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OMERO.iviewer can't open file

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The OMERO.server installation documentation begins here and you can find OMERO.web deployment documentation here.

Re: OMERO.iviewer can't open file

Postby evenhuis » Sat Oct 27, 2018 3:54 am

Hi Kenny,

Here's our current pip installs. Still no luck with those confocal nd2 files

Cheers,

Chris

pip freeze | grep -Ei "(pillow|ice|django*|numpy|matplotlib|omero*|gunicorn)" | sort
You are using pip version 8.1.2, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Django==1.8.18
django-cors-headers==2.4.0
django-pipeline==1.3.20
django-prometheus==1.0.14
django-redis==4.8.0
gunicorn==19.7.1
matplotlib==1.2.0
numpy==1.7.1
omero-figure==3.1.1
omero-iviewer==0.5.0
omero-marshal==0.5.1
Pillow==2.0.0
zeroc-ice==3.6.4
evenhuis
 
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Re: OMERO.iviewer can't open file

Postby kennethgillen » Sat Oct 27, 2018 8:34 am

Hi Chris,

Comparing with my output, your omero-marshal is behind too.

See the requirement at https://github.com/openmicroscopy/openm ... 27.txt#L12

I'd recommend upgrading that, restarting web, and hoping that's enough.

If it's not, then could you please send us all the OMERO.web logs and OMERO.server logs and we can see if we can see any related output from the server. If you could also mention what timepoints you were trying these files, that'd help us locate the correct sections in the server logs.

If you could tar.gz up your OMERO.web and OMERO.server var/log/* directories, and send to us via the following system:

http://qa.openmicroscopy.org.uk/qa/upload/

Thanks,

Kenny
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Re: OMERO.iviewer can't open file

Postby evenhuis » Mon Oct 29, 2018 12:24 am

Hi Kenny,

Im afraid that the uploader is not working for me at the moment,

Code: Select all
SWFUpload is taking a long time to load or the load has failed. Please make sure that the Flash Plugin is enabled and that a working version of the Adobe Flash Player is installed.


I've tried it with Safari and Firefox on OSX and Firefox on Windows but I keep getting the same error.

Cheers,

Chris
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Re: OMERO.iviewer can't open file

Postby kennethgillen » Mon Oct 29, 2018 10:33 am

Hi Chris,

It appears University of Dundee are having some networking issues. Hopefully they'll be resolved soon and we can re-try sending the logs.

Best,

Kenny
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Re: OMERO.iviewer can't open file

Postby kennethgillen » Mon Oct 29, 2018 4:13 pm

Hi Chris,

Networking here all seems to be back.

Resubmission should work.

Thanks for your patience.

Best,

Kenny
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Re: OMERO.iviewer can't open file

Postby evenhuis » Wed Oct 31, 2018 1:08 am

Hi Kenny,

the log files are uploaded to qa, the ID is 27044.

To complicate things some more, the app+db are on one server, web on another and we are using a remote filesystem. I'll try and get the details.

Cheers,

Chris
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Re: OMERO.iviewer can't open file

Postby jburel » Thu Nov 01, 2018 2:25 pm

Hello Chris

Looking at the output you sent previously
Code: Select all
{"symbol_y": "\u00b5m", "symbol_x": "\u00b5m", "symbol_z": "\u00b5m", "unit_y": 0.****************, "unit_x": 0.****************, "unit_z": 10.0, "y": 0.****************, "x": 0.****************, "z": 10.0}

I found the value of unit_y etc, suspicious i.e. 0.****************

What is displayed in the right-hand panel of the original viewer?

Could you also try to retrieve the image infomation using the json-api to see what is returned?
see https://docs.openmicroscopy.org/omero/5 ... n-api.html

Having invalid values will certainly prevent the image to be opened in iviewer

Thanks

Jmarie
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Re: OMERO.iviewer can't open file

Postby evenhuis » Mon Nov 05, 2018 8:53 am

Hi Jmarie,

here's the JSON as you suggested. The request comes back with
SyntaxError: JSON.parse: unterminated fractional number at line 1 column 2147 of the JSON data


the raw JSON is attached at the end of the post. There are **** in the x and y units like you pointed out.

Here's the image viewer details
Screen Shot 2018-11-05 at 7.38.41 pm.png
viewer shot
Screen Shot 2018-11-05 at 7.38.41 pm.png (202.39 KiB) Viewed 1842 times


and the details pane in the browser
Screen Shot 2018-11-05 at 7.38.54 pm.png
image viewer screenshot
Screen Shot 2018-11-05 at 7.38.54 pm.png (126.05 KiB) Viewed 1842 times


Could it be a character encoding issue? In the global metadata there are sections where it looks like the micro / \mu symbol is not handled correctly.

Code: Select all
- Device   Ti ZDrive
- Step   10 �m

Thanks,

Chris



Code: Select all
{"data": {"Name": "tile006.nd2", "omero:details": {"owner": {"UserName": "140407", "FirstName": "Mahsa", "omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rw----", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": false, "isGroupWrite": false, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": false}}, "LastName": "Asadniaye Fard Jahromi", "@id": 664, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter"}, "group": {"omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "@id": 357, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "Name": "Warkiani"}, "@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "url:rois": "http://omero.research.uts.edu.au/api/v0/m/images/92826/rois/", "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Image", "url:datasets": "http://omero.research.uts.edu.au/api/v0/m/images/92826/datasets/", "omero:series": 0, "@id": 92826, "Pixels": {"SizeT": 1, "Type": {"omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": true, "perm": "rwr-r-", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": false, "isGroupWrite": false, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "@id": 6, "@type": "TBD#PixelsType", "value": "uint16"}, "SizeC": 2, "omero:sha1": "2248b4bca28ae705da4da7a1cf837cc908b166c1", "PhysicalSizeY": {"Symbol": "\u00b5m", "Value": 0.****************, "@type": "TBD#LengthI", "Unit": "MICROMETER"}, "omero:details": {"owner": {"UserName": "140407", "FirstName": "Mahsa", "omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rw----", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": false, "isGroupWrite": false, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": false}}, "LastName": "Asadniaye Fard Jahromi", "@id": 664, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter"}, "group": {"omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "@id": 357, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "Name": "Warkiani"}, "@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "PhysicalSizeZ": {"Symbol": "\u00b5m", "Value": 10.0, "@type": "TBD#LengthI", "Unit": "MICROMETER"}, "SizeX": 1024, "SizeY": 1024, "SizeZ": 17, "Channels": [{"Name": "Hoechst33258", "Color": 65535, "omero:details": {"owner": {"UserName": "140407", "FirstName": "Mahsa", "omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rw----", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": false, "isGroupWrite": false, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": false}}, "LastName": "Asadniaye Fard Jahromi", "@id": 664, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter"}, "group": {"omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "@id": 357, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "Name": "Warkiani"}, "@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "omero:photometricInterpretation": {"omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": true, "perm": "rwr-r-", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": false, "isGroupWrite": false, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "@id": 5, "@type": "TBD#PhotometricInterpretation", "value": "Monochrome"}, "SamplesPerPixel": 1, "EmissionWavelength": {"Symbol": "nm", "Value": 450.0, "@type": "TBD#LengthI", "Unit": "NANOMETER"}, "omero:LogicalChannelId": 200031, "@id": 201333, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Channel"}, {"Name": "TD", "Color": -1, "omero:details": {"owner": {"UserName": "140407", "FirstName": "Mahsa", "omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rw----", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": false, "isGroupWrite": false, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": false}}, "LastName": "Asadniaye Fard Jahromi", "@id": 664, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Experimenter"}, "group": {"omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "@id": 357, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#ExperimenterGroup", "Name": "Warkiani"}, "@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": false, "perm": "rwrw--", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": true, "isGroupWrite": true, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "omero:photometricInterpretation": {"omero:details": {"@type": "TBD#Details", "permissions": {"isUserWrite": true, "isWorldWrite": false, "canDelete": true, "isWorldRead": true, "perm": "rwr-r-", "canEdit": true, "canAnnotate": true, "isGroupAnnotate": false, "isGroupWrite": false, "canLink": true, "isUserRead": true, "@type": "TBD#Permissions", "isGroupRead": true}}, "@id": 5, "@type": "TBD#PhotometricInterpretation", "value": "Monochrome"}, "SamplesPerPixel": 1, "omero:LogicalChannelId": 200032, "@id": 201334, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Channel"}], "PhysicalSizeX": {"Symbol": "\u00b5m", "Value": 0.****************, "@type": "TBD#LengthI", "Unit": "MICROMETER"}, "@id": 92826, "@type": "http://www.openmicroscopy.org/Schemas/OME/2016-06#Pixels", "SignificantBits": 12}}}
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Re: OMERO.iviewer can't open file

Postby evenhuis » Tue Nov 06, 2018 8:40 am

Hi,

The same file on our dev servers fails with
Code: Select all
html>
    <head>
        <title>Request Rejected</title>
    </head>
    <body>The requested URL was rejected. Please consult with your administrator.
        <br>
        <br>Your support ID is: 18296077467092126312
        <br>
        <br>
        <a href='javascript:history.back();'>[Go Back]</a>
    </body>
</html>


The two servers are mean to be close to another, dev wil have more recent versions of libraries.

Cheers,

Chris
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Re: OMERO.iviewer can't open file

Postby jburel » Tue Nov 06, 2018 11:17 am

Hi Chris
as I was suspected the JSON is not valid due to
Code: Select all
"PhysicalSizeY": {
                "Symbol": "\u00b5m",
                "Value": 0. ** ** ** ** ** ** ** ** ,
                "@type": "TBD#LengthI",
                "Unit": "MICROMETER"
             },

now we need to figure out why it is correct when I import the image in our system and not in yours.

This is the value I have when querying our server:
Code: Select all
"PhysicalSizeY": {"Symbol": "\u00b5m", "Value": 0.2262397413186163, "@type": "TBD#LengthI", "Unit": "MICROMETER"}


Are you able to open the image in OMERO.figure?

cheers

jmarie
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