New upstream version 3.1.99992 (f6db4e7b) · Commits · Debian Med / invesalius

.dockerignore

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		.git*
		.python-version
		Dockerfile

Dockerfile

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		FROM ubuntu:16.04

		RUN apt-get update
		RUN apt-get install -y \
		cython \
		locales \
		python-concurrent.futures \
		python-gdcm \
		python-matplotlib \
		python-nibabel \
		python-numpy \
		python-pil \
		python-psutil \
		python-scipy \
		python-serial \
		python-skimage \
		python-vtk6 \
		python-vtkgdcm \
		python-wxgtk3.0

		RUN locale-gen en_US.UTF-8
		ENV LANG en_US.UTF-8
		ENV LANGUAGE en_US:en
		ENV LC_ALL en_US.UTF-8

		WORKDIR /usr/local/app

		COPY . .

		RUN python setup.py build_ext --inplace

app.py

100755 → 100644

+203 −38

Original line number	Diff line number	Diff line
		@@ -18,31 +18,42 @@
		# detalhes.
		#-------------------------------------------------------------------------

		from __future__ import print_function

		import multiprocessing
		import optparse as op
		import os
		import sys
		import shutil
		import traceback

		import re

		if sys.platform == 'win32':
		import _winreg
		else:
		if sys.platform != 'darwin':
		import wxversion
		#wxversion.ensureMinimal('2.8-unicode', optionsRequired=True)
		#wxversion.select('2.8-unicode', optionsRequired=True)
		wxversion.ensureMinimal('3.0')
		try:
		import winreg
		except ImportError:
		import _winreg as winreg
		# else:
		# if sys.platform != 'darwin':
		# import wxversion
		# #wxversion.ensureMinimal('2.8-unicode', optionsRequired=True)
		# #wxversion.select('2.8-unicode', optionsRequired=True)
		# # wxversion.ensureMinimal('4.0')

		import wx
		try:
		from wx.adv import SplashScreen
		except ImportError:
		from wx import SplashScreen
		#from wx.lib.pubsub import setupv1 #new wx
		from wx.lib.pubsub import setuparg1# as psv1
		# from wx.lib.pubsub import setuparg1# as psv1
		#from wx.lib.pubsub import Publisher
		#import wx.lib.pubsub as ps
		from wx.lib.pubsub import pub as Publisher

		#import wx.lib.agw.advancedsplash as agw
		#if sys.platform == 'linux2':
		#if sys.platform.startswith('linux'):
		# _SplashScreen = agw.AdvancedSplash
		#else:
		# if sys.platform != 'darwin':
		@@ -61,9 +72,9 @@ if sys.platform == 'win32':
		try:
		USER_DIR = expand_user()
		except:
		USER_DIR = os.path.expanduser('~').decode(FS_ENCODE)
		USER_DIR = utils.decode(os.path.expanduser('~'), FS_ENCODE)
		else:
		USER_DIR = os.path.expanduser('~').decode(FS_ENCODE)
		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')
		@@ -72,6 +83,15 @@ 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
		wx.GetXDisplay = lambda: None
		else:
		del tmp_var


		class InVesalius(wx.App):
		"""
		@@ -86,7 +106,7 @@ class InVesalius(wx.App):
		freeze_support()

		self.SetAppName("InVesalius 3")
		self.splash = SplashScreen()
		self.splash = Inv3SplashScreen()
		self.splash.Show()
		wx.CallLater(1000,self.Startup2)

		@@ -97,7 +117,7 @@ class InVesalius(wx.App):
		Open drag & drop files under darwin
		"""
		path = os.path.abspath(filename)
		Publisher.sendMessage('Open project', path)
		Publisher.sendMessage('Open project', filepath=path)

		def Startup2(self):
		self.control = self.splash.control
		@@ -108,7 +128,7 @@ class InVesalius(wx.App):

		# ------------------------------------------------------------------

		class SplashScreen(wx.SplashScreen):
		class Inv3SplashScreen(SplashScreen):
		"""
		Splash screen to be shown in InVesalius initialization.
		"""
		@@ -175,7 +195,10 @@ class SplashScreen(wx.SplashScreen):
		if lang:
		# print "LANG", lang, _, wx.Locale(), wx.GetLocale()
		import locale
		try:
		locale.setlocale(locale.LC_ALL, '')
		except locale.Error:
		pass
		# For pt_BR, splash_pt.png should be used
		if (lang.startswith('pt')):
		icon_file = "splash_pt.png"
		@@ -196,8 +219,12 @@ class SplashScreen(wx.SplashScreen):

		bmp = wx.Image(path).ConvertToBitmap()

		try:
		style = wx.adv.SPLASH_TIMEOUT \| wx.adv.SPLASH_CENTRE_ON_SCREEN
		except AttributeError:
		style = wx.SPLASH_TIMEOUT \| wx.SPLASH_CENTRE_ON_SCREEN
		wx.SplashScreen.__init__(self,

		SplashScreen.__init__(self,
		bitmap=bmp,
		splashStyle=style,
		milliseconds=1500,
		@@ -218,7 +245,8 @@ class SplashScreen(wx.SplashScreen):
		self.control = Controller(self.main)

		self.fc = wx.FutureCall(1, self.ShowMain)
		wx.FutureCall(1, parse_comand_line)
		options, args = parse_comand_line()
		wx.FutureCall(1, use_cmd_optargs, options, args)

		# Check for updates
		from threading import Thread
		@@ -244,6 +272,24 @@ class SplashScreen(wx.SplashScreen):
		if self.fc.IsRunning():
		self.Raise()


		def non_gui_startup(options, args):
		lang = 'en'
		_ = i18n.InstallLanguage(lang)

		from invesalius.control import Controller
		from invesalius.project import Project

		session = ses.Session()
		if not session.ReadSession():
		session.CreateItens()
		session.SetLanguage(lang)
		session.WriteSessionFile()

		control = Controller(None)

		use_cmd_optargs(options, args)

		# ------------------------------------------------------------------


		@@ -262,49 +308,168 @@ def parse_comand_line():
		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 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', import_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:
		i = len(args)
		while i:
		i -= 1
		file = args[i].decode(sys.stdin.encoding)
		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)
		i = 0
		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 print_events(data):
		def sanitize(text):
		text = str(text).strip().replace(' ', '_')
		return re.sub(r'(?u)[^-\w.]', '', text)


		def check_for_export(options, suffix='', remove_surfaces=False):
		suffix = sanitize(suffix)

		if options.export:
		if not options.threshold:
		print("Need option --threshold when using --export.")
		exit(1)
		threshold_range = tuple([int(n) for n in options.threshold.split(',')])

		if suffix:
		if options.export.endswith('.stl'):
		path_ = '{}-{}.stl'.format(options.export[:-4], suffix)
		else:
		path_ = '{}-{}.stl'.format(options.export, suffix)
		else:
		path_ = options.export

		export(path_, threshold_range, remove_surface=remove_surfaces)
		elif options.export_to_all:
		# noinspection PyBroadException
		try:
		from invesalius.project import Project

		for threshold_name, threshold_range in Project().presets.thresh_ct.iteritems():
		if isinstance(threshold_range[0], int):
		path_ = u'{}-{}-{}.stl'.format(options.export_to_all, suffix, threshold_name)
		export(path_, threshold_range, remove_surface=True)
		except:
		traceback.print_exc()
		finally:
		exit(0)


		def export(path_, threshold_range, remove_surface=False):
		import invesalius.constants as const

		Publisher.sendMessage('Set threshold values',
		threshold_range=threshold_range)

		surface_options = {
		'method': {
		'algorithm': 'Default',
		'options': {},
		}, 'options': {
		'index': 0,
		'name': '',
		'quality': _('Optimal *'),
		'fill': False,
		'keep_largest': False,
		'overwrite': False,
		}
		}
		Publisher.sendMessage('Create surface from index',
		surface_parameters=surface_options)
		Publisher.sendMessage('Export surface to file',
		filename=path_, filetype=const.FILETYPE_STL)
		if remove_surface:
		Publisher.sendMessage('Remove surfaces',
		surface_indexes=(0,))


		def print_events(topic=Publisher.AUTO_TOPIC, **msg_data):
		"""
		Print pubsub messages
		"""
		utils.debug(data.topic)
		utils.debug("%s\n\tParameters: %s" % (topic, msg_data))

		def main():
		"""
		Initialize InVesalius GUI
		"""
		options, args = parse_comand_line()

		if options.no_gui:
		non_gui_startup(options, args)
		else:
		application = InVesalius(0)
		application.MainLoop()

		@@ -316,10 +481,10 @@ if __name__ == '__main__':
		if hasattr(sys,"frozen") and sys.platform.startswith('win'):

		#Click in the .inv3 file support
		root = _winreg.HKEY_CLASSES_ROOT
		root = winreg.HKEY_CLASSES_ROOT
		key = "InVesalius 3.1\InstallationDir"
		hKey = _winreg.OpenKey (root, key, 0, _winreg.KEY_READ)
		value, type_ = _winreg.QueryValueEx (hKey, "")
		hKey = winreg.OpenKey (root, key, 0, winreg.KEY_READ)
		value, type_ = winreg.QueryValueEx (hKey, "")
		path = os.path.join(value,'dist')

		os.chdir(path)

docs/devel/example_singleton_pubsub.py

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		@@ -52,7 +52,7 @@ p3 = Person("Andre ")
		people = [p1, p2, p3]

		print "Everyone eats 2 pieces:"
		for i in xrange(2):
		for i in range(2):
		for person in people:
		person.EatPieceOfPizza()

docs/user_guide_en.pdf

−468 KiB (15.1 MiB)

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