HAS-Motion Software Documentation

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===== Sift Command Line =====
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 it is possible to completely automate processing
===== Running Sift From Command Line ======
To start sift in command line mode, open a command line console, navigate to sifts 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**
==== Command Line Overview ====
  * 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
  * Enter the command **-Help** to get a list of all available commands
  * Pass the parameter **Help** to any command to get a list and description of all of its parameters
  * 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

===== Commands =====
All commands and their parameters are listed below

----
==== -LoadLib / -l ====
----
Load in a library of CMZs
=== Parameters ===
== Directory (Required/Default) ==
Path to the directory containing the CMZs to be loaded, all sub-directories will be searched as well.
=== Example ===
<code>-LoadLib directory "C:\library folder"</code>

----
==== -LoadQuery  / -q ====
----
Load a saved query from a .q3d file
=== Parameters ===
== File (Required/Default) ==
The path to the .q3d file containing the query
=== Example ===
<code>-LoadQuery file "C:\library folder\query.q3d"</code>

----
==== -RunLOF / -lof ====
----
Run Local Outlier Factor
=== Parameters ===
== AutoExclude ==
If passed any outliers found will be excluded automatically
== Grouping ==
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
<sub>//Default:// Combined Groups</sub>
== ManualThreshold ==
The threshold to consider when searching for outliers \\
<sub>//Default:// 2.00</sub>
== NumNeighbors ==
How many neighbors should each point be compared to? \\
<sub>//Default:// 10</sub>
== numPasses ==
How many iterations of the test should be run \\
<sub>//Default:// 1</sub>
== NumPCs ==
How many principal components should the test be run on \\
<sub>//Default:// 2</sub>
== PCsVariance ==
Determine the number of PCs by variance explained (replaces NumPCs if used) \\
<sub>//Default:// 95.0</sub>
== ScaleToVariability ==
If passed scale all calculated values to the variability explained by the PC
=== Example ===
<code>-RunLOF autoExclude manualThreshold "3" numNeighbors "20" numPasses "2" numPCs "2" scaleToVariability</code>

----
==== -RunKMeans / -kmeans ====
----
Run K-Means clustering
=== Parameters ===
== Clusters ==
How many clusters to sort the data into \\
<sub>//Default:// 2</sub>
== CustomSeed ==
If provided use as a seed for the random first centroid (produces repeatable results)
== Grouping ==
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
<sub>//Default:// Combined Groups</sub>
==  Iterations ==
How many iterations of the test should be run \\
<sub>//Default:// 5</sub>
== NumPCs ==
The number of principal components to run the test on \\
<sub>//Default://2</sub>
== PCsVariance ==
Determine the number of principal components by variance explained (replaces NumPCs if used) \\
<sub>//Default:// 95.0</sub>
== ScaleToVariability ==
If passed scale all calculated values to the variability explained by the PC
=== Example ===
<code>-RunKMeans clusters "3" customerSeed "0" grouping "combined groups" iterations "1" numPCs "2" scaleToVariability</code>

----
==== -RunSPE / -spe ====
----
Run squared prediction error
===Parameters===
== AlphaValue ==
The alpha threshold used to determine outliers: 0.1, 0.05, 0.025, 0.01, 0.005 \\
<sub>//Default:// 0.05</sub>
== AutoExclude ==
If passed any outliers will be excluded automatically
== numPCs == 
The number of Principal Components to run the test on //
<sub>//Default:// 2</sub>
== PCsVariance ==
scale calculated values to variability explained //
<sub>//Default:// 95.0</sub>
=== Example ===
<code>-RunSPE alphaValue "0.005" autoExclude numPCs "2"</code>

----
==== -RunMah / -mah ====
----
Run a Mahalanobis distance test
=== Parameters ===
== AlphaValue ==
The threshold used to determine outliers: 0.1, 0.05, 0.025, 0.01, 0.005 \\
<sub>//Default:// 0.05</sub>
== AutoExclude ==
If passed any outliers found will be excluded automatically
== Grouping ==
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
<sub>//Default:// Combined Groups</sub>
== NumPasses ==
How many iterations of the test should be run \\
<sub>//Default:// 1</sub>
== NumPCs ==
The number of principal components to run the test on \\
<sub>//Default:// 2</sub>
== PCsVariance ==
Determining the number of PCs by variance explained \\
<sub>//Default:// 95.0</sub>
== ScaleToVariance ==
If passed scale calculated values to variability explained
=== Example ===
<code>-LoadMah alphaValue "0.1" autoExclude grouping "groups" numPasses "3" numPCs "2" scaleToVariance</code>

----
==== -RegisterCurves / -rc ====
----
=== Parameters ===
== EventSequence ==
Register via events
== LocalMax ==
Use local maximum as a registration point
== LocalMaxLower ==
The lower bounds of the local max
== LocalMaxUpper ==
The upper bounds of the local max
== LocalMin ==
Use the local minimum as a registration point
== LocalMinLower ==
The lower bounds of the local min
== LocalMinUpper ==
The upper bounds of the local min
== Max ==
Register by maximum
== Min ==
Register by minimum
== Name ==
The name for registered curve group created
=== Example ===
<code>-RegisterCurves max name "AnkleAngleX_Reg"</code>

----
==== -CreateGLM / -glm ====
----
Create a General Linear Model
=== Parameters ===
== Grouping ==
The grouping used for the model: Workspace / Group \\
<sub>//Default:// Group</sub>
== Name (Required/Default) ==
The name of the GLM being created
=== Example ===
<code>-CreateGLM name "New GLM" grouping "group"</code>

----
==== -RunSPM / -spm ====
----
Run Statistical Parametric Mapping 
=== Parameters ===
== GLM (Required) ==
The name of the GLM used when creating the SPM
== Group1 (Required) ==
The first grouping to compare
== Group2 (Required) ==
The second grouping to compare
== Name (Required) ==
The name of the SPM being created
=== Example ===
<code>-RunSPM name "New SPM" glm "New GLM" group1 "AnkleAngleX1_Reg" group2 "AnkleAngleX2_Reg"</code>

----
==== -RunDTW / -dtw ====
----
Run Dynamic Time Warping
=== Parameters ===
== Name (Required) ==
The name of the DTW test being run
== StandardDeviations ==
How many standard deviations to test for: 1-3 \\
<sub>//Default:// 1</sub>
=== Example ===
<code>--RunDTW name "New DTW" standardDeviations "2"</code>

---- 
==== -RunV3D / -s / -plpath ====
----
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
=== Parameters ===
== Script (Required) ==
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
=== Example ===
<code>-RunV3d script "C:\library folder\Script One.v3s" script "C:\library folder\Script Two.v3s"</code>

----
==== -RunPCA / -pca ====
----
Run Principal Component Analysis on all queries
=== Parameters ===
== Name (Required/Default) ==
The name for the PCA to be created
== numPCs ==
How many principal components should be created \\
<sub>//Default:// 4</sub>
== WorkspaceMean ==
If passed PCA will be run on the mean of each workspace and not the individual traces
=== Example ===
<code>-RunPCA name "New PCA" numPCs "3" workspaceMean</code>

----
==== -ExportData / -ex ====
Export queried data results in an ascii text file 
=== Parameter ===
== File (Required) ==
The path and name of the .txt file to export 
== Precision == 
How many decimal places to display in exported values \\
<sub>//Default:// 4</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\
<sub>//Default:// Standard</sub>
== NormalizedTo ==
Number of points to normalize the export data to \\
<sub>//Default:// 101</sub>
== GroupMean ==
If passed the group mean will be exported
== GroupStdDev ==
If passed the workspace standard deviation will be exported
== AllSequencesNorm ==
If passed all normalized sequences will be exported
== AllSequencesTime ==
If passed all time based sequences will be exported
=== Example ===
<code>-ExportData file "C:\library folder\exports\Data Export.txt"  precision "2" exportFormat "standard" normalizedTo "100" groupMean groupStdDev workspaceMean workspaceStdDev allSequenceNorm allSequencesTime</code>

----
==== -ExportPCA ====
----
Export PCA results to a .txt file
=== Parameter ===
== File (Required) ==
The path and name of the .txt file to export 
== Precision == 
How many decimal places to display in exported values \\
<sub>//Default:// 4</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\
<sub>//Default:// Standard</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, Transposed, SPSS, P2D
== WorkspaceScores ==
If passed the workspace scores will be exported
== GroupScores ==
If passed the group scores will be exported
== GroupStdDev ==
If passed the group standard deviation will be exported
== VarianceExplained ==
If passed the variance explained by each PC will be exported
== EigenVectors ==
If passed all eigen vectors will be exported
== MeanSD ==
If passed the mean +/- one standard deviation will be exported
== Mean595 ==
If passed the mean +/- 5 and 95% will be exported
=== Example ===
<code>-ExportPCA fileName "C:\library folder\exports\PCA Export.txt" precision "4" exportFormat "transposed" workspaceScores groupScores groupStdDev varianceExplained eigenVectors meanSD mean595</code>

----
==== -ExportSummaryStatistics ====
----
Export summary statistics to a .txt file
=== Parameters ===
== File (Required) ==
The path and name of the .txt file to export 
== Precision == 
How many decimal places to display in exported values \\
<sub>//Default:// 4</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\
<sub>//Default:// Standard</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, Transposed, SPSS, P2D
== Max ==
If passed the maximum value will be exported
== MaxEventPoint ==
If passed the maximum event point will be exported
== MaxStdDev ==
If passed the maximum standard deviation will be exported
== Mean ==
If passed the mean value will be exported
== MeanStdDev ==
If passed the mean standard deviation will be exported
== Min ==
If passed the the minimum value will be exported 
== MinEventPoint ==
If passed the minimum event point will be exported
== MinStdDev ==
If passed the minimum standard deviation will be exported 
== NormalizeMetrics ==
Normalize exported metrics
== Results ==
Export results for: Groups, Workspaces, Instances
=== Example ===
<code>-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"</code>

----
==== -ExportRegisteredCurves ====
Export any results of curve registration
=== Parameters ===
== File (Required) ==
The path and name of the .txt file to export 
== Precision == 
How many decimal places to display in exported values \\
<sub>//Default:// 4</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\
<sub>//Default:// Standard</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, Transposed, SPSS, P2D
== LandmarkAll ==
If passed all landmarks will be exported
== LandmarkMeans ==
If passed the mean of all landmarks will be exported
== RegisteredCurves ==
If passed registered curves will be exported
== WarpingFunctions ==
If passed warping functions will be exported
=== Example ===
<code>-ExportRegisteredCurves file "C:\library folder\exports\Registered Curves Export.txt" precision "3" exportFormat "transposed" landmarkAll landmarkMeans registeredCurves warpingFunctions</code>

----
==== -ExportDTW ====
----
Export Dynamic Time Warping results
=== Parameters ===
== File (Required) ==
The path and name of the .txt file to export 
== Precision == 
How many decimal places to display in exported values \\
<sub>//Default:// 4</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\
<sub>//Default:// Standard</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, Transposed, SPSS, P2D
== CostFunctions ==
If passed cost functions will be exported
== FoundAnomalies ==
If passed all anomalies will be exported
=== Example ===
<code>-ExportDTW file "C:\library folder\exports\Dynamic Time Warping Export.txt" precision "3" exportFormat "transposed"  foundAnomalies costFunctions</code>

----
==== -ExportSPM ====
----
Export Statistical Parametric Mapping Results
=== Parameters ===
== File (Required) ==
The path and name of the .txt file to export 
== Precision == 
How many decimal places to display in exported values \\
<sub>//Default:// 4</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\
<sub>//Default:// Standard</sub>
== ExportFormat ==
The format of the exported ASCII file: Standard, Transposed, SPSS, P2D
== BMatrix ==
If passed the B Matrix used will be exported
== ResidualMatrix ==
If passed the Residual Matrix will be exported
== SPM ==
If passed the Statistical Parametric Map will be exported
=== Example ===
<code>-ExportSPM file "C:\library folder\exports\Statistical Parametric Map Export.txt" precision "5" exportFormat "transposed" bMatrix residualMatrix spm</code>

----
==== -SelectSignals / -sig ====
----
Select all or a selection of Signal groups and workspaces
=== Parameters ===
== Group ==
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
== Workspace ==
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
=== Example ===
<code>-SelectSignals group "AnkleAngleX" group "AnkleAngleY" workspace "Sub004"</code>

---- 
==== -SelectMetrics / -met ====
----
Select all or a selection of Metric groups and workspaces
=== Parameters ===
== Group ==
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
== Workspace ==
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
=== Example ===
<code>-SelectMetrics group "MaxKneeAngleX" group "MinKneeAngleX" workspace "Sub001"</code>

----
==== -SaveProject / -sv ====
----
Save the currently open project to an .i3d file
=== Parameters ===
== file (Required/Default) ==
The name and path of the .i3d file being saved
=== Example ===
<code>-SaveProject file "C:/folder/file.i3d"</code>

----
==== -LoadProject / -ld ====
----
Load the passed project file
=== Parameters ===
== file ==
The name and path of the .i3d file being loaded
=== Example ===
<code>-LoadProject file "C:/folder/file.i3d"</code>

----
==== -ClearProject / -clr ====
----
Clear all data from the current project, no parameters
=== Example ===
<code>-ClearProject</code>