Markov Chain (transition matrix and graph)
Bert
New Altair Community Member
So I'm trying to visualize the output of my clustering with a markov chain, and I'm stuck. It looks like Rapidminer has all the tools for the job, but I don't know how to make this work...
- I have my original dataset as an input, with an additional attribute describing the clusters found by x-means
- I feed this into a transition matrix operator, which shows me the probabilities to transition from one cluster to other clusters
- The second item in the transition matrix is a pairwise table, which is exactly what the transition graph operator needs to display a graph with transition probabilities (i.e., a markov chain)
- but I don't know how to connect those two elements... there doesn't seem to be a way to select the pairwise table from the result of the transition matrix and feed that into the transition graph 
Any idea? Thanks in advance!
Here's my xml:
<?xml version="1.0" encoding="UTF-8"?><process version="7.4.000">
<context>
<input/>
<output/>
<macros/>
</context>
<operator activated="true" class="process" compatibility="7.4.000" expanded="true" name="Process">
<process expanded="true">
<operator activated="true" class="read_csv" compatibility="7.4.000" expanded="true" height="68" name="Read CSV" width="90" x="45" y="34">
<parameter key="csv_file" value="/Users/schneibe/Dropbox/Windows/Kinect/Group/Default82-0-Kinect-Log-2017-03-27 08-23-20.csv"/>
<parameter key="column_separators" value=","/>
<parameter key="first_row_as_names" value="false"/>
<list key="annotations">
<parameter key="0" value="Name"/>
</list>
<parameter key="encoding" value="UTF-8"/>
<list key="data_set_meta_data_information">
<parameter key="0" value="Timestamp.true.polynominal.attribute"/>
<parameter key="1" value="Session.true.polynominal.attribute"/>
<parameter key="2" value="Index.true.integer.attribute"/>
<parameter key="3" value="BodyID.true.integer.attribute"/>
<parameter key="4" value="SpineBase_X.true.real.attribute"/>
<parameter key="5" value="SpineBase_Y.true.real.attribute"/>
<parameter key="6" value="SpineBase_Z.true.real.attribute"/>
<parameter key="7" value="SpineBase_inferred.true.integer.attribute"/>
<parameter key="8" value="SpineMid_X.true.real.attribute"/>
<parameter key="9" value="SpineMid_Y.true.real.attribute"/>
<parameter key="10" value="SpineMid_Z.true.real.attribute"/>
<parameter key="11" value="SpineMid_inferred.true.integer.attribute"/>
<parameter key="12" value="Neck_X.true.real.attribute"/>
<parameter key="13" value="Neck_Y.true.real.attribute"/>
<parameter key="14" value="Neck_Z.true.real.attribute"/>
<parameter key="15" value="Neck_inferred.true.integer.attribute"/>
<parameter key="16" value="Head_X.true.real.attribute"/>
<parameter key="17" value="Head_Y.true.real.attribute"/>
<parameter key="18" value="Head_Z.true.real.attribute"/>
<parameter key="19" value="Head_inferred.true.integer.attribute"/>
<parameter key="20" value="ShoulderLeft_X.true.real.attribute"/>
<parameter key="21" value="ShoulderLeft_Y.true.real.attribute"/>
<parameter key="22" value="ShoulderLeft_Z.true.real.attribute"/>
<parameter key="23" value="ShoulderLeft_inferred.true.integer.attribute"/>
<parameter key="24" value="ElbowLeft_X.true.real.attribute"/>
<parameter key="25" value="ElbowLeft_Y.true.real.attribute"/>
<parameter key="26" value="ElbowLeft_Z.true.real.attribute"/>
<parameter key="27" value="ElbowLeft_inferred.true.integer.attribute"/>
<parameter key="28" value="WristLeft_X.true.real.attribute"/>
<parameter key="29" value="WristLeft_Y.true.real.attribute"/>
<parameter key="30" value="WristLeft_Z.true.real.attribute"/>
<parameter key="31" value="WristLeft_inferred.true.integer.attribute"/>
<parameter key="32" value="HandLeft_X.true.real.attribute"/>
<parameter key="33" value="HandLeft_Y.true.real.attribute"/>
<parameter key="34" value="HandLeft_Z.true.real.attribute"/>
<parameter key="35" value="HandLeft_inferred.true.integer.attribute"/>
<parameter key="36" value="ShoulderRight_X.true.real.attribute"/>
<parameter key="37" value="ShoulderRight_Y.true.real.attribute"/>
<parameter key="38" value="ShoulderRight_Z.true.real.attribute"/>
<parameter key="39" value="ShoulderRight_inferred.true.integer.attribute"/>
<parameter key="40" value="ElbowRight_X.true.real.attribute"/>
<parameter key="41" value="ElbowRight_Y.true.real.attribute"/>
<parameter key="42" value="ElbowRight_Z.true.real.attribute"/>
<parameter key="43" value="ElbowRight_inferred.true.integer.attribute"/>
<parameter key="44" value="WristRight_X.true.real.attribute"/>
<parameter key="45" value="WristRight_Y.true.real.attribute"/>
<parameter key="46" value="WristRight_Z.true.real.attribute"/>
<parameter key="47" value="WristRight_inferred.true.integer.attribute"/>
<parameter key="48" value="HandRight_X.true.real.attribute"/>
<parameter key="49" value="HandRight_Y.true.real.attribute"/>
<parameter key="50" value="HandRight_Z.true.real.attribute"/>
<parameter key="51" value="HandRight_inferred.true.integer.attribute"/>
<parameter key="52" value="HipLeft_X.true.real.attribute"/>
<parameter key="53" value="HipLeft_Y.true.real.attribute"/>
<parameter key="54" value="HipLeft_Z.true.real.attribute"/>
<parameter key="55" value="HipLeft_inferred.true.integer.attribute"/>
<parameter key="56" value="HipRight_X.true.real.attribute"/>
<parameter key="57" value="HipRight_Y.true.real.attribute"/>
<parameter key="58" value="HipRight_Z.true.real.attribute"/>
<parameter key="59" value="HipRight_inferred.true.integer.attribute"/>
<parameter key="60" value="SpineShoulder_X.true.real.attribute"/>
<parameter key="61" value="SpineShoulder_Y.true.real.attribute"/>
<parameter key="62" value="SpineShoulder_Z.true.real.attribute"/>
<parameter key="63" value="SpineShoulder_inferred.true.integer.attribute"/>
<parameter key="64" value="HandTipLeft_X.true.real.attribute"/>
<parameter key="65" value="HandTipLeft_Y.true.real.attribute"/>
<parameter key="66" value="HandTipLeft_Z.true.real.attribute"/>
<parameter key="67" value="HandTipLeft_inferred.true.integer.attribute"/>
<parameter key="68" value="ThumbLeft_X.true.real.attribute"/>
<parameter key="69" value="ThumbLeft_Y.true.real.attribute"/>
<parameter key="70" value="ThumbLeft_Z.true.real.attribute"/>
<parameter key="71" value="ThumbLeft_inferred.true.integer.attribute"/>
<parameter key="72" value="HandTipRight_X.true.real.attribute"/>
<parameter key="73" value="HandTipRight_Y.true.real.attribute"/>
<parameter key="74" value="HandTipRight_Z.true.real.attribute"/>
<parameter key="75" value="HandTipRight_inferred.true.integer.attribute"/>
<parameter key="76" value="ThumbRight_X.true.real.attribute"/>
<parameter key="77" value="ThumbRight_Y.true.real.attribute"/>
<parameter key="78" value="ThumbRight_Z.true.real.attribute"/>
<parameter key="79" value="ThumbRight_inferred.true.integer.attribute"/>
<parameter key="80" value="KneeLeft_X.true.real.attribute"/>
<parameter key="81" value="KneeLeft_Y.true.real.attribute"/>
<parameter key="82" value="KneeLeft_Z.true.real.attribute"/>
<parameter key="83" value="KneeLeft_inferred.true.integer.attribute"/>
<parameter key="84" value="AnkleLeft_X.true.real.attribute"/>
<parameter key="85" value="AnkleLeft_Y.true.real.attribute"/>
<parameter key="86" value="AnkleLeft_Z.true.real.attribute"/>
<parameter key="87" value="AnkleLeft_inferred.true.integer.attribute"/>
<parameter key="88" value="FootLeft_X.true.real.attribute"/>
<parameter key="89" value="FootLeft_Y.true.real.attribute"/>
<parameter key="90" value="FootLeft_Z.true.real.attribute"/>
<parameter key="91" value="FootLeft_inferred.true.integer.attribute"/>
<parameter key="92" value="KneeRight_X.true.real.attribute"/>
<parameter key="93" value="KneeRight_Y.true.real.attribute"/>
<parameter key="94" value="KneeRight_Z.true.real.attribute"/>
<parameter key="95" value="KneeRight_inferred.true.integer.attribute"/>
<parameter key="96" value="AnkleRight_X.true.real.attribute"/>
<parameter key="97" value="AnkleRight_Y.true.real.attribute"/>
<parameter key="98" value="AnkleRight_Z.true.real.attribute"/>
<parameter key="99" value="AnkleRight_inferred.true.integer.attribute"/>
<parameter key="100" value="FootRight_X.true.real.attribute"/>
<parameter key="101" value="FootRight_Y.true.real.attribute"/>
<parameter key="102" value="FootRight_Z.true.real.attribute"/>
<parameter key="103" value="FootRight_inferred.true.integer.attribute"/>
<parameter key="104" value="HandLeftState.true.polynominal.attribute"/>
<parameter key="105" value="HandLeftStateConfidence.true.polynominal.attribute"/>
<parameter key="106" value="HandRightState.true.polynominal.attribute"/>
<parameter key="107" value="HandRightStateConfidence.true.polynominal.attribute"/>
<parameter key="108" value="Lean_X.true.real.attribute"/>
<parameter key="109" value="Lean_Y.true.real.attribute"/>
<parameter key="110" value="Lean_TrackingState.true.polynominal.attribute"/>
<parameter key="111" value="SpineBase_movement.true.real.attribute"/>
<parameter key="112" value="SpineShoulder_movement.true.attribute_value.attribute"/>
<parameter key="113" value="SpineMid_movement.true.real.attribute"/>
<parameter key="114" value="Neck_movement.true.real.attribute"/>
<parameter key="115" value="Head_movement.true.real.attribute"/>
<parameter key="116" value="ShoulderLeft_movement.true.real.attribute"/>
<parameter key="117" value="ElbowLeft_movement.true.real.attribute"/>
<parameter key="118" value="WristLeft_movement.true.real.attribute"/>
<parameter key="119" value="HandLeft_movement.true.real.attribute"/>
<parameter key="120" value="ShoulderRight_movement.true.real.attribute"/>
<parameter key="121" value="ElbowRight_movement.true.real.attribute"/>
<parameter key="122" value="WristRight_movement.true.real.attribute"/>
<parameter key="123" value="HandRight_movement.true.real.attribute"/>
<parameter key="124" value="HipLeft_movement.true.real.attribute"/>
<parameter key="125" value="HipRight_movement.true.attribute_value.attribute"/>
<parameter key="126" value="HandTipLeft_movement.true.real.attribute"/>
<parameter key="127" value="ThumbLeft_movement.true.real.attribute"/>
<parameter key="128" value="HandTipRight_movement.true.attribute_value.attribute"/>
<parameter key="129" value="ThumbRight_movement.true.real.attribute"/>
<parameter key="130" value="KneeLeft_movement.true.real.attribute"/>
<parameter key="131" value="AnkleLeft_movement.true.real.attribute"/>
<parameter key="132" value="FootLeft_movement.true.real.attribute"/>
<parameter key="133" value="KneeRight_movement.true.real.attribute"/>
<parameter key="134" value="AnkleRight_movement.true.real.attribute"/>
<parameter key="135" value="FootRight_movement.true.real.attribute"/>
<parameter key="136" value="Neck_angle.true.real.attribute"/>
<parameter key="137" value="Spine_angle.true.real.attribute"/>
<parameter key="138" value="Hip_angle.true.real.attribute"/>
<parameter key="139" value="ShoulderL_angle.true.real.attribute"/>
<parameter key="140" value="ShoulderR_angle.true.real.attribute"/>
<parameter key="141" value="ElbowL_angle.true.real.attribute"/>
<parameter key="142" value="ElbowR_angle.true.real.attribute"/>
<parameter key="143" value="WristL_angle.true.real.attribute"/>
<parameter key="144" value="WristR_angle.true.real.attribute"/>
<parameter key="145" value="HandL_angle.true.real.attribute"/>
<parameter key="146" value="HandR_angle.true.real.attribute"/>
<parameter key="147" value="Happy.true.attribute_value.attribute"/>
<parameter key="148" value="Engaged.true.attribute_value.attribute"/>
<parameter key="149" value="WearingGlasses.true.attribute_value.attribute"/>
<parameter key="150" value="LeftEyeClosed.true.attribute_value.attribute"/>
<parameter key="151" value="RightEyeClosed.true.attribute_value.attribute"/>
<parameter key="152" value="MouthOpen.true.attribute_value.attribute"/>
<parameter key="153" value="MouthMoved.true.attribute_value.attribute"/>
<parameter key="154" value="LookingAway.true.attribute_value.attribute"/>
<parameter key="155" value="FaceYaw.true.attribute_value.attribute"/>
<parameter key="156" value="FacePitch.true.attribute_value.attribute"/>
<parameter key="157" value="FacenRoll.true.attribute_value.attribute"/>
<parameter key="158" value="Talking.true.integer.attribute"/>
<parameter key="159" value="Posture.true.attribute_value.attribute"/>
</list>
</operator>
<operator activated="true" class="generate_id" compatibility="7.4.000" expanded="true" height="82" name="Generate ID" width="90" x="112" y="136"/>
<operator activated="true" class="select_attributes" compatibility="7.4.000" expanded="true" height="82" name="Select Attributes" width="90" x="179" y="289">
<parameter key="attribute_filter_type" value="subset"/>
<parameter key="attributes" value="WristR_angle|WristL_angle|Spine_angle|ShoulderR_angle|ShoulderL_angle|Neck_angle|Hip_angle|HandR_angle|HandL_angle|ElbowR_angle|ElbowL_angle"/>
</operator>
<operator activated="true" class="x_means" compatibility="7.4.000" expanded="true" height="82" name="X-Means" width="90" x="313" y="34"/>
<operator activated="true" class="join" compatibility="7.4.000" expanded="true" height="82" name="Join" width="90" x="447" y="187">
<list key="key_attributes"/>
</operator>
<operator activated="true" class="transition_matrix" compatibility="7.4.000" expanded="true" height="82" name="Transition Matrix" width="90" x="514" y="34">
<parameter key="attribute" value="cluster"/>
</operator>
<operator activated="false" class="transition_graph" compatibility="7.4.000" expanded="true" height="82" name="Transition Graph" width="90" x="782" y="187">
<parameter key="source_attribute" value="cluster"/>
<parameter key="target_attribute" value="cluster"/>
</operator>
<connect from_op="Read CSV" from_port="output" to_op="Generate ID" to_port="example set input"/>
<connect from_op="Generate ID" from_port="example set output" to_op="Select Attributes" to_port="example set input"/>
<connect from_op="Select Attributes" from_port="example set output" to_op="X-Means" to_port="example set"/>
<connect from_op="Select Attributes" from_port="original" to_op="Join" to_port="right"/>
<connect from_op="X-Means" from_port="clustered set" to_op="Join" to_port="left"/>
<connect from_op="Join" from_port="join" to_op="Transition Matrix" to_port="example set"/>
<connect from_op="Transition Matrix" from_port="example set" to_port="result 1"/>
<connect from_op="Transition Matrix" from_port="transition matrix" to_port="result 2"/>
<portSpacing port="source_input 1" spacing="0"/>
<portSpacing port="sink_result 1" spacing="0"/>
<portSpacing port="sink_result 2" spacing="0"/>
<portSpacing port="sink_result 3" spacing="0"/>
</process>
</operator>
</process>
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Best Answers
-
Great, the Converters extension did the trick. Thanks for your help!!
Here's the xml:
<?xml version="1.0" encoding="UTF-8"?><process version="7.4.000">
<context>
<input/>
<output/>
<macros/>
</context>
<operator activated="true" class="process" compatibility="7.4.000" expanded="true" name="Process">
<process expanded="true">
<operator activated="true" class="read_csv" compatibility="7.4.000" expanded="true" height="68" name="Read CSV" width="90" x="45" y="34">
<parameter key="csv_file" value="/Users/schneibe/Dropbox/Windows/Kinect/Group/Default82-0-Kinect-Log-2017-03-27 08-23-20.csv"/>
<parameter key="column_separators" value=","/>
<parameter key="first_row_as_names" value="false"/>
<list key="annotations">
<parameter key="0" value="Name"/>
</list>
<parameter key="encoding" value="UTF-8"/>
<list key="data_set_meta_data_information">
<parameter key="0" value="Timestamp.true.polynominal.attribute"/>
<parameter key="1" value="Session.true.polynominal.attribute"/>
<parameter key="2" value="Index.true.integer.attribute"/>
<parameter key="3" value="BodyID.true.integer.attribute"/>
<parameter key="4" value="SpineBase_X.true.real.attribute"/>
<parameter key="5" value="SpineBase_Y.true.real.attribute"/>
<parameter key="6" value="SpineBase_Z.true.real.attribute"/>
<parameter key="7" value="SpineBase_inferred.true.integer.attribute"/>
<parameter key="8" value="SpineMid_X.true.real.attribute"/>
<parameter key="9" value="SpineMid_Y.true.real.attribute"/>
<parameter key="10" value="SpineMid_Z.true.real.attribute"/>
<parameter key="11" value="SpineMid_inferred.true.integer.attribute"/>
<parameter key="12" value="Neck_X.true.real.attribute"/>
<parameter key="13" value="Neck_Y.true.real.attribute"/>
<parameter key="14" value="Neck_Z.true.real.attribute"/>
<parameter key="15" value="Neck_inferred.true.integer.attribute"/>
<parameter key="16" value="Head_X.true.real.attribute"/>
<parameter key="17" value="Head_Y.true.real.attribute"/>
<parameter key="18" value="Head_Z.true.real.attribute"/>
<parameter key="19" value="Head_inferred.true.integer.attribute"/>
<parameter key="20" value="ShoulderLeft_X.true.real.attribute"/>
<parameter key="21" value="ShoulderLeft_Y.true.real.attribute"/>
<parameter key="22" value="ShoulderLeft_Z.true.real.attribute"/>
<parameter key="23" value="ShoulderLeft_inferred.true.integer.attribute"/>
<parameter key="24" value="ElbowLeft_X.true.real.attribute"/>
<parameter key="25" value="ElbowLeft_Y.true.real.attribute"/>
<parameter key="26" value="ElbowLeft_Z.true.real.attribute"/>
<parameter key="27" value="ElbowLeft_inferred.true.integer.attribute"/>
<parameter key="28" value="WristLeft_X.true.real.attribute"/>
<parameter key="29" value="WristLeft_Y.true.real.attribute"/>
<parameter key="30" value="WristLeft_Z.true.real.attribute"/>
<parameter key="31" value="WristLeft_inferred.true.integer.attribute"/>
<parameter key="32" value="HandLeft_X.true.real.attribute"/>
<parameter key="33" value="HandLeft_Y.true.real.attribute"/>
<parameter key="34" value="HandLeft_Z.true.real.attribute"/>
<parameter key="35" value="HandLeft_inferred.true.integer.attribute"/>
<parameter key="36" value="ShoulderRight_X.true.real.attribute"/>
<parameter key="37" value="ShoulderRight_Y.true.real.attribute"/>
<parameter key="38" value="ShoulderRight_Z.true.real.attribute"/>
<parameter key="39" value="ShoulderRight_inferred.true.integer.attribute"/>
<parameter key="40" value="ElbowRight_X.true.real.attribute"/>
<parameter key="41" value="ElbowRight_Y.true.real.attribute"/>
<parameter key="42" value="ElbowRight_Z.true.real.attribute"/>
<parameter key="43" value="ElbowRight_inferred.true.integer.attribute"/>
<parameter key="44" value="WristRight_X.true.real.attribute"/>
<parameter key="45" value="WristRight_Y.true.real.attribute"/>
<parameter key="46" value="WristRight_Z.true.real.attribute"/>
<parameter key="47" value="WristRight_inferred.true.integer.attribute"/>
<parameter key="48" value="HandRight_X.true.real.attribute"/>
<parameter key="49" value="HandRight_Y.true.real.attribute"/>
<parameter key="50" value="HandRight_Z.true.real.attribute"/>
<parameter key="51" value="HandRight_inferred.true.integer.attribute"/>
<parameter key="52" value="HipLeft_X.true.real.attribute"/>
<parameter key="53" value="HipLeft_Y.true.real.attribute"/>
<parameter key="54" value="HipLeft_Z.true.real.attribute"/>
<parameter key="55" value="HipLeft_inferred.true.integer.attribute"/>
<parameter key="56" value="HipRight_X.true.real.attribute"/>
<parameter key="57" value="HipRight_Y.true.real.attribute"/>
<parameter key="58" value="HipRight_Z.true.real.attribute"/>
<parameter key="59" value="HipRight_inferred.true.integer.attribute"/>
<parameter key="60" value="SpineShoulder_X.true.real.attribute"/>
<parameter key="61" value="SpineShoulder_Y.true.real.attribute"/>
<parameter key="62" value="SpineShoulder_Z.true.real.attribute"/>
<parameter key="63" value="SpineShoulder_inferred.true.integer.attribute"/>
<parameter key="64" value="HandTipLeft_X.true.real.attribute"/>
<parameter key="65" value="HandTipLeft_Y.true.real.attribute"/>
<parameter key="66" value="HandTipLeft_Z.true.real.attribute"/>
<parameter key="67" value="HandTipLeft_inferred.true.integer.attribute"/>
<parameter key="68" value="ThumbLeft_X.true.real.attribute"/>
<parameter key="69" value="ThumbLeft_Y.true.real.attribute"/>
<parameter key="70" value="ThumbLeft_Z.true.real.attribute"/>
<parameter key="71" value="ThumbLeft_inferred.true.integer.attribute"/>
<parameter key="72" value="HandTipRight_X.true.real.attribute"/>
<parameter key="73" value="HandTipRight_Y.true.real.attribute"/>
<parameter key="74" value="HandTipRight_Z.true.real.attribute"/>
<parameter key="75" value="HandTipRight_inferred.true.integer.attribute"/>
<parameter key="76" value="ThumbRight_X.true.real.attribute"/>
<parameter key="77" value="ThumbRight_Y.true.real.attribute"/>
<parameter key="78" value="ThumbRight_Z.true.real.attribute"/>
<parameter key="79" value="ThumbRight_inferred.true.integer.attribute"/>
<parameter key="80" value="KneeLeft_X.true.real.attribute"/>
<parameter key="81" value="KneeLeft_Y.true.real.attribute"/>
<parameter key="82" value="KneeLeft_Z.true.real.attribute"/>
<parameter key="83" value="KneeLeft_inferred.true.integer.attribute"/>
<parameter key="84" value="AnkleLeft_X.true.real.attribute"/>
<parameter key="85" value="AnkleLeft_Y.true.real.attribute"/>
<parameter key="86" value="AnkleLeft_Z.true.real.attribute"/>
<parameter key="87" value="AnkleLeft_inferred.true.integer.attribute"/>
<parameter key="88" value="FootLeft_X.true.real.attribute"/>
<parameter key="89" value="FootLeft_Y.true.real.attribute"/>
<parameter key="90" value="FootLeft_Z.true.real.attribute"/>
<parameter key="91" value="FootLeft_inferred.true.integer.attribute"/>
<parameter key="92" value="KneeRight_X.true.real.attribute"/>
<parameter key="93" value="KneeRight_Y.true.real.attribute"/>
<parameter key="94" value="KneeRight_Z.true.real.attribute"/>
<parameter key="95" value="KneeRight_inferred.true.integer.attribute"/>
<parameter key="96" value="AnkleRight_X.true.real.attribute"/>
<parameter key="97" value="AnkleRight_Y.true.real.attribute"/>
<parameter key="98" value="AnkleRight_Z.true.real.attribute"/>
<parameter key="99" value="AnkleRight_inferred.true.integer.attribute"/>
<parameter key="100" value="FootRight_X.true.real.attribute"/>
<parameter key="101" value="FootRight_Y.true.real.attribute"/>
<parameter key="102" value="FootRight_Z.true.real.attribute"/>
<parameter key="103" value="FootRight_inferred.true.integer.attribute"/>
<parameter key="104" value="HandLeftState.true.polynominal.attribute"/>
<parameter key="105" value="HandLeftStateConfidence.true.polynominal.attribute"/>
<parameter key="106" value="HandRightState.true.polynominal.attribute"/>
<parameter key="107" value="HandRightStateConfidence.true.polynominal.attribute"/>
<parameter key="108" value="Lean_X.true.real.attribute"/>
<parameter key="109" value="Lean_Y.true.real.attribute"/>
<parameter key="110" value="Lean_TrackingState.true.polynominal.attribute"/>
<parameter key="111" value="SpineBase_movement.true.real.attribute"/>
<parameter key="112" value="SpineShoulder_movement.true.attribute_value.attribute"/>
<parameter key="113" value="SpineMid_movement.true.real.attribute"/>
<parameter key="114" value="Neck_movement.true.real.attribute"/>
<parameter key="115" value="Head_movement.true.real.attribute"/>
<parameter key="116" value="ShoulderLeft_movement.true.real.attribute"/>
<parameter key="117" value="ElbowLeft_movement.true.real.attribute"/>
<parameter key="118" value="WristLeft_movement.true.real.attribute"/>
<parameter key="119" value="HandLeft_movement.true.real.attribute"/>
<parameter key="120" value="ShoulderRight_movement.true.real.attribute"/>
<parameter key="121" value="ElbowRight_movement.true.real.attribute"/>
<parameter key="122" value="WristRight_movement.true.real.attribute"/>
<parameter key="123" value="HandRight_movement.true.real.attribute"/>
<parameter key="124" value="HipLeft_movement.true.real.attribute"/>
<parameter key="125" value="HipRight_movement.true.attribute_value.attribute"/>
<parameter key="126" value="HandTipLeft_movement.true.real.attribute"/>
<parameter key="127" value="ThumbLeft_movement.true.real.attribute"/>
<parameter key="128" value="HandTipRight_movement.true.attribute_value.attribute"/>
<parameter key="129" value="ThumbRight_movement.true.real.attribute"/>
<parameter key="130" value="KneeLeft_movement.true.real.attribute"/>
<parameter key="131" value="AnkleLeft_movement.true.real.attribute"/>
<parameter key="132" value="FootLeft_movement.true.real.attribute"/>
<parameter key="133" value="KneeRight_movement.true.real.attribute"/>
<parameter key="134" value="AnkleRight_movement.true.real.attribute"/>
<parameter key="135" value="FootRight_movement.true.real.attribute"/>
<parameter key="136" value="Neck_angle.true.real.attribute"/>
<parameter key="137" value="Spine_angle.true.real.attribute"/>
<parameter key="138" value="Hip_angle.true.real.attribute"/>
<parameter key="139" value="ShoulderL_angle.true.real.attribute"/>
<parameter key="140" value="ShoulderR_angle.true.real.attribute"/>
<parameter key="141" value="ElbowL_angle.true.real.attribute"/>
<parameter key="142" value="ElbowR_angle.true.real.attribute"/>
<parameter key="143" value="WristL_angle.true.real.attribute"/>
<parameter key="144" value="WristR_angle.true.real.attribute"/>
<parameter key="145" value="HandL_angle.true.real.attribute"/>
<parameter key="146" value="HandR_angle.true.real.attribute"/>
<parameter key="147" value="Happy.true.attribute_value.attribute"/>
<parameter key="148" value="Engaged.true.attribute_value.attribute"/>
<parameter key="149" value="WearingGlasses.true.attribute_value.attribute"/>
<parameter key="150" value="LeftEyeClosed.true.attribute_value.attribute"/>
<parameter key="151" value="RightEyeClosed.true.attribute_value.attribute"/>
<parameter key="152" value="MouthOpen.true.attribute_value.attribute"/>
<parameter key="153" value="MouthMoved.true.attribute_value.attribute"/>
<parameter key="154" value="LookingAway.true.attribute_value.attribute"/>
<parameter key="155" value="FaceYaw.true.attribute_value.attribute"/>
<parameter key="156" value="FacePitch.true.attribute_value.attribute"/>
<parameter key="157" value="FacenRoll.true.attribute_value.attribute"/>
<parameter key="158" value="Talking.true.integer.attribute"/>
<parameter key="159" value="Posture.true.attribute_value.attribute"/>
</list>
</operator>
<operator activated="true" class="generate_id" compatibility="7.4.000" expanded="true" height="82" name="Generate ID" width="90" x="45" y="136"/>
<operator activated="true" class="replace_missing_values" compatibility="7.4.000" expanded="true" height="103" name="Replace Missing Values" width="90" x="45" y="289">
<list key="columns"/>
</operator>
<operator activated="true" class="select_attributes" compatibility="7.4.000" expanded="true" height="82" name="Select Attributes" width="90" x="179" y="289">
<parameter key="attribute_filter_type" value="subset"/>
<parameter key="attributes" value="ElbowL_angle|ElbowR_angle|Hip_angle|Neck_angle|ShoulderL_angle|ShoulderR_angle|Spine_angle|WristR_angle|WristL_angle|HandR_angle|HandL_angle"/>
</operator>
<operator activated="true" class="x_means" compatibility="7.4.000" expanded="true" height="82" name="X-Means" width="90" x="380" y="34"/>
<operator activated="true" class="join" compatibility="7.4.000" expanded="true" height="82" name="Join" width="90" x="514" y="289">
<list key="key_attributes"/>
</operator>
<operator activated="true" class="multiply" compatibility="7.4.000" expanded="true" height="103" name="Multiply" width="90" x="648" y="187"/>
<operator activated="true" class="transition_matrix" compatibility="7.4.000" expanded="true" height="82" name="Transition Matrix" width="90" x="782" y="340">
<parameter key="attribute" value="cluster"/>
</operator>
<operator activated="true" class="converters:matrix_2_example_set" compatibility="0.2.000" expanded="true" height="82" name="Matrix to ExampleSet" width="90" x="782" y="493">
<parameter key="pairwise_list" value="true"/>
</operator>
<operator activated="true" class="extract_prototypes" compatibility="7.4.000" expanded="true" height="82" name="Extract Cluster Prototypes" width="90" x="581" y="34"/>
<operator activated="true" class="python_scripting:execute_python" compatibility="7.2.000" expanded="true" height="103" name="Execute Python (2)" width="90" x="782" y="34">
<parameter key="script" value="import pandas import os import copy import matplotlib.pyplot as plt from scipy import spatial from matplotlib.patches import Ellipse from mpl_toolkits.mplot3d import Axes3D connections = {('Head','Neck'):0.0, ('Neck','SpineMid'):0.0, ('SpineMid','SpineBase'):0.0, ('Neck','ShoulderLeft'):0.3, ('Neck','ShoulderRight'):0.3, ('ShoulderLeft','ElbowLeft'):0.4, ('ShoulderRight','ElbowRight'):0.4, ('ElbowLeft','WristLeft'):0.5, ('ElbowRight','WristRight'):0.5, ('WristLeft','HandLeft'):0.6, ('WristRight','HandRight'):0.6, #('WristLeft','ThumbLeft'):0.7, #('WristRight','ThumbRight'):0.7, #('HandLeft','HandTipLeft'):0.8, #('HandRight','HandTipRight'):0.8, #('SpineBase','HipLeft'):0.0, #('SpineBase','HipRight'):0.0 } def find_rows_kmedoids(data,centers): rows = [] for center_i in range(centers.shape[0]): row = data for col in centers.columns: value = centers.iloc[center_i][col] row = row.loc[(row[col] == value)] if row.shape[0] == 1: break rows.append(row) return rows def find_rows_kmeans(data,centers): # we remove the "unnamed" and "cluster" columns center_cols = list(centers.columns)[1:-1] columns = list(set(data.columns).intersection(center_cols)) tree = spatial.KDTree(data[columns]) rows = [] for center_i in range(centers.shape[0]): row = data similarity,index = tree.query(centers.iloc[center_i][columns]) rows.append(row.loc[(row['id'] == index)]) return rows def save_kinect_centroid(list_rows): fig = plt.figure(figsize=(3, 3*len(list_rows))) for i,df in enumerate(list_rows): ax = fig.add_subplot(len(list_rows),1,i+1, projection='3d') ax.set_xticklabels([]) ax.set_yticklabels([]) ax.set_zticklabels([]) for t,color in connections.items(): a = t[0] b = t[1] x = (df[a+'_X'].values[0], df[b+'_X'].values[0]) y = (df[a+'_Y'].values[0], df[b+'_Y'].values[0]) z = (df[a+'_Z'].values[0], df[b+'_Z'].values[0]) if a == 'Head' and b == 'Neck': ax.plot(x, y, z, color=str(color), solid_capstyle='round', lw=6.0) else: ax.plot(x, y, z, color=str(color), lw=4.0) fig.savefig(os.path.expanduser("~/Desktop/centroid.pdf")) # rm_main is a mandatory function, # the number of arguments has to be the number of input ports (can be none) def rm_main(centers, data): # find complete rows for the cluster centers #rows = find_rows_kmedoids(data,centers) rows = find_rows_kmeans(data,centers) #your code goes here save_kinect_centroid(rows) # connect 2 output ports to see the results return data, centers"/>
</operator>
<operator activated="true" class="transition_graph" compatibility="7.4.000" expanded="true" height="82" name="Transition Graph" width="90" x="782" y="646">
<parameter key="source_attribute" value="First Attribute"/>
<parameter key="target_attribute" value="Second Attribute"/>
<parameter key="strength_attribute" value="Value"/>
</operator>
<connect from_op="Read CSV" from_port="output" to_op="Generate ID" to_port="example set input"/>
<connect from_op="Generate ID" from_port="example set output" to_op="Replace Missing Values" to_port="example set input"/>
<connect from_op="Replace Missing Values" from_port="example set output" to_op="Select Attributes" to_port="example set input"/>
<connect from_op="Select Attributes" from_port="example set output" to_op="X-Means" to_port="example set"/>
<connect from_op="Select Attributes" from_port="original" to_op="Join" to_port="right"/>
<connect from_op="X-Means" from_port="cluster model" to_op="Extract Cluster Prototypes" to_port="model"/>
<connect from_op="X-Means" from_port="clustered set" to_op="Join" to_port="left"/>
<connect from_op="Join" from_port="join" to_op="Multiply" to_port="input"/>
<connect from_op="Multiply" from_port="output 1" to_op="Execute Python (2)" to_port="input 2"/>
<connect from_op="Multiply" from_port="output 2" to_op="Transition Matrix" to_port="example set"/>
<connect from_op="Transition Matrix" from_port="transition matrix" to_op="Matrix to ExampleSet" to_port="matrix"/>
<connect from_op="Matrix to ExampleSet" from_port="example set" to_op="Transition Graph" to_port="example set"/>
<connect from_op="Extract Cluster Prototypes" from_port="example set" to_op="Execute Python (2)" to_port="input 1"/>
<connect from_op="Execute Python (2)" from_port="output 1" to_port="result 1"/>
<connect from_op="Execute Python (2)" from_port="output 2" to_port="result 2"/>
<connect from_op="Transition Graph" from_port="example set" to_port="result 3"/>
<connect from_op="Transition Graph" from_port="transition graph" to_port="result 4"/>
<portSpacing port="source_input 1" spacing="0"/>
<portSpacing port="sink_result 1" spacing="0"/>
<portSpacing port="sink_result 2" spacing="0"/>
<portSpacing port="sink_result 3" spacing="0"/>
<portSpacing port="sink_result 4" spacing="0"/>
<portSpacing port="sink_result 5" spacing="0"/>
</process>
</operator>
</process>2 -
I ended up writing a python script. The input is a dataframe that contains a column named "cluster" and outputs the correct pairwise matrix (that you can can then connect to a transition graph):
import pandas as pd
import numpy as np
# rm_main is a mandatory function,
# the number of arguments has to be the number of input ports (can be none)
def rm_main(data):
# select the column we want to use
column_name = 'cluster'
# get the data
actions = list(data[column_name])
# transform labels into numbers
actions = [str(act) for act in actions]
labels_set = sorted(list(set(actions)))
labels = [labels_set.index(action) for action in actions]
# get the size of the matrix
num_clusters = len(list(set(labels)))
# build the numpy matrix
transitions_matrix = np.zeros((num_clusters, num_clusters))
prev = None
# count the transitions
for lab in labels:
if prev != None:
if not True:
if prev != lab:
transitions_matrix[prev,lab] += 1
else:
transitions_matrix[prev,lab] += 1
prev = lab
# make it a probability matrix
for i in range(num_clusters):
row = transitions_matrix[i,:]
if sum(row) > 0:
transitions_matrix[i,:] = row / sum(row)
for j in range(num_clusters):
transitions_matrix[i,j] = round(transitions_matrix[i,j],3)
matrix = pd.DataFrame(transitions_matrix,
index=labels_set, columns=labels_set)
# building a pairwise matrix
columns_labels = ['First Attribute', 'Second Attribute', 'Value']
num_rows = num_clusters**2
pairwise = pd.DataFrame(index=range(num_rows), columns=columns_labels)
# fill the matrix
index = 0
for col in range(num_clusters):
for row in range(num_clusters):
pairwise.iloc[index][0] = labels_set[col]
pairwise.iloc[index][1] = labels_set[row]
pairwise.iloc[index][2] = matrix.iloc[col][row]
index += 1
pairwise[['Value']] = pairwise[['Value']].apply(pd.to_numeric)
return pairwise3
Answers
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0
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Great, the Converters extension did the trick. Thanks for your help!!
Here's the xml:
<?xml version="1.0" encoding="UTF-8"?><process version="7.4.000">
<context>
<input/>
<output/>
<macros/>
</context>
<operator activated="true" class="process" compatibility="7.4.000" expanded="true" name="Process">
<process expanded="true">
<operator activated="true" class="read_csv" compatibility="7.4.000" expanded="true" height="68" name="Read CSV" width="90" x="45" y="34">
<parameter key="csv_file" value="/Users/schneibe/Dropbox/Windows/Kinect/Group/Default82-0-Kinect-Log-2017-03-27 08-23-20.csv"/>
<parameter key="column_separators" value=","/>
<parameter key="first_row_as_names" value="false"/>
<list key="annotations">
<parameter key="0" value="Name"/>
</list>
<parameter key="encoding" value="UTF-8"/>
<list key="data_set_meta_data_information">
<parameter key="0" value="Timestamp.true.polynominal.attribute"/>
<parameter key="1" value="Session.true.polynominal.attribute"/>
<parameter key="2" value="Index.true.integer.attribute"/>
<parameter key="3" value="BodyID.true.integer.attribute"/>
<parameter key="4" value="SpineBase_X.true.real.attribute"/>
<parameter key="5" value="SpineBase_Y.true.real.attribute"/>
<parameter key="6" value="SpineBase_Z.true.real.attribute"/>
<parameter key="7" value="SpineBase_inferred.true.integer.attribute"/>
<parameter key="8" value="SpineMid_X.true.real.attribute"/>
<parameter key="9" value="SpineMid_Y.true.real.attribute"/>
<parameter key="10" value="SpineMid_Z.true.real.attribute"/>
<parameter key="11" value="SpineMid_inferred.true.integer.attribute"/>
<parameter key="12" value="Neck_X.true.real.attribute"/>
<parameter key="13" value="Neck_Y.true.real.attribute"/>
<parameter key="14" value="Neck_Z.true.real.attribute"/>
<parameter key="15" value="Neck_inferred.true.integer.attribute"/>
<parameter key="16" value="Head_X.true.real.attribute"/>
<parameter key="17" value="Head_Y.true.real.attribute"/>
<parameter key="18" value="Head_Z.true.real.attribute"/>
<parameter key="19" value="Head_inferred.true.integer.attribute"/>
<parameter key="20" value="ShoulderLeft_X.true.real.attribute"/>
<parameter key="21" value="ShoulderLeft_Y.true.real.attribute"/>
<parameter key="22" value="ShoulderLeft_Z.true.real.attribute"/>
<parameter key="23" value="ShoulderLeft_inferred.true.integer.attribute"/>
<parameter key="24" value="ElbowLeft_X.true.real.attribute"/>
<parameter key="25" value="ElbowLeft_Y.true.real.attribute"/>
<parameter key="26" value="ElbowLeft_Z.true.real.attribute"/>
<parameter key="27" value="ElbowLeft_inferred.true.integer.attribute"/>
<parameter key="28" value="WristLeft_X.true.real.attribute"/>
<parameter key="29" value="WristLeft_Y.true.real.attribute"/>
<parameter key="30" value="WristLeft_Z.true.real.attribute"/>
<parameter key="31" value="WristLeft_inferred.true.integer.attribute"/>
<parameter key="32" value="HandLeft_X.true.real.attribute"/>
<parameter key="33" value="HandLeft_Y.true.real.attribute"/>
<parameter key="34" value="HandLeft_Z.true.real.attribute"/>
<parameter key="35" value="HandLeft_inferred.true.integer.attribute"/>
<parameter key="36" value="ShoulderRight_X.true.real.attribute"/>
<parameter key="37" value="ShoulderRight_Y.true.real.attribute"/>
<parameter key="38" value="ShoulderRight_Z.true.real.attribute"/>
<parameter key="39" value="ShoulderRight_inferred.true.integer.attribute"/>
<parameter key="40" value="ElbowRight_X.true.real.attribute"/>
<parameter key="41" value="ElbowRight_Y.true.real.attribute"/>
<parameter key="42" value="ElbowRight_Z.true.real.attribute"/>
<parameter key="43" value="ElbowRight_inferred.true.integer.attribute"/>
<parameter key="44" value="WristRight_X.true.real.attribute"/>
<parameter key="45" value="WristRight_Y.true.real.attribute"/>
<parameter key="46" value="WristRight_Z.true.real.attribute"/>
<parameter key="47" value="WristRight_inferred.true.integer.attribute"/>
<parameter key="48" value="HandRight_X.true.real.attribute"/>
<parameter key="49" value="HandRight_Y.true.real.attribute"/>
<parameter key="50" value="HandRight_Z.true.real.attribute"/>
<parameter key="51" value="HandRight_inferred.true.integer.attribute"/>
<parameter key="52" value="HipLeft_X.true.real.attribute"/>
<parameter key="53" value="HipLeft_Y.true.real.attribute"/>
<parameter key="54" value="HipLeft_Z.true.real.attribute"/>
<parameter key="55" value="HipLeft_inferred.true.integer.attribute"/>
<parameter key="56" value="HipRight_X.true.real.attribute"/>
<parameter key="57" value="HipRight_Y.true.real.attribute"/>
<parameter key="58" value="HipRight_Z.true.real.attribute"/>
<parameter key="59" value="HipRight_inferred.true.integer.attribute"/>
<parameter key="60" value="SpineShoulder_X.true.real.attribute"/>
<parameter key="61" value="SpineShoulder_Y.true.real.attribute"/>
<parameter key="62" value="SpineShoulder_Z.true.real.attribute"/>
<parameter key="63" value="SpineShoulder_inferred.true.integer.attribute"/>
<parameter key="64" value="HandTipLeft_X.true.real.attribute"/>
<parameter key="65" value="HandTipLeft_Y.true.real.attribute"/>
<parameter key="66" value="HandTipLeft_Z.true.real.attribute"/>
<parameter key="67" value="HandTipLeft_inferred.true.integer.attribute"/>
<parameter key="68" value="ThumbLeft_X.true.real.attribute"/>
<parameter key="69" value="ThumbLeft_Y.true.real.attribute"/>
<parameter key="70" value="ThumbLeft_Z.true.real.attribute"/>
<parameter key="71" value="ThumbLeft_inferred.true.integer.attribute"/>
<parameter key="72" value="HandTipRight_X.true.real.attribute"/>
<parameter key="73" value="HandTipRight_Y.true.real.attribute"/>
<parameter key="74" value="HandTipRight_Z.true.real.attribute"/>
<parameter key="75" value="HandTipRight_inferred.true.integer.attribute"/>
<parameter key="76" value="ThumbRight_X.true.real.attribute"/>
<parameter key="77" value="ThumbRight_Y.true.real.attribute"/>
<parameter key="78" value="ThumbRight_Z.true.real.attribute"/>
<parameter key="79" value="ThumbRight_inferred.true.integer.attribute"/>
<parameter key="80" value="KneeLeft_X.true.real.attribute"/>
<parameter key="81" value="KneeLeft_Y.true.real.attribute"/>
<parameter key="82" value="KneeLeft_Z.true.real.attribute"/>
<parameter key="83" value="KneeLeft_inferred.true.integer.attribute"/>
<parameter key="84" value="AnkleLeft_X.true.real.attribute"/>
<parameter key="85" value="AnkleLeft_Y.true.real.attribute"/>
<parameter key="86" value="AnkleLeft_Z.true.real.attribute"/>
<parameter key="87" value="AnkleLeft_inferred.true.integer.attribute"/>
<parameter key="88" value="FootLeft_X.true.real.attribute"/>
<parameter key="89" value="FootLeft_Y.true.real.attribute"/>
<parameter key="90" value="FootLeft_Z.true.real.attribute"/>
<parameter key="91" value="FootLeft_inferred.true.integer.attribute"/>
<parameter key="92" value="KneeRight_X.true.real.attribute"/>
<parameter key="93" value="KneeRight_Y.true.real.attribute"/>
<parameter key="94" value="KneeRight_Z.true.real.attribute"/>
<parameter key="95" value="KneeRight_inferred.true.integer.attribute"/>
<parameter key="96" value="AnkleRight_X.true.real.attribute"/>
<parameter key="97" value="AnkleRight_Y.true.real.attribute"/>
<parameter key="98" value="AnkleRight_Z.true.real.attribute"/>
<parameter key="99" value="AnkleRight_inferred.true.integer.attribute"/>
<parameter key="100" value="FootRight_X.true.real.attribute"/>
<parameter key="101" value="FootRight_Y.true.real.attribute"/>
<parameter key="102" value="FootRight_Z.true.real.attribute"/>
<parameter key="103" value="FootRight_inferred.true.integer.attribute"/>
<parameter key="104" value="HandLeftState.true.polynominal.attribute"/>
<parameter key="105" value="HandLeftStateConfidence.true.polynominal.attribute"/>
<parameter key="106" value="HandRightState.true.polynominal.attribute"/>
<parameter key="107" value="HandRightStateConfidence.true.polynominal.attribute"/>
<parameter key="108" value="Lean_X.true.real.attribute"/>
<parameter key="109" value="Lean_Y.true.real.attribute"/>
<parameter key="110" value="Lean_TrackingState.true.polynominal.attribute"/>
<parameter key="111" value="SpineBase_movement.true.real.attribute"/>
<parameter key="112" value="SpineShoulder_movement.true.attribute_value.attribute"/>
<parameter key="113" value="SpineMid_movement.true.real.attribute"/>
<parameter key="114" value="Neck_movement.true.real.attribute"/>
<parameter key="115" value="Head_movement.true.real.attribute"/>
<parameter key="116" value="ShoulderLeft_movement.true.real.attribute"/>
<parameter key="117" value="ElbowLeft_movement.true.real.attribute"/>
<parameter key="118" value="WristLeft_movement.true.real.attribute"/>
<parameter key="119" value="HandLeft_movement.true.real.attribute"/>
<parameter key="120" value="ShoulderRight_movement.true.real.attribute"/>
<parameter key="121" value="ElbowRight_movement.true.real.attribute"/>
<parameter key="122" value="WristRight_movement.true.real.attribute"/>
<parameter key="123" value="HandRight_movement.true.real.attribute"/>
<parameter key="124" value="HipLeft_movement.true.real.attribute"/>
<parameter key="125" value="HipRight_movement.true.attribute_value.attribute"/>
<parameter key="126" value="HandTipLeft_movement.true.real.attribute"/>
<parameter key="127" value="ThumbLeft_movement.true.real.attribute"/>
<parameter key="128" value="HandTipRight_movement.true.attribute_value.attribute"/>
<parameter key="129" value="ThumbRight_movement.true.real.attribute"/>
<parameter key="130" value="KneeLeft_movement.true.real.attribute"/>
<parameter key="131" value="AnkleLeft_movement.true.real.attribute"/>
<parameter key="132" value="FootLeft_movement.true.real.attribute"/>
<parameter key="133" value="KneeRight_movement.true.real.attribute"/>
<parameter key="134" value="AnkleRight_movement.true.real.attribute"/>
<parameter key="135" value="FootRight_movement.true.real.attribute"/>
<parameter key="136" value="Neck_angle.true.real.attribute"/>
<parameter key="137" value="Spine_angle.true.real.attribute"/>
<parameter key="138" value="Hip_angle.true.real.attribute"/>
<parameter key="139" value="ShoulderL_angle.true.real.attribute"/>
<parameter key="140" value="ShoulderR_angle.true.real.attribute"/>
<parameter key="141" value="ElbowL_angle.true.real.attribute"/>
<parameter key="142" value="ElbowR_angle.true.real.attribute"/>
<parameter key="143" value="WristL_angle.true.real.attribute"/>
<parameter key="144" value="WristR_angle.true.real.attribute"/>
<parameter key="145" value="HandL_angle.true.real.attribute"/>
<parameter key="146" value="HandR_angle.true.real.attribute"/>
<parameter key="147" value="Happy.true.attribute_value.attribute"/>
<parameter key="148" value="Engaged.true.attribute_value.attribute"/>
<parameter key="149" value="WearingGlasses.true.attribute_value.attribute"/>
<parameter key="150" value="LeftEyeClosed.true.attribute_value.attribute"/>
<parameter key="151" value="RightEyeClosed.true.attribute_value.attribute"/>
<parameter key="152" value="MouthOpen.true.attribute_value.attribute"/>
<parameter key="153" value="MouthMoved.true.attribute_value.attribute"/>
<parameter key="154" value="LookingAway.true.attribute_value.attribute"/>
<parameter key="155" value="FaceYaw.true.attribute_value.attribute"/>
<parameter key="156" value="FacePitch.true.attribute_value.attribute"/>
<parameter key="157" value="FacenRoll.true.attribute_value.attribute"/>
<parameter key="158" value="Talking.true.integer.attribute"/>
<parameter key="159" value="Posture.true.attribute_value.attribute"/>
</list>
</operator>
<operator activated="true" class="generate_id" compatibility="7.4.000" expanded="true" height="82" name="Generate ID" width="90" x="45" y="136"/>
<operator activated="true" class="replace_missing_values" compatibility="7.4.000" expanded="true" height="103" name="Replace Missing Values" width="90" x="45" y="289">
<list key="columns"/>
</operator>
<operator activated="true" class="select_attributes" compatibility="7.4.000" expanded="true" height="82" name="Select Attributes" width="90" x="179" y="289">
<parameter key="attribute_filter_type" value="subset"/>
<parameter key="attributes" value="ElbowL_angle|ElbowR_angle|Hip_angle|Neck_angle|ShoulderL_angle|ShoulderR_angle|Spine_angle|WristR_angle|WristL_angle|HandR_angle|HandL_angle"/>
</operator>
<operator activated="true" class="x_means" compatibility="7.4.000" expanded="true" height="82" name="X-Means" width="90" x="380" y="34"/>
<operator activated="true" class="join" compatibility="7.4.000" expanded="true" height="82" name="Join" width="90" x="514" y="289">
<list key="key_attributes"/>
</operator>
<operator activated="true" class="multiply" compatibility="7.4.000" expanded="true" height="103" name="Multiply" width="90" x="648" y="187"/>
<operator activated="true" class="transition_matrix" compatibility="7.4.000" expanded="true" height="82" name="Transition Matrix" width="90" x="782" y="340">
<parameter key="attribute" value="cluster"/>
</operator>
<operator activated="true" class="converters:matrix_2_example_set" compatibility="0.2.000" expanded="true" height="82" name="Matrix to ExampleSet" width="90" x="782" y="493">
<parameter key="pairwise_list" value="true"/>
</operator>
<operator activated="true" class="extract_prototypes" compatibility="7.4.000" expanded="true" height="82" name="Extract Cluster Prototypes" width="90" x="581" y="34"/>
<operator activated="true" class="python_scripting:execute_python" compatibility="7.2.000" expanded="true" height="103" name="Execute Python (2)" width="90" x="782" y="34">
<parameter key="script" value="import pandas import os import copy import matplotlib.pyplot as plt from scipy import spatial from matplotlib.patches import Ellipse from mpl_toolkits.mplot3d import Axes3D connections = {('Head','Neck'):0.0, ('Neck','SpineMid'):0.0, ('SpineMid','SpineBase'):0.0, ('Neck','ShoulderLeft'):0.3, ('Neck','ShoulderRight'):0.3, ('ShoulderLeft','ElbowLeft'):0.4, ('ShoulderRight','ElbowRight'):0.4, ('ElbowLeft','WristLeft'):0.5, ('ElbowRight','WristRight'):0.5, ('WristLeft','HandLeft'):0.6, ('WristRight','HandRight'):0.6, #('WristLeft','ThumbLeft'):0.7, #('WristRight','ThumbRight'):0.7, #('HandLeft','HandTipLeft'):0.8, #('HandRight','HandTipRight'):0.8, #('SpineBase','HipLeft'):0.0, #('SpineBase','HipRight'):0.0 } def find_rows_kmedoids(data,centers): rows = [] for center_i in range(centers.shape[0]): row = data for col in centers.columns: value = centers.iloc[center_i][col] row = row.loc[(row[col] == value)] if row.shape[0] == 1: break rows.append(row) return rows def find_rows_kmeans(data,centers): # we remove the "unnamed" and "cluster" columns center_cols = list(centers.columns)[1:-1] columns = list(set(data.columns).intersection(center_cols)) tree = spatial.KDTree(data[columns]) rows = [] for center_i in range(centers.shape[0]): row = data similarity,index = tree.query(centers.iloc[center_i][columns]) rows.append(row.loc[(row['id'] == index)]) return rows def save_kinect_centroid(list_rows): fig = plt.figure(figsize=(3, 3*len(list_rows))) for i,df in enumerate(list_rows): ax = fig.add_subplot(len(list_rows),1,i+1, projection='3d') ax.set_xticklabels([]) ax.set_yticklabels([]) ax.set_zticklabels([]) for t,color in connections.items(): a = t[0] b = t[1] x = (df[a+'_X'].values[0], df[b+'_X'].values[0]) y = (df[a+'_Y'].values[0], df[b+'_Y'].values[0]) z = (df[a+'_Z'].values[0], df[b+'_Z'].values[0]) if a == 'Head' and b == 'Neck': ax.plot(x, y, z, color=str(color), solid_capstyle='round', lw=6.0) else: ax.plot(x, y, z, color=str(color), lw=4.0) fig.savefig(os.path.expanduser("~/Desktop/centroid.pdf")) # rm_main is a mandatory function, # the number of arguments has to be the number of input ports (can be none) def rm_main(centers, data): # find complete rows for the cluster centers #rows = find_rows_kmedoids(data,centers) rows = find_rows_kmeans(data,centers) #your code goes here save_kinect_centroid(rows) # connect 2 output ports to see the results return data, centers"/>
</operator>
<operator activated="true" class="transition_graph" compatibility="7.4.000" expanded="true" height="82" name="Transition Graph" width="90" x="782" y="646">
<parameter key="source_attribute" value="First Attribute"/>
<parameter key="target_attribute" value="Second Attribute"/>
<parameter key="strength_attribute" value="Value"/>
</operator>
<connect from_op="Read CSV" from_port="output" to_op="Generate ID" to_port="example set input"/>
<connect from_op="Generate ID" from_port="example set output" to_op="Replace Missing Values" to_port="example set input"/>
<connect from_op="Replace Missing Values" from_port="example set output" to_op="Select Attributes" to_port="example set input"/>
<connect from_op="Select Attributes" from_port="example set output" to_op="X-Means" to_port="example set"/>
<connect from_op="Select Attributes" from_port="original" to_op="Join" to_port="right"/>
<connect from_op="X-Means" from_port="cluster model" to_op="Extract Cluster Prototypes" to_port="model"/>
<connect from_op="X-Means" from_port="clustered set" to_op="Join" to_port="left"/>
<connect from_op="Join" from_port="join" to_op="Multiply" to_port="input"/>
<connect from_op="Multiply" from_port="output 1" to_op="Execute Python (2)" to_port="input 2"/>
<connect from_op="Multiply" from_port="output 2" to_op="Transition Matrix" to_port="example set"/>
<connect from_op="Transition Matrix" from_port="transition matrix" to_op="Matrix to ExampleSet" to_port="matrix"/>
<connect from_op="Matrix to ExampleSet" from_port="example set" to_op="Transition Graph" to_port="example set"/>
<connect from_op="Extract Cluster Prototypes" from_port="example set" to_op="Execute Python (2)" to_port="input 1"/>
<connect from_op="Execute Python (2)" from_port="output 1" to_port="result 1"/>
<connect from_op="Execute Python (2)" from_port="output 2" to_port="result 2"/>
<connect from_op="Transition Graph" from_port="example set" to_port="result 3"/>
<connect from_op="Transition Graph" from_port="transition graph" to_port="result 4"/>
<portSpacing port="source_input 1" spacing="0"/>
<portSpacing port="sink_result 1" spacing="0"/>
<portSpacing port="sink_result 2" spacing="0"/>
<portSpacing port="sink_result 3" spacing="0"/>
<portSpacing port="sink_result 4" spacing="0"/>
<portSpacing port="sink_result 5" spacing="0"/>
</process>
</operator>
</process>2 -
One comment: I just realized that you don't get "real" markov chains with this method.
The entire transition matrix sums up to 1:
whereas for a markov chain you would need each column / row to sum up to 1
any idea of a workaround..?
0 -
I ended up writing a python script. The input is a dataframe that contains a column named "cluster" and outputs the correct pairwise matrix (that you can can then connect to a transition graph):
import pandas as pd
import numpy as np
# rm_main is a mandatory function,
# the number of arguments has to be the number of input ports (can be none)
def rm_main(data):
# select the column we want to use
column_name = 'cluster'
# get the data
actions = list(data[column_name])
# transform labels into numbers
actions = [str(act) for act in actions]
labels_set = sorted(list(set(actions)))
labels = [labels_set.index(action) for action in actions]
# get the size of the matrix
num_clusters = len(list(set(labels)))
# build the numpy matrix
transitions_matrix = np.zeros((num_clusters, num_clusters))
prev = None
# count the transitions
for lab in labels:
if prev != None:
if not True:
if prev != lab:
transitions_matrix[prev,lab] += 1
else:
transitions_matrix[prev,lab] += 1
prev = lab
# make it a probability matrix
for i in range(num_clusters):
row = transitions_matrix[i,:]
if sum(row) > 0:
transitions_matrix[i,:] = row / sum(row)
for j in range(num_clusters):
transitions_matrix[i,j] = round(transitions_matrix[i,j],3)
matrix = pd.DataFrame(transitions_matrix,
index=labels_set, columns=labels_set)
# building a pairwise matrix
columns_labels = ['First Attribute', 'Second Attribute', 'Value']
num_rows = num_clusters**2
pairwise = pd.DataFrame(index=range(num_rows), columns=columns_labels)
# fill the matrix
index = 0
for col in range(num_clusters):
for row in range(num_clusters):
pairwise.iloc[index][0] = labels_set[col]
pairwise.iloc[index][1] = labels_set[row]
pairwise.iloc[index][2] = matrix.iloc[col][row]
index += 1
pairwise[['Value']] = pairwise[['Value']].apply(pd.to_numeric)
return pairwise3 -
hi,
could you please help me how we can get this table. means how how can perform transition matrix proability.
thanks
@Bert wrote:One comment: I just realized that you don't get "real" markov chains with this method.
The entire transition matrix sums up to 1:
whereas for a markov chain you would need each column / row to sum up to 1
any idea of a workaround..?
0 -
Could you please explain me how we can get this table
0
Altair Employee
