Package omero :: Package util :: Module populate_roi :: Class MIASPlateAnalysisCtx
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Class MIASPlateAnalysisCtx

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MIAS dataset concrete class implementation of an analysis context. MIAS measurements are aggregated based on a single "log" file. A result file is present for each stitched (of multiple fields) mosaic and contains the actual measured results and ROI.

Nested Classes [hide private]

Inherited from AbstractPlateAnalysisCtx: DEFAULT_ORIGINAL_FILE_PROVIDER

Instance Methods [hide private]
 
__init__(self, images, original_files, original_file_image_map, plate_id, service_factory)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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_populate_log_and_detail_files(self)
Strips out erroneous files and collects the log and result original files based on regular expression matching.
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_populate_measurements(self)
Result original files are only recognizable as part of a given measurement (declared by a log file) based upon their parsed date/time of completion as encoded in the filename.
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get_measurement_count(self)
Returns the number of recognized measurement runs.
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get_measurement_ctx(self, index)
Returns the measurement context for a given index.
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get_result_file_count(self, measurement_index)
Return the number of result files associated with a measurement run.
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Inherited from AbstractPlateAnalysisCtx: colrow_from_wellnumber, guess_geometry, image_from_wellnumber

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

Class Methods [hide private]
 
is_this_type(klass, original_files)
Concrete implementations are to return True if the class pertinent for the original files associated with the plate.
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Class Variables [hide private]
  datetime_format = '%Y-%m-%d-%Hh%Mm%Ss'
  log_regex = re.compile('.*log(\d+-\d+-\d+-\d+h\d+m\d+s).txt$')
  detail_regex = re.compile('^Well(\d+)_(.*)_detail_(\d+-\d+-\d+...
  companion_format = 'Companion/MIAS'
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, images, original_files, original_file_image_map, plate_id, service_factory)
(Constructor)

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

Overrides: object.__init__
(inherited documentation)

_populate_measurements(self)

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Result original files are only recognizable as part of a given measurement (declared by a log file) based upon their parsed date/time of completion as encoded in the filename. This method collects result original files and groups them by collective parsed date/time of completion.

is_this_type(klass, original_files)
Class Method

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Concrete implementations are to return True if the class pertinent for the original files associated with the plate.

Overrides: AbstractPlateAnalysisCtx.is_this_type
(inherited documentation)

get_measurement_count(self)

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Returns the number of recognized measurement runs.

Overrides: AbstractPlateAnalysisCtx.get_measurement_count
(inherited documentation)

get_measurement_ctx(self, index)

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Returns the measurement context for a given index.

Overrides: AbstractPlateAnalysisCtx.get_measurement_ctx
(inherited documentation)

get_result_file_count(self, measurement_index)

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Return the number of result files associated with a measurement run.

Overrides: AbstractPlateAnalysisCtx.get_result_file_count
(inherited documentation)

Class Variable Details [hide private]

detail_regex

Value:
re.compile('^Well(\d+)_(.*)_detail_(\d+-\d+-\d+-\d+h\d+m\d+s).txt$')