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--- visual3d:documentation:pipeline:model_commands:modeling_commands [2024/06/26 20:06] – removed sgranger
+++ visual3d:documentation:pipeline:model_commands:modeling_commands [2024/07/17 15:46] (current) – created sgranger
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+====== Modeling Commands ======
+This page lists several pipeline commands related to modeling. In addition, two examples are presented.
+==== Commands ====
+The commands related to modeling are listed here along with a description of their parameters. The list is not all inclusive.
+=== Add_Landmark ===
+Landmarks (Virtual Markers) are typically added to the model template, but all model commands are also available as pipeline commands.
+=== Add_Functional_Joint_Landmark ===
+This command is based on: **Schwartz MH, Rozumalski A** (2005) A new method for estimating joint parameters from motion data. Journal of Biomechanics, 38, 107-116
+|**Add_Functional_Joint_Landmark**            |                                                                                                                                                                                                                                        |
+|**/LANDMARK_NAME=**                          |The name of the landmark to be created.                                                                                                                                                                                                 |
+|**/CALIBRATION_FILE=**                       |The name of the hybrid model. Use the full pathname.                                                                                                                                                                                    |
+|**/REFERENCE_SEGMENT=**                      |The joint landmark is created relative to an existing segment. For example, for the hip joint center, the pelvis is used.                                                                                                               |
+|**/REFERENCE_TYPES=**                        |The types of reference markers used for defining the landmark.                                                                                                                                                                          |
+|**/REFERENCE_NAMES=**                        |The names of reference markers used for defining the landmark                                                                                                                                                                           |
+|**/SIGNAL_TYPES=**                           |The types of signals used for the tracking markers.                                                                                                                                                                                     |
+|**/SIGNAL_NAMES=**                           |The names of signals used for the tracking markers. Any number of tracking markers may be used.                                                                                                                                         |
+|**/SIGNAL_FOLDER=**                          |The folders for signals used for the tracking markers.                                                                                                                                                                                  |
+|**/MOTION_FILE=**                            |The full pathname of the motion file used. This command allows only one movement file to be used. The user should make sure that a full range of motion about all axes is contained in one file.                                        |
+|**/EVENT_START=**                            |The start frame for the range of data to be used.                                                                                                                                                                                       |
+|**/EVENT_STOP=**                             |The stop frame for the range of frames of data to use.                                                                                                                                                                                  |
+|**/MINIMUM_HELICAL_ROTATION_ACCEPTED=**      |Any combination of three frames for which the helical rotation angle is less than 5 degrees are rejected                                                                                                                                |
+|**/CREATE_100_REPRESENTATIVE_LANDMARKS=**    |A random selection of the intermediate Centers of Rotation will be saved as Landmarks.                                                                                                                                                  |
+|**/APPROXIMATE_NUMBER_OF_COMBINATIONS_USED=**|If there are a large number of frames of data, the possible combinations of 3 frames becomes very big. The can specify an estimate of the number of combination used (these are selected randomly from the total number of combinations)|
+|**/SEARCH_RADIUS=**                          |Only Centers of Rotation within the search radius are used for the mean value.                                                                                                                                                          |
+|**/RATE_OF_VOLUME_REDUCTION=**               |The rate at which the domain of possible solutions is reduced.                                                                                                                                                                          |
+|**/NUMBER_OF_ITERATIONS_REDUCING_RADIUS=**   |The number of times the radius is reduced. At each iteration the cell containing the most crossings is used as the center for the next iteration.                                                                                       |
+This command was changed for Visual3D Version 3.83 to allow the specification of **REFERENCE MARKERS** instead of **REFERENCE SEGMENT**.
+  * If a Reference Segment is specified, the landmark will be created relative to that segment.
+  * If no Reference Segment is specified, the landmark will be created relative to the first three REFERENCE MARKERS (e.g. a Technical Coordinate System will be created from these markers). If more than 3 REFERENCE MARKERS are specified, Visual3D will use all REFERENCE MARKERS to track the Technical Coordinate System.
+=== Create_V3D_Model ===
+Create a Visual3D 6 degree of freedom model. This is the legacy Visual3D model which was developed in collaboration with the National Institutes of Health, Physical Disabilities Branch. It is currently considered a legacy model because all of the features of this model are incorporated in the Visual3D hybrid model.
+<code>
+Create_V3D_Model
+! /CALIBRATION_FILE= the name of the c3d file for the static trial
+;
+</code>
+**Note: Wildcards (*) can be used for the Calibration_File name**
+=== Build_Model ===
+In some circumstances Visual3D does not automatically rebuild the model. For example, landmarks that have been added by a script command do not automatically rebuild the model because sometimes there may be several landmark commands in sequence and rebuilding the model would slow done the processing of the pipeline. The command **Build_Model** will build the model.
+<code>
+Build_Model
+! /CALIBRATION_FILE=  The name of the standing trial associated with the model
+! /REBUILD_ALL_MODELS= TRUE or FALSE to rebuild all models
+! /DISPLAY_RESULTS=  TRUE or FALSE to display results
+;
+</code>
+=== Apply_Model_Template ===
+Apply a Model Template to a Model (Calibration File).
+<code>
+Apply_Model_Template
+/MODEL_TEMPLATE=  The name of the model template
+/CALIBRATION_FILE=  The name of the standing trial associated with the model
+;
+</code>
+**NOTE:** Wildcards (*) can be used for FILE_NAME and MODEL_NAME.
+**NOTE:** In early versions of Visual3D, this command was called **OPEN_MODEL_FILE**. Even though this name no longer appears in the pipeline dialog, if it appears in the Pipeline Script, it will still be recognized and processed correctly by Visual3D.
+=== Save_Model_Template ===
+This command saves the specified link model to a template.
+<code>
+Save_Model_Template
+/CALIBRATION_FILE=  The name of the standing trial associated with the model
+/MODEL_TEMPLATE= The name of the model template
+;
+</code>
+**NOTE:** You can use a wildcard for the calibration_file but you must specify the full model template name.
+An example,
+<code>
+Save_Model_Template
+/CALIBRATION_FILE=*1.c3d
+/MODEL_TEMPLATE=C:\Visual3D\Data\template.mdh
+;
+</code>
+=== Close_Calibration_File ===
+Close an open model and calibration file.
+<code>
+Close_Calibration_File
+/Calibration_File= The name of the standing trial associated with the model
+;
+</code>
+=== Set_Segment_Properties ===
+Sets the inertial properties of a segment. The command allows the user to set the variable value as an expression. For example, the mass could be represented as:
+/MASS=0.12*Mass
+where Mass is a subject property that has already been defined. The user can set one or all of the properties with this command (a blank entry is ignored).
+<code>
+Set_Segment_Properties
+/CALIBRATION_FILE=
+/SEGMENT_NAME=
+! /KINEMATIC_ONLY=
+! /MASS=
+! /CG_FROM_PROX_AXIAL=
+! /CG_FROM_PROX_ML=
+! /CG_FROM_PROX_AP=
+! /INERTIA_XX=
+! /INERTIA_YY=
+! /INERTIA_ZZ=
+! /AP_DIRECTION=
+! /AXIAL_DIRECTION=
+! /MODEL_FILE=
+! /MATERIAL_FILE=
+;
+</code>
+=== Set_Subject_Weight ===
+Set the weight of the subject (kgs). If no LINK_MODEL (Calibration File) is specified, the current model is used. If no Weight is specified, a dialog pops up.
+<code>
+Set_Subject_Weight
+/Calibration_File= The name of the link model (standing trial)
+/Weight= Weight
+;
+</code>
+**NOTE:** If the model is a hybrid model, the Weight parameter can be an expression (e.g. a Model Metric).
+For example, the user enters the Weight of the subject in pounds using a pipeline parameter. This can be converted to Newtons for the model.
+<code>
+Prompt_For_Pipeline_Parameter_Value
+/PIPELINE_PARAMETER_NAME= WEIGHT
+/PROMPT= Enter the Weight of the Subject in Pounds
+/DATA_TYPE=STRING
+/DEFAULT_VALUE=1
+;
+Set_Subject_Weight
+/Calibration_File=
+/Weight= ::WEIGHT/2.2
+;
+</code>
+=== Set_Subject_Height ===
+Set the height of the subject (m). If no LINK_MODEL (Calibration File) is specified, the current model is used. If no Height is specified, a dialog pops up.
+<code>
+Set_Subject_Height
+/Calibration_File= The name of the link model (standing trial)
+/Height= Height
+;
+</code>
+**NOTE:** If the model is a hybrid model, the Height parameter can be an expression (e.g. a Model Metric).
+For example, the user enters the Height of the subject in inches using a pipeline parameter. This can be converted to meters for the model.
+<code>
+Prompt_For_Pipeline_Parameter_Value
+/PIPELINE_PARAMETER_NAME= HEIGHT
+/PROMPT= Enter the Height of the Subject in Inches
+/DATA_TYPE=STRING
+/DEFAULT_VALUE=60
+;
+Set_Subject_Height
+/Calibration_File=
+/Height= ::HEIGHT/39.4
+;
+</code>
+=== Set_Model_Metric ===
+This command was originally part of the model template in Visual3D. In version 4.0 this command will be expanded for general use. This is a convenient way for the user to interact with the model by entering values in a popup dialog rather than by editing the model in model builder mode. This command is a good way to add in a metric that is used in your model.
+The following example will set the proximal radius for the right thigh segment to 0.1
+<code>
+Set_Model_Metric
+! /CALIBRATION_FILE=
+/METRIC_NAME=RTH_Distal_Radius
+/METRIC_VALUE=0.1
+;
+</code>
+==== Examples ====
+Here are two examples utilizing pipeline modeling commands.
+=== Pipeline Example using Create_Hybrid_Model ===
+<code>
+!***********************************************
+! Create Hybrid model example script
+!***********************************************
+Set_Pipeline_Parameter_To_Folder_Path
+/PARAMETER_NAME=FOLDER
+/PARAMETER_VALUE=c:\Visual3D\Data\
+;
+Set_Pipeline_Parameter
+/PARAMETER_NAME=STANDING
+/PARAMETER_VALUE=::FOLDER&*static.c3d
+;
+Create_Hybrid_Model
+/CALIBRATION_FILE=::STANDING
+;
+</code>
+=== Pipeline Example using Assign_Model_File ===
+<code>
+!***********************************************
+! Assign model example script
+!***********************************************
+Set_Pipeline_Parameter_To_Folder_Path
+/PARAMETER_NAME=FOLDER
+/PARAMETER_VALUE=c:\Visual3D\Data\
+;
+Set_Pipeline_Parameter
+/PARAMETER_NAME=STANDING
+/PARAMETER_VALUE=::FOLDER&*static.c3d
+;
+Create_Hybrid_Model
+/CALIBRATION_FILE=::STANDING
+;
+Set_Pipeline_Parameter
+/PARAMETER_NAME=WALKING
+/PARAMETER_VALUE=::FOLDER&*walk*.c3d
+;
+! Prompt for the Movement data files.
+! Multiple files can be selected in the dialog file listing using CTRL-Click
+Open_File
+! /FILE_NAME=
+;
+Assign_Model_File
+/CALIBRATION_FILE=::STANDING
+/MOTION_FILE_NAMES=::WALKING
+;
+</code>