def runner(parser, options, args):
if not hasattr(parser, 'runner'):
options.psf_path = None
options.input_path = None
options.output_path = None
if args:
if len(args) in [2, 3]:
if options.psf_path:
print >> sys.stderr, "WARNING: overwriting psf path %r with %r" % (
options.psf_path, args[0])
options.psf_path = args[0]
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (
options.input_path, args[1])
options.input_path = args[1]
else:
parser.error(
"Incorrect number of arguments (expected 2 or 3 but got %r)" %
((args)))
if len(args) == 3:
if options.output_path:
print >> sys.stderr, "WARNING: overwriting output path %r with %r" % (
options.output_path, args[2])
options.output_path = args[2]
options.input_path = fix_path(options.input_path)
if options.output_path is None:
deconvolve_dir = get_path_dir(options.input_path, 'iocbio.deconvolve')
else:
deconvolve_dir = get_path_dir(options.output_path, 'iocbio.deconvolve')
psf_path = get_psf_path(options)
psf = ImageStack.load(psf_path, options=options)
stack = ImageStack.load(options.input_path, options=options)
deconvolved_image = deconvolve(psf, stack, deconvolve_dir, options=options)
if options.output_path is None:
b, e = os.path.splitext(options.input_path)
suffix = deconvolved_image.pathinfo.suffix
options.output_path = b + suffix + (e or '.tif')
options.output_path = fix_path(options.output_path)
if 1:
print 'Saving result to %r' % (options.output_path)
deconvolved_image.save(options.output_path)
import numpy
from iocbio.ops import convolve
from iocbio.microscope.deconvolution import deconvolve
from iocbio.io import ImageStack
import scipy.stats
from matplotlib import pyplot as plt
kernel = numpy.array([0, 1, 3, 1, 0])
test_data = numpy.array([0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0]) * 50
data = convolve(kernel, test_data)
degraded_data = scipy.stats.poisson.rvs(numpy.where(data <= 0, 1e-16,
data)).astype(data.dtype)
psf = ImageStack(kernel, voxel_sizes=(1, ))
stack = ImageStack(degraded_data, voxel_sizes=(1, ))
deconvolved_data = deconvolve(psf, stack).images
plt.plot(test_data, label='test')
plt.plot(data, label='convolved')
plt.plot(degraded_data, label='degraded')
plt.plot(deconvolved_data, label='deconvolved')
plt.legend()
plt.ylabel('data')
plt.xlabel('index')
plt.title('Deconvolving degraded test data.')
plt.savefig('deconvolve_poisson_1d.png')
plt.show()
import numpy
from iocbio.ops import convolve
from iocbio.microscope.deconvolution import deconvolve
from iocbio.io import ImageStack
import scipy.stats
from matplotlib import pyplot as plt
kernel = numpy.array([0,1,3,1,0])
test_data = numpy.array([0, 0,0,0,2, 0,0,0,0, 0,1,0,1, 0,0,0])*50
data =convolve(kernel, test_data)
degraded_data = scipy.stats.poisson.rvs(numpy.where(data<=0, 1e-16, data)).astype(data.dtype)
psf = ImageStack(kernel, voxel_sizes = (1,))
stack = ImageStack(degraded_data, voxel_sizes = (1,))
deconvolved_data = deconvolve(psf, stack).images
plt.plot(test_data, label='test')
plt.plot (data, label='convolved')
plt.plot (degraded_data, label='degraded')
plt.plot (deconvolved_data, label='deconvolved')
plt.legend()
plt.ylabel('data')
plt.xlabel('index')
plt.title('Deconvolving degraded test data.')
plt.savefig('deconvolve_poisson_1d.png')
plt.show ()