Zeiss CZI: parse Z positions from XML

[melissalinkert]

See http://fiji.sc/bugzilla/show_bug.cgi?id=523

[melissalinkert]

--test zeiss-czi

[ghost]

Looks fine to me.

[ghost]

It does fail with an exception for 'zeiss-czi/olivier/EXP 12 1 CD31 A.czi'

ERROR [16-11-2012 15:23:24.400] 
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
        at java.util.ArrayList.RangeCheck(ArrayList.java:547)
        at java.util.ArrayList.get(ArrayList.java:322)
        at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:489)
        at loci.formats.FormatReader.setId(FormatReader.java:1178)
        at loci.formats.ImageReader.setId(ImageReader.java:729)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:530)
        at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:285)
        at loci.formats.FileStitcher.getUsedFiles(FileStitcher.java:626)
        at loci.formats.ReaderWrapper.getUsedFiles(ReaderWrapper.java:378)
        at loci.tests.testng.FormatReaderTest.initFile(FormatReaderTest.java:2162)
        at loci.tests.testng.FormatReaderTest.initFile(FormatReaderTest.java:2113)
        at loci.tests.testng.FormatReaderTest.testBufferedImageDimensions(FormatReaderTest.java:169)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:644)
        at org.testng.internal.Invoker.invokeMethod(Invoker.java:546)
        at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:700)
        at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1002)
        at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:137)
        at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:121)
        at org.testng.TestRunner.runWorkers(TestRunner.java:908)
        at org.testng.TestRunner.privateRun(TestRunner.java:617)
        at org.testng.TestRunner.run(TestRunner.java:498)
        at org.testng.SuiteRunner.runTest(SuiteRunner.java:329)
        at org.testng.SuiteRunner.access$000(SuiteRunner.java:31)
        at org.testng.SuiteRunner$SuiteWorker.run(SuiteRunner.java:355)
        at org.testng.internal.thread.ThreadUtil$CountDownLatchedRunnable.run(ThreadUtil.java:142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:680)

[melissalinkert]

That exception was fixed in PR #204, so testing with both branches merged should yield no errors.

[ghost]

Now tests with zero failures. However, I do see a lot of the following messages repeated a few hundred times near the end of the tests:

   [testng] [Fatal Error] :10:16: XML document structures must start and end within the same entity.
   [testng] [Fatal Error] :10:5: The element type "DataSchema" must be terminated by the matching end-tag "</DataSchema>".
   [testng] [Fatal Error] :11:3: The element type "METADATA" must be terminated by the matching end-tag "</METADATA>".
   [testng] [Fatal Error] :11:2: XML document structures must start and end within the same entity.
   [testng] [Fatal Error] :9:2: XML document structures must start and end within the same entity.

These errors don't seem to be as fatal as they imply though. If these aren't a problem in practice, looks good to merge.

[melissalinkert]

Those messages are nothing to worry about (and have been there all along).

[melissalinkert]

Merging on Wednesday morning if there are no other objections.

[joshmoore]

Poor PR has been put through enough suffering. Merging now. ;)