Curtis Rueden ctrueden
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ctrueden
/ exclusions.xml
Created
December 10, 2014 16:31
Fiji's Maven Enforcer banDuplicateClasses exclusions
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| <dependencies> | |
| <dependency> | |
| <artifactId>VIB-lib</artifactId> | |
| <ignoreClasses> | |
| <ignoreClass>javax/media/j3d/*</ignoreClass> | |
| </ignoreClasses> | |
| </dependency> | |
| <dependency> | |
| <artifactId>j3d-core</artifactId> | |
| <ignoreClasses> |
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| : curtis@sirius ~/code » | |
| ag net.imglib2.roi | |
| cellprofiler/CellProfiler/imagej/tests/test_imagej2.py:347: "()Lnet/imglib2/roi/RegionOfInterest;") | |
| cellprofiler/CellProfiler/imagej/imagej2.py:777: "net/imglib2/roi/BinaryMaskRegionOfInterest", | |
| cellprofiler/CellProfiler/imagej/imagej2.py:781: "(Lorg/scijava/Context;Lnet/imglib2/roi/BinaryMaskRegionOfInterest;)V", | |
| cellprofiler/CellProfiler/java/src/main/java/org/cellprofiler/ijutils/OverlayUtils.java:30:import net.imglib2.roi.IterableRegionOfInterest; | |
| cellprofiler/CellProfiler/java/src/main/java/org/cellprofiler/ijutils/OverlayUtils.java:31:import net.imglib2.roi.RegionOfInterest; | |
| cellprofiler/CellProfiler/java/src/test/java/org/cellprofiler/ijutils/TestOverlayUtils.java:36:import net.imglib2.roi.AbstractRegionOfInterest; | |
| cellprofiler/CellProfiler/java/src/test/java/org/cellprofiler/ijutils/TestOverlayUtils.java:37:import net.imglib2.roi.RegionOfInterest; | |
| fiji/Colocalisation_Analysis/src/main/java/algorithms/CostesSignificanceTest. |
ctrueden
/ GenericTyping.java
Created
January 24, 2015 16:56
A demonstration of some challenges of recursive typing.
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| /** A demonstration of some challenges of recursive typing. */ | |
| public class GenericTyping { | |
| // -- "Low-level" classes with generic parameters -- | |
| public static interface Generic<T> { | |
| // Object with a non-recursive generic parameter. | |
| } | |
| public static interface Recursive<T extends Recursive<T>> { |
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| import java.util.ArrayList; | |
| import java.util.List; | |
| import net.imglib2.img.Img; | |
| import net.imglib2.type.numeric.RealType; | |
| /** How to have a list of {@link Img}s of mixed type. */ | |
| public class ImgTyping { | |
| public void go() { |
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| java-info === Which versions of Java are installed? === | |
| + /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java -version | |
| java version "1.6.0_65" | |
| Java(TM) SE Runtime Environment (build 1.6.0_65-b14-466.1-11M4716) | |
| Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-466.1, mixed mode) | |
| 54M /System/Library/Java/JavaVirtualMachines/1.6.0.jdk | |
| + /Library/Java/JavaVirtualMachines/1.6.0_45-b06-451.jdk/Contents/Home/bin/java -version | |
| java version "1.6.0_45" |
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| setBatchMode(true); | |
| run("ROI Map"); | |
| roiMap = getImageID(); | |
| run("Duplicate...", " "); | |
| run("8-bit"); | |
| run("Find Edges"); | |
| edgeMap = getImageID(); | |
| // convert edges image to array | |
| edges = newArray(getWidth() * getHeight()); |
ctrueden
/ batch-process-multi-series.ijm
Created
February 17, 2015 17:36
A example of how to batch process image files with multiple image series each.
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| // A macro template for batch processing multi-series images. | |
| function processImage(path, series) { | |
| IJ.log("Processing " + path + "..."); | |
| run("Bio-Formats Importer", | |
| "open=[" + path + "] " + | |
| "autoscale " + | |
| "color_mode=Grayscale " + | |
| "view=Hyperstack " + | |
| "stack_order=XYCZT " + |
ctrueden
/ find-interface-impls.sh
Created
February 20, 2015 16:39
A script to find Java classes which implement a particular interface
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| # Finds Java classes that implement the given interface. | |
| # | |
| # E.g.: find-interface-impls.sh ij.plugin.PlugIn ij-1.49m.jar | |
| usage() { | |
| echo "Usage: find-interface-impls.sh interface jar1 [jar2 ...]" | |
| } | |
| iface="$1" | |
| shift |
ctrueden
/ stack-trace.txt
Created
March 5, 2015 20:48
Transformation of large OME-XML can take awhile
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| "main" #1 prio=5 os_prio=31 tid=0x00007fd10c801000 nid=0xf07 runnable [0x00000001041c2000] | |
| java.lang.Thread.State: RUNNABLE | |
| at org.apache.xpath.patterns.NodeTest.execute(NodeTest.java:576) | |
| at org.apache.xpath.axes.PredicatedNodeTest.acceptNode(PredicatedNodeTest.java:470) | |
| at org.apache.xpath.axes.AxesWalker.nextNode(AxesWalker.java:372) | |
| at org.apache.xpath.axes.WalkingIterator.nextNode(WalkingIterator.java:195) | |
| at org.apache.xpath.axes.NodeSequence.nextNode(NodeSequence.java:335) | |
| at org.apache.xpath.axes.NodeSequence.runTo(NodeSequence.java:494) | |
| at org.apache.xpath.axes.NodeSequence.setRoot(NodeSequence.java:270) | |
| at org.apache.xpath.axes.LocPathIterator.asIterator(LocPathIterator.java:269) |
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| 2015-03-11 14:06:00,019 ERROR [ org.quartz.core.JobRunShell] (2-thread-3) Job DEFAULT.fullTextThreadRun threw an unhandled Exception: | |
| org.springframework.scheduling.quartz.JobMethodInvocationFailedException: Invocation of method 'run' on target class [class ome.services.fulltext.FullTextThread] failed; nested exception is ome.conditions.ApiUsageException: PreparedStatementCallback; bad SQL grammar [SELECT distinct last_value(id) over w as eid, entitytype, entityid, last_value(action) over w, count(id) over w as series FROM eventlog WHERE id > ? and action in (?, ?, ?, ?) AND entitytype in (?, ?, ?, ?, ?) WINDOW w AS ( PARTITION BY entitytype, entityid ORDER BY id range between unbounded preceding and unbounded following ) ORDER BY eid asc limit ?]; nested exception is org.postgresql.util.PSQLException: ERROR: syntax error at or near "over" | |
| Position: 32 | |
| at org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean$MethodInvokingJob.executeInternal(MethodInvokingJobDetailFactoryBe |