Package omero :: Package util :: Module populate_roi :: Class MIASMeasurementCtx
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Class MIASMeasurementCtx

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MIAS measurements are a set of tab delimited text files per well. Each TSV file's content is prefixed by the analysis parameters.

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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get_empty_columns(self, n_columns)
Retrieves a set of empty OmeroTables columns for the analysis results prefixed by an ImageColumn and RoiColumn to handle these linked object indexes.
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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_neo_roi(self, columns)
Parses out ROI from OmeroTables columns for 'NEO' datasets.
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_parse_mnu_roi(self, columns)
Parses out ROI from OmeroTables columns for 'MNU' datasets.
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parse_and_populate_roi(self, columns)
Parses and populates ROI from column data in the OMERO database.
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populate(self, columns)
Query performed:
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Inherited from AbstractMeasurementCtx: create_file_annotation, 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]
  IMAGE_COL = 0
  ROI_COL = 1
  NEO_EXPECTED = 'Image', 'ROI', 'Label', 'Row', 'Col', 'Nucleus...
  MNU_EXPECTED = 'Image', 'ROI', 'row', 'col', 'type'

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)

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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 

Query performed:

       first_roi = columns[self.ROI_COL].values[0]
       first_roi = self.query_service.findByQuery(
               'select roi from Roi as roi '                   'join fetch roi.annotationLinks as link '                       'join fetch link.child '                        'where roi.id = %d' % first_roi, None)
       self.file_annotation = first_roi.copyAnnotationLinks()[0].child
Overrides: AbstractMeasurementCtx.populate

Class Variable Details [hide private]

NEO_EXPECTED

Value:
'Image', 'ROI', 'Label', 'Row', 'Col', 'Nucleus Area', 'Cell Diam.', '\
Cell Type', 'Mean Nucleus Intens.'