[ome-devel] Possible bug in BF ICS/IDS exporter writing to existing files

[Niko Ehrenfeuchter]

Thanks, Melissa!

On 12.11.2018 19:56, Melissa Linkert wrote:
> Hi Niko,
> 
> Thank you for reporting this, and for including a test macro.  I can
> reproduce the problematic ICS/IDS behavior, although it seems like the
> overwritten OME-TIFF dataset is not correct either.
> 
> This is now recorded on our issue tracker:
> 
> https://trello.com/c/CJP1cNxV/292-consistent-behavior-when-writing-to-a-file-that-exists
> 
> The safest thing to do for now is to check if the file exists before
> running the exporter, and delete or rename it as needed (independent
> of the output format).
> 
> Regards,
> -Melissa
> On Sun, Nov 11, 2018 at 6:27 AM Niko Ehrenfeuchter
> <nikolaus.ehrenfeuchter at unibas.ch> wrote:
>>
>> Dear all,
>>
>> I think we have come across a bug in the Bio-Formats ICS/IDS writer. The
>> macro code below illustrates an issue when saving / exporting an image
>> to ICS/IDS using a previously existing filename (i.e. "overwrite" the file).
>>
>> The macro produces four images (six files due to the ICS/IDS separate
>> metadata files), that are supposed to have the same pixel-content
>> independent of their format / suffix (i.e. both "overwrite" images
>> should look identical). Unfortunately the ICS/IDS differs when exporting
>> was done to a previously existing file.
>>
>> Tested it with an up-to-date Fiji + Bio-Formats on Linux and Windows.
>>
>> Cheers,
>> Niko
>>
>>
>> ---- IJ1 macro ----
>> // make sure no images are currently open, clear log:
>> run("Close All");
>> print("\\Clear");
>>
>> // prepare file names and delete them if existing:
>> untouched_omt = getDirectory("temp") + "untouched.ome.tif";
>> untouched_icd = getDirectory("temp") + "untouched.ids";
>> untouched_icc = getDirectory("temp") + "untouched.ics";
>> File.delete(untouched_omt);
>> File.delete(untouched_icd);
>> File.delete(untouched_icc);
>>
>> overwrite_omt = getDirectory("temp") + "overwrite.ome.tif";
>> overwrite_icd = getDirectory("temp") + "overwrite.ids";
>> overwrite_icc = getDirectory("temp") + "overwrite.ics";
>> File.delete(overwrite_omt);
>> File.delete(overwrite_icd);
>> File.delete(overwrite_icc);
>>
>> // create a test image (works with hyperstacks and normal):
>> //newImage("HyperStack", "16-bit color-mode label", 200, 100, 1, 8, 1);
>> newImage("Untitled", "16-bit ramp", 200, 100, 8);
>>
>>
>> // now save the ones to be overwritten:
>> run("Bio-Formats Exporter", "save=[" + overwrite_omt + "]");
>> run("Bio-Formats Exporter", "save=[" + overwrite_icd + "]");
>>
>>
>> // change the test image (rotate by 90 deg, close original):
>> /*
>> id = getImageID();
>> run("TransformJ Rotate", "z-angle=90 adjust");
>> selectImage(id);
>> close();
>> */
>> run("Rotate 90 Degrees Right");
>>
>>
>> // save to "fresh" files:
>> run("Bio-Formats Exporter", "save=[" + untouched_omt + "]");
>> run("Bio-Formats Exporter", "save=[" + untouched_icd + "]");
>>
>> // save (overwrite) to previously existing files:
>> run("Bio-Formats Exporter", "save=[" + overwrite_omt + "]");
>> run("Bio-Formats Exporter", "save=[" + overwrite_icd + "]");
>>
>> // print saving location to log:
>> print(getDirectory("temp"));
>>
>> ---- IJ1 macro ----
>>
>> --
>> Niko Ehrenfeuchter | Image Analysis Specialist
>> University of Basel | Biozentrum | Imaging Core Facility
>> Klingelbergstr. 50/70 | 4056 Basel | Switzerland
>> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>> Phone: +41 (61) 207 26 73 | nikolaus.ehrenfeuchter at unibas.ch
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
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-- 
Niko Ehrenfeuchter | Image Analysis Specialist
University of Basel | Biozentrum | Imaging Core Facility
Klingelbergstr. 50/70 | 4056 Basel | Switzerland
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
Phone: +41 (61) 207 26 73 | nikolaus.ehrenfeuchter at unibas.ch