def OnImportFolder(self, folder):
Publisher.sendMessage('Begin busy cursor')
folder = os.path.abspath(folder)
proj = prj.Project()
proj.load_from_folder(folder)
self.Slice = sl.Slice()
self.Slice._open_image_matrix(proj.matrix_filename,
tuple(proj.matrix_shape),
proj.matrix_dtype)
self.Slice.window_level = proj.level
self.Slice.window_width = proj.window
Publisher.sendMessage('Update threshold limits list',
threshold_range=proj.threshold_range)
session = ses.Session()
filename = proj.name + ".inv3"
filename = filename.replace("/",
"") #Fix problem case other/Skull_DICOM
dirpath = session.CreateProject(filename)
self.LoadProject()
Publisher.sendMessage("Enable state project", state=True)
Publisher.sendMessage('End busy cursor')
def on_show(self):
self.history._config_undo_redo(self.is_shown)
if ses.Session().mask_3d_preview:
Publisher.sendMessage('Show mask preview',
index=self.index,
flag=bool(self.is_shown))
Publisher.sendMessage("Render volume viewer")
def CreateDicomProject(self, dicom, matrix, matrix_filename):
name_to_const = {
"AXIAL": const.AXIAL,
"CORONAL": const.CORONAL,
"SAGITTAL": const.SAGITAL
}
proj = prj.Project()
proj.name = dicom.patient.name
proj.modality = dicom.acquisition.modality
proj.SetAcquisitionModality(dicom.acquisition.modality)
proj.matrix_shape = matrix.shape
proj.matrix_dtype = matrix.dtype.name
proj.matrix_filename = matrix_filename
#proj.imagedata = imagedata
proj.dicom_sample = dicom
proj.original_orientation =\
name_to_const[dicom.image.orientation_label]
# Forcing to Axial
# proj.original_orientation = const.AXIAL
proj.window = float(dicom.image.window)
proj.level = float(dicom.image.level)
proj.threshold_range = int(matrix.min()), int(matrix.max())
proj.spacing = self.Slice.spacing
######
session = ses.Session()
filename = proj.name + ".inv3"
filename = filename.replace("/",
"") #Fix problem case other/Skull_DICOM
dirpath = session.CreateProject(filename)
def OpenProject(self, filepath):
Publisher.sendMessage('Begin busy cursor')
path = os.path.abspath(filepath)
proj = prj.Project()
proj.OpenPlistProject(path)
proj.SetAcquisitionModality(proj.modality)
self.Slice = sl.Slice()
self.Slice._open_image_matrix(proj.matrix_filename,
tuple(proj.matrix_shape),
proj.matrix_dtype)
self.Slice.window_level = proj.level
self.Slice.window_width = proj.window
if proj.affine:
self.Slice.affine = np.asarray(proj.affine).reshape(4, 4)
else:
self.Slice.affine = None
Publisher.sendMessage('Update threshold limits list',
threshold_range=proj.threshold_range)
self.LoadProject()
session = ses.Session()
session.OpenProject(filepath)
Publisher.sendMessage("Enable state project", state=True)
def disable_mask_preview(self):
ses.Session().mask_3d_preview = False
mask = self.Slice.current_mask
if mask is not None:
Publisher.sendMessage("Remove mask preview",
mask_3d_actor=mask.volume._actor)
Publisher.sendMessage("Render volume viewer")
def OnSlideChanging(self, evt):
thresh_min = self.gradient.GetMinValue()
thresh_max = self.gradient.GetMaxValue()
Publisher.sendMessage('Changing threshold values',
threshold_range=(thresh_min, thresh_max))
session = ses.Session()
session.ChangeProject()
def CreateOtherProject(self, name, matrix, matrix_filename):
name_to_const = {"AXIAL": const.AXIAL,
"CORONAL": const.CORONAL,
"SAGITTAL": const.SAGITAL}
proj = prj.Project()
proj.name = name
proj.modality = 'MRI'
proj.SetAcquisitionModality('MRI')
proj.matrix_shape = matrix.shape
proj.matrix_dtype = matrix.dtype.name
proj.matrix_filename = matrix_filename
# Orientation must be CORONAL in order to as_closes_canonical and
# swap axis in img2memmap to work in a standardized way.
# TODO: Create standard import image for all acquisition orientations
orientation = 'CORONAL'
proj.original_orientation =\
name_to_const[orientation]
proj.window = self.Slice.window_width
proj.level = self.Slice.window_level
proj.threshold_range = int(matrix.min()), int(matrix.max())
proj.spacing = self.Slice.spacing
proj.affine = self.affine.tolist()
######
session = ses.Session()
filename = proj.name + ".inv3"
filename = filename.replace("/", "") # Fix problem case other/Skull_DICOM
dirpath = session.CreateProject(filename)
def ShowDialogImportOtherFiles(self, id_type):
# Offer to save current project if necessary
session = ses.Session()
st = session.project_status
if (st == const.PROJ_NEW) or (st == const.PROJ_CHANGE):
filename = session.project_path[1]
answer = dialog.SaveChangesDialog2(filename)
if answer:
self.ShowDialogSaveProject()
self.CloseProject()
# Publisher.sendMessage("Enable state project", False)
Publisher.sendMessage('Set project name')
Publisher.sendMessage("Stop Config Recording")
Publisher.sendMessage("Set slice interaction style",
const.STATE_DEFAULT)
# Warning for limited support to Analyze format
if id_type == const.ID_ANALYZE_IMPORT:
dialog.ImportAnalyzeWarning()
# Import project treating compressed nifti exception
suptype = ('hdr', 'nii', 'nii.gz', 'par')
filepath = dialog.ShowImportOtherFilesDialog(id_type)
if filepath is not None:
name = filepath.rpartition('\\')[-1].split('.')
if name[-1] == 'gz':
name[1] = 'nii.gz'
filetype = name[1].lower()
if filetype in suptype:
Publisher.sendMessage("Open other files", filepath)
else:
dialog.ImportInvalidFiles()
def parse_comand_line():
"""
Handle command line arguments.
"""
session = ses.Session()
# Parse command line arguments
parser = op.OptionParser()
# -d or --debug: print all pubsub messagessent
parser.add_option("-d", "--debug", action="store_true", dest="debug")
parser.add_option('--no-gui', action='store_true', dest='no_gui')
# -i or --import: import DICOM directory
# chooses largest series
parser.add_option("-i", "--import", action="store", dest="dicom_dir")
parser.add_option("--import-all", action="store")
parser.add_option("-s", "--save", help="Save the project after an import.")
parser.add_option(
"-t",
"--threshold",
help="Define the threshold for the export (e.g. 100-780).")
parser.add_option("-e", "--export", help="Export to STL.")
parser.add_option("-a",
"--export-to-all",
help="Export to STL for all mask presets.")
options, args = parser.parse_args()
return options, args
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 UpdateSurfaceInterpolation(self):
interpolation = int(ses.Session().surface_interpolation)
key_actors = self.actors_dict.keys()
for key in self.actors_dict:
self.actors_dict[key].GetProperty().SetInterpolation(interpolation)
Publisher.sendMessage('Render volume viewer')
def redo_history(self, actual_slices):
self.history.redo(self.matrix, actual_slices)
self.modified()
# Marking the project as changed
session = ses.Session()
session.ChangeProject()
def UpdateCheck():
import urllib
import urllib2
import wx
import invesalius.session as ses
def _show_update_info():
from invesalius.gui import dialogs
msg = _(
"A new version of InVesalius is available. Do you want to open the download website now?"
)
title = _("Invesalius Update")
msgdlg = dialogs.UpdateMessageDialog(url)
#if (msgdlg.Show()==wx.ID_YES):
#wx.LaunchDefaultBrowser(url)
msgdlg.Show()
#msgdlg.Destroy()
print "Checking updates..."
# Check if there is a language set
#import invesalius.i18n as i18n import invesalius.session as ses
session = ses.Session()
install_lang = 0
if session.ReadLanguage():
lang = session.GetLanguage()
#if (lang != "False"):
#_ = i18n.InstallLanguage(lang)
#install_lang = 1
#if (install_lang==0):
#return
if session.ReadRandomId():
random_id = session.GetRandomId()
# Fetch update data from server
import invesalius.constants as const
url = "http://www.cti.gov.br/dt3d/invesalius/update/checkupdate.php"
headers = {
'User-Agent': 'Mozilla/5.0 (compatible; MSIE 5.5; Windows NT)'
}
data = {
'update_protocol_version': '1',
'invesalius_version': const.INVESALIUS_VERSION,
'platform': sys.platform,
'architecture': platform.architecture()[0],
'language': lang,
'random_id': random_id
}
data = urllib.urlencode(data)
req = urllib2.Request(url, data, headers)
try:
response = urllib2.urlopen(req, timeout=10)
except:
return
last = response.readline().rstrip()
url = response.readline().rstrip()
if (last != const.INVESALIUS_VERSION):
print " ...New update found!!! -> version:", last #, ", url=",url
wx.CallAfter(wx.CallLater, 1000, _show_update_info)
def TestLoadProjects2(self):
import invesalius.session as ses
session = ses.Session()
projects = session.recent_projects
for tuple in projects:
filename = tuple[1]
path = tuple[0]
self.LoadProject(filename, path)
def CloseProject(self):
proj = prj.Project()
proj.Close()
Publisher.sendMessage('Hide content panel')
Publisher.sendMessage('Close project data')
session = ses.Session()
session.CloseProject()
def _load_user_parameters(self):
session = ses.Session()
if 'surface' in session:
self._default_parameters.update(session['surface'])
else:
session['surface'] = self._default_parameters
session.WriteSessionFile()
def OnLinkExportSurface(self, evt=None):
"OnLinkExportSurface"
project = proj.Project()
n_surface = 0
for index in project.surface_dict:
if project.surface_dict[index].is_shown:
n_surface += 1
if n_surface:
if sys.platform == 'win32':
project_name = project.name
else:
project_name = project.name+".stl"
session = ses.Session()
last_directory = session.get('paths', 'last_directory_3d_surface', '')
dlg = wx.FileDialog(None,
_("Save 3D surface as..."), # title
last_directory, # last used directory
project_name, # filename
WILDCARD_SAVE_3D,
wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
dlg.SetFilterIndex(3) # default is STL
if dlg.ShowModal() == wx.ID_OK:
filetype_index = dlg.GetFilterIndex()
filetype = INDEX_TO_TYPE_3D[filetype_index]
filename = dlg.GetPath()
extension = INDEX_TO_EXTENSION[filetype_index]
if sys.platform != 'win32':
if filename.split(".")[-1] != extension:
filename = filename + "."+ extension
if filename:
session['paths']['last_directory_3d_surface'] = os.path.split(filename)[0]
session.WriteSessionFile()
Publisher.sendMessage('Export surface to file',
filename=filename, filetype=filetype)
if not os.path.exists(filename):
dlg = wx.MessageDialog(None,
_("It was not possible to save the surface."),
_("Error saving surface"),
wx.OK | wx.ICON_ERROR)
dlg.ShowModal()
dlg.Destroy()
else:
dlg = wx.MessageDialog(None,
_("You need to create a surface and make it ") +
_("visible before exporting it."),
'InVesalius 3',
wx.OK | wx.ICON_INFORMATION)
try:
dlg.ShowModal()
finally:
dlg.Destroy()
def UpdateCheck():
try:
from urllib.parse import urlencode
from urllib.request import urlopen, Request
from urllib.error import HTTPError
except ImportError:
from urllib import urlencode
from urllib2 import urlopen, Request, HTTPError
import wx
import invesalius.session as ses
def _show_update_info():
from invesalius.gui import dialogs
msg=_("A new version of InVesalius is available. Do you want to open the download website now?")
title=_("Invesalius Update")
msgdlg = dialogs.UpdateMessageDialog(url)
#if (msgdlg.Show()==wx.ID_YES):
#wx.LaunchDefaultBrowser(url)
msgdlg.Show()
#msgdlg.Destroy()
print("Checking updates...")
# Check if there is a language set
#import invesalius.i18n as i18n import invesalius.session as ses
session = ses.Session()
install_lang = 0
lang = session.GetLanguage()
random_id = session.GetRandomId()
if lang:
# Fetch update data from server
import invesalius.constants as const
url = "https://www.cti.gov.br/dt3d/invesalius/update/checkupdate.php"
headers = { 'User-Agent' : 'Mozilla/5.0 (compatible; MSIE 5.5; Windows NT)' }
data = {'update_protocol_version' : '1',
'invesalius_version' : const.INVESALIUS_VERSION,
'platform' : sys.platform,
'architecture' : platform.architecture()[0],
'language' : lang,
'random_id' : random_id }
data = urlencode(data).encode('utf8')
req = Request(url, data, headers)
try:
response = urlopen(req, timeout=10)
except:
return
last = response.readline().rstrip().decode('utf8')
url = response.readline().rstrip().decode('utf8')
try:
last_ver = LooseVersion(last)
actual_ver = LooseVersion(const.INVESALIUS_VERSION)
except (ValueError, AttributeError):
return
if last_ver > actual_ver:
print(" ...New update found!!! -> version:", last) #, ", url=",url
wx.CallAfter(wx.CallLater, 1000, _show_update_info)
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 CloseProject(self):
proj = prj.Project()
proj.Close()
Publisher.sendMessage('Set slice interaction style', const.STATE_DEFAULT)
Publisher.sendMessage('Hide content panel')
Publisher.sendMessage('Close project data')
session = ses.Session()
session.CloseProject()
def enable_mask_preview(self):
ses.Session().mask_3d_preview = True
mask = self.Slice.current_mask
if mask is not None:
self.Slice.do_threshold_to_all_slices(mask)
mask.create_3d_preview()
Publisher.sendMessage("Load mask preview",
mask_3d_actor=mask.volume._actor,
flag=True)
Publisher.sendMessage("Render volume viewer")
def parse_comand_line():
"""
Handle command line arguments.
"""
session = ses.Session()
# Parse command line arguments
parser = op.OptionParser()
# -d or --debug: print all pubsub messagessent
parser.add_option("-d", "--debug", action="store_true", dest="debug")
parser.add_option('--no-gui', action='store_true', dest='no_gui')
# -i or --import: import DICOM directory
# chooses largest series
parser.add_option("-i", "--import", action="store", dest="dicom_dir")
parser.add_option("--import-all", action="store")
parser.add_option("--import-folder", action="store", dest="import_folder")
parser.add_option("--remote-host", action="store", dest="remote_host")
parser.add_option("-s", "--save", help="Save the project after an import.")
parser.add_option(
"-t",
"--threshold",
help="Define the threshold for the export (e.g. 100-780).")
parser.add_option("-e", "--export", help="Export to STL.")
parser.add_option("-a",
"--export-to-all",
help="Export to STL for all mask presets.")
parser.add_option("--export-project",
help="Export slices and mask to HDF5 or Nifti file.")
parser.add_option(
"--no-masks",
action="store_false",
dest="save_masks",
default=True,
help="Make InVesalius not export mask when exporting project.")
parser.add_option("--use-pedal",
action="store_true",
dest="use_pedal",
help="Use an external trigger pedal")
options, args = parser.parse_args()
return options, args
def LoadPreferences(self):
se = ses.Session()
values = {const.RENDERING:se.rendering,
const.SURFACE_INTERPOLATION:se.surface_interpolation,
const.LANGUAGE:se.language,
const.SLICE_INTERPOLATION: se.slice_interpolation,
}
self.pnl_viewer2d.LoadSelection(values)
self.pnl_viewer3d.LoadSelection(values)
self.pnl_language.LoadSelection(values)
def __init__(self, frame):
self.surface_manager = srf.SurfaceManager()
self.volume = volume.Volume()
self.__bind_events()
self.frame = frame
self.progress_dialog = None
self.cancel_import = False
#Init session
session = ses.Session()
self.measure_manager = measures.MeasurementManager()
Publisher.sendMessage('Load Preferences')
def OnOpenRecentProject(self, filepath):
if os.path.exists(filepath):
session = ses.Session()
st = session.project_status
if (st == const.PROJ_NEW) or (st == const.PROJ_CHANGE):
filename = session.project_path[1]
answer = dialog.SaveChangesDialog2(filename)
if answer:
self.ShowDialogSaveProject()
if session.IsOpen():
self.CloseProject()
self.OpenProject(filepath)
else:
dialog.InexistentPath(filepath)
def SaveProject(self, path=None):
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
proj = prj.Project()
prj.Project().SavePlistProject(dirpath, filename)
session.SaveProject()
Publisher.sendMessage('End busy cursor')
def ReadDicomGroup(dir_):
patient_group = GetDicomGroups(dir_)
if len(patient_group) > 0:
filelist, dicom, zspacing = SelectLargerDicomGroup(patient_group)
filelist = SortFiles(filelist, dicom)
size = dicom.image.size
bits = dicom.image.bits_allocad
imagedata = CreateImageData(filelist, zspacing, size, bits)
session.Session().project_status = const.NEW_PROJECT
return imagedata, dicom
else:
return False
def ShowDialogSaveProject(self, saveas=False):
session = ses.Session()
if saveas or session.temp_item:
proj = prj.Project()
filepath, compress = dialog.ShowSaveAsProjectDialog(proj.name)
if not filepath:
return
else:
proj = prj.Project()
compress = proj.compress
dirpath, filename = session.project_path
filepath = os.path.join(dirpath, filename)
self.SaveProject(filepath, compress)
def modified(self, all_volume=False):
if all_volume:
self.matrix[0] = 1
self.matrix[:, 0, :] = 1
self.matrix[:, :, 0] = 1
if ses.Session().auto_reload_preview:
self._update_imagedata()
self.modified_time = time.monotonic()
callbacks = []
print(self._modified_callbacks)
for callback in self._modified_callbacks:
if callback() is not None:
callback()()
callbacks.append(callback)
self._modified_callbacks = callbacks
def ShowDialogSaveProject(self, saveas=False):
session = ses.Session()
if saveas or session.temp_item:
proj = prj.Project()
filepath = dialog.ShowSaveAsProjectDialog(proj.name)
if filepath:
#session.RemoveTemp()
session.OpenProject(filepath)
else:
return
else:
dirpath, filename = session.project_path
filepath = os.path.join(dirpath, filename)
self.SaveProject(filepath)
