Fiji ships a HandleExtraFileTypes implementation that tries several additional plugins, including Bio-Formats. Code at: https://github.com/fiji/IO/blob/IO_-4.2.2/src/main/java/HandleExtraFileTypes.java#L518-L539
On Wed, Jul 10, 2024 at 2:01 PM Kenneth Sloan <[email protected]> wrote: > I'm told that "I moved the files around". The files were downloaded from > the original source and left as is and...the problem went away. > > Another clue - I had asked for the containing directory to be zipped and > sent to me and...it turned out there was some sort of permissions problem. > > So - we no longer have the problem, but the error handling internal to the > code for loading .tif images could be improved. > > I'm curious - what points to Bio-formats? Does that package handle .tif > files? > > -- > Kenneth Sloan > [email protected] > Vision is the art of seeing what is invisible to others. > > > > > > On Jul 10, 2024, at 14:32, Curtis Rueden <[email protected]> wrote: > > Hi Kenneth, > > Looks like a bug in Bio-Formats. > https://bio-formats.readthedocs.io/en/latest/about/bug-reporting.html > <https://urldefense.com/v3/__https://bio-formats.readthedocs.io/en/latest/about/bug-reporting.html__;!!Mak6IKo!PKVnsC5W5DMYOKi97lmij7k2JbqKecNm4BcHSuhxCQem2_N9xlBDTb15iRbuoZ_DwTwr8gqsLUzfdXehKh7OIfs$> > > Regards, > Curtis > > On Wed, Jul 10, 2024 at 9:00 AM Kenneth Sloan <[email protected]> > wrote: > > Any clues about what might be going wrong? > > I'll have the file soon (this comes from one of my users) > > > (Fiji Is Just) ImageJ 2.14.0/1.53h; Java 1.8.0_322 [64-bit]; Mac OS X > 10.16; 524MB of 5122MB (10%) > > java.lang.IllegalStateException: Too early in import process: current step > is READER, but must be after READER > at loci.plugins.in.ImportProcess.assertStep(ImportProcess.java:749) > at loci.plugins.in.ImportProcess.getBaseReader(ImportProcess.java:233) > at loci.plugins.in.Importer.run(Importer.java:112) > at loci.plugins.LociImporter.run(LociImporter.java:78) > at ij.IJ.runUserPlugIn(IJ.java:241) > at ij.IJ.runPlugIn(IJ.java:204) > at ij.IJ.runPlugIn(IJ.java:193) > at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:524) > at HandleExtraFileTypes.run(HandleExtraFileTypes.java:97) > at ij.IJ.runUserPlugIn(IJ.java:241) > at ij.IJ.runPlugIn(IJ.java:204) > at ij.IJ.runPlugIn(IJ.java:193) > at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:528) > at ij.io.Opener.openUsingHandleExtraFileTypes(Opener.java:382) > at ij.io.Opener.openImage(Opener.java:369) > at ij.io.Opener.openImage(Opener.java:233) > at ij.io.Opener.open(Opener.java:102) > at ij.io.Opener.openAndAddToRecent(Opener.java:302) > at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:194) > at ij.plugin.DragAndDrop.run(DragAndDrop.java:160) > at java.lang.Thread.run(Thread.java:750) > > -- > Kenneth Sloan > [email protected] > Vision is the art of seeing what is invisible to others. > > > > > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > <https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__;!!Mak6IKo!PKVnsC5W5DMYOKi97lmij7k2JbqKecNm4BcHSuhxCQem2_N9xlBDTb15iRbuoZ_DwTwr8gqsLUzfdXehI9VQT7s$> > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > <https://urldefense.com/v3/__http://imagej.nih.gov/ij/list.html__;!!Mak6IKo!PKVnsC5W5DMYOKi97lmij7k2JbqKecNm4BcHSuhxCQem2_N9xlBDTb15iRbuoZ_DwTwr8gqsLUzfdXehI9VQT7s$> > > > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
