Retrieve Parent-Child data

dhavas

Hi Folks, 

I use the first measurement as ROIs and then have a second from which I just have to retrieve the RgnPerArea... 

So I have two classes, the one with the parents (from which I need length, width....) and the second with the children. 

I can retrieve the values to the parents well by this code...

Public Function GetClassDataT() As SimpleScript
        GetClassDataT = New SimpleScript

        Dim im As McImage=ThisApplication.ActiveImage
        If im Is Nothing Then Exit Function 'no image
        Dim md As McMMData=im.MeasurementsData
        'If md.Count=0 Then Exit Function'no data
        Dim classes As MMClasses=McMeasurements.ThisAddin.Options.Classes
        Dim nClasses As Integer=classes.Items.Count



With Automate.ScriptingCommands.CodeCommand(GetClassDataT)
If .Run() Then


For Each cl As MMClassDescr In classes.Items.Values


    For Each sf As McMMSubFeature In md.SubFeatures




    If sf.Value(eMeasures.AnyClass) = 1 Then



                If sf.Value(eMeasures.AnyClass)=cl.Value Then TWidth = sf.value(eMeasures.RgnWidth)
                If sf.Value(eMeasures.AnyClass)=cl.Value Then TLength= sf.value(eMeasures.RgnLength)
                If sf.Value(eMeasures.AnyClass)=cl.Value Then SumTSize = SumTSize + sf.value(eMeasures.RgnArea)

end if end with

YuriG

dhavas,

You could use Parent and PercentAreaParent measures in a macro to get the sum, like this

    Public Sub ParentMeasures
        Dim dict As New System.Collections.Generic.Dictionary(Of String,Double)
        For Each sf As McMMSubFeature In ThisApplication.ActiveImage.MeasurementsData.Subfeatures
            Dim sParent As String=sf.Value(eMeasures.AnyParentName)
            Dim v As Double=sf.Value(eMeasures.RgnPercentParentArea)
            If Not dict.ContainsKey(sParent) Then
                dict.Add(sParent,v)
            Else
                dict(sParent)=dict(sParent)+v'calculate sum
            End If
         Next
         For Each kv As System.Collections.Generic.KeyValuePair(Of String,Double) In dict
            Debug.Print (String.Format("Parent {0} - Percent Area Parent Sum = {1}",kv.Key,kv.Value))
         Next
    End Sub

The easier way is to Classify by Group (after grouping by Parent) , features of different parents will be assigned to different classes



and then collect data to Data Collector, Measurements Class Stats table, Percent Area Parent Sum will give you the value you need



Yuri

dhavas

Sorry was not complete... 
again

How can I get the values of RngPerArea o the children now for each of the parents

Public Function GetClassDataT() As SimpleScript
        GetClassDataT = New SimpleScript

        Dim im As McImage=ThisApplication.ActiveImage
        If im Is Nothing Then Exit Function 'no image
        Dim md As McMMData=im.MeasurementsData
        'If md.Count=0 Then Exit Function'no data
        Dim classes As MMClasses=McMeasurements.ThisAddin.Options.Classes
        Dim nClasses As Integer=classes.Items.Count

dim TWidth, TLength, SumTSize

With Automate.ScriptingCommands.CodeCommand(GetClassDataT)
If .Run() Then


For Each cl As MMClassDescr In classes.Items.Values


    For Each sf As McMMSubFeature In md.SubFeatures



'each parent in class 1
    If sf.Value(eMeasures.AnyClass) = 1 Then



                If sf.Value(eMeasures.AnyClass)=cl.Value Then TWidth = sf.value(eMeasures.RgnWidth)
                If sf.Value(eMeasures.AnyClass)=cl.Value Then TLength= sf.value(eMeasures.RgnLength)
                If sf.Value(eMeasures.AnyClass)=cl.Value Then SumTSize = SumTSize + sf.value(eMeasures.RgnArea)

'XXXXXXXXXXX    HERE I'D NEED THE percent area or area of the children for each parent. 
' in the end I need the % area of the Size of the parent covered by labeling within the parent's outlines


     end if
next
next

end if 
end with

'MANY THANKS

YuriG

dhavas,

There is an easier way to measure Percent Area Parent, which is mentioned in some previous topics:
http://forums.mediacy.com/discussion/comment/1113#Comment_1113 
http://forums.mediacy.com/discussion/comment/1155#Comment_1155 

In short: you just create your parent areas as Measurements (not ROIs), manually or using automatic segmentation, and then Activate "Preserve existing data", "Use as Outlines" and Count objects inside. Then check "Percent Area Parent" statistics, you can optionally group the table "By Parent". Here is the screenshot:



Yuri

dhavas

Hi Yuri, 

This is exactly what I do... 

I need the code to retrieve the data, since I need to calculate with them. 

So how do I get the statistics of the RngPercentParentArea (I found this one :-)) for each parent separately. 

(I'm measuring tumors and  cellular content within). 

My problem is that when I retrieve the single values, they are not sorted to parent. So if I get the class data of the second class (the children) then they are not easy to allocate to the parent so that I can sum them up. 

I'm sure there is a relative simple way, but I don't come on it...

Cheers

Dan

mbatchelor

2018-01-24-131834

Dhavas --

There may be a more sophisticated way to do this but I would use MASKS and HOLE AREA and HOLES NUMBER.

A path through this is shown below where:

AA is the ORIGINAL IMAGE with the ROIs and the AREAS found within the ROIs
BB is the ORIGINAL IMAGE with the ROIs converted to MEASUREMENTS using the FEATURE MANAGER
CC is the ORIGINAL IMAGE with the AREAS and no ROIs
DD is the MASK of BB
EE is the MASK of CC (plus a division by 2 to change 255 to 128)
FF is DD - EE plus a MONO THRESHOLD of 130 to 255 and a COUNT.

I think the information you want is now available in the DATA TABLE.

The only issue I see is if one of your AREAS is at the boundary of the ROI.  I think you can deal with this though by maybe DILATING the DD MASK by a pixel or two or by eroding the EE MASK by a pixel or two.

I hope this information is helpful.

-- Matt

dhavas

Hi Matt, 

I just saw this answer - working  a lot with masks and this would definitely work. 

But there was in the end some code way to retrieve. 

Here a short version of it:

Public Function GetClassDataT() As SimpleScript
        GetClassDataT = New SimpleScript

        Dim im As McImage=ThisApplication.ActiveImage
        If im Is Nothing Then Exit Function 'no image
        Dim md As McMMData=im.MeasurementsData
        'If md.Count=0 Then Exit Function'no data
        Dim classes As MMClasses=McMeasurements.ThisAddin.Options.Classes
        Dim nClasses As Integer=classes.Items.Count


        Dim n, count, area, ClDescription
        ReDim count(nClasses) As Double
        ReDim area(nClasses) As Double

        Dim nObj As Integer = 0
        Dim AreaSum As Double = 0
        Dim currparent, tempparent

        Dim dict As New System.Collections.Generic.Dictionary(Of String,Double)

With Automate.ScriptingCommands.CodeCommand(GetClassDataT)
If .Run() Then

For Each sf As McMMSubFeature In md.SubFeatures Dim sParent As String=sf.Value(eMeasures.AnyParentName) Dim v As Double=sf.Value(eMeasures.RgnPercentParentArea) If Not dict.ContainsKey(sParent) Then dict.Add(sParent,v) Else dict(sParent)=dict(sParent)+v'calculate sum End If Next For Each kv As System.Collections.Generic.KeyValuePair(Of String,Double) In dict 'Debug.Print (String.Format("Parent {0} - Percent Area Parent Sum = {1}",kv.Key,kv.Value)) currparent = kv.Key TCell = kv.Value 'go for subfeatures of Parents For Each sfP As McMMSubFeature In md.SubFeatures ' tempparent = sfP.Name If Trim(tempparent) = Trim(currparent) Then 'DO SOMETHING End If 'this very parent or tumor Next 'sfP Next 'kv Tcell determination and also tumor

End If
End With

End Function

mbatchelor

2018-05-24-104735

Dhavas --

I am glad that you were able to develop a method and code it to provide your solution.

Thank you for posting the code here so others can follow your path and alter it as suits their needs.

-- Matt