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visual3d:tutorials:knowledge_discovery:looking_at_large_public_data_sets [2025/09/09 18:10] – [Inconsistent Subject Prefixes (Stroke Survivors)] wikisysopvisual3d:tutorials:knowledge_discovery:looking_at_large_public_data_sets [2025/09/10 15:13] (current) – [Processing C3Ds into CMZs (Able-Bodied Participants)] wikisysop
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 Below is an explanation of the important sections of the file "convert_subject_prefix_stroke.v3s". Below is an explanation of the important sections of the file "convert_subject_prefix_stroke.v3s".
  
-**Set a pipeline parameter to a list of all dynamic files contained in the "50_Stroke_PiG":**\\ +**Set a pipeline parameter to a list of all dynamic files contained in the "50_Stroke_PiG":**
-''%% Set_Pipeline_Parameter_To_Folder_Path%%''\\ +
-''%%/PARAMETER_NAME=FOLDER%%''\\ +
-''%%! /PARAMETER_VALUE=VISUAL3D_DEFAULT_DATA_FOLDER%%''\\ +
-''%%! /FROM_MOTION_FILE_IN_WORKSPACE=%%''\\ +
-''%%! /PARAMETER_VALUE_SEARCH_FOR=%%''\\ +
-''%%! /PARAMETER_VALUE_REPLACE_WITH=%%''\\ +
-''%%! /PARAMETER_VALUE_APPEND=%%''\\ +
-''%%! /SET_PROMPT=Select a directory%%''\\ +
-''%%! /ALPHABETIZE=TRUE%%''\\ +
-''%%;%%''\\ +
-\\ +
-''%%Set_Pipeline_Parameter_To_List_Of_Files%%''\\ +
-''%%/PARAMETER_NAME=DYNAMIC_FILES%%''\\ +
-''%%/FOLDER=::FOLDER%%''\\ +
-''%%/SEARCH_SUBFOLDERS=TRUE%%''\\ +
-''%%/FILE_MASK=*BWA*.c3d%%''\\ +
-''%%/ALPHABETIZE=FALSE%%''\\ +
-''%%! /RETURN_FOLDER_NAMES=FALSE%%''\\ +
-''%%; %%''\\+
  
 +<code>
 +Set_Pipeline_Parameter_To_Folder_Path
 +/PARAMETER_NAME=FOLDER
 +! /PARAMETER_VALUE=VISUAL3D_DEFAULT_DATA_FOLDER
 +! /FROM_MOTION_FILE_IN_WORKSPACE=
 +! /PARAMETER_VALUE_SEARCH_FOR=
 +! /PARAMETER_VALUE_REPLACE_WITH=
 +! /PARAMETER_VALUE_APPEND=
 +! /SET_PROMPT=Select a directory
 +! /ALPHABETIZE=TRUE
 +;
  
-\\ 
-**Loop through all dynamic files:**\\ 
-''%% For_Each%%''\\ 
-''%%/ITERATION_PARAMETER_NAME=DYNAMIC_FILE%%''\\ 
-''%%! /ITERATION_PARAMETER_COUNT_NAME=%%''\\ 
-''%%/ITEMS=::DYNAMIC_FILES%%''\\ 
-''%%; %%''\\ 
  
 +Set_Pipeline_Parameter_To_List_Of_Files
 +/PARAMETER_NAME=DYNAMIC_FILES
 +/FOLDER=::FOLDER
 +/SEARCH_SUBFOLDERS=TRUE
 +/FILE_MASK=*BWA*.c3d
 +/ALPHABETIZE=FALSE
 +! /RETURN_FOLDER_NAMES=FALSE
 +;
 +</code>
  
-\\ 
-**Open the current file:**\\ 
-''%% File_Open%%''\\ 
-''%%/FILE_NAME=::DYNAMIC_FILE%%''\\ 
-''%%! /FILE_PATH=%%''\\ 
-''%%! /SUFFIX=%%''\\ 
-''%%! /SET_PROMPT=File_Open%%''\\ 
-''%%! /ON_FILE_NOT_FOUND=PROMPT%%''\\ 
-''%%! /FILE_TYPES_ON_PROMPT=%%''\\ 
-''%%; %%''\\ 
  
 +**Loop through all dynamic files:**
 +<code>
 +For_Each
 +/ITERATION_PARAMETER_NAME=DYNAMIC_FILE
 +! /ITERATION_PARAMETER_COUNT_NAME=
 +/ITEMS=::DYNAMIC_FILES
 +;
  
-\\ +</code>
-**Get the Participant ID from PARAMETERS:SUBJECT:NAMES**\\ +
-''%% Set_Pipeline_Parameter_To_Data_Value%%''\\ +
-''%%/SIGNAL_TYPES=PARAMETERS%%''\\ +
-''%%/SIGNAL_FOLDER=SUBJECTS%%''\\ +
-''%%/SIGNAL_NAMES=NAMES%%''\\ +
-''%%! /SIGNAL_COMPONENTS=ALL_COMPONENTS%%''\\ +
-''%%/PARAMETER_NAME=SUBJECT_ID%%''\\ +
-''%%; %%''\\+
  
 +**Open the current file:**
 +<code>
 +File_Open
 +FILE_NAME=::DYNAMIC_FILE
 +! /FILE_PATH=
 +! /SUFFIX=
 +! /SET_PROMPT=File_Open
 +! /ON_FILE_NOT_FOUND=PROMPT
 +! /FILE_TYPES_ON_PROMPT=
 +;
 +</code>
  
-\\ 
-**Get the preceding half of the Participant ID using the STRING_LEFT expression, since all IDs begin with BWA we can hard code the index value:**\\ 
-''%% Set_Pipeline_Parameter_From_Expression%%''\\ 
-''%%/PARAMETER_NAME=LEFT_SUBJECT_ID%%''\\ 
-''%%/EXPRESSION=STRING_LEFT("&::SUBJECT_ID&",3)%%''\\ 
-''%%/AS_INTEGER=FALSE%%''\\ 
-''%%; %%''\\ 
  
 +**Get the Participant ID from PARAMETERS:SUBJECT:NAMES**
 +<code>
 +Set_Pipeline_Parameter_To_Data_Value
 +/SIGNAL_TYPES=PARAMETERS
 +/SIGNAL_FOLDER=SUBJECTS
 +/SIGNAL_NAMES=NAMES
 +! /SIGNAL_COMPONENTS=ALL_COMPONENTS
 +/PARAMETER_NAME=SUBJECT_ID
 +;
 +</code>
  
-\\ +**Get the preceding half of the Participant ID using the STRING_LEFT expression, since all IDs begin with BWA we can hard code the index value:** 
-**Get the length of the participant id using the STRING_LENGTH expression:**\\ +<code> 
-''%% Set_Pipeline_Parameter_From_Expression%%''\\ +Set_Pipeline_Parameter_From_Expression 
-''%%/PARAMETER_NAME=SUBJECT_ID_LENGTH%%''\\ +PARAMETER_NAME=LEFT_SUBJECT_ID 
-''%%/EXPRESSION=STRING_LENGTH("&::SUBJECT_ID&")%%''\\ +EXPRESSION=STRING_LEFT("&::SUBJECT_ID&",3) 
-''%%! /AS_INTEGER=TRUE%%''\\ +/AS_INTEGER=FALSE 
-''%%; %%''\\+; 
 +</code>
  
  
-\\ +**Get the length of the participant id using the STRING_LENGTH expression:** 
-**Get the index of the dash using the STRING_FIND expression**\\ +<code>
-''%% Set_Pipeline_Parameter_From_Expression%%''\\ +
-''%%/PARAMETER_NAME=DASH_INDEX%%''\\ +
-''%%/EXPRESSION=STRING_FIND("&::SUBJECT_ID&","-",0)%%''\\ +
-''%%! /AS_INTEGER=TRUE%%''\\ +
-''%%; %%''+
  
-\\ +Set_Pipeline_Parameter_From_Expression 
-**Subtract the DASH_INDEX from SUBJECT_ID_LENGTH to get the negative index of the dash, subtract that value by one to get the value needed for STRING_RIGHT (the negative index of the character immediately following the dash):**\\ +/PARAMETER_NAME=SUBJECT_ID_LENGTH 
-''%% Set_Pipeline_Parameter_From_Expression%%''\\ +/EXPRESSION=STRING_LENGTH("&::SUBJECT_ID&") 
-''%%/PARAMETER_NAME=RIGHT_SUBJECT_ID%%''\\ +! /AS_INTEGER=TRUE 
-''%%/EXPRESSION=STRING_RIGHT("&::SUBJECT_ID&",&::DASH_NEGATIVE_INDEX&)%%''\\ +; 
-''%%!/AS_INTEGER=FALSE%%''\\ +</code>
-''%%; %%''\\+
  
 +**Get the index of the dash using the STRING_FIND expression**
 +<code>
  
-\\ +Set_Pipeline_Parameter_From_Expression 
-**Get the characters in the subject id following the dash using STRING_RIGHT:**\\ +/PARAMETER_NAME=DASH_INDEX 
-''%% Set_Pipeline_Parameter_From_Expression%%''\\ +/EXPRESSION=STRING_FIND("&::SUBJECT_ID&","-",0) 
-''%%/PARAMETER_NAME=RIGHT_SUBJECT_ID%%''\\ +! /AS_INTEGER=TRUE 
-''%%/EXPRESSION=STRING_RIGHT("&::SUBJECT_ID&",&::DASH_NEGATIVE_INDEX&)%%''\\ +;
-''%%!/AS_INTEGER=FALSE%%''\\ +
-''%%; %%''\\+
  
 +</code>
  
-\\ +**Subtract the DASH_INDEX from SUBJECT_ID_LENGTH to get the negative index of the dash, subtract that value by one to get the value needed for STRING_RIGHT (the negative index of the character immediately following the dash):**
-**Concatenate LEFT_SUBJECT_ID and RIGHT_SUBJECT_ID with an underscore between them:**\\ +
-''%% Set_Pipeline_Parameter%%''\\ +
-''%%/PARAMETER_NAME=SUBJECT_ID_CONVERTED%%''\\ +
-''%%/PARAMETER_VALUE=_%%''\\ +
-''%%! /PARAMETER_VALUE_SEARCH_FOR=%%''\\ +
-''%%! /PARAMETER_VALUE_REPLACE_WITH=%%''\\ +
-''%%/PARAMETER_VALUE_PREFIX=::LEFT_SUBJECT_ID%%''\\ +
-''%%/PARAMETER_VALUE_APPEND=::RIGHT_SUBJECT_ID%%''\\ +
-''%%! /MULTI_PASS=FALSE%%''\\ +
-''%%; %%''\\+
  
 +<code>
  
-\\ +Set_Pipeline_Parameter_From_Expression 
-**Get a list of all target names**\\ +PARAMETER_NAME=RIGHT_SUBJECT_ID 
-''%% Set_Pipeline_Parameter_To_List_Of_Signal_Names%%''\\ +/EXPRESSION=STRING_RIGHT("&::SUBJECT_ID&",&::DASH_NEGATIVE_INDEX&) 
-''%%/PARAMETER_NAME=TARGETS%%''\\ +!/AS_INTEGER=FALSE 
-''%%/SIGNAL_TYPES=TARGET%%''\\ +;
-''%%SIGNAL_FOLDER=ORIGINAL%%''\\ +
-''%%; %%''\\+
  
 +</code>
  
-\\ +**Get the characters in the subject id following the dash using STRING_RIGHT:**
-**Using the updated subject ID and the list of target names, use the modify participants parameters pipeling function the add the neeeded subject prefixes, ensuring OVERWRITE_C3D_FILE is set to true so the changes are preserved:**\\ +
-''%% Modify_C3D_Subjects_Parameters%%''\\ +
-''%%! /INCLUDE_CAL_FILE=TRUE%%''\\ +
-''%%/IS_STATIC=0%%''\\ +
-''%%/SUBJECTS_USES_PREFIXES=1%%''\\ +
-''%%! /REMOVE_EXISTING_LABEL_PREFIXES=TRUE%%''\\ +
-''%%! /REMOVE_EXISTING_PREFIX_PARAMETERS=FALSE%%''\\ +
-''%%/SUBJECTS_LABEL_PREFIXES=::SUBJECT_ID_CONVERTED%%''\\ +
-''%%/PREFIX_MARKERS=::TARGETS%%''\\ +
-''%%! /PREFIX_ROTATIONS=%%''\\ +
-''%%! /PREFIX_C3D_PARAMETERS=%%''\\ +
-''%%! /C3D_PARAMETER_GROUPS=SUBJECTS%%''\\ +
-''%%! /MARKER_SETS=%%''\\ +
-''%%/SUBJECTS_NAMES=::SUBJECT_ID_CONVERTED%%''\\ +
-''%%! /SUBJECTS_DISPLAY_SETS=%%''\\ +
-''%%! /SUBJECTS_MODELS=%%''\\ +
-''%%! /SUBJECTS_MODEL_PARAMS=%%''\\ +
-''%%/OVERWRITE_C3D_FILE=1%%''\\ +
-''%%; %%''\\+
  
 +<code>
 +Set_Pipeline_Parameter_From_Expression
 +/PARAMETER_NAME=RIGHT_SUBJECT_ID
 +/EXPRESSION=STRING_RIGHT("&::SUBJECT_ID&",&::DASH_NEGATIVE_INDEX&)
 +!/AS_INTEGER=FALSE
 +;
  
-\\ +</code> 
-**Clear the workspace to preserve memory, and then close the loop:**\\ + 
-''%% File_New%%''\\ + 
-''%%;%%''\\ +**Concatenate LEFT_SUBJECT_ID and RIGHT_SUBJECT_ID with an underscore between them:** 
-\\ +<code> 
-''%%End the loop%%''\\ +Set_Pipeline_Parameter 
-''%%End_For_Each%%''\\ +/PARAMETER_NAME=SUBJECT_ID_CONVERTED 
-''%%/ITERATION_PARAMETER_NAME=DYNAMIC_FILE%%''\\ +/PARAMETER_VALUE=_ 
-''%%; %%''+! /PARAMETER_VALUE_SEARCH_FOR= 
 +! /PARAMETER_VALUE_REPLACE_WITH= 
 +/PARAMETER_VALUE_PREFIX=::LEFT_SUBJECT_ID 
 +/PARAMETER_VALUE_APPEND=::RIGHT_SUBJECT_ID 
 +! /MULTI_PASS=FALSE 
 +;
  
 +</code>
 +
 +**Get a list of all target names**
 +<code>
 +Set_Pipeline_Parameter_To_List_Of_Signal_Names
 +/PARAMETER_NAME=TARGETS
 +/SIGNAL_TYPES=TARGET
 +/SIGNAL_FOLDER=ORIGINAL
 +;
 +</code>
 +
 +**Using the updated subject ID and the list of target names, use the modify participants parameters pipeline function the add the needed subject prefixes, ensuring OVERWRITE_C3D_FILE is set to true so the changes are preserved:**
 +<code>
 +Modify_C3D_Subjects_Parameters
 +! /INCLUDE_CAL_FILE=TRUE
 +/IS_STATIC=0
 +/SUBJECTS_USES_PREFIXES=1
 +! /REMOVE_EXISTING_LABEL_PREFIXES=TRUE
 +! /REMOVE_EXISTING_PREFIX_PARAMETERS=FALSE
 +/SUBJECTS_LABEL_PREFIXES=::SUBJECT_ID_CONVERTED
 +/PREFIX_MARKERS=::TARGETS
 +! /PREFIX_ROTATIONS=
 +! /PREFIX_C3D_PARAMETERS=
 +! /C3D_PARAMETER_GROUPS=SUBJECTS
 +! /MARKER_SETS=
 +/SUBJECTS_NAMES=::SUBJECT_ID_CONVERTED
 +! /SUBJECTS_DISPLAY_SETS=
 +! /SUBJECTS_MODELS=
 +! /SUBJECTS_MODEL_PARAMS=
 +/OVERWRITE_C3D_FILE=1
 +;
 +
 +</code>
 +
 +**Clear the workspace to preserve memory, and then close the loop:**
 +
 +<code>
 + File_New
 +;
 +</code>
 +
 +**End the loop**
 +<code>
 +End_For_Each
 +/ITERATION_PARAMETER_NAME=DYNAMIC_FILE
 +;
 +</code>
 ==== Inconsistent Subject Prefixes (Able Bodied) ==== ==== Inconsistent Subject Prefixes (Able Bodied) ====
  
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 \\ \\
 **Using the modify C3D subjects parameters pipeline function clear the participant prefixes from the files, set OVERWRITE_C3D_FILE to true to ensure the changes are preserved, keep all other parameters at their default value:**\\ **Using the modify C3D subjects parameters pipeline function clear the participant prefixes from the files, set OVERWRITE_C3D_FILE to true to ensure the changes are preserved, keep all other parameters at their default value:**\\
-''%% Modify_C3D_Subjects_Parameters%%''\\ + 
-''%%! /INCLUDE_CAL_FILE=TRUE%%''\\ +<code> 
-''%%! /IS_STATIC=%%''\\ +Modify_C3D_Subjects_Parameters 
-''%%! /SUBJECTS_USES_PREFIXES=%%''\\ +! /INCLUDE_CAL_FILE=TRUE 
-''%%! /REMOVE_EXISTING_LABEL_PREFIXES=TRUE%%''\\ +! /IS_STATIC= 
-''%%! /REMOVE_EXISTING_PREFIX_PARAMETERS=FALSE%%''\\ +! /SUBJECTS_USES_PREFIXES= 
-''%%! /SUBJECTS_LABEL_PREFIXES=%%''\\ +! /REMOVE_EXISTING_LABEL_PREFIXES=TRUE 
-''%%! /PREFIX_MARKERS=%%''\\ +! /REMOVE_EXISTING_PREFIX_PARAMETERS=FALSE 
-''%%! /PREFIX_ROTATIONS=%%''\\ +! /SUBJECTS_LABEL_PREFIXES= 
-''%%! /PREFIX_C3D_PARAMETERS=%%''\\ +! /PREFIX_MARKERS= 
-''%%! /C3D_PARAMETER_GROUPS=SUBJECTS%%''\\ +! /PREFIX_ROTATIONS= 
-''%%! /MARKER_SETS=%%''\\ +! /PREFIX_C3D_PARAMETERS= 
-''%%! /SUBJECTS_NAMES=%%''\\ +! /C3D_PARAMETER_GROUPS=SUBJECTS 
-''%%! /SUBJECTS_DISPLAY_SETS=%%''\\ +! /MARKER_SETS= 
-''%%! /SUBJECTS_MODELS=%%''\\ +! /SUBJECTS_NAMES= 
-''%%! /SUBJECTS_MODEL_PARAMS=%%''\\ +! /SUBJECTS_DISPLAY_SETS= 
-''%%/OVERWRITE_C3D_FILE=TRUE%%''\\ +! /SUBJECTS_MODELS= 
-''%%; %%''\\+! /SUBJECTS_MODEL_PARAMS= 
 +/OVERWRITE_C3D_FILE=TRUE 
 +; 
 + 
 +</code>
  
  
Line 261: Line 287:
 \\ \\
 **Set a pipeline parameter to the current folder path**\\ **Set a pipeline parameter to the current folder path**\\
-''%% Set_Pipeline_Parameter_To_Folder_Path%%''\\ 
-''%%/PARAMETER_NAME=FOLDER%%''\\ 
-''%%/PARAMETER_VALUE=%%''\\ 
-''%%! /PARAMETER_VALUE_SEARCH_FOR=%%''\\ 
-''%%! /PARAMETER_VALUE_REPLACE_WITH=%%''\\ 
-''%%! /PARAMETER_VALUE_APPEND=%%''\\ 
-''%%; %%''\\ 
  
 +<code>
 +Set_Pipeline_Parameter_To_Folder_Path
 +/PARAMETER_NAME=FOLDER
 +/PARAMETER_VALUE=
 +! /PARAMETER_VALUE_SEARCH_FOR=
 +! /PARAMETER_VALUE_REPLACE_WITH=
 +! /PARAMETER_VALUE_APPEND=
 +; 
 +</code>
  
 \\ \\
 **Get a list of all folders within the 50_StrokePiG folder:**\\ **Get a list of all folders within the 50_StrokePiG folder:**\\
-''%% Set_Pipeline_Parameter_To_List_Of_Files%%''\\ +<code> 
-''%%/PARAMETER_NAME=Folders%%''\\ +Set_Pipeline_Parameter_To_List_Of_Files 
-''%%/FOLDER=::FOLDER%%''\\ +/PARAMETER_NAME=Folders 
-''%%/SEARCH_SUBFOLDERS=TRUE%%''\\ +/FOLDER=::FOLDER 
-''%%/FILE_MASK=*.c3d%%''\\ +/SEARCH_SUBFOLDERS=TRUE 
-''%%! /ALPHABETIZE=TRUE%%''\\ +/FILE_MASK=*.c3d 
-''%%/RETURN_FOLDER_NAMES=TRUE%%''\\ +! /ALPHABETIZE=TRUE 
-''%%; %%''\\ +/RETURN_FOLDER_NAMES=TRUE 
 +; 
 +</code>
  
 \\ \\
 **Loop through the folders:**\\ **Loop through the folders:**\\
-''%% For_Each%%''\\ +<code> 
-''%%/ITERATION_PARAMETER_NAME=sub_folder%%''\\ +For_Each 
-''%%! /ITERATION_PARAMETER_COUNT_NAME=%%''\\ +/ITERATION_PARAMETER_NAME=sub_folder 
-''%%/ITEMS=::Folders%%''\\ +! /ITERATION_PARAMETER_COUNT_NAME= 
-''%%; %%''\\ +/ITEMS=::Folders 
 +; 
 +</code>
  
 \\ \\
 **Calibration files are prefixed with TVC, set a pipeline parameter to all C3D files that start with TVC (there should only be one in each folder):**\\ **Calibration files are prefixed with TVC, set a pipeline parameter to all C3D files that start with TVC (there should only be one in each folder):**\\
-''%% Set_Pipeline_Parameter_To_List_Of_Files%%''\\ +<code> 
-''%%/PARAMETER_NAME=SUBFOLDER_CALIBRATION%%''\\ +Set_Pipeline_Parameter_To_List_Of_Files 
-''%%/FOLDER=::sub_folder%%''\\ +/PARAMETER_NAME=SUBFOLDER_CALIBRATION 
-''%%! /SEARCH_SUBFOLDERS=FALSE%%''\\ +/FOLDER=::sub_folder 
-''%%/FILE_MASK=TVC*.c3d%%''\\ +! /SEARCH_SUBFOLDERS=FALSE 
-''%%! /ALPHABETIZE=TRUE%%''\\ +/FILE_MASK=TVC*.c3d 
-''%%! /RETURN_FOLDER_NAMES=FALSE%%''\\ +! /ALPHABETIZE=TRUE 
-''%%; %%''\\ +! /RETURN_FOLDER_NAMES=FALSE 
 +; 
 +</code>
  
 \\ \\
 **Start a new workspace:**\\ **Start a new workspace:**\\
-''%% File_New%%''\\ +<code> 
-''%%; %%''\\ +File_New 
 +; 
 +</code>
  
 \\ \\
 **Open all dynamic files within the current folder:**\\ **Open all dynamic files within the current folder:**\\
-''%% File_Open%%''\\ +<code> 
-''%%/FILE_NAME=::sub_folder&BWA*.c3d%%''\\ +File_Open 
-''%%! /FILE_PATH=%%''\\ +/FILE_NAME=::sub_folder&BWA*.c3d 
-''%%! /SUFFIX=%%''\\ +! /FILE_PATH= 
-''%%! /SET_PROMPT=File_Open%%''\\ +! /SUFFIX= 
-''%%/ON_FILE_NOT_FOUND=FAIL%%''\\ +! /SET_PROMPT=File_Open 
-''%%! /FILE_TYPES_ON_PROMPT=%%''\\ +/ON_FILE_NOT_FOUND=FAIL 
-''%%; %%''\\ +! /FILE_TYPES_ON_PROMPT= 
 +;  
 +</code>
  
 \\ \\
 **Set all dynamic files to active:**\\ **Set all dynamic files to active:**\\
-''%% Select_Active_File%%''\\ +<code> 
-''%%/FILE_NAME=::sub_folder&BWA*.c3d%%''\\ +Select_Active_File 
-''%%! /QUERY=%%''\\ +/FILE_NAME=::sub_folder&BWA*.c3d 
-''%%! /SUBJECT_TAGS=NO_SUBJECT%%''\\ +! /QUERY= 
-''%%; %%''\\+! /SUBJECT_TAGS=NO_SUBJECT 
 +;  
 +</code>
  
  
 \\ \\
 **Save all the necessary metrics from PARAMETERS:PROCESSING into pipeline parameters:**\\ **Save all the necessary metrics from PARAMETERS:PROCESSING into pipeline parameters:**\\
-''%% Set_Pipeline_Parameter_To_Data_Value%%''\\ +<code> 
-''%%/SIGNAL_TYPES= PARAMETERS%%''\\ +Set_Pipeline_Parameter_To_Data_Value 
-''%%/SIGNAL_FOLDER= PROCESSING%%''\\ +/SIGNAL_TYPES= PARAMETERS 
-''%%/SIGNAL_NAMES= Bodymass%%''\\ +/SIGNAL_FOLDER= PROCESSING 
-''%%! /SIGNAL_COMPONENTS=ALL_COMPONENTS%%''\\ +/SIGNAL_NAMES= Bodymass 
-''%%/PARAMETER_NAME= mass%%''\\ +! /SIGNAL_COMPONENTS=ALL_COMPONENTS 
-''%%;%%''\\ +/PARAMETER_NAME= mass 
-//''%%... see attached pipeline for full list of commands ...%%''//''%% %%''\\+; 
 + 
 +... see attached pipeline for full list of commands ... 
 +</code>
  
  
-\\ 
 **Visual 3Ds expected unit of measurement is meters so the knee widths, ankle widths and height need to be converted from mm to m:**\\ **Visual 3Ds expected unit of measurement is meters so the knee widths, ankle widths and height need to be converted from mm to m:**\\
-''%% Set_Pipeline_Parameter_From_Expression%%''\\ +<code> 
-''%%/PARAMETER_NAME=height%%''\\ +Set_Pipeline_Parameter_From_Expression 
-''%%/EXPRESSION=&::height&/1000.0%%''\\ +/PARAMETER_NAME=height 
-''%%/AS_INTEGER=False%%''\\ +/EXPRESSION=&::height&/1000.0 
-''%%;%%''\\ +/AS_INTEGER=False 
-//''%%... see attached pipeline for full list of commands ...%%''//''%% %%''\\+; 
 + 
 +... see attached pipeline for full list of commands ... 
 +</code>
  
  
-\\ 
 **Get the subject ID from PARAMETERS:SUBJECTS and save it to a pipeline parameter:**\\ **Get the subject ID from PARAMETERS:SUBJECTS and save it to a pipeline parameter:**\\
-''%% Set_Pipeline_Parameter_To_Data_Value%%''\\ +<code> 
-''%%/SIGNAL_TYPES=PARAMETERS%%''\\ +Set_Pipeline_Parameter_To_Data_Value 
-''%%/SIGNAL_FOLDER=SUBJECTS%%''\\ +/SIGNAL_TYPES=PARAMETERS 
-''%%/SIGNAL_NAMES=NAMES%%''\\ +/SIGNAL_FOLDER=SUBJECTS 
-''%%! /SIGNAL_COMPONENTS=ALL_COMPONENTS%%''\\ +/SIGNAL_NAMES=NAMES 
-''%%/PARAMETER_NAME=SUB_NAME%%''\\ +! /SIGNAL_COMPONENTS=ALL_COMPONENTS 
-''%%; %%''\\ +/PARAMETER_NAME=SUB_NAME 
 +; 
 +</code>
  
 \\ \\
 **Create a hybrid model using the calibration file:**\\ **Create a hybrid model using the calibration file:**\\
-''%% Create_Hybrid_Model%%''\\ +<code> 
-''%%/CALIBRATION_FILE=::SUBFOLDER_CALIBRATION%%''\\ +Create_Hybrid_Model 
-''%%! /RANGE=ALL_FRAMES%%''\\ +/CALIBRATION_FILE=::SUBFOLDER_CALIBRATION 
-''%%; %%''\\ +! /RANGE=ALL_FRAMES 
 +; 
 +</code>
  
 \\ \\
 **Apply the model template:**\\ **Apply the model template:**\\
-''%% Apply_Model_Template%%''\\ +<code> 
-''%%/CALIBRATION_FILE=::SUBFOLDER_CALIBRATION%%''\\ +Apply_Model_Template 
-''%%/SUBJECT_PREFIX=::SUB_NAME&:%%''\\ +/CALIBRATION_FILE=::SUBFOLDER_CALIBRATION 
-''%%/MODEL_TEMPLATE=!!! SET PATH TO STROKE MODEL TEMPLATE !!!%%''\\ +/SUBJECT_PREFIX=::SUB_NAME&: 
-''%%! /SET_PROMPT=Open model file%%''\\ +/MODEL_TEMPLATE=!!! SET PATH TO STROKE MODEL TEMPLATE !!! 
-''%%! /VIEW_BUILDMODEL_RESULTS=2%%''\\ +! /SET_PROMPT=Open model file 
-''%%! /MISSING_TARGET_MESSAGE=FALSE%%''\\ +! /VIEW_BUILDMODEL_RESULTS=2 
-''%%; %%''\\ +! /MISSING_TARGET_MESSAGE=FALSE 
 +; 
 +</code>
  
 \\ \\
 **Set all the necessary model metrics and recalculate the model:**\\ **Set all the necessary model metrics and recalculate the model:**\\
-''%% Set_Model_Metric%%''\\ +<code> 
-''%%! /CALIBRATION_FILE=%%''\\ +Set_Model_Metric 
-''%%/METRIC_NAME= Mass%%''\\ +! /CALIBRATION_FILE= 
-''%%/METRIC_VALUE= ::mass%%''\\ +/METRIC_NAME= Mass 
-''%%! /SUBJECT=%%''\\ +/METRIC_VALUE= ::mass 
-''%%;%%''\\ +! /SUBJECT= 
-//''%%... See the attached pipeline for full list of commands ...%%''//''%% %%''\\+; 
 + 
 +... See the attached pipeline for full list of commands ... 
 +</code>
  
  
 \\ \\
 **Assign the model to the dynamic files:**\\ **Assign the model to the dynamic files:**\\
-''%% Assign_Model_File%%''\\ +<code> 
-''%%/CALIBRATION_FILE=::SUBFOLDER_CALIBRATION%%''\\ +Assign_Model_File 
-''%%/MOTION_FILE_NAMES=::sub_folder&BWA*.c3d%%''\\ +/CALIBRATION_FILE=::SUBFOLDER_CALIBRATION 
-''%%! /REMOVE_EXISTING_ASSIGNMENTS=FALSE%%''\\ +/MOTION_FILE_NAMES=::sub_folder&BWA*.c3d 
-''%%; %%''\\+! /REMOVE_EXISTING_ASSIGNMENTS=FALSE 
 +; 
 +</code>
  
  
 \\ \\
 **Set all files to active:**\\ **Set all files to active:**\\
-''%% Select_Active_File%%''\\ +<code> 
-''%%/FILE_NAME= ALL_FILES%%''\\ +Select_Active_File 
-''%%! /QUERY=%%''\\ +/FILE_NAME= ALL_FILES 
-''%%! /SUBJECT_TAGS=NO_SUBJECT%%''\\ +! /QUERY= 
-''%%; %%''\\ +! /SUBJECT_TAGS=NO_SUBJECT 
 +;  
 +</code>
  
 \\ \\
 **Filter and Interpolate available data**\\ **Filter and Interpolate available data**\\
-''%% %%''//''%%...See attached pipeline for examples of computation commands ...%%''//''%% %%''+<code> 
 +...See attached pipeline for examples of computation commands ... 
 +</code>
  
 \\ \\
 **Calculate Gait Events through the use of Kinematic signals**\\ **Calculate Gait Events through the use of Kinematic signals**\\
-''%% %%''//''%%...See attached pipeline for examples of computation commands ...%%''//''%% %%'' +<code> 
 +...See attached pipeline for examples of computation commands ... 
 +</code>
 \\ \\
  
Line 425: Line 476:
 \\ \\
 **Run all desired computations and then save the workspace to a CMZ using the subject ID as the file name and end the loop**\\ **Run all desired computations and then save the workspace to a CMZ using the subject ID as the file name and end the loop**\\
-''%% %%''//''%%...See attached pipeline for examples of computation commands ...%%''//\\ +<code> 
-\\ +..See attached pipeline for examples of computation commands ... 
-''%%File_Save_As%%''\\ + 
-''%%/FILE_NAME=::SUB_NAME%%''\\ +File_Save_As 
-''%%/FOLDER=::sub_folder%%''\\ +/FILE_NAME=::SUB_NAME 
-''%%! /SET_PROMPT=Save CMZ file as%%''\\ +/FOLDER=::sub_folder 
-''%%! /SAVE_EMBEDDED_GRAPHICS=FALSE%%''\\ +! /SET_PROMPT=Save CMZ file as 
-''%%! /CREATE_FOLDER_PATH=FALSE%%''\\ +! /SAVE_EMBEDDED_GRAPHICS=FALSE 
-''%%;%%''\\ +! /CREATE_FOLDER_PATH=FALSE 
-\\ +; 
-''%%End_For_Each%%''\\ +
-''%%/ITERATION_PARAMETER_NAME= sub_folder%%''\\ +
-''%%; %%''+
  
 +End_For_Each
 +/ITERATION_PARAMETER_NAME= sub_folder
 +;
 +</code>
 ==== Processing C3Ds into CMZs (Able-Bodied Participants) ==== ==== Processing C3Ds into CMZs (Able-Bodied Participants) ====
  
Line 447: Line 500:
  
 Run the pipeline **process_c3ds_healthy.v3s**, and select the folder containing the able-bodied participants (138_HealthyPiG_10.05) when prompted. Run the pipeline **process_c3ds_healthy.v3s**, and select the folder containing the able-bodied participants (138_HealthyPiG_10.05) when prompted.
- 
  
 \\ \\
 **Set a pipeline parameter to 0, this will be used for the naming of the CMZ file. The value will be iterated within the loop:**\\ **Set a pipeline parameter to 0, this will be used for the naming of the CMZ file. The value will be iterated within the loop:**\\
-''%% Set_Pipeline_Parameter%%''\\ +<code> 
-''%%/PARAMETER_NAME=SUB_NUM%%''\\ +Set_Pipeline_Parameter 
-''%%/PARAMETER_VALUE=0%%''\\ +/PARAMETER_NAME=SUB_NUM 
-''%%! /PARAMETER_VALUE_SEARCH_FOR=%%''\\ +/PARAMETER_VALUE=0 
-''%%! /PARAMETER_VALUE_REPLACE_WITH=%%''\\ +! /PARAMETER_VALUE_SEARCH_FOR= 
-''%%! /PARAMETER_VALUE_PREFIX=%%''\\ +! /PARAMETER_VALUE_REPLACE_WITH= 
-''%%! /PARAMETER_VALUE_APPEND=%%''\\ +! /PARAMETER_VALUE_PREFIX= 
-''%%! /MULTI_PASS=FALSE%%''\\ +! /PARAMETER_VALUE_APPEND= 
-''%%; %%''\\ +! /MULTI_PASS=FALSE 
 +; 
 +</code>
  
 \\ \\
 **Set a pipeline parameter to a list of folders containing C3Ds within the 138_Healthy_PiG_10.05 folder:**\\ **Set a pipeline parameter to a list of folders containing C3Ds within the 138_Healthy_PiG_10.05 folder:**\\
-\\ +<code> 
-''%%Set_Pipeline_Parameter_To_Folder_Path%%''\\ +Set_Pipeline_Parameter_To_Folder_Path 
-''%%/PARAMETER_NAME=FOLDER%%''\\ +/PARAMETER_NAME=FOLDER 
-''%%! /PARAMETER_VALUE=VISUAL3D_DEFAULT_DATA_FOLDER%%''\\ +! /PARAMETER_VALUE=VISUAL3D_DEFAULT_DATA_FOLDER 
-''%%! /FROM_MOTION_FILE_IN_WORKSPACE=%%''\\ +! /FROM_MOTION_FILE_IN_WORKSPACE= 
-''%%! /PARAMETER_VALUE_SEARCH_FOR=%%''\\ +! /PARAMETER_VALUE_SEARCH_FOR= 
-''%%! /PARAMETER_VALUE_REPLACE_WITH=%%''\\ +! /PARAMETER_VALUE_REPLACE_WITH= 
-''%%! /PARAMETER_VALUE_APPEND=%%''\\ +! /PARAMETER_VALUE_APPEND= 
-''%%! /SET_PROMPT=Select a directory%%''\\ +! /SET_PROMPT=Select a directory 
-''%%! /ALPHABETIZE=TRUE%%''\\ +! /ALPHABETIZE=TRUE 
-''%%;%%''\\ +;
-\\ +
-''%%Set_Pipeline_Parameter_To_List_Of_Files%%''\\ +
-''%%/PARAMETER_NAME=SUB_FOLDERS%%''\\ +
-''%%/FOLDER=::FOLDER%%''\\ +
-''%%/SEARCH_SUBFOLDERS=TRUE%%''\\ +
-''%%/FILE_MASK=*.c3d%%''\\ +
-''%%! /ALPHABETIZE=TRUE%%''\\ +
-''%%/RETURN_FOLDER_NAMES=TRUE%%''\\ +
-''%%; %%''\\+
  
 +Set_Pipeline_Parameter_To_List_Of_Files
 +/PARAMETER_NAME=SUB_FOLDERS
 +/FOLDER=::FOLDER
 +/SEARCH_SUBFOLDERS=TRUE
 +/FILE_MASK=*.c3d
 +! /ALPHABETIZE=TRUE
 +/RETURN_FOLDER_NAMES=TRUE
 +;
 +</code>
  
 \\ \\
 **Loop through the folders:**\\ **Loop through the folders:**\\
-''%% For_Each%%''\\ +<code> 
-''%%/ITERATION_PARAMETER_NAME=FOLDER%%''\\ +For_Each 
-''%%! /ITERATION_PARAMETER_COUNT_NAME=%%''\\ +/ITERATION_PARAMETER_NAME=FOLDER 
-''%%/ITEMS=::FOLDERS%%''\\ +! /ITERATION_PARAMETER_COUNT_NAME= 
-''%%; %%''\\ +/ITEMS=::FOLDERS 
 +; 
 +</code>
  
 \\ \\
 **Calibrations files are numbered (0) so get a list of all files ending with 0) (There should only be one in each folder):**\\ **Calibrations files are numbered (0) so get a list of all files ending with 0) (There should only be one in each folder):**\\
-''%% Set_Pipeline_Parameter_To_List_Of_Files%%''\\ +<code> 
-''%%/PARAMETER_NAME=Cal_File%%''\\ +Set_Pipeline_Parameter_To_List_Of_Files 
-''%%/FOLDER=::FOLDER%%''\\ +/PARAMETER_NAME=Cal_File 
-''%%! /SEARCH_SUBFOLDERS=FALSE%%''\\ +/FOLDER=::FOLDER 
-''%%/FILE_MASK=*0)*.c3d%%''\\ +! /SEARCH_SUBFOLDERS=FALSE 
-''%%! /ALPHABETIZE=TRUE%%''\\ +/FILE_MASK=*0)*.c3d 
-''%%! /RETURN_FOLDER_NAMES=FALSE%%''\\ +! /ALPHABETIZE=TRUE 
-''%%; %%''\\ +! /RETURN_FOLDER_NAMES=FALSE 
 +; 
 +</code>
  
 \\ \\
 **Open a new workspace:**\\ **Open a new workspace:**\\
-''%% File_New%%''\\ +<code> 
-''%%; %%''\\ +File_New 
 +; 
 +</code>
  
 \\ \\
 **Open the calibration file:**\\ **Open the calibration file:**\\
-''%% File_Open%%''\\ +<code> 
-''%%/FILE_NAME=::CAL_FILE%%''\\ +File_Open 
-''%%! /FILE_PATH=%%''\\ +/FILE_NAME=::CAL_FILE 
-''%%! /SUFFIX=%%''\\ +! /FILE_PATH= 
-''%%! /SET_PROMPT=File_Open%%''\\ +! /SUFFIX= 
-''%%/ON_FILE_NOT_FOUND=FAIL%%''\\ +! /SET_PROMPT=File_Open 
-''%%! /FILE_TYPES_ON_PROMPT=%%''\\ +/ON_FILE_NOT_FOUND=FAIL 
-''%%; %%''\\ +! /FILE_TYPES_ON_PROMPT= 
 +; 
 +</code>
  
 \\ \\
 **Set the calibration file to active:**\\ **Set the calibration file to active:**\\
-''%% Select_Active_File%%''\\ +<code> 
-''%%/FILE_NAME=::CAL_FILE%%''\\ +Select_Active_File 
-''%%! /QUERY=%%''\\ +/FILE_NAME=::CAL_FILE 
-''%%! /SUBJECT_TAGS=NO_SUBJECT%%''\\ +! /QUERY= 
-''%%; %%''\\ +! /SUBJECT_TAGS=NO_SUBJECT 
 +; 
 +</code>
  
 \\ \\
 **Save all the necessary information stored in PARAMETERS:PROCESSING into pipeline parameters:**\\ **Save all the necessary information stored in PARAMETERS:PROCESSING into pipeline parameters:**\\
-''%% Set_Pipeline_Parameter_To_Data_Value%%''\\ +<code> 
-''%%/SIGNAL_TYPES= PARAMETERS%%''\\ +Set_Pipeline_Parameter_To_Data_Value 
-''%%/SIGNAL_FOLDER= PROCESSING%%''\\ +/SIGNAL_TYPES= PARAMETERS 
-''%%/SIGNAL_NAMES= Bodymass%%''\\ +/SIGNAL_FOLDER= PROCESSING 
-''%%! /SIGNAL_COMPONENTS=ALL_COMPONENTS%%''\\ +/SIGNAL_NAMES= Bodymass 
-''%%/PARAMETER_NAME= BODYMASS%%''\\ +! /SIGNAL_COMPONENTS=ALL_COMPONENTS 
-''%%;%%''\\ +/PARAMETER_NAME= BODYMASS 
-//''%%... See attached pipeline for full list of commands ...%%''//''%% %%''\\+;
  
 +... See attached pipeline for full list of commands ...
 +</code>
  
 \\ \\
 **Visual 3Ds expected unit of measurement is meters so the knee widths, ankle widths and height need to be converted from mm to m:**\\ **Visual 3Ds expected unit of measurement is meters so the knee widths, ankle widths and height need to be converted from mm to m:**\\
-''%% Set_Pipeline_Parameter_From_Expression%%''\\ +<code> 
-''%%/PARAMETER_NAME=R_KNEE_WIDTH%%''\\ +Set_Pipeline_Parameter_From_Expression 
-''%%/EXPRESSION=&::R_KNEE_WIDTH&/1000.0%%''\\ +/PARAMETER_NAME=R_KNEE_WIDTH 
-''%%/AS_INTEGER=False%%''\\ +/EXPRESSION=&::R_KNEE_WIDTH&/1000.0 
-''%%;%%''\\ +/AS_INTEGER=False 
-//''%%... See attached pipeline for full list of commands ...%%''//''%% %%''\\+;
  
 +... See attached pipeline for full list of commands ...
 +</code>
  
 \\ \\
 **Close the calibration file:**\\ **Close the calibration file:**\\
-''%% File_Close%%''\\ +<code> 
-''%%/FILE_NAME=::CAL_FILE%%''\\ +File_Close 
-''%%! /QUERY=%%''\\ +/FILE_NAME=::CAL_FILE 
-''%%! /CLOSE_ASSOCIATED_MODELS=FALSE%%''\\ +! /QUERY= 
-''%%; %%''\\ +! /CLOSE_ASSOCIATED_MODELS=FALSE 
 +; 
 +</code>
  
 \\ \\
 **To open the dynamic files without re-opening the calibration file, list all C3D files within the current folder:**\\ **To open the dynamic files without re-opening the calibration file, list all C3D files within the current folder:**\\
-''%% Set_Pipeline_Parameter_To_List_Of_Files%%''\\ +<code> 
-''%%/PARAMETER_NAME=DYNAMIC_FILES%%''\\ +Set_Pipeline_Parameter_To_List_Of_Files 
-''%%/FOLDER=::FOLDER%%''\\ +/PARAMETER_NAME=DYNAMIC_FILES 
-''%%! /SEARCH_SUBFOLDERS=FALSE%%''\\ +/FOLDER=::FOLDER 
-''%%/FILE_MASK=*.c3d%%''\\ +! /SEARCH_SUBFOLDERS=FALSE 
-''%%! /ALPHABETIZE=TRUE%%''\\ +/FILE_MASK=*.c3d 
-''%%! /RETURN_FOLDER_NAMES=FALSE%%''\\ +! /ALPHABETIZE=TRUE 
-''%%; %%''\\ +! /RETURN_FOLDER_NAMES=FALSE 
 +; 
 +</code>
  
 \\ \\
 **Loop through each file:**\\ **Loop through each file:**\\
-''%% For_Each%%''\\ +<code> 
-''%%/ITERATION_PARAMETER_NAME=DYNAMIC_FILE%%''\\ +For_Each 
-''%%! /ITERATION_PARAMETER_COUNT_NAME=%%''\\ +/ITERATION_PARAMETER_NAME=DYNAMIC_FILE 
-''%%/ITEMS=::DYNAMIC_FILES%%''\\ +! /ITERATION_PARAMETER_COUNT_NAME= 
-''%%; %%''\\ +/ITEMS=::DYNAMIC_FILES 
 +; 
 +</code>
  
 \\ \\
 **Use a conditional statement to check that the current file name does not match the calibrations file name:**\\ **Use a conditional statement to check that the current file name does not match the calibrations file name:**\\
-''%% Conditional_Statement%%''\\ +<code> 
-''%%/ITERATION_PARAMETER_NAME=IS_DYNAMIC%%''\\ +Conditional_Statement 
-''%%/EXPRESSION= "&::DYNAMIC_FILE&" >< "&::CAL_FILE&"%%''\\ +/ITERATION_PARAMETER_NAME=IS_DYNAMIC 
-''%%! /AS_INTEGER=TRUE%%''\\ +/EXPRESSION= "&::DYNAMIC_FILE&" >< "&::CAL_FILE&" 
-''%%; %%''\\ +! /AS_INTEGER=TRUE 
 +; 
 +</code>
  
 \\ \\
 **if the file names do not match open the selected file:**\\ **if the file names do not match open the selected file:**\\
-''%% File_Open%%''\\ +<code> 
-''%%/FILE_NAME=::DYNAMIC_FILE%%''\\ +File_Open 
-''%%! /FILE_PATH=%%''\\ +/FILE_NAME=::DYNAMIC_FILE 
-''%%! /SUFFIX=%%''\\ +! /FILE_PATH= 
-''%%! /SET_PROMPT=File_Open%%''\\ +! /SUFFIX= 
-''%%! /ON_FILE_NOT_FOUND=PROMPT%%''\\ +! /SET_PROMPT=File_Open 
-''%%! /FILE_TYPES_ON_PROMPT=%%''\\ +! /ON_FILE_NOT_FOUND=PROMPT 
-''%%; %%''\\ +! /FILE_TYPES_ON_PROMPT= 
 +; 
 +</code>
  
 \\ \\
 **Close the conditional statement and the loop**\\ **Close the conditional statement and the loop**\\
-''%% Conditional_Statement_End%%''\\ +<code> 
-''%%/ITERATION_PARAMETER_NAME=IS_DYNAMIC%%''\\ +Conditional_Statement_End 
-''%%;%%''\\ +/ITERATION_PARAMETER_NAME=IS_DYNAMIC 
-\\ +;
-''%%End_For_Each%%''\\ +
-''%%/ITERATION_PARAMETER_NAME=DYNAMIC_FILE%%''\\ +
-''%%; %%''\\+
  
 +End_For_Each
 +/ITERATION_PARAMETER_NAME=DYNAMIC_FILE
 +;
 +</code>
  
 \\ \\
 **Set all dynamic files to active:**\\ **Set all dynamic files to active:**\\
-''%% Select_Active_File%%''\\ +<code> 
-''%%/FILE_NAME=::FOLDER&SUBJ*.c3d%%''\\ +Select_Active_File 
-''%%! /QUERY=%%''\\ +/FILE_NAME=::FOLDER&SUBJ*.c3d 
-''%%! /SUBJECT_TAGS=NO_SUBJECT%%''\\ +! /QUERY= 
-''%%; %%''\\ +! /SUBJECT_TAGS=NO_SUBJECT 
 +; 
 +</code>
  
 \\ \\
 **Create a hybrid model using the calibration file:**\\ **Create a hybrid model using the calibration file:**\\
-''%% Create_Hybrid_Model%%''\\ +<code> 
-''%%/CALIBRATION_FILE=::CAL_FILE%%''\\ +Create_Hybrid_Model 
-''%%! /RANGE=ALL_FRAMES%%''\\ +/CALIBRATION_FILE=::CAL_FILE 
-''%%; %%''\\ +! /RANGE=ALL_FRAMES 
 +; 
 +</code>
  
 \\ \\
 **Apply the model template:**\\ **Apply the model template:**\\
-''%% /CALIBRATION_FILE=::CAL_FILE%%''\\ +<code> 
-''%%!/SUBJECT_PREFIX=%%''\\ +/CALIBRATION_FILE=::CAL_FILE 
-''%%/MODEL_TEMPLATE=!!! SET PATH TO HEALTHY MODEL TEMPLATE !!!%%''\\ +!/SUBJECT_PREFIX= 
-''%%! /SET_PROMPT=Open model file%%''\\ +/MODEL_TEMPLATE=!!! SET PATH TO HEALTHY MODEL TEMPLATE !!! 
-''%%! /VIEW_BUILDMODEL_RESULTS=2%%''\\ +! /SET_PROMPT=Open model file 
-''%%! /MISSING_TARGET_MESSAGE=FALSE%%''\\ +! /VIEW_BUILDMODEL_RESULTS=2 
-''%%; %%''\\ +! /MISSING_TARGET_MESSAGE=FALSE 
 +; 
 +</code>
  
 \\ \\
 **Set the necessary model metrics using the parameters saved from the calibration file and then recalculate the model:**\\ **Set the necessary model metrics using the parameters saved from the calibration file and then recalculate the model:**\\
-''%% Set_Model_Metric%%''\\ +<code> 
-''%%! /CALIBRATION_FILE=%%''\\ +Set_Model_Metric 
-''%%/METRIC_NAME= Mass%%''\\ +! /CALIBRATION_FILE= 
-''%%/METRIC_VALUE= ::BODYMASS%%''\\ +/METRIC_NAME= Mass 
-''%%! /SUBJECT=%%''\\ +/METRIC_VALUE= ::BODYMASS 
-''%%;%%''\\ +! /SUBJECT= 
-//''%%... See the attached pipeline for full list of commands ...%%''//''%% %%''\\+;
  
 +... See the attached pipeline for full list of commands ...
 +</code>
  
 \\ \\
 **Assign model to the dynamic files:**\\ **Assign model to the dynamic files:**\\
-''%% Assign_Model_File%%''\\ +<code> 
-''%%/CALIBRATION_FILE=::CAL_FILE%%''\\ +Assign_Model_File 
-''%%/MOTION_FILE_NAMES=::FOLDER&SUBJ*.c3d%%''\\ +/CALIBRATION_FILE=::CAL_FILE 
-''%%! /REMOVE_EXISTING_ASSIGNMENTS=FALSE%%''\\ +/MOTION_FILE_NAMES=::FOLDER&SUBJ*.c3d 
-''%%; %%''\\ +! /REMOVE_EXISTING_ASSIGNMENTS=FALSE 
 +; 
 +</code>
  
 \\ \\
 **Run all desired computations, and then iterate the SUB_NUM pipeline parameter:**\\ **Run all desired computations, and then iterate the SUB_NUM pipeline parameter:**\\
-''%% %%''//''%%... See attached pipeline for examples of computation commands ...%%''//\\ +<code> 
-''%%Set_Pipeline_Parameter_From_Expression%%''\\ +... See attached pipeline for examples of computation commands ...
-''%%/PARAMETER_NAME=SUB_NUM%%''\\ +
-''%%/EXPRESSION=&::SUB_NUM&+1%%''\\ +
-''%%! /AS_INTEGER=TRUE%%''\\ +
-''%%; %%''\\+
  
 +Set_Pipeline_Parameter_From_Expression
 +/PARAMETER_NAME=SUB_NUM
 +/EXPRESSION=&::SUB_NUM&+1
 +! /AS_INTEGER=TRUE
 +;
 +</code>
  
 \\ \\
 **Save the workspace as a CMZ appending the SUB_NUM variable to the name, then close the loop:**\\ **Save the workspace as a CMZ appending the SUB_NUM variable to the name, then close the loop:**\\
-''%% /FILE_NAME=SUBJ&::SUB_NUM&.cmz%%''\\ +<code> 
-''%%/FOLDER=::FOLDER%%''\\ +/FILE_NAME=SUBJ&::SUB_NUM&.cmz 
-''%%! /SET_PROMPT=Save CMZ file as%%''\\ +/FOLDER=::FOLDER 
-''%%! /SAVE_EMBEDDED_GRAPHICS=FALSE%%''\\ +! /SET_PROMPT=Save CMZ file as 
-''%%! /CREATE_FOLDER_PATH=FALSE%%''\\ +! /SAVE_EMBEDDED_GRAPHICS=FALSE 
-''%%;%%''\\ +! /CREATE_FOLDER_PATH=FALSE 
-\\ +; 
-''%%End_For_Each%%''\\ + 
-''%%/ITERATION_PARAMETER_NAME= FOLDER%%''\\ +End_For_Each 
-''%%; %%''+/ITERATION_PARAMETER_NAME= FOLDER 
 +; 
 +</code>
  
 ==== Missing Parameters ==== ==== Missing Parameters ====
visual3d/tutorials/knowledge_discovery/looking_at_large_public_data_sets.1757441432.txt.gz · Last modified: 2025/09/09 18:10 by wikisysop