Differences

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

--- visual3d:documentation:pipeline:pipeline_commands:manage_file_merge [2025/05/28 18:34] – wikisysop
+++ visual3d:documentation:pipeline:pipeline_commands:manage_file_merge [2025/06/09 20:18] (current) – wikisysop
@@ Line 20: / Line 20: @@
 ! /TAGS=ACTION
 ! /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
-! /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_SUBJECT_TAG=
-! /THEIA3D_COLOR=
+! /PRIMARY_COLOR=
-! /THEIA3D_SEX=UNKNOWN
+! /PRIMARY_SEX=UNKNOWN
 ! /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=
 ! /SAVE_DEFAULT_CMZ_FILES=TRUE
@@ Line 66: / Line 66: @@
 |**! /TAGS=ACTION**|If/how file tags should be added onto the files by. Default is to the Action.|
 |**! /IMPORT_ANALOG_FILES=FALSE**|Merge primary files with analog files, such as force plate data (mutually exclusive).|
-|**! /MERGE_THEIA3D_FILES=FALSE**|Merge primary files into other files (mutually exclusive)|
+|**! /MERGE_PRIMARY_FILES=FALSE**|Merge primary files into other files (mutually exclusive)|
-|**! /MERGE_THEIA3D_AND_OTHER_FILES=FALSE**|Merge primary files with other data, such as marker-based files (mutually exclusive).|
+|**! /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 between Primary and Secondary .c3d files.|
-|**! /THEIA3D_SESSION_FOLDER=**|Folder mask for primary session files (directory within top level directory to search for primary files).|
+|**! /PRIMARY_SESSION_FOLDER=**|Folder mask for primary session files (directory within top level directory to search for primary files).|
-|**! /THEIA3D_FILE_MASK=*.c3d**|File name mask for primary files. Can include wildcards.|
+|**! /PRIMARY_FILE_MASK=*.c3d**|File name mask for primary files. Can include wildcards.|
-|**! /THEIA3D_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.|
+|**! /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=**|Subject Prefixes for Primary files.|
 |**! /THEIA3D_SUBJECT_TAG=**|Subject tags for Primary files.|
-|**! /THEIA3D_COLOR=**|The color of the Primary file skeleton.|
+|**! /PRIMARY_COLOR=**|The color of the Primary file skeleton.|
-|**! /THEIA3D_SEX=UNKNOWN**|Sex of the primary file.|
+|**! /PRIMARY_SEX=UNKNOWN**|Sex of the primary file.|
 |**! /CREATE_MODEL_FOR_EACH_C3D_FILE=FALSE**|For automated model building for Theia3D files, creating a new model for each .c3d. |
-|**! /OTHER3D_SESSION_FOLDER=**|Folder mask for merged files (directory within top level directory to search for merged files).|
+|**! /OTHER_SESSION_FOLDER=**|Folder mask for merged files (directory within top level directory to search for merged files).|
-|**! /OTHER3D_FILE_MASK=**|File name mask for merged files. Can include wildcards.|
+|**! /OTHER_FILE_MASK=**|File name mask for merged files. Can include wildcards.|
-|**! /OTHER3D_MODEL_MASK=**|File name mask for static merged files. Can include wildcards.|
+|**! /OTHER_MODEL_MASK=**|File name mask for static merged files. Can include wildcards.|
-|**! /OTHER3D_MODEL_TEMPLATE_MASK=**|File name mask for model files (if needed). Can include wildcards.|
+|**! /OTHER_MODEL_TEMPLATE_MASK=**|File name mask for model files (if needed). Can include wildcards.|
-|**! /OTHER3D_PREFIX=**|Subject prefixes for merged files.|
+|**! /OTHER_PREFIX=**|Subject prefixes for merged files.|
-|**! /OTHER3D_SUBJECT_TAG=**|Subject tags for merged files.|
+|**! /OTHER_SUBJECT_TAG=**|Subject tags for merged files.|
-|**! /OTHER3D_COLOR=**|The color of the secondary data files.|
+|**! /OTHER_COLOR=**|The color of the secondary data files.|
 |**! /NUMBER_OF_SESSION_FILES_ALLOWED=**|Restricts the number of session files used.|
 |**! /SAVE_DEFAULT_CMZ_FILES=TRUE**|Automatically save default CMZ file with specified name.|
@@ Line 101: / Line 101: @@
 ====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.
+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]
@@ Line 121: / Line 159: @@
 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:
-  - Study
+|**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.|
-  - Group
+|**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.|
-  - Session
+|**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.|
-  - Task
+|**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]].|
-  - Trial
+|**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:\\
+**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
@@ Line 135: / Line 173: @@
   - pose_filt_0.c3d
-|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.|
-|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.|
-|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.|
-|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]].|
-|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.|