Initialization Files
Updated for release version: 1.0.3-alpha
This page introduces the initialization process utilized my mgui; in particular, the use of initialization files ("init files") to set up the environment at launch time. It explains where to find an init file, how to specify it when launching mgui, and the various commands used to set up the environment.
Introduction
ModelGUI uses an init file to set up the session environment (which is implemented by the static class InterfaceEnvironment). This includes a specification of the version, locale, and look-and-feel of the mgui session, as well as all the interface panels, possible interface graphics windows, and possible input/output (I/O) types. Objects such as session files, shape models, graphics window instances, etc., can also be specified in this file. Such a setup allows a highly customizable session for modelGUI; a user can choose from a variety of session types (e.g., one that is customized strictly for processing a specific fMRI project versus one for general purposes), and these session types can also be shared between users (e.g., if you wanted a colleague to view a particular session as-it-is, without requiring them to set it up themselves).
What follows is a description of how init files accomplish these tasks. At present, init files must be specified manually (i.e., by editing the text file in a text editor). In the future, a GUI will be provided to simplify this process.
File locations
In a standard installation of mgui, the init files will be located in the directory "resources/init". The default init file that comes with the installation is called "mgui.model.init". It is recommended to put all custom init files in this location as well, which is expected by the launch process.
Init file commands
Init file commands are processed sequentially, which means that order is potentially important. For instance, it is important to specify a database driver class before attempting to load a data source which depends on that driver. This is discussed further below. What follows is a list of the commands interpreted by mgui and a description of their syntax and how they function.
Default init file
This is the default init file for mgui-1.0.0-alpha. Comments (starting with "#") are added to explain the parts in better detail.
# set version setVersion 1.0.21 [dev] # set locale setLocale en CA # set units addUnit spatial millimeter mm 0.001 addUnit spatial centimeter cm 0.01 addUnit spatial kilometer km 1000 addUnit spatial micrometer μm 0.000001 addUnit spatial mile mi 1609.344 # set logging setLogFileAndConsole mgui_session setLoggingType debug # colour maps # This command loads all the colour maps found in the specified directory loadColourMaps cmaps # node shapes # This command loads all the graph node shapes found in the specified directory loadGraphNodeShapes node_shapes # set data source key file # This command sets the current private key for password encryption from the specified file/URL. # The command is optional; if not specified, a generic key will be used. Note that this file/URL should be # stored in a trusted environment; it is the responsibility of the user to set permissions properly. A # file can be generated using the generate_db_key script; see the README file for more. # URLs which do not specify a protocol will be treated as files. Files which do not start with "/" will # be treated as relative to the mgui home directory. setDataSourceKey data_sources/.dbkey # jdbc drivers # This command tells the environment to register the given classes as JDBC drivers, and make them available for use # in the session. The optional third argument specifies an instance of DataSourceDialogPanel, which will be # used to provide a specialized set up of the data source (if not specified, the default panel is used). #addKnownDataSourceDriver mysql.driver mgui.interfaces.datasources.DataSourceListDialogPanel #addKnownDataSourceDriver jdbc_odbc.driver #addKnownDataSourceDriver tinysql.driver #addKnownDataSourceDriver postgresql.driver mgui.interfaces.datasources.DataSourceListDialogPanel addKnownDataSourceDrivers # set look and feel # Java uses a "look-and-feel" concept to provide customized GUI rendering for Swing components. Such libraries # are available online, and can be used with mgui by setting them here. This command sets the look-and-feel # to "NimROD" (see http://personales.ya.com/nimrod/index-en.html) # setLookAndFeel native # setLookAndFeel java setLookAndFeel com.nilo.plaf.nimrod.NimRODLookAndFeel # preloaded data sources # This command loads all datasources in the specified directory from parameters specified in a text files. # If the specified driver has not already been loaded using addKnownDataSourceDriver, mgui attempts to add a # new driver to the environment as well. loadDataSources data_sources # load graphic window classes (can also do this explicitly for efficiency) # This command loads the various interface graphics types, which specifies which graphics windows are available # in the session. loadInterfaceGraphicClass Graphic3D mgui.interfaces.graphics.InterfaceGraphic3D loadInterfaceGraphicClass Graphic2D mgui.interfaces.graphics.InterfaceGraphic2D loadInterfaceGraphicClass Graph mgui.interfaces.graphs.InterfaceGraphDisplay loadInterfaceGraphicClass "Data Table" mgui.interfaces.tables.InterfaceDataTable loadInterfaceGraphicClass Console mgui.interfaces.console.InterfaceConsoleDisplay loadInterfaceGraphicClass Plot mgui.interfaces.plots.InterfacePlotDisplay # load interface panel classes # This command loads the various interface panels into the session, which will show up as selections in the # interface combo box. loadInterfacePanelClass "Windows Panel" mgui.interfaces.graphics.InterfaceGraphicPanel loadInterfacePanelClass "Section Set Panel" mgui.interfaces.shapes.InterfaceSectionSetPanel loadInterfacePanelClass "File Panel" mgui.interfaces.io.InterfaceFilePanel loadInterfacePanelClass "Datasource Panel" mgui.interfaces.datasources.InterfaceDatasourcePanel loadInterfacePanelClass "Volume Panel" mgui.interfaces.shapes.volume.InterfaceVolumePanel loadInterfacePanelClass "Mesh Panel" mgui.interfaces.shapes.mesh.InterfaceMeshPanel loadInterfacePanelClass "Maps Panel" mgui.interfaces.maps.InterfaceMapPanel loadInterfacePanelClass "Cortical Thickness Panel" mgui.interfaces.neuro.InterfaceCorticalThicknessPanel loadInterfacePanelClass "Selection Panel" mgui.interfaces.InterfaceSelectionPanel loadInterfacePanelClass "Queries Panel" mgui.interfaces.queries.InterfaceQueryPanel loadInterfacePanelClass "Tools Panel" mgui.interfaces.tools.InterfaceToolPanel loadInterfacePanelClass "Shapes Panel" mgui.interfaces.shapes.InterfaceShapesPanel loadInterfacePanelClass "Shape Stats Panel" mgui.interfaces.shapes.ShapeStatsPanel loadInterfacePanelClass "Pipelines Panel" mgui.interfaces.pipelines.InterfacePipelinesPanel # load plot classes loadInterfacePlotClass "Multiline Plot" mgui.interfaces.plots.sgt.SgtMultilinePlot loadInterfacePlotClass "XY Scatter Plot" mgui.interfaces.plots.sgt.SgtScatterplot # load video task classes # This command loads video task types (instances of VideoTask) available for video processes loadVideoTaskType SetView3D mgui.interfaces.graphics.video.SetView3DTask mgui.interfaces.graphics.video.SetView3DTaskDialogPanel loadVideoTaskType RotateView3D mgui.interfaces.graphics.video.RotateView3DTask mgui.interfaces.graphics.video.RotateView3DTaskDialogPanel loadVideoTaskType AttributeUpdate mgui.interfaces.attributes.video.AttributeObjectVideoTask mgui.interfaces.attributes.video.AttributeObjectVideoTaskDialogPanel # initial windows # This command adds a graphic window to the display panel on launch addGraphicsWindow Graphic3D "3D Window" # load IO types: name, type (input or output), class (instance of InterfaceIO), dialog class, options class, file description, file extension filters # This command loads the available I/O classes (instances of FileLoader or FileWriter) available in the session. # These classes determine the type of data that can be input or output in the session. The command also specifies # which dialog and options classes are associated with the I/O class; mgui uses these to provide user interaction. # If no such class is available, the string "null" is used. Finally, the file description and associated extensions # are provided, which are used by the file browser. loadIOType Workspace_out output mgui.io.domestic.WorkspaceWriter null mgui.io.domestic.WorkspaceOutputOptions "Mgui Workspaces (*.workspace)" workspace loadIOType ShapeModel3D_out output mgui.io.domestic.shapes.ShapeModel3DWriter mgui.io.domestic.shapes.ShapeModel3DOutputDialog mgui.io.domestic.shapes.ShapeModel3DOutputOptions "Mgui shape models (*.smod, *.smod.gz, *.xml)" smod smod.gz xml loadIOType ShapeModel3D_in input mgui.io.domestic.shapes.ShapeModel3DLoader mgui.io.domestic.shapes.ShapeModel3DInputDialog mgui.io.domestic.shapes.ShapeModel3DInputOptions "Mgui Shape models (*.smod, *.smod.gz, *.xml)" smod smod.gz xml loadIOType Minc_surf_in input mgui.io.foreign.minc.MincSurfaceLoader mgui.io.domestic.shapes.SurfaceInputDialogBox mgui.io.domestic.shapes.SurfaceInputOptions "Minc surfaces (*.obj)" obj loadIOType Minc_surf_out output mgui.io.foreign.minc.MincSurfaceWriter mgui.io.domestic.shapes.SurfaceOutputDialogBox mgui.io.domestic.shapes.SurfaceOutputOptions "Minc surfaces (*.obj)" obj loadIOType Minc_surf_data_out output mgui.io.foreign.minc.MincSurfaceDataWriter mgui.io.foreign.minc.MincSurfaceDataOutDialogBox mgui.io.foreign.minc.MincSurfaceDataOutOptions "Minc surface data (*.txt)" txt loadIOType Minc_surf_data_in input mgui.io.foreign.minc.MincSurfaceDataLoader mgui.io.domestic.shapes.SurfaceDataInputDialogBox mgui.io.domestic.shapes.SurfaceDataInputOptions "Minc surface data (*.txt)" txt loadIOType Caret_surf_paint_in input mgui.io.foreign.caret.CaretPaintLoader mgui.io.foreign.caret.CaretPaintInDialogBox mgui.io.foreign.caret.CaretPaintInOptions "Caret paint data (*.paint)" paint loadIOType Caret_surf_paint_out output mgui.io.foreign.caret.CaretPaintWriter mgui.io.domestic.shapes.SurfaceDataOutputDialogBox mgui.io.foreign.caret.CaretPaintOutOptions "Caret paint data (*.paint)" paint loadIOType Caret_surf_metric_in input mgui.io.foreign.caret.CaretMetricLoader mgui.io.foreign.caret.CaretMetricInDialogBox mgui.io.foreign.caret.CaretMetricInOptions "Caret metric data (*.metric)" metric loadIOType Caret_surf_out output mgui.io.foreign.caret.CaretSurfaceWriter mgui.io.foreign.caret.CaretSurfaceOutDialogBox mgui.io.foreign.caret.CaretSurfaceOutOptions "Caret surfaces (*.topo, *.coord)" topo coord loadIOType Caret_surf_in input mgui.io.foreign.caret.CaretSurfaceLoader mgui.io.foreign.caret.CaretSurfaceInDialogBox mgui.io.foreign.caret.CaretSurfaceInOptions "Caret surfaces (*.topo, *.coord)" topo coord loadIOType Caret_area_colour_in input mgui.io.foreign.caret.CaretAreaColourLoader mgui.io.foreign.caret.CaretAreaColourInDialogBox mgui.io.foreign.caret.CaretAreaColourInOptions "Caret area colour files (*.areacolor)" areacolor loadIOType Caret_area_colour_out output mgui.io.foreign.caret.CaretAreaColourWriter mgui.io.foreign.caret.CaretAreaColourOutDialogBox mgui.io.foreign.caret.CaretAreaColourOutputOptions "Caret area colour files (*.areacolor)" areacolor loadIOType NameMap_in input mgui.io.domestic.maps.NameMapLoader null mgui.io.domestic.maps.NameMapInOptions "Name maps (*.txt, *.nmap)" txt nmap loadIOType NameMap_out output mgui.io.domestic.maps.NameMapWriter mgui.io.domestic.maps.NameMapOutDialogBox mgui.io.domestic.maps.NameMapOutOptions "Name maps (*.txt, *.nmap)" txt nmap loadIOType MricroLut_in input mgui.io.foreign.mricro.MricroLutLoader mgui.io.domestic.maps.DiscreteColourMapInDialogBox mgui.io.domestic.maps.DiscreteColourMapInOptions "Mricro LUT (*.lut)" lut loadIOType Network_in input mgui.io.domestic.network.CorticalNetworkMatrixLoader mgui.io.domestic.network.CorticalNetworkMatrixInDialogBox mgui.io.domestic.network.CorticalNetworkMatrixInOptions "Network matrix files (*.net, *.txt)" net txt loadIOType Mesh3D_in input mgui.io.domestic.shapes.Mesh3DLoader mgui.io.domestic.shapes.SurfaceInputDialogBox mgui.io.domestic.shapes.SurfaceInputOptions "Tri surfaces (*.tri)" tri loadIOType Mesh3D_out output mgui.io.domestic.shapes.Mesh3DWriter mgui.io.domestic.shapes.SurfaceOutputDialogBox mgui.io.domestic.shapes.SurfaceOutputOptions "Tri surfaces (*.tri)" tri loadIOType Duff_surface_in input mgui.io.foreign.duff.DuffSurfaceLoader mgui.io.domestic.shapes.SurfaceInputDialogBox mgui.io.domestic.shapes.SurfaceInputOptions "Duff surfaces (*.dfs)" dfs loadIOType Nifti_volume_in input mgui.io.standard.nifti.NiftiVolumeLoader mgui.io.domestic.shapes.VolumeInputDialogBox mgui.io.domestic.shapes.VolumeInputOptions "Nifti volumes (*.hdr, *.nii, *.gz)" hdr nii gz loadIOType Nifti_volume_out output mgui.io.standard.nifti.NiftiVolumeWriter mgui.io.domestic.shapes.VolumeOutputDialogBox mgui.io.domestic.shapes.VolumeOutputOptions "Nifti volumes (*.hdr, *.nii, *.gz)" hdr nii gz loadIOType FSL_surface_in input mgui.io.foreign.fsl.FSLSurfaceLoader mgui.io.domestic.shapes.SurfaceInputDialogBox mgui.io.domestic.shapes.SurfaceInputOptions "FSL surfaces (*.off)" off loadIOType Freesurfer_surface_in input mgui.io.foreign.freesurfer.FreesurferSurfaceLoader mgui.io.domestic.shapes.SurfaceInputDialogBox mgui.io.domestic.shapes.SurfaceInputOptions "Freesurfer surfaces (*.*)" * loadIOType Freesurfer_surface_out output mgui.io.foreign.freesurfer.FreesurferSurfaceWriter mgui.io.domestic.shapes.SurfaceOutputDialogBox mgui.io.foreign.freesurfer.FreesurferSurfaceOutputOptions "Freesurfer surfaces (*.*)" * loadIOType Freesurfer_surface_data_in input mgui.io.foreign.freesurfer.FreesurferVertexDataLoader mgui.io.foreign.freesurfer.FreesurferVertexDataDialogBox mgui.io.foreign.freesurfer.FreesurferVertexDataInOptions "Freesurfer surface data (*.curv, *.annot, *.label)" * loadIOType Pajek_graph_in input mgui.io.foreign.pajek.PajekGraphLoader mgui.io.foreign.pajek.PajekGraphInputDialog mgui.io.foreign.pajek.PajekGraphInputOptions "Pajek graphs (*.net)" net loadIOType Discrete_cmap_out output mgui.io.domestic.maps.DiscreteColourMapWriter mgui.io.domestic.maps.DiscreteColourMapOutDialogBox mgui.io.domestic.maps.DiscreteColourMapOutOptions "Discrete colour maps (*.cmap)" cmap loadIOType Discrete_cmap_in input mgui.io.domestic.maps.DiscreteColourMapLoader mgui.io.domestic.maps.DiscreteColourMapInDialogBox mgui.io.domestic.maps.DiscreteColourMapInOptions "Discrete colour maps (*.cmap)" cmap loadIOType TrackVis_tracts_in input mgui.io.foreign.trackvis.TrackVisTractLoader mgui.io.domestic.shapes.PolygonSet3DInputDialogBox mgui.io.domestic.shapes.PolygonSet3DInputOptions "TrackVis tract files (*.trk)" trk loadIOType Point_set_3D_in input mgui.io.domestic.shapes.PointSet3DLoader mgui.io.domestic.shapes.PointSet3DInputDialogBox mgui.io.domestic.shapes.PointSet3DInputOptions "PointSet 3D file (*.txt, *.pset3d)" txt pset3d loadIOType Point_set_3D_data_in input mgui.io.domestic.shapes.PointSet3DDataLoader mgui.io.domestic.shapes.PointSet3DDataInputDialogBox mgui.io.domestic.shapes.PointSet3DDataInputOptions "PointSet 3D data file (*.txt)" txt loadIOType Point_set_2D_in input mgui.io.domestic.shapes.PointSet2DLoader mgui.io.domestic.shapes.PointSet2DInputDialogBox mgui.io.domestic.shapes.PointSet2DInputOptions "PointSet 2D file (*.txt, *.pset2d)" txt pset2d loadIOType Polygon_set_3D_in input mgui.io.domestic.shapes.PolygonSet3DLoader mgui.io.domestic.shapes.PolygonSet3DInputDialogBox mgui.io.domestic.shapes.PolygonSet3DInputOptions "PolygonSet 3D files (*.txt *.poly3d)" txt poly3d loadIOType Vector_set_3D_in input mgui.io.domestic.shapes.VectorSet3DLoader mgui.io.domestic.shapes.VectorSet3DInputDialogBox mgui.io.domestic.shapes.VectorSet3DInputOptions "VectorSet 3D files (*.txt *.vect3d)" txt vect3d loadIOType Matrix_in input mgui.io.domestic.variables.DefaultMatrixFileLoader mgui.io.domestic.variables.MatrixInDialogBox mgui.io.domestic.variables.MatrixInOptions "Matrix files (*.txt, *.matrix)" txt matrix loadIOType Matrix_out output mgui.io.domestic.variables.DefaultMatrixFileWriter null null "Matrix files (*.txt, *.matrix)" txt matrix loadIOType Shape_3D_data_in input mgui.io.domestic.shapes.ShapeDataLoader mgui.io.domestic.shapes.ShapeDataInputDialogBox mgui.io.domestic.shapes.ShapeDataInputOptions "Shape data files (*.txt *.sdata)" txt sdata loadIOType Wunil_volume_in input mgui.io.foreign.wunil.WunilVolumeLoader mgui.io.domestic.shapes.VolumeInputDialogBox mgui.io.domestic.shapes.VolumeInputOptions "Wunil volumes (*.ifh)" ifh loadIOType View3D_out output mgui.io.domestic.views.View3DWriter mgui.io.domestic.views.View3DOutputDialogBox mgui.io.domestic.views.View3DOutputOptions "View3Ds (*.view3d)" view3d loadIOType View3D_in input mgui.io.domestic.views.View3DLoader null mgui.io.domestic.views.View3DInputOptions "View3Ds (*.view3d)" view3d loadIOType ImportDataTableText input mgui.io.domestic.datasources.ImportDataTableTextLoader mgui.io.domestic.datasources.ImportDataTableDialogBox mgui.io.domestic.datasources.ImportDataTableTextOptions "Delimited Text (*.txt, *.csv)" txt csv loadIOType ExportDataTableText output mgui.io.domestic.datasources.ExportDataTableTextWriter mgui.io.domestic.datasources.ExportDataTableDialogBox mgui.io.domestic.datasources.ExportDataTableTextOptions "Delimited Text (*.txt, *.csv)" txt csv loadIOType String_vector_in input mgui.io.domestic.variables.StringVectorLoader null mgui.io.domestic.variables.StringVectorInOptions "String vector (*.txt, *.svector)" txt svector loadIOType Shape_xml_out output mgui.io.domestic.shapes.InterfaceShapeWriter mgui.io.domestic.shapes.InterfaceShapeOutputDialogBox mgui.io.domestic.shapes.InterfaceShapeOutputOptions "Mgui Shape (*.xml, *.shape)" xml shape loadIOType Gifti_in input mgui.io.standard.gifti.GiftiSurfaceLoader mgui.io.domestic.shapes.SurfaceInputDialogBox mgui.io.standard.gifti.GiftiInputOptions "Gifti Surface (*.gii)" gii loadIOType Gifti_out output mgui.io.standard.gifti.GiftiSurfaceWriter mgui.io.standard.gifti.GiftiSurfaceOutDialogBox mgui.io.standard.gifti.GiftiOutputOptions "Gifti Surface (*.gii)" gii loadIOType FSL_volume_in input mgui.io.foreign.fsl.FSLVolumeLoader mgui.io.domestic.shapes.VolumeInputDialogBox mgui.io.domestic.shapes.VolumeInputOptions "FSL volumes (*.mgz, *.mgh)" mgz mgh loadIOType Minc_volume_in input mgui.io.foreign.minc.MincVolumeLoader mgui.io.domestic.shapes.VolumeInputDialogBox mgui.io.foreign.minc.MincVolumeInputOptions "Minc volumes (*.mnc)" mnc # Pipeline Process Libraries loadPipelineProcessLibraries pipeline_process_libraries
page revision: 19, last edited: 19 Feb 2014 13:21