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sift:tutorials:visualizing_healthy_human_walking [2024/11/29 15:54] – [Cleaning the data set in Sift] wikisysopsift:tutorials:visualizing_healthy_human_walking [2024/11/29 18:26] (current) – [Data] wikisysop
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 We are interested in the .c3d files that can be downloaded [[https://doi.org/10.6084/m9.figshare.c.5897423.v1|here]]. We are interested in the .c3d files that can be downloaded [[https://doi.org/10.6084/m9.figshare.c.5897423.v1|here]].
  
-Also necessary are the Visual3D pipeline scripts, model templates, and Sift query definitions that can be downloaded [[https://www.has-motion.com/download/examples/Inspect3D/I3D_Tutorial_Healthy_Human_Walking.zip|here]].+Also necessary are the Visual3D pipeline scripts, model templates, and Sift query definitions that can be downloaded [[https://www.has-motion.com/download/examples/Sift_Tutorial_Healthy_Human_Walking.zip|here]].
  
   * **Create_CMO.v3s**: Script for creating a participant's CMZ file from the data set's C3D files.   * **Create_CMO.v3s**: Script for creating a participant's CMZ file from the data set's C3D files.
   * **CleanForceAssignments**: Folder of scripts called by **Create_CMO.v3s** to clean force assignments.   * **CleanForceAssignments**: Folder of scripts called by **Create_CMO.v3s** to clean force assignments.
   * **HealthyHumanWalking_ModelTemplate.mdh**: [[Visual3D:Documentation:Modeling:Modeling_Overview|Visual3D model]] for the C3D files.   * **HealthyHumanWalking_ModelTemplate.mdh**: [[Visual3D:Documentation:Modeling:Modeling_Overview|Visual3D model]] for the C3D files.
-  * **HealthyHumanWalking-ReportTemplate.rgt**: [[Visual3D:Documentation:Reports:Reports_Overview#Report_Template|Report template]] for the CMZ file.+  * **HealthyHumanWalking_ReportTemplate.rgt**: [[Visual3D:Documentation:Reports:Reports_Overview#Report_Template|Report template]] for the CMZ file.
   * **HealthyHumanWalking-GRF.q3d**: Query definitions for the three components of both the left and right ground reaction forces.   * **HealthyHumanWalking-GRF.q3d**: Query definitions for the three components of both the left and right ground reaction forces.
   * **HealthyHumanWalking-XComponent.q3d**: Query definitions for the X component of all signals of interest, with signals not combined across sides of the body.   * **HealthyHumanWalking-XComponent.q3d**: Query definitions for the X component of all signals of interest, with signals not combined across sides of the body.
   * **HealthyHumanWalking-LeftRight.xml**: Color palette matching the colours used in Figure 3 to denote the left and right sides of the body.   * **HealthyHumanWalking-LeftRight.xml**: Color palette matching the colours used in Figure 3 to denote the left and right sides of the body.
 +  * **Participant_1.cmz/cmz**: The .cmz and .cmz files built in the next section (in case you would like to skip it)
  
 ===== Creating CMZ files in Visual3D ===== ===== Creating CMZ files in Visual3D =====
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   - To create Participant 1's CMZ file, choose p1_c3dfiles/p1_standing_1.c3d file as the static calibration file.   - To create Participant 1's CMZ file, choose p1_c3dfiles/p1_standing_1.c3d file as the static calibration file.
-  - Choose Model_Template_CMotion_v2.mdh as the model file.+  - Choose HealthyHumanWalking_ModelTemplate.mdh as the model file.
   - Set Participant 1's weight, height, and foot width according to the [[https://www.nature.com/articles/s41597-022-01817-1/tables/2|anthropometric information]] included in the paper.   - Set Participant 1's weight, height, and foot width according to the [[https://www.nature.com/articles/s41597-022-01817-1/tables/2|anthropometric information]] included in the paper.
   - Choose the remaining 33 .c3d files in the p1_c3dfiles folder as the dynamic trials.   - Choose the remaining 33 .c3d files in the p1_c3dfiles folder as the dynamic trials.
-  - Choose Sample_Report_Template.rgt as the report template. \\ {{:Tutorial-HHW-V3DReports.PNG?1000x651}} \\+  - Choose Sample_Report_Template.rgt as the report template.
   - Save the results as Participant_1.cmz.   - Save the results as Participant_1.cmz.
  
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 The processing done in Visual3D allows us to extract signal traces from all of our desired gait sequences from the .c3d files, but not all of these are suitable for further analysis. The number of traces involved makes it impractical to clean this data set in Visual3D, there are more than 3000 traces for Participant 1 alone, but Sift gives us the ability to visualize the ground reaction forces and make inclusion/exclusion decisions for each trace. A detailed explanation of this process can be found in the [[Sift:Tutorials:Clean_your_Data|Clean your data]] tutorial. The processing done in Visual3D allows us to extract signal traces from all of our desired gait sequences from the .c3d files, but not all of these are suitable for further analysis. The number of traces involved makes it impractical to clean this data set in Visual3D, there are more than 3000 traces for Participant 1 alone, but Sift gives us the ability to visualize the ground reaction forces and make inclusion/exclusion decisions for each trace. A detailed explanation of this process can be found in the [[Sift:Tutorials:Clean_your_Data|Clean your data]] tutorial.
  
 +
 +  - Open color prefs dialog via the [[Sift:Application:Data_Options_Dialog|Data Options Dialog]] and load the palette "HealthyHumanWalking-LeftRight.xml"
   - Load **Participant_1.cmz** into the library.   - Load **Participant_1.cmz** into the library.
-  - Open the {{:sift_query_builder.png}} **Query Builder** dialog and apply the GRF.q3d query definitions to compute three groups, one for each component of the ground reaction force.+  - Open the {{:sift_query_builder.png?20}} **Query Builder** dialog, load and compute the HealthyHumanWalking-GRF.q3d query definitions to compute three groups, one for each component of the ground reaction force.
   - Navigate to the [[Sift:Application:Explore_Page|Explore Page]].   - Navigate to the [[Sift:Application:Explore_Page|Explore Page]].
-  - Select the GRF_Z group and **Plot all sequences**.+  - Select the GRF_Z group and **Plot all Traces**.
   - In the plot, iteratively select traces that look anomalous and exclude them. The end result should look like the figure on the right.   - In the plot, iteratively select traces that look anomalous and exclude them. The end result should look like the figure on the right.
-  - Open the {{:sift_update_cmz.png}} **Update CMZs** dialog from the toolbar, select **Update Force Assignments...**, and then **Update CMOs**. +  - Plot all sequences for each GRF component in turn, verifying that there are no included traces that should be excluded. If there are any erroneous traces left, repeat steps 4 and 5 as necessary until you are satisfied with the remaining traces.
-  - Plot all sequences for each GRF component in turn, verifying that there are no included traces that should be excluded. If there are any bad traces left, repeat steps 4 and 5 as necessary until you are satisfied with the remaining traces. +
- +
-----+
  
 ===== Visualizing the data ===== ===== Visualizing the data =====
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 Now that Participant 1's CMZ file has been cleaned of any unwanted traces, we are ready to perform some preliminary analysis and visualize the data set. Our goal in this section is to reproduce [[https://www.nature.com/articles/s41597-022-01817-1/figures/3|Figure 3]] in the paper. Now that Participant 1's CMZ file has been cleaned of any unwanted traces, we are ready to perform some preliminary analysis and visualize the data set. Our goal in this section is to reproduce [[https://www.nature.com/articles/s41597-022-01817-1/figures/3|Figure 3]] in the paper.
  
-  - Open the {{:sift_general_options.png}} **Show Options** dialog, and set both **Graph Rows** and **Graph Columns** to 3. This will create a 3x3 layout of grids in the plot area.\\ +  - Open the {{:sift_general_options.png?20}} **Show Options** dialog, and set both **Graph Rows** and **Graph Columns** to 3. This will create a 3x3 layout of grids in the plot area \\ {{:sift_row_col_count.png?500}} \\  
-{{:sift_row_col_count.png}}\\ +  - Open the {{:sift_plot_options.png?20}} Plot Options dialog, and deselect auto-scaling for the X and Y axis \\ {{:sift_auto_scale.png?500}} \\ 
- +  - Open the {{:sift_query_builder.png?20}} **Query Builder** dialog and load the HealthyHumanWalking-XComponent.q3d query definitions. This extracts the X-component for all signals in the library without combining signals across the left and right sides of the body.
-  - Open the {{:sift_plot_options.png}} Plot Options dialog, and deselect auto-scaling for the X and Y axis\\ +
-{{:sift_auto_scale.png}}\\ +
- +
-  - Open color prefs dialog via the [[Sift:Application:Data_Options_Dialog|Data Options Dialog]] and load the palette "HealthyHumanWalking-LeftRight.xml" +
-  - Open the {{:sift_query_builder.png}} **Query Builder** dialog and apply the HealthyHumanWalking-X.q3d query definitions. This extracts the X-component for all signals in the library without combining signals across the left and right sides of the body.+
   - Make sure that the top left graph (1,1) is active, indicated by the grey border. Select the RAnkleAngle_X LAnkleAngle_X groups and plot the Group Means.   - Make sure that the top left graph (1,1) is active, indicated by the grey border. Select the RAnkleAngle_X LAnkleAngle_X groups and plot the Group Means.
   - Repeat Step 3 for the remaining graphs with the following groups:   - Repeat Step 3 for the remaining graphs with the following groups:
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     * Bottom centre (3,2) - RKneePower_X and LKneePower_X     * Bottom centre (3,2) - RKneePower_X and LKneePower_X
     * Bottom right (3,3) - RHipPower_X and LHipPower_X     * Bottom right (3,3) - RHipPower_X and LHipPower_X
-  - With the group means plotted for each of our signals, all that remains is to assign the appropriate graph and axis titles. To do this, open the {{:sift_plot_options.png}} **Plot Styles** dialog and for the top left graph (1,1), provide the following input:+  - With the group means plotted for each of our signals, all that remains is to assign the appropriate graph and axis titles. To do this, open the {{:sift_plot_options.png?20}} **Plot Styles** dialog and for the top left graph (1,1), provide the following input:
     * Deselect **Display Group Name as Title**     * Deselect **Display Group Name as Title**
     * Use the title "Ankle", set the Title Font to Bold and Size 24.     * Use the title "Ankle", set the Title Font to Bold and Size 24.
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   - Repeat Step 5 for the remaining graphs using the titles from Figure 3.   - Repeat Step 5 for the remaining graphs using the titles from Figure 3.
  
-{{:27_132546.png}}+{{:healthy_human_all.png}}
  
  
sift/tutorials/visualizing_healthy_human_walking.1732895692.txt.gz · Last modified: 2024/11/29 15:54 by wikisysop