def use_cmd_optargs(options, args):
# If import DICOM argument...
if options.dicom_dir:
import_dir = options.dicom_dir
Publisher.sendMessage('Import directory',
directory=import_dir,
use_gui=not options.no_gui)
if options.save:
Publisher.sendMessage('Save project',
filepath=os.path.abspath(options.save))
exit(0)
check_for_export(options)
return True
elif options.import_folder:
Publisher.sendMessage('Import folder', folder=options.import_folder)
if options.save:
Publisher.sendMessage('Save project',
filepath=os.path.abspath(options.save))
exit(0)
check_for_export(options)
elif options.import_all:
import invesalius.reader.dicom_reader as dcm
for patient in dcm.GetDicomGroups(options.import_all):
for group in patient.GetGroups():
Publisher.sendMessage('Import group',
group=group,
use_gui=not options.no_gui)
check_for_export(options,
suffix=group.title,
remove_surfaces=False)
Publisher.sendMessage('Remove masks', mask_indexes=(0, ))
return True
# Check if there is a file path somewhere in what the user wrote
# In case there is, try opening as it was a inv3
else:
for arg in reversed(args):
file = utils.decode(arg, FS_ENCODE)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', filepath=path)
check_for_export(options)
return True
file = utils.decode(arg, sys.stdin.encoding)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', filepath=path)
check_for_export(options)
return True
return False
def use_cmd_optargs(options, args):
# If debug argument...
if options.debug:
Publisher.subscribe(print_events, Publisher.ALL_TOPICS)
session = ses.Session()
session.debug = 1
# If import DICOM argument...
if options.dicom_dir:
import_dir = options.dicom_dir
Publisher.sendMessage('Import directory', {
'directory': import_dir,
'gui': not options.no_gui
})
if options.save:
Publisher.sendMessage('Save project',
os.path.abspath(options.save))
exit(0)
check_for_export(options)
return True
elif options.import_all:
import invesalius.reader.dicom_reader as dcm
for patient in dcm.GetDicomGroups(options.import_all):
for group in patient.GetGroups():
Publisher.sendMessage('Import group', {
'group': group,
'gui': not options.no_gui
})
check_for_export(options,
suffix=group.title,
remove_surfaces=False)
Publisher.sendMessage('Remove masks', [0])
return True
# Check if there is a file path somewhere in what the user wrote
# In case there is, try opening as it was a inv3
else:
for arg in reversed(args):
file = utils.decode(arg, FS_ENCODE)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', path)
check_for_export(options)
return True
file = utils.decode(arg, sys.stdin.encoding)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', path)
check_for_export(options)
return True
return False
def use_cmd_optargs(options, args):
# If debug argument...
if options.debug:
Publisher.subscribe(print_events, Publisher.ALL_TOPICS)
session = ses.Session()
session.debug = 1
# If import DICOM argument...
if options.dicom_dir:
import_dir = options.dicom_dir
Publisher.sendMessage('Import directory', directory=import_dir, use_gui=not options.no_gui)
if options.save:
Publisher.sendMessage('Save project', filepath=os.path.abspath(options.save))
exit(0)
check_for_export(options)
return True
elif options.import_all:
import invesalius.reader.dicom_reader as dcm
for patient in dcm.GetDicomGroups(options.import_all):
for group in patient.GetGroups():
Publisher.sendMessage('Import group',
group=group,
use_gui=not options.no_gui)
check_for_export(options, suffix=group.title, remove_surfaces=False)
Publisher.sendMessage('Remove masks', mask_indexes=(0,))
return True
# Check if there is a file path somewhere in what the user wrote
# In case there is, try opening as it was a inv3
else:
for arg in reversed(args):
file = utils.decode(arg, FS_ENCODE)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', filepath=path)
check_for_export(options)
return True
file = utils.decode(arg, sys.stdin.encoding)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', filepath=path)
check_for_export(options)
return True
return False
def SaveProject(self, path=None, compress=False):
Publisher.sendMessage('Begin busy cursor')
session = ses.Session()
if path:
dirpath, filename = os.path.split(path)
else:
dirpath, filename = session.project_path
if isinstance(filename, str):
filename = utils.decode(filename, const.FS_ENCODE)
proj = prj.Project()
try:
prj.Project().SavePlistProject(dirpath, filename, compress)
except PermissionError as err:
if wx.GetApp() is None:
print(
"Error: Permission denied, you don't have permission to write at {}"
.format(dirpath))
else:
dlg = dialogs.ErrorMessageBox(
None, "Save project error",
"It was not possible to save because you don't have permission to write at {}\n{}"
.format(dirpath, err))
dlg.ShowModal()
dlg.Destroy()
else:
session.SaveProject((dirpath, filename))
Publisher.sendMessage('End busy cursor')
def OnExportSurface(self, filename, filetype):
ftype_prefix = {
const.FILETYPE_STL: '.stl',
const.FILETYPE_VTP: '.vtp',
const.FILETYPE_PLY: '.ply',
const.FILETYPE_STL_ASCII: '.stl',
}
if filetype in ftype_prefix:
temp_file = tempfile.mktemp(suffix=ftype_prefix[filetype])
if _has_win32api:
utl.touch(temp_file)
_temp_file = temp_file
temp_file = win32api.GetShortPathName(temp_file)
os.remove(_temp_file)
temp_file = utl.decode(temp_file, const.FS_ENCODE)
try:
self._export_surface(temp_file, filetype)
except ValueError:
if wx.GetApp() is None:
print(
"It was not possible to export the surface because the surface is empty"
)
else:
wx.MessageBox(
_("It was not possible to export the surface because the surface is empty"
), _("Export surface error"))
return
shutil.move(temp_file, filename)
def Extract(filename, folder):
if _has_win32api:
folder = win32api.GetShortPathName(folder)
folder = decode(folder, const.FS_ENCODE)
tar = tarfile.open(filename, "r")
idir = decode(os.path.split(tar.getnames()[0])[0], 'utf8')
os.mkdir(os.path.join(folder, idir))
filelist = []
for t in tar.getmembers():
fsrc = tar.extractfile(t)
fname = os.path.join(folder, decode(t.name, 'utf-8'))
fdst = open(fname, 'wb')
shutil.copyfileobj(fsrc, fdst)
filelist.append(fname)
fsrc.close()
fdst.close()
del fsrc
del fdst
tar.close()
return filelist
def Extract(filename, folder):
if _has_win32api:
folder = win32api.GetShortPathName(folder)
folder = decode(folder, const.FS_ENCODE)
tar = tarfile.open(filename, "r")
idir = decode(os.path.split(tar.getnames()[0])[0], 'utf8')
os.mkdir(os.path.join(folder, idir))
filelist = []
for t in tar.getmembers():
fsrc = tar.extractfile(t)
fname = os.path.join(folder, decode(t.name, 'utf-8'))
fdst = open(fname, 'wb')
shutil.copyfileobj(fsrc, fdst)
filelist.append(fname)
fsrc.close()
fdst.close()
del fsrc
del fdst
tar.close()
return filelist
def OnOpenOtherFiles(self, filepath):
filepath = utils.decode(filepath, const.FS_ENCODE)
if not (filepath) == None:
name = os.path.basename(filepath).split(".")[0]
group = oth.ReadOthers(filepath)
if group:
matrix, matrix_filename = self.OpenOtherFiles(group)
self.CreateOtherProject(name, matrix, matrix_filename)
self.LoadProject()
Publisher.sendMessage("Enable state project", state=True)
else:
dialog.ImportInvalidFiles(ftype="Others")
def OnOpenOtherFiles(self, filepath):
filepath = utils.decode(filepath, const.FS_ENCODE)
if not(filepath) == None:
name = filepath.rpartition('\\')[-1].split('.')
group = oth.ReadOthers(filepath)
if group:
matrix, matrix_filename = self.OpenOtherFiles(group)
self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
self.LoadProject()
Publisher.sendMessage("Enable state project", state=True)
else:
dialog.ImportInvalidFiles(ftype="Others")
def OnOpenOtherFiles(self, pubsub_evt):
filepath = utils.decode(pubsub_evt.data, const.FS_ENCODE)
if not (filepath) == None:
name = filepath.rpartition('\\')[-1].split('.')
group = oth.ReadOthers(filepath)
if group:
matrix, matrix_filename = self.OpenOtherFiles(group)
self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
self.LoadProject()
Publisher.sendMessage("Enable state project", True)
else:
dialog.ImportInvalidFiles(ftype="Others")
def GetPixelSpacingFromInfoFile(filepath):
filepath = utils.decode(filepath, const.FS_ENCODE)
if filepath.endswith('.DS_Store'):
return False
fi = open(filepath, 'r')
lines = fi.readlines()
measure_scale = 'mm'
values = []
if len(lines) > 0:
#info text from avizo
if '# Avizo Stacked Slices' in lines[0]:
value = lines[2].split(' ')
spx = float(value[1])
spy = float(value[2])
value = lines[5].split(' ')
spz = float(value[1])
return [spx * 0.001, spy * 0.001, spz * 0.001]
else:
#info text from skyscan
for l in lines:
if 'Pixel Size' in l:
if 'um' in l:
measure_scale = 'um'
value = l.split("=")[-1]
values.append(value)
if len(values) > 0:
value = values[-1]
value = value.replace('\n','')
value = value.replace('\r','')
#convert um to mm (InVesalius default)
if measure_scale == 'um':
value = float(value) * 0.001
measure_scale = 'mm'
elif measure_scale == 'nm':
value = float(value) * 0.000001
return [value, value, value]
else:
return False
else:
return False
def GetPixelSpacingFromInfoFile(filepath):
filepath = utils.decode(filepath, const.FS_ENCODE)
if filepath.endswith(".DS_Store"):
return False
fi = open(filepath, "r")
lines = fi.readlines()
measure_scale = "mm"
values = []
if len(lines) > 0:
# info text from avizo
if "# Avizo Stacked Slices" in lines[0]:
value = lines[2].split(" ")
spx = float(value[1])
spy = float(value[2])
value = lines[5].split(" ")
spz = float(value[1])
return [spx * 0.001, spy * 0.001, spz * 0.001]
else:
# info text from skyscan
for l in lines:
if "Pixel Size" in l:
if "um" in l:
measure_scale = "um"
value = l.split("=")[-1]
values.append(value)
if len(values) > 0:
value = values[-1]
value = value.replace("\n", "")
value = value.replace("\r", "")
# convert um to mm (InVesalius default)
if measure_scale == "um":
value = float(value) * 0.001
measure_scale = "mm"
elif measure_scale == "nm":
value = float(value) * 0.000001
return [value, value, value]
else:
return False
else:
return False
def GetPixelSpacingFromInfoFile(filepath):
filepath = utils.decode(filepath, const.FS_ENCODE)
if filepath.endswith('.DS_Store'):
return False
fi = open(filepath, 'r')
lines = fi.readlines()
measure_scale = 'mm'
values = []
if len(lines) > 0:
#info text from avizo
if '# Avizo Stacked Slices' in lines[0]:
value = lines[2].split(' ')
spx = float(value[1])
spy = float(value[2])
value = lines[5].split(' ')
spz = float(value[1])
return [spx * 0.001, spy * 0.001, spz * 0.001]
else:
#info text from skyscan
for l in lines:
if 'Pixel Size' in l:
if 'um' in l:
measure_scale = 'um'
value = l.split("=")[-1]
values.append(value)
if len(values) > 0:
value = values[-1]
value = value.replace('\n', '')
value = value.replace('\r', '')
#convert um to mm (InVesalius default)
if measure_scale == 'um':
value = float(value) * 0.001
measure_scale = 'mm'
elif measure_scale == 'nm':
value = float(value) * 0.000001
return [value, value, value]
else:
return False
else:
return False
def SaveProject(self, path=None, compress=False):
Publisher.sendMessage('Begin busy cursor')
session = ses.Session()
if path:
dirpath, filename = os.path.split(path)
session.SaveProject((dirpath, filename))
else:
dirpath, filename = session.project_path
if isinstance(filename, str):
filename = utils.decode(filename, const.FS_ENCODE)
proj = prj.Project()
prj.Project().SavePlistProject(dirpath, filename, compress)
session.SaveProject()
Publisher.sendMessage('End busy cursor')
def OnExportSurface(self, filename, filetype):
ftype_prefix = {
const.FILETYPE_STL: '.stl',
const.FILETYPE_VTP: '.vtp',
const.FILETYPE_PLY: '.ply',
const.FILETYPE_STL_ASCII: '.stl',
}
if filetype in ftype_prefix:
temp_file = tempfile.mktemp(suffix=ftype_prefix[filetype])
if _has_win32api:
utl.touch(temp_file)
_temp_file = temp_file
temp_file = win32api.GetShortPathName(temp_file)
os.remove(_temp_file)
temp_file = utl.decode(temp_file, const.FS_ENCODE)
try:
self._export_surface(temp_file, filetype)
except ValueError:
if wx.GetApp() is None:
print(
"It was not possible to export the surface because the surface is empty"
)
else:
wx.MessageBox(
_("It was not possible to export the surface because the surface is empty"
), _("Export surface error"))
return
try:
shutil.move(temp_file, filename)
except PermissionError as err:
dirpath = os.path.split(filename)[0]
if wx.GetApp() is None:
print(
_("It was not possible to export the surface because you don't have permission to write to {} folder: {}"
.format(dirpath, err)))
else:
dlg = dialogs.ErrorMessageBox(
None, _("Export surface error"),
"It was not possible to export the surface because you don't have permission to write to {}:\n{}"
.format(dirpath, err))
dlg.ShowModal()
dlg.Destroy()
os.remove(temp_file)
def SaveProject(self, path=None, compress=False):
Publisher.sendMessage('Begin busy cursor')
session = ses.Session()
if path:
dirpath, filename = os.path.split(path)
session.SaveProject((dirpath, filename))
else:
dirpath, filename = session.project_path
if isinstance(filename, str):
filename = utils.decode(filename, const.FS_ENCODE)
proj = prj.Project()
prj.Project().SavePlistProject(dirpath, filename, compress)
session.SaveProject()
Publisher.sendMessage('End busy cursor')
def Compress(folder, filename, filelist, compress=False):
tmpdir, tmpdir_ = os.path.split(folder)
current_dir = os.path.abspath(".")
temp_inv3 = tempfile.mktemp()
if _has_win32api:
touch(temp_inv3)
temp_inv3 = win32api.GetShortPathName(temp_inv3)
temp_inv3 = decode(temp_inv3, const.FS_ENCODE)
#os.chdir(tmpdir)
#file_list = glob.glob(os.path.join(tmpdir_,"*"))
if compress:
tar = tarfile.open(temp_inv3, "w:gz")
else:
tar = tarfile.open(temp_inv3, "w")
for name in filelist:
tar.add(name, arcname=os.path.join(tmpdir_, filelist[name]))
tar.close()
shutil.move(temp_inv3, filename)
def Compress(folder, filename, filelist, compress=False):
tmpdir, tmpdir_ = os.path.split(folder)
current_dir = os.path.abspath(".")
temp_inv3 = tempfile.mktemp()
if _has_win32api:
touch(temp_inv3)
temp_inv3 = win32api.GetShortPathName(temp_inv3)
temp_inv3 = decode(temp_inv3, const.FS_ENCODE)
#os.chdir(tmpdir)
#file_list = glob.glob(os.path.join(tmpdir_,"*"))
if compress:
tar = tarfile.open(temp_inv3, "w:gz")
else:
tar = tarfile.open(temp_inv3, "w")
for name in filelist:
tar.add(name, arcname=os.path.join(tmpdir_, filelist[name]))
tar.close()
shutil.move(temp_inv3, filename)
def OnExportSurface(self, filename, filetype):
ftype_prefix = {
const.FILETYPE_STL: '.stl',
const.FILETYPE_VTP: '.vtp',
const.FILETYPE_PLY: '.ply',
const.FILETYPE_STL_ASCII: '.stl',
}
if filetype in ftype_prefix:
temp_file = tempfile.mktemp(suffix=ftype_prefix[filetype])
if _has_win32api:
utl.touch(temp_file)
_temp_file = temp_file
temp_file = win32api.GetShortPathName(temp_file)
os.remove(_temp_file)
temp_file = utl.decode(temp_file, const.FS_ENCODE)
self._export_surface(temp_file, filetype)
shutil.move(temp_file, filename)
def OnExportSurface(self, filename, filetype):
ftype_prefix = {
const.FILETYPE_STL: '.stl',
const.FILETYPE_VTP: '.vtp',
const.FILETYPE_PLY: '.ply',
const.FILETYPE_STL_ASCII: '.stl',
}
if filetype in ftype_prefix:
temp_file = tempfile.mktemp(suffix=ftype_prefix[filetype])
if _has_win32api:
utl.touch(temp_file)
_temp_file = temp_file
temp_file = win32api.GetShortPathName(temp_file)
os.remove(_temp_file)
temp_file = utl.decode(temp_file, const.FS_ENCODE)
self._export_surface(temp_file, filetype)
shutil.move(temp_file, filename)
_("Vasculature - Hard"): (240, 80),
_("Vasculature - Soft"): (650, 160),
_("Contour"): (255, 127)
}
REDUCE_IMAGEDATA_QUALITY = 0
# PATHS
FS_ENCODE = sys.getfilesystemencoding()
if sys.platform == 'win32':
from invesalius.expanduser import expand_user
try:
USER_DIR = expand_user()
except:
USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
else:
USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
USER_INV_DIR = os.path.join(USER_DIR, u'.invesalius')
USER_PRESET_DIR = os.path.join(USER_INV_DIR, u'presets')
USER_LOG_DIR = os.path.join(USER_INV_DIR, u'logs')
FILE_PATH = utils.decode(os.path.split(__file__)[0], FS_ENCODE)
if hasattr(sys,"frozen") and (sys.frozen == "windows_exe"\
or sys.frozen == "console_exe"):
abs_path = os.path.abspath(FILE_PATH, u'..', u'..', u'..')
ICON_DIR = os.path.join(abs_path, u"icons")
SAMPLE_DIR = os.path.join(FILE_PATH, u'samples')
DOC_DIR = os.path.join(FILE_PATH, u'docs')
def SetLastDicomFolder(self, folder):
self.last_dicom_folder = decode(folder, FS_ENCODE)
self.WriteSessionFile()
def SavePlistProject(self, dir_, filename, compress=False):
dir_temp = decode(tempfile.mkdtemp(), const.FS_ENCODE)
self.compress = compress
filename_tmp = os.path.join(dir_temp, u'matrix.dat')
filelist = {}
project = {
# Format info
"format_version": const.INVESALIUS_ACTUAL_FORMAT_VERSION,
"invesalius_version": const.INVESALIUS_VERSION,
"date": datetime.datetime.now().isoformat(),
"compress": self.compress,
# case info
"name": self.name, # patient's name
"modality": self.modality, # CT, RMI, ...
"orientation": self.original_orientation,
"window_width": self.window,
"window_level": self.level,
"scalar_range": self.threshold_range,
"spacing": self.spacing,
"affine": self.affine,
}
# Saving the matrix containing the slices
matrix = {
'filename': u'matrix.dat',
'shape': self.matrix_shape,
'dtype': self.matrix_dtype,
}
project['matrix'] = matrix
filelist[self.matrix_filename] = 'matrix.dat'
#shutil.copyfile(self.matrix_filename, filename_tmp)
# Saving the masks
masks = {}
for index in self.mask_dict:
masks[str(index)] = self.mask_dict[index].SavePlist(dir_temp,
filelist)
project['masks'] = masks
# Saving the surfaces
surfaces = {}
for index in self.surface_dict:
surfaces[str(index)] = self.surface_dict[index].SavePlist(dir_temp,
filelist)
project['surfaces'] = surfaces
# Saving the measurements
measurements = self.GetMeasuresDict()
measurements_filename = 'measurements.plist'
temp_mplist = tempfile.mktemp()
plistlib.writePlist(measurements,
temp_mplist)
filelist[temp_mplist] = measurements_filename
project['measurements'] = measurements_filename
# Saving the annotations (empty in this version)
project['annotations'] = {}
# Saving the main plist
temp_plist = tempfile.mktemp()
plistlib.writePlist(project, temp_plist)
filelist[temp_plist] = 'main.plist'
# Compressing and generating the .inv3 file
path = os.path.join(dir_,filename)
Compress(dir_temp, path, filelist, compress)
# Removing the temp folder.
shutil.rmtree(dir_temp)
for f in filelist:
if filelist[f].endswith('.plist'):
os.remove(f)
def run(self):
grouper = self.grouper
reader = gdcm.ImageReader()
if _has_win32api:
try:
reader.SetFileName(
utils.encode(win32api.GetShortPathName(self.filepath),
const.FS_ENCODE))
except TypeError:
reader.SetFileName(win32api.GetShortPathName(self.filepath))
else:
try:
reader.SetFileName(utils.encode(self.filepath,
const.FS_ENCODE))
except TypeError:
reader.SetFileName(self.filepath)
if (reader.Read()):
file = reader.GetFile()
# Retrieve data set
dataSet = file.GetDataSet()
# Retrieve header
header = file.GetHeader()
stf = gdcm.StringFilter()
stf.SetFile(file)
field_dict = {}
data_dict = {}
tag = gdcm.Tag(0x0008, 0x0005)
ds = reader.GetFile().GetDataSet()
if ds.FindDataElement(tag):
encoding_value = str(
ds.GetDataElement(tag).GetValue()).split('\\')[0]
if encoding_value.startswith("Loaded"):
encoding = "ISO_IR 100"
else:
try:
encoding = const.DICOM_ENCODING_TO_PYTHON[
encoding_value]
except KeyError:
encoding = 'ISO_IR 100'
else:
encoding = "ISO_IR 100"
# Iterate through the Header
iterator = header.GetDES().begin()
while (not iterator.equal(header.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not (utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(
data[1], encoding)
else:
data_dict[group][field] = "Invalid Character"
# Iterate through the Data set
iterator = dataSet.GetDES().begin()
while (not iterator.equal(dataSet.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
# if (tag.GetGroup() == 0x0009 and tag.GetElement() == 0x10e3) \
# or (tag.GetGroup() == 0x0043 and tag.GetElement() == 0x1027):
# continue
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not (utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(
data[1], encoding, 'replace')
else:
data_dict[group][field] = "Invalid Character"
# -------------- To Create DICOM Thumbnail -----------
try:
data = data_dict[str(0x028)][str(0x1050)]
level = [float(value) for value in data.split('\\')][0]
data = data_dict[str(0x028)][str(0x1051)]
window = [float(value) for value in data.split('\\')][0]
except (KeyError, ValueError):
level = None
window = None
if _has_win32api:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(
win32api.GetShortPathName(self.filepath), window, level)
else:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(
self.filepath, window, level)
#------ Verify the orientation --------------------------------
img = reader.GetImage()
direc_cosines = img.GetDirectionCosines()
orientation = gdcm.Orientation()
try:
_type = orientation.GetType(tuple(direc_cosines))
except TypeError:
_type = orientation.GetType(direc_cosines)
label = orientation.GetLabel(_type)
# ---------- Refactory --------------------------------------
data_dict['invesalius'] = {'orientation_label': label}
# -------------------------------------------------------------
dict_file[self.filepath] = data_dict
#---------- Verify is DICOMDir -------------------------------
is_dicom_dir = 1
try:
if (data_dict[str(0x002)][str(0x002)] !=
"1.2.840.10008.1.3.10"): #DICOMDIR
is_dicom_dir = 0
except (KeyError):
is_dicom_dir = 0
if not (is_dicom_dir):
parser = dicom.Parser()
parser.SetDataImage(dict_file[self.filepath], self.filepath,
thumbnail_path)
dcm = dicom.Dicom()
#self.l.acquire()
dcm.SetParser(parser)
grouper.AddFile(dcm)
def __init__(self, grouper, filepath):
self.grouper = grouper
self.filepath = utils.decode(filepath, const.FS_ENCODE)
self.run()
def SavePlistProject(self, dir_, filename, compress=False):
dir_temp = decode(tempfile.mkdtemp(), const.FS_ENCODE)
self.compress = compress
filename_tmp = os.path.join(dir_temp, u'matrix.dat')
filelist = {}
project = {
# Format info
"format_version": const.INVESALIUS_ACTUAL_FORMAT_VERSION,
"invesalius_version": const.INVESALIUS_VERSION,
"date": datetime.datetime.now().isoformat(),
"compress": self.compress,
# case info
"name": self.name, # patient's name
"modality": self.modality, # CT, RMI, ...
"orientation": self.original_orientation,
"window_width": self.window,
"window_level": self.level,
"scalar_range": self.threshold_range,
"spacing": self.spacing,
"affine": self.affine,
}
# Saving the matrix containing the slices
matrix = {
'filename': u'matrix.dat',
'shape': self.matrix_shape,
'dtype': self.matrix_dtype,
}
project['matrix'] = matrix
filelist[self.matrix_filename] = 'matrix.dat'
#shutil.copyfile(self.matrix_filename, filename_tmp)
# Saving the masks
masks = {}
for index in self.mask_dict:
masks[str(index)] = self.mask_dict[index].SavePlist(
dir_temp, filelist)
project['masks'] = masks
# Saving the surfaces
surfaces = {}
for index in self.surface_dict:
surfaces[str(index)] = self.surface_dict[index].SavePlist(
dir_temp, filelist)
project['surfaces'] = surfaces
# Saving the measurements
measurements = self.GetMeasuresDict()
measurements_filename = 'measurements.plist'
temp_mplist = tempfile.mktemp()
plistlib.writePlist(measurements, temp_mplist)
filelist[temp_mplist] = measurements_filename
project['measurements'] = measurements_filename
# Saving the annotations (empty in this version)
project['annotations'] = {}
# Saving the main plist
temp_plist = tempfile.mktemp()
plistlib.writePlist(project, temp_plist)
filelist[temp_plist] = 'main.plist'
# Compressing and generating the .inv3 file
path = os.path.join(dir_, filename)
Compress(dir_temp, path, filelist, compress)
# Removing the temp folder.
shutil.rmtree(dir_temp)
for f in filelist:
if filelist[f].endswith('.plist'):
os.remove(f)
def run(self):
grouper = self.grouper
reader = gdcm.ImageReader()
if _has_win32api:
try:
reader.SetFileName(utils.encode(win32api.GetShortPathName(self.filepath),
const.FS_ENCODE))
except TypeError:
reader.SetFileName(win32api.GetShortPathName(self.filepath))
else:
try:
reader.SetFileName(utils.encode(self.filepath, const.FS_ENCODE))
except TypeError:
reader.SetFileName(self.filepath)
if (reader.Read()):
file = reader.GetFile()
# Retrieve data set
dataSet = file.GetDataSet()
# Retrieve header
header = file.GetHeader()
stf = gdcm.StringFilter()
stf.SetFile(file)
field_dict = {}
data_dict = {}
tag = gdcm.Tag(0x0008, 0x0005)
ds = reader.GetFile().GetDataSet()
if ds.FindDataElement(tag):
encoding_value = str(ds.GetDataElement(tag).GetValue()).split('\\')[0]
if encoding_value.startswith("Loaded"):
encoding = "ISO_IR 100"
else:
try:
encoding = const.DICOM_ENCODING_TO_PYTHON[encoding_value]
except KeyError:
encoding = 'ISO_IR 100'
else:
encoding = "ISO_IR 100"
# Iterate through the Header
iterator = header.GetDES().begin()
while (not iterator.equal(header.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not(utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(data[1], encoding)
else:
data_dict[group][field] = "Invalid Character"
# Iterate through the Data set
iterator = dataSet.GetDES().begin()
while (not iterator.equal(dataSet.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
# if (tag.GetGroup() == 0x0009 and tag.GetElement() == 0x10e3) \
# or (tag.GetGroup() == 0x0043 and tag.GetElement() == 0x1027):
# continue
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not(utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(data[1], encoding, 'replace')
else:
data_dict[group][field] = "Invalid Character"
# -------------- To Create DICOM Thumbnail -----------
try:
data = data_dict[str(0x028)][str(0x1050)]
level = [float(value) for value in data.split('\\')][0]
data = data_dict[str(0x028)][str(0x1051)]
window = [float(value) for value in data.split('\\')][0]
except(KeyError, ValueError):
level = None
window = None
if _has_win32api:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(win32api.GetShortPathName(self.filepath), window, level)
else:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(self.filepath, window, level)
#------ Verify the orientation --------------------------------
img = reader.GetImage()
direc_cosines = img.GetDirectionCosines()
orientation = gdcm.Orientation()
try:
_type = orientation.GetType(tuple(direc_cosines))
except TypeError:
_type = orientation.GetType(direc_cosines)
label = orientation.GetLabel(_type)
# ---------- Refactory --------------------------------------
data_dict['invesalius'] = {'orientation_label' : label}
# -------------------------------------------------------------
dict_file[self.filepath] = data_dict
#---------- Verify is DICOMDir -------------------------------
is_dicom_dir = 1
try:
if (data_dict[str(0x002)][str(0x002)] != "1.2.840.10008.1.3.10"): #DICOMDIR
is_dicom_dir = 0
except(KeyError):
is_dicom_dir = 0
if not(is_dicom_dir):
parser = dicom.Parser()
parser.SetDataImage(dict_file[self.filepath], self.filepath, thumbnail_path)
dcm = dicom.Dicom()
#self.l.acquire()
dcm.SetParser(parser)
grouper.AddFile(dcm)
def __init__(self, bmp_file, filepath):
self.bmp_file = bmp_file
self.filepath = utils.decode(filepath, const.FS_ENCODE)
self.run()
def __init__(self, grouper, filepath):
self.grouper = grouper
self.filepath = utils.decode(filepath, const.FS_ENCODE)
self.run()
def __init__(self, bmp_file, filepath):
self.bmp_file = bmp_file
self.filepath = utils.decode(filepath, const.FS_ENCODE)
self.run()
_("Vasculature - Hard"):(240,80),
_("Vasculature - Soft"):(650,160),
_("Contour"): (255, 127)}
REDUCE_IMAGEDATA_QUALITY = 0
# PATHS
FS_ENCODE = sys.getfilesystemencoding()
if sys.platform == 'win32':
from invesalius.expanduser import expand_user
try:
USER_DIR = expand_user()
except:
USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
else:
USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
USER_INV_DIR = os.path.join(USER_DIR, u'.invesalius')
USER_PRESET_DIR = os.path.join(USER_INV_DIR, u'presets')
USER_LOG_DIR = os.path.join(USER_INV_DIR, u'logs')
FILE_PATH = utils.decode(os.path.split(__file__)[0], FS_ENCODE)
if hasattr(sys,"frozen") and (sys.frozen == "windows_exe"\
or sys.frozen == "console_exe"):
abs_path = os.path.abspath(FILE_PATH, u'..', u'..', u'..')
ICON_DIR = os.path.join(abs_path, u"icons")
SAMPLE_DIR = os.path.join(FILE_PATH, u'samples')
DOC_DIR = os.path.join(FILE_PATH, u'docs')
# _SplashScreen = wx.SplashScreen
import invesalius.gui.language_dialog as lang_dlg
import invesalius.i18n as i18n
import invesalius.session as ses
import invesalius.utils as utils
FS_ENCODE = sys.getfilesystemencoding()
if sys.platform == 'win32':
from invesalius.expanduser import expand_user
try:
USER_DIR = expand_user()
except:
USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
else:
USER_DIR = utils.decode(os.path.expanduser('~'),FS_ENCODE)
USER_INV_DIR = os.path.join(USER_DIR, u'.invesalius')
USER_PRESET_DIR = os.path.join(USER_INV_DIR, u'presets')
USER_RAYCASTING_PRESETS_DIRECTORY = os.path.join(USER_PRESET_DIR, u'raycasting')
USER_LOG_DIR = os.path.join(USER_INV_DIR, u'logs')
# ------------------------------------------------------------------
if sys.platform in ('linux2', 'linux', 'win32'):
try:
tmp_var = wx.GetXDisplay
except AttributeError:
# A workaround to make InVesalius run with wxPython4 from Ubuntu 18.04
# _SplashScreen = wx.SplashScreen
import invesalius.gui.language_dialog as lang_dlg
import invesalius.i18n as i18n
import invesalius.session as ses
import invesalius.utils as utils
FS_ENCODE = sys.getfilesystemencoding()
if sys.platform == 'win32':
from invesalius.expanduser import expand_user
try:
USER_DIR = expand_user()
except:
USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
else:
USER_DIR = utils.decode(os.path.expanduser('~'),FS_ENCODE)
USER_INV_DIR = os.path.join(USER_DIR, u'.invesalius')
USER_PRESET_DIR = os.path.join(USER_INV_DIR, u'presets')
USER_RAYCASTING_PRESETS_DIRECTORY = os.path.join(USER_PRESET_DIR, u'raycasting')
USER_LOG_DIR = os.path.join(USER_INV_DIR, u'logs')
# ------------------------------------------------------------------
if sys.platform in ('linux2', 'linux', 'win32'):
try:
tmp_var = wx.GetXDisplay
except AttributeError:
# A workaround to make InVesalius run with wxPython4 from Ubuntu 18.04