def LoadHTTP(self, filename):
'''Load PYMEs semi-custom HDF5 image data format. Offloads all the
hard work to the HDFDataSource class'''
import tables
from PYME.Analysis.DataSources import HTTPDataSource, BGSDataSource
#from PYME.Analysis.LMVis import inpFilt
#open hdf5 file
self.dataSource = HTTPDataSource.DataSource(filename)
#chain on a background subtraction data source, so we can easily do
#background subtraction in the GUI the same way as in the analysis
self.data = BGSDataSource.DataSource(self.dataSource) #this will get replaced with a wrapped version
#try: #should be true the whole time
self.mdh = MetaData.TIRFDefault
self.mdh.copyEntriesFrom(self.dataSource.getMetadata())
#except:
# self.mdh = MetaData.TIRFDefault
# wx.MessageBox("Carrying on with defaults - no gaurantees it'll work well", 'ERROR: No metadata found in file ...', wx.OK)
# print("ERROR: No metadata fond in file ... Carrying on with defaults - no gaurantees it'll work well")
#attempt to estimate any missing parameters from the data itself
MetaData.fillInBlanks(self.mdh, self.dataSource)
#calculate the name to use when we do batch analysis on this
#from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = filename
self.events = self.dataSource.getEvents()
def LoadQueue(self, filename):
'''Load data from a remote PYME.ParallelTasks.HDFTaskQueue queue using
Pyro.
Parameters:
filename the name of the queue
'''
import Pyro.core
from PYME.Analysis.DataSources import TQDataSource
from PYME.misc.computerName import GetComputerName
compName = GetComputerName()
if self.queueURI == None:
#do a lookup
taskQueueName = 'TaskQueues.%s' % compName
self.tq = Pyro.core.getProxyForURI('PYRONAME://' + taskQueueName)
else:
self.tq = Pyro.core.getProxyForURI(self.queueURI)
self.seriesName = filename[len('QUEUE://'):]
self.dataSource = TQDataSource.DataSource(self.seriesName, self.tq)
self.data = self.dataSource #this will get replaced with a wrapped version
self.mdh = MetaDataHandler.QueueMDHandler(self.tq, self.seriesName)
MetaData.fillInBlanks(self.mdh, self.dataSource)
#self.timer.WantNotification.append(self.dsRefresh)
self.events = self.dataSource.getEvents()
def _loadHTTP(self, filename):
"""Load PYMEs semi-custom HDF5 image data format. Offloads all the
hard work to the HDFDataSource class"""
import tables
from PYME.IO.DataSources import HTTPDataSource, BGSDataSource
#from PYME.LMVis import inpFilt
#open hdf5 file
self.dataSource = HTTPDataSource.DataSource(filename)
#chain on a background subtraction data source, so we can easily do
#background subtraction in the GUI the same way as in the analysis
self.data = BGSDataSource.DataSource(
self.dataSource) #this will get replaced with a wrapped version
#try: #should be true the whole time
self.mdh = MetaData.TIRFDefault
self.mdh.copyEntriesFrom(self.dataSource.getMetadata())
#except:
# self.mdh = MetaData.TIRFDefault
# wx.MessageBox("Carrying on with defaults - no gaurantees it'll work well", 'ERROR: No metadata found in file ...', wx.OK)
# print("ERROR: No metadata fond in file ... Carrying on with defaults - no gaurantees it'll work well")
#attempt to estimate any missing parameters from the data itself
MetaData.fillInBlanks(self.mdh, self.dataSource)
#calculate the name to use when we do batch analysis on this
#from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = filename
self.events = self.dataSource.getEvents()
self.mode = 'LM'
def _loadClusterPZF(self, filename):
"""Load PYMEs semi-custom HDF5 image data format. Offloads all the
hard work to the HDFDataSource class"""
from PYME.IO.DataSources import ClusterPZFDataSource, BGSDataSource
self.dataSource = ClusterPZFDataSource.DataSource(filename)
#chain on a background subtraction data source, so we can easily do
#background subtraction in the GUI the same way as in the analysis
self.data = BGSDataSource.DataSource(
self.dataSource) #this will get replaced with a wrapped version
#try: #should be true the whole time
self.mdh = MetaData.TIRFDefault
self.mdh.copyEntriesFrom(self.dataSource.getMetadata())
#attempt to estimate any missing parameters from the data itself
MetaData.fillInBlanks(self.mdh, self.dataSource)
#calculate the name to use when we do batch analysis on this
#from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = filename
self.events = self.dataSource.getEvents()
self.mode = 'LM'
def LoadQueue(self, filename):
'''Load data from a remote PYME.ParallelTasks.HDFTaskQueue queue using
Pyro.
Parameters:
filename the name of the queue
'''
import Pyro.core
from PYME.Analysis.DataSources import TQDataSource
from PYME.misc.computerName import GetComputerName
compName = GetComputerName()
if self.queueURI == None:
#do a lookup
taskQueueName = 'TaskQueues.%s' % compName
self.tq = Pyro.core.getProxyForURI('PYRONAME://' + taskQueueName)
else:
self.tq = Pyro.core.getProxyForURI(self.queueURI)
self.seriesName = filename[len('QUEUE://'):]
self.dataSource = TQDataSource.DataSource(self.seriesName, self.tq)
self.data = self.dataSource #this will get replaced with a wrapped version
self.mdh = MetaDataHandler.QueueMDHandler(self.tq, self.seriesName)
MetaData.fillInBlanks(self.mdh, self.dataSource)
#self.timer.WantNotification.append(self.dsRefresh)
self.events = self.dataSource.getEvents()
def _loadh5(self, filename):
"""Load PYMEs semi-custom HDF5 image data format. Offloads all the
hard work to the HDFDataSource class"""
import tables
from PYME.IO.DataSources import HDFDataSource, BGSDataSource
from PYME.IO import tabular
self.dataSource = HDFDataSource.DataSource(filename, None)
#chain on a background subtraction data source, so we can easily do
#background subtraction in the GUI the same way as in the analysis
self.data = BGSDataSource.DataSource(
self.dataSource) #this will get replaced with a wrapped version
if 'MetaData' in self.dataSource.h5File.root: #should be true the whole time
self.mdh = MetaData.TIRFDefault
self.mdh.copyEntriesFrom(
MetaDataHandler.HDFMDHandler(self.dataSource.h5File))
else:
self.mdh = MetaData.TIRFDefault
import wx
wx.MessageBox(
"Carrying on with defaults - no gaurantees it'll work well",
'ERROR: No metadata found in file ...', wx.OK)
print(
"ERROR: No metadata fond in file ... Carrying on with defaults - no gaurantees it'll work well"
)
#attempt to estimate any missing parameters from the data itself
try:
MetaData.fillInBlanks(self.mdh, self.dataSource)
except:
logger.exception('Error attempting to populate missing metadata')
#calculate the name to use when we do batch analysis on this
#from PYME.IO.FileUtils.nameUtils import getRelFilename
self.seriesName = getRelFilename(filename)
#try and find a previously performed analysis
fns = filename.split(os.path.sep)
cand = os.path.sep.join(fns[:-2] + [
'analysis',
] + fns[-2:]) + 'r'
print(cand)
if False: #os.path.exists(cand):
h5Results = tables.open_file(cand)
if 'FitResults' in dir(h5Results.root):
self.fitResults = h5Results.root.FitResults[:]
self.resultsSource = tabular.H5RSource(h5Results)
self.resultsMdh = MetaData.TIRFDefault
self.resultsMdh.copyEntriesFrom(
MetaDataHandler.HDFMDHandler(h5Results))
self.events = self.dataSource.getEvents()
self.mode = 'LM'
def Loadh5(self, filename):
'''Load PYMEs semi-custom HDF5 image data format. Offloads all the
hard work to the HDFDataSource class'''
import tables
from PYME.Analysis.DataSources import HDFDataSource, BGSDataSource
from PYME.Analysis.LMVis import inpFilt
#open hdf5 file
self.dataSource = HDFDataSource.DataSource(filename, None)
#chain on a background subtraction data source, so we can easily do
#background subtraction in the GUI the same way as in the analysis
self.data = BGSDataSource.DataSource(self.dataSource) #this will get replaced with a wrapped version
if 'MetaData' in self.dataSource.h5File.root: #should be true the whole time
self.mdh = MetaData.TIRFDefault
self.mdh.copyEntriesFrom(MetaDataHandler.HDFMDHandler(self.dataSource.h5File))
else:
self.mdh = MetaData.TIRFDefault
wx.MessageBox("Carrying on with defaults - no gaurantees it'll work well", 'ERROR: No metadata found in file ...', wx.OK)
print("ERROR: No metadata fond in file ... Carrying on with defaults - no gaurantees it'll work well")
#attempt to estimate any missing parameters from the data itself
MetaData.fillInBlanks(self.mdh, self.dataSource)
#calculate the name to use when we do batch analysis on this
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
#try and find a previously performed analysis
fns = filename.split(os.path.sep)
cand = os.path.sep.join(fns[:-2] + ['analysis',] + fns[-2:]) + 'r'
print(cand)
if False:#os.path.exists(cand):
h5Results = tables.openFile(cand)
if 'FitResults' in dir(h5Results.root):
self.fitResults = h5Results.root.FitResults[:]
self.resultsSource = inpFilt.h5rSource(h5Results)
self.resultsMdh = MetaData.TIRFDefault
self.resultsMdh.copyEntriesFrom(MetaDataHandler.HDFMDHandler(h5Results))
self.events = self.dataSource.getEvents()
def _loadQueue(self, filename):
"""Load data from a remote PYME.ParallelTasks.HDFTaskQueue queue using
Pyro.
Parameters:
-----------
filename : string
the name of the queue
"""
import Pyro.core
from PYME.IO.DataSources import TQDataSource
from PYME.misc.computerName import GetComputerName
compName = GetComputerName()
if self.queueURI is None:
#do a lookup
taskQueueName = 'TaskQueues.%s' % compName
try:
from PYME.misc import pyme_zeroconf
ns = pyme_zeroconf.getNS()
URI = ns.resolve(taskQueueName)
except:
URI = 'PYRONAME://' + taskQueueName
self.tq = Pyro.core.getProxyForURI(URI)
else:
self.tq = Pyro.core.getProxyForURI(self.queueURI)
self.seriesName = filename[len('QUEUE://'):]
self.dataSource = TQDataSource.DataSource(self.seriesName, self.tq)
self.data = self.dataSource #this will get replaced with a wrapped version
self.mdh = MetaDataHandler.QueueMDHandler(self.tq, self.seriesName)
MetaData.fillInBlanks(self.mdh, self.dataSource)
#self.timer.WantNotification.append(self.dsRefresh)
self.events = self.dataSource.getEvents()
self.mode = 'LM'
def __init__(self, dsviewer):
self.dsviewer = dsviewer
if 'tq' in dir(dsviewer):
self.tq = dsviewer.tq
else:
self.tq = None
self.image = dsviewer.image
self.view = dsviewer.view
self.do = dsviewer.do
#this should only occur for files types which we weren't expecting to process
#as LM data (eg tiffs)
if not 'EstimatedLaserOnFrameNo' in self.image.mdh.getEntryNames():
from PYME.Analysis import MetaData
#try:
MetaData.fillInBlanks(self.image.mdh, self.image.dataSource)
#except IndexError:
# pass
if 'fitResults' in dir(self.image):
self.fitResults = self.image.fitResults
else:
self.fitResults = []
if 'resultsMdh' in dir(self.image):
self.resultsMdh = self.image.resultsMdh
mTasks = wx.Menu()
TASKS_STANDARD_2D = wx.NewId()
TASKS_CALIBRATE_SPLITTER = wx.NewId()
TASKS_2D_SPLITTER = wx.NewId()
TASKS_3D = wx.NewId()
TASKS_3D_SPLITTER = wx.NewId()
TASKS_PRI = wx.NewId()
mTasks.Append(TASKS_STANDARD_2D, "Normal 2D analysis", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_CALIBRATE_SPLITTER, "Calibrating the splitter", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_2D_SPLITTER, "2D with splitter", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D, "3D analysis", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D_SPLITTER, "3D with splitter", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_PRI, "PRI", "", wx.ITEM_NORMAL)
self.dsviewer.menubar.Append(mTasks, "Set defaults for")
wx.EVT_MENU(self.dsviewer, TASKS_CALIBRATE_SPLITTER, self.OnCalibrateSplitter)
wx.EVT_MENU(self.dsviewer, TASKS_STANDARD_2D, self.OnStandard2D)
wx.EVT_MENU(self.dsviewer, TASKS_2D_SPLITTER, self.OnSpitter2D)
wx.EVT_MENU(self.dsviewer, TASKS_3D, self.OnStandard3D)
wx.EVT_MENU(self.dsviewer, TASKS_3D_SPLITTER, self.OnSpliter3D)
wx.EVT_MENU(self.dsviewer, TASKS_PRI, self.OnPRI3D)
BG_SUBTRACT = wx.NewId()
self.dsviewer.view_menu.AppendCheckItem(BG_SUBTRACT, 'Subtract Background')
wx.EVT_MENU(self.dsviewer, BG_SUBTRACT, self.OnToggleBackground)
#a timer object to update for us
self.timer = mytimer()
self.timer.Start(10000)
self.analDispMode = 'z'
self.numAnalysed = 0
self.numEvents = 0
dsviewer.pipeline = pipeline.Pipeline()
self.ds = None
dsviewer.paneHooks.append(self.GenPointFindingPanel)
dsviewer.paneHooks.append(self.GenAnalysisPanel)
dsviewer.paneHooks.append(self.GenFitStatusPanel)
dsviewer.updateHooks.append(self.update)
dsviewer.statusHooks.append(self.GetStatusText)
if 'Protocol.DataStartsAt' in self.image.mdh.getEntryNames():
self.do.zp = self.image.mdh.getEntry('Protocol.DataStartsAt')
else:
self.do.zp = self.image.mdh.getEntry('EstimatedLaserOnFrameNo')
def __init__(self, dsviewer):
self.dsviewer = dsviewer
if 'tq' in dir(dsviewer):
self.tq = dsviewer.tq
else:
self.tq = None
self.image = dsviewer.image
self.view = dsviewer.view
self.do = dsviewer.do
#this should only occur for files types which we weren't expecting to process
#as LM data (eg tiffs)
if not 'EstimatedLaserOnFrameNo' in self.image.mdh.getEntryNames():
from PYME.Analysis import MetaData
#try:
MetaData.fillInBlanks(self.image.mdh, self.image.dataSource)
#except IndexError:
# pass
if 'fitResults' in dir(self.image):
self.fitResults = self.image.fitResults
else:
self.fitResults = []
if 'resultsMdh' in dir(self.image):
self.resultsMdh = self.image.resultsMdh
mTasks = wx.Menu()
TASKS_STANDARD_2D = wx.NewId()
TASKS_CALIBRATE_SPLITTER = wx.NewId()
TASKS_2D_SPLITTER = wx.NewId()
TASKS_3D = wx.NewId()
TASKS_3D_SPLITTER = wx.NewId()
TASKS_PRI = wx.NewId()
mTasks.Append(TASKS_STANDARD_2D, "Normal 2D analysis", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_CALIBRATE_SPLITTER, "Calibrating the splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_2D_SPLITTER, "2D with splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D, "3D analysis", "", wx.ITEM_NORMAL)
mTasks.Append(TASKS_3D_SPLITTER, "3D with splitter", "",
wx.ITEM_NORMAL)
mTasks.Append(TASKS_PRI, "PRI", "", wx.ITEM_NORMAL)
self.dsviewer.menubar.Append(mTasks, "Set defaults for")
wx.EVT_MENU(self.dsviewer, TASKS_CALIBRATE_SPLITTER,
self.OnCalibrateSplitter)
wx.EVT_MENU(self.dsviewer, TASKS_STANDARD_2D, self.OnStandard2D)
wx.EVT_MENU(self.dsviewer, TASKS_2D_SPLITTER, self.OnSpitter2D)
wx.EVT_MENU(self.dsviewer, TASKS_3D, self.OnStandard3D)
wx.EVT_MENU(self.dsviewer, TASKS_3D_SPLITTER, self.OnSpliter3D)
wx.EVT_MENU(self.dsviewer, TASKS_PRI, self.OnPRI3D)
BG_SUBTRACT = wx.NewId()
self.dsviewer.view_menu.AppendCheckItem(BG_SUBTRACT,
'Subtract Background')
wx.EVT_MENU(self.dsviewer, BG_SUBTRACT, self.OnToggleBackground)
#a timer object to update for us
self.timer = mytimer()
self.timer.Start(10000)
self.analDispMode = 'z'
self.numAnalysed = 0
self.numEvents = 0
dsviewer.pipeline = pipeline.Pipeline()
self.ds = None
dsviewer.paneHooks.append(self.GenPointFindingPanel)
dsviewer.paneHooks.append(self.GenAnalysisPanel)
dsviewer.paneHooks.append(self.GenFitStatusPanel)
dsviewer.updateHooks.append(self.update)
dsviewer.statusHooks.append(self.GetStatusText)
if 'Protocol.DataStartsAt' in self.image.mdh.getEntryNames():
self.do.zp = self.image.mdh.getEntry('Protocol.DataStartsAt')
else:
self.do.zp = self.image.mdh.getEntry('EstimatedLaserOnFrameNo')
