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)

🔧 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,
  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)

🩹 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)

🩹 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
  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)

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)

✨ Highlights

• Integrated pelvis, lumbar, and thorax models into a consistent trunk model in
  preparation for a full thoracic model in AMMR 4.
• 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
  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.

• 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
  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" 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
  argument in the 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 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)

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)

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)

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)

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)

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
  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
  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), 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)

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)

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)

{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)

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 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)

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). 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
  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"</anybody_path_body>

// 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"
};
```</anybody_path_body></anybody_path_body></anybody_path_body></anybody_path_body>

:::{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)

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)

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)

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
  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"</anybody_path_modelutils>

AnySwitchVar file_exists = PyUtils.os.path.exist("some-file")
```

AMMR 2.2 (2019-04-03)

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 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)

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). This is
handled by 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)

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 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)

Major changes:

New lower extremity model (TLEM2.1)

• The Twente Lower Extremity Model version 2.0
  dataset, developed in the
  TLEMsafe 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
  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.
  The tool requires that FFmpeg is installed. The
  class template can be found in:
  <ANYBODY_PATH_MODELUTILS>/Video/CameraClassTemplate.any. See this blog
  post.

• 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