Big images fs 9701 (develop) #634

will-moore · 2013-01-21T14:42:31Z

This fixes the PanoJS big image viewer in Web to handle zoom factors other than 50% between levels.

Currently the required scaling factors for zoom levels is not provided by the server (http://trac.openmicroscopy.org.uk/ome/ticket/9813) so it is hard-coded in the BlitzGateway will-moore@4c07e3f

This PR should be put on hold awaiting #9813.

To test, browse an SVS image in 'develop'.

Zoom in/out, Pan around the image etc.
Check that viewer remains centered on the same spot
Check that thumbnail view and main viewport correspond

joshmoore · 2013-01-21T15:35:11Z

@chris-allan/@melissalinkert : did either of you have any prior art and/or a particular interface method you wanted added for the scaling factors?

ghost · 2013-01-21T16:40:36Z

Could we add a getResolutionScaleFactor method to IFormatReader which returns sizeX[n]/sizeX[0]?

melissalinkert · 2013-01-21T17:26:59Z

If the scale factor is always getSizeX() / core.get(0).sizeX, then I'm not convinced that it belongs in IFormatReader. I'd rather see the scale factor calculation as a utility method somewhere (FormatTools?), if there isn't one already (which there is not, as far as I know).

pwalczysko · 2013-01-22T10:31:14Z

Tested on Safari Mac OS 10.8, and on WindowsXP in: Chrome, Firefox and IE8.
Works as expected in all except IE8.

The panning is very slow in IE8, nearly unusable (see screenshot).

The panning using the "birds eye" (the red tool in right-bottom corner mini-view) is impossible in IE8 (neither does it really move in real-time, nor is the action performed after a long wait)
The zoom 200% is broken (see screenshot)

joshmoore · 2013-01-25T09:28:48Z

@will-moore, any thoughts on next steps here?

will-moore · 2013-01-25T10:42:11Z

@joshmoore The issues we have with PanoJS in IE8 are not new to this PR. This PR is mostly waiting on #9813, so that I don't have to hard-code the zoom scaling. Then it needs testing on all our big image formats.

Provide a list of ResolutionDescription objects which should eventually represent the entire geometry of the tiled plane.

joshmoore · 2013-02-01T00:45:25Z

NB: Closed my PR since it's been cherry-picked here.

will-moore · 2013-02-04T09:37:28Z

@ximenesuk If possible, this could really do with testing on a bunch of different big image formats. Only tried on svs so far. Thanks

ximenesuk · 2013-02-04T11:25:54Z

@will-moore @pwalczysko Do you know if there are any other big image formats on gretzky - I found the svs ones under user-5 If there are other formats already imported I'll test further but importing from home given my upload speed is probably a barrier.

The zooming and panning seemed to work well using Safari on Mac OS 10.6.8 despite being on the end of a relatively slow ADSL connection. At one point the Testis.svs seemed to stall in providing new tiles but re-opening the image viewer seemed to fix that and then I couldn't reproduce - maybe a temporary connectivity issue due to my connection?

pwalczysko · 2013-02-04T12:35:07Z

Hi Colin
see below.

data_repo/from_skyking/gatan/biosamplefullframe.dm3
data_repo/test_images_good/jpeg/8kx8k.jpg

These are pre-loaded to Gretzky.
Check here
https://docs.google.com/spreadsheet/ccc?key=0AoKiTAl8UOxndER5UF9mczRNNklxbWFfakN4clhDaXc#gid=0
what user/group.

Cheers
Petr

On 4 Feb 2013, at 11:25, Colin Blackburn <notifications@github.com mailto:notifications@github.com>
wrote:

@will-moorehttps://github.com/will-moore @pwalczyskohttps://github.com/pwalczysko Do you know if there are any other big image formats on gretzky - I found the svs ones under user-5 If there are other formats already imported I'll test further but importing from home given my upload speed is probably a barrier.

The zooming and panning seemed to work well using Safari on Mac OS 10.6.8 despite being on the end of a relatively slow ADSL connection. At one point the Testis.svs seemed to stall in providing new tiles but re-opening the image viewer seemed to fix that and then I couldn't reproduce - maybe a temporary connectivity issue due to my connection?

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/634#issuecomment-13071922.

The University of Dundee is a registered Scottish Charity, No: SC015096

ximenesuk · 2013-02-04T12:54:27Z

Thanks @pwalczysko

pwalczysko · 2013-02-04T13:15:42Z

@ximenesuk : wait a minute please, josh is just kicking the auto-import script on - the images are not there yet (sorry)

pwalczysko · 2013-02-04T14:03:43Z

@ximenesuk - importing some big images formats manually as well - see user-8, group read-only, project "for Colin".
hamamatsu/.ndpi, pyramids, trestle, ....
Pyramids are there already. The others will come as import progresses.

joshmoore · 2013-02-04T14:08:46Z

Some of the formats failed due to OutOfMemory. If something is required, please let me know.

pwalczysko · 2013-02-04T14:21:08Z

Manual import of test_images_good/hamamtsu/david/2009-12-18 09.20.56.ndpi failed due to IceCommunicationDestroyed. See ticket https://trac.openmicroscopy.org.uk/ome/ticket/10287.

ximenesuk · 2013-02-04T17:51:38Z

Tested on svs and omero pyramid files with everything looking good. If further testing is needed on other formats I can pick up on Tuesday lunchtime if no-one else wants to take it.

jburel · 2013-02-07T16:08:36Z

@pwalczysko: to test with big images format other than svs, as long as do not take too long. If you have already imported some big images, could you indicate under which user/group and the location? Thanks

pwalczysko · 2013-02-07T18:03:38Z

@jburel
Import is in progress now on.
user-8
read-only-1
Project: big images to test PR 08-02-13
Datasets names are self-explaining.

@jburel :
mporting the big images for tomorrows testing, the "Cannot create thumbnail" error in importer was spotted.
Please see below - I thought it was claimed to be sorted ?
If not, I cannot find the particular ticket - do you want me to file a new ticket for this ?

pwalczysko · 2013-02-08T16:36:05Z

Problems:

Web: Being at Scale 100% and clciking once at minus sign in Web goes to Scale:523.53%. Another click on minus brings goes to Scale: 3.03%.
Tiles are not corresponding correctly with the birds eye red square position (both Web and Insight). (See screenshots)
Insight: First click on minus goes to x0.8 - all the tiles are black. Second click on minus goes to x0.64 - tiles never show up (because the whole image is perched in the topmost leftmost tile, see screenshot). The placement of red square in birds eye is okay when panning is used. When the red square itself is moved, it becomes displaced.
Web: Image scales numerically well (1-- - 5- -25 ...) and is displayed sensibly in birds eye, but full viewer is just grey. Also, it causes Stacktrace.

Screenshots: squig- team/screenshots/pwalczysko/08-02-13/PR634

These problems are connected to following files:

1,
(Problems 1.,2., 3.) ticket http://trac.openmicroscopy.org.uk/ome/ticket/10353#comment:1
/ome/data_repo/test_images_good/cellsens/anda/Image_01_V76 K2 11_lung/stack1/frame_t.ets [frame_t.ets]

2,
(Problems 1.,2., 3.) ticket http://trac.openmicroscopy.org.uk/ome/ticket/10353#comment:1
/Volumes/ome/data_repo/test_images_good/cellsens/anda/Image_01_V76 K2 11_lung.vsi [Image_01_V76 K2 11_lung.vsi]

3.
(Problem 4.) made comment to ticket http://trac.openmicroscopy.org.uk/ome/ticket/10287#comment:2
/Volumes/ome/data_repo/test_images_good/hamamatsu/david/2009-12-18 09.20.56.ndpi - the other two .ndpi files had the same problem, see ticket

Works as expected (the scaling and panning):

/Volumes/ome/data_repo/test_images_good/gatan/biosamplefullframe.dm3
/Volumes/ome/data_repo/test_images_good/gatan/DMtest2.dm3
/Volumes/ome/data_repo/test_images_good/hamamatsu/philippe/fluorescence/green redZ.ndpis [green redZ.ndpis]
/Volumes/ome/data_repo/test_images_good/hamamatsu/philippe/fluorescence/green redZ.ndpis [green redZ.ndpis](2nd image with the same name)
/Volumes/ome/data_repo/test_images_good/jpeg2000/8kx8k.jpf
/Volumes/ome/data_repo/test_images_good/jpeg/8kx8k.jpg
/Volumes/ome/data_repo/test_images_good/mrw/1600R PICT0005.MRW (not really a large image though)
/Volumes/ome/data_repo/test_images_good/trestle/openslide/CMU-1/CMU-1.tif [Series 1](no thumbnail display and birds eye small insert not displaying in Web - okay in Insight, but tiles and scaling okay)
- 14. /Volumes/ome/data_repo/test_images_good/trestle/openslide/CMU-1/CMU-1.tif [Series 2-7]
/Volumes/ome/data_repo/test_images_good/trestle/openslide/CMU-2/CMU-2.tif [Series 1](no thumbnail display and birds eye small insert not displaying in Web - okay in Insight, but tiles and scaling okay)
- 16. /Volumes/ome/data_repo/test_images_good/trestle/openslide/CMU-2/CMU-2.tif [Series 2-7]

pwalczysko · 2013-02-08T18:35:43Z

See ticket http://trac.openmicroscopy.org.uk/ome/ticket/10356 for specific trestle problems. These do not seem to have anything to do with scaling and panning.

will-moore · 2013-02-13T14:49:58Z

@joshmoore @pwalczysko I don't know how much the problems with images above are due to this PR, e.g. http://trac.openmicroscopy.org.uk/ome/ticket/10353#comment:2. Do we just want to keep this PR open until everything is working (maybe with an 'onhold' label) or merge it?

jburel · 2013-02-13T20:05:42Z

@will-moore: let see how the file formats testing goes tomorrow and access where we are on that front after.

joshmoore · 2013-02-15T10:04:46Z

Even though FTS and a few other file formats may not be working, we're merging, since it's possible to state that some readers won't be supported.

Big images fs 9701 (develop)

Will Moore added 4 commits January 21, 2013 13:22

TEMP workaround for #9813

4c07e3f

Image marshal includes zoomLevelScaling

874d85e

viewport.js $ viewportImage.js pass zoomLevelScaling down to PanoJS

a6788ad

PanoJS handles zoomLevelScaling - default is still 50%

7d12bf2

joshmoore and others added 2 commits January 31, 2013 21:42

Add PyramidService.getResolutionDescriptions method (See #9813)

36d58d2

Provide a list of ResolutionDescription objects which should eventually represent the entire geometry of the tiled plane.

Use zoom scaling levels from server

36cc004

joshmoore mentioned this pull request Feb 1, 2013

Add PyramidService.getResolutionDescriptions method (See #9813) #680

Closed

joshmoore added a commit that referenced this pull request Feb 15, 2013

Merge pull request #634 from will-moore/big_images_FS_9701

19cf1f1

Big images fs 9701 (develop)

joshmoore merged commit 19cf1f1 into ome:develop Feb 15, 2013

joshmoore deleted the big_images_FS_9701 branch February 15, 2013 10:05

will-moore mentioned this pull request Apr 2, 2013

Big images fs 9701 dev44 #979

Merged

sbesson modified the milestones: 5.0.0, 5.0.0-alpha1 Nov 29, 2017

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Big images fs 9701 (develop) #634

Big images fs 9701 (develop) #634

will-moore commented Jan 21, 2013

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Big images fs 9701 (develop) #634

Big images fs 9701 (develop) #634

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