===== 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 the argument **--NoGUI** ==== Command Line Overview ==== * Commands are prefixed with two dashes (--) these are considered a reserved character, so file and parameter names can not contain two consecutive dashes * Commands and parameters are case insensitive * any parameters containing a space (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 * 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) ===== Commands ===== All commands and their parameters are listed below ---- ==== LoadLib ==== ---- Load in a library of CMZs === Parameters === == Directory (Required) == Path to the directory containing the CMZs to be loaded, all sub-directories will be searched as well. === Example === --LoadLib directory "C:\library folder" ---- ==== LoadQuery ==== ---- Load a saved query from a .q3d file === Parameters === == File (Required) == The path to the .q3d file containing the query === Example === --LoadQuery file "C:\library folder\query.q3d" ---- ==== RunLOF ==== ---- 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 //Default:// Combined Groups == ManualThreshold == The threshold to consider when searching for outliers \\ //Default:// 2.00 == NumNeighbors == How many neighbors should each point be compared to? \\ //Default:// 10 == numPasses == How many iterations of the test should be run \\ //Default:// 1 == NumPCs == How many principal components should the test be run on \\ //Default:// 2 == PCsVariance == Determine the number of PCs by variance explained (replaces NumPCs if used) \\ //Default:// 95.0 == ScaleToVariability == If passed scale all calculated values to the variability explained by the PC === Example === --RunLOF autoExclude manualThreshold "3" numNeighbors "20" numPasses "2" numPCs "2" scaleToVariability ---- ==== RunKMeans ==== ---- Run K-Means clustering === Parameters === == Clusters == How many clusters to sort the data into \\ //Default:// 2 == 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 //Default:// Combined Groups == Iterations == How many iterations of the test should be run \\ //Default:// 5 == NumPCs == The number of principal components to run the test on \\ //Default://2 == PCsVariance == Determine the number of principal components by variance explained (replaces NumPCs if used) \\ //Default:// 95.0 == ScaleToVariability == If passed scale all calculated values to the variability explained by the PC === Example === --RunKMeans clusters "3" customerSeed "0" grouping "combined groups" iterations "1" numPCs "2" scaleToVariability ---- ==== RunSPE ==== ---- Run squared prediction error ===Parameters=== == AlphaValue == The alpha threshold used to determine outliers: 0.1, 0.05, 0.025, 0.01, 0.005 \\ //Default:// 0.05 == AutoExclude == If passed any outliers will be excluded automatically == numPCs == The number of Principal Components to run the test on // //Default:// 2 == PCsVariance == scale calculated values to variability explained // //Default:// 95.0 === Example === --RunSPE alphaValue "0.005" autoExclude numPCs "2" ---- ==== RunMah ==== ---- Run a Mahalanobis distance test === Parameters === == AlphaValue == The threshold used to determine outliers: 0.1, 0.05, 0.025, 0.01, 0.005 \\ //Default:// 0.05 == 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 //Default:// Combined Groups == NumPasses == How many iterations of the test should be run \\ //Default:// 1 == NumPCs == The number of principal components to run the test on \\ //Default:// 2 == PCsVariance == Determining the number of PCs by variance explained \\ //Default:// 95.0 == ScaleToVariance == If passed scale calculated values to variability explained === Example === --LoadMah alphaValue "0.1" autoExclude grouping "groups" numPasses "3" numPCs "2" scaleToVariance ---- ==== RegisterCurves ==== ---- === 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 === --RegisterCurves max name "AnkleAngleX_Reg" ---- ==== CreateGLM ==== ---- Create a General Linear Model === Parameters === == Grouping == The grouping used for the model: Workspace / Group \\ //Default:// Group == Name (Required) == The name of the GLM being created === Example === --CreateGLM name "New GLM" grouping "group" ---- ==== RunSPM ==== ---- 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 === --RunSPM name "New SPM" glm "New GLM" group1 "AnkleAngleX1_Reg" group2 "AnkleAngleX2_Reg" ---- ==== RunDTW ==== ---- 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 \\ //Default:// 1 === Example === --RunDTW name "New DTW" standardDeviations "2" ---- ==== RunV3D ==== ---- 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 === --RunV3d script "C:\library folder\Script One.v3s" script "C:\library folder\Script Two.v3s" ---- ==== RunPCA ==== ---- Run Principal Component Analysis on all queries === Parameters === == Name (Required) == The name for the PCA to be created == numPCs == How many principal components should be created \\ //Default:// 4 == WorkspaceMean == If passed PCA will be run on the mean of each workspace and not the individual traces === Example === --RunPCA name "New PCA" numPCs "3" workspaceMean ---- ==== ExportData ==== 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 \\ //Default:// 4 == ExportFormat == The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\ //Default:// Standard == NormalizedTo == Number of points to normalize the export data to \\ //Default:// 101 == 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 === --ExportData file "C:\library folder\exports\Data Export.txt" precision "2" exportFormat "standard" normalizedTo "100" groupMean groupStdDev workspaceMean workspaceStdDev allSequenceNorm allSequencesTime ---- ==== 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 \\ //Default:// 4 == ExportFormat == The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\ //Default:// Standard == 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 === --ExportPCA fileName "C:\library folder\exports\PCA Export.txt" precision "4" exportFormat "transposed" workspaceScores groupScores groupStdDev varianceExplained eigenVectors meanSD mean595 ---- ==== 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 \\ //Default:// 4 == ExportFormat == The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\ //Default:// Standard == 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 === --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" ---- ==== 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 \\ //Default:// 4 == ExportFormat == The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\ //Default:// Standard == 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 === --ExportRegisteredCurves file "C:\library folder\exports\Registered Curves Export.txt" precision "3" exportFormat "transposed" landmarkAll landmarkMeans registeredCurves warpingFunctions ---- ==== 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 \\ //Default:// 4 == ExportFormat == The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\ //Default:// Standard == 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 === --ExportDTW file "C:\library folder\exports\Dynamic Time Warping Export.txt" precision "3" exportFormat "transposed" foundAnomalies costFunctions ---- ==== 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 \\ //Default:// 4 == ExportFormat == The format of the exported ASCII file: Standard, SPSS, Transposed, P2D \\ //Default:// Standard == 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 === --ExportSPM file "C:\library folder\exports\Statistical Parametric Map Export.txt" precision "5" exportFormat "transposed" bMatrix residualMatrix spm