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--- visual3d:documentation:emg:processing_tools [2024/07/03 17:25] – removed sgranger
+++ visual3d:documentation:emg:processing_tools [2024/07/17 15:45] (current) – created sgranger
@@ Line 1: / Line 1: @@
+====== Processing Tools ======
+==== Introduction ====
+The purpose is to offset trial data to accommodate for any DC shift. Quantifying the EMG background noise based on a "Resting Trial" using the following algorithm:
+Find overall mean of trial:
+if positive, subtract mean from all values to offset overall average to zero
+if negative, add mean to all values to offset overall average to zero.
+Rectify trial around the zero baselines
+Calculate threshold values for each channel of EMG (level of digitized baseline noise).
+Determine noise threshold (i.e., the value determined from the resting EMG values fall below; calculated by passing a ceiling through data at successively higher levels until all data values for the 5 second duration fall below the ceiling.
+==== EMG_Resting_Background ====
+You can remove the background using a Meta-Command (as described below), or you can see [[Visual3D:Documentation:EMG:Filtering:Resting_Background_Noise_Offset|here]] for an example implementing this in a script.
+==== EMG_Resting_Background Meta-Command ====
+The following Meta Command can be Cut-and-Paste into a file named **EMG_Resting_Background.v3m**
+<code>
+! BEGIN_META
+! META_CMD_NAME=EMG_Resting_Background
+! META_PARAM= SIGNAL_NAMES:string::yes
+! META_PARAM= SIGNAL_FOLDER:string::yes
+! META_PARAM= RESULT_FOLDER:string::yes
+! END_META
+Set_Pipeline_Parameter
+/PARAMETER_NAME=FOLDER
+/PARAMETER_VALUE=::SIGNAL_FOLDER
+! /PARAMETER_VALUE_SEARCH_FOR=
+! /PARAMETER_VALUE_REPLACE_WITH=
+! /PARAMETER_VALUE_PREFIX=
+! /PARAMETER_VALUE_APPEND=
+;
+Set_Pipeline_Parameter
+/PARAMETER_NAME=RESULT
+/PARAMETER_VALUE=::RESULT_FOLDER
+! /PARAMETER_VALUE_SEARCH_FOR=
+! /PARAMETER_VALUE_REPLACE_WITH=
+! /PARAMETER_VALUE_PREFIX=
+! /PARAMETER_VALUE_APPEND=
+;
+! ---------------------------------------------------------------
+! Offset trial data to accommodate for any DC shift
+! (find overall mean of trial&ldots;if positive,
+! subtract mean from all values to offset overall average to zero&ldots;
+! if negative, add mean to all values to offset overall average to zero).
+! Rectify trial around the zero baselines
+! (all values set to absolute values).
+! ---------------------------------------------------------------
+For_Each
+/ITERATION_PARAMETER_NAME=INDEX
+/ITEMS=::SIGNAL_NAMES
+;
+Metric_Mean
+/RESULT_METRIC_NAME=_MEAN
+/APPLY_AS_SUFFIX_TO_SIGNAL_NAME=TRUE
+! /RESULT_METRIC_FOLDER=PROCESSED
+/SIGNAL_TYPES=ANALOG
+/SIGNAL_NAMES=::INDEX
+/SIGNAL_FOLDER=::FOLDER
+! /SIGNAL_COMPONENTS=X
+/EVENT_SEQUENCE=
+/EXCLUDE_EVENTS=
+/GENERATE_MEAN_AND_STDDEV=FALSE
+! /APPEND_TO_EXISTING_VALUES=FALSE
+;
+Evaluate_Expression
+/EXPRESSION=ABS(ANALOG&:&:&::FOLDER&:&:&::INDEX&-&METRIC::PROCESSED&:&:&::INDEX&_MEAN)
+/RESULT_NAME=::INDEX
+/RESULT_TYPE=ANALOG
+/RESULT_FOLDER=::RESULT
+;
+End_For_Each
+/ITERATION_PARAMETER_NAME=INDEX
+;
+! ---------------------------------------------------------------
+! Calculated threshold values for each channel of EMG
+! (level of digitized baseline noise).
+! Apply noise threshold (i.e., the value determined from the
+! resting EMG values fall below).  Calculated by passing a
+! ceiling through data at successively higher levels until
+! all data values for the 5 second duration fall below the ceiling.
+! ---------------------------------------------------------------
+Metric_Maximum
+/RESULT_METRIC_NAME=_REST
+/APPLY_AS_SUFFIX_TO_SIGNAL_NAME=TRUE
+/RESULT_METRIC_FOLDER=::RESULT
+/SIGNAL_TYPES=ANALOG
+/SIGNAL_NAMES=
+/SIGNAL_FOLDER=::RESULT
+/SIGNAL_COMPONENTS=X
+/EVENT_SEQUENCE=
+/EXCLUDE_EVENTS=
+/GENERATE_MEAN_AND_STDDEV=FALSE
+! /APPEND_TO_EXISTING_VALUES=FALSE
+/CREATE_GLOBAL_MAXIMUM=TRUE
+;
+</code>
+==== Madonna EMG Remove Background Meta-Command ====
+The following Meta Command removes the background noise from the EMG signals and can be Cut-and-Paste into a file named **Madonna_EMG_Remove_Background.v3m**
+<code>
+! BEGIN_META
+! META_CMD_NAME=Madonna EMG Remove Background
+! META_PARAM= SIGNAL_NAMES:string::yes
+! META_PARAM= SIGNAL_FOLDER:string::yes
+! META_PARAM= RESULT_FOLDER:string::yes
+! META_PARAM= BACKGROUND_FOLDER:string::yes
+! END_META
+Set_Pipeline_Parameter
+/PARAMETER_NAME=FOLDER
+/PARAMETER_VALUE=::SIGNAL_FOLDER
+;
+Set_Pipeline_Parameter
+/PARAMETER_NAME=RESULT
+/PARAMETER_VALUE=::RESULT_FOLDER
+;
+! ---------------------------------------------------------------
+! Remove the EMG background noise
+! ---------------------------------------------------------------
+For_Each
+/ITERATION_PARAMETER_NAME=INDEX
+/ITEMS=::SIGNAL_NAMES
+;
+Evaluate_Expression
+/EXPRESSION=ABS(ANALOG&:&:&::FOLDER&:&:&::INDEX&& - GLOBAL::METRIC&:&:&::BACKGROUND_FOLDER&:&:&::INDEX&_REST_MAX)
+/RESULT_NAME=::INDEX
+/RESULT_TYPE=ANALOG
+/RESULT_FOLDER=::RESULT
+;
+Set_Data_To_New_Values
+/SIGNAL_TYPES=ANALOG
+/SIGNAL_NAMES=::INDEX
+/SIGNAL_FOLDER=::RESULT
+! /SIGNAL_COMPONENTS=ALL_COMPONENTS
+! /RESULT_SUFFIX=
+/RESULT_FOLDER=::RESULT
+! /EVENT_SEQUENCE=
+! /EXCLUDE_EVENTS=
+/START_FRAME=1
+/END_FRAME=EOF
+! /USE_POINT_RATE=TRUE
+/REPLACEMENT_VALUES=0
+/THRESHOLD_HIGH=DATA_NOT_FOUND
+/THRESHOLD_LOW=GLOBAL::METRIC&:&:&::BACKGROUND_FOLDER&:&:&::INDEX&_REST_MAX
+;
+End_For_Each
+/ITERATION_PARAMETER_NAME=INDEX
+;
+</code>
+==== An example Visual3D Pipeline Command to call these Meta-Commands ====
+In this example, some files are TAGGED as REST, EMG, and GAIT.
+<code>
+!Make the Resting Trial the Active File.
+For_Each
+/ITERATION_PARAMETER_NAME=TAGS
+/ITEMS=REST
+;
+Select_Active_File
+/FILE_NAME=::TAGS
+!/QUERY=
+;
+! Calculates resting background by calling the EMG_Resting_Background Meta-Command.
+EMG_Resting_Background
+/SIGNAL_NAMES=LGAS+LGLU+LMED+LTIB+LVAS+RGAS+RGLU+RMED+RTIB+RVAS
+/SIGNAL_FOLDER=EMG_FILTERED
+/RESULT_FOLDER=EMG_BACKGROUND
+;
+End_For_Each
+/ITERATION_PARAMETER_NAME=TAGS
+;
+! This loop will remove the resting background from the signals.
+For_Each
+/ITERATION_PARAMETER_NAME=TAGS
+/ITEMS=EMG+GAIT
+;
+Select_Active_File
+/FILE_NAME=::TAGS
+!/QUERY=
+;
+! Call the EMG_Remove_Background Meta-Command
+EMG_Remove_Background
+/SIGNAL_NAMES=LGAS+LGLU+LMED+LTIB+LVAS+RGAS+RGLU+RMED+RTIB+RVAS
+/SIGNAL_FOLDER=EMG_FILTERED
+/BACKGROUND_FOLDER=EMG_BACKGROUND
+/RESULT_FOLDER=EMG_PROCESSED
+;
+End_For_Each
+/ITERATION_PARAMETER_NAME=TAGS
+;
+</code>