def convolveDisk(bimage, radius, convolve_t, testlog):
#make disk binaray image
disk = makeDisk(radius)
diskshape = numpy.shape(disk)
# convolve
c = convolver.Convolver()
intimage = bimage.astype(numpy.int8)
c.setKernel(disk)
cmask = c.convolve(image=intimage)
# convolve two disks to get maximum correlation
c = convolver.Convolver()
c.setKernel(disk)
cref = c.convolve(image=disk)
testlog = outputTestImage(cmask, 'maskc', 'Convolved filled edge mask',
testlog)
# Thresholding to binary mask
cmax = cref.max() * convolve_t
masked_cmask = ma.masked_greater(cmask, cmax)
mask = ma.getmask(masked_cmask)
testlog = outputTestImage(mask, 'maskct', 'Thresholded Convolved mask',
testlog)
return mask, testlog
def __init__(self, node):
self.node = node
## if tilts are below these thresholds, no need to correct
self.alpha_threshold = 0.02
self.bt_threshold = 0.000001
gauss = convolver.gaussian_kernel(2.0)
self.filter = convolver.Convolver(kernel=gauss)
def __init__(self):
## These are the results that are maintained by this
## object for external use through the __getitem__ method.
self.__results = {
'original': None,
'template': None,
'correlation': None,
'threshold': None,
'blobs': None,
'vector': None,
'lattice': None,
'holes': None,
'markedholes': None,
'holes2': None,
'markedholes2': None,
}
## This defines which dependent results should be cleared
## when a particular result is updated.
## Read this as:
## If you update key, clear everything in the dependent tuple
self.__dependents = {
'original': ('correlation', ),
'template': ('correlation', ),
'correlation': ('threshold', 'blobs'),
'threshold': ('blobs', 'vector'),
'blobs': ('lattice', ),
'vector': ('lattice', ),
'lattice': ('holes', ),
'holes': ('holes2', 'markedholes'),
'markedholes': (),
'holes2': ('markedholes2', ),
'markedholes2': (),
}
## other necessary components
self.convolver = convolver.Convolver()
self.peakfinder = peakfinder.PeakFinder()
self.circle = CircleMaskCreator()
self.icecalc = ice.IceCalculator()
## some default configuration parameters
self.save_mrc = False
self.template_config = {'ring_list': [(25, 30)]}
self.correlation_config = {'cortype': 'cross', 'corfilt': (1.0, )}
self.threshold = 3.0
self.threshold_method = "Threshold = mean + A * stdev"
self.blobs_config = {'border': 20, 'maxblobsize': 50, 'maxblobs': 100}
self.lattice_config = {
'tolerance': 0.1,
'vector': 100.0,
'minspace': 20,
'extend': 'off'
}
self.holestats_config = {'radius': 20}
self.ice_config = {'i0': None, 'min': 0.0, 'max': 0.1, 'std': 0.05}
def __init__(self):
## These are the results that are maintained by this
## object for external use through the __getitem__ method.
self.__results = {
'original': None,
'edges': None,
'template': None,
'correlation': None,
'threshold': None,
'blobs': None,
'holes': None,
'markedholes': None,
}
## This defines which dependent results should be cleared
## when a particular result is updated.
## Read this as:
## If you update key, clear everything in the dependent tuple
self.__dependents = {
'original': ('edges', ),
'edges': ('correlation', ),
'template': ('correlation', ),
'correlation': ('threshold', ),
'threshold': ('blobs', ),
'blobs': (),
'holes': ('markedholes', ),
'markedholes': (),
}
## other necessary components
self.edgefinder = convolver.Convolver()
self.peakfinder = peakfinder.PeakFinder()
self.circle = CircleMaskCreator()
self.oval = OvalMaskCreator()
self.icecalc = ice.IceCalculator()
## some default configuration parameters
self.save_mrc = False
self.edges_config = {
'filter': 'sobel',
'size': 9,
'sigma': 1.4,
'abs': False,
'lp': True,
'lpsig': 1.0,
'thresh': 100.0,
'edges': True
}
self.template_config = {'ring_list': [(25, 30)], 'tilt_axis': 0.0}
self.correlation_config = {'cortype': 'cross', 'corfilt': (1.0, )}
self.threshold = 3.0
self.blobs_config = {'border': 20, 'maxblobsize': 50, 'maxblobs': 100}
self.makeblobs_config = {'center_list': [(100, 100)]}
self.dist_config = {'binned_pixel': 2e-10}
self.pickhole_config = {'center_list': [(100, 100)]}
self.holestats_config = {'radius': 20}
def filterImg(img, apix, bin, rad):
# low pass filter image to res resolution
if rad == 0:
print " ... skipping low pass filter"
return (img)
else:
print " ... performing low pass filter"
sigma = float(rad) / apix / 3.0 / float(bin)
kernel = convolver.gaussian_kernel(sigma)
c = convolver.Convolver()
return (c.convolve(image=img, kernel=kernel))
def __init__(self, id, session, managerlocation, **kwargs):
self.mosaicselectionmapping = {}
targetfinder.ClickTargetFinder.__init__(self, id, session,
managerlocation, **kwargs)
self.calclients = {
'image shift':
calibrationclient.ImageShiftCalibrationClient(self),
'stage position':
calibrationclient.StageCalibrationClient(self),
'modeled stage position':
calibrationclient.ModeledStageCalibrationClient(self)
}
self.images = {
'Original': None,
'Extra Crispy': None,
'Filtered': None,
'Thresholded': None
}
parameter = self.settings['calibration parameter']
self.mosaic = mosaic.EMMosaic(self.calclients[parameter])
self.mosaicimagelist = None
self.mosaicimage = None
self.mosaicimagescale = None
self.mosaicimagedata = None
self.convolver = convolver.Convolver()
self.currentposition = []
self.mosaiccreated = threading.Event()
self.presetsclient = presets.PresetsClient(self)
self.mosaic.setCalibrationClient(self.calclients[parameter])
self.existing_targets = {}
self.clearTiles()
self.reference_target = None
if self.__class__ == MosaicClickTargetFinder:
self.start()
def __init__(self):
self.peakfinder = peakfinder.PeakFinder()
self.conv = convolver.Convolver()
def __init__(self):
Plugin.__init__(self)
self.convolver = convolver.Convolver()
