Hi, Melissa,<div><br></div><div>I tried updating loci_tools.jar to the latest version and that didn't help, but I did track it down to a different plugin that I had manually installed, which included some of the bio-formats image reading classes from an older version, which were apparently being used instead of those in loci_tools.jar. I removed the other plugin and now things are working with the latest build.</div>
<div><br></div><div>Apologies for the trouble and thanks!</div><div><br></div><div>Colin<br><br><div class="gmail_quote">On Sat, Jun 2, 2012 at 5:09 PM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Colin,<br>
<br>
> When attempting to read a micromanager file using the bio-formats ImageJ<br>
> plugin (v. 4.3.3 as well as the latest trunk build, running latest Fiji on<br>
> ubuntu 12.04), I've encountered an exception with the stack trace included<br>
> below. I think this results from micromanager having created a metadata<br>
> field with a value of only empty square brackets in the metadata.txt file.<br>
> I've attached a sample metadata.txt file (one of the empty fields is<br>
> "CustomIntervals_ms": [] at line 47, e.g.); I'm happy to ftp the actual<br>
> images to you as well, though they are too large to attach.<br>
*snip*<br>
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of<br>
> range: -1<br>
> at java.lang.String.substring(String.java:1937)<br>
> at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:285)<br>
> at loci.formats.FormatReader.setId(FormatReader.java:1072)<br>
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)<br>
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)<br>
> at loci.plugins.in.Importer.showDialogs(Importer.java:125)<br>
> at loci.plugins.in.Importer.run(Importer.java:77)<br>
> at loci.plugins.LociImporter.run(LociImporter.java:79)<br>
> at ij.IJ.runUserPlugIn(IJ.java:185)<br>
> at ij.IJ.runPlugIn(IJ.java:152)<br>
> ... 8 more<br>
<br>
Thank you for the bug report.<br>
<br>
I wasn't able to duplicate this error message using the very latest<br>
trunk build, or the latest version that is in the Fiji updater (and in<br>
fact, I do recall fixing this very bug a while back).<br>
<br>
Could you please run the Fiji updater ("Help > Update Fiji", making sure<br>
to update "plugins/loci_tools.jar"), restart Fiji, and then see if the<br>
file opens correctly?<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Fri, Jun 01, 2012 at 03:37:54PM -0700, Colin Fuller wrote:<br>
> Hi--<br>
><br>
> When attempting to read a micromanager file using the bio-formats ImageJ<br>
> plugin (v. 4.3.3 as well as the latest trunk build, running latest Fiji on<br>
> ubuntu 12.04), I've encountered an exception with the stack trace included<br>
> below. I think this results from micromanager having created a metadata<br>
> field with a value of only empty square brackets in the metadata.txt file.<br>
> I've attached a sample metadata.txt file (one of the empty fields is<br>
> "CustomIntervals_ms": [] at line 47, e.g.); I'm happy to ftp the actual<br>
> images to you as well, though they are too large to attach.<br>
><br>
> Thanks,<br>
><br>
> Colin Fuller<br>
><br>
> Stack trace:<br>
><br>
> java.lang.reflect.InvocationTargetException<br>
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
> at<br>
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)<br>
> at<br>
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br>
> at java.lang.reflect.Method.invoke(Method.java:597)<br>
> at ij.Command.runPlugIn(Command.java:146)<br>
> at ij.Command.runCommand(Command.java:95)<br>
> at ij.Executer.run(Executer.java:64)<br>
> at java.lang.Thread.run(Thread.java:680)<br>
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of<br>
> range: -1<br>
> at java.lang.String.substring(String.java:1937)<br>
> at loci.formats.in.MicromanagerReader.initFile(MicromanagerReader.java:285)<br>
> at loci.formats.FormatReader.setId(FormatReader.java:1072)<br>
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:481)<br>
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)<br>
> at loci.plugins.in.Importer.showDialogs(Importer.java:125)<br>
> at loci.plugins.in.Importer.run(Importer.java:77)<br>
> at loci.plugins.LociImporter.run(LociImporter.java:79)<br>
> at ij.IJ.runUserPlugIn(IJ.java:185)<br>
> at ij.IJ.runPlugIn(IJ.java:152)<br>
> ... 8 more<br>
<br>
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> "MicroManagerVersion": "1.4.10",<br>
> "ROI": [<br>
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> "ChNames": [<br>
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> "IJType": 1,<br>
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> "Height": 1040,<br>
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> "CoolsnapHQ-Description": "PVCAM API device adapter",<br>
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> "Core-AutoFocus": "",<br>
> "COM7-StopBits": "1",<br>
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> "CoolsnapHQ-CCDTemperatureSetPoint": "-30",<br>
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> "COM8-AnswerTimeout": "500.0000",<br>
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> "UUID": "d1a7d3e2-1853-47e9-a8b6-bf5de37b5c76",<br>
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> "CoolsnapHQ-Trigger Timeout (secs)": "2",<br>
> "ZStage-Description": "ASI Z-stage driver adapter",<br>
> "ElapsedTime-ms": 1213,<br>
> "Wheel-A-Name": "Wheel-A",<br>
> "Wheel-B-Speed": "3",<br>
> "CoolsnapHQ-TransposeXY": "0",<br>
> "CoolsnapHQ-Firmware Version": "2132",<br>
> "Wheel-A-Description": "Sutter Lambda filter wheel adapter",<br>
> "Frame": 0,<br>
> "Wheel-A-Port": "COM7",<br>
> "Core-ChannelGroup": "Channel",<br>
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> "Width": 1392,<br>
> "WaitInterval": 0,<br>
> "PositionName": null,<br>
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> "Summary": {<br>
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> "Source": "Micro-Manager",<br>
> "Channels": 3,<br>
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> "Width": 1392,<br>
> "WaitInterval": null,<br>
> "PositionName": null,<br>
> "PixelSizeUm": 0,<br>
> "Height": 1040,<br>
> "Summary": {<br>
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> "UUID": "775aaa0b-87c9-4142-9586-d508da358802",<br>
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> "ChNames": [<br>
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> "Height": 1040,<br>
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> "Prefix": "20120601_fiberspreads_flowcell_T",<br>
> "PixelSize_um": 0,<br>
> "Frames": 0,<br>
> "BitDepth": 12,<br>
> "KeepShutterOpenChannels": true,<br>
> "Source": "Micro-Manager",<br>
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> "ComputerName": "horntail",<br>
> "CustomIntervals_ms": [],<br>
> "KeepShutterOpenSlices": false,<br>
> "ChColors": [<br>
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> "Positions": 0,<br>
> "Directory": "C:\\Documents and Settings\\Colin Fuller/Images"<br>
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> "Source": "CoolsnapHQ",<br>
> "Wheel-A-Delay_ms": "0.0000",<br>
> "CoolsnapHQ-PrescanPixels": "21",<br>
> "CoolsnapHQ-CCDTemperature": "-30",<br>
> "COM8-DataBits": "8",<br>
> "Epi-Mode": "Fast",<br>
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> "CoolsnapHQ-OutputTriggerFirstMissing": "0",<br>
> "CoolsnapHQ-Y-dimension": "1040",<br>
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> "Epi-State": "1",<br>
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<br>
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</blockquote></div><br></div>