def runner(parser, options, args):
if not hasattr(parser, 'runner'):
options.output_path = None
if args:
if len(args) == 1:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (
options.input_path, args[0])
options.input_path = args[0]
elif len(args) == 2:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (
options.input_path, args[0])
options.input_path = args[0]
if options.output_path:
print >> sys.stderr, "WARNING: overwriting output path %r with %r" % (
options.output_path, args[1])
options.output_path = args[1]
else:
parser.error(
"Incorrect number of arguments (expected upto 2 but got %s)" %
(len(args)))
if options.input_path is None:
parser.error('Expected --input-path but got nothing')
options.input_path = fix_path(options.input_path)
stack = ImageStack.load(options.input_path, options=options)
numpy_types = numpy.typeDict.values()
if options.output_type in ['<detect>', None]:
if str(stack.images.dtype).startswith('float'):
output_type_name = 'float32'
elif str(stack.images.dtype).startswith('int'):
output_type_name = 'int32'
elif str(stack.images.dtype).startswith('uint'):
output_type_name = 'uint32'
else:
output_type_name = 'int32'
else:
output_type_name = options.output_type.lower()
output_type = getattr(numpy, output_type_name, None)
mn, mx = stack.images.min(), stack.images.max()
print 'Input minimum and maximum: %s, %s' % (mn, mx)
if options.scale and 'int' in output_type_name:
tmn, tmx = get_dtype_min_max(output_type)
new_images = (tmn + float(tmx - tmn) * (stack.images - float(mn)) /
(mx - mn)).astype(output_type)
else:
new_images = stack.images.astype(output_type)
print 'Output minimum and maximum: %s, %s' % (new_images.min(),
new_images.max())
output_path = options.output_path
output_ext = options.output_ext
if output_path is None:
dn = os.path.dirname(options.input_path)
bn = os.path.basename(options.input_path)
if os.path.isfile(options.input_path):
fn, ext = os.path.splitext(bn)
type_part = None
for t in numpy_types:
if fn.endswith('_' + t.__name__):
type_part = t.__name__
break
if type_part is None:
output_path = os.path.join(
dn, fn + '_' + output_type_name + '.' + output_ext)
else:
output_path = os.path.join(
dn,
fn[:-len(type_part)] + output_type_name + '.' + output_ext)
elif os.path.isdir(options.input_path):
output_path = os.path.join(
dn, bn + '_' + output_type_name + '.' + output_ext)
else:
raise NotImplementedError('%s is not file nor directory' %
(options.input_path))
output_path = fix_path(output_path)
print 'Saving new stack to', output_path
if output_ext == 'tif':
ImageStack(new_images, stack.pathinfo,
options=options).save(output_path)
elif output_ext == 'data':
from iocbio.microscope.psf import normalize_unit_volume, discretize
value_resolution = stack.pathinfo.get_value_resolution()
normal_images = normalize_unit_volume(new_images,
stack.get_voxel_sizes())
discrete = discretize(new_images / value_resolution)
signal_indices = numpy.where(discrete > 0)
new_value_resolution = value_resolution * normal_images.max(
) / new_images.max()
ImageStack(normal_images,
stack.pathinfo,
value_resolution=new_value_resolution).save(
output_path, zip(*signal_indices))
elif output_ext == 'vtk':
from pyvtk import VtkData, StructuredPoints, PointData, Scalars
vtk = VtkData(StructuredPoints(new_images.shape),
PointData(Scalars(new_images.T.ravel())))
vtk.tofile(output_path, 'binary')
else:
raise NotImplementedError( ` output_ext `)
def runner (parser, options, args):
if not hasattr(parser, 'runner'):
options.output_path = None
if args:
if len (args)==1:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (options.input_path, args[0])
options.input_path = args[0]
elif len(args)==2:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (options.input_path, args[0])
options.input_path = args[0]
if options.output_path:
print >> sys.stderr, "WARNING: overwriting output path %r with %r" % (options.output_path, args[1])
options.output_path = args[1]
else:
parser.error("Incorrect number of arguments (expected upto 2 but got %s)" % (len(args)))
if options.input_path is None:
parser.error('Expected --input-path but got nothing')
options.input_path = fix_path (options.input_path)
stack = ImageStack.load(options.input_path, options=options)
numpy_types = numpy.typeDict.values()
if options.output_type in ['<detect>', None]:
if str (stack.images.dtype).startswith ('float'):
output_type_name = 'float32'
elif str (stack.images.dtype).startswith ('int'):
output_type_name = 'int32'
elif str (stack.images.dtype).startswith ('uint'):
output_type_name = 'uint32'
else:
output_type_name = 'int32'
else:
output_type_name = options.output_type.lower()
output_type = getattr (numpy, output_type_name, None)
mn, mx = stack.images.min (), stack.images.max ()
print 'Input minimum and maximum: %s, %s' % (mn, mx)
if options.scale and 'int' in output_type_name:
tmn, tmx = get_dtype_min_max(output_type)
new_images = (tmn + float(tmx - tmn) * (stack.images-float(mn)) / (mx - mn)).astype (output_type)
else:
new_images = stack.images.astype (output_type)
print 'Output minimum and maximum: %s, %s' % (new_images.min (), new_images.max ())
output_path = options.output_path
output_ext = options.output_ext
if output_path is None:
dn = os.path.dirname(options.input_path)
bn = os.path.basename(options.input_path)
if os.path.isfile(options.input_path):
fn, ext = os.path.splitext (bn)
type_part = None
for t in numpy_types:
if fn.endswith('_' + t.__name__):
type_part = t.__name__
break
if type_part is None:
output_path = os.path.join(dn, fn + '_' + output_type_name + '.' + output_ext)
else:
output_path = os.path.join(dn, fn[:-len(type_part)] + output_type_name + '.' + output_ext)
elif os.path.isdir (options.input_path):
output_path = os.path.join (dn, bn+'_'+output_type_name + '.' + output_ext)
else:
raise NotImplementedError ('%s is not file nor directory' % (options.input_path))
output_path = fix_path(output_path)
print 'Saving new stack to',output_path
if output_ext=='tif':
ImageStack(new_images, stack.pathinfo, options=options).save(output_path)
elif output_ext=='data':
from iocbio.microscope.psf import normalize_unit_volume, discretize
value_resolution = stack.pathinfo.get_value_resolution()
normal_images = normalize_unit_volume(new_images, stack.get_voxel_sizes())
discrete = discretize(new_images / value_resolution)
signal_indices = numpy.where(discrete>0)
new_value_resolution = value_resolution * normal_images.max() / new_images.max()
ImageStack(normal_images, stack.pathinfo,
value_resolution = new_value_resolution).save(output_path, zip(*signal_indices))
elif output_ext=='vtk':
from pyvtk import VtkData, StructuredPoints, PointData, Scalars
vtk = VtkData (StructuredPoints (new_images.shape), PointData(Scalars(new_images.T.ravel())))
vtk.tofile(output_path, 'binary')
else:
raise NotImplementedError (`output_ext`)
def runner (parser, options, args):
if not hasattr(parser, 'runner'):
options.output_path = None
if args:
if len (args)==1:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (options.input_path, args[0])
options.input_path = args[0]
elif len(args)==2:
if options.input_path:
print >> sys.stderr, "WARNING: overwriting input path %r with %r" % (options.input_path, args[0])
options.input_path = args[0]
if options.output_path:
print >> sys.stderr, "WARNING: overwriting output path %r with %r" % (options.output_path, args[1])
options.output_path = args[1]
else:
parser.error("Incorrect number of arguments (expected upto 2 but got %s)" % (len(args)))
if options.input_path is None:
parser.error('Expected --input-path but got nothing')
options.input_path = fix_path (options.input_path)
stack = ImageStack.load(options.input_path, options=options)
numpy_types = numpy.typeDict.values()
if options.output_type in ['<detect>', None]:
output_type_name = stack.images.dtype.name
else:
output_type_name = options.output_type.lower()
output_type = getattr (numpy, output_type_name, None)
nof_stacks = stack.get_nof_stacks()
old_shape = stack.images.shape
new_shape = (nof_stacks, old_shape[0]//nof_stacks) + old_shape[1:]
new_images = numpy.zeros (new_shape[1:], dtype=output_type_name)
first_stack = None
last_stack = None
for i, stacki in enumerate(stack.images.reshape(new_shape)):
if i==0:
first_stack = stacki.astype (float)
new_images[:] = stacki
else:
err_first = abs(stacki - first_stack).mean()
err_last = abs(stacki - last_stack).mean()
print ('Stack %i: mean abs difference from first and last stack: %.3f, %.3f' % (i+1, err_first, err_last))
new_images += stacki
last_stack = stacki.astype(float)
output_path = options.output_path
output_ext = options.output_ext
if output_path is None:
dn = os.path.dirname(options.input_path)
bn = os.path.basename(options.input_path)
if os.path.isfile(options.input_path):
fn, ext = os.path.splitext (bn)
fn += '_sumstacks%s' % (nof_stacks)
type_part = None
for t in numpy_types:
if fn.endswith('_' + t.__name__):
type_part = t.__name__
break
if type_part is None:
output_path = os.path.join(dn, fn + '_' + output_type_name + '.' + output_ext)
else:
output_path = os.path.join(dn, fn[:-len(type_part)] + output_type_name + '.' + output_ext)
elif os.path.isdir (options.input_path):
bn += '_sumstacks%s' % (nof_stacks)
output_path = os.path.join (dn, bn+'_'+output_type_name + '.' + output_ext)
else:
raise NotImplementedError ('%s is not file nor directory' % (options.input_path))
output_path = fix_path(output_path)
print 'Saving new stack to',output_path
if output_ext=='tif':
ImageStack(new_images, stack.pathinfo, options=options).save(output_path)
elif output_ext=='data':
from iocbio.microscope.psf import normalize_unit_volume, discretize
value_resolution = stack.pathinfo.get_value_resolution()
normal_images = normalize_unit_volume(new_images, stack.get_voxel_sizes())
discrete = discretize(new_images / value_resolution)
signal_indices = numpy.where(discrete>0)
new_value_resolution = value_resolution * normal_images.max() / new_images.max()
ImageStack(normal_images, stack.pathinfo,
value_resolution = new_value_resolution).save(output_path, zip(*signal_indices))
elif output_ext=='vtk':
from pyvtk import VtkData, StructuredPoints, PointData, Scalars
vtk = VtkData (StructuredPoints (new_images.shape), PointData(Scalars(new_images.T.ravel())))
vtk.tofile(output_path, 'binary')
else:
raise NotImplementedError (`output_ext`)
