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The ordering of the Z and T indices is reversed when only the channel index is stored in the file.
If the specified file name ends in ".ids", then a v1.0 dataset (.ics and .ids file) will be written. If the specified file name ends in ".ics", then a v2.0 file will be written as before.
This allows names and wavelengths to be assigned correctly, even if the first index is neither 0 nor 1 and there are gaps in the indices.
This group defines which tests should be run by Hudson/Jenkins.
This reverts commit 556185b. This commit is not at all necessary, because it only served to work around a very, very stupid bug in the ICS writer.
This fixes the very, very stupid bug alluded to in the commit message for 51e4fbd. Previously, the .ics file contained the pixel data and the .ids file contained the metadata. This is the opposite of what it is supposed to be.
This prevents OutOfMemoryErrors during report generation, which caused the build to fail even when all of the tests had passed.
Instead of assuming that every series will produce a thumbnail of the same size, we now explicitly check the length of the thumbnail's byte array.
These files represent surface wind speeds for hurricanes. While not technically image data, someone somewhere might think it's interesting to visualize this data as an image. See the format description: http://www.aoml.noaa.gov/hrd/Storm_pages/grid.html Datasets available here: http://www.aoml.noaa.gov/hrd/data_sub/wind.html
Closes #6219.
Some TIFF-based formats specify that the tiles in an image should overlap by some number of pixels. So we now have a getSamples(...) signature that can accept overlap values in X and Y, though nothing is done with these values at the moment. See #6616.
X and Y overlap values are now parsed, and the image dimensions are adjusted accordingly. See #6616.
Closes #6616.
The only missing piece now is that the reference graphs are not checked.
This means that the graphs {Objective:0:0, Image:0 => Objective:0:0} and
{Objective:0:0, Image:0 => Objective:1:0} are considered to be equal when
they are in fact not equal.
Closes #7282.
Reference checks are now in place, so that two OMEXMLMetadata objects will be considered equal if their graphs are equal (regardless of the specific IDs used). Closes #7280.
Remember, this is a Java 1.6 feature, so of course it will not compile under 1.5.
Some software thinks that it is cute to write BitsPerSample = 1, even when there really truly are 8 bits per sample. This is wrong. As a result, we must now check the number of reported bits per sample and, if less than 8, set it to 8.
Closed
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Dec 17, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2694 simleo 'Options propagation: FileStitcher' (user: simleo) # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (user: rleigh-codelibre) # PR 2700 hflynn 'Remove tabularcolumns from docs' (user: hflynn) # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' (user: rleigh-codelibre) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' (user: mabruce) # PR 2704 snoopycrimecop 'Update POM version numbers to 5.3.2-SNAPSHOT' (user: snoopycrimecop) # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' (user: melissalinkert) Already up-to-date. Merged PRs: # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' Generated by BIOFORMATS-DEV-breaking-push#711 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-breaking-push/711/)
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Dec 18, 2016
…om MetaMorph headers (ome#1))
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Dec 18, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' # PR 2700 hflynn 'Remove tabularcolumns from docs' # PR 2704 snoopycrimecop 'Update POM version numbers to 5.3.2-SNAPSHOT' Generated by BIOFORMATS-DEV-merge-push#849 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-merge-push/849/)
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Dec 18, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2694 simleo 'Options propagation: FileStitcher' (user: simleo) # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (user: rleigh-codelibre) # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' (user: mabruce) # PR 2700 hflynn 'Remove tabularcolumns from docs' (user: hflynn) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2704 snoopycrimecop 'Update POM version numbers to 5.3.2-SNAPSHOT' (user: snoopycrimecop) # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' (user: melissalinkert) # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' (user: rleigh-codelibre) Already up-to-date. Merged PRs: # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' Generated by BIOFORMATS-DEV-breaking-push#712 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-breaking-push/712/)
snoopycrimecop
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Dec 18, 2016
snoopycrimecop
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Dec 18, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' # PR 2700 hflynn 'Remove tabularcolumns from docs' # PR 2704 snoopycrimecop 'Update POM version numbers to 5.3.2-SNAPSHOT' Generated by OME-FILES-CPP-DEV-merge-push-superbuild#468 (https://ci.openmicroscopy.org/job/OME-FILES-CPP-DEV-merge-push-superbuild/468/)
snoopycrimecop
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Dec 19, 2016
…om MetaMorph headers (ome#1))
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Dec 19, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' # PR 2700 hflynn 'Remove tabularcolumns from docs' # PR 2704 snoopycrimecop 'Update POM version numbers to 5.3.2-SNAPSHOT' Generated by BIOFORMATS-DEV-merge-push#850 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-merge-push/850/)
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Dec 19, 2016
snoopycrimecop
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Dec 19, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' # PR 2700 hflynn 'Remove tabularcolumns from docs' # PR 2704 snoopycrimecop 'Update POM version numbers to 5.3.2-SNAPSHOT' Generated by OME-FILES-CPP-DEV-merge-push-superbuild#469 (https://ci.openmicroscopy.org/job/OME-FILES-CPP-DEV-merge-push-superbuild/469/)
snoopycrimecop
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Dec 19, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2700 hflynn 'Remove tabularcolumns from docs' (user: hflynn) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2694 simleo 'Options propagation: FileStitcher' (user: simleo) # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (user: rleigh-codelibre) # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' (user: rleigh-codelibre) # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' (user: mabruce) # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' (user: melissalinkert) Already up-to-date. Merged PRs: # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' Generated by BIOFORMATS-DEV-breaking-push#713 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-breaking-push/713/)
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Dec 19, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' (user: mabruce) # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' (user: melissalinkert) # PR 2694 simleo 'Options propagation: FileStitcher' (user: simleo) # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (user: rleigh-codelibre) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' (user: rleigh-codelibre) Already up-to-date. Merged PRs: # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' Generated by BIOFORMATS-DEV-breaking-push#714 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-breaking-push/714/)
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Dec 20, 2016
…om MetaMorph headers (ome#1))
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Dec 20, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' Generated by BIOFORMATS-DEV-merge-push#851 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-merge-push/851/)
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Dec 20, 2016
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Dec 20, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' Generated by OME-FILES-CPP-DEV-merge-push-superbuild#470 (https://ci.openmicroscopy.org/job/OME-FILES-CPP-DEV-merge-push-superbuild/470/)
snoopycrimecop
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Dec 20, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' (user: mabruce) # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' (user: rleigh-codelibre) # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (user: rleigh-codelibre) # PR 2694 simleo 'Options propagation: FileStitcher' (user: simleo) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' (user: melissalinkert) Already up-to-date. Merged PRs: # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' Generated by BIOFORMATS-DEV-breaking-push#715 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-breaking-push/715/)
snoopycrimecop
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Dec 20, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' (user: mabruce) # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' (user: melissalinkert) # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' (user: rleigh-codelibre) # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (user: rleigh-codelibre) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (status: pending) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2694 simleo 'Options propagation: FileStitcher' (user: simleo) Already up-to-date. Merged PRs: # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' Generated by BIOFORMATS-DEV-breaking-push#716 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-breaking-push/716/)
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Dec 21, 2016
…om MetaMorph headers (ome#1))
snoopycrimecop
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Dec 21, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' Generated by BIOFORMATS-DEV-merge-push#852 (https://ci.openmicroscopy.org/job/BIOFORMATS-DEV-merge-push/852/)
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Dec 21, 2016
snoopycrimecop
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Dec 21, 2016
Repository: openmicroscopy/bioformats Excluded PRs: # PR 2701 rleigh-codelibre 'Build Sphinx docs with maven' (label: exclude) # PR 2670 MichaelEllis 'Include BioFormats channel name, into the ImagePlus slice label' (label: breaking) # PR 2625 michaelgoelzer 'Bugfixes for Leica LIFReader' (user: michaelgoelzer) # PR 2556 csachs 'Use chunkmap for Nikon ND2 files to speed up processing' (label: breaking) Already up-to-date. Merged PRs: # PR 2658 rleigh-codelibre 'DeltaVision: Improve accuracy of isThisType stream checks' # PR 2694 simleo 'Options propagation: FileStitcher' # PR 2696 melissalinkert 'ImageJ: preserve original pixel values when exporting signed data' # PR 2698 mabruce 'Read refractive index from MetaMorph headers (ome#1)' Generated by OME-FILES-CPP-DEV-merge-push-superbuild#471 (https://ci.openmicroscopy.org/job/OME-FILES-CPP-DEV-merge-push-superbuild/471/)
sbesson
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Dec 21, 2016
Read refractive index from MetaMorph headers (#1)
simleo
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Apr 27, 2017
This should fix WellSample indexing, so that the reader does not attempt to populate WellSample ome#1 without WellSample #0 being present. openBytes will also now return a blank plane if the appropriate file is missing.
snoopycrimecop
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Apr 1, 2020
Update swg08/bioformats
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These are all of the remaining commits that were in the develop branch of dev.loci.wisc.edu:bio-formats.git prior to our switching entirely to GitHub on 3 January 2011.