def OpenPlistProject(self, filename):
import invesalius.data.measures as ms
import invesalius.data.mask as msk
import invesalius.data.surface as srf
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
# Opening the main file from invesalius 3 project
main_plist = os.path.join(dirpath, 'main.plist')
project = plistlib.readPlist(main_plist)
# case info
self.name = project["name"]
self.modality = project["modality"]
self.original_orientation = project["orientation"]
self.window = project["window_width"]
self.level = project["window_level"]
self.threshold_range = project["scalar_range"]
self.spacing = project["spacing"]
# Opening the matrix containing the slices
filepath = os.path.join(dirpath, project["matrix"]["filename"])
self.matrix_filename = filepath
self.matrix_shape = project["matrix"]['shape']
self.matrix_dtype = project["matrix"]['dtype']
# Opening the masks
self.mask_dict = {}
for index in project["masks"]:
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.OpenPList(filepath)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in project["surfaces"]:
filename = project["surfaces"][index]
filepath = os.path.join(dirpath, filename)
s = srf.Surface(int(index))
s.OpenPList(filepath)
self.surface_dict[s.index] = s
# Opening the measurements
self.measurement_dict = {}
measurements = plistlib.readPlist(
os.path.join(dirpath, project["measurements"]))
for index in measurements:
measure = ms.Measurement()
measure.Load(measurements[index])
self.measurement_dict[int(index)] = measure
def load_from_folder(self, dirpath):
"""
Loads invesalius3 project files from dipath.
"""
import invesalius.data.measures as ms
import invesalius.data.mask as msk
import invesalius.data.surface as srf
# Opening the main file from invesalius 3 project
main_plist = os.path.join(dirpath, 'main.plist')
project = plistlib.readPlist(main_plist)
format_version = project["format_version"]
if format_version > const.INVESALIUS_ACTUAL_FORMAT_VERSION:
from invesalius.gui.dialogs import ImportOldFormatInvFile
ImportOldFormatInvFile()
# case info
self.name = project["name"]
self.modality = project["modality"]
self.original_orientation = project["orientation"]
self.window = project["window_width"]
self.level = project["window_level"]
self.threshold_range = project["scalar_range"]
self.spacing = project["spacing"]
if project.get("affine", ""):
self.affine = project["affine"]
# self.affine = project.get("affine")
Publisher.sendMessage('Update affine matrix',
affine=np.asarray(self.affine).reshape(4, 4),
status=True)
self.compress = project.get("compress", True)
# Opening the matrix containing the slices
filepath = os.path.join(dirpath, project["matrix"]["filename"])
self.matrix_filename = filepath
self.matrix_shape = project["matrix"]['shape']
self.matrix_dtype = project["matrix"]['dtype']
# Opening the masks
self.mask_dict = {}
for index in project.get("masks", []):
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.spacing = self.spacing
m.OpenPList(filepath)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in project.get("surfaces", []):
filename = project["surfaces"][index]
filepath = os.path.join(dirpath, filename)
s = srf.Surface(int(index))
s.OpenPList(filepath)
self.surface_dict[s.index] = s
# Opening the measurements
self.measurement_dict = {}
measures_file = os.path.join(
dirpath, project.get("measurements", "measurements.plist"))
if os.path.exists(measures_file):
measurements = plistlib.readPlist(measures_file)
for index in measurements:
if measurements[index]["type"] in (const.DENSITY_ELLIPSE,
const.DENSITY_POLYGON):
measure = ms.DensityMeasurement()
else:
measure = ms.Measurement()
measure.Load(measurements[index])
self.measurement_dict[int(index)] = measure
def OpenPlistProject(self, filename):
import invesalius.data.measures as ms
import invesalius.data.mask as msk
import invesalius.data.surface as srf
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
filelist = Extract(filename, tempfile.mkdtemp())
dirpath = os.path.abspath(os.path.split(filelist[0])[0])
# Opening the main file from invesalius 3 project
main_plist = os.path.join(dirpath ,'main.plist')
project = plistlib.readPlist(main_plist)
format_version = project["format_version"]
if format_version > const.INVESALIUS_ACTUAL_FORMAT_VERSION:
from invesalius.gui.dialogs import ImportOldFormatInvFile
ImportOldFormatInvFile()
# case info
self.name = project["name"]
self.modality = project["modality"]
self.original_orientation = project["orientation"]
self.window = project["window_width"]
self.level = project["window_level"]
self.threshold_range = project["scalar_range"]
self.spacing = project["spacing"]
if project.get("affine"):
self.affine = project["affine"]
Publisher.sendMessage('Update affine matrix',
affine=self.affine, status=True)
self.compress = project.get("compress", True)
# Opening the matrix containing the slices
filepath = os.path.join(dirpath, project["matrix"]["filename"])
self.matrix_filename = filepath
self.matrix_shape = project["matrix"]['shape']
self.matrix_dtype = project["matrix"]['dtype']
# Opening the masks
self.mask_dict = {}
for index in project["masks"]:
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.OpenPList(filepath)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in project["surfaces"]:
filename = project["surfaces"][index]
filepath = os.path.join(dirpath, filename)
s = srf.Surface(int(index))
s.OpenPList(filepath)
self.surface_dict[s.index] = s
# Opening the measurements
self.measurement_dict = {}
measurements = plistlib.readPlist(os.path.join(dirpath,
project["measurements"]))
for index in measurements:
if measurements[index]["type"] in (const.DENSITY_ELLIPSE, const.DENSITY_POLYGON):
measure = ms.DensityMeasurement()
else:
measure = ms.Measurement()
measure.Load(measurements[index])
self.measurement_dict[int(index)] = measure