HAS-Motion Software Documentation

The Manage File Merge command is designed to merge multiple files that recorded data from the same motion capture trial. This command merges data types from each .c3d file into one trial in the Visual3D workspace. This command was originally called Manage_Theia3D_Merge, but since has been updated to be used for file types other than from Theia3D.

This command can be found in the Pipeline Workshop Dialog under Pipeline Control.

Manage_File_Merge can be used to combine motion capture files from the same recording session. A popular use case for this command would be to merge force plate recordings from a QTM file with a Theia3D motion capture file. The analog signals from the QTM .c3d file would be merge into the Theia3D .c3d file.

This command requires data files to be stored in a particular folder structure to match .c3d files appropriately. Please carefully review the Notes section of this page for more details.

Below is the full pipeline command and parameters for Manage_File_Merge

Manage_File_Merge
! /ROOT_FOLDER=
! /HMX_INDEX_MASK=
! /USE_HMX_INDEX=FALSE
! /ACTION=
! /TAGS=ACTION
! /IMPORT_ANALOG_FILES=FALSE
! /MERGE_THEIA3D_FILES=FALSE
! /MERGE_THEIA3D_AND_OTHER_FILES=FALSE
! /MERGE_EVENT_LABELS=FALSE
! /THEIA3D_SESSION_FOLDER=
! /THEIA3D_FILE_MASK=*.c3d
! /THEIA3D_FILE_MASK_FOR_MODEL=
! /THEIA3D_PREFIX=
! /THEIA3D_SUBJECT_TAG=
! /THEIA3D_COLOR=
! /THEIA3D_SEX=UNKNOWN
! /CREATE_MODEL_FOR_EACH_C3D_FILE=FALSE
! /OTHER3D_SESSION_FOLDER=
! /OTHER3D_FILE_MASK=
! /OTHER3D_MODEL_MASK=
! /OTHER3D_MODEL_TEMPLATE_MASK=
! /OTHER3D_PREFIX=
! /OTHER3D_SUBJECT_TAG=
! /OTHER3D_COLOR=
! /NUMBER_OF_SESSION_FILES_ALLOWED=
! /SAVE_DEFAULT_CMZ_FILES=TRUE
! /DEFAULT_CMZ_NAME=<SESSION>
! /OPEN_CMZ_LIBRARY=FALSE
! /VIRTUAL_LAB=
! /INPUT_DATA_FOLDER_PRIMARY=DEFAULT
! /INPUT_DATA_FOLDER_SECONDARY=DEFAULT
! /INPUT_STATIC_DATA_FOLDER=DEFAULT
! /KINETIC_THORAX=RTA
! /ANALOG_FILTER_CUTOFF=12
! /TARGET_FILTER_CUTOFF=12
! /FP_AUTO_BASELINE=DO_NOT_COMPUTE
! /VISUAL3D_PIPELINE_POST_MERGE=
! /VISUAL3D_PIPELINE_PREMERGE=
;

The following table shows the command parameters and descriptions:

The command can be edited in a text editor or in a dialog form. To edit in the dialog pop up form either click on the Edit button in the pipeline workshop or double-click on the pipeline command. The dialog is shown below. There are a variety of inputs that can be used to generate CMZs from Theia3D files:

• Root path to search: The directory root to search for all of the Files.
• Open CMZ Library After Processing:
• Automatically save default CMZ files: How the CMZ file should be saved as.
• Use Index Theia Files (.hmx): If you would like to use a .hmx file to supersede Theia3D files information.
• File Tags: If/how file tags should be added onto the files by.

Primary Files:

• Primary Data Folder: Method by which Theia3D data is stored.
• Primary Session Folder Mask: Folder mask for Theia3d files (directory within top level directory to search for Theia3D files).
• Primary File Mask: File name mask for Theia3D files. Can include wildcards.
• Primary File Mask for Model: File name mask for model file. If blank it will select the first file as the model file. Can include wildcards.
• Theia3D Subject Tags: Subject tags for Theia3D files.
• Theia Prefixes: Subject prefixes for Theia3D files.
• Theia Color: The color of the Theia3D skeleton.
• Sex: The sex of the Theia3D file for model inertial properties.
• Choose Kinetic Thorax: Choose which type of thorax to model.

• Merge Primary Files: Merge primary files into other primary files (mutually exclusive).
• Import Analog Files: Merge primary files with analog files, such as force plate data (mutually exclusive).
• Merge Primary Files and Other Files: Merge primary files with other data, such as marker-based files (mutually exclusive).
• Treat Session Files as Independent: …

Secondary Files:

• Secondary Data Folder: Method by which secondary data is stored.
• Static Data Folder: Method by which static secondary data is stored.
• Other Session Folder Mask: Folder mask for merged files (directory within top level directory to search for merged files).
• Other File Mask: File name mask for merged files. Can include wildcards.
• Other Static File Mask: File name mask for static merged files. Can include wildcards.
• Other Model Template Mask: File name mask for model files (if needed). Can include wildcards.
• Other Subject Tags: Subject tags for merged files.
• Other Prefixes: Subject prefixes for merged files.
• Other Color: The color of the secondary data files.
• Analog Filter Cutoff: The lowpass filter cutoff for the analog files.
• Target Filter Cutoff: The lowpass filter cutoff for the target files.
• FP_Auto_Baseline: Method by which forceplate data was collected.

• Restrict Number of Session Files: Restricts the number of session files used.
• Visual3D Pipeline Pre-Merge: Visual 3D pipeline to run before the merge occurs.
• Visual3D Pipeline Post-Merge: Visual 3D pipeline to run after the merge occurs.

There is an assumed basic directory structure for this command's input data that aligns with some useful concepts from the experiments that produced the data. This directory structure organizes the CMZ files and C3D files that contain the information relevant for analysis. This structure has 5 levels, from root folder to deepest leaf they are:

If you are using Theia3D files, and use TMBATCH, the default folder structure will have 6 levels. From root folder to deepest leaf they are:

1. Study
2. Group
3. Session
4. Task
5. Trial
6. pose_filt_0.c3d