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sift:command_line [2024/09/04 17:59] – sgrangersift:command_line [2025/04/04 19:57] (current) – sgranger
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   * Creating a bat file it is possible to completely automate processing   * Creating a bat file it is possible to completely automate processing
 ===== Running Sift From Command Line ====== ===== 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**+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 ==== ==== 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 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   * Commands and parameters are case insensitive
-  * any parameters containing a space (e.g. a folder path) must be wrapped in double quotes ("")+  * 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   * 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   * 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 +  * 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 +  * 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)+  * 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 ===== ===== Commands =====
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 ---- ----
-==== LoadLib ====+==== -LoadLib / -l ====
 ---- ----
 Load in a library of CMZs Load in a library of CMZs
 === Parameters === === Parameters ===
-== Directory (Required) ==+== Directory (Required/Default) ==
 Path to the directory containing the CMZs to be loaded, all sub-directories will be searched as well. Path to the directory containing the CMZs to be loaded, all sub-directories will be searched as well.
 === Example === === Example ===
-<code>--LoadLib directory "C:\library folder"</code>+<code>-LoadLib directory "C:\library folder"</code>
  
 ---- ----
-==== LoadQuery ====+==== -LoadQuery  / -q ====
 ---- ----
 Load a saved query from a .q3d file Load a saved query from a .q3d file
 === Parameters === === Parameters ===
-== File (Required) ==+== File (Required/Default) ==
 The path to the .q3d file containing the query The path to the .q3d file containing the query
 === Example === === Example ===
-<code>--LoadQuery file "C:\library folder\query.q3d"</code>+<code>-LoadQuery file "C:\library folder\query.q3d"</code>
  
 ---- ----
-==== RunLOF ====+==== -RunLOF / -lof ====
 ---- ----
 Run Local Outlier Factor Run Local Outlier Factor
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 If passed scale all calculated values to the variability explained by the PC If passed scale all calculated values to the variability explained by the PC
 === Example === === Example ===
-<code>--RunLOF autoExclude manualThreshold "3" numNeighbors "20" numPasses "2" numPCs "2" scaleToVariability</code>+<code>-RunLOF autoExclude manualThreshold "3" numNeighbors "20" numPasses "2" numPCs "2" scaleToVariability</code>
  
 ---- ----
-==== RunKMeans ====+==== -RunKMeans / -kmeans ====
 ---- ----
 Run K-Means clustering Run K-Means clustering
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 If passed scale all calculated values to the variability explained by the PC If passed scale all calculated values to the variability explained by the PC
 === Example === === Example ===
-<code>--RunKMeans clusters "3" customerSeed "0" grouping "combined groups" iterations "1" numPCs "2" scaleToVariability</code>+<code>-RunKMeans clusters "3" customerSeed "0" grouping "combined groups" iterations "1" numPCs "2" scaleToVariability</code>
  
 ---- ----
-==== RunSPE ====+==== -RunSPE / -spe ====
 ---- ----
 Run squared prediction error Run squared prediction error
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 <sub>//Default:// 95.0</sub> <sub>//Default:// 95.0</sub>
 === Example === === Example ===
-<code>--RunSPE alphaValue "0.005" autoExclude numPCs "2"</code>+<code>-RunSPE alphaValue "0.005" autoExclude numPCs "2"</code>
  
 ---- ----
-==== RunMah ====+==== -RunMah / -mah ====
 ---- ----
 Run a Mahalanobis distance test Run a Mahalanobis distance test
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 If passed scale calculated values to variability explained If passed scale calculated values to variability explained
 === Example === === Example ===
-<code>--LoadMah alphaValue "0.1" autoExclude grouping "groups" numPasses "3" numPCs "2" scaleToVariance</code>+<code>-LoadMah alphaValue "0.1" autoExclude grouping "groups" numPasses "3" numPCs "2" scaleToVariance</code>
  
 ---- ----
-==== RegisterCurves ====+==== -RegisterCurves / -rc ====
 ---- ----
 === Parameters === === Parameters ===
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 The name for registered curve group created The name for registered curve group created
 === Example === === Example ===
-<code>--RegisterCurves max name "AnkleAngleX_Reg"</code>+<code>-RegisterCurves max name "AnkleAngleX_Reg"</code>
  
 ---- ----
-==== CreateGLM ====+==== -CreateGLM / -glm ====
 ---- ----
 Create a General Linear Model Create a General Linear Model
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 The grouping used for the model: Workspace / Group \\ The grouping used for the model: Workspace / Group \\
 <sub>//Default:// Group</sub> <sub>//Default:// Group</sub>
-== Name (Required) ==+== Name (Required/Default) ==
 The name of the GLM being created The name of the GLM being created
 === Example === === Example ===
-<code>--CreateGLM name "New GLM" grouping "group"</code>+<code>-CreateGLM name "New GLM" grouping "group"</code>
  
 ---- ----
-==== RunSPM ====+==== -RunSPM / -spm ====
 ---- ----
 Run Statistical Parametric Mapping  Run Statistical Parametric Mapping 
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 The name of the SPM being created The name of the SPM being created
 === Example === === Example ===
-<code>--RunSPM name "New SPM" glm "New GLM" group1 "AnkleAngleX1_Reg" group2 "AnkleAngleX2_Reg"</code>+<code>-RunSPM name "New SPM" glm "New GLM" group1 "AnkleAngleX1_Reg" group2 "AnkleAngleX2_Reg"</code>
  
 ---- ----
-==== RunDTW ====+==== -RunDTW / -dtw ====
 ---- ----
 Run Dynamic Time Warping Run Dynamic Time Warping
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 ----  ---- 
-==== RunV3D ====+==== -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 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
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 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 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 === === Example ===
-<code>--RunV3d script "C:\library folder\Script One.v3s" script "C:\library folder\Script Two.v3s"</code>+<code>-RunV3d script "C:\library folder\Script One.v3s" script "C:\library folder\Script Two.v3s"</code>
  
 ---- ----
-==== RunPCA ====+==== -RunPCA / -pca ====
 ---- ----
 Run Principal Component Analysis on all queries Run Principal Component Analysis on all queries
 === Parameters === === Parameters ===
-== Name (Required) ==+== Name (Required/Default) ==
 The name for the PCA to be created The name for the PCA to be created
 == numPCs == == numPCs ==
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 If passed PCA will be run on the mean of each workspace and not the individual traces If passed PCA will be run on the mean of each workspace and not the individual traces
 === Example === === Example ===
-<code>--RunPCA name "New PCA" numPCs "3" workspaceMean</code>+<code>-RunPCA name "New PCA" numPCs "3" workspaceMean</code> 
 + 
 +---- 
 +==== -ExportPlotSignalTime / -ExportPlotST / -EPST ==== 
 +---- 
 +Export the selected traces on a signal time 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 == 
 +Which data style type to use when generating the plot, options are: Workspace, Group, Sub Group, Cluster \\ 
 +<sub>//Default:// Workspace</sub> 
 +== GroupDispersion == 
 +If passed the group dispersion will be plotted 
 +== GroupDispersionType == 
 +The method of dispersion to plot, options are: One Standard Deviation, Two Standard Deviations, Interquartile Range \\ 
 +<sub>//Default:// One Standard Deviation</sub> 
 +== GroupMean == 
 +If passed group mean will be plotted 
 +== WorkspaceDispersion == 
 +If passed the workspace dispersion will be plotted 
 +== WorkspaceDispersionType == 
 +The method of dispersion to plot, options are: One Standard Deviation, Two Standard Deviations, Interquartile Range \\ 
 +<sub>//Default:// One Standard Deviation</sub> 
 +== WorkspaceMean == 
 +If passed workspace mean will be plotted 
 +== XRange == 
 +The range of values displayed on the X Axis of the plot, format: "min,max" 
 +== YRange == 
 +The range of values displayed on the Y Axis of the plot, format: "min,max" 
 +== RawTraces == 
 +If passed individual traces will be plotted, if no other items are plotted, raw traces will be plotted by default 
 +=== Example === 
 +<code>-ExportPlotSignalTime filePath "C:\Export Folder\signal_time_plot.png" rawTraces workspaceMean workspaceDispersion workspaceDispersionType "Interquartile Range" legend "Bottom Left"</code> 
 + 
 +---- 
 + 
 +==== -ExportPlotMetric / -ExportPlotM / -EPM ==== 
 +Export the select metrics on a metric 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 \\ 
 +<sub> 
 +== RawTraces == 
 +If passed individual traces will be displayed 
 +== GroupMean == 
 +If passed group mean will be plotted 
 +== GroupDispersion == 
 +If passed group dispersion will be plotted 
 +== GroupDispersionType ==  
 +The method of dispersion used, options are: One Standard Deviation, Two Standard Deviations, Interquartile Range \\ 
 +<sub>//Default:// One Standard Deviation</sub> 
 +== WorkspaceMean == 
 +If passed workspace mean will be plotted 
 +== WorkspaceDispersion == 
 +If passed workspace dispersion will be plotted  
 +== WorkspaceDispersionType == 
 +The method of dispersion used, options are: One Standard Deviation, Two Standard Deviations, Interquartile Range \\ 
 +<sub>//Default:// One Standard Deviation</sub> 
 +== MeanPlotStyle == 
 +Method used for plotting means, options are Bar Chart, Stacked Bar Chart, Box Plot 
 +<sub>//Default:// Bar Chart</sub> 
 +== MetricGrouping == 
 +How should workspace means be grouped, options are No Group, Group, Workspace 
 +<sub>//Default:// No Group</sub> 
 +=== Example === 
 +<code>
  
 ---- ----
-==== ExportData ====+==== -ExportData / -ex ====
 Export queried data results in an ascii text file  Export queried data results in an ascii text file 
 === Parameter === === Parameter ===
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 If passed all time based sequences will be exported If passed all time based sequences will be exported
 === Example === === Example ===
-<code>--ExportData file "C:\library folder\exports\Data Export.txt"  precision "2" exportFormat "standard" normalizedTo "100" groupMean groupStdDev workspaceMean workspaceStdDev allSequenceNorm allSequencesTime</code>+<code>-ExportData file "C:\library folder\exports\Data Export.txt"  precision "2" exportFormat "standard" normalizedTo "100" groupMean groupStdDev workspaceMean workspaceStdDev allSequenceNorm allSequencesTime</code>
  
 ---- ----
-==== ExportPCA ====+==== -ExportPCA ====
 ---- ----
 Export PCA results to a .txt file Export PCA results to a .txt file
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 If passed the mean +/- 5 and 95% will be exported If passed the mean +/- 5 and 95% will be exported
 === Example === === Example ===
-<code>--ExportPCA fileName "C:\library folder\exports\PCA Export.txt" precision "4" exportFormat "transposed" workspaceScores groupScores groupStdDev varianceExplained eigenVectors meanSD mean595</code>+<code>-ExportPCA fileName "C:\library folder\exports\PCA Export.txt" precision "4" exportFormat "transposed" workspaceScores groupScores groupStdDev varianceExplained eigenVectors meanSD mean595</code>
  
 ---- ----
-==== ExportSummaryStatistics ====+==== -ExportSummaryStatistics ====
 ---- ----
 Export summary statistics to a .txt file Export summary statistics to a .txt file
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 Export results for: Groups, Workspaces, Instances Export results for: Groups, Workspaces, Instances
 === Example === === 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>+<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 ====+==== -ExportRegisteredCurves ====
 Export any results of curve registration Export any results of curve registration
 === Parameters === === Parameters ===
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 If passed warping functions will be exported If passed warping functions will be exported
 === Example === === Example ===
-<code>--ExportRegisteredCurves file "C:\library folder\exports\Registered Curves Export.txt" precision "3" exportFormat "transposed" landmarkAll landmarkMeans registeredCurves warpingFunctions</code>+<code>-ExportRegisteredCurves file "C:\library folder\exports\Registered Curves Export.txt" precision "3" exportFormat "transposed" landmarkAll landmarkMeans registeredCurves warpingFunctions</code>
  
 ---- ----
-==== ExportDTW ====+==== -ExportDTW ====
 ---- ----
 Export Dynamic Time Warping results Export Dynamic Time Warping results
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 If passed all anomalies will be exported If passed all anomalies will be exported
 === Example === === Example ===
-<code>--ExportDTW file "C:\library folder\exports\Dynamic Time Warping Export.txt" precision "3" exportFormat "transposed"  foundAnomalies costFunctions</code>+<code>-ExportDTW file "C:\library folder\exports\Dynamic Time Warping Export.txt" precision "3" exportFormat "transposed"  foundAnomalies costFunctions</code>
  
 ---- ----
-==== ExportSPM ====+==== -ExportSPM ====
 ---- ----
 Export Statistical Parametric Mapping Results Export Statistical Parametric Mapping Results
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 If passed the Statistical Parametric Map will be exported If passed the Statistical Parametric Map will be exported
 === Example === === Example ===
-<code>--ExportSPM file "C:\library folder\exports\Statistical Parametric Map Export.txt" precision "5" exportFormat "transposed" bMatrix residualMatrix spm</code>+<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>
  
sift/command_line.1725472782.txt.gz · Last modified: 2024/09/04 17:59 by sgranger