/DataTools.java
components/loci-legacy/src/loci/common/DateTools.java
components/loci-legacy/src/loci/common/DebugTools.java
@hinerm
hinerm / scifio javadoc warnings
Last active December 25, 2015 04:38
[WARNING] Javadoc Warnings
[WARNING] /Users/mhiner/loci/scifio/scifio/src/main/java/io/scif/formats/TIFFFormat.java:990: warning - Tag @link: can't find initStandardMetadata(Metadata) in io.scif.formats.TIFFFormat.BaseTIFFParser
[WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/package-info.java:347: warning - Tag @link: reference not found: Plane
[WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/package-info.java:347: warning - Tag @link: reference not found: RandomAccessInputStream
[WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/img/package-info.java:51: warning - Tag @link: reference not found: net.imglib2.img.ImgPlus
[WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/img/package-info.java:51: warning - Tag @link: reference not found: net.imglib2.img.ImgPlus
[WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/img/package-info.java:51: warning - Tag @link: reference not found: io.scif.io.img.ImgOpener
[WARNING] /Users/m
@hinerm
hinerm / Calculate_UnMixing_Fiji.m
Last active August 29, 2015 14:05
% @matrix Image
% @matrix dSpectrum
% @matrix aSpectrum
% @matrix tSpectrum
% @double dQY
% @double aQY
% @double BackGround
% @double Threshold
% @OUTPUT double[] KDA
% @OUTPUT double[] KAD
@hinerm
hinerm / fiji-failures
Created November 7, 2014 20:05
[INFO] Scanning for projects...
[INFO]
[INFO] Using the builder org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder with a thread count of 1
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Top-level Fiji project 2.0.0-beta-1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- scijava-maven-plugin:0.2.1-SNAPSHOT:verify-no-snapshots (default-cli) @ fiji ---
[ERROR] Could not resolve dependency: Dependency {groupId=sc.fiji, artifactId=fiji-lib, version=2.0.0, type=jar} of path:
@hinerm
hinerm / licenses
Created November 14, 2014 21:05
Fiji is GPL v3
SCIFIO is bsd2
scifio-bf-compat is gplv2
scifio-omero is gplv2
scifio-tutorials is cc0
scifio-lifesci is gplv2
scijava is bsd2
scripting-r is gplv2
@hinerm
hinerm / TIFF profile
Created January 25, 2015 18:15
<?xml version="1.0" encoding="UTF-8"?>
<?JvmMonitor version="3.8.1"?>
<cpu-profile date="2015/01/25 12:09:02" runtime="8608@localhost" mainClass="org.eclipse.jdt.internal.junit.runner.RemoteTestRunner" arguments="-Dscijava.log.level=error -Dfile.encoding=UTF-8">
<thread name="main">
<frame name="io.scif.services.SCIFIODatasetService.create(net.imagej.ImgPlus)" cnt="1" time="0">
<frame name="io.scif.services.SCIFIODatasetService.datasetService()" cnt="1" time="0"/>
</frame>
<frame name="io.scif.services.DefaultDatasetIOService.open(java.lang.String)" cnt="7676" time="175061">
<frame name="io.scif.config.SCIFIOConfig.imgOpenerSetIndex(int)" cnt="7676" time="0">
<frame name="io.scif.config.SCIFIOConfig.imgOpenerSetRange(io.scif.img.Range)" cnt="7676" time="0"/>
@hinerm
hinerm / Main.java
Created June 18, 2015 17:50
Test for URLClassLoader.close
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.URL;
import java.net.URLClassLoader;
public class Main {
@hinerm
hinerm / Main.java
Created June 18, 2015 18:14
Test the ability of a jar to overwrite itself
package org.scijava;
import java.io.FileOutputStream;
import java.io.IOException;
public class Main {
public static void main(String... args) throws IOException {
//FIXME: set this path to the location of the jar containing this main class.
String url = "C:/Users/Johannes/loci/test/target/scijava-tests-2.43.1-SNAPSHOT.jar";