Package omero :: Package util :: Module populate_roi :: Class AbstractMeasurementCtx
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Class AbstractMeasurementCtx

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Abstract class which aggregates and represents all the results produced from a given measurement run. It also provides a scaffold for interacting with the OmeroTables infrastructure.

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_well_images(self, row, col)
Takes a row and a col index and returns a tuple of Well and image.
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update_table(self, columns)
Updates the OmeroTables instance backing our results.
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create_file_annotation(self, set_of_columns)
Creates a file annotation to represent a set of columns from our measurment.
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update_rois(self, rois, batches, batch_no)
Updates a set of ROI for a given batch updating the batches dictionary with the saved IDs.
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image_from_original_file(self, original_file)
Returns the image from which an original file has originated.
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parse_and_populate(self)
Calls parse and populate, updating the OmeroTables instance backing our results and the OMERO database itself.
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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)
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 object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  ROI_UPDATE_LIMIT = 1000
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)

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

Overrides: object.__init__
(inherited documentation)

get_well_images(self, row, col)

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Takes a row and a col index and returns a tuple of Well and image. Either might be None. Uses the first image found to find the Well and therefore must be loaded (image->wellSample->well)