UpdateBot: Nightly -> 4.8

2017-10-18T07:07:50Z

Nightly -> 4.8

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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:'''Contact:''' Andras Lasso, <email>lasso@queensu.ca</email><br>
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{{documentation/{{documentation/version}}/module-section|Module Description}}
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{{documentation/{{documentation/version}}/module-section|Use Cases}}
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|valign="top"|Examples:
* Add/edit tables in Tables module and in tables view (layout: Four-up table view)
* Import tables from and save tables to/csv, tsv, txt files
* Copy-paste table between Slicer and other applications (Excel, etc.)
* Use tables as inputs or outputs in CLI modules. See for example [[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] module.
* Use tables to show results generated by Python scripted. See for example [[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label statistics]] module

See this '''[https://youtu.be/tNrAut6WD_k short demo video]''' for an overview of Tables module's features.
|valign="top"|[[File:Slicer45-Tables-TableView.png|left|300px|Table view used as scripted module output]]
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}

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|valign="top"| A list of all the panels in the interface, their features, what they mean, and how to use them. {{documentation/{{documentation/version}}/module-parametersdescription}}
|valign="top"| [[File:Slicer45-Tables-GUI.png|thumb|200px]]
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
* [[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] CLI module uses table as output.
* [[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label statistics]] scripted module can optionally create a table as output.


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N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}

===Create a table node===
Tables can be created and values can be defined using [http://slicer.org/doc/html/classvtkMRMLTableNode.html Table node]. For example:
<pre>
tableNode = slicer.vtkMRMLTableNode()
col=tableNode.AddColumn()
col.SetName('First')
col=tableNode.AddColumn()
col.SetName('Seconf')
tableNode.AddEmptyRow()
tableNode.AddEmptyRow()
tableNode.SetCellText(0,0,'some value in col 1')
tableNode.SetCellText(0,0,'some value 2')
tableNode.SetCellText(0,0,'second column value 1')
tableNode.SetCellText(0,0,'second column value 2')
slicer.mrmlScene.AddNode(tableNode)
</pre>
If large amount of data is to be added to the table then either temporarily disable table updates using
<pre>
tableWasModified = tableNode.StartModify()
...
tableNode.EndModify(tableWasModified)
</pre>
or populate a ''vtkStringArray'' object and add it to the table using ''AddColumn''.

===How to display a table in the view layout===
Switch to a layout where tables are visible, set the table node as active and propagate the selection to views
<pre>
slicer.app.layoutManager().setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpTableView)
slicer.app.applicationLogic().GetSelectionNode().SetReferenceActiveTableID(tableNode.GetID())
slicer.app.applicationLogic().PropagateTableSelection()
</pre>

==How to display a table in a module GUI==
A table view can be used to show table contents by simply setting the input table using setMRMLTableNode. See details in [http://slicer.org/doc/html/classqMRMLTableView.html qMRMLTableView documentation].
<pre>
tableView=slicer.qMRMLTableView()
tableView.setMRMLTableNode(tableNode)
tableView.show()
</pre>

===Use table in CLI modules===
Add a ''table'' element in your module XML file:
<pre>
<table>
<name>inputDT</name>
<channel>input</channel>
<label>Input Table</label>
<longflag>inputTable</longflag>
<description><![CDATA[Array of Table values to process]]></description>
</table>
<table>
<name>outputDT</name>
<channel>output</channel>
<label>Output Table</label>
<longflag>outputTable</longflag>
<description><![CDATA[Array of processed (output) Table values]]></description>
</table>
</pre>
Notes:
* ''fileExtensions'' attribute may be specified to change type of the output file. Allowed types: .tsv (default), .txt, .csv. See their description at [http://slicer.org/doc/html/classvtkMRMLTableStorageNode.html table storage node documentation]
* The same ''table'' element may be used for passing color tables along with volumes. For this case ''type="color"'' is specified for the element and the data is read from/written to a color table node instead of a table node.

===Table column properties===

Properties can be defined for each column of the table using a schema file. Standard properties include data type, default value, long name, description, unit label. See complete list in [http://apidocs.slicer.org/master/classvtkMRMLTableNode.html#a01b263899f7eedb5ebfbc74298c2a1ca table node API documentation]. Properties are stored in a separate .csv file, with exactly the same name and extension as the table file, but with the ''.schema'' word inserted before the extension (ExampleTable.csv -> ExampleTable.schema.csv).

Example table file:
<pre>
ID,Structure,Volume,Surface,Verified
1,bone,12.4,11.2,1
2,tumor,32.1,22.5,1
3,cartilage,33.2,63.2,0
4,soft tissue,66.5,19.3,1
</pre>

Example schema file:
<pre>
columnName,type,defaultValue,longName,description,unitLabel
ID,string,,Measurement identifier,This text describes in detail what the column content is.,
Structure,string,,Structure name,Description <b>can</b> use html for formatting.,
Volume,double,0,Measured volume,,cc
Surface,double,0,Measured surface,,mm2
Verified,bit,0,Correctness verified,This column appears as a checkbox in the user interface.,
</pre>

Table display in Slicer:
[[File:Slicer47-ExampleTableProperties.png|left|Table properties are displayed in the tooltip and may be used for defining the column appearance (values in bit type column appear as checkbox)]]


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Documentation/4.8/Modules/Tables - Revision history

UpdateBot: Nightly -> 4.8