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--- a +++ b/CHANGELOG.md @@ -0,0 +1,2070 @@ +# Changelog + +% A rendered version of the CHANGELOG is avaible here: +% https://anyscript.org/ammr/beta/changelog.html + +(ammr-3.1.0-changelog)= +## AMMR 3.1.0 (2025-03-31) +[](https://doi.org/10.5281/zenodo.15094590) +[](https://www.anybodytech.com/resources/customer-downloads/) + + + +### 🔧 Changed: + +* Modified the Human-Ground residual implementation in MoCap models to use + rotational measures configured for angular velocities. This change enhances + the robustness of the residuals and makes the residual output easier to + interpret geometrically, without affecting the results. +* Updated the insertion and origin points of the Gluteus Medius to ensure + correct moment arms for external rotation in specific postures. The posterior + Gluteus Medius now twists inside the anterior part and attaches more + anteriorly on the femoral trochanter. +* The wrapping surface for muscles at the wrist has been changed from a cylinder + to an ellipsoid. This lowers the risk of muscle via points penetrating the + wrapping surface in postures involving both flexion/extension and + abduction/adduction at the wrist. +* Excluded force plates from the parameter identification study, as they were + unnecessary. This change may slightly speed up the parameter identification + process. +* The coordinate system used when scaling the shank segment has been aligned + with same reference frame used when scaling the thigh segment, instead of + using the anatomical frame of the shank. Now both segments use the direction + given by the femoral epicondyles as the lateral direction. This change + ensures consistent scaling across the knee joint. + +### ➕ Added: + +* Introduced a new class template, + [`CreateCoMRefNode`](#Utilities.center-of-mass.createcomrefnode.createcomrefnode), + for generating a reference node at the center of mass of a segment, aligned + with its principal axes of inertia. +* Added the `TRI(N)` macro to create a lower triangular (NxN) matrix. +* Added the `TOTAL_POLYLINE_LENGTH(P)` macro to compute the total length of a + polyline defined by a set of points. + +### 🩹 Fixed: + +* Corrected the PelvisGround rotation drivers in the {ref}`Free Posture Static + example<example_freeposture>`. The X and Z rotation drivers were previously + mixed up and are now properly assigned. +* Resolved an issue that prevented disabling the drawing of marker arrows in + `CreateMarkerDriverClass` within MoCap models. The search string in + `Main.ModelSetup.Views.All_MarkerArrows.Objects` has been updated to correctly + identify the arrow drawing objects. +* Fixed a spelling typo in the disc stiffness BM control statements. The + `BM_TRUNK_*_DISC_STIFNESS` parameters have been renamed to `BM_TRUNK_*_DISC_STIFFNESS`. + The misspelled parameter names have been deprecated. +* The data points for the femoral epicondyles with respect to the shank in the + neutral posture have been corrected. These values were not updated when the + knee axis in shank was redefined in TLEM 2.2 and AMMR 3. This change has no + influence on the default AnyBody Models, but it fixes an issue if the model + was configured to use the {bm_constant}`special 'bony landmark' defined <_JOINT_TYPE_BONY_LANDMARK_>` + joint axis configuration. + +### Removed: + +* Removed the python hooks to check for modified AMMR folder. This feature was + not used and has been removed to simplify the AMMR codebase. + +(ammr-3.0.4-changelog)= +## AMMR 3.0.4 (2024-07-02) +[](https://doi.org/10.5281/zenodo.12592455) +[](https://www.anybodytech.com/resources/customer-downloads/) + +### 🩹 Fixed: +* Fixed an issue in the {ref}`Bike Model example <example_bikemodel>` that + included thoracic support in the full body model also. +* Fixed an issue with the visualization of the marker coordinate system arrows. They now + correctly update while running running parameter identification in the MoCap models. + +(ammr-3.0.3-changelog)= +## AMMR 3.0.3 (2024-06-10) +[](https://doi.org/10.5281/zenodo.11191711) +[](https://www.anybodytech.com/resources/customer-downloads/) + +### 🩹 Fixed: +* Fixed a penetration warning for the pectoralis muscles when the thoracic + segments are scaled very non-uniformly. The fix involves a small (5 deg) + adjustment to the orientation of the pectoralis wrapping surface. +* Fixed default limits in [Range of Motion limits](#Utilities.Kinematic-limits.RangeOfMotionLimits_template.any) + class template. The default limits for PelvisThoraxExtension, PelvisThoraxLateralBending, + Right/LeftWristFlexion had the upper and lower limits flipped. This is now fixed and a + check is added in the class template to catch this kind of error. +* Fixed an issue where blinking Windows would appear when loading models stored + in git repositories. This issue was caused by a python subprocess that queried + the git repository for branch information. +* Updated the foot marker position in the Xsens protocol to accommodate the + changes made to the foot anatomical frame in the TLEM 2.2 leg model. The + R/LTOE and R/LTOE2 markers have been moved upwards by 1.5 cm. + +(ammr-3.0.1-changelog)= +## AMMR 3.0.1 (2024-02-13) +[](https://doi.org/10.5281/zenodo.10803883) +[](https://www.anybodytech.com/download/anybodysetup-8-0-1-11638_x64/) + + +This minor release of AMMR contains no updates to the models compared to the major AMMR 3.0.0 released the previous month. It only has a few minor changes to the documentation and new tolerances in the FDK models. + +### 🔧 Changed: + +* Finer FDK tolerances for the {ref}`Knee Simulator example + <example_kneesimulator>`, to take avantage of the improved robustness of the + AnyBody FDK solver in version 8.0.1. + + +(ammr-3.0-changelog)= +## AMMR 3.0 (2024-02-13) +[](https://doi.org/10.5281/zenodo.10527958) +[](https://www.anybodytech.com/download/anybodysetup-8-0-0-11540_x64/) + + +### ✨ Highlights + +* Integrated pelvis, lumbar, and thorax models into a consistent trunk model in + preparation for a full thoracic model in [AMMR 4](https://anyscript.org/ammr/beta/body/thoracic_model.html). +* Updated the leg model (TLEM 2.2) with improvements to the ankle complex, + shank orientation, and alignment of the patella tendon. +* Added new wrapping surfaces to the Achilles tendon around the + ankle in the TLEM 2.2 leg model. +* Made numerous improvements and fixes to the Body models, MoCap models, + and application examples. + +:::{Warning} Care must be taken when porting existing MoCap models to the +new AMMR. Changes to the pelvic tilt, and changes to the foot anatomical +frame can cause MoCap markers on Pelvis and feet to have moved slightly. + +If migrating models from AMMR 2.4, be sure to check markers on +pelvis and the foot segments. The Y component may need to be adjusted to +achieve same marker position and joint angle output. +::: + + +### 🩹 Fixed: +* Fixed a couple of bugs in the {ref}`Seated Human model <example_seatedhuman>`: + - Reactions for subtalar joint driver are switched off. + - GHDriverLeft was using velocity value from GHExternalRotation instead of GHAbduction. + This is now fixed. +* The `Main.ModelSetup.CreateVideo` operation was missing in some of the MoCap + examples. This has been fixed. If you have this problem update the + `CreateVideo.any` file in your application. +* Fixed a wrapping problem with the posterior deltoid muscle in the 2-parameter + shoulder calibration. +* Fixed a bug in the LegPressMachine example that caused the model view to zoom + to infinity. +* Improved the robustness of muscle recruitment for abdominal muscles (`buckle + support`) by increasing the strength of recruited reactions on buckle segment + balance. +* Updated scaling functions (`Scale`) for segments in trunk model (lumbar, + thoracic and cervical) to account for pelvis segment morphing into leg pelvis + coordinate system using `BM_LEG_TRUNK_INTERFACE` setting. +* Fixed a bug in the `AnatomicalFrame` of TLEM 2.2 foot and talus that caused the + ARel to be constructed from unscaled landmarks. +* Fixed small inaccuracy in the mass scaling of the shank. It did not account for the + mass of the patella segment which uses the same scaling coefficient as the shank. +* Visualizaiton of muscles in AMMR now use the builtin `.viewMuscle` drawing objects + in the muscle class. Hence, all manually created `AnyDrawMuscle` objects, usually named + `DrwMus` have been removed. +* The kinematic start guess for left patalla joint has been adjusted to improve + robustness of the kinematic solver. This does not changed the result of + models. + + +### ➕ Added: +* Added two small helper code macros: + `NON_UNIQUE_VALUES()`/`NON_UNIQUE_POINTERS()` for finding duplicate + (non-unique) entries in arrays of values and pointers. + +* Added new set of hip joint measures (`Interface.Right.HipISB`) that strictly + follow the International Society of Biomechanics' (ISB) definitions. These + measures are similar to existing angles but do not have zero hip-flexion in + neutral position due to different definition of pelvis coordinate system with + respect to a plane defined by ASIS-PSIS points. + +* Segments in trunk model (lumbar, thoracic and cervical) now explicitly define + a `ScalingNode` node indicating coordinate system for segment scaling. + +* Improved error message when MoCap markers in marker protocol are missing from + C3D file. + +* Add an option to override the default kinematic joint limits in the MoCap + framework + +### 🔧 Changed: + +* The trunk joint reaction force in `SelectedOutputs` + is now expressed in new reference nodes that are aligned with the vertebral body. + Therefore, the names of the outputs now include CompressionForce and + ShearForce. The new reference nodes are created inside the joint node on the proximal + segment. The implementation from AMMR 2.4 can be enabled by using the compatibility + switch: `#define BM_COMPATIBILITY_24_TRUNK_SELECTED_OUTPUTS_JRF ON` + +* Adjustments to pelvic tilt have changed the position of MoCap markers on the + pelvis segment. This mostly affects markers with hardcoded positions. + Particularly PSIS markers furthest posterior from the origin between ASIS. + When migrating from AMMR 2.4 models without adjusting marker positions, PSIS + markers may move 2 cm lower. + + - Most [non-MoCap model examples](#example-gallery) + have been updated to account for the new pelvic tilt value. Either by using the + `AnatomicalFrameTrunk` reference frame in the pelvic driver or by adjusting the + Pelvis-Thorax Extension slightly. + +* The Twente Lower Extremity Model (TLEM) 2 leg model has several updates and is + now designated as [TLEM 2.2](#TLEM2-v2.2). + + - The ankle complex and the knee joint axis have been redefined to compensate for + the non-neutral position in which the cadaver was scanned. This improves the + alignment of the tibia, talus, and calcaneus bones. The updated knee joint ensures + that the patella tendon is straight in the neutral position. The net effect is + rotation of the tibia about its long axis with the feet still pointing in the + same direction in the neutral position. + + - Wrapping surfaces have been added to the Achilles tendon around the ankle in + the TLEM 2.2 leg model, giving a more even ratio of moment arms between + the soleus and gastrocnemius muscles. Hence, gastrocnemius is recruited + less, especially during downhill walking and stair descent, solving the + tendency of the model to over-predict the knee contact forces at toe off. + This is the first of a number of improvements to the leg model by Dr. Enrico + De Pieri, who is working on a publication on improvements and validation of + the TLEM 2 leg model. + - The foot and talus models in TLEM 2.2 leg model have several updates in + preparation for the release of advanced multi-segment foot models in the + future: + + - The coordinate system of the talus is updated to be coincident with the foot + coordinate system. A new reference node, `TalusCompatibilityFrameAMMR24`, + is created in the talus segment to be consistent with the previous + coordinate system for backwards compatibility. + - Subtalar and ankle joint parameters for the talus have been updated to be + expressed in the new coordinate system. The implementation of the joints + is still consistent with the previous implementation. + - The anatomical frames of the foot and talus are updated and defined using + bony landmarks on the foot. This updates the neutral position of the foot + and talus. This will also update the ankle plantarflexion and subtalar + joint angles. + - The malleoli coordinates in the foot coordinate system have been fixed to + match the malleoli on the shank in the neutral position. + - The model tree has been updated. The talus segment is moved inside the + foot segment. For backwards compatibility, a pointer to the talus segment + still exists outside the foot segment. + + - The implementation of the TLEM model has been split into two separate folders, + `LegTLEM/` and `LegTLEM1/`. All references to TLEM 1 code have been removed in + the code implementing the TLEM 2 model. + + - The TLEM 1 model now triggers a deprecation warning suggesting using TLEM 2. + +* The InverseDynamics analysis in MoCap models now uses the first step of Marker + tracking as a start guess (initial conditions) + for the kinematic solver. This improves robustness in certain cases. + +* The marker protocol in the {ref}`"ADL gait (MoCap model)" + <sphx_glr_auto_examples_MoCap_plot_ADL_Gait.py>` was updated/tweaked to + improve the robustness of the model. Some special exceptions were added to + trials where we discovered that some markers were swapped by accident in the + original open access dataset. + +* Scaling laws defined by the `BM_SCALING` setting have been updated to calculate + offsets between different scaling regions and apply them at load time. Scaling + remains the same, but users can now create scaling functions that account for + offsets between regions with different scaling. + +* Glenoid reaction forces are now expressed in the coordinate system of the glenoid + cup instead of the general scapula coordinate system. Variables + `GlenoHumeral_DistractionForce`, `GlenoHumeral_InferoSuperiorForce`, + `GlenoHumeral_AnteroPosteriorForce` represent three directions given by the + glenoid cup. Variables may differ slightly even if the force remains the same. + +* Resolved inconsistencies in arm muscle parameters. The same underlying parameters + are now used for both simple and 3-element muscle models. + +* MoCap marker protocols: Users must now explicitly specify a coordinate system + relative to which markers are placed on the segment using the + [`PlaceMarkerAt`](#MoCap.Markers.CreateMarkerDriverClass.CreateMarkerDriver:PlaceMarkerAt) + argument in the class template. Previously, this defaulted to the `AnatomicalFrame` of + the segment. + +* The organization of segmental scaling functions was reworked and now configured + slightly simpler. This modification is expected not to affect users working + with default and non-default scaling laws and patient-specific morphing. + Additionally, all spinal segments share a scaling reference frame. + +* We updated how the class `AnySurfCylinderFit` is used in the {ref}`Knee + Simulator example <example_kneesimulator>`. The deprecated way of using the + `AnySurfCylinderFit` has been changed. Since `AnySurfCylinderFit` is now a + subclass of `AnyRefNode`, it should no longer be nested inside another + parent reference frame to provide the pos `sRel` and orientation `ARel`. This + fixes a number of deprecated warnings that would have triggered with AnyBody version 8. + +* Added the new `AnatomicalFrameTrunk` reference frame to the pelvis segment consistent + with anatomical frames in the rest of the trunk model. All joint angles relative + to the pelvis segment now use this frame. This aligns the neutral position of + the model with the neutral position of the trunk dataset and results in more + pelvic tilt in the neutral position, better reflecting reported values in + literature. Existing `PelvisSeg.AnatomicalFrame` defined by the ASIS and pubic bony + landmarks remains unchanged. + +* Updated trend validation in ["Wilke Spine Pressure validation + models"](example_wilkespinepressure) to reflect changes to the thoracic model + and the pelvis frame. Although absolute pressures in the spine have changed, + trends (relative changes in spine pressure between models) remain the same. + +* Reduced discretization (number of elements) of the pectoralis major and + semispinalis muscles for consistency with textbook anatomy. Pectoralis no + longer has its origin on rib 2, and semispinalis no longer inserts on the + lumbar region. + +* Refactored the implementation of muscle parameters in the arm model. All + parameters are now given as muscle volume, optimal fiber length, and tendon + slack length. Physiological cross-sectional area (PCSA), previously a + hardcoded parameter, is now an intermediate value used for calculating muscle + strength from muscle volume and optimal fiber length. + + This new structure allows for overwriting the complete set of muscle volumes with + an alternative dataset. + +* The [`MarkerName`](#MoCap.Markers.CreateMarkerDriverClass.CreateMarkerDriver:MarkerName) + argument in the [`CreateMarkerDriver`](#MoCap.Markers.CreateMarkerDriverClass.CreateMarkerDriver) + template for MoCap models is no longer necessary. The argument can still be used + if the marker class and data entry in the C3D file differ. + +* Updated the implementation of muscle parameters section in models to use the new + `??=` (optional assignment) operator introduced in AnyBody 7.4.1. This allows + for direct overriding/redefinition of muscle parameters and volumes. + + For example, muscle volumes can be overridden with new data. + + ```{code-block} AnyScriptDoc + Main.HumanModel.BodyModel.Right.Leg.ModelParameters.Muscles = { + SoleusMedialis.MuscleVolume = 540; //ml + SoleusLateralis.MuscleVolume = 450; //ml + }; + ``` + +* Updated methods for distributing muscle volume among discretized muscle + elements. This allows for different optimal fiber lengths among elements of a + muscle. If one element has a smaller optimal fiber length (e.g., through + calibration), the volume of muscle elements is redistributed, and PCSA remains + constant across elements. + + If the optimal fiber length of different elements is + the same, this method yields the same result as before. + +* Renamed the folders holding muscle models from `MusPar` to `MuscleModels` for + better clarity. + +* The `CameraClassTemplate.any` include file in model utilities has been renamed to + [`VideoLookAtCamera.any`](#Video-tools.Video.VideoLookAtCamera.any) to have the same name as the class template it + contains. + +### 🧹 Removed: + +- The template `DEFAULT_PARAMETER_FOLDER` has been removed. It is no longer needed + since the same functionality is now provided by the `??=` operator. + +- The three scaling laws `_SCALING_UNIFORM_EXTMEASUREMENTS_`, + `_SCALING_LENGTHMASS_EXTMEASUREMENTS_`, + `_SCALING_LENGTHMASSFAT_EXTMEASUREMENTS_` have been deprecated. They are + superseeded by the "Statistical Scaling Plugin" which cover the same + functionality. The AMMR guide on scaling have been updated to reflect this + change. + + + + +(ammr-2.4-changelog)= +## AMMR 2.4.4 (2023-04-03) +[](https://doi.org/10.5281/zenodo.7764841) +[](https://www.anybodytech.com/download/anybodysetup-7-4-4-8907_x64/) + + +This version of AMMR adds a number fixes and tweaks to the body models which +improves robustness of various kinematic and recruitment solvers. + +**Added:** + +* Added kinematic joint angle limits in MoCap models for elbow and wrist joints + to prevent the kinematic solver from finding postures that are physiologically + impossible, such as bending the elbow backwards. These limits are active where + marker tracking solver would occasionally find a local minima with + unphysiological posture. + +* Tables with body model configuration parameter in the AMMR documentation now + contain links showing their options. For example, see the page on {doc}`Leg + model parameter </bm_config/leg>`. + +**Fixed:** + +* Fixed an issue with wrist joint segment's load time position (start guess). + This greatly improves kinematic robustness of all models with arms as it + creates a 'universal-joint' mechanism for wrist movement. + +* Further fixes made to pectoralis wrapping segment's robustness by optimizing + initial load time positions to ensure model kinematics can more easily solve. + +* Fixed missing `LoadParameters` operation in `LoadAndReplay` operation in MoCap + examples. + +* Fixed a problem with oblique muscles introduced in AMMR 2.4. A weak residual + force was added to Y rotation of buckle to eliminate this problem. + +* Corrected wrong order of nonlinear intervertebral disc stiffness polynomial + coefficients (affects only those who used polynomial disc stiffness). + +* Corrected small asymmetry in function for nonlinear intervertebral disc + stiffness in coronal plane (affects only those who used polynomial disc + stiffness). + + +## AMMR 2.4.3 (2023-01-27) +[](https://doi.org/10.5281/zenodo.7572879) [](https://www.anybodytech.com/download/anybodysetup-7-4-3-8899_x64/) + + +**Added:** + +* Added a few utility helper class templates + + - `Template_OperationSaveValues` + - `Template_OperationLoadValues` + - `Template_OperationUpdateValues` + + to make it easier to do common class operations without manually having to + create the operations with macros. + + To create an operation which loads a file, do: + + ```{code-block} AnyScriptDoc + Template_OperationLoadValues LoadAnySetFile = { + FileName= "MyFile.anyset"; + }; + ``` +* A more helpful error message is now printed when MoCap markers in the marker + protocol are missing the C3D file. + +**Changed:** +* The load-time position of the box in the {ref}`BVH_BoxLift model + <sphx_glr_auto_examples_Mocap_plot_BVH_BoxLift.py>` is now calculated using + the position of the hands. Also, + `Main.ModelSetup.EnvironmentParameters.GravityDirection` defined in the + `box.any` file is now calculated automatically from + `Main.ModelSetup.LabSpecificData.Gravity` defined in the `LabSpecificData.any` + file. These changes should make the model more robust when dealing with + different BVH files. +* It is no longer necessasry to supply the `MarkerName` argument in the + CreateMarkerDriver template MoCap models. The argument can still be used if + the marker name and the data entry in the c3d file are different. +* The references to muscle models in the joint muscles of the detailed hand have + been renamed to avoid future naming conflicts. +* The "via-points" for the Psoas Major muscle have been adjusted to ensure that + the muscles can better act the role of stabilizing muscle for the lumbar + spine. + +**Fixed:** +* The `Main.ModelSetup.CreateVideo` operation was missing in some of the MoCap + examples. This has been fixed. If you have this problem please update the + `CreateVideo.any` file in your application. +* Fixed a wrapping problem with the posterior deltoid muscle in the + two-parameter shoulder calibration. +* Fixed a bug in the LegPressMachine example that caused the model view to zoom + to infinity. +* The robustness of muscle recruitment with the abdominal muscles (`buckle + support`) was futher tweaked by increasing the the strength of the recruited + reactions on the balance of the buckle segment. + + +## AMMR 2.4.2 (2022-07-08) +[](https://doi.org/10.5281/zenodo.6809697) [](https://www.anybodytech.com/download/anybodysetup-7-4-2-8845_x64/) + +AMMR version 2.4.2 contains only a few minor changes and fixes compared to +version 2.4.1. + + +**Changed:** + +* Changed defintion (sign) of the `SkullThoraxRotation` and + `SkullThoraxLateralbending` variable in the `interface` folder. They are now + consistent with similar difinitions in the rest of the spine. +* The location of the foot drawing generated by the `OptimizeBVH_Origin` class + template for visualization of the target location and orientation of "LFOOT" + and "RFOOT" has been updated to better match the expected actual foot + location. + + +**Fixed:** + +* Fixed the {ref}`Evaluate moments arms example + <sphx_glr_auto_examples_Validation_plot_EvaluateMomentArms.py>` where a few + branches of the latisimus dorsi, pectoralis major and trapezius muscles were + not included. +* Fixed a problem that caused the `OptimizeBVH_Origin` class template to fail to + load if the same human segment was used more than one time in the same model. + + + +## AMMR 2.4.1 (2022-05-30) +[](https://doi.org/10.5281/zenodo.6533249) [](https://www.anybodytech.com/download/anybodysetup-7-4-1-8830_x64/) + + +**New example models:** + +- Added a model using a new class template to optimize the origin of BVH model. + This model shows how to optimize the origin of the BVH model such that a + target segment of the human model (Left/Right Foot/Hand) hits a known position + and orientation in a given time interval while following the recorded motion + from the trial. <{ref}`See more + <sphx_glr_auto_examples_Mocap_plot_BVH_OptimizeOrigin.py>`> + + +**Fixed:** +* Fixed a small syntax error which caused the BVH example `S1/S01_Trial02/` to + fail loading. +* Fixed a problem with the "interface" morphing between the TLEM2 pelvis and + Trunk Pelvis at the tip of the scarum bone. This bug was visible when using + `#define BM_LEG_TRUNK_INTERFACE _MORPH_LEG_TO_TRUNK_`, (i.e. when using the + trunk pelvis morphology with the TLEM2 model), which is not the default. +* Fixed missing calibration for the new latissimus dorsi elements introduced in + AMMR 2.4. This fix also ensures that all latissimus dorsi elements are + calibrated in the same arm posture. + + +**Changed:** + +* The anyscript implemenatation of the acromio-clavicuala, sterno-clavicular, + gleno-humeral, and elbow joints have been refactored. They now use explicit + AnyScript joint classes (e.g. `AnySphericalJoint`) instead of implementing the + joints directly with measures and constraints. This simplifies the + implementation, but also changes the structure of the model tree. However, it + has no influence the kinematics of the model, which remains identical. + + The new names of the explicit joint objects in `ShoulderArm.Jnt` are: + + * `SternoClavicularJoint` (-3 DOF) + * `AcromioClavicularJoint` (-3 DOF) + * `GlenoHumeralJoint` (-3 DOF) + * `HumeroUlnarJoint` (-5 DOF) + * `HumeroRadialJoint` (-1 DOF) + * `ProximalRadioUlnarJoint` (-2 DOF) + * `DistalRadioUlnarJoint` (-2 DOF) + +The `HumeroUlnarJoint` is the elbow flexion extension, and together +`HumeroRadialJoint`, `ProximalRadioUlnarJoint` and `DistalRadioUlnarJoint` adds +5 constraints leaving the forearm rotation degree of freedom. + + +**Added:** +* A few previously renamed nodes in pelvis were added back to improve backwards + compatibility when loading old seating models. + + +## AMMR 2.4 (2022-04-28) +[](https://doi.org/10.5281/zenodo.6471999) [](https://www.anybodytech.com/download/anybodysetup-7-4-0-8782_x64/) + + +**New example models:** + +- Added a new trunk exoskeleton concept model for simulating assistance at the + trunk in a box lifting task. This simple example shows how to apply assistive + torque directly to the human model. <{ref}`See more + <sphx_glr_auto_examples_Other_plot_ExoConceptTrunk_BoxLift.py>`> +- Added a new exoskeleton concept model for simulation-driven conceptual design + of exoskeletons. The model was developed by Prof. John Rasmussen from Aalborg + University. Please see the [web + cast](https://www.anybodytech.com/download/simulation-driven-conceptual-design-of-exoskeletons/) + for more details. <{ref}`See more + <sphx_glr_auto_examples_Other_plot_ExoConcept_BoxLift.py>`> +- Added a new femoral torsion tool to apply femoral torsion to the TLEM2.0 leg + model. This model tool was developed by Dr. Enrico De Pieri from University of + Basel Children’s Hospital (UKBB). Please see the documentation or the [web + cast](https://www.anybodytech.com/download/modeling-subject-specific-femoral-torsion-for-the-analysis-of-lower-limb-joint-loads/) + by Enrico on his work and publication on femoral torsion. <{ref}`See more + <sphx_glr_auto_examples_Orthopedics_and_rehab_plot_FemoralTorsionTool.py>`> +- Added a new knee force model example. The model shows how to calculate a + simple estimate of the medial and lateral knee force. <{ref}`See more + <sphx_glr_auto_examples_Orthopedics_and_rehab_plot_KneeForcesExample.py>`> +- A new box lifting motion capture model has been added. The model is based on + data from an inertial measurement unit based suit + ([Xsens](https://www.movella.com/products/wearables/xsens-mtw-awinda)), and + illustrates how to connect MoCap models with objects in the environment. + <{ref}`See more <sphx_glr_auto_examples_mocap_plot_bvh_boxlift.py>`> + + +**New features:** + +- Many AnyScript example models now include an option to automatically create a + video from the model. To use this functionality find and run the new + `VideoTool.CreateVideo` operation under the Study folder. This will + automatically run the example model, output still frames, and combine them + into a video afterwards. The script can easily be adapted and moved to other + examples. +- Two new utility macros, which make it easier to create 3D grid arrays, have + been added to the model repository. `MESHTRIPLES(xarr, yarr, zarr)` and + `MESHGRID(xarr,yarr,zarr)`. i.e. for creating arrays of all points in a 3D + grid array. More information in the file: {menuselection}`Body --> AAUHuman + --> BodyModels --> GenericBodyModel --> Helper.ClassTemplates.any` + +- Added a warning when the glenohumeral flexion/abduction in the mannequin + values can cause problems as start guess for the kinematic solver. A small + automatic pertubation of the Humerus orientation (`Axes0`) is also added in + these cases so the shoulder rhythm will work as expected. +- There is a new option to override more settings in the + `DefaultMannequinDrivers` section. Now the driver type (`CType=Hard/Soft`), + can be overridden directly by the users. +- Fixed a lack of robustness with muscle recruitment of the abdominal muscles + (`buckle support`). Muscle recruitment could previously fail with high lumbar + flexion. A small support "artificial muscle" has beeen added to the buckle + segment, preventing muscle recruitment from failing. + +**Fixed:** + +- Improved the selected output by adding the m. Semimembranosus and m. + Semitendinosus contributions to the knee flexor group for both muscle activity + (`KneeFlexorMuscleActivity`) and muscle force (`KneeFlexorMuscleForce`). +- Updated and improved origin of the hamstring muscles. The muscles biceps + femoris, semitendinosus and semimembranosus have been updated to improve their + moment arms in certain lunge movements. The origin points at pelvis has been + moved down a bit to ensure the muscles wraps correctly in lunge movements, + while maintaining the same moment arm in gait etc. +- Fixed a bug in scaling where the mass of the trunk model pelvis was used in + some cases instead of the pelvis mass from the leg model. This could cause a + slightly incorrect mass to be used for the pelvis segment. +- Fixed wrong sign for the WristJoint flexion variable. The values users provided in the mannequin + section was incorrectly interpreted as wrist extension. +- Fixed a problem where custom scaling and {bm_constant}`_SCALING_XYZ_` would + prevent the model from loading. +- Fixed some logical issues with the `ContactSurfaceDistanceAndVelocityDepLinPush.any` file. + + - Fix length calculation and drawing of the normal force + - Fixed an extrapolation error when changing the internal setting + `_SMOOTHING_FUNCTION_PROFILE_` to `FUNC_PROFILE_BSPLINE`. We now cap the + height ratio to only be in the interpolation area. Values outside this area + infer that no contact is present. + +- Refactored the way Trunk nodes are mirrored between left and right. This is + more consistent with the remaining body parts and handled in the cadaver data + files. +- Fixed a problem in MoCap models where calibration studies were not run + automatically in models that only had 3-element muscles on the upper body. +- The {ref}`example to evaluate moments arms <sphx_glr_auto_examples_Validation_plot_EvaluateMomentArms.py>` + now works when the shoulder rhythm is enabled. + + +**Changed:** + +- Improve the trunk model's strength for trunk external rotation. This change + improves the implementation of the internal/external obliques and latissimus + dorsi muscles. More branches are added to the internal obliques and the + geometry is updated to better match anatomical text books. Likewise, the + latissimus dorsi muscles is discretized into more branches so it has branches + inserting on every vertebra. +- The `clavicle` entry in the `Anthropometric.SegmentMasses` folder have been + renamed to `shoulder`. This makes it consistent with the rest of varaibles in + the folder, and correctly reflect that the mass is assigned to both the + scapula and clavicle segment. +- The `OptimalFiberLength` and `TotalTendonLength` in the TLEM leg models are no + longer 'DesignVar' when the parameters are also calibrated. This prevents the + huge amount of warnings when calibrating the leg muscles. +- The `L5LContactNode`,`L4LContactNode`,`L3LContactNode`, + `L4LContactNode`,`L1LContactNode` nodes were scaled using the Right node + Z-axis. This is now changed to use the Left node Z-axis. +- The trunk model has been restructured in preparation for a full Thoracic + model. This means that all the vertebra and ribs have been created in the + model structure, but only as `AnyFolder&` references to the single rigid + thorax segment. + + :::{note} A number of nodes have been renamed in the process. If you have + problems loading old model due to missing nodes, please consult the new model + examples to find the new names. + ::: + +- Updated the neutral scapula position and scapula sliding. The default neutral + scapula position (medial rotation) has been updated to a more realistic + position. Additionally, the node at scapula TS point, on which the scapula + slides, has been moved to provide a more realistic clearance between the + scapula and the ellipsoid sliding surface representing thorax. + Thanks to Johanna Menze (@menzejo) from the University of Bern for updating + the model. +- Renamed a few variables named `r` which could collide with built-in `r` + variable. + +**Removed:** + +- The previously deprecated BM keyword `_LEG_MODEL_Leg_` has been completely + removed. +- The special mannequin driver switches for the old leg model + (`BM_MANNEQUIN_DRIVER_ANKLE_EVERSION_RIGHT/LEFT`) have been deprecated. + Instead the switch used for the TLEM1/2 leg models + ({bm_statement}`BM_MANNEQUIN_DRIVER_ANKLE_SUBTALAR_EVERSION_RIGHT`) can now be + used for all leg models. +- Renamed all deprecated ligament class names. `AnyViaPointLigament`-> + `AnyLigamentViaPoint`. + +## AMMR 2.3.4 (2021-07-05) +[](https://doi.org/10.5281/zenodo.5060249) [](https://www.anybodytech.com/download/anybodysetup-7-3-4-8518_x64/) + +**Fixed:** + +- Improved the intial guess for Latissimus dorsi wrapping, so the wrapping + solutions becomes more robust to extreeme starting postions. +- Fix a problem with `<ANYBODY_PATH_MODELUTILS>/Reactions` support files + preventing models from loading correctly. Thanks to prof. Michael Skipper + Andersen (Aalborg University) for finding this bug. + +**Added:** + +- Add small helper class template `DriverBasedOnLoadPos` which makes it easy to + add constraints between two segments based on their load time positions. +- Refactor the way pelvis rotations are measured in the interface folder. This + allows the user to override the default implicit global reference frame and + thus output pelvis rotation relative to a custom frame. +- Add a new ability to evaluate trunk strength into the built-in studies for + {ref}`joint strength evaluation + <sphx_glr_auto_examples_Validation_plot_EvaluateJointStrength.py>`. +- New ligaments connecting the Sacrum and Pelvis segments are added. They are + enabled togehter with the ligaments on the lumbar spine through the + `BM_TRUNK_LUMBAR_LIGAMENTS` define statement. + +**Changed:** + +- The {ref}`"ADL gait (MoCap model)" + <sphx_glr_auto_examples_MoCap_plot_ADL_Gait.py>` has been updated with most + recent improvements from our internal projects. The marker protocol has been + adjust and a lot of small data problems (marker dropouts etc) has been fixed. +- The posture of the {ref}`standing lift example + <sphx_glr_auto_examples_ADLs_and_ergonomics_plot_StandingLift.py>` have been + modified to make the example more robust. +- The `Tuber_ischiadicum` node to `Seat_contact` as it was misaligned to the + actual bony landmark position. New `Tuber_ischiadicum` nodes have been added + at the bony landmark. The renaming also makes it easier to identify what the + node is used for across the ammr models. +- Changed the way the arm joint moment measures are calculated. This affect the + output when no muscles are added to the model, and the + moments are now calculated and expressed in same way as when muscles are + included. The moments are expressed in a fixed proximal reference frame + instead of using the euler axis of rotation which may not be othogonal. All + moment contribution also now found using search function which will be more + robust. + +## AMMR 2.3.3 (2021-03-24) + +[](https://doi.org/10.5281/zenodo.4616316) [](https://www.anybodytech.com/download/anybodysetup-7-3-3-8440_x64/) + + + +**Fixed:** + + `OptimizeAnthropometricsOnOff.any` preventing models with only one leg +- Fix a problem single leg models in AnyMocap. The file + included from being loaded. +- Removed two unused measures with references to thorax in the scapula and + clavicula segments. The references could cause problems for ´AnyKinCOM\` which + uses search when including segments. Thanks to Handa Kensuke from Terrabyte + helping fix this error. +- Fix bug in initial wrapping guess for Triceps LH muscle wrapping. This bug + could cause the left side Triceps LH muscle to wrap incorrectly at shoulder. +- Fix calibration of of element 4 and 5 of the latissimus dorsi muscle. These + two stands of the muscles where not included correctly in the calibration + study when using the three element muscles model. + +**Changed:** + +- The settings of the {ref}`Knee Simulator example <example_kneesimulator>` has been + tweaked to make it run faster. + +## AMMR 2.3.2 (2021-01-21) + + +[](https://doi.org/10.5281/zenodo.4305559) [](https://www.anybodytech.com/download/anybodysetup-7-3-2-8354_x64/) + + + + +```{rst-class} without-title +``` + +:::{warning} **Model results can change!** + +A bug related to scaling was fixed in AMMR 2.3.2. This affect models using the +{bm_constant}`length-mass-fat<_SCALING_LENGTHMASSFAT_>` and +{bm_constant}`uniform <_SCALING_UNIFORM_>` scaling, when only Body Height is +specified. The results can change as models more accurately match the +requested body height. +::: + + +**Fixed:** + +- Fixed tibialis anterior/posterior variables in the `SelectedOutput` section. + The force values were represented as the `max()` of the muscle elements + instead of the `sum()`. Thanks to Dr. Enrico De Pierie from University + Children's Hospital Basel for fixing this issue. +- Fixed a bug when using {bm_constant}`_SCALING_LENGTHMASSFAT_` and + {bm_constant}`_SCALING_UNIFORM_` and only specifying the body height as input. + The segment lengths were set to slightly smaller values, which caused the + total body height to be less than what was used as input. The bug occurred + since a standard body height in some 'AnyMan' files was assumed to be 1.8 m + instead of the correct 1.75 m. This fix aligns the results with + {bm_constant}`_SCALING_XYZ_` (used in the MoCap models) and + {bm_constant}`_SCALING_STANDARD_` (50 percentile) which were both correct. +- Fixed a problem with foot support in the {ref}`"Spine Pressure validation + model" <sphx_glr_auto_examples_Validation_plot_WilkeSpinePressure.py>` lying + flat on the back. The foot is now supported in the right direction. +- Fixed a problem with the Standing Model template which was using an alternate + mode where foot constraints were disabled. +- Fixed a problem with the ADL gait MoCap example, where the batch processing + script would report some trials as failed even if they succeeded correctly. +- Use correct times in the Xsens example MoCap (trial "S01-Trial2"). The model + stopped walking after a number of time steps + because `tEnd` was set after the last data point in the BVH data file. +- Fixed/improved the wrapping surface for the subscapularis muscles. The muscles + can no longer slide off + its wrapping surface in extreme range of motions. +- Fixed infraspinatus muscle wrapping for high arm positions. This fix adds a + torus for infraspinatus wrapping on the humerus. + It fixes a problem where infraspinatus could slide of its wrapping surface in + high arm postures. +- Fix problem with latissimus dorsi muscle wrapping in over-head arm postures. A + new wrapping ellipsoid has been added at the humeral head. + +**Changed:** + +- The rectus femoris muscle wrapping surface at the hip has been adjusted to + prevent collision between the rectus femoris origin and the wrapping surface. + Further, the surface is now used for both the straight and reflected head of + the rectus femoris. +- Increase the discretization (StringMesh) on approx 30 muscles to improve + wrapping. +- The results for the {ref}`"Wilke Spine Pressure" + <sphx_glr_auto_examples_Validation_plot_WilkeSpinePressure.py>` validation + model has been updated due to the fix for the + {bm_constant}`_SCALING_UNIFORM_`. The updated model improved the validation + results slightly. +- The new large scale {ref}`" MoCap model (ADL gait)" + <sphx_glr_auto_examples_MoCap_plot_ADL_Gait.py>` has been updated so the + results of running all standing reference trials have been added to the model. + This means that all the dynamic trials will work even if the user forgets to + first run the standing reference trials. It is still necessary to run the + standing reference trials again if any changes are made to the model. +- The wrapping for the "Triceps Long Head" muscle has been updated at the + humeral head to avoid the muscle wrapping incorrectly in over-head arm + postures. This fix also adds a via point at the middle of the humerus to make + the wrapping solution more robust. +- The `VideoLookAtCamera` camera class template in the AMMR now saves videos as + they look in the model view. I.e. if things are hidden in the model view they + will not show up in the video. This feature is enabled by a new setting + `AnyCameraLookAt.RenderUserInterfaceViewState` in AnyBody version 7.3.2. The + old behavior can be restored by setting + `Camera.RenderUserInterfaceViewState=Off;` in the class template. + + +## AMMR 2.3.1 (2020-09-30) + +[](https://doi.org/10.5281/zenodo.4023956) [](https://www.anybodytech.com/download/anybodysetup-7-3-1-8217_x64/) + +**Added:** + +- All models now run with the new wrapping solver by default, which makes all + models with wrapping muscles run much faster. Hence the + `AnyBody73_ExperimentalShortestPathSolver` setting is deprecated and no + effect. The old wrapping algorithm can be enabled (not recommended) by + setting: + + ```{code-block} AnyScriptDoc + System.Compatibility.ShortestPathSolverVersion = 2; // 4 is default (new wrapping) + ``` + +- New dedicated wrapping ellipsoid for Triceps at the glenohumeral head. This + addition solves a few problems with overhead arm postures. + +**Changed:** + +- Improvements to the new {ref}`"ADL Gait" + <sphx_glr_auto_examples_MoCap_plot_ADL_Gait.py>` example. The model now has + muscles enabled and the marker protocol has been adjusted for a better + shoulder posture. Also, the batch processing script now runs all trials + without hickups. +- Improve the shoulder rhythm. Scapula position when using the shoulder rhythm + is now determined by the Conoideum ligament driver, like how scapula kinematic + is controlled with no shoulder rhythm. The rhythm is now controlled based on + the **plane of elevation** and **humerus elevation** from the 'ThoraxHumerus' + measures in the interface folder. This tracks the original specification of + the shoulder rhythm in "De Groot, J. H. *The shoulder: a kinematic and dynamic + analysis of motion and loading.* (1998)". One difference is still shoulder + protraction/retraction where regression coefficients needed to be tweaked for + the shoulder to work in the full range of motion. De Groot et al (1998) had + only based their shoulder rhythm on arm position in front of the body (e.i. + positive elevation planes). +- Removed metabolic power (`Pmet`) contributions from artificial muscles defined + as `AnyMuscle` derived classes. `Pmet` contributions from tools, such as GRF + prediction, modelled as `AnyGeneralMuscles` will no longer be part of studies' + Pmet calculations. +- Adjusted the wrapping segments for deltoid posterior so it doesn't affect the + muscle in overhead arm posturess. +- Teres minor now uses a torus for wrapping at the humeral head. + +**Fixed:** + +- Fixed incorrect values in "SelectedOutput" for four reaction moments + variables, which were wrong due an implementation change of + `AnyRevoluteJoint`. The following variables in + `SelectedOutput.Trunk.JointReactionForce` were incorrect. + + - `C2C1FlexionExtensionMoment` + - `C2C1LateralMoment` + - `C1C0AxialMoment` + - `C1C0LateralMoment` + + The values were wrong because they referered to the internal generalized force + output of `AnyRevoluteJoint`. (i.e. `Constraints.Reactions.Fout`). The values + `Fout[3]` and `Fout[4]` can not be interpreted as real physical reaction + moments because `AnyRevoluteJoint` is implemented using euler angles. + + :::{warning} + The use of generalized forces (`Fout`) is + discouraged, and will be removed in the AMMR. Instead use the force and moment + variables in `AnyRefFrameOutput` subfolder instead. + ::: + +- Fixed incorrect volume of Satorius muscle in TLEM1 and TLEM2. Thanks to Dr. + Adam D. Sylvester from Johns Hopkins School of Medicine and Dr. Patricia A. + Kramer from the University of Washington for pointing out the error. The error + occurred since the satorius in the original [TLEM1 + paper](https://doi.org/10.1016/j.clinbiomech.2006.10.003) was muscles in + series with a pseudo insertion/origin on the femur. Both of these muscle + elements were therefore listed with the full PSCA of Satorius. This detail was + missed in the AnyBody TLEM1 and TLEM2 implementation where Satorius was + implemented two parallel elements (TLEM1) and a single element (TLEM2). Hence + the Satorius had twice the correct volume. + +- Fixed a problem when C3D files are malformed and doesn't contain a + `FORCE_PLATFORM.ZERO` variable. The C3D standard specifies that the variable + should exist but since it not used in the models the reference could just be + remvoed. + +- Fixed an problem which prevented the ANSUR scaling plugin example from working + correctly 7.3.0 + +- Fixed incorrect output of `ThoraxHumerus` interface measures. The mesure + wasn't used by other parts of the AMMR until now so the bug had no + consequences in previous AMMR versions. + +- Fixed mass calculation of the foot and talus segments in the `GaitVaughan` + validation model. + +**Removed:** + +- Removed unused `BM_TRUNK_CERVICAL_LIGAMENTS` switch which had no effect since + there were no ligaments defined in the neck model. + +## AMMR 2.3 (2020-07-07) + +[](https://doi.org/10.5281/zenodo.3932764) [](https://www.anybodytech.com/download/anybodysetup-7-3-0-8065_x64/) + + +**Added:** + +- Added a new Full Body {ref}`"ADL Gait" + <sphx_glr_auto_examples_MoCap_plot_ADL_Gait.py>` MoCap Example based on the + "Rehazenter Adult Walking Dataset" by [Schreiber and Moissenet + (2019)](https://doi.org/10.1038/s41597-019-0124-4). The model is configured to + run all 50 subjects and 1145 trials in the data set. However, you must + download the actual data separately from + [FigShare](https://figshare.com/articles/dataset/A_multimodal_dataset_of_human_gait_at_different_walking_speeds/7734767) + where it is hosted under a Creative Commons license. + +- New GUI plugin which uses statistical information from the ANSUR database to + set anthropometric values in AnyBody. A small example model is added + `Examples/StatisticalScalingPlugin` which shows how to use the plugin. + +- Added a new option to optimize "head width" / "head depth" / "neck length" / + "Tibia torsion" / "hand breadth" as part of the `OptimizeAnthropometricsOnOff` + class_template in the AnyMoCap framework. + +- Added new rotation vector based measures in the interface folder for the arm + degrees of freedom. These measures (`Interface.Right.RotVectorMeasures.*`) for + joint angles do not have a clinical meaning but are useful when exporting and + importing joint angles. + +- Added a new {ammr:bm_statement}`option for setting custom muscle calibration + <BM_CALIBRATION_TYPE>`. I.e. an option which disables calibration so the user + can add their own code. + + ```{code-block} AnyScriptDoc + #define BM_CALIBRATION_TYPE _CALIBRATION_TYPE_CUSTOM_ + + #include "<ANYBODY_PATH_BODY>\HumanModel.any" + + // Manually include calibration code. + Main.HumanModel.Calibration = { + #include "<ANYBODY_PATH_BODY>/LegTLEM/Calibration/CalibrationSequenceRight.any" + #include "<ANYBODY_PATH_BODY>/LegTLEM/Calibration/CalibrationSequenceLeft.any" + #include "<ANYBODY_PATH_BODY>/Arm/Calibration/CalibrationSequenceRight.any" + #include "<ANYBODY_PATH_BODY>/Arm/Calibration/CalibrationSequenceLeft.any" + }; + ``` + + :::{note} + If you need to modify the calibration code, copy it to the application folder + and include it from there. + ::: + +**Changed:** + +- All application examples use the new and fast experimental wrapping algorithmn + in the AnyBody Modeling System 7.3.0. A notice is shown in the output window to + remind the users that the algorithm is enabled. The experimental wrapping + algorithm + can be used in all models by setting: + + ```{code-block} AnyScriptDoc + System.Compatibility.AnyBody73_ExperimentalShortestPathSolver = On; + ``` + + :::{seealso} + The release notes for the AnyBoy Modeling System has more information + on the new and faster experimental wrapping algorithm. + ::: + +- Split the SternoCleidomastoid muscle up into two muscle branches. This makes + the two heads of the muscle able to work independent. + +- Add extra muscle-via points on for the Latissimus dorsi on the Thorax segment. + This change fixes wrapping problems where the Latissimus dorsi muscle strands + would slide off the wrapping surface representing the thorax segment. + +- Renamed all deprecated muscle class names. `AnyViaPointMuscle`-> `AnyMuscleViaPoint` + and `AnyShortestPathMuscle`-> `AnyMuscleShortestPath` + +- The AnyMoCap framework now uses a more robust way of saving optimized + parameters from the parameter optimization studies, when using AMS 7.3. + +- Pectoralis Major has been split from 5 into 10 branches to better represent + the real fiber direction of the muscle. Similarly the origins of the new + Pectoralis Major muscles have been moved to align with real anatomy of the + muscle. + +- Changed the format used by the AnyMoCap models when transferring joint angles + from the mrker tracking step to inverse dynamics simulation. The joint-angles + for the arms and pelvis rotation are now written in terms of rotation vectors + instead of Euler angles. This fixes potential singularity problems. The + temporary joint angle files produced by the MoCap models have been renamed to + indicate the data is no longer Euler angles. + + :::{note} + This means that the data in these temporary files can not easily be interpreted from a clinical + point of view. Create your own output files with physiological joint angles if you need to export that data. + ::: + +- The body model configuration plugin have been updated. This fixes a number of + smaller issues and bugs. + +- The via points of PeroneusLongus and PeroneusBrevis have been adjusted to + ensure the muscles maintain moment arm in a larger range of motion. + +- Rectus abdominis muscle has been split into eight branches to better represent + geometry, than what is possible with one branch. The strength between the new + branches has been split evenly. Additionally, the PCSA has been increased from + $2.6 cm^2$ to $7.9 cm^2$ according to McGill et al 1988, the $2.6 cm^2$ + originates from a study with elderly subjects, the McGill study used mid age + subjects. + +- Adjusted the origin of Serratus Anterior 1 so it aligns with the geometry of + the rib on which it originates. + +- Changed the way the deltoid wrapping surfaces move relative to humerus. This + changes makes it wrapping more robust to deltoid flipping over to the wrong + side of the wrapping surface in extreme postures. + +- The BVH virtual marker protocol have been adjusted. If older BVH models is + used with AMMR 2.3 a warning/error is triggered to warn the user that the + protocol needs to be updated. + +**Fixed:** + +- Fixed problems with the following variables in the `SelectedOuput` folder: + `HipAbductorMuscleForce`, `HipExtensorMuscleActivity`, + `HipExtensorMuscleForce`, `KneeFlexorMuscleActivity` and + `KneeFlexorMuscleForce`. +- Markers on BVH stick-figure model in the AnyMoCap framework now respects the + setting: `Main.ModelSetup.BVHFileData.ModelDrawOnOff`. +- Fixed occasional kinematics problems with FullBody MoCap models during inverse + dynamics simulation. This was fixed by changing the internal representation of + the shoulder joint angles when transferring kinematics from marker tracking to + the Inverse Dynamics simulations. +- Fixed a problem with the Body Model configurator plugin showing reporting: "No + Human Model" when a configuration file already exists. +- Corrected the location of via points of Flexor_Digitorum_Superficialis_Digit2 + to avoid wrapping surface collisions in certain hand positions. +- Corrected the location of via points of Flexor_Digitorum_Superficialis_Digit3 + and 4, Palmaris_Longus, Extensor_Carpi_Radialis_Brevis and + Extensor_Digitorum_Digit2 to avoid wrapping surface collisions in certain hand + positions. +- The muscle via point representing the bicipital groove have been adjusted to + ensure the Biceps Caput Longum wraps the humeral head correctly in +- Fixed a bug in the FreePosture model, where input for the Left/Right arm + drivers was switched in some places. +- Fixed missing visual color indication of force plate forces for type 3 force + plates in the MoCap models. +- Fixed a bug with in the built-in studies to {ref}`evaluate arm joint strength + <sphx_glr_auto_examples_Validation_plot_EvaluateJointStrength.py>`. The range + of motion for the left arm elbow pronation/supination were not correct. +- Fixed a bug preventing the model from loading with with + {bm_constant}`_SCALING_XYZ_` and both legs excluded. +- Fixed the load-time position of the head segment when neck scaling is changed. +- Fixed a problem with visualization in GRF prediction class which prevented GRF + prediction to be used with moving base frames (i.e. treadmills). Thanks to + Marco Antonio Marra (University of Twente) for fixing this. +- Fixed the marker node orientation for BVH (inertial based) MoCap models in the + CreateMarkerDriver class template. Marker orientations are now handles + identical to normal C3D based markers.\`\`\` +- Fixed incorrect wrapping of teres minor and teres major at extreme shoulder + range of motion. New wrapping surfaces have been added. One in Humerus and one + on scapula. The meet at the glenohumeral joint to prevent the muscles from + sliding to the wrong side of the humerus. + +**Removed:** + +- Removed unused support files for muscle contact. `Tools/ModelUtilities/ContactMuscles/*` + +## AMMR 2.2.3 (2019-11-13) + +[](https://doi.org/10.5281/zenodo.3521521) [](https://www.anybodytech.com/download/anybodysetup-7-2-3-7075_x64/) + + +**Added:** + +- Add new option to set the type of wrapping surface used in the deltoid + wrapping implementation. The following will force the use of cylinders (which + is faster) instead of ellipsoids. + + ```{code-block} AnyScriptDoc + #define BM_ARM_DELTOID_WRAPPING _DELTOID_WRAPPING_CYLINDERS_ + ``` + + See {bm_statement}`BM_ARM_DELTOID_WRAPPING` for possible options. + +**Fixed:** + +- Fixed problems with BVH models that have jumping angular data due to multiple + solutions to the Euler angle equations when gimbal locks occur. The fix + requires a new structure of the BVH model, where virtual marker trajectories + are calculated by the `AnyInputBVH` class. See the updated {ref}`BVH_Xsens + example <sphx_glr_auto_examples_Mocap_plot_BVH.py>`, and port your existing + BVH models to the new example structure. +- Fixed a problem in {ref}`AnyMoCap models <anymocap>`, where model view + operations in `Main.ModelSetup.Views.SetViewMacros` would not trigger a redraw + of the model view when executed directly. + +**Changed:** + +- Increase the time offset when running MoCap inverse dynamics simulations. The + offset was 2 frames which were skipped at the start/end of inverse dynamics + simulations. But the accelerations of 4th order b-spline are only stable on + the fourth frame, and hence the offset has been increased to three frames + instead of two. +- ScalingXYZ scaling law has been extended to respect the following new + variables in the `HumanModel.Anthropometrics.SegmentDimensions` folder: + (`HeadWidth`, `HeadDepth`, `TrunkDepth`, `NeckLength`, `FootWidth`) + +**Removed:** + +- Remove the joint muscles' strength dependency on the range of motion. Joint + muscles are the torque actuators embedded in the joints when the model is + loaded without muscles. Previously, joint muscles would reduce their strength + to 10% when the joint was outside the range of motion. The lower strength + outside the range of motion was originally implemented to prevent + inverse-inverse simulations finding non-physiological solutions. However, this + problem is now better solved with kinematic joint limits, and the change in + joint strength could sometimes cause models to fail with a muscle recruitment + failure. +- Remove the warning for modified Body model files. The warning can still be enabled + by setting the switch `#define ANYBODY_ENABLE_MODIFIED_AMMR_NOTICE` + +**Added:** + +- Added a warning to MoCap models when the number of frames is below 8. Since + the low number of frames causes problems with both low-pass filters and + b-spline interpolation. *Note:* C3D files with only a single frame works fine + since that is handled specially and often used for static trials. + +## AMMR 2.2.2 (2019-09-12) + +[](https://doi.org/10.5281/zenodo.3404750) [](https://www.anybodytech.com/download/anybodysetup-7-2-2-7000_x64/) + + +**Fixed:** + +- Fixed kinematic problems when driving specific wrist-flexion/abduction values. + The definition of wrist flexion in `BodyModel.Interface` now measures the + flexion between the radius and small artificial `WristJointSeg` segment + between the radius and the hand segment. This ensures that there is always + unique solution when driving the wrist flexion and abduction. +- Fixed a bug in the AnyMoCap examples when setting {bm_statement}`BM_SCALING` + to {bm_constant}`_SCALING_LENGTHMASSFAT_`. +- Fixed a number of smaller bugs with Body Model configuration plugin. +- Fixed a bug in calibration of 3 element leg muscles in the TLEM1 and TLEM2 + model. The problem was that the first calibration study (`LegCal1`) included + muscles which were also calibrated specifically in later calibrations. This + could in some cases (certain scaling) lead to a problem where `LegCal1` would + be forces to change the fiber-length even though later specific calibration of + the muscle did not need that. Now, `LegCal1` only calibrates muscles which are + not included in the later calibration studies. + +**Changed:** + +- Changed the posture of the push-up model example to something which looks more + natural, and reduces the max muscle activity. + +## AMMR 2.2.1 (2019-05-13) + +[](https://doi.org/10.5281/zenodo.2657673) [](https://www.anybodytech.com/download/anybodysetup-7-2-1-6927_x64/) + + +**Fixed:** + +- Fixed a symmetry issue with Scapula scaling in the + {bm_constant}`_SCALING_XYZ_` scaling law. +- Fixed a bug in the Knee Simulator example regarding an extra tibiofemoral + `AnyForceSurfaceContact`. +- Fixed a bug in how the Conoid driver scales with scapula size. +- Fix bug in reference axes for SacrumPelvis Moment measures in selected output. + Thanks to Divyaksh Chander from [Politecnico di Torino](https://www.polito.it) + for fixing this. +- Attempt to fix muscle wrapping errors with Latissimus dorsi when the model + bends forward. This was done by increasing the Augmented Lagrangian + coefficient `SPLine.AugLagCoef` value and the using full wrapping solver. +- Fix some muscle wrapping problems with subscapularis muscle by increasing the + number of points in the string mesh. +- Fixed minor symmetry issue in the head markers of the Full Body MoCap example. + +**Changed:** + +- Changed the recruitment criterion to the power of 2 (quadratic) in the two + MoCap examples using GRF prediction and weak human-ground residuals. + ({ref}`link 1 + <sphx_glr_auto_examples_MoCap_plot_Plug-in-gait_Simple_FullBody_GRFPrediction.py>` + and {ref}`link 2 <sphx_glr_auto_examples_MoCap_plot_BVH.py>`). This greatly + increases the robustness of recruitment solver and prevents many muscle + recruitment failures. + +**Added:** + +- New options to optimize pelvis-, trunk- and head- widths and depths in the + `OptimizeAnthropometricsOnOff` class template. + +- Simple library of Python utility functions which can be used from AnyScript. + This first version only adds a few functions from the Python's `os.path` + module. They are used by including the `Python.Utils.any` file: + + ```{code-block} AnyScriptDoc + #include "<ANYBODY_PATH_MODELUTILS>/Python/Utils.any" + + AnySwitchVar file_exists = PyUtils.os.path.exist("some-file") + ``` + +## AMMR 2.2 (2019-04-03) + +[](https://doi.org/10.5281/zenodo.1481635) [](https://www.anybodytech.com/download/anybodysetup-7-2-0-6876_x64/) + + +**Added:** + +- New implementation of the Deltoid muscles that uses wrapping instead of + previous rake-segment/via-point approach. The new wrapping deltoid was + developed by Marta Strzelczak from Ecole de technologie superieure, Montreal, + CA. The new implementation is used by default but the old implementation can + be enabled with the {bm_statement}`BM_ARM_DELTOID_WRAPPING` switch. + Please see the {ref}`Shoulder-Arm Documentation <DeltoidWrapping>` for more + information. + +- Added new example model of a Knee Simulator using a knee implant model and + force-dependent kinematics (FDK). See the {ref}`Knee Simulator example + <example_kneesimulator>` for more information. + +- New model plugin (BodyModel Configurator) which provides a graphical user + interface to configure the Body Model (i.e. setting the `BM_*` parameters). + Please see the [blog + post](https://anyscript.org/tools/body-model-configurator/) introducing the BM + plugin. + +- Added a new {ref}`Posture prediction model + <sphx_glr_auto_examples_ADLs_and_ergonomics_plot_PosturePredictionModel.py>` + based on standing posture. The model can predict posture as a consequence of + applied loads in hands. It does this by minimizing joint torques and applying + balance drivers which account for external applied loads. + +- Added new standing model example which uses soft constraints and GRF + prediction. {ref}`See this link + <sphx_glr_auto_examples_ADLs_and_ergonomics_plot_StandingModel.py>`. This new + model is good starting point for making standing/balancing models, and the + corresponding standing model in the template generator has also been updated. + +- Added new kinematic rhythm to determine the Sterno-Clavicular axial rotation, + effectively removing the degree of freedom from the shoulder model. The + rhythm distributes the axial rotation equally between SC and AC joint. The + rhythm is active by default, but can be disabled with + {bm_statement}`BM_ARM_CLAVICULA_ROTATION_RHYTHM` switch. + +- More documentation on the {ref}`AnyMoCap framework and the settings available + <anymocap-settings>` . + +- New measures for shoulder angles based on recommendation from International + Society of Biomechanics (ISB). The measures are available in the + `BodyModel.Interface` folder. The new measures are: + + - `AcromioClavicular` ([Wu et al. 2005] section 2.4.3) + + - `Protraction` + - `MedialRotation` + - `PosteriorTilt` + + - `ScapulaHumerus` ([Wu et al. 2005] section 2.4.4) + + - `PlaneOfElevation` + - `Elevation` + - `InternalAxialRotation` + + - `ThoraxScapula` ([Wu et al. 2005] section 2.4.6) + + - `Protraction` + - `MedialRotation` + - `PosteriorTilt` + + - `ThoraxHumerus` ([Wu et al. 2005] section 2.4.7) + + - `PlaneOfElevation` + - `Elevation` + - `InternalAxialRotation` + +- Three new BM switches to control add default drivers for the individual neck + degrees of freedom: + + - {bm_statement}`BM_MANNEQUIN_DRIVER_SKULL_THORAX_FLEXION` + - {bm_statement}`BM_MANNEQUIN_DRIVER_SKULL_THORAX_LATERALBENDING` + - {bm_statement}`BM_MANNEQUIN_DRIVER_SKULL_THORAX_ROTATION` + +- A default center of mass kinematic measure were added + + - `Main.HumanModel.BodyModel.Interface.CenterOfMass` + +- Markers in MoCap models now changes color to gray when they drop out (i.e. + have a weight of zero). + +- Added new `ASIS`/`PSIS`/`PT` bony-landmark nodes to the + `PelvisSeg.Right`/`Left` folders. This ensures the bony landmarks are easily + available as nodes in all models even if the legs are not included. + +- Added a new setting (`#define MOCAP_FILTER_JOINT_ANGLES ON/OFF`) to the + AnyMoCap frame work. If enabled a filter will be applied to the intermediate + set of joint angles generated by the Marker Tracking step. This can be useful + to remove high accelerations due to kinematic limit constraints (e.g. Joint + angle limits, surface contacts etc.). + +- Added a `#define MOCAP_PARAMETER_FILE_PREFIX` switch to override the prefix + for parameter identification files (containing marker position and scaling). + This can be useful in special cases where subjects share a common parameter + identification file. + +- Added two new default arguments (`MANNEQUIN_FOLDER`, `BODYMODEL_FOLDER`) to + the class_template `Template_MannequinDrivers`, making it easier to reuse the + class template as a general-purpose driver for all joint angles. + +- Added a `PreAnalysis` step to the video recorder template + (`CameraClassTemplate.any`). Operations placed in the `PreAnalysis` step will + be executed before the video recorder starts. + +- Added a new warning if using low-pass filters in the AnyMoCap model without a + zero phase filter (e.g. warn if `FilterForwardBackwardOnOff` is set to `Off`) + +- Added a new option for choosing a different implementation of the kinematic + sliding between scapula and thorax. The new scapula sliding implementation + uses multiple points on the ribs and a norm measures to surfaces on the + scapula. This work is preparation of a new thoracic model where ribs are + individual segments. Note that this implementation is still a + work-in-progress. The new thorax-scapula contact can be enabled with the + {bm_statement}`BM_ARM_THORAX_SCAPULA_CONTACT` switch: + + ```{code-block} AnyScriptDoc + #define BM_ARM_THORAX_SCAPULA_CONTACT _MULTIPLE_POINT_CONTACT_ + ``` + +- New `DEFAULT_PARAMETER_FOLDER` class template for creating folders with + default values which can be overridden. See the following example: + + ```{code-block} AnyScriptDoc + DEFAULT_PARAMETER_FOLDER Settings( + NPARAM = 2, + PARAM_1 = TibialRotation, PARAM_1_TYPE = AnyMat33, + PARAM_2 = Offset, PARAM_2_TYPE = AnyVar + ) = { + // Default values are specified in the defaults folder. + Default.TibialRotation = RotMat(5*pi/180,y); + Default.Offset = 0.005; + }; + + // Parameters can now be overridden if desired. + Settings.TibialRotation = RotMat(10*pi/180,y); + ``` + +**Changed:** + +- Re-implemented the origins for the Semitendinosus and Biceps Caput Longum + muscles in the TLEM-2.1 model based on the original digitized insertions and + MRI scans. Better correspondence with the original MRI scans increases the + moment-arms through range of motion. + +- New wrapping surfaces for Semitendinosus and Biceps Caput Longum muscles based + on original MRI scans. New surfaces ensure that muscles don't penetrate the + pelvis bone at high hip flexion angles. + +- Reimplement insertion of Gluteus Medius/Minimus of the TLEM2.1 model based on + original TLEM2 dataset. This improves range of motion in which Gluteus Medius + and Gluteus Minimus has a moment arm for internal rotation of the hip. + +- Kinematic rhythms for the shoulder, lumber-spine and cervical-spine can now be + specified as soft contraints. The setting is controlled by setting the BM + control statement `BM_XXX RHYTHM` to {bm_constant}`_RHYTHM_SOFT_`. For + example: + + ```{code-block} AnyScriptDoc + #define BM_ARM_SHOULDER_RHYTHM _RHYTHM_SOFT_ + ``` + +- Re-implemented the origins for the Semitendinosus and Biceps Caput Longum + muscles in the TLEM-2.1 model based on the original digitized insertions and + MRI scans. Better correspondence with the original MRI scans increases the + moment-arms through range of motion. + +- New wrapping surfaces for Semitendinosus and Biceps Caput Longum muscles based + on original MRI scans. New surfaces ensure that muscles don't penetrate the + pelvis bone at high hip flexion angles. + +- Reimplement insertion of Gluteus Medius/Minimus of the TLEM2.1 model based on + original TLEM2 dataset. This improves range of motion in which Gluteus Medius + and Gluteus Minimus has a moment arm for internal rotation of the hip. + +- The {doc}`TLEM2 model</body/leg_tlem2_model>` is now the default leg model + unless the model is configured otherwise. + +- All AnyMoCap examples where changed to use the {bm_constant}`_SCALING_XYZ_` + scaling law. This scaling law is similar to + {bm_constant}`_SCALING_LENGTHMASSFAT_`, but allows for optimization of all + segment dimensions (hence the `XYZ` name). + +- Scaling law {ammr:bm_constant}`_SCALING_XYZ_` now has a scaling factors to + control the neck scaling. Before neck scaling were controlled by + the head scale factors. + +- All MoCap model examples now use the option (`UseC3DWeightResiduals=ON`) in + the marker protocols. This ensures that the marker weights are reduced to zero + when a marker drops out (i.e. when the residual value in the C3D file becomes + negative). + +- AnyMoCap examples are updated with extra margin at the start/end of the + analysis compared to the data in the C3D file. This prevents inaccurate + kinematics due to low-pass filter transients. + +- Add warning to AnyMoCap models when `tStart`/`tEnd` are very close to the + start/end times of the data in the C3D file. This can cause inaccurate + kinematics at the very start/end of the simulation due to low-pass filter + transients. + +- Increased the resolution tibia bones for the TLEM1 and TLEM2 models. + +- All examples now have their body model configuration in a separate file + (usually, `BodyModelConfiguration.any`) to accommodate the new Body Model + Configurator plugin. + +- The MoCap models now use joint angles for all degrees of freedom when + transferring motion from MarkerTracking study to the Inverse dynamic study. + This means that rhythms can now be soft constraints when running the Marker + tracking study, and markers can override the kinematic rhythms if needed. + +- Refactored all examples to avoid the confusing paradigm with a reference + called `Model.HumanModel` pointing to `HumanModel.BodyModel`. + +- Improvements to the accuracy of the wrapping cylinder used by Teres Minor and + Teres Major. + +- The interface morphing algorithm (which morphs pelvis of the trunk or leg + dataset to match) now includes the ASIS/PSIS/PT bony landmarks as control + points. This change ensures that bony-landmarks of the Trunk and Leg datasets + map to the exact same point. + +- Models generated from templates now fail with a descriptive error message if + they are loaded with an older unsupported version of the AMMR. + +**Fixed:** + +- Fixed problem with the initial guess for Vastus wrapping which could cause the + Vastus muscle to wrap incorrectly when the knee started in slightly over + stretched posture. +- Fixed location of bicep longus via points to pass through bicipital groove +- Fixed a regression in bike model where the foot crank connection did not + rotate around the correct point (`PedalConnectNode`). The point in the foot + coordinate system was also updated to a more posteriorly location beneath the + meta tarsal joints. +- Fixed an issue with over-constraint default mannequin drivers when shoulder + rhythm was enabled. Now the default mannequin drivers will not create drivers + for sterno-clavicular rotation, elevation, protraction when the shoulder + rhythm is enabled. +- Fixed the initial wrapping guess for Teres Minor to prevent incorrect wrapping + when starting model in postures which are close to range of motion. +- Fixed typo in `Flexor_Digitorum_Profundus_Digit5` name. +- Fixed an interpolation issue with BVH based AnyMoCap models when the models + were using all frames in a BVH file. +- Added missing hand length/breadth values needed by Detailed Hand to the + `CustomScaling.any` for custom scaling scenarios +- Fixed missing possibility for overriding the reaction forces for the Trunk + flexion/extension/rotation drivers in `HumanModel.DefaultMannequinDrivers`. +- Add missing strength scaling factor to `pectoralis_major_thoracic_part_3` in + the simple muscle configuration. +- Fixed issue with the {ref}`Standing Model example + <sphx_glr_auto_examples_ADLs_and_ergonomics_plot_StandingModel.py>`, where the + elbow flexion velocity was incorrectly set to a non zero value. +- Fixed the problem with over-constraint models when adding the shoulder rhythm. +- Fixed a bug with the Video class (`CameraClassTemplate.any`) when specifying + direct path to ffmpeg. +- Fixed a problem with the FullBody AnyMoCap example where a relative high + weight on the soft clavicula rotation constraints could cause the model to + fail kinematically in with the AnyBody Modeling System 7.2. + +**Removed:** + +- Removed previously deprecated MoCap model which were not based on the AnyMoCap + framework. + +- Removed all references to the previously deprecated `BM_TRUNK_NECK` switch. + +- Removed outdated versions of `JointLimits_template.any` and + `KinLimitsDriver_template.any` from the AnyMoCap folder. Updated version of + the files still exists in the `Tools\ModelUtilities\KinematicLimits` folder. + +- All uses of the Sterno-Clavicular axial rotation in all examples, since this + DOF is now handled by a kinematic rhythm which distributes the rotation + equally between SC and AC joint. + +- The `BM_MANNEQUIN_DRIVER_INDIVIDUAL_WEIGHTS` switch was removed, since the + individual weights can be set directly using + + ```{code-block} AnyScriptDoc + Main.HumanModel.DefaultMannequinDrivers.KneeDriverRight.WeakDriverWeight = 0.1; + ``` + +## AMMR 2.1.1 (2018-06-12) + +[](https://doi.org/10.5281/zenodo.1287730) [](https://www.anybodytech.com/download/anybodysetup-7-1-2-6044_x64/) + + +The AMMR 2.1.1 version is a minor release of the AMMR with smaller changes and +bugfixes. The AnyBody Managed Model Repository now has a DOI +([10.5281/zenodo.1250764](https://doi.org/10.5281/zenodo.1250764)). This is +handled by [Zenodo.org](https://zenodo.org/) (The European Open Science platform +hosted at CERN). + +**Added:** + + model. This RefNode was also present in the TLEM1 model and was used by few +- Added a `Leg.Seg.Foot.GroundJoint` RefNode to the foot segment of the TLEM2 + applications. +- New `GroundVelocity` setting added to the `ForcePlateAutoDetection` + class_template, which makes class usable with instrumented treadmills. +- All force plate types now have a user-definable `ForcePlate.CalMatrix` + variable. The feature is useful to easily compensate for errors in the c3d + file (i.e. swapped channel and wrong sign) + +**Changed:** + +- Enhanced the {ref}`multi-trial MoCap example + <sphx_glr_auto_examples_Mocap_plot_Plug-in-gait_MultiTrial_StandingRef.py>` + for best practice for MoCap trials with multiple subjects and trials. The + example now shows how to deal with multiple subjects and storing the c3d files + in a separate folder. + +**Fixed:** + +- Corrected the default mass of the patella segment in the TLEM2 model from zero + to 0.025. + +- Add missing unilateral reaction between TS node on Scapula and the Thorax when + using the shoulder rhythm. + +- Adjusted the initial wrapping vectors for the semitendinosus, semimembranosus, + and biceps caput breve muscles around the knee. This has no influence on the + output of the model, and is only done to reduce the risk of the muscles + wrapping the wrong direction around the wrapping surface. + +- AnyMoCap: + + - The high memory usage of the AnyMoCap BVH model has been fixed. The high + memory usage was due to a reference in the `CreateMarkerDriver` class + template which caused the studies to include the BVH input data multiple + times in the output. + - The BVH and multi-trial examples now use zero phase shift filtering of force + plate forces. The zero-phase filter can be important to ensure that forces + are synchronized with kinematic data. + - Fix bug in Type 1 Force plate when data is not in meters (i.e. + `PointScaleFactor != 1`). The PointScaleFactor was applied twice to the z + moment component. + - Fix a problem reading C3D files where force plate meta information is saved + with the wrong dimensionality. Such a issue can, for example, happen if the + c3d files are created manually in MATLAB. + - The option to load parameter optimization results is no longer hidden when + the `MOCAP_CREATE_PARAMETER_ID_SHORTCUT` is set to `OFF`. + +## AMMR 2.1.0 (2018-03-22) + +[](https://doi.org/10.5281/zenodo.1251276) +[](https://www.anybodytech.com/download/anybodysetup-7-1-1-6029_x64/) + +**Added:** + +- New {ref}`squat example + <sphx_glr_auto_examples_ADLs_and_ergonomics_plot_Squat.py>` model which + demonstrates a parameterized squatting motion. + +- New `#class_template` for adding limit drivers to kinematic measures. Can be + included with `#include + "<ANYBODY_PATH_MODELUTILS>/KinematicLimits/KinLimit_template.any"` + +- Muscle ColorScale can now be set from the + `Main.DrawSettings.Muscles.ColorScale`. If you port an older model to the new + AMMR you will need to update your `DrawSettings.any` file. + +- AnyMoCap framework: + + - New argument `DRAW_SCALE` in the `CreateMarkerDriver` class_template to + control the visual size of markers. + - Added an option to the ForcePlateAutoDetection class template to make the + limb1/2 contact detection mutually exclusive. Setting the option + `ALLOW_MULTI_LIMB_CONTACT=OFF` will ensure that both legs cant be in contact + with the plate at the same time. This can prevent accidental contact + detection for the collateral leg in the swing phase. + - New option to specify the contact nodes in ForcePlateAutoDetection class + template. This makes the class useful for connecting force plate to other + limbs than the feet. + - Add support for the Shoulder Rhythm in AnyMoCap based models. + - Add support for the {doc}`/body/detailed_hand_model` in AnyMoCap based + models. + +- New `BM_FOOT_MODEL` parameter, as preparation for integrating the + Glasgow-Maastricht foot model (GM-Foot) back into the AMMR. Currently, the + parameter can only be used for excluding the feet (`#define BM_FOOT_MODEL + _FOOT_MODEL_NONE_`). making it easier to work on integrating the GM foot + model. + +:::{seealso} +Adding the GM-Foot to the TLEM2 model is a work in progress. An early version is +released on GitHub: <https://github.com/AnyBody/gm-foot> +::: + +**Changed:** + +- Default mannequin drivers for the Pelvis are changed to drive the Pelvis + anatomical frame instead of the segmental reference frame. This also fixes the + discrepancy between the load time position and the mannequin driver position + and makes the driver consistent with the interface measures + `BodyModel.Interface.Trunk.PelvisPosX/Y/Z`. + +:::{warning} +This change will affect models using the default mannequin drivers unless +the driver values are updated. +::: + +- The Wilke spine pressure validation examples have been updated and now uses + the TLEM2 lower extremity model. + +- In {bm_constant}`_SCALING_XYZ_` scaling law the definition of + length/depth/width of the scapula is corrected to match the anatomical + definitions. + +- Updated the AAU Mandible Model introduced in AMMR 2.0.0. By accident the + authors did not share the exact same version of the model that was used in the + publication by [Andersen et al. 2017](https://doi.org/10.1115/1.4037100) This + is now corrected and the validation example produces the same results as + published version. + +- TLEM 2 model + + - Pectineus implementation has been adjusted based on the original MRI Scans. + Only the most lateral element of the pectineus muscle was changed. This was + done to prevent it from penetrating the femoral head in some situations. + - Tweaked the Gluteus Maximum Superior implementation to reduce the risk of + collisions between muscle insertions and the wrapping surface. The two most + proximal insertion points of the Gluteus Superior are shifted more distally, + and the locations of the wrapping surfaces are tweaked. + +- AnyMoCap Framework: + + - Models now uses the default kinematic solver for the inverse dynamic + analysis. + - Changed the set joint drivers used for transferring the joint angles from + the over-determinate marker tracking to the inverse dynamic analysis. To + improve the stability of the scapula kinematics the Scapula Thorax Elevation + angle is used instead of the sterno clavicula elevation angle. + - Changed the way marker drivers are excluded from the Inverse Dynamic + analysis. The drivers are now excluded using the new `AnyMechObjectExcluder` + class instead of the `MechObjectExlcude` member of the Study. This has no + practical effect on model output but means that the `MechObjectExlcude` can + now be assigned by the users. + - Update to the BVH MoCap example. Pre-processing the BVH data is now a + separate operation which saves the virtual marker positions to a file. Thus, + this step can be skipped the next time the model is reloaded. + - Changed the AnyMoCap Multi trial example + `Plug-in-gait_MultiTrial_StandingRef` to make it a better starting point for + creating new models. 1. Moved the Human-Ground residuals from the Trunk to + the Pelvis segment. 2. Use the TLEM 2 lower body model in the example. 3. + Disable upper bounds for the muscle recruitment `Criterion.UpperBoundOnOff = + Off;` to improve the stability of the simulations. + +**Fixed:** + +- Shoulder-arm model: + + - Fixed problems with Pectoralis Major wrapping. Wrapping could fail + unpredictively when muscles wrapped in the intersection between the coracoid + wrapping and pectoralis minor cylinder. The coracoid wrapping cylinder has + been removed, and the others has been made longer. This creates a more + robust wrapping for the Pectoralis Major muscle. + - Better initial position for scapula and clavicula. The initial position is + now calculated from the initial position of the chain from thorax through + the clavicula to scapula. This will not change the model output but should + make the arm model more robust solving the first step. + - Improve the Teres Minor wrapping by adjusting the wrapping surface, and + ensure that the insertion point is not directly on the surface. + - The "Evaluate joint strength" studies now also work when the shoulder rhythm + is enabled. + - Fixed problems with via points of the wrist extensor muscles colliding with + the wrist wrapping surface in normal range of motion. The via point of + Extensor indicis `Via_Extensor_Indicis_pos` has been slightly adjusted and + the location of the wrist wrapping cylinder `MedialExtensorCyl` has been + improved. + +- Detailed hand model: + + - Fix a problem causing the hand to scale incorrectly. + - Fix a problem with the default mannequin drivers for the left thumb, where + CMC and MCP abduction was treated as adduction. + - Fixed compatibility between the detailed hand and scaling law + {bm_constant}`_SCALING_XYZ_`. + +- Lower extremity models: + + - Fixed various warnings when running calibration routines with the lower + extremity models. + - Fixed muscle insertions for the old leg model (`#define BM_LEG_MODEL + _LEG_MODEL_LEG_`). The misaligned pelvis muscles insertions was a regression + due to the updated Trunk pelvis introduced in AMMR 2.0. The pelvis muscles + insertions have been translated and rotated to fit the new Trunk geometry as + best as possible. + - Fix missing left leg calibration operations when right leg was excluded. + +- MoCap models: + + - Weak residuals for GRF prediction: Ensure the same strength is used in all + directions for the weak recruited actuators. + - Fix bug in `CreateMarkerDriver` class template which prevented the + `UseC3DWeightResiduals` from having any effect. + - Fix the wrong visualization of the contact area in ground reaction force + prediction class template, when the base frame is different from the global + coordinate system. + - Wrong masses in the deprecated "old" MOCAP models. The model was not using + the body mass specified in `Main.TrialSpecificData.Anthropometrics.BodyMass` + +- Other fixes: + + - Wrapping convergence for multiple muscles has been improved. This was done + by tweaking the string-mesh of the muscles to improve the wrapping solvers + ability to find the solution within the given number of iterations. + +## AMMR 2.0.0 (2017-11-29) + +[](https://doi.org/10.5281/zenodo.1251274) +[](https://www.anybodytech.com/download/anybodysetup-7-1-0-5957_x64/) + +### Major changes: + +#### New lower extremity model (TLEM2.1) + +- The [Twente Lower Extremity Model version 2.0 + dataset](https://dx.doi.org/10.1016/j.jbiomech.2014.12.034), developed in the + TLEM*safe* EU project was implemented in the AMMR repository. The model is not + the default model, but can be enabled with the {ref}`BM parameter <bm-config>` + `#define BM_LEG_MODEL _LEG_MODEL_TLEM2_` + +- The model is versioned TLEM 2.1, to indicate the number of changes and + correction which has been added in the process. The changes and updates to the + TLEM2 dataset was done in the [Life Long + Joints](https://web.archive.org/web/20230108081423/https://lifelongjoints.eu/) + EU research project (paper submitted for publication). + +- The most important changes to the TLEM 2 dataset include the following: + + - Updated wrapping for the Gluteus Maximus, Iliacus, Psoas around the hip. + - Reworked muscle topology for Gluteus Medius and Gluteus Minimus + - Updated wrapping for Hamstring muscles, and Gastrocnemius around the knee. + - Redefined revolute knee axis and patella joint axis and patella tendon + length based on the bone geometry. The original TLEM knee axis was + estimated using a functional method, and was only valid for very small + flexion angles. Thanks to Marco Antonio Marra (Radboudumc) for this for this + improvement. + - The ratio of volume between Gluteus Maximus superior/inferior has been + re-estimated based on the original cadaver MRI scans. + - Update the Sartorius via points. + - Re-implemented the Hip Joint location for the pelvis and the femur by + fitting spheres to the femoral head and the acetabulum. This is in contrast + to the original TLEM2.0 implementation where the hip joint center was found + using a functional method. + - Included a more detailed version of the patella bone. + - Various minor bug fixes from the original implementation used in the + TLEMSafe project. + - Corrected the femoral attachment points for the popliteus muscle + - Update ankle joint nodes with positions fitted to the bone geometry + - Small correction to wrong insertion points for Adductor Longus and Vastus + Medialis. + +- See the dedicated {doc}`TLEM2.1 page </body/leg_tlem2_model>` page for more + information. + +#### AnyMoCap + +- New framework for running MoCap models. The AnyMoCap framework is an effort to + create a simple and unified framework for doing any kind of MoCap analysis + with the AnyBody Modeling System. See the {ref}`AnyMoCap example gallery + <mocap_examples>` for more information. +- Algorithms and file for Ground reaction force prediction are added to: + `ammr/tools/GRFPrediction/`. See the {ref}`MoCap examples + <sphx_glr_auto_examples_Mocap_plot_Plug-in-gait_Simple_FullBody_GRFPrediction.py>` + for how they are used. + +#### TLEM 1 updates + +- The cumulated smaller bug fixes and updates to the TLEM1 model mean that we + now denote the model 1.2. +- Changed the position of the Heel contact node, to align the heights of the + TLEM1 and TLEM2 models. +- Added missing `GeomScale` function to the patella segment. +- Update ankle joint nodes with positions fitted to the bone geometry +- PSCA is now calculated based on the scaled fiber length. This aligns the TLEM + 1 model with the new TLEM 2 model. It also means that scaling the model + without changing the muscle volumes will change the strength of the model. +- Update scaling of the Patella tendon to work with non-linear scaling laws. +- Added visualization of the Fibula bone. + +#### AMMR restructure + +- Added a top-level `Tools` folder helper files and other models which don't + belong in `Body/` or `Application`. +- Moved `Body/AAUHuman/Toolbox` to `Tools/ModelUtilities` +- Renamed the `Body/AUHuman` to `Body/Mandible_AU` +- Restructured the anthropometric ("AnyMan") folder. The folder + `HumanModel.AnthroDataSubject` is renamed to `HumanModel.Anthropometics`. The + structure of the folder has also changed with a `SegmentDimensions` and + `SegmentMasses` subfolder. + +#### Configuration parameters + +- The previously used system to configure human body using a BodyPartSetup file + was completely replaced with the new body model (BM) parameters. +- Please see the documentation on: {ref}`BM parameters <bm-config>`. + +#### Scaling laws + +- An additional scaling law based on individual segmental scaling factors was + added to the repository. It can be enabled using this {ref}`BM + parameter<bm-config>` `#define BM_SCALING _SCALING_XYZ_`. See the {ref}`guide + on scaling <scaling-intro>`. +- Default scaling is now {any}`_SCALING_STANDARD_` (e.g `#define BM_SCALING + _SCALING_STANDARD_`) which scales all models to default standard 50% male. +- Introduced {any}`_SCALING_NONE_`, which disables scaling. E.g. models gets the + original unscaled size. + +#### New Mandible model + +- Added new mandible model based on a CT scan of a 40 year old male. For more + information see {doc}`the documentation for the model + </body/aalborg_mandible>` or the {ref}`validation example + <sphx_glr_auto_examples_Validation_plot_AalborgMandible.py>`. + +#### Spine model + +- {ref}`BM parameters <bm-trunk-config>` were updated to have control over each + section of the spine and relevant components. +- The anatomical reference frame of the thorax segment was modified. This change + reflects a change in the pelvic anatomical reference, and ensures upright + posture for the standing postures, to align C1C0 joint with the hip joint + centers. +- Boney surfaces of both pelvis and sacrum were updated and now correspond + better to the relevant muscle attachments. These segments now also share a + common scaling function. Hip joint centers were corrected for the old Leg + model. +- Improved wrapping surface for Psoas Major muscles based on the TLEM2.0 MR + scans +- Insertion, via, and attachment nodes of relevant muscles have been updated to + match new geometries of pelvis and sacrum. + +#### Arm model + +- The model now facilitates individual personalization for each side using + nonlinear morphing schemes in a more consistent manner. Previously the + morphing needed to be done on the right side and then reflect to have the left + side morphing. This change removes an extra mirroring step. +- Arm calibration was updated +- {ref}`BM parameters <bm-arm-config>` have been updated for more convenient + use. `BM_ARM_DETAILED_HAND` and `BM_ARM_SHOULDER_RHYTHM` are now used instead + of individual switches for right and left side, which were deprecated. +- Muscle wrapping surfaces were updated for more physiological behavior. +- Scapula reaction contact forces were simplified, and do not longer utilize + slider segments. +- Conoid ligament length now scales along with the scapula width. +- Add a `GeomScale` function the Clavicula segment. + +#### Muscle models + +- All muscle models are updated to support the structure of the new + `AnyMuscleModel3E` and `AnyMuscleModel` in the AnyBody Modeling System 7.1. + The following variables are renamed: + + > - The "optimal fiber length" variable renamed from `Lfbar` to `Lf0` + > - The "Pennation angle" variable renamed from `Gammabar` to `Gamma0` + > - The "Tendon strain at F0" variable renamed from `Epsilonbar` to `Epsilon0` + +- Restructured the muscle model section of both TLEM1 and TLEM2 models. + + - All the original TLEM based muscle parameter are now located under: + `Leg/ModelParameters/Muscles` + + - All scaled muscle parameters are located in `Leg/MusPar/SubjectMusPar`. This + folder references the TLEM muscle and applies strength scaling etc. The + `SubjectMusPar` folder and all subfolders are implemented with + `class_template`. Thus, all muscle parameter can now be overridden in + applications by just assigning the variables a new value: E.g. + + ```{code-block} AnyScriptDoc + Main.HumanModel.BodyModel.Right.Leg.MusPar.SubjectMusPar = { + GastrocnemiusMedialis.MuscleVolume = 300; // Volume in mililiters + GastrocnemiusMedialis.Pennationangle = 15; // (in degrees) + }; + ``` + +#### Calibration + +- Updated calibration for Arms and TLEM legs in the Body Model to + + > - include muscles to the calibration study with search functions. + > - drive the postures using the measures from the interface folder to remain + > anatomically similar throughout future versions. + +- Added new **experimental** two-parameter calibration, which is based on + range-of-motion postures. The calibration type is controlled by the + {any}`BM_CALIBRATION_TYPE` parameter. + + For example: + + ```{code-block} AnyScriptDoc + #define BM_CALIBRATION_TYPE _CALIBRATION_TYPE_2PAR_ + ``` + +### Minor Changes: + +- Added new initial guess for wrapping muscles, which make the wrapping more + when the model starts in extreme postures. + +- Updated many examples to use the TLEM 2.1 model. See the {ref}`example gallery + <example-gallery>`. + +- BM mannequin drivers are now implemented with a class_template allowing all + weights and other settings to be customized. + +- A default `HumanModel.Mannequin` folder is now automatically created with a + `class_template` when no user-defined Mannequin file is set. + +- A default `Main.DrawSettings` folder is now automatically created with a + `class_template` when no user-defined {bm_statement}`DrawSettings + <BM_DRAWSETTINGS_FILE>` file is set. + +- Extra Mannequin drivers for the individual shoulder degrees of freedom: + {any}`Sterno clavicula protraction <BM_MANNEQUIN_DRIVER_STERNOCLAVICULAR_PROTRACTION_RIGHT>`, + {any}`Sterno clavicula elevation <BM_MANNEQUIN_DRIVER_STERNOCLAVICULAR_ELEVATION_RIGHT>`, + {any}`Sterno clavicula axial rotation <BM_MANNEQUIN_DRIVER_STERNOCLAVICULAR_AXIAL_ROTATION_RIGHT>` + +- The initial positions of the pelvis now use the anatomical reference frame. + This follows the logic from the initial rotation of the pelvis which also uses + the anatomical frame. + +- DeltoidMuscleConnector segment loading time positioning now depends on the + Humerus segment. + +- Added [class template to easily create videos from AnyScript + model](https://anyscript.org/tips-n-tricks/creating-videos-from-your-simulations/). + The tool requires that [FFmpeg](https://www.ffmpeg.org/) is installed. The + class template can be found in: + `<ANYBODY_PATH_MODELUTILS>/Video/CameraClassTemplate.any`. See [this blog + post](https://anyscript.org/tips-n-tricks/creating-videos-from-your-simulations/). + +- In TLEM models make the opacity of the patellar tendon dependent on the + opacity of the patellar surface. + +- New `AnyDoc` classes are added to the different body model, so the GUI can + create direct links to the documentation. + +- Simplify the Scapular reactions to the thorax segment. + +- Foot contact nodes are aligned with the AnatomicalFrame + +- Updated the Wilke Validation example to reflect the forces for the AMMR 2.0 + repository. + +- Updates to BM parameters: + + - New {bm_statement}`BM_ARM_DETAILED_HAND` parameter for the detailed hand. + The old `BM_ARM_DETAIL_HAND_RIGHT`/`LEFT` are deprecated. + - New {bm_statement}`BM_ARM_SHOULDER_RHYTHM` parameter for controlling the shoulder rhythm. + The old `BM_ARM_SHOULDER_RHYTHM_RIGHT`/`LEFT` are deprecated. + - Added new `BM_JOINT_TYPE_<joint>_<side>` parameter for completely + disabling joint and associated nodes in the lower extremity models. (See: + for example {bm_statement}`BM_JOINT_TYPE_HIP_RIGHT`) + - New {bm_statement}`BM_LEG_MODEL` parameter for setting the type of leg model + used. The {bm_statement}`BM_LEG_RIGHT`/{bm_statement}`LEFT <BM_LEG_LEFT>` are + now only {bm_constant}`ON`/{bm_constant}`OFF` options. + +### Fixed: + +- Sign for the plantar flexion variable were reversed in some section of the + model. This has been fixed. +- Bug in Mannequin drivers for the neck, where velocities were not set + correctly. (Thanks to Assoc. Prof. Michael Skipper Andersen for reporting + this) +- Fix small bug preventing `StandingModelScalingDisplay` from loading when using + the {ref}`Leg <old-leg-model>` model. +- Fixed the opacity of the patellar surface in TLEM models, which pointing + erroneously to the opacity of the talus. +- Fixed wrong symmetry of nodes on the C7 segment of full neck model. +- Latissimus Dorsi 5 fascicle was missing in `MuscleNames.any` and thus from + many symmetry measures. +- Fixed a symmetry problem for the Deltoid muscles at the shoulder. +- Fixed a symmetry problem for the Disc stiffness from L1 to L5 +- Fix white surfaces in examples with flat STL surfaces. For example + {ref}`sphx_glr_auto_examples_Sports_plot_CrossTrainer.py`. +- Fixed an issue preventing + {ref}`sphx_glr_auto_examples_ADLs_and_ergonomics_plot_StandingModel.py` from + working with one leg. +- Fixed a problem with the drawings of the bones in the Arm model which were not + always symmetrical. +- Fixed symmetry issues in scaling laws for scapula and clavicula, and humerus. +- Fixed a bug where a the Pectoralis wrapping cylinder was not a included in the + calibration study. +- Fixed wrong sign for the AnklePlantarFlexion variable. +- Added missing GeomScale and AnatomicalFrame for Ulna segment. +- Fixed ScalingCustom.any to use Thorax folder instead of Trunk. + +### Removed: + +- Old MoCap examples have been moved to `Application/Examples/Deprecated` +- Removed the deprecated AMMR1.4 hip rotation sequences. +- The GM-foot model. A new version of this in the pipeline. Contact us if you + are interested in this work. +- All older BodyModels which were deprecated in AMMR1.3 + + +[wu et al. 2005]: https://isbweb.org/images/documents/standards/Wu%20et%20al%20J%20Biomech%2038%20(2005)%20981%E2%80%93992.pdf