python-microscopy/PYME/Analysis/MetaData.py at master · python-microscopy/python-microscopy

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#!/usr/bin/python

##################

# MetaData.py

# Copyright David Baddeley, 2009

# [email protected]

# This program is free software: you can redistribute it and/or modify

# it under the terms of the GNU General Public License as published by

# the Free Software Foundation, either version 3 of the License, or

# (at your option) any later version.

# This program is distributed in the hope that it will be useful,

# but WITHOUT ANY WARRANTY; without even the implied warranty of

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License

# along with this program. If not, see <http://www.gnu.org/licenses/>.

##################

import numpy

from PYME.IO.MetaDataHandler import NestedClassMDHandler, HDFMDHandler

from PYME import pyme_warnings as warnings

#class VoxelSize:

# def __init__(self, x, y, z, unit='um'):

# self.x = x

# self.y = y

# self.z = z

# self.unit = unit

#class CCDMetaDataIXonDefault:

# #all at 10Mhz, e.m. amplifier

# name = 'Andor IXon DV97'

# ADOffset = 1100 #counts (@ T ~ -70, em gain ~ 150)

# ReadNoise = 109.8 #electrons

# noiseFactor = 1.41

# electronsPerCount = 27.32

#class MetaData:

# def __init__(self, voxSize, CCDMD = None):

# self.voxelsize = voxSize

# self.CCD = CCDMD

##FIXME - THIS SHOULD ALL BE EXTRACTED FROM LOG FILES OR THE LIKE

#TIRFDefault = MetaData(VoxelSize(0.07, 0.07, 0.2), CCDMetaDataIXonDefault())

# NOTE - if using these metadatahandlers as defaults be sure to

# copy into a new metadatahandler rather than using them directly

TIRFDefault = NestedClassMDHandler()

#voxelsize

TIRFDefault.setEntry('voxelsize.x',0.07)

TIRFDefault.setEntry('voxelsize.y',0.07)

TIRFDefault.setEntry('voxelsize.z',0.2)

TIRFDefault.setEntry('voxelsize.units','um')

#camera properties - for Andor camera - see above

#TIRFDefault.setEntry('Camera.ADOffset',1100)

TIRFDefault.setEntry('Camera.ReadNoise',109.8)

TIRFDefault.setEntry('Camera.NoiseFactor',1.41)

TIRFDefault.setEntry('Camera.ElectronsPerCount',27.32)

TIRFDefault.setEntry('Camera.TrueEMGain',20) #mostly use gain register setting of 150 - this will hopefully be overwitten

ConfocDefault = NestedClassMDHandler()

#voxelsize

ConfocDefault.setEntry('voxelsize.x',0.09)

ConfocDefault.setEntry('voxelsize.y',0.09)

ConfocDefault.setEntry('voxelsize.z',0.2)

ConfocDefault.setEntry('voxelsize.units','um')

#camera properties - placeholder values - real vlaues will depend on gain etc...

ConfocDefault.setEntry('Camera.ReadNoise',0)

ConfocDefault.setEntry('Camera.NoiseFactor',1)

ConfocDefault.setEntry('Camera.ElectronsPerCount',1)

ConfocDefault.setEntry('Camera.TrueEMGain',1)

ConfocDefault.setEntry('Camera.ADOffset',0)

ConfocDefault.setEntry('tIndex',0)

#bare bones metadata

BareBones = NestedClassMDHandler()

#voxelsize

BareBones.setEntry('voxelsize.units','um')

#camera properties - placeholder values - real vlaues will depend on gain etc...

BareBones.setEntry('Camera.ReadNoise',0)

BareBones.setEntry('Camera.NoiseFactor',1)

BareBones.setEntry('Camera.ElectronsPerCount',1)

BareBones.setEntry('Camera.TrueEMGain',1)

BareBones.setEntry('Camera.ADOffset',0)

BareBones.setEntry('tIndex',0)

#PCO default metadata

PCODefault = NestedClassMDHandler()

#voxelsize

PCODefault.setEntry('voxelsize.x',0.07)

PCODefault.setEntry('voxelsize.y',0.07)

PCODefault.setEntry('voxelsize.z',0.2)

PCODefault.setEntry('voxelsize.units','um')

#camera properties - for Andor camera - see above

#TIRFDefault.setEntry('Camera.ADOffset',1100)

PCODefault.setEntry('Camera.ReadNoise',4)

PCODefault.setEntry('Camera.NoiseFactor',1)

PCODefault.setEntry('Camera.ElectronsPerCount',2)

PCODefault.setEntry('Camera.TrueEMGain',1) #mostly use gain register setting of 150 - this will hopefully be overwitten

#def genMetaDataFromHDF(h5File):

# md = TIRFDefault

# if 'MetaData' in h5File.root: #should be true the whole time

# mdh5 = HDFMDHandler(h5File)

# md.copyEntriesFrom(mdh5)

# #once we start putting everything into data file properly,

# #grab the relavant bits here

# #Guestimate when the laser was turned on

# #Laser turn on will result in large spike - look at derivative

# dI = numpy.diff(h5File.root.ImageData[:200, :,:].mean(2).mean(1))

# tLon = numpy.argmax(dI)

# print tLon

# dIm = dI[tLon]

# #Now do some sanity checks ...

# if tLon > 100: #shouldn't bee this late

# tLon = 0

# #expect magnitude of differential to be much larger at turn on than later ...

# elif not dIm > 10*dI[(tLon + 50):(tLon + 100)].max():

# tLon = 0 # assume laser was already on

# #also expect the intensity to be decreasing after the initial peak faster than later on in the piece

# elif not dI[(tLon + 5):(tLon + 15)].mean() < -abs(dI[(tLon + 50):(tLon + 100)].mean()):

# tLon = 0

# md.setEntry('EstimatedLaserOnFrameNo', tLon)

# #Estimate the offset during the dark time before laser was turned on

# #N.B. this will not work if other lights (e.g. room lights, arc lamp etc... are on

# if not tLon == 0:

# md.setEntry('Camera.ADOffset', numpy.median(h5File.root.ImageData[:max(tLon - 1, 1), :,:].ravel()))

# else: #if laser was on to start with our best estimate is at maximal bleaching where the few molecules that are still on will hopefully have little influence on the median

# md.setEntry('Camera.ADOffset',numpy.median(h5File.root.ImageData[-5:, :,:].ravel()))

# print """WARNING: No clear laser turn on signature found - assuming laser was already on

# and fudging ADOffset Estimation"""

# if not 'MetaData' in h5File.root:

# #something went wrong - should only happen for very early (mid 2008) .h5 files or for files taken

# #in last couple of weeks of Jan 2009

# import wx

# if not None == wx.GetApp():

# wx.MessageBox('Guessing that the EM Gain setting was 150 - if this is wrong fix in console', 'ERROR: No metadata fond in file ...', wx.ERROR|wx.OK)

# print 'ERROR: No metadata fond in file ... Guessing that the EM Gain setting was 150'

# md.setEntry('Camera.TrueEMGain', 20)

# return md

# #Quick hack for approximate EMGain for gain register settings of 150 & 200

# #FIXME to use a proper calibration

# if 'Camera.EMGain' in md.getEntryNames():

# if md.Camera.EMGain == 200: #gain register setting

# md.setEntry('Camera.TrueEMGain', 100) #real gain @ -50C - from curve in performance book - need proper calibration

# elif md.Camera.EMGain == 150: #gain register setting

# md.setEntry('Camera.TrueEMGain', 20) #real gain @ -50C - need proper calibration

# else: #early file, or from camera without EMGain - assume early file - gain was usually 150

# md.setEntry('Camera.TrueEMGain', 20)

# if 'Camera.Name' in md.getEntryNames(): #new improved metadata

# if md.Camera.Name == 'Simulated Standard CCD Camera': #em gain for simulated camera is _real_ em gain rather than gain register setting

# md.Camera.TrueEMGain = md.Camera.EMGain

# return md

def genMetaDataFromSourceAndMDH(dataSource, mdh=None):

md = TIRFDefault

if not mdh is None: #should be true the whole time

md.copyEntriesFrom(mdh)

#guestimate whatever wasn't in the metadata from remaining metadata

#and image data

fillInBlanks(md, dataSource)

return md

def fillInBlanks(md, dataSource):

if 'Protocol.DataStartsAt' in md.getEntryNames():

md.setEntry('EstimatedLaserOnFrameNo', md.getEntry('Protocol.DataStartsAt'))

if not 'Protocol.DataStartsAt' in md.getEntryNames() and not 'EstimatedLaserOnFrameNo' in md.getEntryNames():

# FIXME - Do we still need this - this is a backwards compatibility fix for **really** old files

#Guestimate when the laser was turned on

if dataSource.getNumSlices() < 200: #not long enough to bother

md.setEntry('EstimatedLaserOnFrameNo', 0)

else:

#mean intensity in first 200 frames

I_t = numpy.array([dataSource.getSlice(i).mean(1).mean(0) for i in range(200)])

#Laser turn on will result in large spike - look at derivative

dI = numpy.diff(I_t)

tLon = numpy.argmax(dI)

#print tLon

dIm = dI[tLon]

#Now do some sanity checks ...

if tLon > 100: #shouldn't bee this late

tLon = 0

#expect magnitude of differential to be much larger at turn on than later ...

elif not dIm > 10*dI[(tLon + 50):(tLon + 100)].max():

tLon = 0 # assume laser was already on

#also expect the intensity to be decreasing after the initial peak faster than later on in the piece

elif not dI[(tLon + 5):(tLon + 15)].mean() < -abs(dI[(tLon + 50):(tLon + 100)].mean()):

tLon = 0

md.setEntry('EstimatedLaserOnFrameNo', tLon)

if not 'Camera.ADOffset' in md.getEntryNames():

if 'Protocol.DarkFrameRange' in md.getEntryNames(): #prefered way

darkFrStart, darkFrStop = md.getEntry('Protocol.DarkFrameRange')

md.setEntry('Camera.ADOffset', numpy.median(numpy.array([dataSource.getSlice(i) for i in range(darkFrStart,darkFrStop)]).ravel()))

else: #use hueristics

tLon = md.getOrDefault('EstimatedLaserOnFrameNo', 0)

#Estimate the offset during the dark time before laser was turned on

#N.B. this will not work if other lights (e.g. room lights, arc lamp etc... are on

if not tLon == 0:

md.setEntry('Camera.ADOffset', numpy.median(numpy.array([dataSource.getSlice(i) for i in range(0, max(tLon - 1, 1))]).ravel()))

else: #if laser was on to start with our best estimate is at maximal bleaching where the few molecules that are still on will hopefully have little influence on the median

md.setEntry('Camera.ADOffset', numpy.median(numpy.array([dataSource.getSlice(i) for i in range(0, min(10, dataSource.getNumSlices()))]).ravel()))

warnings.warn("ADOffset fudged as %d and probably wrong\n\nTo change ADOffset, execute the following in the console: image.mdh['Camera.ADOffset'] = newValue\n\nOr use the Metadata pane in the GUI (right click on value to change)" % md.getEntry('Camera.ADOffset'))#,'Did not find laser turn on signature')

#md.setEntry('Camera.ADOffset',numpy.median(numpy.array([dataSource.getSlice(i) for i in range(dataSource.getNumSlices()-5, dataSource.getNumSlices())]).ravel()))

#print """WARNING: No clear laser turn on signature found - assuming laser was already on

# and fudging ADOffset Estimation"""

fixEMGain(md)

def fixEMGain(md):

#Quick hack for approximate EMGain for gain register settings of 150 & 200

#FIXME to use a proper calibration

if 'Camera.EMGain' in md.getEntryNames() and not 'Camera.TrueEMGain' in md.getEntryNames():

if md.getEntry('Camera.EMGain') == 200: #gain register setting

md.setEntry('Camera.TrueEMGain', 100) #real gain @ -50C - from curve in performance book - need proper calibration

elif md.getEntry('Camera.EMGain') == 150: #gain register setting

md.setEntry('Camera.TrueEMGain', 20) #real gain @ -50C - need proper calibration

elif md.getOrDefault('Camera.EMGain', 0) == 0:

md.setEntry('Camera.TrueEMGain', 1.0)

if 'Camera.Name' in md.getEntryNames(): #new improved metadata

if md.getEntry('Camera.Name') == 'Simulated Standard CCD Camera': #em gain for simulated camera is _real_ em gain rather than gain register setting

md.setEntry('Camera.TrueEMGain', md.getEntry('Camera.EMGain'))

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