OME Tiffs and macros

[nellypledge]

Hi all.

It appears I've created some ome.tifs using micro-manager (MM) that will open when I drag and drop, but not in a macro.  It tells me that the file is not a supported format when I try to open it from a macro loop.  It's weird as the drag and drop works well.  This is in both Fiji stand alone and Fiji and ImageJ that comes with OpenSPIM and MM respectively.

The files were created from the multiD acq in the OpenSPIM version of MM, which has a Fiji main program compared to the ImageJ main program on all the other MM installs I have in place.

In a for loop in the macro it stops and shows a error dialog in addition to the console and log.  If I remove the loop and setup just the single file open in a macro it gives me the console, and then slowly pops up the INFO lines of reading and populating metadata and then finally opens.  The console window is pasted below.

Thanks in advance for your time.  Any pointers would be much appreciated.

Neil

[WARNING] Opening was canceled.
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Checking comment style
java.io.IOException: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: Invalid TIFF file
        at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:134)
        at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:109)
        at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75)
        at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
        at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
        at net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:328)
        at ij.IJ.open(IJ.java)
        at ij.macro.Functions.open(Functions.java:2651)
        at ij.macro.Functions.doFunction(Functions.java:156)
        at ij.macro.Interpreter.doStatement(Interpreter.java:227)
        at ij.macro.Interpreter.doBlock(Interpreter.java:605)
        at ij.macro.Interpreter.doStatement(Interpreter.java:269)
        at ij.macro.Interpreter.doFor(Interpreter.java:527)
        at ij.macro.Interpreter.doStatement(Interpreter.java:251)
        at ij.macro.Interpreter.doStatements(Interpreter.java:215)
        at ij.macro.Interpreter.run(Interpreter.java:112)
        at ij.macro.Interpreter.run(Interpreter.java:82)
        at ij.macro.Interpreter.run(Interpreter.java:93)
        at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
        at ij.IJ.runMacro(IJ.java:129)
        at ij.IJ.runMacro(IJ.java:118)
        at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:917)
        at net.imagej.legacy.IJ1Helper$3.call(IJ1Helper.java:914)
        at net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:880)
        at net.imagej.legacy.IJ1Helper.runMacro(IJ1Helper.java:914)
        at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:116)
        at net.imagej.legacy.plugin.IJ1MacroEngine.eval(IJ1MacroEngine.java:163)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:174)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
        at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask.run(FutureTask.java:262)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
        at java.lang.Thread.run(Thread.java:745)
Caused by: io.scif.img.ImgIOException: java.io.IOException: io.scif.FormatException: Invalid TIFF file
        at io.scif.img.ImgOpener.createReader(ImgOpener.java:556)
        at io.scif.img.ImgOpener.openImgs(ImgOpener.java:146)
        at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:123)
        ... 35 more
Caused by: java.io.IOException: io.scif.FormatException: Invalid TIFF file
        at io.scif.AbstractReader.setSource(AbstractReader.java:274)
        at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
        at io.scif.img.ImgOpener.createReader(ImgOpener.java:547)
        ... 37 more
Caused by: io.scif.FormatException: Invalid TIFF file
        at io.scif.formats.MinimalTIFFFormat$Parser.typedParse(MinimalTIFFFormat.java:415)
        at io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:891)
        at io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:873)
        at io.scif.AbstractParser.parse(AbstractParser.java:253)
        at io.scif.AbstractParser.parse(AbstractParser.java:336)
        at io.scif.AbstractParser.parse(AbstractParser.java:52)
        at io.scif.AbstractReader.setSource(AbstractReader.java:270)
        ... 39 more
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Reading IFDs
[INFO] Populating metadata

[Roger Leigh-2]

On 08/04/2016 01:52, nellypledge wrote:
> Hi all.
>
> It appears I've created some ome.tifs using micro-manager (MM) that will
> open when I drag and drop, but not in a macro.  It tells me that the file is
> not a supported format when I try to open it from a macro loop.

> Thanks in advance for your time.  Any pointers would be much appreciated.

> /[WARNING] Opening was canceled.
> [INFO] Reading IFDs
> [INFO] Populating metadata
> [INFO] Checking comment style
> java.io.IOException: io.scif.img.ImgIOException: java.io.IOException:
> io.scif.FormatException: Invalid TIFF file
>       at
> io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:134)
>       at
> io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:109)

It looks like ImageJ is using scifio to open the file, rather than
Bio-Formats.  I would suggest turning this off and retrying
(Edit->Options->ImageJ2) to see if this makes any difference.

If you still have problems, please do let us know.


Kind regards,
Roger Leigh

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
School of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: [phone]

The University of Dundee is a registered Scottish Charity, No: SC015096

--
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