def find_resource(where):
""" Return the absolute file name of a resource inside the project.
This function is necessary as bbfreeze cannot embed arbitrary files.
"""
# Try first as a local application using MediPy
command_name = sys.argv[0]
abs_path = os.path.realpath(command_name)
dirname = os.path.dirname(abs_path)
elements = dirname.split(os.path.sep)
resource_path = None
while len(elements) > 0:
path = os.path.sep.join(elements)
if os.path.exists(os.path.join(path, where)):
resource_path = os.path.join(path, where)
break
else:
elements.pop()
if resource_path is not None:
return resource_path
# Try in MediPy and plugins
import medipy
for path in medipy.__path__:
resource_path = os.path.join(path, where)
if os.path.exists(resource_path):
return resource_path
# Resource was not found, raise an exception
raise exception.Exception("Cannot find resource %s" % where)
def _default_direction(self):
""" Return the default image direction, according to the data type.
"""
dim = None
if self.data_type == "scalar":
dim = self.data.ndim
elif self.data_type == "vector":
dim = self.data.ndim - 1
elif self.data_type == "matrix":
dim = self.data.ndim - 2
else:
raise exception.Exception("Unknown data_type : %s" %
self.data_type)
return numpy.identity(dim, dtype=numpy.float32)
def remove_observer(self, event, observer):
"""Remove an observer from the object.
Return False if the observer was not in the list. Otherwise return True
"""
self._remove_dead_observers()
if not self.is_allowed_event(event):
raise exception.Exception("Event " + event +
" is not allowed for type " +
str(type(self)))
if "im_self" in dir(observer) and "im_func" in dir(observer):
return self._remove_bound_method_observer(event, observer)
else:
return self._remove_function_observer(event, observer)
def __init__(self,
shape=(0, ),
dtype=numpy.single,
spacing=None,
origin=None,
direction=None,
data_type="scalar",
image_type="normal",
annotations=None,
metadata=None,
**kwargs):
""" Create an image. Extra arguments may contain :
* data or value (mutually exclusive)
* dti
* any other argument of numpy.ndarray.__init__
"""
##################
# Public members #
##################
# Numpy array holding the voxel values
self.data = None
# Type/dimensionality of the data : can be one of scalar, vector, or matrix
self.data_type = data_type
# Acquisition modality of the image : can be normal or spectroscopy. TODO : use metadata
self.image_type = image_type
# Annotations on the image. TODO : store them in metadata
self.annotations = ObservableList(annotations or [])
# Metadata
self.metadata = metadata or {}
############################
# Property-related members #
############################
# Spacing between pixels, in mm
self._spacing = None
# Origin of the image, in mm
self._origin = None
# Matrix of direction cosines that specify the direction between samples
self._direction = None
self._index_to_physical_matrix = None
self._physical_to_index_matrix = None
##################
# Initialization #
##################
Observable.__init__(self, ["modified"])
# Modify the shape of DTI images
if "dti" in kwargs:
self.data_type = "vector"
if kwargs["dti"] == "tensor_2":
self.image_type = "tensor_2"
shape = list(shape)
shape.append(6)
# elif kwargs["dti"] == "tensor_4" :
# pass
else:
raise exception.Exception("Unkown DTI model : %s" %
kwargs["dti"])
del kwargs["dti"]
# Array initialization : either data or value
if "data" in kwargs and "value" in kwargs:
raise exception.Exception("Only one of data and value is allowed")
if "data" in kwargs:
self.data = numpy.asarray(kwargs["data"])
del kwargs["data"]
else:
if "value" in kwargs:
value = kwargs["value"]
del kwargs["value"]
else:
value = None
self.data = numpy.ndarray(shape, dtype, **kwargs)
if value is not None:
self.data.fill(value)
if spacing is None:
self._set_spacing(self._default_spacing())
else:
self._set_spacing(spacing)
if origin is None:
self._set_origin(self._default_origin())
else:
self._set_origin(origin)
if direction is None:
self._set_direction(self._default_direction())
else:
self._set_direction(direction)