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visual3d:tutorials:pipeline:generic_pipeline_to_create_cmz

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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.

download sample script

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

load static trial

  1. create_hybrid_model: load static c3d file
  2. apply_model_template: apply model template (mdh file)
    1. tutorial to build a model template can be found here.
  3. set necessary model metrics (most metrics should be calculated based on markers, but height and weight always need to be entered manually):

load dynamic trials

  1. file_open: load dynamic c3d files
  2. assign_model_file: associated static trial with appropriate dynamic trials
    1. 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

  1. select_active_file: set active file to all_files
  2. set_force_platform_threshold: common minimum values are:
    1. overground plates: 20 n
    2. treadmill: 50 n
  3. gap fill & filter target data:
  4. filter analog data:
  5. if using treadmill data only use fp_auto_baseline

gait events

gait events with force platforms

      1. plot vertical component of kinetic_kinematic::lft::force_1
      1. plot vertical component of kinetic_kinematic::rft::force_1
    1. open_force_dialogs: open force assignment dialog
    2. switch_between_tabs: switch to signals and events tag
    3. pipeline_breakpoint: pause pipeline to manually check force assignments
      1. remove any force assignment that is not clean
      2. remove any partial force assignments (this includes force assignments at the start/end of the trial)
  1. select_active_file: set active file to all_files
  2. automatic_gait_events: create gait events

gait events without force platforms

report and data review

  1. open_report_template: load report template (rgt file)
  2. stop pipeline to review data prior to export:

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 here
  • the report template contains any signals defined using the compute model based function

signal definitions and processing

export

save

visual3d/tutorials/pipeline/generic_pipeline_to_create_cmz.1718801701.txt.gz · Last modified: 2024/06/19 12:55 by sgranger