Package omero :: Package util :: Module populate_roi :: Class InCellMeasurementCtx
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Class InCellMeasurementCtx

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InCell Analyzer measurements are located deep within an XML file container.

Instance Methods [hide private]
 
__init__(self, analysis_ctx, service_factory, original_file_provider, original_file, result_files)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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check_sparse_data(self, columns)
Checks a set of columns for sparse data (one column shorter than the rest) and adds -1 where appropriate.
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get_name(self, set_of_columns=None)
Returns the name of the measurement, and a set of columns.
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parse(self)
Parses result files, returning a MeasurementParsingResult.
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parse_and_populate_roi(self, columns_as_list)
Parses and populates ROI from column data in the OMERO database.
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populate(self, columns)
Populates an OmeroTables instance backing our results and ROI linkages.
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Inherited from AbstractMeasurementCtx: create_file_annotation, get_well_images, image_from_original_file, parse_and_populate, update_rois, update_table

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  CELLS_CG_EXPECTED = ['Cell: cgX', 'Cell: cgY']
  NUCLEI_CG_EXPECTED = ['Nucleus: cgX', 'Nucleus: cgY']
  CELLS_SOURCE = 'Cells'
  NUCLEI_SOURCE = 'Nuclei'
  ORGANELLES_SOURCE = 'Organelles'

Inherited from AbstractMeasurementCtx: ROI_UPDATE_LIMIT

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, analysis_ctx, service_factory, original_file_provider, original_file, result_files)
(Constructor)

source code 

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

get_name(self, set_of_columns=None)

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Returns the name of the measurement, and a set of columns.

Overrides: AbstractMeasurementCtx.get_name
(inherited documentation)

parse(self)

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Parses result files, returning a MeasurementParsingResult.

Overrides: AbstractMeasurementCtx.parse
(inherited documentation)

parse_and_populate_roi(self, columns_as_list)

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Parses and populates ROI from column data in the OMERO database.

Overrides: AbstractMeasurementCtx.parse_and_populate_roi
(inherited documentation)

populate(self, columns)

source code 

Populates an OmeroTables instance backing our results and ROI linkages.

Overrides: AbstractMeasurementCtx.populate
(inherited documentation)