Biomechanical Analysis

From iPiSoft Wiki

(Difference between revisions)

Latest revision as of 10:26, 4 March 2021

Get Linear and Angular Quantities for selected bones, including
- Linear coordinate, velocity, acceleration
- Euler angles, angular velocity and angular acceleration
- Quaternions and Rotation matrices
Select convenient coordinate systems
- Linear: Absolute (relative to floor), Relative to parent joint, Relative to center of mass
- Angular: Absolute (relative to floor), Relative to parent joint
Select Euler angles system
Plot values of selected Quantities for selected bones
Export bones motion data to file
- Tab-separated text format (for Excel)
- MATLAB format

Export point clouds obtained from depth sensors to file
- PCD format
- MATLAB format

Note. iPi Biomech Add-on requires separate license key, which you need to activate in addition to iPi Mocap Studio license key. 30-days free trial provided.

Glossary

Linear quantities

Quantities derived from linear coordinate of the joint which connects bone to it's parent bone, including:

Coordinate
Velocity
Acceleration

Angular quantities

Quantities derived from bones's Euler angle, including:

Linear coordinate system

Coordinate system used for linear quantities, can be:

Absolute (relative to ground) — axes are shown by selecting Move tool; center is automatically set during calibration (it's z-coordinate is always 0)
Relative to center of mass — axes are shown by selecting Move tool; center is in the actor model's center of mass
Relative to parent joint — axes are shown by selecting Move tool; center coincides with the coordinates of the parent bone

Angular coordinate system

Coordinate system used for angular quantities, can be:

Absolute (relative to ground) — in this system rotations are defined relative to ground
Local (Relative to parent bone) — in this system rotations are defined relative to the parent bone

Euler angles system: Set of rotations which defines Euler angles, see here

Unit: Measurement unit of physical quantity

License and Trial

iPi Biomech Add-on requires separate license key, which you need to activate in addition to iPi Mocap Studio license key. You can order your license here, or activate 30-days free trial. As soon as you install (or auto-update to) version 2.6 or higher, Biomech tab will appear in iPi Mocap Studio control panel. Follow the steps below to start working with iPi Biomech Add-on

Switch to Biomech tab.
Press Activate button
Press Start 30-days Free Trial Period or Enter Biomech License Key and follow further on-screen instructions

Note. If you do not have iPi Mocap Studio license key, you can order it here or activate 30-days free trial. If your Studio trial has expired, you will not be able to export biomech data as well as animation. But you can still plot biomech data.

Select Data for Analysis

First you need to select data that you will analyze

Select bones
- (1) Check corresponding bones to include them in analysis
- (2) On the top of the list you can see "special" bones — Center of mass, Center of mass projection to the ground. The rest of the list are the bones from the internal iPi rig.
- (3) You can include finger bones into analysis by expanding hand bone (RHand and / or LHand). However, fingers are not tracked due to insufficient resolution of off-the-shelf cameras, so they just keep attached to hand joint (RHand or LHand), remaining in default position related to hand
- (4) You can select all bones by clicking to the checkbox in the header. Fingers will be included only if the hand bone is expanded.
- (5) You can change bones listbox height using splitter at the bottom.
Select linear quantities for analysis
Select output units for each quantity
Select linear coordinate system
Select angular quantities for analysis
Select output units for each quantity
Select angular coordinate system
Select Euler angles system

Plot Data

You can plot values of the selected quantities for the selected bones within the Region-of-Interest (except Quaternions and Rotation matrices, as it makes no sense to see them on plots due to their physical meaning).

Select the Region-of-Interest
Press Plot Selected Data button
Plot window will be opened. If it is already opened it's contents will be updated. In the Plot window you see bones in rows and quantities in columns. Plot controls:
Plot controls button shows plot control keys (focus should be set to Plot window).
Mouse wheel — zoom in / out for the horizontal axis
'Page Up' key — zoom in for the horizontal axis
'Page Down' key — zoom out for the horizontal axis
Right mouse button drag over plots — horizontal shift of all plots
Left mouse button drag over table header title — change columns order
'Right arrow' key — shift all plots to the left
'Left arrow' key — shift all plots to the right
Left mouse key click — show plot values for particular frame
'A' key — cancel zoom and shift, restore initial state of all plots
Reload plot data reloads plot's data. Useful when selection of bones, quantities, Region-of-Interest changed or any tracking / refined / filtering applied to motion data. You will get the same effect if you press Plot button.
Scroll to current frame button shifts all plots along horizontal axis, in order to make current frame visible in the plot area. Nothing happens, if current frame is already visible on plots.
Show / hide series button allows to select particular components of the corresponding quantity that will be shown on graph.

Export Motion Data

To export values of the selected quantities for the selected bones within the Region-of-Interest:

Select the Region-of-Interest
Press Export Selected Data button
Select export option:
- Tab-separated text file: text format easily importable to Excel. Header will contain information on parameters such as coordinate systems and units
- Copy to clipboard / paste to Excel: text data will be copied to clipboard. You just need to open empty Excel sheet and paste data to it. Information on parameters such as coordinate systems and units will be in the top rows.
- MATLAB file: binary file in MATLAB format.

Export Point Cloud

To export point cloud captured with depth sensors within the Region-of-Interest:

Select the Region-of-Interest
Select the cameras you want to export point cloud from (if you select several cameras, you will get one aggregate point cloud)
Turn on / off background subtraction (if checked, background will not be included in point cloud)
Turn on / off RGB export (if checked, color information will be added to points)
Press Export Selected Data button
Select export option:
- One point cloud from current frame (PCD): export single point cloud from the current frame to a file in PCD format
- All frames of ROI (multiple PCD files): export multiple point clouds (one point cloud from each frame of the Region-of-Interest) to PCD format, each point cloud is saved to a separate file
- One point cloud from current frame (MAT): export single point cloud from the current frame to a file in MATLAB format
- All frames of ROI (MAT): export multiple point clouds (one point cloud from each frame of the Region-of-Interest) to a file in MATLAB format

Biomech Export Profile

You can save all interface settings (1) to an XML file, and later load them from the file (2). It is useful if you work with several projects that require to analyze different bones and / or quantities. The following settings are stored:

Selected bones, bones list view height
Selected quantities, coordinate systems, euler angles system, units
Settings of point cloud export
Plot window settings (order on columns, visible series, window size and position)

@@ Line 1: / Line 1: @@
 === Introduction ===
-Starting from version 2.6, [[iPi Mocap Studio]] includes '''iPi Biomech Extension'''.
+Starting from version 2.6, [[iPi Mocap Studio]] includes '''iPi Biomech Add-on'''.
-'''iPi Biomech Add-on''' is a convenient tool for in-depth biomechanical analysis on tracking data. It includes visualization of tracking data and its export to various formats. It can be used for:
+'''iPi Biomech Add-on''' is a convenient tool for in-depth biomechanical analysis of human motions. It includes visualization of tracking data and its export to various formats. It can be used for:
 * Gait analysis and rehabilitation
 * Sports motion analysis
@@ Line 13: / Line 13: @@
 * Get '''Linear and Angular Quantities''' for selected bones, including
 ** Linear coordinate, velocity, acceleration
-** [http://en.wikipedia.org/wiki/Euler_angles Euler angles], angular velocity and acceleration
+** [http://en.wikipedia.org/wiki/Euler_angles Euler angles], [http://en.wikipedia.org/wiki/Angular_velocity angular velocity] and [http://en.wikipedia.org/wiki/Angular_acceleration angular acceleration]
+** [http://en.wikipedia.org/wiki/Quaternion Quaternions] and [http://en.wikipedia.org/wiki/Rotation_matrix Rotation matrices]
 * Select convenient '''coordinate systems'''
 ** Linear: Absolute (relative to floor), Relative to parent joint, Relative to center of mass
 ** Angular: Absolute (relative to floor), Relative to parent joint
-* '''Plot''' values of selected metrics
+* Select '''[http://en.wikipedia.org/wiki/Euler_angles#Conventions Euler angles system]'''
+* '''Plot''' values of selected '''Quantities''' for selected bones
 * '''Export''' bones motion data to file
-** [http://en.wikipedia.org/wiki/Tab-separated_values Tab-separated text] (for Excel)
+** [http://en.wikipedia.org/wiki/Tab-separated_values Tab-separated text] format (for Excel)
-** [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf MATLAB]
+** [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf MATLAB] format
 * '''Export point clouds''' obtained from depth sensors to file
-**[http://pointclouds.org/documentation/tutorials/pcd_file_format.php PCD]
+**[http://pointclouds.org/documentation/tutorials/pcd_file_format.php PCD] format
-**[http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf MATLAB]
+**[http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf MATLAB] format
 </td>
@@ Line 35: / Line 37: @@
 === Glossary ===
-;Linear quantities: Quantities derived from linear coordinate of joint in which bone is connected to parent bone, include:
+;Linear quantities: Quantities derived from linear coordinate of the joint which connects bone to it's parent bone, including:
 ::* Coordinate
 ::* Velocity
 ::* Acceleration
-;Angular quantities: Quantities derived from Euler angle of bone, include:
+;Angular quantities: Quantities derived from bones's Euler angle, including:
 ::* [http://en.wikipedia.org/wiki/Euler_angles Euler angle]
-::* Angular velocity
+::* [http://en.wikipedia.org/wiki/Angular_velocity Angular velocity]
-::* Angular acceleration
+::* [http://en.wikipedia.org/wiki/Angular_acceleration Angular acceleration]
+::* [http://en.wikipedia.org/wiki/Quaternion Quaternions]
+::* [http://en.wikipedia.org/wiki/Rotation_matrix Rotation matrices]
 ;Linear coordinate system: Coordinate system used for '''linear quantities''', can be:
-::* Absolute (relative to ground) - axis are shown by selecting Move tool; center is automatically set during calibration (it's z-coordinate is always 0)
+::* Absolute (relative to ground) &mdash; axes are shown by selecting Move tool; center is automatically set during calibration (it's z-coordinate is always 0)
-::* Relative to center of mass - axis are shown by selecting Move tool; center is in the actor model center of mass
+::* Relative to center of mass &mdash; axes are shown by selecting Move tool; center is in the actor model's center of mass
-::* Relative to parent joint - axis are shown by selecting Move tool; center coincides with the coordinates of parent bone
+::* Relative to parent joint &mdash; axes are shown by selecting Move tool; center coincides with the coordinates of the parent bone
 ;Angular coordinate system: Coordinate system used for '''angular quantities''', can be:
-::* Absolute (relative to ground) - in this system rotations are defined relative to ground
+::* Absolute (relative to ground) &mdash; in this system rotations are defined relative to ground
-::* Local (Relative to parent bone) - in this system rotations are defined relative to parent bone
+::* Local (Relative to parent bone) &mdash; in this system rotations are defined relative to the parent bone
 ;Euler angles system: Set of rotations which defines Euler angles, see [http://en.wikipedia.org/wiki/Euler_angles#Conventions here]
@@ Line 60: / Line 64: @@
 === License and Trial ===
-'''iPi Biomech Extension''' requires separate license key, which you need to activate in addition to [[iPi Mocap Studio]] license key. You can order your license [http://ipisoft.com/biomech here], or activate 30-days free trial. As soon as you install (or auto-update to) version 2.6 or higher, '''Biomech''' tab will appear in [[iPi Mocap Studio]] control panel. Follow the steps below to start working with '''iPi Biomech Extension'''
+'''iPi Biomech Add-on''' requires separate license key, which you need to activate in addition to [[iPi Mocap Studio]] license key. You can order your license [https://ipisoft.com/software/biomech-add-on/ here], or activate 30-days free trial. As soon as you install (or auto-update to) version 2.6 or higher, '''Biomech''' tab will appear in [[iPi Mocap Studio]] control panel. Follow the steps below to start working with '''iPi Biomech Add-on'''
 # Switch to '''Biomech''' tab.
 # Press '''Activate''' button
 # Press '''Start 30-days Free Trial Period''' or '''Enter Biomech License Key''' and follow further on-screen instructions
-#: [[Image:iPi-Biomech-2-1.png]]
+#: [[Image:iPi-Biomech-2-1.png|600px]]
-<blockquote>'''Note.''' If you do not have [[iPi Mocap Studio]] license key, you can order it [http://ipisoft.com/store here] or activate 30-days free trial. If your Studio trial has expired, you will not be able to export biomech data as well as animation. But you can still plot biomech data.</blockquote>
+<blockquote>'''Note.''' If you do not have [[iPi Mocap Studio]] license key, you can order it [https://ipisoft.com/store here] or activate 30-days free trial. If your Studio trial has expired, you will not be able to export biomech data as well as animation. But you can still plot biomech data.</blockquote>
 === Select Data for Analysis ===
@@ Line 72: / Line 76: @@
 # Select bones
 #* (1) Check corresponding bones to include them in analysis
-#* (2) On the top of the list you can see "special" bones - Center of mass, Center of mass projection to the ground. The rest of the list are bones from internal iPi rig.
+#* (2) On the top of the list you can see "special" bones &mdash; ''Center of mass'', ''Center of mass projection to the ground''. The rest of the list are the bones from the internal iPi rig.
 #* (3) You can include finger bones into analysis by expanding hand bone (RHand and / or LHand). However, fingers are not tracked due to insufficient resolution of off-the-shelf cameras, so they just keep attached to hand joint (RHand or LHand), remaining in default position related to hand
-#* (4) You can select all bones by clicking to checkbox in the header. Fingers will be included only if hand bone is expanded.
+#* (4) You can select all bones by clicking to the checkbox in the header. Fingers will be included only if the hand bone is expanded.
 #* (5) You can change bones listbox height using splitter at the bottom.
-#: [[Image:iPi-Biomech-2-2.png]]
+#: [[Image:iPi-Biomech-2-2.png|400px]]
 # Select '''linear quantities''' for analysis
 # Select output '''units''' for each quantity
@@ Line 84: / Line 88: @@
 # Select '''angular coordinate system'''
 # Select '''Euler angles system'''
-#: [[Image:iPi-Biomech-2-3.png]]
+#: [[Image:iPi-Biomech-2-3.png|400px]]
 === Plot Data ===
+You can plot values of the selected '''quantities''' for the selected bones within the ''Region-of-Interest'' (except Quaternions and Rotation matrices, as it makes no sense to see them on plots due to their physical meaning).
+# Select the ''Region-of-Interest''
+# Press '''Plot Selected Data''' button
+#: Plot window will be opened. If it is already opened it's contents will be updated. In the Plot window you see bones in rows and '''quantities''' in columns. Plot controls:
+# '''Plot controls''' button shows plot control keys (focus should be set to '''Plot''' window).
+#:'''Mouse wheel''' &mdash; zoom in / out for the horizontal axis
+#:''''Page Up' key''' &mdash; zoom in for the horizontal axis
+#:''''Page Down' key''' &mdash; zoom out for the horizontal axis
+#:'''Right mouse button drag over plots''' &mdash; horizontal shift of all plots
+#:'''Left mouse button drag over table header title''' &mdash; change columns order
+#:''''Right arrow' key''' &mdash; shift all plots to the left
+#:''''Left arrow' key''' &mdash; shift all plots to the right
+#:'''Left mouse key click''' &mdash; show plot values for particular frame
+#:''''A' key''' &mdash; cancel zoom and shift, restore initial state of all plots
+# '''Reload plot data''' reloads plot's data. Useful when selection of bones, '''quantities''', ''Region-of-Interest'' changed or any tracking / refined / filtering applied to motion data. You will get the same effect if you press '''Plot''' button.
+# '''Scroll to current frame''' button shifts all plots along horizontal axis, in order to make current frame visible in the plot area. Nothing happens, if current frame is already visible on plots.
+# '''Show / hide series''' button allows to select particular components of the corresponding '''quantity''' that will be shown on graph.
+#: [[Image:iPi-Biomech-2-4.png|700px]]
 === Export Motion Data ===
+To export values of the selected '''quantities''' for the selected bones within the ''Region-of-Interest'':
+# Select the ''Region-of-Interest''
+# Press '''Export Selected Data''' button
+# Select export option:
+#* ''Tab-separated text file'': text format easily importable to Excel. Header will contain information on parameters such as '''coordinate systems''' and '''units'''
+#* ''Copy to clipboard / paste to Excel'': text data will be copied to clipboard. You just need to open empty Excel sheet and paste data to it. Information on parameters such as '''coordinate systems''' and '''units''' will be in the top rows.
+#* ''MATLAB file'': binary file in [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf MATLAB] format.
+#: [[Image:iPi-Biomech-2-5.png|400px]]
+=== Export Point Cloud ===
+To export point cloud captured with depth sensors within the ''Region-of-Interest'':
+# Select the ''Region-of-Interest''
+# Select the cameras you want to export point cloud from (if you select several cameras, you will get one aggregate point cloud)
+# Turn on / off background subtraction (if checked, background will not be included in point cloud)
+# Turn on / off RGB export (if checked, color information will be added to points)
+# Press '''Export Selected Data''' button
+# Select export option:
+#* ''One point cloud from current frame (PCD)'': export single point cloud from the current frame to a file in [http://pointclouds.org/documentation/tutorials/pcd_file_format.php PCD] format
+#* ''All frames of ROI (multiple PCD files)'': export multiple point clouds (one point cloud from each frame of the ''Region-of-Interest'') to [http://pointclouds.org/documentation/tutorials/pcd_file_format.php PCD] format, each point cloud is saved to a separate file
+#* ''One point cloud from current frame (MAT)'': export single point cloud from the current frame to a file in [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf MATLAB] format
+#* ''All frames of ROI (MAT)'': export multiple point clouds (one point cloud from each frame of the ''Region-of-Interest'') to a file in [http://www.mathworks.com/help/pdf_doc/matlab/matfile_format.pdf MATLAB] format
+#: [[Image:iPi-Biomech-2-6.png|400px]]
+=== Biomech Export Profile  ===
+You can save all interface settings '''<span style="color: red">(1)</span>''' to an XML file, and later load them from the file '''<span style="color: red">(2)</span>'''. It is useful if you work with several projects that require to analyze different bones and / or '''quantities'''. The following settings are stored:
-=== Export Point Cloud ===
+* Selected bones, bones list view height
+* Selected '''quantities''', '''coordinate systems''', '''euler angles system''', '''units'''
+* Settings of point cloud export
+* Plot window settings (order on columns, visible series, window size and position)
+: [[Image:iPi-Biomech-2-7.png|400px]]

Biomechanical Analysis

Latest revision as of 10:26, 4 March 2021

Contents

Introduction

Glossary

License and Trial

Select Data for Analysis

Plot Data

Export Motion Data

Export Point Cloud

Biomech Export Profile

Views

Personal tools

Navigation

Search

Toolbox