[ome-users] strange (bad?) meta data with bfopen for MetaXpress
Curtis Rueden
ctrueden at wisc.edu
Wed Apr 15 18:13:28 BST 2015
Hi Melissa,
> When we have a proposed fix, we will update the ticket with a link to
> the pull request on GitHub. At that point, you can build the patch by
> adding the correct remote (SOMEUSER will be the username shown in the
> pull request):
>
>
http://www.openmicroscopy.org/site/support/contributing/using-git.html#github-remotes
>
> fetch the remote as shown on that page, and then merge the branch name
> given in the pull request.
There is actually an easier way to fetch pull requests, without needing to
add additional remotes:
$ git fetch origin pull/1200/head
$ git checkout FETCH_HEAD
$ git checkout -b shiny-new-local-branch # OPTIONAL STEP
$ ant jars # or whatever, to build it
Regards,
Curtis
On Wed, Apr 15, 2015 at 11:57 AM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:
> Hi Mario,
>
> > I've seen progress reported in your issue tracker for this!
> > But I could not easily understand if its in a state that would
> > make sense for me to try? Even if incomplete, I might be able
> > to aid development by testing the current snapshot on our ~5k
> > image sets?
> >
> > If you think it makes sense, can you point out how I fetch the
> > patch and integrate it in my local GIT? From there on I know my
> > way...
>
> This ticket:
>
> > >> http://trac.openmicroscopy.org/ome/ticket/12802
>
> currently does not have a proposed fix - we've investigated enough to
> know that we won't have time to fix it for the upcoming 5.1.1, but we
> expect to have a fix for 5.1.2. Apologies for any confusion there.
>
> When we have a proposed fix, we will update the ticket with a link to
> the pull request on GitHub. At that point, you can build the patch by
> adding the correct remote (SOMEUSER will be the username shown in the
> pull request):
>
>
> http://www.openmicroscopy.org/site/support/contributing/using-git.html#github-remotes
>
> fetch the remote as shown on that page, and then merge the branch name
> given in the pull request. We can certainly provide more detailed
> commands once a pull request is open and the remote name/branch name is
> known.
>
> Regards,
> -Melissa
>
> On Wed, Apr 15, 2015 at 09:53:54AM +0200, Mario Emmenlauer wrote:
> >
> > Dear Melissa and all,
> >
> > I've seen progress reported in your issue tracker for this!
> > But I could not easily understand if its in a state that would
> > make sense for me to try? Even if incomplete, I might be able
> > to aid development by testing the current snapshot on our ~5k
> > image sets?
> >
> > If you think it makes sense, can you point out how I fetch the
> > patch and integrate it in my local GIT? From there on I know my
> > way...
> >
> > Thanks for your help, and Cheers,
> >
> > Mario
> >
> >
> >
> > On 26.03.2015 14:34, Mario Emmenlauer wrote:
> > >
> > > Dear Melissa,
> > >
> > > On 25.03.2015 23:13, Melissa Linkert wrote:
> > >>> correcting my own email from 30min ago:
> > >>>
> > >>> I've checked the current trunk for below-mentioned fix, and I think
> > >>> several values are fine now. There are some exceptions where I'm
> > >>> uncertain about the value:
> > >>> "AbsoluteZ" = "2096309"
> > >>> "CameraChipOffset" = "2096260"
> > >>> "Gamma" = "2096317"
> > >>> "PlaneProperty" = "2097094"
> > >>> "StagePosition" = "2096244"
> > >>>
> > >>> To me, these look possibly incorrect (and actually look more like
> TIFF
> > >>> offsets than values). Is that possible?
> > >>
> > >> That certainly seems likely. As with the PageNumber issue, we won't
> > >> have a fix for this in 5.1.0, but a ticket is now open:
> > >>
> > >> http://trac.openmicroscopy.org/ome/ticket/12802
> > >
> > > Thanks for the very fast follow-up! I'll follow the ticket!
> > >
> > > Cheers,
> > >
> > > Mario
> > >
> > >
> > >
> > >
> > >> Regards,
> > >> -Melissa
> > >>
> > >> On Wed, Mar 25, 2015 at 12:48:12PM +0100, Mario Emmenlauer wrote:
> > >>>
> > >>> Dear Bio-Formats developers,
> > >>>
> > >>> correcting my own email from 30min ago:
> > >>>
> > >>> I've checked the current trunk for below-mentioned fix, and I think
> > >>> several values are fine now. There are some exceptions where I'm
> > >>> uncertain about the value:
> > >>> "AbsoluteZ" = "2096309"
> > >>> "CameraChipOffset" = "2096260"
> > >>> "Gamma" = "2096317"
> > >>> "PlaneProperty" = "2097094"
> > >>> "StagePosition" = "2096244"
> > >>>
> > >>> To me, these look possibly incorrect (and actually look more like
> TIFF
> > >>> offsets than values). Is that possible?
> > >>>
> > >>> The image I used is the same as before:
> > >>> http://data.marssoft.de/b0BCDSL-T070_wD07_s4_z0_t1_cCy5_u001.tif
> > >>>
> > >>> Cheers,
> > >>>
> > >>> Mario
> > >>>
> > >>>
> > >>>
> > >>> On 22.01.2015 15:44, Mario Emmenlauer wrote:
> > >>>>
> > >>>> Hi Melissa,
> > >>>>
> > >>>> On 21.01.2015 23:31, Melissa Linkert wrote:
> > >>>>> Hi Mario,
> > >>>>>
> > >>>>>> attached is an image from MetaXpress, where I try to read all
> > >>>>>> available meta data. However there are some values that seem not
> > >>>>>> to make sense, can you please help if there is a bug, or if the
> > >>>>>> values are indeed correct, or possibly if the issue is in Meta-
> > >>>>>> Xpress that stores weired values? Examples are:
> > >>>>>> Channel #0 Laser focus score 8.2890462076516E-310
> > >>>>>> Channel #0 Camera Bit Depth 8.289046E-317
> > >>>>>
> > >>>>> Thank you for the bug report - this is indeed a bug in
> Bio-Formats. We
> > >>>>> have a fix under review now:
> > >>>>>
> > >>>>> http://github.com/openmicroscopy/bioformats/pull/1537
> > >>>>>
> > >>>>> I would expect that to be included in the upcoming 5.0.7 and 5.1.0
> > >>>>> releases.
> > >>>>
> > >>>> Thanks for the very quick fix, its appreciated! I'll wait for the
> > >>>> 5.0.7 or 5.1.0 releases to check the result.
> > >>>>
> > >>>> All the best,
> > >>>>
> > >>>> Mario
> > >>>>
> > >>>>
> > >>>>
> > >>>>> Regards,
> > >>>>> -Melissa
> > >>>>>
> > >>>>> On Wed, Jan 21, 2015 at 08:52:41PM +0100, Mario Emmenlauer wrote:
> > >>>>>>
> > >>>>>> Dear Bio-Formats developers,
> > >>>>>>
> > >>>>>> attached is an image from MetaXpress, where I try to read all
> > >>>>>> available meta data. However there are some values that seem not
> > >>>>>> to make sense, can you please help if there is a bug, or if the
> > >>>>>> values are indeed correct, or possibly if the issue is in Meta-
> > >>>>>> Xpress that stores weired values? Examples are:
> > >>>>>> Channel #0 Laser focus score 8.2890462076516E-310
> > >>>>>> Channel #0 Camera Bit Depth 8.289046E-317
> > >>>>>>
> > >>>>>> These (and some others) seem not to make sense(?) Attached is
> > >>>>>> also the meta data that I can extract with Bio-Formats from the
> > >>>>>> latest Fiji, I believe version Bio-Formats 5.0.6.
> > >>>>>>
> > >>>>>> All the best,
> > >>>>>>
> > >>>>>> Mario
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>> Mario Emmenlauer BioDataAnalysis Mobil:
> +49-(0)151-68108489
> > >>>>>> Balanstrasse 43 mailto: mario.emmenlauer *
> unibas.ch
> > >>>>>> D-81669 München
> http://www.marioemmenlauer.de/
> > >>>>>
> > >>>>>
> > >>>>>> Key Value
> > >>>>>> BitsPerPixel 16
> > >>>>>> DimensionOrder XYCZT
> > >>>>>> IsInterleaved false
> > >>>>>> IsRGB false
> > >>>>>> LittleEndian true
> > >>>>>> PixelType uint16
> > >>>>>> Series 0 Name
> > >>>>>> SizeC 1
> > >>>>>> SizeT 1
> > >>>>>> SizeX 1392
> > >>>>>> SizeY 1040
> > >>>>>> SizeZ 1
> > >>>>>> AbsoluteZ 2096309
> > >>>>>> AbsoluteZValid 0
> > >>>>>> AutoScale 1
> > >>>>>> AutoScaleHiInfo 0/1
> > >>>>>> AutoScaleLoInfo 0/1
> > >>>>>> Binning 1 x 1
> > >>>>>> BitsPerSample 16
> > >>>>>> CalibrationUnits ume
> > >>>>>> Camera Shutter Always Open
> > >>>>>> CameraBin 1x1
> > >>>>>> CameraChipOffset 2096260
> > >>>>>> Channel #0 Camera Bit Depth 8.289046E-317
> > >>>>>> Channel #0 ImageXpress Micro Filter Cube Cy5
> > >>>>>> Channel #0 ImageXpress Micro Objective 10X S Fluor
> > >>>>>> Channel #0 ImageXpress Micro Shutter Open
> > >>>>>> Channel #0 Laser focus score 8.2890462076516E-310
> > >>>>>> Channel #0 Lumencor Blue Intensity 8.289046E-317
> > >>>>>> Channel #0 Lumencor Blue Shutter Closed
> > >>>>>> Channel #0 Lumencor Cyan Intensity 8.289046E-317
> > >>>>>> Channel #0 Lumencor Cyan Shutter Closed
> > >>>>>> Channel #0 Lumencor Green/Yellow Intensity 8.289046E-317
> > >>>>>> Channel #0 Lumencor Green/Yellow Shutter Closed
> > >>>>>> Channel #0 Lumencor Red Intensity 8.289046E-317
> > >>>>>> Channel #0 Lumencor Red Shutter Closed
> > >>>>>> Channel #0 Lumencor Teal Intensity 8.289046E-317
> > >>>>>> Channel #0 Lumencor Teal Shutter Closed
> > >>>>>> Channel #0 Lumencor UV Intensity 8.289046E-317
> > >>>>>> Channel #0 Lumencor UV Shutter Closed
> > >>>>>> Channel #0 _IllumSetting_ Cy5
> > >>>>>> Channel #0 _MagNA_ 8.28904606E-316
> > >>>>>> Channel #0 _MagRI_ 8.289046E-317
> > >>>>>> Channel #0 _MagSetting_ 10X S Fluor
> > >>>>>> Clear Count 2
> > >>>>>> Clear Mode CLEAR PRE SEQUENCE
> > >>>>>> Compression LZW
> > >>>>>> DateTime 19/03/2014 12:59:47:667
> > >>>>>> Digitizer 20 MHz
> > >>>>>> Exposure 100 ms
> > >>>>>> FillOrder Pixels with lower column values are stored in the
> higher order bits of a byte
> > >>>>>> Frames to Average 1
> > >>>>>> Gain Gain 1 (1x)
> > >>>>>> Gamma 2096317
> > >>>>>> ImageLength 1040
> > >>>>>> ImageWidth 1392
> > >>>>>> LastSavedTime 19/03/2014 12:59:47:790
> > >>>>>> Location /tmp/b0BCDSL-T070_wD07_s4_z0_t1_cCy5_u001.tif
> > >>>>>> MaxScale 4095
> > >>>>>> MetaDataPhotometricInterpretation Monochrome
> > >>>>>> MinScale 194
> > >>>>>> Name Cy5
> > >>>>>> NewLUT 8
> > >>>>>> NewSubfileType 0
> > >>>>>> NumberOfChannels 1
> > >>>>>> PhotometricInterpretation BlackIsZero
> > >>>>>> PlanarConfiguration Chunky
> > >>>>>> PlaneProperty 2097094
> > >>>>>> Predictor Horizontal differencing
> > >>>>>> Region 1392 x 1040, offset at (0, 0)
> > >>>>>> ResolutionUnit Inch
> > >>>>>> SamplesPerPixel 1
> > >>>>>> Shading Off
> > >>>>>> Software MetaMorph 3.1.0.79
> > >>>>>> Spatial Calibration on
> > >>>>>> StagePosition 2096244
> > >>>>>> StandardLUT monochrome
> > >>>>>> Subtract Off
> > >>>>>> Temperature -29.85
> > >>>>>> ThreshState off
> > >>>>>> ThreshStateBlue 64
> > >>>>>> ThreshStateGreen 128
> > >>>>>> ThreshStateHi 65535
> > >>>>>> ThreshStateLo 0
> > >>>>>> ThreshStateRed 255
> > >>>>>> Trigger Mode Normal (TIMED)
> > >>>>>> Wavelength 692
> > >>>>>> XCalibration 645/1000
> > >>>>>> XResolution 72
> > >>>>>> YCalibration 645/1000
> > >>>>>> YResolution 72
> > >>>>>> Zoom 35
> > >>>>>> grayFit 4
> > >>>>>> grayMax -1/1
> > >>>>>> grayMin -1/1
> > >>>>>> grayPointCount 0
> > >>>>>> grayX -1/1
> > >>>>>> grayY -1/1
> > >>>>>
> > >>>>>> _______________________________________________
> > >>>>>> ome-users mailing list
> > >>>>>> ome-users at lists.openmicroscopy.org.uk
> > >>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> > >>>>>
> > >>>>>
> > >>>>
> > >>>
> > >>> --
> > >>> A: Yes.
> > >>>> Q: Are you sure?
> > >>>>> A: Because it reverses the logical flow of conversation.
> > >>>>>> Q: Why is top posting annoying in email?
> > >>>
> > >>> Mario Emmenlauer BioDataAnalysis Mobil:
> +49-(0)151-68108489
> > >>> Balanstrasse 43 mailto: mario.emmenlauer *
> unibas.ch
> > >>> D-81669 München
> http://www.biodataanalysis.de/
> > >>> _______________________________________________
> > >>> ome-users mailing list
> > >>> ome-users at lists.openmicroscopy.org.uk
> > >>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> > >>
> > >
> >
> > --
> > A: Yes.
> > > Q: Are you sure?
> > >> A: Because it reverses the logical flow of conversation.
> > >>> Q: Why is top posting annoying in email?
> >
> > Mario Emmenlauer BioDataAnalysis Mobil: +49-(0)151-68108489
> > Balanstrasse 43 mailto: mario.emmenlauer * unibas.ch
> > D-81669 München http://www.biodataanalysis.de/
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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