# > Input parameter
numFramesToAnalyze = 1
fitMod = 'LatGaussFitFR'
threshold = 1.0
bIndiceRange = [-20, 0]
# > File names
# filename = r'data\1004x1002.tif'
filename = r'data\100x140x170.tif'
# > Metadata
metadata = NestedClassMDHandler()
metadata.setEntry('voxelsize.x', 0.08)
metadata.setEntry('voxelsize.y', 0.08)
metadata.setEntry('voxelsize.z', 0.2)
metadata.setEntry('voxelsize.units', 'um')
metadata.setEntry('Camera.ADOffset', 0)
metadata.setEntry('Camera.ReadNoise', 0)
metadata.setEntry('Camera.NoiseFactor', 1)
metadata.setEntry('Camera.ElectronsPerCount', 1)
metadata.setEntry('Camera.TrueEMGain', 1)
metadata.setEntry('Analysis.FitModule', fitMod)
# > Runtime arguments
results = []
# 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())
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()
# 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())
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)
# region : Initialize parameters
# > Input parameter
numFramesToAnalyze = 5
fitMod = 'LatGaussFitFR'
threshold = 0.6
bIndiceRange = [-20, 0]
# > File names
filename = r'data\100x140x170.tif'
# > Metadata
metadata = NestedClassMDHandler()
metadata.setEntry('voxelsize.x', 0.08)
metadata.setEntry('voxelsize.y', 0.08)
metadata.setEntry('voxelsize.z', 0.2)
metadata.setEntry('voxelsize.units', 'um')
metadata.setEntry('Camera.ADOffset', 0)
metadata.setEntry('Camera.ReadNoise', 0)
metadata.setEntry('Camera.NoiseFactor', 1)
metadata.setEntry('Camera.ElectronsPerCount', 1)
metadata.setEntry('Camera.TrueEMGain', 1)
metadata.setEntry('Analysis.FitModule', fitMod)
# > Runtime arguments
results = []