pwem.viewers.mdviewer.sqlite_dao module

class pwem.viewers.mdviewer.sqlite_dao.ScipionColumn(name, renderer=None, callback=None)

Bases: Column

calculate(row, values)

setCallback(callback)

Callback to compute the value for this column. The callback will receives the row

class pwem.viewers.mdviewer.sqlite_dao.ScipionSetsDAO(sqliteFile)

Bases: IDAO

Class to serve data from scipion sets files (sqlite).

addChimera(renderer: ImageRenderer, imageExt: str)

addExternalProgram(renderer: ImageRenderer, imageExt: str)

addImageJ(renderer: ImageRenderer)

addImageViewer(renderer: ImageRenderer, imageExt: str)

close()

composeDataTables(tablesNames)

This method is used to generate a dictionary with the principal tables mapping the dependencies with other tables

composeImageFilename(row, values)

composeObjectType()

Define the different objects types

composeTableAlias(tableName)

Create an alias for the given table

createSubsetCallback(table: Table, objectType: str, objectManager)

Create a subset

exctractAngularValue(values, offset, position)

Extract the euler angle form the matrix

exctractShift(values, offset, position)

Extract offset value

fillPage(page, actualColumn: str, orderAsc=True)

Read the given table from the sqlite and fill the page(add rows)

fillTable(table: ScipionTable, objectManager)

Create the table structure (columns) and set the table alias

generateTableActions(table, objectManager)

Generate actions for a given table in order to create subsets

getColumnsValues(tableName, columns, xAxis, selection, limit, useSelection, reverse=True)

Get the values of the selected columns in order to plot them

classmethod getCompatibleFileTypes()

Return a list of compatible extension of files

getRowsCount(tableName)

Return the number of elements in the given table.

getScipionObjectId()

Returns Scipion object id

getScipionPort()

Returns Scipion port or None if not in the environment

getSelectedRangeRowsIds(tableName, startRow, numberOfRows, column, reverse=True)

Return a range of rows starting at ‘startRow’ an amount of ‘numberOfRows’

getTableRow(tableName, rowIndex, **kwargs)

Get a given row by index. Extra args are passed to iterTable.

getTableRowCount(tableName)

getTableWithAdditionalInfo()

Return a tuple with the table that need to show additional info and the column that we need to show

getTables()

Return all the table names found in the database.

iterTable(tableName, **kwargs)

Method to iterate over the table’s rows :param tableName: the name of the table :param kwargs:

limit: integer value to limit the number of elements start: start from a given element classes: read column names from a ‘classes’ table orderBy: clause to sort given a column name mode: sort direction ASC or DESC

sendSubsetCreationMessage(selectionFile, outputClassName, label)

writeSelection(table: Table, path)

Create a file with the selected rows ids

class pwem.viewers.mdviewer.sqlite_dao.ScipionTable(name, definitionTable)

Bases: Table

getDefinitionTable()