emxlib.utils module

MODIFICATION ADVICE:

Please, do not generate or distribute a modified version of this file under its original name.

class emxlib.utils.EmxData

Bases: object

Class to group EMX objects

addObject(obj)

clear()

getFirstObject(className)

Return the first object of a given className. This function should be called after read.

getObject(mapPK)

Return an object given its primary key.

iterClasses(className)

Iterate through objects of a particular class.

read(emxFile)

Read data from an emxFile.

readFirstObject(className, emxFile)

Read only the first object of a given className from file.

size()

write(emxFile)

Write data to an emxFile.

class emxlib.utils.EmxImage(fileName=None, index=None)

Bases: emxlib.utils.EmxObject

Base class for EmxMicrograph and EmxParticle. Both share that have FILENAME and INDEX as primary keys.

class emxlib.utils.EmxLabel(type, unit=None)

Bases: object

Auxiliary class to assign data type (i.e.: int, str, etc) and unit to each attribute/label pair.

getType()

getUnit()

hasUnit()

class emxlib.utils.EmxMicrograph(fileName=None, index=None)

Bases: emxlib.utils.EmxImage

Class for Micrographs

class emxlib.utils.EmxObject

Bases: object

Base class for all EMX objects/classes name is the class type so far micrograph or particles

clear()

Generic clean. PK cannot be modified or clean.

get(key, default=None)

Given a key (attribute name) returns the value assigned to it. If not present, the default will be returned.

has(key)

iterAttributes()

Returns list with valid keys (attribute names) and values for this class. Primary keys are ignored

iterForeignKeys()

Returns list with valid primary keys (attribute names) and values for this class

iterPrimaryKeys()

Returns list with valid primary keys (attribute names) and values for this class

set(key, value=None)

Given a key (attribute name) assigns a value to it.

strongEq(other)

true if both objects are truly identical

class emxlib.utils.EmxParticle(fileName=None, index=None)

Bases: emxlib.utils.EmxImage

Class for Particles

getMicrograph()

Return the micrograph associated with this particles.

setMicrograph(micrograph)

Set the micrograph associated with this particle.

class emxlib.utils.EmxXmlMapper(emxData)

Bases: object

Mapper for XML

createObject(elem)

firstObject(classname, fileName)

Iterate over the tags elements and find the first one of type ‘classname’, build the object and return it. The foreing keys will be not updated.

objectToXML(object)

Given an object persist it in XML dataBase. Each object goes to a different element. Much much faster…

readEMXFile(fileName, classElement=None)

create tree from xml file If classElement is not None, the first element of this class will be returned

readObjectPK(elem)

read primary key. So far all entities has the same PK. We may need to specialize or use dictPrimaryKeys in the future

writeEMXFile(fileName)

write xml file and store it in a document

exception emxlib.utils.ValidateError(code, message)

Bases: Exception

getCode()

getMessage()

emxlib.utils.validateSchema(filename, schema_file=None)

Code from astropy project released under BSD licence Validates an XML file against a schema or DTD.

Functions to do XML schema and DTD validation. At the moment, this makes a subprocess call first to xerces then to xmllint. This could use a Python-based library at some point in the future, if something appropriate could be found. lxml is a possibility but has too many dependences if anyone knows about a pure python validator let my know

Parameters

• filename (str) – The path to the XML file to validate

• schema (str) – The path to the XML schema or DTD

Returns

returncode, stdout, stderr – Returns the returncode from validator and the stdout and stderr as strings

Return type

int, str, str