def create_project_file(self, name, spacing, modality, orientation, window_width, window_level, image, affine='', folder=None):
if folder is None:
folder = tempfile.mkdtemp()
if not os.path.exists(folder):
os.mkdir(folder)
image_file = os.path.join(folder, 'matrix.dat')
image_mmap = imagedata_utils.array2memmap(image, image_file)
matrix = {
'filename': 'matrix.dat',
'shape': image.shape,
'dtype': str(image.dtype)
}
project = {
# Format info
"format_version": const.INVESALIUS_ACTUAL_FORMAT_VERSION,
"invesalius_version": const.INVESALIUS_VERSION,
"date": datetime.datetime.now().isoformat(),
"compress": True,
# case info
"name": name, # patient's name
"modality": modality, # CT, RMI, ...
"orientation": orientation,
"window_width": window_width,
"window_level": window_level,
"scalar_range": (int(image.min()), int(image.max())),
"spacing": spacing,
"affine": affine,
"matrix": matrix,
}
path = os.path.join(folder, 'main.plist')
with open(path, 'w+b') as f:
plistlib.dump(project, f)
def create_project_from_matrix(self,
name,
matrix,
orientation="AXIAL",
spacing=(1.0, 1.0, 1.0),
modality="CT",
window_width=None,
window_level=None,
new_instance=False):
"""
Creates a new project from a Numpy 3D array.
name: Name of the project.
matrix: A Numpy 3D array. It only works with int16 arrays.
spacing: The spacing between the center of the voxels in X, Y and Z direction.
modality: Imaging modality.
"""
if window_width is None:
window_width = (matrix.max() - matrix.min())
if window_level is None:
window_level = (matrix.max() + matrix.min()) // 2
window_width = int(window_width)
window_level = int(window_level)
name_to_const = {
"AXIAL": const.AXIAL,
"CORONAL": const.CORONAL,
"SAGITTAL": const.SAGITAL
}
if new_instance:
self.start_new_inv_instance(matrix, name, spacing, modality,
name_to_const[orientation],
window_width, window_level)
else:
# Verifying if there is a project open
s = ses.Session()
if s.IsOpen():
Publisher.sendMessage('Close Project')
Publisher.sendMessage('Disconnect tracker')
# Check if user really closed the project, if not, stop project creation
if s.IsOpen():
return
mmap_matrix = image_utils.array2memmap(matrix)
self.Slice = sl.Slice()
self.Slice.matrix = mmap_matrix
self.Slice.matrix_filename = mmap_matrix.filename
self.Slice.spacing = spacing
self.Slice.window_width = window_width
self.Slice.window_level = window_level
proj = prj.Project()
proj.name = name
proj.modality = modality
proj.SetAcquisitionModality(modality)
proj.matrix_shape = matrix.shape
proj.matrix_dtype = matrix.dtype.name
proj.matrix_filename = self.Slice.matrix_filename
proj.window = window_width
proj.level = window_level
proj.original_orientation =\
name_to_const[orientation]
proj.threshold_range = int(matrix.min()), int(matrix.max())
proj.spacing = self.Slice.spacing
Publisher.sendMessage('Update threshold limits list',
threshold_range=proj.threshold_range)
######
session = ses.Session()
filename = proj.name + ".inv3"
filename = filename.replace("/", "")
dirpath = session.CreateProject(filename)
self.LoadProject()
Publisher.sendMessage("Enable state project", state=True)
