def input_volume(self, filename, n_dimensions=MI_ORIGINAL_TYPE,
dim_names=None,
nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE, voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE, create_flag=1):
"""construct Volume object from existing MINC file
Usage: input_volume(filename, n_dimensions, dim_names, nc_data_type,
signed_flag, voxel_min, voxel_max, create_flag)
Arguments:
string filename (required)
integer n_dimensions
tuple of strings | None dim_names
integer nc_data_type
integer signed_flag
floating point voxel_min
floating point voxel_max
integer create_flag
"""
if hasattr(self, 'volume_io_obj'):
raise RuntimeError, \
'volume_io_obj can only be created by a constructor'
self.volume_io_obj, self.input_info, self.attributes = \
VolumeIO._start_volume_input(filename, n_dimensions,
dim_names, nc_data_type,
signed_flag, float(voxel_min),
float(voxel_max), create_flag)
if self.volume_io_obj is None:
raise IOError, "input of volume %s failed" % filename
Volume._prune_header(self)
VolumeIO._finish_volume_input(self.volume_io_obj, self.input_info)
del self.input_info
def set_cache_output_parameters(self, filename, history="",
nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE,
voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE,
original_filename=None):
VolumeIO._set_cache_output_volume_parameters(self.volume_io_obj,
filename, nc_data_type, signed_flag, float(voxel_min), float(voxel_max),
original_filename, history)
def __del__(self):
if hasattr(self, 'input_info'):
VolumeIO._delete_volume_input(self.input_info)
if hasattr(self, 'volume_io_obj'):
if VolumeIO_a.volume_is_cached(self.volume_io_obj) and \
not VolumeIO_a.volume_is_alloced(self.volume_io_obj):
# this is memory leak; however, there is a bug in
# delete_volume that can't handle this case
pass
else:
VolumeIO_a.delete_volume(self.volume_io_obj)
def output(self, filename, comment = "Tag file created by py_minc"):
if self.n_volumes == 2:
VolumeIO._output_tag_file(filename, comment, self.n_volumes, self.number(),
numpy.array(self.locations[0]), numpy.array(self.locations[1]),
self.weights, self.structure_ids, self.patient_ids,
self.labels)
else:
VolumeIO._output_tag_file(filename, comment, self.n_volumes, len(self.weights),
numpy.array(self.locations), numpy.array([]),
self.weights, self.structure_ids, self.patient_ids,
self.labels)
def __del__(self):
if hasattr(self, 'input_info'):
VolumeIO._delete_volume_input(self.input_info)
if hasattr(self, 'volume_io_obj'):
if VolumeIO_a.volume_is_cached(self.volume_io_obj) and \
not VolumeIO_a.volume_is_alloced(self.volume_io_obj):
# this is memory leak; however, there is a bug in
# delete_volume that can't handle this case
pass
else:
VolumeIO_a.delete_volume(self.volume_io_obj)
def set_cache_output_parameters(self,
filename,
history="",
nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE,
voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE,
original_filename=None):
VolumeIO._set_cache_output_volume_parameters(self.volume_io_obj,
filename, nc_data_type,
signed_flag,
float(voxel_min),
float(voxel_max),
original_filename,
history)
def output(self, filename, comment="Tag file created by py_minc"):
if self.n_volumes == 2:
VolumeIO._output_tag_file(filename, comment, self.n_volumes,
self.number(),
numpy.array(self.locations[0]),
numpy.array(self.locations[1]),
self.weights, self.structure_ids,
self.patient_ids, self.labels)
else:
VolumeIO._output_tag_file(filename, comment, self.n_volumes,
len(self.weights),
numpy.array(self.locations),
numpy.array([]), self.weights,
self.structure_ids, self.patient_ids,
self.labels)
def output(self, filename, history="", nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE, voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE):
"""output(filename, history, nc_data_type, signed_flag, voxel_min, voxel_max)
Arguments:
string filename
string history
integer nc_data_type
integer signed_flag
floating point voxel_min
floating point voxel_max
Returns:
None
"""
VolumeIO._output_volume(filename, self.volume_io_obj,
history, nc_data_type, signed_flag,
float(voxel_min), float(voxel_max))
def input_volume(self,
filename,
n_dimensions=MI_ORIGINAL_TYPE,
dim_names=None,
nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE,
voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE,
create_flag=1):
"""construct Volume object from existing MINC file
Usage: input_volume(filename, n_dimensions, dim_names, nc_data_type,
signed_flag, voxel_min, voxel_max, create_flag)
Arguments:
string filename (required)
integer n_dimensions
tuple of strings | None dim_names
integer nc_data_type
integer signed_flag
floating point voxel_min
floating point voxel_max
integer create_flag
"""
if hasattr(self, 'volume_io_obj'):
raise RuntimeError, \
'volume_io_obj can only be created by a constructor'
self.volume_io_obj, self.input_info, self.attributes = \
VolumeIO._start_volume_input(filename, n_dimensions,
dim_names, nc_data_type,
signed_flag, float(voxel_min),
float(voxel_max), create_flag)
if self.volume_io_obj is None:
raise IOError, "input of volume %s failed" % filename
Volume._prune_header(self)
VolumeIO._finish_volume_input(self.volume_io_obj, self.input_info)
del self.input_info
def copy_volume(self, existing_volume, starts=None, sizes=None):
"""create a Volume object by copying an existing Volume
Usage: copy_volume(existing_volume [, start=(s0,s1, ...), sizes=(n0,n1,...)])
Arguments:
Volume : existing_volume
start : extract a subvolume starting at given voxel (optional)
size : extract a subvolume of given dimensions (optional)
"""
if hasattr(self, 'volume_io_obj'):
raise RuntimeError, \
'volume_io_obj can only be created by a constructor'
if existing_volume.__class__ is not Volume:
raise TypeError, ("Cannot create volume of type %s from type Volume."
+ " Try copy='definition' instead.") \
% existing_volume.__class
# copy the whole volume
if starts is None and sizes is None:
self.volume_io_obj = VolumeIO_a.copy_volume(
existing_volume.volume_io_obj)
# or copy only a subvolume
else:
Volume._copy_sub_volume_definition_no_alloc(
self, existing_volume, starts, sizes)
VolumeIO_a.alloc_volume_data(self.volume_io_obj)
hyperslab = VolumeIO._get_real_subvolume(
existing_volume.volume_io_obj, tuple(starts), tuple(sizes))
VolumeIO._set_real_subvolume(self.volume_io_obj, (0, ) *
existing_volume.get_n_dimensions(),
hyperslab)
if self.volume_io_obj is None:
raise RuntimeError
self._copy_attributes(existing_volume.attributes)
def copy_volume(self, existing_volume, starts=None, sizes=None):
"""create a Volume object by copying an existing Volume
Usage: copy_volume(existing_volume [, start=(s0,s1, ...), sizes=(n0,n1,...)])
Arguments:
Volume : existing_volume
start : extract a subvolume starting at given voxel (optional)
size : extract a subvolume of given dimensions (optional)
"""
if hasattr(self, 'volume_io_obj'):
raise RuntimeError, \
'volume_io_obj can only be created by a constructor'
if existing_volume.__class__ is not Volume:
raise TypeError, ("Cannot create volume of type %s from type Volume."
+ " Try copy='definition' instead.") \
% existing_volume.__class
# copy the whole volume
if starts is None and sizes is None:
self.volume_io_obj = VolumeIO_a.copy_volume(existing_volume.volume_io_obj)
# or copy only a subvolume
else:
Volume._copy_sub_volume_definition_no_alloc(self, existing_volume, starts, sizes)
VolumeIO_a.alloc_volume_data(self.volume_io_obj)
hyperslab = VolumeIO._get_real_subvolume(existing_volume.volume_io_obj,
tuple(starts), tuple(sizes))
VolumeIO._set_real_subvolume(self.volume_io_obj,
(0,) * existing_volume.get_n_dimensions(),
hyperslab)
if self.volume_io_obj is None:
raise RuntimeError
self._copy_attributes(existing_volume.attributes)
def output(self,
filename,
history="",
nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE,
voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE):
"""output(filename, history, nc_data_type, signed_flag, voxel_min, voxel_max)
Arguments:
string filename
string history
integer nc_data_type
integer signed_flag
floating point voxel_min
floating point voxel_max
Returns:
None
"""
VolumeIO._output_volume(filename, self.volume_io_obj, history,
nc_data_type, signed_flag, float(voxel_min),
float(voxel_max))
def copy_volume_definition(self,
existing_volume,
nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE,
voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE,
starts=None,
sizes=None):
"""create a Volume object based on the definition of an existing Volume
Usage: copy_volume_definition(existing_volume, nc_data_type,
signed_flag, voxel_min, voxel_max, start, size
Arguments:
Volume existing_volume : (required)
integer nc_data_type
integer signed_flag
floating point voxel_min
floating point voxel_max
tuple starts : voxel coordinate of subvolume starts
tuple size : voxel dimensions of subvolume
"""
if hasattr(self, 'volume_io_obj'):
raise RuntimeError,\
'volume_io_obj can only be created by a constructor'
# copy the whole volume
if starts is None and sizes is None:
self.volume_io_obj = VolumeIO._copy_volume_definition(
existing_volume.volume_io_obj, nc_data_type, signed_flag,
float(voxel_min), float(voxel_max))
else:
Volume._copy_sub_volume_definition_no_alloc(
self, existing_volume, starts, sizes, nc_data_type,
signed_flag, voxel_min, voxel_max)
VolumeIO_a.alloc_volume_data(self.volume_io_obj)
if self.volume_io_obj is None:
raise RuntimeError
self.attributes = {}
def copy_volume_definition(self, existing_volume,
nc_data_type=MI_ORIGINAL_TYPE,
signed_flag=MI_ORIGINAL_TYPE,
voxel_min=MI_ORIGINAL_TYPE,
voxel_max=MI_ORIGINAL_TYPE,
starts=None, sizes=None):
"""create a Volume object based on the definition of an existing Volume
Usage: copy_volume_definition(existing_volume, nc_data_type,
signed_flag, voxel_min, voxel_max, start, size
Arguments:
Volume existing_volume : (required)
integer nc_data_type
integer signed_flag
floating point voxel_min
floating point voxel_max
tuple starts : voxel coordinate of subvolume starts
tuple size : voxel dimensions of subvolume
"""
if hasattr(self, 'volume_io_obj'):
raise RuntimeError,\
'volume_io_obj can only be created by a constructor'
# copy the whole volume
if starts is None and sizes is None:
self.volume_io_obj = VolumeIO._copy_volume_definition(
existing_volume.volume_io_obj, nc_data_type, signed_flag,
float(voxel_min), float(voxel_max))
else:
Volume._copy_sub_volume_definition_no_alloc(self, existing_volume, starts, sizes,
nc_data_type, signed_flag,
voxel_min, voxel_max)
VolumeIO_a.alloc_volume_data(self.volume_io_obj)
if self.volume_io_obj is None:
raise RuntimeError
self.attributes = {}
def __init__(self, arg0):
"If arg0 is a filename, read tags from file. Otherwise, if arg0 is 1, 2 create an empty tags structure appropriate for the specified number of volumes"
if type(arg0) is types.StringType:
r = VolumeIO._input_tag_file(arg0)
self.n_volumes = r[0]
if(self.n_volumes == 1):
self.locations = r[1]
r = r[2:]
else:
self.locations = [r[1], r[2]]
r = r[3:]
self.weights, self.structure_ids, self.patient_ids, self.labels = r
elif arg0 in [1, 2]:
self.n_volumes = arg0
self.locations = ([], [[], []])[arg0 == 2]
self.weights = []
self.structure_ids = []
self.patient_ids = []
self.labels = []
else:
raise TypeError, "Unknown argument type for VolumeTags"
def __init__(self, arg0):
"If arg0 is a filename, read tags from file. Otherwise, if arg0 is 1, 2 create an empty tags structure appropriate for the specified number of volumes"
if type(arg0) is types.StringType:
r = VolumeIO._input_tag_file(arg0)
self.n_volumes = r[0]
if (self.n_volumes == 1):
self.locations = r[1]
r = r[2:]
else:
self.locations = [r[1], r[2]]
r = r[3:]
self.weights, self.structure_ids, self.patient_ids, self.labels = r
elif arg0 in [1, 2]:
self.n_volumes = arg0
self.locations = ([], [[], []])[arg0 == 2]
self.weights = []
self.structure_ids = []
self.patient_ids = []
self.labels = []
else:
raise TypeError, "Unknown argument type for VolumeTags"
def fill(self, value):
"fill all voxels with given value"
VolumeIO._fill_volume_real_value(self.volume_io_obj, value)
def set_hyperslab(self, start, data):
"set an n dimensional array of real values in the volume."
VolumeIO._set_real_subvolume(self.volume_io_obj,
tuple(start), data)
def get_hyperslab(self, start, size, typecode=numpy.float_):
"get an n dimensional array of real values from the volume"
return self._cast(VolumeIO._get_real_subvolume(self.volume_io_obj,
tuple(start), tuple(size)), typecode)
def get_all_values(self, typecode=numpy.float_):
"""Return a numpy array of the specified type with all values from the volume.
Note that integer types are produced by rounding using floor(x+0.5).
"""
return VolumeIO._get_volume_all_real_values(self.volume_io_obj, numpy.dtype(typecode).char)
def get_dimension_names(self):
"get_dimension_names()"
return VolumeIO._get_volume_dimension_names(self.volume_io_obj)
def get_dimension_names(self):
"get_dimension_names()"
return VolumeIO._get_volume_dimension_names(self.volume_io_obj)
def get_all_values(self, typecode=numpy.float_):
"""Return a numpy array of the specified type with all values from the volume.
Note that integer types are produced by rounding using floor(x+0.5).
"""
return VolumeIO._get_volume_all_real_values(self.volume_io_obj,
numpy.dtype(typecode).char)
def get_hyperslab(self, start, size, typecode=numpy.float_):
"get an n dimensional array of real values from the volume"
return self._cast(
VolumeIO._get_real_subvolume(self.volume_io_obj, tuple(start),
tuple(size)), typecode)
def set_hyperslab(self, start, data):
"set an n dimensional array of real values in the volume."
VolumeIO._set_real_subvolume(self.volume_io_obj, tuple(start), data)
def fill(self, value):
"fill all voxels with given value"
VolumeIO._fill_volume_real_value(self.volume_io_obj, value)