====== Generic Pipeline to Create CMZ ======

Almost every step that can be accomplished using the user interface can also be accomplished using a pipeline command - the pipeline is essentially a set of commands/functions that allow you to streamline your data processing and reproducible for other subjects.

It's always recommended to learn the manual steps PRIOR to writing a pipeline command - learning the interface will help you build your pipeline.

[[https://www.has-motion.com/download/examples/Pipelines/Building_CMZ.zip|Download sample script]]

When writing a pipeline to build a CMZ file, your script should follow the general procedure outlined below.

===== Load Static Trial =====

  - [[Visual3D:Documentation:Pipeline:Model_Commands:Create_Hybrid_Model|Create_Hybrid_Model]]: Load static C3D file
  - [[Visual3D:Documentation:Pipeline:Model_Commands:Apply_Model_Template|Apply_Model_Template]]: Apply model template (MDH file)
    - Tutorial to build a model template can be found [[Visual3D:Tutorials:Modeling:Building_a_6_DOF_Model_|here]].
  - Set necessary model metrics (most metrics should be calculated based on markers, but height and weight always need to be entered manually):
    - [[Visual3D:Documentation:Pipeline:Model_Commands:Set_Subject_Height|Set_Subject_Height]]
    - [[Visual3D:Documentation:Pipeline:Model_Commands:Set_Subject_Weight|Set_Subject_Weight]]

===== Load Dynamic Trials =====

  - [[Visual3D:Documentation:Pipeline:File_Commands:File_Open|File_Open]]: Load dynamic C3D files
  - [[Visual3D:Documentation:Pipeline:Model_Commands:Assign_Model_File|Assign_Model_File]]: Associated static trial with appropriate dynamic trials
    - Note: If a marker falls off during data collection, you should re-take a static trial and associate the appropriate dynamic trials

===== Process Target and Analog Signals =====

  - [[Visual3D:Documentation:Pipeline:File_Commands:Select_Active_File|Select_Active_File]]: Set active file to ALL_FILES
  - [[Visual3D:Documentation:Visual3D_Signal_Types:Used_Process|Set Use Processed:]]
    - [[Visual3D:Documentation:Pipeline:Other_Commands:Set_Use_Processed_Targets|Set_Use_Processed_Targets]]: Set to TRUE
    - [[Visual3D:Documentation:Pipeline:Other_Commands:Set_Use_Processed_Analog|Set_Use_Processed_Analog]]: Set to TRUE
  - [[Visual3D:Documentation:Pipeline:Force_Commands:Set_Force_Platform_Threshold|Set_Force_Platform_Threshold]]: Common minimum values are:
    - Overground plates: 20 N
    - Treadmill: 50 N
  - Gap fill & Filter Target Data:
    - [[Visual3D:Documentation:Pipeline:Signal_Commands:Interpolate|Interpolate]]
    - [[Visual3D:Documentation:Pipeline:Signal_Commands:Lowpass_Filter|Lowpass_Filter]]
  - Filter Analog data:
    - [[Visual3D:Documentation:Pipeline:Signal_Commands:Lowpass_Filter|Lowpass_Filter]]
  - If using treadmill data ONLY use [[Visual3D:Documentation:Pipeline:Force_Commands:FP_Auto_Baseline|FP_Auto_Baseline]]
  - [[Visual3D:Documentation:Pipeline:File_Commands:Recalc|Recalc]]

===== Gait Events =====

==== Gait Events with Force Platforms ====

  - [[Visual3D:Documentation:Definitions:Clean_Foot_Strike|Check for clean force assignments]]
    - [[Visual3D:Documentation:Pipeline:Report_Commands:Interactive_Graph_Signals|Interactive_Graph_Signals]]:
      - Plot vertical component of KINETIC_KINEMATIC::LFT::FORCE_1
    - [[Visual3D:Documentation:Pipeline:Report_Commands:Interactive_Graph_Signals|Interactive_Graph_Signals]]:
      - Plot vertical component of KINETIC_KINEMATIC::RFT::FORCE_1
    - [[Visual3D:Documentation:Pipeline:Other_Commands:Open_Force_Dialogs|Open_Force_Dialogs]]: Open force assignment dialog
    - [[Visual3D:Documentation:Pipeline:Other_Commands:Switch_Between_Tabs|Switch_Between_Tabs]]: Switch to Signals and Events tag
    - [[Visual3D:Documentation:Pipeline:Pipeline_Commands:Pipeline_Breakpoint|Pipeline_Breakpoint]]: Pause pipeline to manually check force assignments
      - Remove any force assignment that is not [[Visual3D:Documentation:Definitions:Clean_Foot_Strike|clean]]
      - Remove any partial force assignments (this includes force assignments at the start/end of the trial)
  - [[Visual3D:Documentation:Pipeline:File_Commands:Select_Active_File|Select_Active_File]]: Set active file to ALL_FILES
  - [[Visual3D:Documentation:Pipeline:Event_Commands:Automatic_Gait_Events|Automatic_Gait_Events]]: Create gait events

==== Gait Events WITHOUT Force Platforms ====

  - [[Visual3D:Documentation:Pipeline:Event_Commands:Example_-_Gait_Events_using_Kinematic_Data|Kinematic Gait Events]]

===== Report and Data Review =====

  - [[Visual3D:Documentation:Pipeline:Report_Commands:Open_Report_Template|Open_Report_Template]]: Load report template (RGT file)
  - Stop pipeline to review data prior to export:
    - [[Visual3D:Documentation:Pipeline:Other_Commands:Switch_Between_Tabs|Switch_Between_Tabs]]
    - [[Visual3D:Documentation:Pipeline:Pipeline_Commands:Pipeline_Breakpoint|Pipeline_Breakpoint]]

Notes:

  * Many users are skipping report templates - but it's highly recommended to even create a simple report template to review data prior to export. No data collection is perfect, and reviewing the data prior to exporting ensures the data is a quality assurance step.
  * Instructions to create a report template can be found [[Visual3D:Tutorials:Reports:Creating_a_Report|here]]
  * The report template contains any signals defined using the [[Visual3D:Documentation:Visual3D_Signal_Types:LINK_MODEL_BASED_Data_Type#Link_Model_Based_Items|Compute Model Based Function]]

===== Signal Definitions and Processing =====

  - [[Visual3D:Documentation:Pipeline:Signal_Commands:Signal_Commands_Overview|Calculate Additional Signals]]
  - [[Visual3D:Documentation:Pipeline:Metric_Commands:Metric_Commands_Overview|Calculate Metrics]]

===== Export =====

  - [[Visual3D:Documentation:Pipeline:File_Commands:Export_Data_To_ASCII_File|Export data to a text file]]

===== Save =====

  - [[Visual3D:Documentation:Pipeline:File_Commands:File_Save|Save CMZ]]