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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image_from_original_file(self, original_file)
Overriding the abstract implementation since the companion files are no longer attached to the images, but only to the plate for MIAS.
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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, get_well_images, 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)

image_from_original_file(self, original_file)

source code 

Overriding the abstract implementation since the companion files are no longer attached to the images, but only to the plate for MIAS. Instead, we use the filename itself to find the image.

Overrides: AbstractMeasurementCtx.image_from_original_file

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)

source code 

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.'