Base Armature¶
Armature definition procedure¶
Armature are configured based on a Python dictionary object that can be modified in a dedicated editor included in the Stereotaxic Frame module.
The frame geometry is given as a series of translation and rotation transforms representative of each stereotaxic frame joints.
# Armature configuration definition example
{
'_armature_joints': {
'Joint 1 (x translation only)': {
'translation_0': {
'args': ['x', 0.05],
'_is_editable': False,
}
},
'Joint 2 (z translation + z rotation + y translation)': {
'translation_0': {
'args': ['z', 0.01],
'_is_editable': False
},
'rotation_0': {
'args': ['z', 20.0, 'degrees'],
'_is_editable': True,
'_edit_increment': 1,
'_unit': 'deg'
},
'translation_1': {
'args': ['y', 0.07],
'_is_editable': True,
'_edit_increment': 0.0005,
'_unit': 'm'
}
}
}
}
These dictionaries are constructed through carreful measurements of the stereotaxic frame geometry.
Joints with constant dimensions can reference values defined in a constant dictionary. These can be used as transformation arguments by providing a string that will be evaluated 'args': ['x', "-csts['L2'] + csts['d1']/2"] when displaying the armature. Fixed joints can be hidden from the GUI editor by setting _is_editable to False.
Armature definition validation¶
Proper armature definition should results in simulated armature geometries matching their actual counterpart in a large range of configurations.
- In this example, the stereotaxic frame has been defined as a series of 3 discrete armatures:
Bregma loc correction → bridging the rodent head location, with the Arm origin.
Arm 2 → The main arm possessing 5 degrees of freedom (\(x\), \(y\), \(z\) translations + \(x\), \(z\) rotations)
Dummy probe → a detachable probe holder which is in this case constitutes of a single rod with no attachments.
Configuration dictionaries for these armatures have been defined as follows:
Bregma loc correction
Armature
# Armature configuration definition
{
'_armature_joints': {
'AP Bregma': {
'translation_0': {
'args': ['x', 0.0787],
'_is_editable': True,
'_edit_increment': 0.0005,
'_unit': 'm'
}
},
'ML Bregma': {
'translation_0': {
'args': ['y', 0.0938],
'_is_editable': True,
'_edit_increment': 0.0005,
'_unit': 'm'
}
},
'DV Bregma': {
'translation_0': {
'args': ['z', 0.0225],
'_is_editable': True,
'_edit_increment': 0.0005,
'_unit': 'm'
}
}
}
}
Arm 2
Armature
# Armature constant definition
{
'L1': 0.0215,
'L2': 0.135,
'L3': 0.0483,
'L4': 0.077,
'L5': 0.0245,
'L6': 0.1152,
'L7': 0.013,
'L8': 0.0303,
'L9': 0.014,
'L10': 0.0053,
'L11': 0.0128,
'L12': 0.136,
'L13': 0.0245,
'L14': 0.014,
'd1': 0.0332,
'd2': 0.0095,
'd3': 0.0096,
'd4': 0.008
}
# Armature configuration definition
{
'_armature_joints': {
'ML0': {
'translation_0': {
'args': ['y', "csts['L1']/2"],
'_is_editable': False
}
},
'AP Knob': {
'translation_0': {
'args': ['x', 0.0029],
'_is_editable': True,
'_force_gui_location_to': 0,
'_edit_increment': 0.0005,
'_color': 'x_RED',
'_unit': 'm'
}
},
'AP0': {
'translation_0': {
'args': ['x', "-csts['L2'] + csts['d1']/2"],
'_is_editable': False
}
},
'DV0': {
'translation_0': {
'args': ['z', "csts['L3'] - csts['d2']/2"],
'_is_editable': False
},
'rotation_0': {
'args': ['z', 20.0, 'degrees'],
'_is_editable': True,
'_edit_increment': 1,
'_unit': 'deg'
}
},
'DV1': {
'translation_0': {
'args': ['z', "csts['d2']/2 + csts['L4'] - csts['L5']"],
'_is_editable': False
},
'rotation_0': {
'args': ['x', 0.0, 'degrees'],
'_is_editable': True,
'_edit_increment': 1,
'_unit': 'deg'
}
},
'DV Knob': {
'translation_0': {
'args': ['z', 0.0128],
'_is_editable': True,
'_force_gui_location_to': 2,
'_color': 'z_BLUE',
'_edit_increment': 0.0005,
'_unit': 'm'
}
},
'ML Knob': {
'translation_0': {
'args': ['y', 0.013000000000000001],
'_is_editable': True,
'_force_gui_location_to': 1,
'_edit_increment': 0.0005,
'_color': 'y_GREEN',
'_unit': 'm'
}
},
'AP2': {
'translation_0': {
'args': ['x', "csts['d3']/2 - csts['L7'] + csts['L8'] - csts['L9'] - csts['L10'] - csts['d4']/2"],
'_is_editable': False
}
},
'ML2': {
'translation_0': {
'args': ['y', "-csts['d3']/2 + csts['L11'] - csts['L12'] + csts['d4']/2"],
'_is_editable': False
}
},
'DV2': {
'translation_0': {
'args': ['z', "csts['L13'] - csts['L14']"],
'_is_editable': False
}
}
}
}
Dummy probe attachment
Armature
# Armature configuration definition
{
'_armature_joints': {
'DummyProbe arm': {
'translation_0': {
'args': ['z', -0.1465]
}
}
}
}
Base Armature API reference¶
- class coperniFUS.modules.armatures.base_armature.Armature(armature_display_name, parent_viewer, stereotax_frame_instance, **kwargs)[source]¶
Bases:
object- property uneval_armature_config_dict¶
Unevaluated armature configuration dictionary. A non-jsonable copy of the dict with expression strings evaluated is available by calling armature_config_dict
- property armature_config_dict¶
Armature configuration dictionary with expression strings fully evaluated.
- property armature_config_csts¶
Set of constants defined by the user in the armature configuration panel (dictionary).
- get_joints(armature_config_dict=None)[source]¶
Get the list of joints names defined in the _armature_joints section of the armature_config_dict
- get_joint_transforms(joint_id, armature_config_dict=None)[source]¶
Get the affine transmation matrix associated to a given armature joint_id. Joint identifiers can be obtained by calling get_joints().
- property end_transform_mat¶
Returns the transform matrix of the last joint in the armature
- property armature_tooltip_tmat¶
- property visible¶
Armature visibility in viewer
- property rgba_color¶
Armature joints color in viewer
- property glline_width¶
Armature joints line width in viewer
- get_armature_user_param(param_name, default_value=None)[source]¶
Get armature configuration parameter stored in cache (or default values if non existant)