visual3d:tutorials:pipeline:generic_pipeline_to_create_cmz
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Table of Contents
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.
when writing a pipeline to build a cmz file, your script should follow the general procedure outlined below.
load static trial
- create_hybrid_model: load static c3d file
- apply_model_template: apply model template (mdh file)
- tutorial to build a model template can be found here.
- 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
- file_open: load dynamic c3d files
- 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
- select_active_file: set active file to all_files
-
- set_use_processed_targets: set to true
- set_use_processed_analog: set to true
- set_force_platform_threshold: common minimum values are:
- overground plates: 20 n
- treadmill: 50 n
- gap fill & filter target data:
- filter analog data:
- if using treadmill data only use fp_auto_baseline
gait events
gait events with force platforms
-
-
- plot vertical component of kinetic_kinematic::lft::force_1
-
- plot vertical component of kinetic_kinematic::rft::force_1
- open_force_dialogs: open force assignment dialog
- switch_between_tabs: switch to signals and events tag
- pipeline_breakpoint: pause pipeline to manually check force assignments
- remove any force assignment that is not clean
- remove any partial force assignments (this includes force assignments at the start/end of the trial)
-
- select_active_file: set active file to all_files
- automatic_gait_events: create gait events
gait events without force platforms
report and data review
- open_report_template: load report template (rgt file)
- 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