HAS-Motion Software Documentation

User Tools

Site Tools

You are here: Main Page » visual3d » documentation » pipeline » pipeline_commands » Manage_File_Merge
visual3d:documentation:pipeline:pipeline_commands:manage_file_merge

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
visual3d:documentation:pipeline:pipeline_commands:manage_file_merge [2025/05/28 15:41] – wikisysopvisual3d:documentation:pipeline:pipeline_commands:manage_file_merge [2025/06/09 20:18] (current) – wikisysop
Line 20: Line 20:
 ! /TAGS=ACTION ! /TAGS=ACTION
 ! /IMPORT_ANALOG_FILES=FALSE ! /IMPORT_ANALOG_FILES=FALSE
-! /MERGE_THEIA3D_FILES=FALSE +! /MERGE_PRIMARY_FILES=FALSE 
-! /MERGE_THEIA3D_AND_OTHER_FILES=FALSE+! /MERGE_PRIMARY_AND_OTHER_FILES=FALSE
 ! /MERGE_EVENT_LABELS=FALSE ! /MERGE_EVENT_LABELS=FALSE
-! /THEIA3D_SESSION_FOLDER= +! /PRIMARY_SESSION_FOLDER= 
-! /THEIA3D_FILE_MASK=*.c3d +! /PRIMARY_FILE_MASK=*.c3d 
-! /THEIA3D_FILE_MASK_FOR_MODEL=+! /PRIMARY_FILE_MASK_FOR_MODEL=
 ! /THEIA3D_PREFIX= ! /THEIA3D_PREFIX=
 ! /THEIA3D_SUBJECT_TAG= ! /THEIA3D_SUBJECT_TAG=
-! /THEIA3D_COLOR= +! /PRIMARY_COLOR= 
-! /THEIA3D_SEX=UNKNOWN+! /PRIMARY_SEX=UNKNOWN
 ! /CREATE_MODEL_FOR_EACH_C3D_FILE=FALSE ! /CREATE_MODEL_FOR_EACH_C3D_FILE=FALSE
-! /OTHER3D_SESSION_FOLDER= +! /OTHER_SESSION_FOLDER= 
-! /OTHER3D_FILE_MASK= +! /OTHER_FILE_MASK= 
-! /OTHER3D_MODEL_MASK= +! /OTHER_MODEL_MASK= 
-! /OTHER3D_MODEL_TEMPLATE_MASK= +! /OTHER_MODEL_TEMPLATE_MASK= 
-! /OTHER3D_PREFIX= +! /OTHER_PREFIX= 
-! /OTHER3D_SUBJECT_TAG= +! /OTHER_SUBJECT_TAG= 
-! /OTHER3D_COLOR=+! /OTHER_COLOR=
 ! /NUMBER_OF_SESSION_FILES_ALLOWED= ! /NUMBER_OF_SESSION_FILES_ALLOWED=
 ! /SAVE_DEFAULT_CMZ_FILES=TRUE ! /SAVE_DEFAULT_CMZ_FILES=TRUE
Line 60: Line 60:
  
 |**Parameter**   |**Description**| |**Parameter**   |**Description**|
-|**! /ROOT_FOLDER=**|| +|**! /ROOT_FOLDER=**| The directory root search containing all C3D files that contain the information relevant for analysis.| 
-|**! /HMX_INDEX_MASK=**|...| +|**! /HMX_INDEX_MASK=**|file mask for Theia .hmx file (if applicable).| 
-|**! /USE_HMX_INDEX=FALSE**|...|+|**! /USE_HMX_INDEX=FALSE**|If you would like to use a .hmx file to supersede this information.|
 |**! /ACTION=**|...| |**! /ACTION=**|...|
-|**! /TAGS=ACTION**|...| +|**! /TAGS=ACTION**|If/how file tags should be added onto the files by. Default is to the Action.| 
-|**! /IMPORT_ANALOG_FILES=FALSE**|...| +|**! /IMPORT_ANALOG_FILES=FALSE**|Merge primary files with analog files, such as force plate data (mutually exclusive).| 
-|**! /MERGE_THEIA3D_FILES=FALSE**|...| +|**! /MERGE_PRIMARY_FILES=FALSE**|Merge primary files into other files (mutually exclusive)| 
-|**! /MERGE_THEIA3D_AND_OTHER_FILES=FALSE**|...| +|**! /MERGE_PRIMARY_AND_OTHER_FILES=FALSE**|Merge primary files with other data, such as marker-based files (mutually exclusive).| 
-|**! /MERGE_EVENT_LABELS=FALSE**|...| +|**! /MERGE_EVENT_LABELS=FALSE**|Merge event labels between Primary and Secondary .c3d files.| 
-|**! /THEIA3D_SESSION_FOLDER=**|...| +|**! /PRIMARY_SESSION_FOLDER=**|Folder mask for primary session files (directory within top level directory to search for primary files).| 
-|**! /THEIA3D_FILE_MASK=*.c3d**|...| +|**! /PRIMARY_FILE_MASK=*.c3d**|File name mask for primary files. Can include wildcards.| 
-|**! /THEIA3D_FILE_MASK_FOR_MODEL=**|...| +|**! /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_PREFIX=**|...| +|**! /THEIA3D_PREFIX=**|Subject Prefixes for Primary files.| 
-|**! /THEIA3D_SUBJECT_TAG=**|...| +|**! /THEIA3D_SUBJECT_TAG=**|Subject tags for Primary files.| 
-|**! /THEIA3D_COLOR=**|...| +|**! /PRIMARY_COLOR=**|The color of the Primary file skeleton.| 
-|**! /THEIA3D_SEX=UNKNOWN**|...| +|**! /PRIMARY_SEX=UNKNOWN**|Sex of the primary file.| 
-|**! /CREATE_MODEL_FOR_EACH_C3D_FILE=FALSE**|...| +|**! /CREATE_MODEL_FOR_EACH_C3D_FILE=FALSE**|For automated model building for Theia3D files, creating a new model for each .c3d. | 
-|**! /OTHER3D_SESSION_FOLDER=**|...| +|**! /OTHER_SESSION_FOLDER=**|Folder mask for merged files (directory within top level directory to search for merged files).| 
-|**! /OTHER3D_FILE_MASK=**|...| +|**! /OTHER_FILE_MASK=**|File name mask for merged files. Can include wildcards.| 
-|**! /OTHER3D_MODEL_MASK=**|...| +|**! /OTHER_MODEL_MASK=**|File name mask for static merged files. Can include wildcards.| 
-|**! /OTHER3D_MODEL_TEMPLATE_MASK=**|...| +|**! /OTHER_MODEL_TEMPLATE_MASK=**|File name mask for model files (if needed). Can include wildcards.| 
-|**! /OTHER3D_PREFIX=**|...| +|**! /OTHER_PREFIX=**|Subject prefixes for merged files.| 
-|**! /OTHER3D_SUBJECT_TAG=**|...| +|**! /OTHER_SUBJECT_TAG=**|Subject tags for merged files.| 
-|**! /OTHER3D_COLOR=**|...| +|**! /OTHER_COLOR=**|The color of the secondary data files.| 
-|**! /NUMBER_OF_SESSION_FILES_ALLOWED=**|...| +|**! /NUMBER_OF_SESSION_FILES_ALLOWED=**|Restricts the number of session files used.| 
-|**! /SAVE_DEFAULT_CMZ_FILES=TRUE**|...| +|**! /SAVE_DEFAULT_CMZ_FILES=TRUE**|Automatically save default CMZ file with specified name.| 
-|**! /DEFAULT_CMZ_NAME=<SESSION>**|...| +|**! /DEFAULT_CMZ_NAME=<SESSION>**|The name that CMZ file should be saved as, related to the hierarchy of the folder structure (either Session or Group+Session).| 
-|**! /OPEN_CMZ_LIBRARY=FALSE**|...| +|**! /OPEN_CMZ_LIBRARY=FALSE**|Open CMZ Library after processing.| 
-|**! /VIRTUAL_LAB=**|...| +|**! /VIRTUAL_LAB=**|Set virtual lab ("None" if not desired).| 
-|**! /INPUT_DATA_FOLDER_PRIMARY=DEFAULT**|...| +|**! /INPUT_DATA_FOLDER_PRIMARY=DEFAULT**| Method by which primary data is stored. DEFAULT is | 
-|**! /INPUT_DATA_FOLDER_SECONDARY=DEFAULT**|...| +|**! /INPUT_DATA_FOLDER_SECONDARY=DEFAULT**|Method by which secondary data is stored. DEFAULT is | 
-|**! /INPUT_STATIC_DATA_FOLDER=DEFAULT**|...| +|**! /INPUT_STATIC_DATA_FOLDER=DEFAULT**|Method by which static secondary data is stored. DEFAULT is | 
-|**! /KINETIC_THORAX=RTA**|...| +|**! /KINETIC_THORAX=RTA**|Choice of Kinetic Thorax for automated model with Theia3D specific files.| 
-|**! /ANALOG_FILTER_CUTOFF=12**|...| +|**! /ANALOG_FILTER_CUTOFF=12**|The lowpass filter cutoff for the analog files.| 
-|**! /TARGET_FILTER_CUTOFF=12**|...| +|**! /TARGET_FILTER_CUTOFF=12**|The lowpass filter cutoff for the target files.| 
-|**! /FP_AUTO_BASELINE=DO_NOT_COMPUTE**|...| +|**! /FP_AUTO_BASELINE=DO_NOT_COMPUTE**|Method by which forceplate data was collected.| 
-|**! /VISUAL3D_PIPELINE_POST_MERGE=**|...| +|**! /VISUAL3D_PIPELINE_POST_MERGE=**|Visual 3D pipeline to run after the merge occurs.| 
-|**! /VISUAL3D_PIPELINE_PREMERGE=**|...|+|**! /VISUAL3D_PIPELINE_PREMERGE=**|Visual 3D pipeline to run before the merge occurs.|
  
 ====Dialog==== ====Dialog====
 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. 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:
  
-{{visual3d:documentation:pipeline:pipeline_commands:manage_file_merge_dialog.png}}+{{ visual3d:documentation:pipeline:pipeline_commands:manage_file_merge_dialog.png}} 
 +  * **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.
  
-- Brief description of components (Combo boxes, acronyms, etc.)+**Primary Files:** 
 +  * **Primary Data Folder:** Method by which Primary data is stored. 
 +  * **Primary Session Folder Mask:** Folder mask for Primary files (directory within top level directory to search for Primary files). 
 +  * **Primary File Mask:** File name mask for Primary 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 Primary files. 
 +  * **Theia Prefixes:** Subject prefixes for Theia3D Primary files. 
 +  * **Theia Color:** The color of the Primary skeleton. 
 +  * **Sex:** The sex of the Primary 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.
  
 |[IMAGE] |[IMAGE]
Line 117: Line 155:
  
  
-====Notes==== +=====Notes===== 
-- Important considerations (anything included in the page before the reformat)+==== Folder Structure ==== 
 +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 [[Visual3D:Documentation:Definitions:File_Formats:CMZ_Format_|CMZ files]] and [[Visual3D:Documentation:C3D_Signal_Types:C3D_Format|C3D files]] that contain the information relevant for analysis. This structure has 5 levels, from root folder to deepest leaf they are:
  
 +|**1. Study**|Although the name of this directory level suggests that the data it contains is only used for one study, this is not necessary. As a top-level concept this is the largest, most general database that is stored in one location. This could be specific to a study, or it could be specific to a project, researcher, lab, or consortium. In these latter cases it is possible to define [[Other:Inspect3D:Documentation:Dialogs:Advanced_Query_Section|queries]] to extract the specific signals that are desired for an individual study.|
 +|**2. Group**|This level of the directory structure is optional, but it allows the researcher to divide c3d files according to desired parameters, e.g., Women - Men, Old - Young. If this level is omitted from the structure then individual C3D files can be [[Visual3D:Documentation:Definitions:Tag|tagged]] with the necessary parameters to allow for their specific selection.|
 +|**3. Session**|This directory level can be conceived as a single day (or single effort) of data collection within the database. This is the most important level as this is where the [[Visual3D:Documentation:Definitions:File_Formats:CMZ_Format_|CMZ file]] and log files get stored. This is also the level of the directory where static models are stored for all subjects involved in the session.|
 +|**4. Task**|This level of the directory allows the researcher to divide c3d files according to the desired activity, e.g., walking, running, jumping, etc. As with group-level parameters, C3D files can be coded with these different tasks by using [[Visual3D:Documentation:Definitions:Tag|tags]].|
 +|**5. Trial**|At this level of the directory structure we have individual trials. This means that we have the individual C3D files that are recorded by the motion capture system.|
  
 +**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:\\
 +  - Study
 +  - Group
 +  - Session
 +  - Task
 +  - Trial
 +  - pose_filt_0.c3d
  
  
visual3d/documentation/pipeline/pipeline_commands/manage_file_merge.1748446908.txt.gz · Last modified: 2025/05/28 15:41 by wikisysop