Make Movie script handles units for scalebar

[will-moore]

This fixes the Make Movie script to work with units changes.

All other scripts seem to have been fixed already.

To test, check that you can create a movie with a scalebar.

--no-rebase

[pwalczysko]

Error on Kymograph Script when Pixelsize is populated (entered "6")

• select an image with line propagated over T, like http://trout.openmicroscopy.org/merge/webclient/?show=image-21966
• start Kyjmograph script, in the dialog fill into the Pixel Size row number 6
• execute the script, the script will end up in errror, see the error
• the same workflow is fine on octopus (5.0)
• the workflows were executed in Insight

WARNING:omero.gateway:ValueError on <class 'omero.gateway.OmeroGatewaySafeCallWrapper'> to <5bcfa3b0-6ceb-4987-a076-7a75d17f0a51omero.api.IUpdate> saveObject((object #0 (::omero::model::Pixels)
{
    _id = object #1 (::omero::RLong)
    {
        _val = 21001
    }
    _details = object #2 (::omero::model::Details)
    {
        _owner = object #3 (::omero::model::Experimenter)
        {
            _id = object #4 (::omero::RLong)
            {
                _val = 5
            }
            _details = <nil>
            _loaded = False
            _version = <nil>
            _groupExperimenterMapSeq = 
            {
            }
            _groupExperimenterMapLoaded = False
            _omeName = <nil>
            _firstName = <nil>
            _middleName = <nil>
            _lastName = <nil>
            _institution = <nil>
            _ldap = <nil>
            _email = <nil>
            _annotationLinksSeq = 
            {
            }
            _annotationLinksLoaded = False
            _annotationLinksCountPerOwner = 
            {
            }
        }
        _group = object #5 (::omero::model::ExperimenterGroup)
        {
            _id = object #6 (::omero::RLong)
            {
                _val = 8
            }
            _details = object #7 (::omero::model::Details)
            {
                _owner = <nil>
                _group = <nil>
                _creationEvent = <nil>
                _updateEvent = <nil>
                _permissions = object #8 (::omero::model::Permissions)
                {
                    _restrictions = 
                    {
                        [0] = False
                        [1] = True
                        [2] = True
                        [3] = True
                    }
                    _perm1 = -56
                }
                _externalInfo = <nil>
                _call = 
                {
                    key = omero.session.uuid
                    value = 53e73aaa-34d2-4f51-a007-50aa5bcc858c

                    key = omero.client.uuid
                    value = 5bcfa3b0-6ceb-4987-a076-7a75d17f0a51
                }
                _event = object #9 (::omero::sys::EventContext)
                {
                    shareId = -1
                    sessionId = 10768
                    sessionUuid = *********
                    userId = 5
                    userName = user-4
                    groupId = 8
                    groupName = read-only-1
                    isAdmin = False
                    eventId = -1
                    eventType = User
                    memberOfGroups = 
                    {
                        [0] = 8
                        [1] = 6
                        [2] = 1
                        [3] = 853
                    }
                    leaderOfGroups = 
                    {
                        [0] = 6
                        [1] = 853
                    }
                    groupPermissions = object #10 (::omero::model::Permissions)
                    {
                        _restrictions = 
                        {
                        }
                        _perm1 = -56
                    }
                }
            }
            _loaded = True
            _version = object #11 (::omero::RInt)
            {
                _val = 0
            }
            _name = object #12 (::omero::RString)
            {
                _val = read-only-1
            }
            _ldap = object #13 (::omero::RBool)
            {
                _val = False
            }
            _groupExperimenterMapSeq = 
            {
            }
            _groupExperimenterMapLoaded = False
            _config = 
            {
            }
            _annotationLinksSeq = 
            {
            }
            _annotationLinksLoaded = False
            _annotationLinksCountPerOwner = 
            {
            }
            _description = <nil>
        }
        _creationEvent = object #14 (::omero::model::Event)
        {
            _id = object #15 (::omero::RLong)
            {
                _val = 221069
            }
            _details = <nil>
            _loaded = False
            _status = <nil>
            _time = <nil>
            _experimenter = <nil>
            _experimenterGroup = <nil>
            _type = <nil>
            _containingEvent = <nil>
            _logsSeq = 
            {
            }
            _logsLoaded = False
            _session = <nil>
        }
        _updateEvent = object #16 (::omero::model::Event)
        {
            _id = object #17 (::omero::RLong)
            {
                _val = 221070
            }
            _details = <nil>
            _loaded = False
            _status = <nil>
            _time = <nil>
            _experimenter = <nil>
            _experimenterGroup = <nil>
            _type = <nil>
            _containingEvent = <nil>
            _logsSeq = 
            {
            }
            _logsLoaded = False
            _session = <nil>
        }
        _permissions = object #18 (::omero::model::Permissions)
        {
            _restrictions = 
            {
            }
            _perm1 = -56
        }
        _externalInfo = <nil>
        _call = 
        {
            key = omero.session.uuid
            value = 53e73aaa-34d2-4f51-a007-50aa5bcc858c

            key = omero.client.uuid
            value = 5bcfa3b0-6ceb-4987-a076-7a75d17f0a51
        }
        _event = object #19 (::omero::sys::EventContext)
        {
            shareId = -1
            sessionId = 10768
            sessionUuid = *********
            userId = 5
            userName = user-4
            groupId = 8
            groupName = read-only-1
            isAdmin = False
            eventId = -1
            eventType = User
            memberOfGroups = 
            {
                [0] = 8
                [1] = 6
                [2] = 1
                [3] = 853
            }
            leaderOfGroups = 
            {
                [0] = 6
                [1] = 853
            }
            groupPermissions = object #20 (::omero::model::Permissions)
            {
                _restrictions = 
                {
                }
                _perm1 = -56
            }
        }
    }
    _loaded = True
    _version = <object #11>
    _image = object #21 (::omero::model::Image)
    {
        _id = object #22 (::omero::RLong)
        {
            _val = 23201
        }
        _details = <nil>
        _loaded = False
        _version = <nil>
        _acquisitionDate = <nil>
        _archived = <nil>
        _partial = <nil>
        _format = <nil>
        _imagingEnvironment = <nil>
        _objectiveSettings = <nil>
        _instrument = <nil>
        _stageLabel = <nil>
        _experiment = <nil>
        _pixelsSeq = 
        {
        }
        _pixelsLoaded = False
        _wellSamplesSeq = 
        {
        }
        _wellSamplesLoaded = False
        _roisSeq = 
        {
        }
        _roisLoaded = False
        _datasetLinksSeq = 
        {
        }
        _datasetLinksLoaded = False
        _datasetLinksCountPerOwner = 
        {
        }
        _fileset = <nil>
        _annotationLinksSeq = 
        {
        }
        _annotationLinksLoaded = False
        _annotationLinksCountPerOwner = 
        {
        }
        _name = <nil>
        _description = <nil>
    }
    _relatedTo = <nil>
    _pixelsType = object #23 (::omero::model::PixelsType)
    {
        _id = object #24 (::omero::RLong)
        {
            _val = 5
        }
        _details = <nil>
        _loaded = False
        _value = <nil>
        _bitSize = <nil>
    }
    _significantBits = <nil>
    _sizeX = object #25 (::omero::RInt)
    {
        _val = 243
    }
    _sizeY = object #26 (::omero::RInt)
    {
        _val = 28
    }
    _sizeZ = object #27 (::omero::RInt)
    {
        _val = 1
    }
    _sizeC = object #28 (::omero::RInt)
    {
        _val = 1
    }
    _sizeT = object #29 (::omero::RInt)
    {
        _val = 1
    }
    _sha1 = object #30 (::omero::RString)
    {
        _val = e4a205fd627beb5030a152f0a24edde81915654f
    }
    _dimensionOrder = object #31 (::omero::model::DimensionOrder)
    {
        _id = object #32 (::omero::RLong)
        {
            _val = 1
        }
        _details = <nil>
        _loaded = False
        _value = <nil>
    }
    _physicalSizeX = <invalid value - expected ::omero::model::Length>
    _physicalSizeY = <nil>
    _physicalSizeZ = <nil>
    _waveStart = <nil>
    _waveIncrement = <nil>
    _timeIncrement = <nil>
    _methodology = <nil>
    _planeInfoSeq = 
    {
    }
    _planeInfoLoaded = False
    _pixelsFileMapsSeq = 
    {
    }
    _pixelsFileMapsLoaded = False
    _pixelsFileMapsCountPerOwner = 
    {
    }
    _channelsSeq = 
    {
    }
    _channelsLoaded = False
    _settingsSeq = 
    {
    }
    _settingsLoaded = False
    _thumbnailsSeq = 
    {
    }
    _thumbnailsLoaded = False
},), {})
Traceback (most recent call last):
  File "/opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/python/omero/gateway/__init__.py", line 4094, in __call__
    return self.f(*args, **kwargs)
  File "/opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/python/omero_api_IUpdate_ice.py", line 107, in saveObject
    return _M_omero.api.IUpdate._op_saveObject.invoke(self, ((obj, ), _ctx))
ValueError: invalid value for ::omero::model::Pixels member `_physicalSizeX'
Traceback (most recent call last):
  File "./script", line 538, in <module>
    newImages, message = processImages(conn, scriptParams)
  File "./script", line 466, in processImages
    conn.getUpdateService().saveObject(px)
  File "/opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/python/omero/gateway/__init__.py", line 4097, in __call__
    return self.handle_exception(e, *args, **kwargs)
  File "/opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/python/omero/gateway/__init__.py", line 4094, in __call__
    return self.f(*args, **kwargs)
  File "/opt/hudson/workspace/OMERO-5.1-merge-deploy/src/dist/lib/python/omero_api_IUpdate_ice.py", line 107, in saveObject
    return _M_omero.api.IUpdate._op_saveObject.invoke(self, ((obj, ), _ctx))
ValueError: invalid value for ::omero::model::Pixels member `_physicalSizeX'

[pwalczysko]

The calibrated values in the Kymograph analysis csv are empty:

[pwalczysko]

Bug: Movie ROI figure script throws error

• In Insight, draw a rectangle on a multi-T image and execute Movei ROI figure.
• Activities show an error

Traceback (most recent call last):
  File "./script", line 846, in <module>
    runAsScript()
  File "./script", line 835, in runAsScript
    fileAnnotation, message = roiFigure(conn, commandArgs)
  File "./script", line 565, in roiFigure
    log("  Date: %s" % date.fromtimestamp(imageDate/1000))
TypeError: unsupported operand type(s) for /: 'datetime.datetime' and 'int'

[pwalczysko]

Bug: Split view Figure gives error

• In Insight, go to image ID 21907 on trout merge, user-4
• execute Split View Figure script with the default Scalebar size 5 microns
• error reported in Activities

Traceback (most recent call last):
  File "./script", line 826, in <module>
    runAsScript()
  File "./script", line 815, in runAsScript
    [fileAnnotation, message] = splitViewFigure(conn, scriptParams)
  File "./script", line 563, in splitViewFigure
    log("  Date: %s" % date.fromtimestamp(imageDate/1000))
TypeError: unsupported operand type(s) for /: 'datetime.datetime' and 'int'

[pwalczysko]

Bug: ROI Split Figure - analogous error and workflow as https://github.com/ome/scripts/pull/94#issuecomment-66763468

[pwalczysko]

Bug: Make Movie throws error

• in Insight, select a multi-z image ID 21966 user-4 trout/merge
• execute Make Movie
• execution is fine, but there is also an error report in Activities

[swscaler @ 0x2d369e0] BICUBIC scaler, from bgra to yuv420p using MMX2
[VD_FFMPEG] DRI failure.

[pwalczysko]

Bug: Movie Figure does not execute

• in Insight, find select a multi-z image ID 21966 user-4 trout/merge
• execute Movie Figure, ticking the scalebar at 5 microns box
• nothing happens

[pwalczysko]

In summary: Bugs:

• kymograph 1 (error) https://github.com/ome/scripts/pull/94#issuecomment-66759440
• kymograph 2 (missing calibrated values in csv) https://github.com/ome/scripts/pull/94#issuecomment-66759885
• Movie ROI Figure (error) https://github.com/ome/scripts/pull/94#issuecomment-66760760
• Split View Figure (error) https://github.com/ome/scripts/pull/94#issuecomment-66763468
• ROI Split Figure (error) https://github.com/ome/scripts/pull/94#issuecomment-66763712
• Make Movie (error) https://github.com/ome/scripts/pull/94#issuecomment-66764007
• Movie Figure (no execution) https://github.com/ome/scripts/pull/94#issuecomment-66764883

[will-moore]

@pwalczysko As long at the "Make Movie" creates a movie OK, then I think we can ignore the error output. That is just mencoder printing something to stderr which we then pick up as error. Other issues have been addressed above.

[gusferguson]

@will-moore Tested using OMERO.insight-5.1.0-m3-59-c29ae39-ice35-b364-mac trout user-3 read-only-1

Make Movie script: Using Image ID: 9461 /home/hudson/for_import_to_howe/archived-imoprt-case/user-3/read-only-1/Project-user-3/archivedv/CFPNEAT01_R3D.dv.log Movie created and scale bar present. Using Image ID: 21612 multi-channel-z-series.ome.tif Movie created but no scale bar present. See screenshot 1.

Is this because of lack of metadata in the second image?

Retesting Petr’s bug summary:

kymograph 1 (error) #94 (comment)

• runs fine and creates kymograph
• no error message just warning: ROI: 5654 had no lines or polylines

kymograph 2 (missing calibrated values in csv) #94 (comment)

• using images ID 21966 and ID 9463
• no output at all in downloaded CSV files - completely blank

Movie ROI Figure (error) #94 (comment)

• using images ID 21966 and ID 9463
• works as expected
• no errors reported

Split View Figure (error) #94 (comment)

• script failed to run at all
• no errors in Insight log
• quit and restart Insight
• worked as expected

ROI Split Figure (error) #94 (comment)

• script failed to run at all
• no errors in Insight log
• quit and restart Insight
• worked as expected

Make Movie (error) #94 (comment)

• works as expected
• same line in info but appears to be inconsequential

Movie Figure (no execution) #94 (comment)

• executes but comes up with “Error Info” in Activities window
• if I just run with defaults or just select scale bar this info shows no obvious error - but figure is not created
• Error message: {'Figure_Name': '/home/hudson/for_import_to_howe/archived-imoprt-case/user-3/read-only-1/no_projects/archivedv/test11_R3D', 'Show_Scalebar': True, 'Image_Labels': 'Image Name', 'Algorithm': 'Maximum Intensity', 'Data_Type': 'Image', 'Format': 'JPEG', 'Scalebar': 5, 'Scalebar_Colour': 'White', 'Time_Units': 'SECS', 'Height': 256, 'Width': 256, 'T_Indexes': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199], 'Z_Projection': True, 'Stepping': 1, 'Merged_Names': False, 'Max_Columns': 10, 'Overlay_Colour': 'White', 'IDs': [9472L]} Movie figure created by OMERO on 2014-12-18 Time units are in seconds Image details: Image: /home/hudson/for_import_to_howe/archived-imoprt-case/user-3/read-only-1/no_projects/archivedv/test11_R3D.dv ID: 9472
• if I deselect some time points then it gives the following error:
• Error message: Traceback (most recent call last): File "./script", line 679, in runAsScript() File "./script", line 669, in runAsScript fileAnnotation, message = movieFigure(conn, commandArgs) File "./script", line 435, in movieFigure log(" Date: %s" % date.fromtimestamp(imageDate/1000)) TypeError: unsupported operand type(s) for /: 'datetime.datetime' and 'int' }}}

A lot improved but still some issues.

[will-moore]

The Kymograph analysis script needs to run on the output image from the Kymograph script after drawing a diagonal line(s) on it. E.g. http://trout.openmicroscopy.org/merge/webclient/?show=image-23463 now generates a valid csv file with that script.

I've fixed the TypeError: unsupported operand type(s) for /: 'datetime.datetime' and 'int' and display of Scalebar in Movie_Figure. I've updated this script on trout and it seems to be fine:

[gusferguson]

@will-moore Tested using http://trout.openmicroscopy.org/merge/webclient/ and OMERO.insight-5.1.0-m3-87-35e2530-ice35-b365-mac user-3 read-only-1 image-23463

Kymograph analysis works on image as above - Calibrated values are showing up in csv. See screenshot.

Movie Figure - works as expected, Scalar appears on final thumbnail. No error seen in information log.

[jburel]

It will probably be necessary to adjust the scale bar to the units used. It is still in microns. This can be done in a follow-up PR Also noticed on make_movie.figure that colour is used instead of color

[jburel]

@gusferguson: Ok to merge?

[gusferguson]

@jburel Fine by me if the little things are noted to be done at another stage.

[jburel]

Other points to be addressed in another PR. Merging