def OpenPlist(self, filename):
translate_to_x = {
"Bone": _("Bone"),
"Soft Tissue": _("Soft Tissue"),
"Enamel (Adult)": _("Enamel (Adult)"),
"Enamel (Child)": _("Enamel (Child)"),
"Compact Bone (Adult)": _("Compact Bone (Adult)"),
"Compact Bone (Child)": _("Compact Bone (Child)"),
"Spongial Bone (Adult)": _("Spongial Bone (Adult)"),
"Spongial Bone (Child)": _("Spongial Bone (Child)"),
"Muscle Tissue (Adult)": _("Muscle Tissue (Adult)"),
"Muscle Tissue (Child)": _("Muscle Tissue (Child)"),
"Fat Tissue (Adult)": _("Fat Tissue (Adult)"),
"Fat Tissue (Child)": _("Fat Tissue (Child)"),
"Skin Tissue (Adult)": _("Skin Tissue (Adult)"),
"Skin Tissue (Child)": _("Skin Tissue (Child)"),
"Custom": _("Custom")
}
with open(filename, 'rb') as f:
p = plistlib.load(f, fmt=plistlib.FMT_XML)
thresh_mri = p['thresh_mri'].copy()
thresh_ct = p['thresh_ct'].copy()
thresh_ct_new = {}
for name in thresh_ct.keys():
thresh_ct_new[translate_to_x[name]] = thresh_ct[name]
thresh_mri_new = {}
for name in thresh_mri.keys():
thresh_mri_new[translate_to_x[name]] = thresh_mri[name]
self.thresh_mri = TwoWaysDictionary(thresh_mri_new)
self.thresh_ct = TwoWaysDictionary(thresh_ct_new)
def OpenPlist(self, filename):
translate_to_x = {
"Bone": "Bone",
"Soft Tissue": "Soft Tissue",
"Enamel (Adult)": "Enamel (Adult)",
"Enamel (Child)": "Enamel (Child)",
"Compact Bone (Adult)": "Compact Bone (Adult)",
"Compact Bone (Child)": "Compact Bone (Child)",
"Spongial Bone (Adult)": "Spongial Bone (Adult)",
"Spongial Bone (Child)": "Spongial Bone (Child)",
"Muscle Tissue (Adult)": "Muscle Tissue (Adult)",
"Muscle Tissue (Child)": "Muscle Tissue (Child)",
"Fat Tissue (Adult)": "Fat Tissue (Adult)",
"Fat Tissue (Child)": "Fat Tissue (Child)",
"Skin Tissue (Adult)": "Skin Tissue (Adult)",
"Skin Tissue (Child)": "Skin Tissue (Child)",
"Custom": "Custom"
}
p = plistlib.readPlist(filename)
thresh_mri = p['thresh_mri'].copy()
thresh_ct = p['thresh_ct'].copy()
thresh_ct_new = {}
for name in thresh_ct.keys():
thresh_ct_new[translate_to_x[name]] = thresh_ct[name]
thresh_mri_new = {}
for name in thresh_mri.keys():
thresh_mri_new[translate_to_x[name]] = thresh_mri[name]
self.thresh_mri = TwoWaysDictionary(thresh_mri_new)
self.thresh_ct = TwoWaysDictionary(thresh_ct_new)
def OpenPlist(self, filename):
translate_to_x = {"Bone":_("Bone"),
"Soft Tissue":_("Soft Tissue"),
"Enamel (Adult)":_("Enamel (Adult)"),
"Enamel (Child)": _("Enamel (Child)"),
"Compact Bone (Adult)": _("Compact Bone (Adult)"),
"Compact Bone (Child)":_("Compact Bone (Child)"),
"Spongial Bone (Adult)":_("Spongial Bone (Adult)"),
"Spongial Bone (Child)":_("Spongial Bone (Child)"),
"Muscle Tissue (Adult)":_("Muscle Tissue (Adult)"),
"Muscle Tissue (Child)":_("Muscle Tissue (Child)"),
"Fat Tissue (Adult)":_("Fat Tissue (Adult)"),
"Fat Tissue (Child)":_("Fat Tissue (Child)"),
"Skin Tissue (Adult)":_("Skin Tissue (Adult)"),
"Skin Tissue (Child)":_("Skin Tissue (Child)"),
"Custom":_("Custom")}
p = plistlib.readPlist(filename)
thresh_mri = p['thresh_mri'].copy()
thresh_ct = p['thresh_ct'].copy()
thresh_ct_new = {}
for name in thresh_ct.keys():
thresh_ct_new[translate_to_x[name]] = thresh_ct[name]
thresh_mri_new = {}
for name in thresh_mri.keys():
thresh_mri_new[translate_to_x[name]] = thresh_mri[name]
self.thresh_mri = TwoWaysDictionary(thresh_mri_new)
self.thresh_ct = TwoWaysDictionary(thresh_ct_new)
def __init__(self):
# Patient/ acquistion information
self.name = ''
self.modality = ''
self.original_orientation = ''
self.window = ''
self.level = ''
self.affine = ''
# Masks (vtkImageData)
self.mask_dict = TwoWaysDictionary()
# Surfaces are (vtkPolyData)
self.surface_dict = {}
self.last_surface_index = -1
# Measurements
self.measurement_dict = {}
# TODO: Future ++
self.annotation_dict = {}
self.compress = False
# InVesalius related data
# So we can find bugs and reproduce user-related problems
self.invesalius_version = version.get_svn_revision()
self.presets = Presets()
self.threshold_modes = self.presets.thresh_ct
self.threshold_range = ''
self.raycasting_preset = ''
def RemoveMask(self, index):
new_dict = TwoWaysDictionary()
new_index = 0
for i in self.mask_dict:
if i == index:
mask = self.mask_dict[i]
mask.cleanup()
else:
new_dict[new_index] = self.mask_dict[i]
self.mask_dict[i] = new_index
new_index += 1
self.mask_dict = new_dict
def __init__(self):
self.thresh_ct = TwoWaysDictionary({
_("Bone"): (226, 3071),
_("Soft Tissue"): (-700, 225),
_("Enamel (Adult)"): (1553, 2850),
_("Enamel (Child)"): (2042, 3071),
_("Compact Bone (Adult)"): (662, 1988),
_("Compact Bone (Child)"): (586, 2198),
_("Spongial Bone (Adult)"): (148, 661),
_("Spongial Bone (Child)"): (156, 585),
_("Muscle Tissue (Adult)"): (-5, 135),
_("Muscle Tissue (Child)"): (-25, 139),
_("Fat Tissue (Adult)"): (-205, -51),
_("Fat Tissue (Child)"): (-212, -72),
_("Skin Tissue (Adult)"): (-718, -177),
_("Skin Tissue (Child)"): (-766, -202),
_("Custom"): (0, 0)
})
self.thresh_mri = TwoWaysDictionary({
_("Bone"): (1250, 4095),
_("Soft Tissue"): (324, 1249),
_("Enamel (Adult)"): (2577, 3874),
_("Enamel (Child)"): (3066, 4095),
_("Compact Bone (Adult)"): (1686, 3012),
_("Compact Bone (Child)"): (1610, 3222),
_("Spongial Bone (Adult)"): (1172, 1685),
_("Spongial Bone (Child)"): (1180, 1609),
_("Muscle Tissue (Adult)"): (1019, 1159),
_("Muscle Tissue (Child)"): (999, 1163),
_("Fat Tissue (Adult)"): (819, 973),
_("Fat Tissue (Child)"): (812, 952),
_("Skin Tissue (Adult)"): (306, 847),
_("Skin Tissue (Child)"): (258, 822),
_("Custom"): (0, 0)
})
self.__bind_events()
def __init__(self):
self.thresh_ct = TwoWaysDictionary({
_("Bone"):(226,3071),
_("Soft Tissue"):(-700,225),
_("Enamel (Adult)"):(1553,2850),
_("Enamel (Child)"):(2042,3071),
_("Compact Bone (Adult)"):(662,1988),
_("Compact Bone (Child)"):(586,2198),
_("Spongial Bone (Adult)"):(148,661),
_("Spongial Bone (Child)"):(156,585),
_("Muscle Tissue (Adult)"):(-5,135),
_("Muscle Tissue (Child)"):(-25,139),
_("Fat Tissue (Adult)"):(-205,-51),
_("Fat Tissue (Child)"):(-212,-72),
_("Skin Tissue (Adult)"):(-718,-177),
_("Skin Tissue (Child)"):(-766,-202),
_("Custom"):('', '')
})
self.thresh_mri = TwoWaysDictionary({
_("Bone"):(1250,4095),
_("Soft Tissue"):(324,1249),
_("Enamel (Adult)"):(2577,3874),
_("Enamel (Child)"):(3066,4095),
_("Compact Bone (Adult)"):(1686,3012),
_("Compact Bone (Child)"):(1610,3222),
_("Spongial Bone (Adult)"):(1172,1685),
_("Spongial Bone (Child)"):(1180,1609),
_("Muscle Tissue (Adult)"):(1019,1159),
_("Muscle Tissue (Child)"):(999,1163),
_("Fat Tissue (Adult)"):(819,973),
_("Fat Tissue (Child)"):(812,952),
_("Skin Tissue (Adult)"):(306,847),
_("Skin Tissue (Child)"):(258,822),
_("Custom"):('', '')
})
self.__bind_events()
class Presets():
def __init__(self):
self.thresh_ct = TwoWaysDictionary({
_("Bone"): (226, 3071),
_("Soft Tissue"): (-700, 225),
_("Enamel (Adult)"): (1553, 2850),
_("Enamel (Child)"): (2042, 3071),
_("Compact Bone (Adult)"): (662, 1988),
_("Compact Bone (Child)"): (586, 2198),
_("Spongial Bone (Adult)"): (148, 661),
_("Spongial Bone (Child)"): (156, 585),
_("Muscle Tissue (Adult)"): (-5, 135),
_("Muscle Tissue (Child)"): (-25, 139),
_("Fat Tissue (Adult)"): (-205, -51),
_("Fat Tissue (Child)"): (-212, -72),
_("Skin Tissue (Adult)"): (-718, -177),
_("Skin Tissue (Child)"): (-766, -202),
_("Custom"): (0, 0)
})
self.thresh_mri = TwoWaysDictionary({
_("Bone"): (1250, 4095),
_("Soft Tissue"): (324, 1249),
_("Enamel (Adult)"): (2577, 3874),
_("Enamel (Child)"): (3066, 4095),
_("Compact Bone (Adult)"): (1686, 3012),
_("Compact Bone (Child)"): (1610, 3222),
_("Spongial Bone (Adult)"): (1172, 1685),
_("Spongial Bone (Child)"): (1180, 1609),
_("Muscle Tissue (Adult)"): (1019, 1159),
_("Muscle Tissue (Child)"): (999, 1163),
_("Fat Tissue (Adult)"): (819, 973),
_("Fat Tissue (Child)"): (812, 952),
_("Skin Tissue (Adult)"): (306, 847),
_("Skin Tissue (Child)"): (258, 822),
_("Custom"): (0, 0)
})
self.__bind_events()
def __bind_events(self):
Publisher.subscribe(self.UpdateThresholdModes,
'Update threshold limits list')
def UpdateThresholdModes(self, threshold_range):
thresh_min, thresh_max = threshold_range
presets_list = (self.thresh_ct, self.thresh_mri)
for presets in presets_list:
for key in presets:
(t_min, t_max) = presets[key]
print(key, t_min, t_max)
if (t_min is None) or (t_max is None): # setting custom preset
t_min = thresh_min
t_max = thresh_max
if (t_min < thresh_min):
t_min = thresh_min
if (t_max > thresh_max):
t_max = thresh_max
# This has happened in Analyze files
# TODO: find a good solution for presets in Analyze files
if (t_min > thresh_max):
t_min = thresh_min
if (t_max < thresh_min):
t_max = thresh_max
presets[key] = (t_min, t_max)
Publisher.sendMessage('Update threshold limits',
threshold_range=(thresh_min, thresh_max))
def SavePlist(self, filename):
filename = "%s$%s" % (filename, 'presets.plist')
preset = {}
translate_to_en = {
_("Bone"): "Bone",
_("Soft Tissue"): "Soft Tissue",
_("Enamel (Adult)"): "Enamel (Adult)",
_("Enamel (Child)"): "Enamel (Child)",
_("Compact Bone (Adult)"): "Compact Bone (Adult)",
_("Compact Bone (Child)"): "Compact Bone (Child)",
_("Spongial Bone (Adult)"): "Spongial Bone (Adult)",
_("Spongial Bone (Child)"): "Spongial Bone (Child)",
_("Muscle Tissue (Adult)"): "Muscle Tissue (Adult)",
_("Muscle Tissue (Child)"): "Muscle Tissue (Child)",
_("Fat Tissue (Adult)"): "Fat Tissue (Adult)",
_("Fat Tissue (Child)"): "Fat Tissue (Child)",
_("Skin Tissue (Adult)"): "Skin Tissue (Adult)",
_("Skin Tissue (Child)"): "Skin Tissue (Child)",
_("Custom"): "Custom"
}
thresh_mri_new = {}
for name in self.thresh_mri.keys():
thresh_mri_new[translate_to_en[name]] = self.thresh_mri[name]
thresh_ct_new = {}
for name in self.thresh_ct.keys():
thresh_ct_new[translate_to_en[name]] = self.thresh_ct[name]
preset['thresh_mri'] = thresh_mri_new
preset['thresh_ct'] = thresh_ct_new
with open(filename, 'w+b') as f:
plistlib.dump(preset, f)
return os.path.split(filename)[1]
def OpenPlist(self, filename):
translate_to_x = {
"Bone": _("Bone"),
"Soft Tissue": _("Soft Tissue"),
"Enamel (Adult)": _("Enamel (Adult)"),
"Enamel (Child)": _("Enamel (Child)"),
"Compact Bone (Adult)": _("Compact Bone (Adult)"),
"Compact Bone (Child)": _("Compact Bone (Child)"),
"Spongial Bone (Adult)": _("Spongial Bone (Adult)"),
"Spongial Bone (Child)": _("Spongial Bone (Child)"),
"Muscle Tissue (Adult)": _("Muscle Tissue (Adult)"),
"Muscle Tissue (Child)": _("Muscle Tissue (Child)"),
"Fat Tissue (Adult)": _("Fat Tissue (Adult)"),
"Fat Tissue (Child)": _("Fat Tissue (Child)"),
"Skin Tissue (Adult)": _("Skin Tissue (Adult)"),
"Skin Tissue (Child)": _("Skin Tissue (Child)"),
"Custom": _("Custom")
}
with open(filename, 'rb') as f:
p = plistlib.load(f, fmt=plistlib.FMT_XML)
thresh_mri = p['thresh_mri'].copy()
thresh_ct = p['thresh_ct'].copy()
thresh_ct_new = {}
for name in thresh_ct.keys():
thresh_ct_new[translate_to_x[name]] = thresh_ct[name]
thresh_mri_new = {}
for name in thresh_mri.keys():
thresh_mri_new[translate_to_x[name]] = thresh_mri[name]
self.thresh_mri = TwoWaysDictionary(thresh_mri_new)
self.thresh_ct = TwoWaysDictionary(thresh_ct_new)
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')
with open(main_plist, 'r+b') as f:
project = plistlib.load(f, fmt=plistlib.FMT_XML)
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"]
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']
if project.get("affine", ""):
self.affine = project["affine"]
# Opening the masks
self.mask_dict = TwoWaysDictionary()
for index in sorted(project.get("masks", []), key=lambda x: int(x)):
filename = project["masks"][index]
filepath = os.path.join(dirpath, filename)
m = msk.Mask()
m.spacing = self.spacing
m.OpenPList(filepath)
m.index = len(self.mask_dict)
self.mask_dict[m.index] = m
# Opening the surfaces
self.surface_dict = {}
for index in sorted(project.get("surfaces", []), key=lambda x: int(x)):
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):
with open(measures_file, 'r+b') as f:
measurements = plistlib.load(f, fmt=plistlib.FMT_XML)
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
class Presets():
def __init__(self):
self.thresh_ct = TwoWaysDictionary({
_("Bone"):(226,3071),
_("Soft Tissue"):(-700,225),
_("Enamel (Adult)"):(1553,2850),
_("Enamel (Child)"):(2042,3071),
_("Compact Bone (Adult)"):(662,1988),
_("Compact Bone (Child)"):(586,2198),
_("Spongial Bone (Adult)"):(148,661),
_("Spongial Bone (Child)"):(156,585),
_("Muscle Tissue (Adult)"):(-5,135),
_("Muscle Tissue (Child)"):(-25,139),
_("Fat Tissue (Adult)"):(-205,-51),
_("Fat Tissue (Child)"):(-212,-72),
_("Skin Tissue (Adult)"):(-718,-177),
_("Skin Tissue (Child)"):(-766,-202),
_("Custom"):('', '')
})
self.thresh_mri = TwoWaysDictionary({
_("Bone"):(1250,4095),
_("Soft Tissue"):(324,1249),
_("Enamel (Adult)"):(2577,3874),
_("Enamel (Child)"):(3066,4095),
_("Compact Bone (Adult)"):(1686,3012),
_("Compact Bone (Child)"):(1610,3222),
_("Spongial Bone (Adult)"):(1172,1685),
_("Spongial Bone (Child)"):(1180,1609),
_("Muscle Tissue (Adult)"):(1019,1159),
_("Muscle Tissue (Child)"):(999,1163),
_("Fat Tissue (Adult)"):(819,973),
_("Fat Tissue (Child)"):(812,952),
_("Skin Tissue (Adult)"):(306,847),
_("Skin Tissue (Child)"):(258,822),
_("Custom"):('', '')
})
self.__bind_events()
def __bind_events(self):
Publisher.subscribe(self.UpdateThresholdModes,
'Update threshold limits list')
def UpdateThresholdModes(self, evt):
thresh_min, thresh_max = evt.data
presets_list = (self.thresh_ct, self.thresh_mri)
for presets in presets_list:
for key in presets:
(t_min, t_max) = presets[key]
if (t_min is None) or (t_max is None): # setting custom preset
t_min = thresh_min
t_max = thresh_max
if (t_min < thresh_min):
t_min = thresh_min
if (t_max > thresh_max):
t_max = thresh_max
# This has happened in Analyze files
# TODO: find a good solution for presets in Analyze files
if (t_min > thresh_max):
t_min = thresh_min
if (t_max < thresh_min):
t_max = thresh_max
presets[key] = (t_min, t_max)
Publisher.sendMessage('Update threshold limits', (thresh_min,
thresh_max))
def SavePlist(self, filename):
filename = "%s$%s" % (filename, 'presets.plist')
preset = {}
translate_to_en = {_("Bone"):"Bone",
_("Soft Tissue"):"Soft Tissue",
_("Enamel (Adult)"):"Enamel (Adult)",
_("Enamel (Child)"): "Enamel (Child)",
_("Compact Bone (Adult)"):"Compact Bone (Adult)",
_("Compact Bone (Child)"):"Compact Bone (Child)",
_("Spongial Bone (Adult)"):"Spongial Bone (Adult)",
_("Spongial Bone (Child)"):"Spongial Bone (Child)",
_("Muscle Tissue (Adult)"):"Muscle Tissue (Adult)",
_("Muscle Tissue (Child)"):"Muscle Tissue (Child)",
_("Fat Tissue (Adult)"):"Fat Tissue (Adult)",
_("Fat Tissue (Child)"):"Fat Tissue (Child)",
_("Skin Tissue (Adult)"):"Skin Tissue (Adult)",
_("Skin Tissue (Child)"):"Skin Tissue (Child)",
_("Custom"):"Custom"}
thresh_mri_new = {}
for name in self.thresh_mri.keys():
thresh_mri_new[translate_to_en[name]] = self.thresh_mri[name]
thresh_ct_new = {}
for name in self.thresh_ct.keys():
thresh_ct_new[translate_to_en[name]] = self.thresh_ct[name]
preset['thresh_mri'] = thresh_mri_new
preset['thresh_ct'] = thresh_ct_new
plistlib.writePlist(preset, filename)
return os.path.split(filename)[1]
def OpenPlist(self, filename):
translate_to_x = {"Bone":_("Bone"),
"Soft Tissue":_("Soft Tissue"),
"Enamel (Adult)":_("Enamel (Adult)"),
"Enamel (Child)": _("Enamel (Child)"),
"Compact Bone (Adult)": _("Compact Bone (Adult)"),
"Compact Bone (Child)":_("Compact Bone (Child)"),
"Spongial Bone (Adult)":_("Spongial Bone (Adult)"),
"Spongial Bone (Child)":_("Spongial Bone (Child)"),
"Muscle Tissue (Adult)":_("Muscle Tissue (Adult)"),
"Muscle Tissue (Child)":_("Muscle Tissue (Child)"),
"Fat Tissue (Adult)":_("Fat Tissue (Adult)"),
"Fat Tissue (Child)":_("Fat Tissue (Child)"),
"Skin Tissue (Adult)":_("Skin Tissue (Adult)"),
"Skin Tissue (Child)":_("Skin Tissue (Child)"),
"Custom":_("Custom")}
p = plistlib.readPlist(filename)
thresh_mri = p['thresh_mri'].copy()
thresh_ct = p['thresh_ct'].copy()
thresh_ct_new = {}
for name in thresh_ct.keys():
thresh_ct_new[translate_to_x[name]] = thresh_ct[name]
thresh_mri_new = {}
for name in thresh_mri.keys():
thresh_mri_new[translate_to_x[name]] = thresh_mri[name]
self.thresh_mri = TwoWaysDictionary(thresh_mri_new)
self.thresh_ct = TwoWaysDictionary(thresh_ct_new)
