Package omero :: Package gateway
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Package gateway

source code

Submodules [hide private]

Classes [hide private]
  BlitzObjectWrapper
Object wrapper class which provides various methods for hierarchy traversing, saving, handling permissions etc.
  NoProxies
A dummy placeholder to indicate that proxies haven't been created
  _BlitzGateway
Connection wrapper.
  OmeroGatewaySafeCallWrapper
Function or method wrapper that handles certain types of server side exceptions and debugging of errors.
  SafeCallWrapper
Function or method wrapper that handles certain types of server side exceptions and debugging of errors.
  BlitzGateway
Connection wrapper.
  ProxyObjectWrapper
Wrapper for services.
  AnnotationWrapper
omero_model_AnnotationI class wrapper extends BlitzObjectWrapper.
  _AnnotationLinkWrapper
omero_model_AnnotationLinkI class wrapper extends omero.gateway.BlitzObjectWrapper.
  AnnotationLinkWrapper
omero_model_AnnotationLinkI class wrapper extends omero.gateway.BlitzObjectWrapper.
  FileAnnotationWrapper
omero_model_FileAnnotatio class wrapper extends AnnotationWrapper.
  _OriginalFileWrapper
omero_model_OriginalFileI class wrapper extends BlitzObjectWrapper.
  OriginalFileWrapper
omero_model_OriginalFileI class wrapper extends BlitzObjectWrapper.
  TimestampAnnotationWrapper
omero_model_TimestampAnnotatio class wrapper extends AnnotationWrapper.
  BooleanAnnotationWrapper
omero_model_BooleanAnnotationI class wrapper extends AnnotationWrapper.
  TagAnnotationWrapper
omero_model_BooleanAnnotationI class wrapper extends AnnotationWrapper.
  CommentAnnotationWrapper
omero_model_CommentAnnotationI class wrapper extends AnnotationWrapper.
  LongAnnotationWrapper
omero_model_LongAnnotationI class wrapper extends AnnotationWrapper.
  DoubleAnnotationWrapper
omero_model_DoubleAnnotationI class wrapper extends AnnotationWrapper.
  TermAnnotationWrapper
omero_model_TermAnnotationI class wrapper extends AnnotationWrapper.
  XmlAnnotationWrapper
omero_model_XmlAnnotationI class wrapper extends CommentAnnotationWrapper.
  _EnumerationWrapper
  EnumerationWrapper
  _ExperimenterWrapper
omero_model_ExperimenterI class wrapper extends BlitzObjectWrapper.
  ExperimenterWrapper
omero_model_ExperimenterI class wrapper extends BlitzObjectWrapper.
  _ExperimenterGroupWrapper
omero_model_ExperimenterGroupI class wrapper extends BlitzObjectWrapper.
  ExperimenterGroupWrapper
omero_model_ExperimenterGroupI class wrapper extends BlitzObjectWrapper.
  DetailsWrapper
omero_model_DetailsI class wrapper extends BlitzObjectWrapper.
  _DatasetWrapper
omero_model_DatasetI class wrapper extends BlitzObjectWrapper.
  DatasetWrapper
omero_model_DatasetI class wrapper extends BlitzObjectWrapper.
  _ProjectWrapper
omero_model_ProjectI class wrapper extends BlitzObjectWrapper.
  ProjectWrapper
omero_model_ProjectI class wrapper extends BlitzObjectWrapper.
  _ScreenWrapper
omero_model_ScreenI class wrapper extends BlitzObjectWrapper.
  ScreenWrapper
omero_model_ScreenI class wrapper extends BlitzObjectWrapper.
  _PlateWrapper
omero_model_PlateI class wrapper extends BlitzObjectWrapper.
  PlateWrapper
omero_model_PlateI class wrapper extends BlitzObjectWrapper.
  _WellWrapper
omero_model_WellI class wrapper extends BlitzObjectWrapper.
  WellWrapper
omero_model_WellI class wrapper extends BlitzObjectWrapper.
  _WellSampleWrapper
omero_model_WellSampleI class wrapper extends BlitzObjectWrapper.
  WellSampleWrapper
omero_model_WellSampleI class wrapper extends BlitzObjectWrapper.
  ColorHolder
Stores color internally as (R,G,B,A) and allows setting and getting in multiple formats
  _LogicalChannelWrapper
omero_model_LogicalChannelI class wrapper extends BlitzObjectWrapper.
  LogicalChannelWrapper
omero_model_LogicalChannelI class wrapper extends BlitzObjectWrapper.
  _LightPathWrapper
base Light Source class wrapper, extends BlitzObjectWrapper.
  LightPathWrapper
base Light Source class wrapper, extends BlitzObjectWrapper.
  _PixelsWrapper
omero_model_PixelsI class wrapper extends BlitzObjectWrapper.
  PixelsWrapper
omero_model_PixelsI class wrapper extends BlitzObjectWrapper.
  _ChannelWrapper
omero_model_ChannelI class wrapper extends BlitzObjectWrapper.
  ChannelWrapper
omero_model_ChannelI class wrapper extends BlitzObjectWrapper.
  assert_re
Function decorator to make sure that rendering engine is prepared before call.
  _ImageWrapper
omero_model_ImageI class wrapper extends BlitzObjectWrapper.
  ImageWrapper
omero_model_ImageI class wrapper extends BlitzObjectWrapper.
  _ImageStageLabelWrapper
omero_model_StageLabelI class wrapper extends BlitzObjectWrapper.
  ImageStageLabelWrapper
omero_model_StageLabelI class wrapper extends BlitzObjectWrapper.
  _ImagingEnvironmentWrapper
omero_model_ImagingEnvironment class wrapper extends BlitzObjectWrapper.
  ImagingEnvironmentWrapper
omero_model_ImagingEnvironment class wrapper extends BlitzObjectWrapper.
  _ImagingEnviromentWrapper
omero_model_ImagingEnvironmentI class wrapper extends BlitzObjectWrapper.
  ImagingEnviromentWrapper
omero_model_ImagingEnvironmentI class wrapper extends BlitzObjectWrapper.
  _TransmittanceRangeWrapper
omero_model_TransmittanceRangeI class wrapper extends BlitzObjectWrapper.
  TransmittanceRangeWrapper
omero_model_TransmittanceRangeI class wrapper extends BlitzObjectWrapper.
  _DetectorSettingsWrapper
omero_model_DetectorSettingsI class wrapper extends BlitzObjectWrapper.
  DetectorSettingsWrapper
omero_model_DetectorSettingsI class wrapper extends BlitzObjectWrapper.
  _BinningWrapper
omero_model_BinningI class wrapper extends BlitzObjectWrapper.
  BinningWrapper
omero_model_BinningI class wrapper extends BlitzObjectWrapper.
  _DetectorWrapper
omero_model_DetectorI class wrapper extends BlitzObjectWrapper.
  DetectorWrapper
omero_model_DetectorI class wrapper extends BlitzObjectWrapper.
  _ObjectiveWrapper
omero_model_ObjectiveI class wrapper extends BlitzObjectWrapper.
  ObjectiveWrapper
omero_model_ObjectiveI class wrapper extends BlitzObjectWrapper.
  _ObjectiveSettingsWrapper
omero_model_ObjectiveSettingsI class wrapper extends BlitzObjectWrapper.
  ObjectiveSettingsWrapper
omero_model_ObjectiveSettingsI class wrapper extends BlitzObjectWrapper.
  _FilterWrapper
omero_model_FilterI class wrapper extends BlitzObjectWrapper.
  FilterWrapper
omero_model_FilterI class wrapper extends BlitzObjectWrapper.
  _DichroicWrapper
omero_model_DichroicI class wrapper extends BlitzObjectWrapper.
  DichroicWrapper
omero_model_DichroicI class wrapper extends BlitzObjectWrapper.
  _FilterSetWrapper
omero_model_FilterSetI class wrapper extends BlitzObjectWrapper.
  FilterSetWrapper
omero_model_FilterSetI class wrapper extends BlitzObjectWrapper.
  _OTFWrapper
omero_model_OTFI class wrapper extends BlitzObjectWrapper.
  OTFWrapper
omero_model_OTFI class wrapper extends BlitzObjectWrapper.
  _LightSettingsWrapper
base Light Source class wrapper, extends BlitzObjectWrapper.
  LightSettingsWrapper
base Light Source class wrapper, extends BlitzObjectWrapper.
  _LightSourceWrapper
base Light Source class wrapper, extends BlitzObjectWrapper.
  _FilamentWrapper
omero_model_FilamentI class wrapper extends LightSourceWrapper.
  FilamentWrapper
omero_model_FilamentI class wrapper extends LightSourceWrapper.
  _ArcWrapper
omero_model_ArcI class wrapper extends FilamentWrapper.
  ArcWrapper
omero_model_ArcI class wrapper extends FilamentWrapper.
  _LaserWrapper
omero_model_LaserI class wrapper extends LightSourceWrapper.
  LaserWrapper
omero_model_LaserI class wrapper extends LightSourceWrapper.
  _LightEmittingDiodeWrapper
omero_model_LightEmittingDiodeI class wrapper extends LightSourceWrapper.
  LightEmittingDiodeWrapper
omero_model_LightEmittingDiodeI class wrapper extends LightSourceWrapper.
  _MicroscopeWrapper
omero_model_MicroscopeI class wrapper extends BlitzObjectWrapper.
  MicroscopeWrapper
omero_model_MicroscopeI class wrapper extends BlitzObjectWrapper.
  _InstrumentWrapper
omero_model_InstrumentI class wrapper extends BlitzObjectWrapper.
  InstrumentWrapper
omero_model_InstrumentI class wrapper extends BlitzObjectWrapper.
Functions [hide private]
omero.rtype
omero_type(val)
Converts rtypes from static factory methods:
source code
string
fileread(fin, fsize, bufsize)
Reads everything from fin, in chunks of bufsize.
source code
generator
fileread_gen(fin, fsize, bufsize)
Generator helper function that yields chunks of the file of size fsize.
source code
list of Ints
splitHTMLColor(color)
splits an hex stream of characters into an array of bytes in format (R,G,B,A).
source code
 
_letterGridLabel(i)
Convert number to letter label.
source code
Function
assert_pixels(func)
Function decorator to make sure that pixels are loaded before call
source code
 
LightSourceWrapper(conn, obj, **kwargs)
Creates wrapper instances for omero.model light source objects
source code
 
refreshWrappers()
this needs to be called by modules that extend the base wrappers
source code
Variables [hide private]
  THISPATH = os.path.dirname(os.path.abspath(__file__))
  logger = logging.getLogger('blitz_gateway')
  _LightSourceClasses = {}
  KNOWN_WRAPPERS = {}

Imports: os, sys, shutil, tempfile, IntType, LongType, UnicodeType, ListType, TupleType, StringType, StringTypes, datetime, ConfigParser, omero, timeit, TimeIt, Ice, Glacier2, traceback, time, array, math, logging, Image, ImageDraw, ImageFont, StringIO, sqrt, omero_Constants_ice, omero_ROMIO_ice, rstring, rint, rlong, rbool, rtime, rlist, rdouble, unwrap, FileAnnotationI, TimestampAnnotationI, BooleanAnnotationI, TagAnnotationI, CommentAnnotationI, LongAnnotationI, DoubleAnnotationI, TermAnnotationI, XmlAnnotationI


Function Details [hide private]

omero_type(val)

source code 

Converts rtypes from static factory methods:

  • StringType to rstring
  • UnicodeType to rstring
  • IntType to rint
  • LongType to rlong

elswere return the argument itself

Parameters:
  • val - value
Returns: omero.rtype
matched RType or value

fileread(fin, fsize, bufsize)

source code 

Reads everything from fin, in chunks of bufsize.

Parameters:
  • fin (file) - filelike readable object
  • fsize (int) - total number of bytes to read
  • fsize (int) - size of each chunk of data read from fin
  • bufsize (int)
Returns: string
string buffer holding the contents read from the file

fileread_gen(fin, fsize, bufsize)

source code 

Generator helper function that yields chunks of the file of size fsize.

Parameters:
  • fin (file) - filelike readable object
  • fsize (int) - total number of bytes to read
  • fsize (int) - size of each chunk of data read from fin that gets yielded
  • bufsize (int)
Returns: generator
generator of string buffers of size up to bufsize read from fin

splitHTMLColor(color)

source code 

splits an hex stream of characters into an array of bytes in format (R,G,B,A).

  • abc -> (0xAA, 0xBB, 0xCC, 0xFF)
  • abcd -> (0xAA, 0xBB, 0xCC, 0xDD)
  • abbccd -> (0xAB, 0xBC, 0xCD, 0xFF)
  • abbccdde -> (0xAB, 0xBC, 0xCD, 0xDE)
Parameters:
  • color - Characters to split.
Returns: list of Ints
rgba

_letterGridLabel(i)

source code 

Convert number to letter label. E.g. 0 -> 'A' and 100 -> 'CW'

assert_pixels(func)

source code 

Function decorator to make sure that pixels are loaded before call

Parameters:
  • func (Function) - Function
Returns: Function
Decorated function

LightSourceWrapper(conn, obj, **kwargs)

source code 

Creates wrapper instances for omero.model light source objects

Parameters:
Returns:
_LightSourceWrapper subclass