<div dir="ltr">Hi Melissa,<div><div><br></div><div>> When we have a proposed fix, we will update the ticket with a link to</div><div>> the pull request on GitHub. At that point, you can build the patch by</div><div>> adding the correct remote (SOMEUSER will be the username shown in the</div><div>> pull request):</div><div>> </div><div>> <a href="http://www.openmicroscopy.org/site/support/contributing/using-git.html#github-remotes">http://www.openmicroscopy.org/site/support/contributing/using-git.html#github-remotes</a></div><div>> </div><div>> fetch the remote as shown on that page, and then merge the branch name</div><div>> given in the pull request.</div></div><div><br></div><div>There is actually an easier way to fetch pull requests, without needing to add additional remotes:</div><div><br></div><div> $ git fetch origin pull/1200/head</div><div> $ git checkout FETCH_HEAD</div><div> $ git checkout -b shiny-new-local-branch # OPTIONAL STEP</div><div> $ ant jars # or whatever, to build it</div><div><br></div><div>Regards,</div><div>Curtis</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 15, 2015 at 11:57 AM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Mario,<br>
<span class=""><br>
> I've seen progress reported in your issue tracker for this!<br>
> But I could not easily understand if its in a state that would<br>
> make sense for me to try? Even if incomplete, I might be able<br>
> to aid development by testing the current snapshot on our ~5k<br>
> image sets?<br>
><br>
> If you think it makes sense, can you point out how I fetch the<br>
> patch and integrate it in my local GIT? From there on I know my<br>
> way...<br>
<br>
</span>This ticket:<br>
<br>
> >> <a href="http://trac.openmicroscopy.org/ome/ticket/12802" target="_blank">http://trac.openmicroscopy.org/ome/ticket/12802</a><br>
<br>
currently does not have a proposed fix - we've investigated enough to<br>
know that we won't have time to fix it for the upcoming 5.1.1, but we<br>
expect to have a fix for 5.1.2. Apologies for any confusion there.<br>
<br>
When we have a proposed fix, we will update the ticket with a link to<br>
the pull request on GitHub. At that point, you can build the patch by<br>
adding the correct remote (SOMEUSER will be the username shown in the<br>
pull request):<br>
<br>
<a href="http://www.openmicroscopy.org/site/support/contributing/using-git.html#github-remotes" target="_blank">http://www.openmicroscopy.org/site/support/contributing/using-git.html#github-remotes</a><br>
<br>
fetch the remote as shown on that page, and then merge the branch name<br>
given in the pull request. We can certainly provide more detailed<br>
commands once a pull request is open and the remote name/branch name is<br>
known.<br>
<br>
Regards,<br>
-Melissa<br>
<div class="HOEnZb"><div class="h5"><br>
On Wed, Apr 15, 2015 at 09:53:54AM +0200, Mario Emmenlauer wrote:<br>
><br>
> Dear Melissa and all,<br>
><br>
> I've seen progress reported in your issue tracker for this!<br>
> But I could not easily understand if its in a state that would<br>
> make sense for me to try? Even if incomplete, I might be able<br>
> to aid development by testing the current snapshot on our ~5k<br>
> image sets?<br>
><br>
> If you think it makes sense, can you point out how I fetch the<br>
> patch and integrate it in my local GIT? From there on I know my<br>
> way...<br>
><br>
> Thanks for your help, and Cheers,<br>
><br>
> Mario<br>
><br>
><br>
><br>
> On <a href="tel:26.03.2015%2014" value="+12603201514">26.03.2015 14</a>:34, Mario Emmenlauer wrote:<br>
> ><br>
> > Dear Melissa,<br>
> ><br>
> > On <a href="tel:25.03.2015%2023" value="+12503201523">25.03.2015 23</a>:13, Melissa Linkert wrote:<br>
> >>> correcting my own email from 30min ago:<br>
> >>><br>
> >>> I've checked the current trunk for below-mentioned fix, and I think<br>
> >>> several values are fine now. There are some exceptions where I'm<br>
> >>> uncertain about the value:<br>
> >>> "AbsoluteZ" = "2096309"<br>
> >>> "CameraChipOffset" = "2096260"<br>
> >>> "Gamma" = "2096317"<br>
> >>> "PlaneProperty" = "2097094"<br>
> >>> "StagePosition" = "2096244"<br>
> >>><br>
> >>> To me, these look possibly incorrect (and actually look more like TIFF<br>
> >>> offsets than values). Is that possible?<br>
> >><br>
> >> That certainly seems likely. As with the PageNumber issue, we won't<br>
> >> have a fix for this in 5.1.0, but a ticket is now open:<br>
> >><br>
> >> <a href="http://trac.openmicroscopy.org/ome/ticket/12802" target="_blank">http://trac.openmicroscopy.org/ome/ticket/12802</a><br>
> ><br>
> > Thanks for the very fast follow-up! I'll follow the ticket!<br>
> ><br>
> > Cheers,<br>
> ><br>
> > Mario<br>
> ><br>
> ><br>
> ><br>
> ><br>
> >> Regards,<br>
> >> -Melissa<br>
> >><br>
> >> On Wed, Mar 25, 2015 at 12:48:12PM +0100, Mario Emmenlauer wrote:<br>
> >>><br>
> >>> Dear Bio-Formats developers,<br>
> >>><br>
> >>> correcting my own email from 30min ago:<br>
> >>><br>
> >>> I've checked the current trunk for below-mentioned fix, and I think<br>
> >>> several values are fine now. There are some exceptions where I'm<br>
> >>> uncertain about the value:<br>
> >>> "AbsoluteZ" = "2096309"<br>
> >>> "CameraChipOffset" = "2096260"<br>
> >>> "Gamma" = "2096317"<br>
> >>> "PlaneProperty" = "2097094"<br>
> >>> "StagePosition" = "2096244"<br>
> >>><br>
> >>> To me, these look possibly incorrect (and actually look more like TIFF<br>
> >>> offsets than values). Is that possible?<br>
> >>><br>
> >>> The image I used is the same as before:<br>
> >>> <a href="http://data.marssoft.de/b0BCDSL-T070_wD07_s4_z0_t1_cCy5_u001.tif" target="_blank">http://data.marssoft.de/b0BCDSL-T070_wD07_s4_z0_t1_cCy5_u001.tif</a><br>
> >>><br>
> >>> Cheers,<br>
> >>><br>
> >>> Mario<br>
> >>><br>
> >>><br>
> >>><br>
> >>> On 22.01.2015 15:44, Mario Emmenlauer wrote:<br>
> >>>><br>
> >>>> Hi Melissa,<br>
> >>>><br>
> >>>> On 21.01.2015 23:31, Melissa Linkert wrote:<br>
> >>>>> Hi Mario,<br>
> >>>>><br>
> >>>>>> attached is an image from MetaXpress, where I try to read all<br>
> >>>>>> available meta data. However there are some values that seem not<br>
> >>>>>> to make sense, can you please help if there is a bug, or if the<br>
> >>>>>> values are indeed correct, or possibly if the issue is in Meta-<br>
> >>>>>> Xpress that stores weired values? Examples are:<br>
> >>>>>> Channel #0 Laser focus score 8.2890462076516E-310<br>
> >>>>>> Channel #0 Camera Bit Depth 8.289046E-317<br>
> >>>>><br>
> >>>>> Thank you for the bug report - this is indeed a bug in Bio-Formats. We<br>
> >>>>> have a fix under review now:<br>
> >>>>><br>
> >>>>> <a href="http://github.com/openmicroscopy/bioformats/pull/1537" target="_blank">http://github.com/openmicroscopy/bioformats/pull/1537</a><br>
> >>>>><br>
> >>>>> I would expect that to be included in the upcoming 5.0.7 and 5.1.0<br>
> >>>>> releases.<br>
> >>>><br>
> >>>> Thanks for the very quick fix, its appreciated! I'll wait for the<br>
> >>>> 5.0.7 or 5.1.0 releases to check the result.<br>
> >>>><br>
> >>>> All the best,<br>
> >>>><br>
> >>>> Mario<br>
> >>>><br>
> >>>><br>
> >>>><br>
> >>>>> Regards,<br>
> >>>>> -Melissa<br>
> >>>>><br>
> >>>>> On Wed, Jan 21, 2015 at 08:52:41PM +0100, Mario Emmenlauer wrote:<br>
> >>>>>><br>
> >>>>>> Dear Bio-Formats developers,<br>
> >>>>>><br>
> >>>>>> attached is an image from MetaXpress, where I try to read all<br>
> >>>>>> available meta data. However there are some values that seem not<br>
> >>>>>> to make sense, can you please help if there is a bug, or if the<br>
> >>>>>> values are indeed correct, or possibly if the issue is in Meta-<br>
> >>>>>> Xpress that stores weired values? Examples are:<br>
> >>>>>> Channel #0 Laser focus score 8.2890462076516E-310<br>
> >>>>>> Channel #0 Camera Bit Depth 8.289046E-317<br>
> >>>>>><br>
> >>>>>> These (and some others) seem not to make sense(?) Attached is<br>
> >>>>>> also the meta data that I can extract with Bio-Formats from the<br>
> >>>>>> latest Fiji, I believe version Bio-Formats 5.0.6.<br>
> >>>>>><br>
> >>>>>> All the best,<br>
> >>>>>><br>
> >>>>>> Mario<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>><br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> --<br>
> >>>>>> Mario Emmenlauer BioDataAnalysis Mobil: +49-(0)151-68108489<br>
> >>>>>> Balanstrasse 43 mailto: mario.emmenlauer * <a href="http://unibas.ch" target="_blank">unibas.ch</a><br>
> >>>>>> D-81669 München <a href="http://www.marioemmenlauer.de/" target="_blank">http://www.marioemmenlauer.de/</a><br>
> >>>>><br>
> >>>>><br>
> >>>>>> Key Value<br>
> >>>>>> BitsPerPixel 16<br>
> >>>>>> DimensionOrder XYCZT<br>
> >>>>>> IsInterleaved false<br>
> >>>>>> IsRGB false<br>
> >>>>>> LittleEndian true<br>
> >>>>>> PixelType uint16<br>
> >>>>>> Series 0 Name<br>
> >>>>>> SizeC 1<br>
> >>>>>> SizeT 1<br>
> >>>>>> SizeX 1392<br>
> >>>>>> SizeY 1040<br>
> >>>>>> SizeZ 1<br>
> >>>>>> AbsoluteZ 2096309<br>
> >>>>>> AbsoluteZValid 0<br>
> >>>>>> AutoScale 1<br>
> >>>>>> AutoScaleHiInfo 0/1<br>
> >>>>>> AutoScaleLoInfo 0/1<br>
> >>>>>> Binning 1 x 1<br>
> >>>>>> BitsPerSample 16<br>
> >>>>>> CalibrationUnits ume<br>
> >>>>>> Camera Shutter Always Open<br>
> >>>>>> CameraBin 1x1<br>
> >>>>>> CameraChipOffset 2096260<br>
> >>>>>> Channel #0 Camera Bit Depth 8.289046E-317<br>
> >>>>>> Channel #0 ImageXpress Micro Filter Cube Cy5<br>
> >>>>>> Channel #0 ImageXpress Micro Objective 10X S Fluor<br>
> >>>>>> Channel #0 ImageXpress Micro Shutter Open<br>
> >>>>>> Channel #0 Laser focus score 8.2890462076516E-310<br>
> >>>>>> Channel #0 Lumencor Blue Intensity 8.289046E-317<br>
> >>>>>> Channel #0 Lumencor Blue Shutter Closed<br>
> >>>>>> Channel #0 Lumencor Cyan Intensity 8.289046E-317<br>
> >>>>>> Channel #0 Lumencor Cyan Shutter Closed<br>
> >>>>>> Channel #0 Lumencor Green/Yellow Intensity 8.289046E-317<br>
> >>>>>> Channel #0 Lumencor Green/Yellow Shutter Closed<br>
> >>>>>> Channel #0 Lumencor Red Intensity 8.289046E-317<br>
> >>>>>> Channel #0 Lumencor Red Shutter Closed<br>
> >>>>>> Channel #0 Lumencor Teal Intensity 8.289046E-317<br>
> >>>>>> Channel #0 Lumencor Teal Shutter Closed<br>
> >>>>>> Channel #0 Lumencor UV Intensity 8.289046E-317<br>
> >>>>>> Channel #0 Lumencor UV Shutter Closed<br>
> >>>>>> Channel #0 _IllumSetting_ Cy5<br>
> >>>>>> Channel #0 _MagNA_ 8.28904606E-316<br>
> >>>>>> Channel #0 _MagRI_ 8.289046E-317<br>
> >>>>>> Channel #0 _MagSetting_ 10X S Fluor<br>
> >>>>>> Clear Count 2<br>
> >>>>>> Clear Mode CLEAR PRE SEQUENCE<br>
> >>>>>> Compression LZW<br>
> >>>>>> DateTime 19/03/2014 12:59:47:667<br>
> >>>>>> Digitizer 20 MHz<br>
> >>>>>> Exposure 100 ms<br>
> >>>>>> FillOrder Pixels with lower column values are stored in the higher order bits of a byte<br>
> >>>>>> Frames to Average 1<br>
> >>>>>> Gain Gain 1 (1x)<br>
> >>>>>> Gamma 2096317<br>
> >>>>>> ImageLength 1040<br>
> >>>>>> ImageWidth 1392<br>
> >>>>>> LastSavedTime 19/03/2014 12:59:47:790<br>
> >>>>>> Location /tmp/b0BCDSL-T070_wD07_s4_z0_t1_cCy5_u001.tif<br>
> >>>>>> MaxScale 4095<br>
> >>>>>> MetaDataPhotometricInterpretation Monochrome<br>
> >>>>>> MinScale 194<br>
> >>>>>> Name Cy5<br>
> >>>>>> NewLUT 8<br>
> >>>>>> NewSubfileType 0<br>
> >>>>>> NumberOfChannels 1<br>
> >>>>>> PhotometricInterpretation BlackIsZero<br>
> >>>>>> PlanarConfiguration Chunky<br>
> >>>>>> PlaneProperty 2097094<br>
> >>>>>> Predictor Horizontal differencing<br>
> >>>>>> Region 1392 x 1040, offset at (0, 0)<br>
> >>>>>> ResolutionUnit Inch<br>
> >>>>>> SamplesPerPixel 1<br>
> >>>>>> Shading Off<br>
> >>>>>> Software MetaMorph 3.1.0.79<br>
> >>>>>> Spatial Calibration on<br>
> >>>>>> StagePosition 2096244<br>
> >>>>>> StandardLUT monochrome<br>
> >>>>>> Subtract Off<br>
> >>>>>> Temperature -29.85<br>
> >>>>>> ThreshState off<br>
> >>>>>> ThreshStateBlue 64<br>
> >>>>>> ThreshStateGreen 128<br>
> >>>>>> ThreshStateHi 65535<br>
> >>>>>> ThreshStateLo 0<br>
> >>>>>> ThreshStateRed 255<br>
> >>>>>> Trigger Mode Normal (TIMED)<br>
> >>>>>> Wavelength 692<br>
> >>>>>> XCalibration 645/1000<br>
> >>>>>> XResolution 72<br>
> >>>>>> YCalibration 645/1000<br>
> >>>>>> YResolution 72<br>
> >>>>>> Zoom 35<br>
> >>>>>> grayFit 4<br>
> >>>>>> grayMax -1/1<br>
> >>>>>> grayMin -1/1<br>
> >>>>>> grayPointCount 0<br>
> >>>>>> grayX -1/1<br>
> >>>>>> grayY -1/1<br>
> >>>>><br>
> >>>>>> _______________________________________________<br>
> >>>>>> ome-users mailing list<br>
> >>>>>> <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
> >>>>>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
> >>>>><br>
> >>>>><br>
> >>>><br>
> >>><br>
> >>> --<br>
> >>> A: Yes.<br>
> >>>> Q: Are you sure?<br>
> >>>>> A: Because it reverses the logical flow of conversation.<br>
> >>>>>> Q: Why is top posting annoying in email?<br>
> >>><br>
> >>> Mario Emmenlauer BioDataAnalysis Mobil: <a href="tel:%2B49-%280%29151-68108489" value="+4915168108489">+49-(0)151-68108489</a><br>
> >>> Balanstrasse 43 mailto: mario.emmenlauer * <a href="http://unibas.ch" target="_blank">unibas.ch</a><br>
> >>> D-81669 München <a href="http://www.biodataanalysis.de/" target="_blank">http://www.biodataanalysis.de/</a><br>
> >>> _______________________________________________<br>
> >>> ome-users mailing list<br>
> >>> <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
> >>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
> >><br>
> ><br>
><br>
> --<br>
> A: Yes.<br>
> > Q: Are you sure?<br>
> >> A: Because it reverses the logical flow of conversation.<br>
> >>> Q: Why is top posting annoying in email?<br>
><br>
> Mario Emmenlauer BioDataAnalysis Mobil: <a href="tel:%2B49-%280%29151-68108489" value="+4915168108489">+49-(0)151-68108489</a><br>
> Balanstrasse 43 mailto: mario.emmenlauer * <a href="http://unibas.ch" target="_blank">unibas.ch</a><br>
> D-81669 München <a href="http://www.biodataanalysis.de/" target="_blank">http://www.biodataanalysis.de/</a><br>
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</div></div></blockquote></div><br></div>