def combine_maps(maps, return_validMap=False):
destarr = None
mapimgs = []
for map in maps:
mapimg = ImageStack(filename=map)
mapimgs.append(mapimg)
if destarr is None:
mdh = NestedClassMDHandler(mapimg.mdh)
destarr = mkdestarr(mapimg)
validMap = np.zeros_like(destarr, dtype='int')
else:
checkMapCompat(mapimg, mdh)
insertvmap(mapimg, destarr, validMap)
mdh.setEntry('CameraMap.combinedFromMaps', maps)
mdh.setEntry('CameraMap.ValidROI.ROIHeight',
mapimgs[0].mdh['Camera.SensorHeight'])
mdh.setEntry('CameraMap.ValidROI.ROIWidth',
mapimgs[0].mdh['Camera.SensorWidth'])
mdh.setEntry('CameraMap.ValidROI.ROIOriginX', 0)
mdh.setEntry('CameraMap.ValidROI.ROIOriginY', 0)
combinedMap = ImageStack(destarr, mdh=mdh)
if return_validMap:
vmdh = NestedClassMDHandler(mdh)
vmdh.setEntry('CameraMap.ValidMask', True)
return (combinedMap, ImageStack(validMap, mdh=vmdh))
else:
return combinedMap
def insert_into_full_map(dark, variance, metadata, sensor_size=(2048, 2048)):
"""
Embeds partial-sensor camera maps into full-sized camera map by padding with basic values in metadata. Alternatively
can be used to create boring maps to use in place of metadata scalars.
Parameters
----------
dark: ndarray or None
darkmap for valid ROI, or None to generate a uniform, ~useless metadata map
variance: ndarray
variance for valid ROI, or None to generate a uniform, ~useless metadata map
metadata: dict-like
ROI informatrion and camera noise parameters to use when padding maps
sensor_size: 2-int tuple
x and y camera sensor size
Returns
-------
full_dark: ndarray
padded dark map
full_var: ndarray
padded variance map
mdh: PYME.IO.MetadataHandler.NestedClassMDHandler
metadata handler to be associated with full maps while maintaining information about the original/valid ROI.
"""
mdh = NestedClassMDHandler()
mdh.copyEntriesFrom(metadata)
mdh.setEntry('Analysis.name', 'mean-variance')
x_origin, y_origin = get_camera_roi_origin(mdh)
mdh.setEntry('Analysis.valid.ROIOriginX', x_origin)
mdh.setEntry('Analysis.valid.ROIOriginY', y_origin)
mdh.setEntry('Analysis.valid.ROIWidth', mdh['Camera.ROIWidth'])
mdh.setEntry('Analysis.valid.ROIHeight', mdh['Camera.ROIHeight'])
mdh['Camera.ROIOriginX'], mdh['Camera.ROIOriginY'] = 0, 0
mdh['Camera.ROIWidth'], mdh['Camera.ROIHeight'] = sensor_size
mdh['Camera.ROI'] = (0, 0, sensor_size[0], sensor_size[1])
if dark is not None and variance is not None:
full_dark = mdh['Camera.ADOffset'] * np.ones(sensor_size,
dtype=dark.dtype)
full_var = (mdh['Camera.ReadNoise']**2) * np.ones(sensor_size,
dtype=variance.dtype)
xslice = slice(x_origin, x_origin + metadata['Camera.ROIWidth'])
yslice = slice(y_origin, y_origin + metadata['Camera.ROIHeight'])
full_dark[xslice, yslice] = dark
full_var[xslice, yslice] = variance
else:
logger.warning('Generating uniform maps')
full_dark = mdh['Camera.ADOffset'] * np.ones(sensor_size)
full_var = (mdh['Camera.ReadNoise']**2) * np.ones(sensor_size)
return full_dark, full_var, mdh
def insertIntoFullMap(m, ve, smdh, chipsize=(2048, 2048)):
x0, y0 = get_camera_roi_origin(smdh)
validROI = {
'PosX': x0 + 1,
'PosY': x0 + 1,
'Width': smdh['Camera.ROIWidth'],
'Height': smdh['Camera.ROIHeight']
}
bmdh = NestedClassMDHandler()
bmdh.copyEntriesFrom(smdh)
bmdh.setEntry('Analysis.name', 'mean-variance')
bmdh.setEntry('Analysis.valid.ROIPosX', validROI['PosX'])
bmdh.setEntry('Analysis.valid.ROIPosY', validROI['PosY'])
bmdh.setEntry('Analysis.valid.ROIWidth', validROI['Width'])
bmdh.setEntry('Analysis.valid.ROIHeight', validROI['Height'])
bmdh['Camera.ROIOriginX'] = 0
bmdh['Camera.ROIOriginY'] = 0
bmdh['Camera.ROIWidth'] = chipsize[0]
bmdh['Camera.ROIHeight'] = chipsize[1]
bmdh['Camera.ROI'] = (0, 0, chipsize[0], chipsize[1])
if m is None:
mfull = np.zeros(chipsize, dtype='float64')
vefull = np.zeros(chipsize, dtype='float64')
else:
mfull = np.zeros(chipsize, dtype=m.dtype)
vefull = np.zeros(chipsize, dtype=ve.dtype)
mfull.fill(smdh['Camera.ADOffset'])
vefull.fill(smdh['Camera.ReadNoise']**2)
if m is not None:
mfull[validROI['PosX'] - 1:validROI['PosX'] - 1 + validROI['Width'],
validROI['PosY'] - 1:validROI['PosY'] - 1 +
validROI['Height']] = m
vefull[validROI['PosX'] - 1:validROI['PosX'] - 1 + validROI['Width'],
validROI['PosY'] - 1:validROI['PosY'] - 1 +
validROI['Height']] = ve
return mfull, vefull, bmdh
def main():
chipsize = (
2048, 2048
) # we currently assume this is correct but could be chosen based
# on camera model in meta data
darkthreshold = 1e4 # this really should depend on the gain mode (12bit vs 16 bit etc)
variancethreshold = 300**2 # again this is currently picked fairly arbitrarily
blemishvariance = 1e8
# options parsing
op = argparse.ArgumentParser(
description='generate offset and variance maps from darkseries.')
op.add_argument('filename',
metavar='filename',
nargs='?',
default=None,
help='filename of the darkframe series')
op.add_argument('-s',
'--start',
type=int,
default=0,
help='start frame to use')
op.add_argument('-e',
'--end',
type=int,
default=-1,
help='end frame to use')
op.add_argument('-u',
'--uniform',
action='store_true',
help='make uniform map using metadata info')
op.add_argument(
'-i',
'--install',
action='store_true',
help='install map in default location - the filename argument is a map'
)
op.add_argument(
'-d',
'--dir',
metavar='destdir',
default=None,
help='destination directory (default is PYME calibration path)')
op.add_argument('-l',
'--list',
action='store_true',
help='list all maps in default location')
args = op.parse_args()
if args.list:
listCalibrationDirs()
sys.exit(0)
# body of script
filename = args.filename
if filename is None:
op.error('need a file name if -l or --list not requested')
print('Opening image series...', file=sys.stderr)
source = im.ImageStack(filename=filename)
if args.install:
if source.mdh.getOrDefault('Analysis.name', '') != 'mean-variance':
print(
'Analysis.name is not equal to "mean-variance" - probably not a map',
file=sys.stderr)
sys.exit('aborting...')
if source.mdh['Analysis.resultname'] == 'mean':
maptype = 'dark'
else:
maptype = 'variance'
mapname = mkDefaultPath(maptype, source.mdh)
saveasmap(source.dataSource.getSlice(0), mapname, mdh=source.mdh)
sys.exit(0)
start = args.start
end = args.end
if end < 0:
end = int(source.dataSource.getNumSlices() + end)
print('Calculating mean and variance...', file=sys.stderr)
m, ve = (None, None)
if not args.uniform:
m, v = meanvards(source.dataSource, start=start, end=end)
eperADU = source.mdh['Camera.ElectronsPerCount']
ve = v * eperADU * eperADU
# occasionally the cameras seem to have completely unusable pixels
# one example was dark being 65535 (i.e. max value for 16 bit)
if m.max() > darkthreshold:
ve[m > darkthreshold] = blemishvariance
if ve.max() > variancethreshold:
ve[ve > variancethreshold] = blemishvariance
nbad = np.sum((m > darkthreshold) * (ve > variancethreshold))
# if the uniform flag is set, then m and ve are passed as None
# which makes sure that just the uniform defaults from meta data are used
mfull, vefull, basemdh = insertIntoFullMap(m,
ve,
source.mdh,
chipsize=chipsize)
#mfull, vefull, basemdh = (m, ve, source.mdh)
print('Saving results...', file=sys.stderr)
if args.dir is None:
print('installing in standard location...', file=sys.stderr)
mname = mkDefaultPath('dark', source.mdh)
vname = mkDefaultPath('variance', source.mdh)
else:
mname = mkDestPath(args.dir, 'dark', source.mdh)
vname = mkDestPath(args.dir, 'variance', source.mdh)
print('dark map -> %s...' % mname, file=sys.stderr)
print('var map -> %s...' % vname, file=sys.stderr)
commonMD = NestedClassMDHandler()
commonMD.setEntry('Analysis.name', 'mean-variance')
commonMD.setEntry('Analysis.start', start)
commonMD.setEntry('Analysis.end', end)
commonMD.setEntry('Analysis.SourceFilename', filename)
commonMD.setEntry('Analysis.darkThreshold', darkthreshold)
commonMD.setEntry('Analysis.varianceThreshold', variancethreshold)
commonMD.setEntry('Analysis.blemishVariance', blemishvariance)
commonMD.setEntry('Analysis.NBadPixels', nbad)
if args.uniform:
commonMD.setEntry('Analysis.isuniform', True)
mmd = NestedClassMDHandler(basemdh)
mmd.copyEntriesFrom(commonMD)
mmd.setEntry('Analysis.resultname', 'mean')
mmd.setEntry('Analysis.units', 'ADU')
vmd = NestedClassMDHandler(basemdh)
vmd.copyEntriesFrom(commonMD)
vmd.setEntry('Analysis.resultname', 'variance')
vmd.setEntry('Analysis.units', 'electrons^2')
saveasmap(mfull, mname, mdh=mmd)
saveasmap(vefull, vname, mdh=vmd)
# 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()
def main():
logging.basicConfig(
) # without it got 'No handlers could be found for logger...'
defaultSensorSize = (
2048, 2048
) # we currently assume this is correct but could be chosen based
# on camera model in meta data TODO - add CCD size to camera metadata
darkthreshold = 1e4 # this really should depend on the gain mode (12bit vs 16 bit etc)
variancethreshold = 300**2 # again this is currently picked fairly arbitrarily
blemishvariance = 1e8
# options parsing
op = argparse.ArgumentParser(
description='generate offset and variance maps from darkseries.')
op.add_argument('filename',
metavar='filename',
nargs='?',
default=None,
help='filename of the darkframe series')
op.add_argument('-s',
'--start',
type=int,
default=0,
help='start frame to use')
op.add_argument('-e',
'--end',
type=int,
default=-1,
help='end frame to use')
op.add_argument('-u',
'--uniform',
action='store_true',
help='make uniform map using metadata info')
op.add_argument(
'-i',
'--install',
action='store_true',
help='install map in default location - the filename argument is a map'
)
op.add_argument(
'-d',
'--dir',
metavar='destdir',
default=None,
help='destination directory (default is PYME calibration path)')
op.add_argument('-l',
'--list',
action='store_true',
help='list all maps in default location')
op.add_argument('-p',
'--prefix',
metavar='prefix',
default='',
help='prefix for dark/variance map filenames')
args = op.parse_args()
if args.list:
listCalibrationDirs()
sys.exit(0)
# body of script
filename = args.filename
prefix = args.prefix
if filename is None:
op.error('need a file name if -l or --list not requested')
if args.install:
#copy the map to the default maps directory
install_map(filename)
sys.exit(0)
logger.info('Opening image series...')
source = ImageStack(filename=filename)
start = args.start
end = args.end
if end < 0:
end = int(source.dataSource.getNumSlices() + end)
# pre-checks before calculations to minimise the pain
sensorSize = list(defaultSensorSize)
try:
sensorSize[0] = source.mdh['Camera.SensorWidth']
except AttributeError:
logger.warning('no valid sensor width in metadata - using default %d' %
sensorSize[0])
try:
sensorSize[1] = source.mdh['Camera.SensorHeight']
except AttributeError:
logger.warning(
'no valid sensor height in metadata - using default %d' %
sensorSize[1])
if not ((source.mdh['Camera.ROIWidth'] == sensorSize[0]) and
(source.mdh['Camera.ROIHeight'] == sensorSize[1])):
logger.warning(
'Generating a map from data with ROI set. Use with EXTREME caution.\nMaps should be calculated from the whole chip.'
)
if args.dir is None:
logger.error(
'Maps with an ROI set cannot be stored to the default map directory\nPlease specify an output directory.'
)
sys.exit(-1)
logger.info('Calculating mean and variance...')
m, ve = (None, None)
if not args.uniform:
m, v = _meanvards(source.dataSource, start=start, end=end)
eperADU = source.mdh['Camera.ElectronsPerCount']
ve = v * eperADU * eperADU
# occasionally the cameras seem to have completely unusable pixels
# one example was dark being 65535 (i.e. max value for 16 bit)
if m.max() > darkthreshold:
ve[m > darkthreshold] = blemishvariance
if ve.max() > variancethreshold:
ve[ve > variancethreshold] = blemishvariance
nbad = np.sum((m > darkthreshold) * (ve > variancethreshold))
else:
logger.warning('Simulating uniform maps - use with care')
nbad = 0
if args.dir is None:
logger.error(
'Uniform maps cannot be stored to the default map directory\nPlease specify an output directory.'
)
sys.exit(-1)
# if the uniform flag is set, then m and ve are passed as None
# which makes sure that just the uniform defaults from meta data are used
mfull, vefull, basemdh = insert_into_full_map(m,
ve,
source.mdh,
sensor_size=sensorSize)
logger.info('Saving results...')
if args.dir is None:
logger.info('installing in standard location...')
mname = mkDefaultPath('dark', source.mdh)
vname = mkDefaultPath('variance', source.mdh)
else:
mname = mkDestPath(args.dir, prefix + 'dark', source.mdh)
vname = mkDestPath(args.dir, prefix + 'variance', source.mdh)
logger.info('dark map -> %s...' % mname)
logger.info('var map -> %s...' % vname)
commonMD = NestedClassMDHandler()
commonMD.setEntry('Analysis.name', 'mean-variance')
commonMD.setEntry('Analysis.start', start)
commonMD.setEntry('Analysis.end', end)
commonMD.setEntry('Analysis.SourceFilename', filename)
commonMD.setEntry('Analysis.darkThreshold', darkthreshold)
commonMD.setEntry('Analysis.varianceThreshold', variancethreshold)
commonMD.setEntry('Analysis.blemishVariance', blemishvariance)
commonMD.setEntry('Analysis.NBadPixels', nbad)
if args.uniform:
commonMD.setEntry('Analysis.isuniform', True)
mmd = NestedClassMDHandler(basemdh)
mmd.copyEntriesFrom(commonMD)
mmd.setEntry('Analysis.resultname', 'mean')
mmd.setEntry('Analysis.units', 'ADU')
vmd = NestedClassMDHandler(basemdh)
vmd.copyEntriesFrom(commonMD)
vmd.setEntry('Analysis.resultname', 'variance')
vmd.setEntry('Analysis.units', 'electrons^2')
ImageStack(mfull, mdh=mmd).Save(filename=mname)
ImageStack(vefull, mdh=vmd).Save(filename=vname)