def __init__(self,
spooler,
seriesName,
analysisMetadata,
resultsFilename=None,
startAt=0,
serverfilter=clusterIO.local_serverfilter,
**kwargs):
# TODO - reduce duplication of `LocalisationRule.__init__()` and `LocalisationRule._setup()`
from PYME.IO import MetaDataHandler
from PYME.Analysis import MetaData
from PYME.IO.FileUtils.nameUtils import genClusterResultFileName
from PYME.IO import unifiedIO
self.spooler = spooler
if resultsFilename is None:
resultsFilename = genClusterResultFileName(seriesName)
resultsFilename = verify_cluster_results_filename(resultsFilename)
logger.info('Results file: ' + resultsFilename)
resultsMdh = MetaDataHandler.DictMDHandler()
# NB - anything passed in analysis MDH will wipe out corresponding entries in the series metadata
resultsMdh.update(self.spooler.md)
resultsMdh.update(analysisMetadata)
resultsMdh['EstimatedLaserOnFrameNo'] = resultsMdh.getOrDefault(
'EstimatedLaserOnFrameNo',
resultsMdh.getOrDefault('Analysis.StartAt', 0))
MetaData.fixEMGain(resultsMdh)
self._setup(seriesName, resultsMdh, resultsFilename, startAt,
serverfilter)
Rule.__init__(self, **kwargs)
def __init__(self,
seriesName,
analysisMetadata,
resultsFilename=None,
startAt=0,
dataSourceModule=None,
serverfilter=clusterIO.local_serverfilter,
**kwargs):
from PYME.IO import MetaDataHandler
from PYME.Analysis import MetaData
from PYME.IO.FileUtils.nameUtils import genClusterResultFileName
from PYME.IO import unifiedIO
unifiedIO.assert_uri_ok(seriesName)
if resultsFilename is None:
resultsFilename = genClusterResultFileName(seriesName)
resultsFilename = verify_cluster_results_filename(resultsFilename)
logger.info('Results file: ' + resultsFilename)
resultsMdh = MetaDataHandler.NestedClassMDHandler()
# NB - anything passed in analysis MDH will wipe out corresponding entries in the series metadata
resultsMdh.update(
json.loads(unifiedIO.read(seriesName + '/metadata.json')))
resultsMdh.update(analysisMetadata)
resultsMdh['EstimatedLaserOnFrameNo'] = resultsMdh.getOrDefault(
'EstimatedLaserOnFrameNo',
resultsMdh.getOrDefault('Analysis.StartAt', 0))
MetaData.fixEMGain(resultsMdh)
self._setup(seriesName, resultsMdh, resultsFilename, startAt,
serverfilter)
#load data source
if dataSourceModule is None:
DataSource = DataSources.getDataSourceForFilename(seriesName)
else:
DataSource = __import__(
'PYME.IO.DataSources.' + dataSourceModule,
fromlist=['PYME', 'io',
'DataSources']).DataSource #import our data source
self.ds = DataSource(seriesName)
logger.debug('DataSource.__class__: %s' % self.ds.__class__)
Rule.__init__(self, **kwargs)
def launch_localize(analysisMDH, seriesName):
"""
Pushes an analysis task for a given series to the distributor
Parameters
----------
analysisMDH : dictionary-like
MetaDataHandler describing the analysis tasks to launch
seriesName : str
cluster path, e.g. pyme-cluster:///example_folder/series
Returns
-------
"""
#import logging
import json
#from PYME.ParallelTasks import HTTPTaskPusher
from PYME.IO import MetaDataHandler
from PYME.Analysis import MetaData
from PYME.IO.FileUtils.nameUtils import genClusterResultFileName
from PYME.IO import unifiedIO
unifiedIO.assert_uri_ok(seriesName)
seriesName = seriesName
resultsFilename = verify_cluster_results_filename(
genClusterResultFileName(seriesName))
logger.info('Results file: ' + resultsFilename)
resultsMdh = MetaDataHandler.NestedClassMDHandler()
# NB - anything passed in analysis MDH will wipe out corresponding entries in the series metadata
resultsMdh.update(json.loads(unifiedIO.read(seriesName +
'/metadata.json')))
resultsMdh.update(analysisMDH)
resultsMdh['EstimatedLaserOnFrameNo'] = resultsMdh.getOrDefault(
'EstimatedLaserOnFrameNo',
resultsMdh.getOrDefault('Analysis.StartAt', 0))
MetaData.fixEMGain(resultsMdh)
# resultsMdh['DataFileID'] = fileID.genDataSourceID(image.dataSource)
# TODO - do we need to keep track of the pushers in some way (we currently rely on the fact that the pushing thread
# will hold a reference
pusher = HTTPRulePusher(dataSourceID=seriesName,
metadata=resultsMdh,
resultsFilename=resultsFilename)
logging.debug('Queue created')
