HAS-Motion Software Documentation

It is possible to run sift from the command line, this offers several advantages:

• With no need to update a GUI or plots the application will run much faster
• With experience it makes it possible to quickly execute commands
• Creating a bat file or python script it is possible to completely automate processing

To start sift in command line mode, open a command line console, navigate to Sift's install directory and run sift with any argument that starts with a single dash (-) if you do not want to run any commands as Sift is launched you can instead pass -NoGUI

• Commands are prefixed with a dash these are considered a reserved character, but Sift will ignore any dashes that are within double quotes so file-name.txt will cause an error, where “file-name.txt” will not.
• Commands and parameters are case insensitive
• any parameters containing a space or a dash (e.g. a folder path) must be wrapped in double quotes (“”)
• Command parameters are named not positional, so the order they are passed does not matter
• Some commands have a default parameter, in these cases the parameter name can be omitted, for example with -loadLib the directory parameter name is optional. so either of the following will work: -loadLib directory “folder path” or -loadLib “folder path”. These parameters are marked as default in the list below
• Commands can be entered all at once in the same command that launches sift, or one at a time
• To exit pass the command -Exit, or press Ctrl + C to quickly exit at any time (Sift will exit once the current command finishes executing)
• Most commands have one or more aliases that will be accepted

If at any point you need help remembering a command or its parameters you can use the help function. Enter the command -Help to receive a list of all available commands within the command line:

This will display the commands default name and any aliases separated by |'s, below each will be a brief description of the command as well as a list of all it's parameters

From here, if you want some more information about a specific command and its parameters you can enter the command of interest and pass it the help parameter, this will give a more detailed description of the command and its parameters:

This will display the command name and any accepted aliases, and below that a list of all parameters complete with a description and some more details about the parameter:

• Whether or not this parameter is required for the command to run
• The default value of the parameter if its not passed
• The expected data type of the parameter

Load in a library of CMZs

Path to the directory containing the CMZs to be loaded, all sub-directories will be searched as well.

-LoadLib directory "C:\library folder"

Load a saved query from a .q3d file

The path to the .q3d file containing the query

-LoadQuery file "C:\library folder\query.q3d"

Select all or a selection of Signal groups and workspaces

The name of a group to be selected, this parameter can be passed multiple times to select more than one group, if this parameter is not passed, all groups will be selected

The name of a workspace to be selected, this parameter can be passed multiple times to select more than one workspace, if this parameter is not passed, all workspaces will be selected

-SelectSignals group "AnkleAngleX" group "AnkleAngleY" workspace "Sub004"

Select all or a selection of Metric groups and workspaces

The name of a group to be selected, this parameter can be passed multiple times to select more than one group, if this parameter is not passed, all groups will be selected

The name of a workspace to be selected, this parameter can be passed multiple times to select more than one workspace, if this parameter is not passed, all groups will be selected

-SelectMetrics group "MaxKneeAngleX" group "MinKneeAngleX" workspace "Sub001"

Save the currently open project to an .i3d file

The name and path of the .i3d file being saved

-SaveProject file "C:/folder/file.i3d"

Load the passed project file

The name and path of the .i3d file being loaded

-LoadProject file "C:/folder/file.i3d"

Clear all data from the current project, no parameters

-ClearProject

Run Principal Component Analysis on all queries

The name for the PCA to be created

How many principal components should be created
_{Default: 4}

If passed PCA will be run on the mean of each workspace and not the individual traces

-RunPCA name "New PCA" numPCs "3" workspaceMean

Run Local Outlier Factor

If passed any outliers found will be excluded automatically

How should data be grouped before running?

• Combined Groups: All data points will be compared
• Groups: Data will be compared within groups
• Workspace: Data will be compared within workspaces

_{Default: Combined Groups}

The threshold to consider when searching for outliers
_{Default: 2.00}

How many neighbors should each point be compared to?
_{Default: 10}

How many iterations of the test should be run
_{Default: 1}

How many principal components should the test be run on
_{Default: 2}

Determine the number of PCs by variance explained (replaces NumPCs if used)
_{Default: 95.0}

If passed scale all calculated values to the variability explained by the PC

-RunLOF autoExclude manualThreshold "3" numNeighbors "20" numPasses "2" numPCs "2" scaleToVariability

Run K-Means clustering

How many clusters to sort the data into
_{Default: 2}

If provided use as a seed for the random first centroid (produces repeatable results)

How should data be grouped before running:

• Combined Groups: All data points will be compared
• Groups: Data will be compared within groups
• Workspaces: Data will be compared within workspaces

_{Default: Combined Groups}

How many iterations of the test should be run
_{Default: 5}

The number of principal components to run the test on
_Default:2

Determine the number of principal components by variance explained (replaces NumPCs if used)
_{Default: 95.0}

If passed scale all calculated values to the variability explained by the PC

-RunKMeans clusters "3" customSeed "0" grouping "combined groups" iterations "1" numPCs "2" scaleToVariability

Run squared prediction error

The alpha threshold used to determine outliers: 0.1, 0.05, 0.025, 0.01, 0.005
_{Default: 0.05}

If passed any outliers will be excluded automatically

The number of Principal Components to run the test on _{Default: 2} == PCsVariance == scale calculated values to variability explained _{Default: 95.0}

-RunSPE alphaValue "0.005" autoExclude numPCs "2"

Run a Mahalanobis distance test

The threshold used to determine outliers: 0.1, 0.05, 0.025, 0.01, 0.005
_{Default: 0.05}

If passed any outliers found will be excluded automatically

How should data be grouped before running:

• Combined Groups: All data points will be compared
• Groups: Data will be compared within groups
• Workspace: Data will be compared within workspaces

_{Default: Combined Groups}

How many iterations of the test should be run
_{Default: 1}

The number of principal components to run the test on
_{Default: 2}

Determining the number of PCs by variance explained
_{Default: 95.0}

If passed scale calculated values to variability explained

-LoadMah alphaValue "0.1" autoExclude grouping "groups" numPasses "3" numPCs "2" scaleToVariance

Execute one or more Visual3D pipeline scripts via the V3D Engine, currently this only works if a library has be loaded and a query run

A path to a .v3s script file, this parameter can be used more than once to load multiple scripts, the scripts will be executed in the order the are passed

-RunV3d script "C:\library folder\Script One.v3s" script "C:\library folder\Script Two.v3s"

Run a single V3D pipeline command (Can be use multiple times to execute multiple commands)

The pipeline command to be executed

-RunV3DCommand command "Set_Default_Folders C:\Folder Path\;"

Set a global parameter within the Visual3D Engine to be used later

The path you want to set the global variable to

-DirPath path "C:\Program Files\Directory Path\"

Register via events

Use local maximum as a registration point

The lower bounds of the local max

The upper bounds of the local max

Use the local minimum as a registration point

The lower bounds of the local min

The upper bounds of the local min

Register by maximum

Register by minimum

The name for registered curve group created

-RegisterCurves max name "AnkleAngleX_Reg"

Create a General Linear Model

The grouping used for the model: Workspace / Group
_{Default: Group}

The name of the GLM being created

-CreateGLM name "New GLM" grouping "group"

Run Statistical Parametric Mapping One-Sample T-Test

The name of the SPM created

The name of the group to test

The name of the GLM to use when creating the SPM

The alpha value to threshold with

If two-tailed inference (as opposed to one-tailed)

-RunSPM1TTest name "NEW_SPM_TEST" glm "GLM" group "AnkleAngleX" alpha "0.5" twoTailed

Run Statistical Parameteric Mapping Two-Sample T-Test

The name of the SPM created

The name of the first group to test

The name of the second group to test

The name of the GLM to use when creating the SPM

The alpha value to threshold with

It two-tailed inference (as opposed to one-tailed)

-RunSPM2TTest name "NEW_SPM_TEST" glm "GLM" group1 "Ankle_AngleX_Healthy" group2 "Ankle_AngleX_Affected" alpha "0.5" twoTailed

Run Statistical Parametric Mapping Paired T-Test

The name of the SPM created

The name of the first group to test

The name of the second group to test

The name of the GLM to use when creating the SPM

The alpha value to threshold with

It two-tailed inference (as opposed to one-tailed)

-RunSPMPairedTTest name "NEW_SPM_TEST" glm "GLM" group1 "Ankle_AngleX_Healthy" group2 "Ankle_AngleX_Affected" alpha "0.5" twoTailed

Run Statistical Parametric Mapping Paired T-Test

The name of the SPM being created

The name of the GLM to use when creating the SPM

The Alpha value to threshold with

If two-tailed inference (as opposed to one-tailed)

-RunSPMOneWayAnova name "NEW_SPM_TEST" glm "GLM" alpha "0.5" twoTailed

Run Dynamic Time Warping

The name of the DTW test being run

How many standard deviations to test for: 1-3
_{Default: 1}

--RunDTW name "New DTW" standardDeviations "2"

Export the selected traces on a signal time plot

The file path the plot will be saved to, pass the desired image extension. Accepted image formats are .png, .pdf, .bmp, and .jpg

The height in pixels of the generated plot
_{Default: 1000}

The width in pixels of the generated plot
_{Default: 1000}

The title displayed at the top of the plot

The label displayed along the X Axis of the plot

The label displayed along the Y Axis of the plot

Where the legend will be displayed, options are: Top Right, Top Left, Bottom Right, Bottom Left. If this is not passed no legend will be displayed.

Which data style type to use when generating the plot, options are: Workspace, Group, Sub Group, Cluster
_{Default: Workspace}

If passed the group dispersion will be plotted

The method of dispersion to plot, options are: One Standard Deviation, Two Standard Deviations, Interquartile Range
_{Default: One Standard Deviation}

If passed group mean will be plotted

If passed the workspace dispersion will be plotted

The method of dispersion to plot, options are: One Standard Deviation, Two Standard Deviations, Interquartile Range
_{Default: One Standard Deviation}

If passed workspace mean will be plotted

The range of values displayed on the X Axis of the plot, format: “min,max”

The range of values displayed on the Y Axis of the plot, format: “min,max”

If passed individual traces will be plotted, if no other items are plotted, raw traces will be plotted by default

-ExportPlotSignalTime filePath "C:\Export Folder\signal_time_plot.png" rawTraces workspaceMean workspaceDispersion workspaceDispersionType "Interquartile Range" legend "Bottom Left"

Export the selected metrics on a metric plot

The file path the plot will be saved to, pass the desired image extension. Accepted image formats are .png, .pdf, .bmp, and .jpg

The height in pixels of the generated plot
_{Default: 1000}

The width in pixels of the generated plot
_{Default: 1000}

The title displayed at the top of the plot

The label displayed along the X Axis of the plot

The label displayed along the Y Axis of the plot

Where the legend will be displayed, options are: Top Right, Top Left, Bottom Right, Bottom Left. If this is not passed no legend will be displayed.

-ExportPlotMetric filePath "C:\Export Folder\metric_plot.png" rawTraces workspaceMean workspaceDispersion workspaceDispersionType "Interquartile Range" legend "Bottom Left"

Export the selected signals on a Signal-Signal plot

The path to the desired export location

Add a pair of two groups, seperate group names with '|' eg. “GROUP_1|GROUP_2”

The data style to use when generating the plot, options include: Workspace, Group, Sub Group, Cluster

If passed group dispersion will be plotted

The type of dispersion to be displayed for groups

If passed the group mean will be plotted

The height in pixels of the image being exported

Which corner should the legend be displayed in, if not passed no legend will be displayed

If passed individual traces will be plotted

The title of the plot

The width in pixels of the image being exported

If passed the workspace dispersion will be plotted

The type of dispersion to be displayed for workspaces

If passed workspace mean will be plotted

Label for the X Axis

The display range of the X Axis: “High,Low”

Label for the Y Axis

The display range of the Y Axis: “High,Low”

-ExportPlotPairSignal filePath "C:\Export Folder\signal_signal_plot.png" pair "Ankle_Angle_X|Elbow_Angle_X" rawTraces workspaceMean

Export the selected metrics on a Metric-Metric plot

The data style to use when generating plot

The file path the plot will be saved to

If passed group dispersion will be plotted

The type of dispersion to be displayed for groups

If passed group mean will be plotted

The height in pixels of the image exported

The random offset of each pointer on the X Axis

The random offset of each pointer on the Y Axis

Which corner should the legend be displayed in, if not passed no legend will be displayed

Add a pair of two groups, separate group names with '|' eg. “GROUP_1|GROUP_2”

If passed individual traces will be plotted

The title of the plot

The width in pixels of the image exported

If passed workspace dispersion will be plotted

The type of dispersion to be displayed for the workspaces

If passed workspace mean will be plotted

Label for the X-Axis

The display range of the X-Axis: “High,Low”

Label for the Y-Axis

The display range of the Y Axis: “High,Low”

-ExportPlotPairMetric filePath "C:\Export Folder\metric_metric_plot.png" pair "Ankle_Angle_X|Elbow_Angle_X" rawTraces workspaceMean

----
==== -ExportPlotSPM /  -EPSPM ====
----
Export the active SPM plot
=== Parameters ===
== FilePath (Required/Default) ==
The file path the plot will be saved to, pass the desired image extension. Accepted image formats are .png, .pdf, .bmp, and .jpg
== Height ==
The height in pixels of the generated plot \\
<sub>//Default:// 1000</sub>
== Width ==
The width in pixels of the generated plot \\
<sub>//Default:// 1000</sub>
== Title ==
The title displayed at the top of the plot
== XLabel ==
The label displayed along the X Axis of the plot
== YLabel ==
The label displayed along the Y Axis of the plot
== Legend ==
Where the legend will be displayed, options are: Top Right, Top Left, Bottom Right, Bottom Left. If this is not passed no legend will be displayed.
== DataStyle ==
What data style used when plotting, options are: Workspace, Group, Sub Group, Cluster \\
=== Example ===
<code>-ExportPlotSPM filePath "C:\Export Folder\spm_plot.png" legend "Bottom Left"

Export the active GLMs residual plot

The data style to use when generating plot

The file path the plot will be saved to

The height in pixels of the image exported

Which corner should the legend be displayed in, if not passed no legend will be displayed, Options: Top Left, Top Right, Bottom Left, Bottom Right

The title of the plot

The width in pixels of the image exported

Label for the X-Axis

The display range of the X Axis: “High,Low”

Label for the Y-Axis

The display range of the Y Axis: “High,Low”

-ExportPlotResiduals filePath "C:\Export Folder\glm_residuals.png"

Export queried data results in an ascii text file

The path and name of the .txt file to export

How many decimal places to display in exported values
_{Default: 4}

The format of the exported ASCII file: Standard, SPSS, Transposed, P2D
_{Default: Standard}

Number of points to normalize the export data to
_{Default: 101}

If passed the group mean will be exported

If passed the workspace standard deviation will be exported

If passed all normalized sequences will be exported

If passed all time based sequences will be exported

-ExportData file "C:\library folder\exports\Data Export.txt"  precision "2" exportFormat "standard" normalizedTo "100" groupMean groupStdDev workspaceMean workspaceStdDev allSequenceNorm allSequencesTime

Export PCA results to a .txt file

The path and name of the .txt file to export

How many decimal places to display in exported values
_{Default: 4}

The format of the exported ASCII file: Standard, SPSS, Transposed, P2D
_{Default: Standard}

The format of the exported ASCII file: Standard, Transposed, SPSS, P2D

If passed the workspace scores will be exported

If passed the group scores will be exported

If passed the group standard deviation will be exported

If passed the variance explained by each PC will be exported

If passed all eigen vectors will be exported

If passed the mean +/- one standard deviation will be exported

If passed the mean +/- 5 and 95% will be exported

-ExportPCA fileName "C:\library folder\exports\PCA Export.txt" precision "4" exportFormat "transposed" workspaceScores groupScores groupStdDev varianceExplained eigenVectors meanSD mean595

Export summary statistics to a .txt file

The path and name of the .txt file to export

How many decimal places to display in exported values
_{Default: 4}

The format of the exported ASCII file: Standard, SPSS, Transposed, P2D
_{Default: Standard}

The format of the exported ASCII file: Standard, Transposed, SPSS, P2D

If passed the maximum value will be exported

If passed the maximum event point will be exported

If passed the maximum standard deviation will be exported

If passed the mean value will be exported

If passed the mean standard deviation will be exported

If passed the the minimum value will be exported

If passed the minimum event point will be exported

If passed the minimum standard deviation will be exported

Normalize exported metrics

Export results for: Groups, Workspaces, Instances

-ExportSummaryStatistics file "C:\library folder\exports\Summary Statistics Export.txt" precision "2" exportFormat "SPSS" max maxEventPoint maxStdDev mean meanStdDev min minEventPoint minStdDev normalizeMetrics results "groups"

Export any results of curve registration

The path and name of the .txt file to export

How many decimal places to display in exported values
_{Default: 4}

The format of the exported ASCII file: Standard, SPSS, Transposed, P2D
_{Default: Standard}

The format of the exported ASCII file: Standard, Transposed, SPSS, P2D

If passed all landmarks will be exported

If passed the mean of all landmarks will be exported

If passed registered curves will be exported

If passed warping functions will be exported

-ExportRegisteredCurves file "C:\library folder\exports\Registered Curves Export.txt" precision "3" exportFormat "transposed" landmarkAll landmarkMeans registeredCurves warpingFunctions

Export Dynamic Time Warping results

The path and name of the .txt file to export

How many decimal places to display in exported values
_{Default: 4}

The format of the exported ASCII file: Standard, SPSS, Transposed, P2D
_{Default: Standard}

The format of the exported ASCII file: Standard, Transposed, SPSS, P2D

If passed cost functions will be exported

If passed all anomalies will be exported

-ExportDTW file "C:\library folder\exports\Dynamic Time Warping Export.txt" precision "3" exportFormat "transposed"  foundAnomalies costFunctions

Export Statistical Parametric Mapping Results

The path and name of the .txt file to export

How many decimal places to display in exported values
_{Default: 4}

The format of the exported ASCII file: Standard, SPSS, Transposed, P2D
_{Default: Standard}

The format of the exported ASCII file: Standard, Transposed, SPSS, P2D

If passed the B Matrix used will be exported

If passed the Residual Matrix will be exported

If passed the Statistical Parametric Map will be exported

-ExportSPM file "C:\library folder\exports\Statistical Parametric Map Export.txt" precision "5" exportFormat "transposed" bMatrix residualMatrix spm