Number of frames and McImageSetLocationsClass

davek604

Hello

I'm using the code below to perform an EDF on a 3D timelapse image. The code is not tested yet because although its basically the recorded code from the Record Macro option I get the following error "Type identifier is invalid referring to the line below.

.SetFrames = New System.Collections.Generic.List(Of MediaCy.IQL.Sets.McImageSetLocations)

Also which command do you use to get the number of z and number of timepoints in an image

Full code below

Public Function MergeRed()
        Dim x As Integer
        Dim doc1, image1, doc2, image2, doc3

        With Application.DocumentCommands.Active(MergeRed)
            .Run(ThisApplication.ActiveImage)
        End With

        With Process.FramesCommands.Extract(MergeRed)
            .SetFrames = New System.Collections.Generic.List(Of MediaCy.IQL.Sets.McImageSetLocations)
                Dim locations As MediaCy.IQL.Sets.McImageSetLocationsClass

                For x = 0 To 5
                    locations = New MediaCy.IQL.Sets.McImageSetLocationsClass
                    locations.Add(MediaCy.IQL.Sets.mcImageSetDimensions.mcisdChannel, 1)
                    locations.Add(MediaCy.IQL.Sets.mcImageSetDimensions.mcisdZ, x)
                    locations.Add(MediaCy.IQL.Sets.mcImageSetDimensions.mcisdScan, 0)
                    locations.Add(MediaCy.IQL.Sets.mcImageSetDimensions.mcisdSite, 0)
                    locations.Add(MediaCy.IQL.Sets.mcImageSetDimensions.mcisdTime, 0)
                    locations.Add(MediaCy.IQL.Sets.mcImageSetDimensions.mcisdResolution, 0)
                    locations.Add(MediaCy.IQL.Sets.mcImageSetDimensions.mcisdUser2, 0)
                    .SetFrames.Add(locations)
                Next x
                .ViewClassName = "McGalleryView"
                .FrameByFrame = False
                .BestFocusPlane = False
                .NormalizeIllumination = False
                .BottomUp = False
                .Prefilter = MediaCy.IQL.Align.mcefPreFilterType.mcpftVarDilation3x3
                .VarianceThreshold = 50
                .Run(doc1, image1)

        End With

End Function

YuriG

Hi David,

Low level set operations are not covered by commands, so you have to use IQL functions to get all these parameters. Below is a sample macro that prints all dimensions of the active set from the active location:

    Public Sub GetSetDimentions()
        If ThisApplication.ActiveDocument Is Nothing Then Exit Sub
        Dim imSet As McImageSet=ThisApplication.ActiveDocument.GetData(GetType(McImageSet),Nothing)
        If imSet IsNot Nothing Then
            Dim lc As McImageSetLocations=imSet.GetCurrentLocation
            For Each ilc As McImageSetLocation In lc
                Dim length As Integer=imSet.GetDimensionLength(ilc.Dimension,lc)
                If length>1 Then
                    Debug.Print (ilc.Dimension.ToString() & " = " &  length)
                End If
            Next
        End If
    End Sub

For other set operations you have to check IQL functions in MediaCy.IQL.Sets namespace of the automation help.

Yuri 

YuriG

Hi David,

It looks like the references to MediaCy.IQL.Sets.dll and MediaCy.IQL.Align.dll are not added automatically.

Please try to add them manually (Project workbench - References).

Yuri

davek604

Hello Yuri

The references worked, but which commands would you use to find how many timepoints and how many z are in an image.

Regards

David

YuriG

David,

I've created an example macro that extracts maximum Projection image from every time point stack and merges it to a sequence. 

Imports MediaCy.IQL.Sets

...

    Public Sub CreateMIPSequenceOfActiveChannel()
        If ThisApplication.ActiveDocument Is Nothing Then Exit Sub
        Dim imSet As McImageSet=ThisApplication.ActiveDocument.GetData(GetType(McImageSet),Nothing)
        If imSet Is Nothing Then Exit Sub 'not a set
        Dim seqOp As New MediaCy.IQL.Operations.McOperations

        Dim lc As McImageSetLocations=imSet.GetCurrentLocation
        'get number of time points
        Dim timeLength As Integer=imSet.GetDimensionLength(mcImageSetDimensions.mcisdTime,lc)
        Dim outIm As McImage
        Dim pm As McBusyState =ThisApplication.SetBusyState(,True)
        pm.SetProgressInfo("Creating MIP sequence",Interop.mcProgressAllowCancel.mcpacTopLevelCancelOnly,0,timeLength-1)
        For i As Integer =0 To timeLength-1
            If pm.SetProgress(i) Then Exit Sub'user cancel
            'get Z planes for every time point
            lc.Item(mcImageSetDimensions.mcisdTime).Location=i
            Dim src As McImageSetSources=imSet.GetSourcesAlongDimension(lc,mcImageSetDimensions.mcisdZ)
            'create maximum intensity projection image, as invisible
            Dim im As mcimage=seqOp.MaxFrames(src,mcImageCreateFlags.mcicfNotVisible Or mcImageCreateFlags.mcicfNoAddToCollection)
            If outIm Is Nothing Then
                outIm=im
            Else
                'append frame
                im.MoveFrames(0,1,outIm,outIm.FrameCount)
            End If
        Next
        'make image visible
        outIm.Visible=True
    End Sub

You can use this macro as a reference for your processing.

Yuri

davek604

Hello Yuri

Thanks for code to extract the max projections over time it works well. I'm now trying to extend it to work on 2 or 3 colour images but using the debugger its very difficult to figure out what the various variables contain and therefore what they are doing so that I can modify the correct bit. In the debugger each variable seems to hold a hex memory location rather than readable values. I've been using the .DisplayName you suggested in a previous post but this doesn't work on most of the variables is there another way to figure out what the variables are doing. I've searched the help files for the commands but I'm struggling a bit with them

 

Regards

 

David 

davek604

Hello Yuri

Got it, you select the channel then run your code

Regards

David

YuriG

Yes, the macro uses CurrentLocation of the set, which defines what channel is currently selected. 

If you want to specify channel programmatically you can set it to the msisdChannel dimension of the location:

        Dim lc As McImageSetLocations=imSet.GetCurrentLocation
        Dim ChannelIndex As Integer=0
        'process my channel
        lc.Item(mcImageSetDimensions.mcisdChannel).Location=ChannelIndex

Yuri