pwem.viewers.showj module

Configuration definition for launching the ShowJ visualization utility. The name of ShowJ is due historical reasons. This data visualization tools was first called xmipp_show. And later was re-written using Java and became xmipp_showj.

class pwem.viewers.showj.ColumnProperties(col, allowRender, defaultColumnLayoutProperties)

Bases: object

Store some properties to customize how each column will be display in the table.

allowsRenderable()

getColumnType()

getLabel()

getName()

getValues()

isRenderable()

setValues(defaultColumnLayoutProperties)

class pwem.viewers.showj.ColumnsConfig(table, allowRender=True, defaultColumnsLayout={})

Bases: object

Store the configuration of the columns for a given table in a dataset. The order of the columns will be stored and configuration for each columns. For each column, we store properties: - visible - allowSetVisible - renderable - allowSetRenderable - editable - allowSetEditable - renderFunc - renderFuncExtra

configColumn(colName, **kwargs)

Configure properties of a given column.

getColumnProperty(colName, propName)

Get some property value of a given column.

getRenderableColumns(extra=None)

Return a list with the name of renderable columns. extra: parameter used to keep some rendering columns.

hasEnableColumn()

printColumns()

class pwem.viewers.showj.MySocketServer(server_address, RequestHandlerClass, bind_and_activate=True)

Bases: TCPServer

Constructor. May be extended, do not override.

serve_forever()

Handle one request at a time until shutdown.

Polls for shutdown every poll_interval seconds. Ignores self.timeout. If you need to do periodic tasks, do them in another thread.

class pwem.viewers.showj.ProtocolTCPRequestHandler(request, client_address, server)

Bases: BaseRequestHandler

handle()

pwem.viewers.showj.getArchitecture()

pwem.viewers.showj.getJavaBin()

pwem.viewers.showj.getJavaIJappArguments(memory, appName, appArgs)

Build the command line arguments to launch a Java application based on ImageJ. memory: the amount of memory passed to the JVM. appName: the qualified name of the java application. appArgs: the arguments specific to the application.

pwem.viewers.showj.getJavaVersion()

pwem.viewers.showj.getJvmMaxMemory()

pwem.viewers.showj.initProtocolTCPServer(protocol)

pwem.viewers.showj.launchSupervisedPickerGUI(micsFn, outputDir, protocol, mode=None, memory=None, pickerProps=None, inTmpFolder=False)

pwem.viewers.showj.launchTiltPairPickerGUI(micsFn, outputDir, protocol, mode=None)

pwem.viewers.showj.runJavaIJapp(memory, appName, args, env=None)