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--- visual3d:documentation:pipeline:signal_commands:signal_management_commands [2024/07/03 17:30] – removed sgranger
+++ visual3d:documentation:pipeline:signal_commands:signal_management_commands [2024/07/17 15:46] (current) – created sgranger
@@ Line 1: / Line 1: @@
+====== Signal Management Commands ======
+==== Contents ====
+  * [[#Signal_Management|1 Signal Management]]
+    * [[#Global_Normalized_Signal_Mean|1.1 Global_Normalized_Signal_Mean]]
+      * [[#Meta-Command_-_Create_Global_Means_For_Left_Right|1.1.1 Meta-Command - Create_Global_Means_For_Left_Right]]
+    * [[#Find_Representative_Signal|1.2 Find Representative Signal]]
+    * [[#Merge_Data|1.3 Merge_Data]]
+    * [[#Copy_Folder|1.4 Copy_Folder]]
+    * [[#Rename_Folder|1.5 Rename_Folder]]
+    * [[#Delete_Folder|1.6 Delete_Folder]]
+    * [[#Remove_Signals|1.7 Remove_Signals]]
+    * [[#Rename_Signals|1.8 Rename_Signals]]
+==== Signal Management ====
+=== Global_Normalized_Signal_Mean ===
+Time normalize a signal (in this case Knee Flexion Angle) between events (RHS to RHS) for Right Knee angles and (LHS to LHS) for Left Knee angles, and compute a GLOBAL mean and Standard Deviation. Note: the Global_Normalized_Signal_Mean command only works on one component at at time for each signal. (You must select either Y, Y or Z as the SIGNAL_COMPONENTS.)
+First add the Global_Normalized_Signal_Mean command to the pipeline. Double click on the command to launch the dialog.
+{{:GMSM_1.jpg}}
+select the RKNEE_ANGLE Signal and the event sequence (e.g RHS to RHS) and select **Add A New Signal**
+{{:GNSM_2.jpg}}
+select the LKNEE_ANGLE Signal and the event sequence (e.g LHS to LHS) and select **Add A New Signal**
+{{:GNSM_3.jpg}}
+Enter the **P2D Result Signal Name** and click **Create Standard Deviation** Button {{:GNSM_4.jpg}}
+When you select **OK** the text representation of the command should be as follows:
+<code>
+Global_Normalized_Signal_Mean
+/SIGNAL_TYPES=LINK_MODEL_BASED+LINK_MODEL_BASED
+/SIGNAL_NAMES=RKNEE_ANGLE+LKNEE_ANGLE
+/SIGNAL_FOLDER=ORIGINAL+ORIGINAL
+/SIGNAL_COMPONENTS=X+X
+/START_LABEL=
+/END_LABEL=
+/EVENT_SEQUENCE= RHS+RHS++LHS+LHS
+! /EXCLUDE_EVENTS=
+/RESULT_NAME=KNEE_FLEXION
+! /RESULT_FOLDER=ORIGINAL
+/NORMALIZE_POINTS=101
+/CREATE_STANDARD_DEVIATION=TRUE
+! /CALCULATE_PER_FILE=FALSE
+;
+</code>
+**Note:** If **CALCULATE_PER_FILE=FALSE** Signals from all active files are used to compute the mean.
+**Note:** If **CALCULATE_PER_FILE=TRUE** The mean value is computed for Signals from each active files. The global mean value is then the mean value of the mean values.
+**Note:** The Output signal is a P2D Signal, which is associated with every file. The resulting signal, therefore, is stored in the GLOBAL_WORKPACE
+== Meta-Command - Create_Global_Means_For_Left_Right ==
+A Meta-Command can be created for processing all 3 components of a number of model based signals using one pipeline command.
+Let the original cmo file contain the following signals: **RANKLE_ANGLE**, **RKNEE_ANGLE**, **RHIP_ANGLE**, **LANKLE_ANGLE**, **LKNEE_ANGLE**, and **LHIP_ANGLE**.
+Let the events for heel strike be labeled **LHS** and **RHS**. The mean signal should be computed from heel strike to heel strike.
+The Pipeline call for the Meta-Command below is:
+<code>
+Create_Global_Means_For_Left_Right
+/TYPE=ANGLE
+/JOINTS=ANKLE+KNEE+HIP
+/START_EVENT=HS
+/END_EVENT=HS
+;
+</code>
+The Meta-Command, which should be placed in the Meta_Command folder within the Plugins folder is as follows:
+<code>
+! BEGIN_META
+! META_CMD_NAME=Create_Global_Means_For_Left_Right
+! META_PARAM= TYPE  : string ::yes
+! META_PARAM= JOINTS  : string ::yes
+! META_PARAM= START_EVENT  : string ::yes
+! META_PARAM= END_EVENT  : string ::yes
+! END_META
+! Create a Global_Normalized_Signal_Mean event for left and right sides with common labels (e.g.RHS and LHS)
+For_Each /ITERATION_PARAMETER_NAME=INDEX1
+/ITEMS=::JOINTS
+;
+For_Each
+/ITERATION_PARAMETER_NAME=INDEX2
+/ITEMS=X+Y+Z
+;
+Global_Normalized_Signal_Mean
+/SIGNAL_TYPES=LINK_MODEL_BASED+LINK_MODEL_BASED
+/SIGNAL_NAMES=R&::INDEX1&_&::TYPE+L&::INDEX1&_&::TYPE
+/SIGNAL_FOLDER=ORIGINAL+ORIGINAL
+/SIGNAL_COMPONENTS=::INDEX2+::INDEX2
+/START_LABEL=R&::START_EVENT+L&::END_EVENT
+/END_LABEL=R&::START_EVENT+L&::END_EVENT
+! /EVENT_SEQUENCE=
+! /EXCLUDE_EVENTS=
+/RESULT_NAME=::INDEX1&_&::TYPE&_&::INDEX2
+! /RESULT_FOLDER=ORIGINAL
+! /NORMALIZE_POINTS=101
+! /CREATE_STANDARD_DEVIATION=FALSE
+! /CALCULATE_PER_FILE=FALSE
+;
+End_For_Each
+/ITERATION_PARAMETER_NAME=INDEX2
+;
+End_For_Each
+/ITERATION_PARAMETER_NAME=INDEX1
+;
+</code>
+=== Find Representative Signal ===
+Find the signal that is most representative of a set of signals. This implementation is based on the following article:
+Shadmehr R and Mussa-Ivaldi FA (1994) **Adaptive Representation of Dynamics during Learning of a Motor Task**. J. Neuroscience 14(5), pp 3208-3224.
+**Note:** that there is an error in the appendix that we have accounted for.
+For example, to find the representative Knee Flexion Angle over the range RHS to RHS.
+<code>
+Find_Representative_Signal
+/SIGNAL_TYPES=LINK_MODEL_BASED
+/SIGNAL_NAMES=RKNEE_ANGLE
+/SIGNAL_FOLDER=ORIGINAL
+/SIGNAL_COMPONENTS=X
+/EVENT_SEQUENCE=RHS+RHS
+! /EXCLUDE_EVENTS=
+! /NORMALIZE_RESULT_POINTS=
+/RESULT_NAME=RKNEE_ANGLE_REP
+! /RESULT_FOLDER=ORIGINAL
+;
+</code>
+=== Merge_Data ===
+Merges data from more than one data name into a single signal either by **APPEND_TO_END** (appending one signal to the end of another signal) or by **MERGE_AS_NEW_COMPONENTS** (treat each original signal as a component of the new signal)
+For example, create a vector from 3 analog signals.
+<code>
+Merge_Data
+/SIGNAL_NAMES=Analog1+Analog2+Analog3
+/SIGNAL_TYPES=ANALOG+ANALOG+ANALOG
+/SIGNAL_FOLDER=ORIGINAL+ORIGINAL+ORIGINAL
+/SIGNAL_COMPONENTS=0+0+0
+/RESULT_NAME=Vector
+/RESULT_TYPE=DERIVED
+/RESULT_FOLDER=PROCESSED
+/MERGE_TYPE=MERGE_AS_NEW_COMPONENTS
+;
+</code>
+**Note:** If the Signal_Components parameter is empty, all components of the signals will be used.
+=== Copy_Folder ===
+Makes a copy of an existing folder. If the new folder already exists, select whether these signals should be overwritten (replaced).
+<code>
+Copy_Folder
+/SIGNAL_TYPE=
+/EXISTING_FOLDER=
+/NEW_FOLDER_NAME=
+/OVERWRITE_EXISTING_SIGNALS=FALSE
+;
+</code>
+=== Rename_Folder ===
+Rename the specified data tree folder.
+<code>
+Rename_Folder
+/SIGNAL_TYPE=
+/EXISTING_FOLDER=
+/NEW_FOLDER_NAME=
+;
+</code>
+=== Delete_Folder ===
+Deletes the specified folder. **Note:** that ORIGINAL folders cannot be deleted.
+<code>
+Delete_Folder
+/SIGNAL_TYPE=
+/FOLDER=
+;
+</code>
+=== Remove_Signals ===
+Remove a signal from the Workspace. **Note:** that Visual3D will not allow the user to delete ORIGINAL signals.
+<code>
+Remove_Signals
+/SIGNAL_TYPES=
+/SIGNAL_NAMES=
+! /SIGNAL_FOLDER=ORIGINAL
+;
+</code>
+For example, remove one Derived signal and one Metric
+<code>
+Remove_Signals
+/SIGNAL_TYPES=DERIVED+METRIC
+/SIGNAL_NAMES=  DERIVED1+METRIC1
+! /SIGNAL_FOLDER=PROCESSED+PROCESSED
+;
+</code>
+=== Rename_Signals ===
+Rename a signal in the Workspace.
+For example, rename a DERIVED signal in all of the ACTIVE files
+<code>
+Rename_Signals
+! /FILE_NAME=
+/SIGNAL_TYPES=DERIVED
+/SIGNAL_NAMES=Derived1
+/SIGNAL_FOLDER=PROCESSED
+/NEW_SIGNAL_NAME=Derived2
+! /APPEND_TO_OLD_SIGNAL_NAME=FALSE
+;
+</code>