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 LoadDBL(self, filename):
'''Load Bewersdorf custom STED data.
'''
mdfn = self.FindAndParseMetadata(filename)
self.data = numpy.memmap(filename, dtype='<f4', mode='r', offset=128, shape=(self.mdh['Camera.ROIWidth'],self.mdh['Camera.ROIHeight'],self.mdh['NumImages']), order='F')
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
def LoadNPY(self, filename):
'''Load numpy .npy data.
'''
mdfn = self.FindAndParseMetadata(filename)
self.data = numpy.load(filename)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
def LoadNPY(self, filename):
'''Load numpy .npy data.
'''
mdfn = self.FindAndParseMetadata(filename)
self.data = numpy.load(filename)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
def LoadImageSeries(self, filename):
#from PYME.FileUtils import readTiff
from PYME.Analysis.DataSources import ImageSeriesDataSource
self.dataSource = ImageSeriesDataSource.DataSource(filename, None)
self.dataSource = BufferedDataSource.DataSource(self.dataSource, min(self.dataSource.getNumSlices(), 50))
self.data = self.dataSource #this will get replaced with a wrapped version
#self.data = readTiff.read3DTiff(filename)
self.FindAndParseMetadata(filename)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
def LoadImageSeries(self, filename):
#from PYME.FileUtils import readTiff
from PYME.Analysis.DataSources import ImageSeriesDataSource
self.dataSource = ImageSeriesDataSource.DataSource(filename, None)
self.dataSource = BufferedDataSource.DataSource(
self.dataSource, min(self.dataSource.getNumSlices(), 50))
self.data = self.dataSource #this will get replaced with a wrapped version
#self.data = readTiff.read3DTiff(filename)
self.FindAndParseMetadata(filename)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
def LoadPSF(self, filename):
'''Load PYME .psf data.
.psf files consist of a tuple containing the data and the voxelsize.
'''
self.data, vox = numpy.load(filename)
self.mdh = MetaData.ConfocDefault
self.mdh.setEntry('voxelsize.x', vox.x)
self.mdh.setEntry('voxelsize.y', vox.y)
self.mdh.setEntry('voxelsize.z', vox.z)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'psf'
def LoadPSF(self, filename):
'''Load PYME .psf data.
.psf files consist of a tuple containing the data and the voxelsize.
'''
self.data, vox = numpy.load(filename)
self.mdh = MetaData.ConfocDefault
self.mdh.setEntry('voxelsize.x', vox.x)
self.mdh.setEntry('voxelsize.y', vox.y)
self.mdh.setEntry('voxelsize.z', vox.z)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'psf'
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 LoadDBL(self, filename):
'''Load Bewersdorf custom STED data.
'''
mdfn = self.FindAndParseMetadata(filename)
self.data = numpy.memmap(filename,
dtype='<f4',
mode='r',
offset=128,
shape=(self.mdh['Camera.ROIWidth'],
self.mdh['Camera.ROIHeight'],
self.mdh['NumImages']),
order='F')
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
def LoadKdf(self, filename):
'''load khorus formatted data - pretty much deprecated by now'''
import PYME.cSMI as cSMI
self.data = cSMI.CDataStack_AsArray(cSMI.CDataStack(filename), 0).squeeze()
self.mdh = MetaData.TIRFDefault
try: #try and get metadata from the .log file
lf = open(os.path.splitext(filename)[0] + '.log')
from PYME.DSView import logparser
lp = logparser.logparser()
log = lp.parse(lf.read())
lf.close()
self.mdh.setEntry('voxelsize.z', log['PIEZOS']['Stepsize'])
except:
pass
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'psf'
def LoadKdf(self, filename):
'''load khorus formatted data - pretty much deprecated by now'''
import PYME.cSMI as cSMI
self.data = cSMI.CDataStack_AsArray(cSMI.CDataStack(filename),
0).squeeze()
self.mdh = MetaData.TIRFDefault
try: #try and get metadata from the .log file
lf = open(os.path.splitext(filename)[0] + '.log')
from PYME.DSView import logparser
lp = logparser.logparser()
log = lp.parse(lf.read())
lf.close()
self.mdh.setEntry('voxelsize.z', log['PIEZOS']['Stepsize'])
except:
pass
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'psf'
def LoadTiff(self, filename):
#from PYME.FileUtils import readTiff
from PYME.Analysis.DataSources import TiffDataSource
mdfn = self.FindAndParseMetadata(filename)
self.dataSource = TiffDataSource.DataSource(filename, None)
self.dataSource = BufferedDataSource.DataSource(self.dataSource, min(self.dataSource.getNumSlices(), 50))
self.data = self.dataSource #this will get replaced with a wrapped version
#if we have a multi channel data set, try and pull in all the channels
if 'ChannelFiles' in self.mdh.getEntryNames():
try:
from PYME.DSView.dataWrap import ListWrap
#pull in all channels
chans = []
for cf in self.mdh.getEntry('ChannelFiles'):
cfn = os.path.join(os.path.split(filename)[0], cf)
ds = TiffDataSource.DataSource(cfn, None)
ds = BufferedDataSource.DataSource(ds, min(ds.getNumSlices(), 50))
chans.append(ds)
self.data = ListWrap(chans) #this will get replaced with a wrapped version
self.filename = mdfn
except:
pass
elif 'ChannelNames' in self.mdh.getEntryNames() and len(self.mdh['ChannelNames']) == self.data.getNumSlices():
from PYME.DSView.dataWrap import ListWrap
chans = [numpy.atleast_3d(self.data.getSlice(i)) for i in range(len(self.mdh['ChannelNames']))]
self.data = ListWrap(chans)
elif filename.endswith('.lsm') and 'LSM.images_number_channels' in self.mdh.keys() and self.mdh['LSM.images_number_channels'] > 1:
from PYME.DSView.dataWrap import ListWrap
nChans = self.mdh['LSM.images_number_channels']
chans = []
for n in range(nChans):
ds = TiffDataSource.DataSource(filename, None, n)
ds = BufferedDataSource.DataSource(ds, min(ds.getNumSlices(), 50))
chans.append(ds)
self.data = ListWrap(chans)
#self.data = readTiff.read3DTiff(filename)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
def OnBStartSpoolButton(self, event=None, stack=False):
'''GUI callback to start spooling.
NB: this is also called programatically by the start stack button.'''
#fn = wx.FileSelector('Save spooled data as ...', default_extension='.log',wildcard='*.log')
#if not fn == '': #if the user cancelled
# self.spooler = Spooler.Spooler(self.scope, fn, self.scope.pa, self)
# self.bStartSpool.Enable(False)
# self.bStopSpooling.Enable(True)
# self.stSpoolingTo.Enable(True)
# self.stNImages.Enable(True)
# self.stSpoolingTo.SetLabel('Spooling to ' + fn)
# self.stNImages.SetLabel('0 images spooled in 0 minutes')
fn = self.tcSpoolFile.GetValue()
if fn == '': #sanity checking
wx.MessageBox('Please enter a series name', 'No series name given',
wx.OK)
return #bail
if not os.path.exists(self.dirname):
os.makedirs(self.dirname)
if not self.dirname[-1] == os.sep:
self.dirname += os.sep
if (fn + '.h5') in os.listdir(
self.dirname): #check to see if data with the same name exists
ans = wx.MessageBox('A series with the same name already exists',
'Error', wx.OK)
#overwriting doesn't work ... so just bail
#increment the series counter first, though, so hopefully we don't get the same error on the next try
self.seriesCounter += 1
self.seriesName = self._GenSeriesName()
self.tcSpoolFile.SetValue(self.seriesName)
#if ans == wx.NO:
return #bail
if self.cbCompress.GetValue():
compLevel = 2
else:
compLevel = 0
if stack:
protocol = self.protocolZ
print(protocol)
else:
protocol = self.protocol
if not preflight.ShowPreflightResults(self,
self.protocol.PreflightCheck()):
return #bail if we failed the pre flight check, and the user didn't choose to continue
spoolType = self.rbQueue.GetStringSelection()
#if self.cbQueue.GetValue():
if spoolType == 'Queue':
self.queueName = getRelFilename(self.dirname + fn + '.h5')
self.spooler = QueueSpooler.Spooler(self.scope,
self.queueName,
self.scope.pa,
protocol,
self,
complevel=compLevel)
self.bAnalyse.Enable(True)
elif spoolType == 'HTTP':
self.queueName = self.dirname + fn + '.h5'
self.spooler = HTTPSpooler.Spooler(self.scope,
self.queueName,
self.scope.pa,
protocol,
self,
complevel=compLevel)
self.bAnalyse.Enable(True)
else:
self.spooler = HDFSpooler.Spooler(self.scope,
self.dirname + fn + '.h5',
self.scope.pa,
protocol,
self,
complevel=compLevel)
#if stack:
# self.spooler.md.setEntry('ZStack', True)
self.bStartSpool.Enable(False)
self.bStartStack.Enable(False)
self.bStopSpooling.Enable(True)
self.stSpoolingTo.Enable(True)
self.stNImages.Enable(True)
self.stSpoolingTo.SetLabel('Spooling to ' + fn)
self.stNImages.SetLabel('0 images spooled in 0 minutes')
if sampInf:
sampleInformation.getSampleData(self, self.spooler.md)
def OnBStartSpoolButton(self, event=None, stack=False):
'''GUI callback to start spooling.
NB: this is also called programatically by the start stack button.'''
#fn = wx.FileSelector('Save spooled data as ...', default_extension='.log',wildcard='*.log')
#if not fn == '': #if the user cancelled
# self.spooler = Spooler.Spooler(self.scope, fn, self.scope.pa, self)
# self.bStartSpool.Enable(False)
# self.bStopSpooling.Enable(True)
# self.stSpoolingTo.Enable(True)
# self.stNImages.Enable(True)
# self.stSpoolingTo.SetLabel('Spooling to ' + fn)
# self.stNImages.SetLabel('0 images spooled in 0 minutes')
fn = self.tcSpoolFile.GetValue()
if fn == '': #sanity checking
wx.MessageBox('Please enter a series name', 'No series name given', wx.OK)
return #bail
if not os.path.exists(self.dirname):
os.makedirs(self.dirname)
if not self.dirname[-1] == os.sep:
self.dirname += os.sep
if (fn + '.h5') in os.listdir(self.dirname): #check to see if data with the same name exists
ans = wx.MessageBox('A series with the same name already exists', 'Error', wx.OK)
#overwriting doesn't work ... so just bail
#increment the series counter first, though, so hopefully we don't get the same error on the next try
self.seriesCounter +=1
self.seriesName = self._GenSeriesName()
self.tcSpoolFile.SetValue(self.seriesName)
#if ans == wx.NO:
return #bail
if self.cbCompress.GetValue():
compLevel = 2
else:
compLevel = 0
if stack:
protocol = self.protocolZ
print(protocol)
else:
protocol = self.protocol
if not preflight.ShowPreflightResults(self, self.protocol.PreflightCheck()):
return #bail if we failed the pre flight check, and the user didn't choose to continue
spoolType = self.rbQueue.GetStringSelection()
#if self.cbQueue.GetValue():
if spoolType == 'Queue':
self.queueName = getRelFilename(self.dirname + fn + '.h5')
self.spooler = QueueSpooler.Spooler(self.scope, self.queueName, self.scope.pa, protocol, self, complevel=compLevel)
self.bAnalyse.Enable(True)
elif spoolType == 'HTTP':
self.queueName = self.dirname + fn + '.h5'
self.spooler = HTTPSpooler.Spooler(self.scope, self.queueName, self.scope.pa, protocol, self, complevel=compLevel)
self.bAnalyse.Enable(True)
else:
self.spooler = HDFSpooler.Spooler(self.scope, self.dirname + fn + '.h5', self.scope.pa, protocol, self, complevel=compLevel)
#if stack:
# self.spooler.md.setEntry('ZStack', True)
self.bStartSpool.Enable(False)
self.bStartStack.Enable(False)
self.bStopSpooling.Enable(True)
self.stSpoolingTo.Enable(True)
self.stNImages.Enable(True)
self.stSpoolingTo.SetLabel('Spooling to ' + fn)
self.stNImages.SetLabel('0 images spooled in 0 minutes')
if sampInf:
sampleInformation.getSampleData(self, self.spooler.md)
def LoadTiff(self, filename):
#from PYME.FileUtils import readTiff
from PYME.Analysis.DataSources import TiffDataSource
mdfn = self.FindAndParseMetadata(filename)
self.dataSource = TiffDataSource.DataSource(filename, None)
self.dataSource = BufferedDataSource.DataSource(
self.dataSource, min(self.dataSource.getNumSlices(), 50))
self.data = self.dataSource #this will get replaced with a wrapped version
#if we have a multi channel data set, try and pull in all the channels
if 'ChannelFiles' in self.mdh.getEntryNames():
try:
from PYME.DSView.dataWrap import ListWrap
#pull in all channels
chans = []
for cf in self.mdh.getEntry('ChannelFiles'):
cfn = os.path.join(os.path.split(filename)[0], cf)
ds = TiffDataSource.DataSource(cfn, None)
ds = BufferedDataSource.DataSource(
ds, min(ds.getNumSlices(), 50))
chans.append(ds)
self.data = ListWrap(
chans) #this will get replaced with a wrapped version
self.filename = mdfn
except:
pass
elif 'ChannelNames' in self.mdh.getEntryNames() and len(
self.mdh['ChannelNames']) == self.data.getNumSlices():
from PYME.DSView.dataWrap import ListWrap
chans = [
numpy.atleast_3d(self.data.getSlice(i))
for i in range(len(self.mdh['ChannelNames']))
]
self.data = ListWrap(chans)
elif filename.endswith(
'.lsm') and 'LSM.images_number_channels' in self.mdh.keys(
) and self.mdh['LSM.images_number_channels'] > 1:
from PYME.DSView.dataWrap import ListWrap
nChans = self.mdh['LSM.images_number_channels']
chans = []
for n in range(nChans):
ds = TiffDataSource.DataSource(filename, None, n)
ds = BufferedDataSource.DataSource(ds,
min(ds.getNumSlices(), 50))
chans.append(ds)
self.data = ListWrap(chans)
#self.data = readTiff.read3DTiff(filename)
from PYME.ParallelTasks.relativeFiles import getRelFilename
self.seriesName = getRelFilename(filename)
self.mode = 'default'
