melage 0.0.65__py3-none-any.whl

melage/utils/glScientific_bc.py

@@ -0,0 +1,1585 @@
+# -*- coding: utf-8 -*-
+__author__= 'Bahram Jafrasteh'
+import numpy as np
+import sys
+sys.path.append('../')
+from melage.graphics import GLViewWidget, GLAxisItem, GLScatterPlotItem, GLGridItem, GLVolumeItem, GLPolygonItem
+from OpenGL.GL import *
+from collections import defaultdict
+from PyQt5.QtWidgets import QApplication, QWidget, QMenu, QAction, QSlider, QFileDialog
+from PyQt5.QtGui import QVector3D, QMatrix4x4
+from PyQt5.QtCore import Qt
+import cv2
+#from utils.polygontessellator import PolygonTessellator
+from melage.utils.utils import ConvertPointsToPolygons, ConvertPToPolygons, fillInsidePol, Polygon, LargestCC
+from PyQt5.QtCore import pyqtSignal
+from functools import partial
+
+class glScientific(GLViewWidget):
+    """
+
+    """
+    point3dpos=pyqtSignal(object, object) #qt signal
+    def __init__(self, colorsCombinations, parent = None, id =0, source_directory=''):
+        """
+
+        :param colorsCombinations: a dictionary containing color information
+        :param parent: parent
+        :param id: id of the GL
+        :param source_directory: source folder
+        """
+
+        super( glScientific, self).__init__(parent)
+        self.traces = dict()
+        #self = gl.GLViewWidget()
+        #self.installEventFilter()
+        self.id = id
+        self._lastZ = 1
+        self._image = None
+        self._image_seg = None
+        self._renderMode = 'Img'
+        self._threshold = 0
+        self._artistic = False
+
+        self._updatePaint = True
+        self._gotoLoc = False
+        self.colorsCombinations = colorsCombinations
+        self.totalPolyItems = []
+        self.maxXYZ = [100, 100, 100]
+        self._excluded_inds = np.zeros((100,100,100), bool)
+        self.setWindowTitle('3D view')
+        self._enabledPolygon = False
+        #self.setGeometry(0, 110, 600, 600)
+        self.setGeometry(0,0,1000,1000)
+        self.el_az_dis.connect(
+            lambda points : self.emit_viewport(points)
+        )
+        self._indices = None
+        self._rendered = 'seg'
+        self._numPolys = 0
+        self.totalpolys = defaultdict(list)
+        self.totalpolys_camer = defaultdict(list)
+
+        self._sPoints = []
+        self.intensitySeg = 1.0
+        self.totalItems = defaultdict(list)
+        self.totalItems['axis'] = []
+        self.totalItems['polys'] = []
+        self.colorInd = 9876#len(self.colorsCombinations)
+        self.colorInds= [9876]
+        self.setContextMenuPolicy(Qt.CustomContextMenu) # enable right click
+
+        self.customContextMenuRequested.connect(self.ShowContextMenu)
+
+        self.createGridAxis(self.maxXYZ)
+        self.source_dir = source_directory
+        self.GLV = GLVolumeItem(sliceDensity=1, smooth=True, glOptions='translucent',
+                                intensity_seg = self.intensitySeg)
+        self.GLSC = GLScatterPlotItem(pxMode=True, size=5)
+        self.GLPl = GLPolygonItem()
+        #self.GLV.smooth = True
+        self._UseScatter = False
+
+        self._verticalSlider_1 = QSlider(self)
+        self._verticalSlider_1.setOrientation(Qt.Vertical)
+        self._verticalSlider_1.setObjectName("verticalSlider_6")
+        self._verticalSlider_1.setRange(1, 50)
+        self._verticalSlider_1.setValue(1)
+        self._verticalSlider_1.setVisible(False)
+        #self.label_1 = QLabel(self)
+        #self.label_1.setAlignment(Qt.AlignCenter)
+        #self.label_1.setObjectName("label_1")
+        #self._verticalSlider_1.valueChanged.connect(self.label_1.setNum)
+        self._verticalSlider_1.valueChanged.connect(self.threshold_change)
+
+        self._seg_im = None
+
+        #self.opts['bgcolor'] = [0.5, 1, 0.0, 1]
+        self.opts['bgcolor'] = [0.3, 0.3, 0.3, 1] # background color
+
+    def threshold_change(self, value):
+        """
+        Threshold in 3D rendering
+        :param value:
+        :return:
+        """
+        if self._rendered != 'image':
+            self._verticalSlider_1.setValue(1)
+            return
+        self._threshold = value
+        self.cmap_image(self._lastmap_type,reset=False)
+
+    def take_screenshot(self):
+        """
+        Take screenshot from 3D rendering
+        :return:
+        """
+        if self._seg_im is None:
+            return
+        filters = "png(*.png)"
+        opts = QFileDialog.DontUseNativeDialog
+        fileObj = QFileDialog.getSaveFileName(self, "Open File", self.source_dir, filters, options=opts)
+        if fileObj[0] == '':
+            return
+        filename = fileObj[0] + '.png'
+        init_width, init_height = self.width(), self.height()
+        maxhw = max(init_width, init_height)
+        width, height = init_width, init_height
+        while maxhw <3000:
+            width, height = width*1.5, height*1.5
+            maxhw = max(width, height)
+        self.setFixedWidth(int(width))
+        self.setFixedHeight(int(height))
+        maxhw = max(self.width(), self.height())
+        #self.setGeometry()
+        self.removeItem('scatter_total')
+        self.GLV.setData(self._seg_im, self._artistic)
+        self.GLV.setDepthValue(10)
+        self.addItem(self.GLV, 'vol_total')
+        self.showEvent(0)
+        maxhw = max(self.width(), self.height())
+        img = glReadPixels(0, 0, maxhw, maxhw, GL_RGB, GL_FLOAT)
+        img = img[::-1]
+        img = img[:self.height(), :self.width(), :]
+        from matplotlib.image import imsave
+
+        imsave(filename, img)
+        self.setFixedWidth(init_width)
+        self.setFixedHeight(init_height)
+
+    def initiate_actions(self):
+        """
+
+        :return:
+        """
+        self.axis_action = QAction("Axis")
+        self.axis_action.setCheckable(True)
+        self.axis_action.setChecked(True)
+        self.axis_action.triggered.connect(self.axis_status)
+
+
+        self.goto_action = QAction("GoTo")
+        self.goto_action.setCheckable(True)
+        self.goto_action.setChecked(False)
+        self.goto_action.triggered.connect(self.goto_status)
+
+        self.grid_action = QAction("Grid")
+        self.grid_action.setCheckable(True)
+        self.grid_action.setChecked(True)
+        self.grid_action.triggered.connect(self.grid_status)
+
+
+        self.one_third_action = QAction("slice disp.")
+        self.one_third_action.setCheckable(True)
+        self.one_third_action.setChecked(False)
+        self.one_third_action.triggered.connect(self.artistic_status)
+
+
+        self.seg_action = QAction("Show Seg.")
+        self.seg_action.setCheckable(True)
+        self.seg_action.setChecked(False)
+        self.seg_action.triggered.connect(self.seg_status)
+
+        self.im_seg_action = QAction("Show Img+Seg")
+        self.im_seg_action.setCheckable(True)
+        self.im_seg_action.setChecked(False)
+        self.im_seg_action.triggered.connect(self.im_seg_status)
+
+
+
+        self.screenshot_action = QAction("ScreenShot")
+        self.screenshot_action.triggered.connect(self.take_screenshot)
+
+        self.draw_action = QAction("Draw")
+        self.draw_action.setCheckable(True)
+        self.draw_action.setChecked(False)
+        self.draw_action.triggered.connect(self.draw_status)
+
+
+        self.draw_art = QAction("Artistic")
+        self.draw_art.setCheckable(True)
+        self.draw_art.setChecked(False)
+        self.draw_art.triggered.connect(self.draw_art_action)
+
+        self.clear_action = QAction("Show Total")
+        self.clear_action.triggered.connect(self.showTotal)
+
+
+
+    def showTotal(self):
+        """
+        Show all the part of image in 3D
+        :return:
+        """
+        self._excluded_inds[:] = False
+        self._artistic = False
+
+
+    def remove_painting(self):
+        """
+        Excluding 3D ares from demonstration
+        :return:
+        """
+        def filledPoly(poly):
+            """
+            Fill inside polygons
+            Args:
+                poly:
+
+            Returns:
+
+            """
+            from matplotlib.path import Path
+
+            try:
+                coords = np.array(poly.exterior.coords)
+
+                p = Path(coords)
+                xmin, ymin, xmax, ymax = poly.bounds
+                x = np.arange(np.floor(xmin), np.ceil(xmax), 1)
+                y = np.arange(np.floor(ymin), np.ceil(ymax), 1)
+                points = np.transpose([np.tile(x, len(y)), np.repeat(y, len(x))])
+                ind_points = p.contains_points(points)
+                selected_points = points[ind_points]
+
+                return selected_points
+            except:
+                return []
+        def adjustVals(selected):
+            for i in [0,1,2]:
+                ind = selected[:,i]>=self.maxXYZ[i]
+                selected[ind, i] = self.maxXYZ[i]-1
+                ind = selected[:,i]<=0
+                selected[ind, i] = 1
+            return selected
+        def findIndices(vls):
+            pl = Polygon(vls)
+            if not pl.is_valid:
+                pls = ConvertPToPolygons(vls)
+                for ij, pl in enumerate(pls):
+                    if ij == 0:
+                        #pl = spline_points(pl)
+                        selected_points = filledPoly(pl)
+                    else:
+                        #pl = spline_points(pl)
+                        n_points = filledPoly(pl)
+                        selected_points = np.vstack([selected_points, n_points])
+            else:
+                #pl = spline_points(pl)
+                selected_points = filledPoly(pl)
+            return selected_points
+        if len(self.totalpolys[0])<5:
+            return
+        if 'vol_total' in self.items:
+            self.SubUpdateSegScatterItem()
+        else:
+            return
+        #points = self._compute_coordinates(self.mousePos)
+        if 'scatter_total' in self.items:
+
+            self.removeItem('scatter_total')
+            self.GLV.setData(self._seg_im, self._artistic)
+            self.GLV.setDepthValue(20)
+            self.addItem(self.GLV, 'vol_total')
+
+        invM = np.linalg.inv(self.mvpProj.reshape((4, 4)).transpose())
+        xmax, ymax, zmax = self.maxCoord
+        filled_polygon = np.array(self._sPoints)
+        filled_polygon = findIndices(filled_polygon)
+        filled_polygon = np.concatenate([filled_polygon, np.ones((len(filled_polygon), 2))], 1)
+        filled_polygon[:, 0] = 2 * filled_polygon[:,0] / self.width() - 1
+        filled_polygon[:, 1] = 1 - 2 * filled_polygon[:,1] / self.height()
+        filled_polygon[:, 3] = 1
+        filled_polygon[:, 2] = 2 * 1- 1
+
+
+
+        Tpoints = []
+        #self._z[self._z>0].min(), #self._z[self._z<1].max()
+        opt=1e-4
+        #round(self._z[self._z < 1].max() + 0.0001, 4)
+        for z in np.arange(0.9985- 0.0006, round(self._z[self._z < 1].max() + 0.0001, 4), 1e-6):
+            A = filled_polygon.copy()
+            A[:, 2] = 2 * z - 1
+
+            Tpoints = np.matmul(invM,
+                                A.T).T
+            Tpoints /= Tpoints[:, 3, None]
+            # Tpoints = Tpoints.astype('int')
+
+            selected = Tpoints.astype('int')[:, :3]
+
+
+            selected[:, 2] = self.maxXYZ[0] - selected[:, 2]
+            selected[:, 0] = self.maxXYZ[2] - selected[:, 0]
+
+            ind = 0
+            for j, xyzm in enumerate([zmax, ymax, xmax]):
+                ind += ((selected[:, j] < xyzm) * (selected[:, j] >= 0))
+            ind = ind >= 3
+            selected = selected[ind, :]
+            selected = selected[:, [2, 1, 0]]
+
+            self._excluded_inds[selected[:, 0], selected[:, 1], selected[:, 2]] = True
+
+
+        #from scipy.ndimage import binary_fill_holes
+        #self._excluded_inds = binary_fill_holes(self._excluded_inds)
+        self._indices = (self._indices.astype('int')- self._excluded_inds.astype('int'))>0
+        self._seg_im[self._excluded_inds, :] = 0
+
+        #print('removing')
+        self.clear_points()
+        self.GLV.setData(self._seg_im, self._artistic)
+        self.GLV.update()
+        return
+
+
+    def clear_points(self):
+        """
+        Clear information
+        :return:
+        """
+        self.totalpolys = defaultdict(list)
+        self.totalpolys_camer = defaultdict(list)
+        self._numPolys = 0
+        self._lastZ=1
+        self.GLPl.update_points(self.totalpolys)
+        self.update()
+
+
+    def paintGL(self, region=None, viewport=None, useItemNames=False):
+        """
+        Paint GL
+        :param region:
+        :param viewport:
+        :param useItemNames:
+        :return:
+        """
+        super(glScientific, self).paintGL()
+        elev = self.opts['elevation'] #* np.pi/180.
+        azim = self.opts['azimuth'] #* np.pi/180.
+        #print(elev, azim)
+
+    def _endIMage(self, x, y, z, tol=10): # to check if we are at the end of the image
+        zmax, xmax, ymax = self.maxCoord
+        zmax, xmax, ymax = zmax+tol, ymax+tol, xmax+tol
+        endIm = False
+        if x<-tol:
+            endIm = True
+            x = -tol
+        elif x>xmax:
+            endIm = True
+            x = xmax
+        if y <-tol:
+            endIm = True
+            y = -tol
+        elif y > ymax:
+            endIm = True
+            y = ymax
+        if z <-tol:
+            endIm = True
+            z = -tol
+        elif z > zmax:
+            endIm = True
+            z = zmax
+        return endIm, x, y, z
+
+    def mouseReleaseEvent(self, a0) -> None:
+        """
+        Mouse events
+        :param a0:
+        :return:
+        """
+        if self._enabledPolygon:
+            if len(self._sPoints)==0:
+                return
+            self.totalpolys[self._numPolys].append(self.totalpolys[self._numPolys][0])
+            self._sPoints.append(self._sPoints[0])
+
+            if self.GLV._ax==0:
+                self.totalpolys_camer[self._numPolys] = ['sagittal', self.GLV._d]
+            elif self.GLV._ax == 1:
+                self.totalpolys_camer[self._numPolys] = ['coronal', self.GLV._d]
+            elif self.GLV._ax == 2:
+                self.totalpolys_camer[self._numPolys] = ['axial', self.GLV._d]
+            self._numPolys = 0
+            self.GLPl.update_points(self.totalpolys)
+
+            #polygonC = ConvertPointsToPolygons(self.totalpolys[self._numPolys], width=0)
+            #if polygonC.is_valid:
+            #    Mpl = ConvertPToPolygons(self.totalpolys[self._numPolys])
+            try:
+                self.remove_painting()
+            except Exception as e:
+                print(e)
+            self._sPoints = []
+            self._enabledPolygon = False
+            self.draw_action.setChecked(False)
+
+
+        if 'scatter_total' in self.items:
+
+            self.removeItem('scatter_total')
+            self.GLV.setData(self._seg_im, self._artistic)
+            self.GLV.setDepthValue(20)
+            self.addItem(self.GLV, 'vol_total')
+
+    def _custom_viewMatrix(self, distance):
+        tr = QMatrix4x4()
+        tr.translate( 0.0, 0.0, -distance)
+        tr.rotate(self.opts['elevation']-90, 1, 0, 0)
+        tr.rotate(self.opts['azimuth']+90, 0, 0, -1)
+        center = self.opts['center']
+        tr.translate(-center.x(), -center.y(), -center.z())
+        return tr
+
+    def _custom_projectionMatrix(self, dist):
+
+        dpr = self.devicePixelRatio()
+        region = (0, 0, self.width() * dpr, self.height() * dpr)
+
+        x0, y0, w, h = self.getViewport()
+
+        nearClip = dist * 0.001
+        farClip = dist * 1000.
+
+        r = nearClip * np.tan(self.opts['fov'] * 0.5 * np.pi / 180.)
+        t = r * h / w
+
+        ## Note that X0 and width in these equations must be the values used in viewport
+        left = r * ((region[0] - x0) * (2.0 / w) - 1)
+        right = r * ((region[0] + region[2] - x0) * (2.0 / w) - 1)
+        bottom = t * ((region[1] - y0) * (2.0 / h) - 1)
+        top = t * ((region[1] + region[3] - y0) * (2.0 / h) - 1)
+
+        tr = QMatrix4x4()
+        tr.frustum(left, right, bottom, top, nearClip, farClip)
+        return tr
+
+    def _compute_coordinates(self, ev, z=None):
+        if z is None:
+            self.showEvent(0)
+            z = glReadPixels(ev.x(), self.height() - ev.y(), 1, 1, GL_DEPTH_COMPONENT, GL_FLOAT)[0][0]
+        if z == 0:
+            return [0,0,0,0]
+        if z==1:
+            z=self._lastZ
+            #a = np.argwhere(self._z != 1)
+            #_y, _x = self.height() - ev.y(), ev.x()
+            #ind = np.abs(a-np.array([_y, _x])).sum(-1).argmin()
+            #z = self._z[a[ind][0], a[ind][1]]
+        self._lastZ = z
+
+
+
+        #per = np.array(self.m.copyDataTo()).reshape((4, 4)).transpose().flatten()
+        #zFar = 0.5 * per[14] * (1.0 - ((per[10] - 1.0) / (per[10] + 1.0)))
+        # zNear = zFar * (per[10] + 1.0) / (per[10] - 1.0)
+
+        # z = (2.0 * z) - 1.0
+        # z = (2.0 * zNear * zFar) / (zFar + zNear - (z * (zFar - zNear)))
+
+        ndcx = 2 * self.mousePos.x() / self.width() - 1
+        ndcy = 1 - 2 * self.mousePos.y() / self.height()
+        a= [self.mousePos.x(), self.mousePos.y()]
+
+        #z=0.998
+
+        invM = np.linalg.inv(self.mvpProj.reshape((4, 4)).transpose())
+
+        points = np.matmul(invM,
+                           np.array([ndcx, ndcy, 2 * z - 1, 1]))
+        points /= points[3]
+        return points,a
+
+    def mouseMoveEvent(self, ev):
+        #print(self.opts['azimuth'], self.opts['elevation'])
+        if not hasattr(self, 'mousePos'):
+            return
+        diff = ev.pos() - self.mousePos
+        self.mousePos = ev.pos()
+        if self._enabledPolygon:
+
+            #self.SubUpdateSegScatterItem()
+
+            #z = self._z[self.height()-ev.y(), ev.x()]
+            z=1.0
+            points, _ = self._compute_coordinates(ev, z=z)
+            #points[0] -= 1
+            #points[-1] -= 1
+            # points[1] -= 1
+            #points[2] = self.maxXYZ[2] - points[2]
+            #points[0] = self.maxXYZ[2] - points[0]
+            p1, xo = self._compute_coordinates(ev, 1)
+
+            # self.points = []
+            x,y, z, _ = points
+            if z == 0:
+                return
+            endIm = self._endIMage(x, y, z)
+
+            if endIm[0]:
+                # update x and y
+                #return
+                x = endIm[1]
+                y = endIm[2]
+                z = endIm[3]
+            endIm2 = self._endIMage(p1[0], p1[2], p1[3])
+            self._sPoints.append(xo)
+            #if not endIm2[0]:
+            #    self._sPoints.append(p1)
+            self.totalpolys[self._numPolys].append([x, y, z])
+            if len(self.totalpolys[self._numPolys]) > 2:
+                self.GLPl.update_points(self.totalpolys)
+                self.addItem(self.GLPl, 'pol_total')
+                self.GLPl.setDepthValue(100)
+            #if 'scatter_total' in self.items:
+            #    self.removeItem('scatter_total')
+            #    self.GLV.setData(self._seg_im)
+            #    self.GLV.setDepthValue(0)
+            #    self.addItem(self.GLV, 'vol_total')
+
+        else:
+            if ev.buttons() == Qt.LeftButton:
+                if (ev.modifiers() & Qt.ControlModifier):
+                    self.pan(diff.x(), diff.y(), 0, relative='view')
+                else:
+                    self.orbit(-diff.x(), diff.y())
+            elif ev.buttons() == Qt.MidButton:
+                if (ev.modifiers() & Qt.ControlModifier):
+                    self.pan(diff.x(), 0, diff.y(), relative='view-upright')
+                else:
+                    self.pan(diff.x(), diff.y(), 0, relative='view-upright')
+            self.point3dpos.emit([self.opts['elevation'], self.opts['azimuth'], self.opts['distance']],None)
+    def emit_viewport(self, points):
+        self.point3dpos.emit(points, None)
+
+    def mousePressEvent(self, ev):
+        """
+        By Bahram Jafrasteh
+        :param ev:
+        :return:
+        """
+        #self.opts['azimuth'] = 0
+        #self.opts['elevation'] = 0
+
+        self.mousePos = ev.localPos()
+        if not (self._gotoLoc or self._enabledPolygon):
+            return
+
+        if ev.button()==Qt.RightButton:
+            return
+        if 'vol_total' in self.items:
+            self.SubUpdateSegScatterItem()
+        else:
+            return
+        points, _ = self._compute_coordinates(ev)
+
+        #points[1] -= 1
+        #print(points)
+
+        if self._enabledPolygon:
+            #self.addItem(self.GLPl, 'pol_total')
+            #self.points = []
+            #points[2] = self.maxXYZ[2] - points[2]
+            #points[0] = self.maxXYZ[2] - points[0]
+            p1, xo = self._compute_coordinates(ev, 1)
+            self._sPoints = []
+            self.totalpolys[self._numPolys] =[]
+            if points[-2] == 0:
+                return
+            #print(points)
+            x, y, z , _=points
+            endIm = self._endIMage(x, y, z)
+            if endIm[0]:
+                # update x and y
+                x = endIm[1]
+                y = endIm[2]
+                z = endIm[3]
+            endIm2 = self._endIMage(p1[0], p1[2], p1[3])
+            #if not endIm2[0]:
+            #    self._sPoints.append(p1)
+
+            self._sPoints.append(xo)
+            self.totalpolys[self._numPolys].append([x, y, z])
+            if len(self.totalpolys[self._numPolys])>1:
+                self.GLPl.update_points(self.totalpolys)
+
+
+
+        #print(points)
+        elif self._gotoLoc:
+            #points[0] -= 1
+            #points[-1] -= 1
+            points[2] = self.maxXYZ[0] - points[2]
+            points[0] = self.maxXYZ[2] - points[0]
+            if self.GLV._ax==0:
+                windowName = 'sagittal'
+            elif self.GLV._ax == 1:
+                windowName = 'coronal'
+            elif self.GLV._ax == 2:
+                windowName = 'axial'
+            self.point3dpos.emit(points, windowName)
+        else:
+            self.point3dpos.emit(points, None)
+        #self.updateSegVolItem(self._seg_im, None)
+        if 'scatter_total' in self.items:
+
+            self.removeItem('scatter_total')
+            self.GLV.setData(self._seg_im, self._artistic)
+            self.GLV.setDepthValue(20)
+            self.addItem(self.GLV, 'vol_total')
+
+
+
+    """
+    
+    def changedata(self):
+        self._artistic = False
+        if self._UseScatter:
+            self._UseScatter=False
+            #self.paint(self._seg_im)
+            self.SubUpdateSegScatterItem()
+        elif not self._UseScatter:
+            self._UseScatter=True
+
+        self.update()
+    """
+    def _localUpdate(self):
+
+        self.removeItem('scatter_total')
+        if self._seg_im is not None:
+            self.GLV.setData(self._seg_im.copy(), self._artistic)
+        else:
+            self.GLV.data = None
+        self.GLV.setDepthValue(20)
+        self.addItem(self.GLV, 'vol_total')
+
+    def draw_art_action(self, value):
+        self._artistic = False
+        if value:
+            self._artistic = True
+        self.update()
+
+    def draw_status(self, value):
+        try:
+            if not value:
+                self.removeItem('pol_total')
+                self.totalpolys = defaultdict(list)
+                totalpolys_camer = defaultdict(list)
+                self.GLPl.update_points(self.totalpolys)
+                self._enabledPolygon = value
+            else:
+                self.GLV.setDepthValue(0)
+                self._enabledPolygon = value
+
+
+                """
+                
+                if self.GLV._ax==0: #sagittal
+                    if self.GLV._d==1:
+                        self.opts['elevation'] = 0
+                        self.opts['azimuth'] = 0
+                    else:
+                        self.opts['elevation'] = 0
+                        self.opts['azimuth'] = -180
+                elif self.GLV._ax==1:#coronal
+                    if self.GLV._d == 1:
+                        self.opts['elevation'] = 0
+                        self.opts['azimuth'] = 90
+                    else:
+                        self.opts['elevation'] = 0
+                        self.opts['azimuth'] = -90
+                elif self.GLV._ax==2:#axial
+                    if self.GLV._d == 1:
+                        self.opts['elevation'] = 90
+                        self.opts['azimuth'] = 0
+                    else:
+                        self.opts['elevation'] = -90
+                        self.opts['azimuth'] = 0
+                """
+                self.SubUpdateSegScatterItem()
+                self.showEvent(0)
+                self._z = glReadPixels(0, 0, self.height(),self.width(), GL_DEPTH_COMPONENT, GL_FLOAT)
+                if 'scatter_total' in self.items:
+                    self.removeItem('scatter_total')
+                    self.GLV.setData(self._seg_im, self._artistic)
+                    self.GLV.setDepthValue(0)
+                    self.addItem(self.GLV, 'vol_total')
+        except Exception as e:
+            print(e)
+    def axis_status(self, value):
+        if not value:
+            self.removeItem('ax')
+        else:
+            self.addItem(self.ax,'ax')
+            self.axis_action.setChecked(True)
+
+    def grid_status(self, value):
+        if not value:
+            self.removeItem('xyz')
+        else:
+            self.addItem(self.gx, 'xyz')
+            self.grid_action.setChecked(True)
+    def artistic_status(self, value):
+        self._artistic = True
+        if not value:
+            self._artistic = False
+        self._localUpdate()
+
+
+    def im_seg_status(self, value):
+        self.seg_action.setChecked(False)
+        if value:
+            self._renderMode = 'Seg'
+            self._threshold=0
+            self.im_seg_action.setChecked(True)
+            self.updateSegVolItem(self._image, self._seg_im)
+
+            #self.removeItem('vol_total')
+
+        else:
+            self._renderMode = 'Img'
+            self.im_seg_action.setChecked(False)
+
+            self.removeItem('vol_total')
+            self.paintGL()
+
+
+
+    def seg_status(self, value):
+        self.im_seg_action.setChecked(False)
+
+        if value:
+            self._renderMode = 'Seg'
+            self._threshold=0
+
+            self.seg_action.setChecked(True)
+            #self.removeItem('vol_total')
+
+        else:
+            self._renderMode = 'Img'
+            self.seg_action.setChecked(False)
+            self.removeItem('vol_total')
+            self.paintGL()
+        #if hasattr(self, 'GLV'):
+        #    self.GLV.smooth = value
+        #    self.GLV._needUpload = True
+        #    self._localUpdate()
+        #    self.paintGL()
+
+
+    def goto_status(self, value):
+        self._gotoLoc = value
+        if not value:
+            self.point3dpos.emit(np.array([0,0,0,1]),None)
+
+
+    def changeBG(self, cl):
+        self.opts['bgcolor'] = cl
+        self._localUpdate()
+        self.paintGL()
+
+    def cmap_image(self, map_type, reset=True):
+        if self._image is None:
+            return
+        if reset:
+            self._threshold = 0
+        self._renderMode = 'Seg'
+        self.seg_action.setChecked(False)
+        self._verticalSlider_1.setVisible(True)
+        mask = self._image<=(self._image.max()*self._threshold/100)
+        if map_type=='original':
+            cm = np.repeat(self._image[...,None], 4, -1)
+        else:
+            import matplotlib.pyplot as plt
+            cm = plt.get_cmap(map_type, lut=256)
+            cm = cm(self._image / self._image.max()) * 255.0
+            #if map_type!='gist_rainbow_r':
+            #    cm[...,3]=self._image
+        self.removeItem('vol_total')
+
+        self._seg_im = cm
+        self._seg_im[mask,:]=0
+        #if self._indices is not None:
+        self._indices = (1-mask.astype('int'))>0
+        self._indices = (self._indices.astype('int') - self._excluded_inds.astype('int')) > 0
+        self._seg_im[self._excluded_inds,:]=0
+        self.GLV.setData(self._seg_im, self._artistic)
+        self.GLV.setDepthValue(20)
+        self.addItem(self.GLV, 'vol_total')
+        self.paintGL()
+        self._lastmap_type = map_type
+        self._rendered = 'image'
+
+    def ShowContextMenu(self, pos):
+        # Main Edit Menu
+        menu = QMenu("Edit")
+
+        # Submenu for Background Colors
+        self.bgColorMenu = QMenu('Background Color')
+
+        grc = QAction('Gray')
+        gc = QAction("Green")
+        oc = QAction("Orange")
+        pc = QAction("Pink")
+        vc = QAction("Violet")
+        rc = QAction("Red")
+        bc = QAction("Blue")
+        wc = QAction("White")
+        yc = QAction("Yellow")
+        blc = QAction("Black")
+
+        gc.triggered.connect(partial(self.changeBG, [0.5, 1, 0.0, 1]))
+        oc.triggered.connect(partial(self.changeBG, [1, 0.7, 0.1, 1]))
+        pc.triggered.connect(partial(self.changeBG, [1, 0.41, 0.79, 1]))
+
+        vc.triggered.connect(partial(self.changeBG, [0.93, 0.51, 0.93, 1]))
+        wc.triggered.connect(partial(self.changeBG, [0.96, 0.96, 0.86, 1]))
+        rc.triggered.connect(partial(self.changeBG, [0.98, 0.5, 0.44, 1]))
+        bc.triggered.connect(partial(self.changeBG, [0.25, 0.87, 0.82, 1]))
+        yc.triggered.connect(partial(self.changeBG, [1, 0.87, 0.0, 1]))
+        blc.triggered.connect(partial(self.changeBG, [0.05, 0.05, 0.05, 1]))
+        grc.triggered.connect(partial(self.changeBG, [0.3, 0.3, 0.3, 1]))
+        self.bgColorMenu.addAction(gc)
+        self.bgColorMenu.addAction(grc)
+        self.bgColorMenu.addAction(rc)
+        self.bgColorMenu.addAction(bc)
+        self.bgColorMenu.addAction(vc)
+        self.bgColorMenu.addAction(wc)
+        self.bgColorMenu.addAction(oc)
+        self.bgColorMenu.addAction(pc)
+        self.bgColorMenu.addAction(yc)
+        self.bgColorMenu.addAction(blc)
+
+
+        # Submenu for Image Rendering/Colormap Options
+        self.imageRenderMenu = QMenu("Image Render")
+
+        gis_rainbow = QAction("RainBow")
+        gis_rainbow.triggered.connect(partial(self.cmap_image, 'gist_rainbow_r'))
+
+        gray = QAction("Gray")
+        gray.triggered.connect(partial(self.cmap_image, 'gray_r'))
+
+        original = QAction("Original")
+        original.triggered.connect(partial(self.cmap_image, 'original'))
+
+        jet = QAction("JET")
+        jet.triggered.connect(partial(self.cmap_image, 'jet_r'))
+
+        CMRmap = QAction("gnuplot")
+        CMRmap.triggered.connect(partial(self.cmap_image, 'gnuplot2'))
+
+        gnuplot_r = QAction("gnuplot2")
+        gnuplot_r.triggered.connect(partial(self.cmap_image, 'gnuplot_r'))
+        self.imageRenderMenu.addAction(gis_rainbow)
+        self.imageRenderMenu.addAction(gray)
+        self.imageRenderMenu.addAction(jet)
+        self.imageRenderMenu.addAction(CMRmap)
+        self.imageRenderMenu.addAction(gnuplot_r)
+        self.imageRenderMenu.addAction(original)
+
+
+        # Submenu for Segmentation Options
+        self.segmentationMenu = QMenu('Segmentation')
+        self.segmentationMenu.addAction(self.im_seg_action)
+        self.segmentationMenu.addAction(self.seg_action)
+
+        # Submenu for Drawing Options
+        self.paintingMenu = QMenu('Painting')
+        self.paintingMenu.addAction(self.draw_action)
+        self.paintingMenu.addAction(self.draw_art)
+        self.paintingMenu.addAction(self.clear_action)
+        self.paintingMenu.addMenu(self.imageRenderMenu)  # Nested menu for image rendering
+
+        # View Options (Axis, Grid, Slice)
+        self.viewMenu = QMenu("View Options")
+        self.viewMenu.addAction(self.axis_action)
+        self.viewMenu.addAction(self.grid_action)
+        self.viewMenu.addAction(self.one_third_action)
+
+        # Actions directly in the main menu
+        menu.addMenu(self.bgColorMenu)  # Background Color
+        menu.addMenu(self.paintingMenu)  # Painting and Image Rendering
+        menu.addMenu(self.segmentationMenu)  # Segmentation
+        menu.addMenu(self.viewMenu)  # View Options
+        menu.addAction(self.screenshot_action)  # Screenshot
+        menu.addAction(self.goto_action)  # GoTo
+
+        menu.exec_(self.mapToGlobal(pos))
+
+    def ShowContextMenu_old(self, pos):
+        menu = QMenu("Edit")
+        #remove_action = QAction("Unknown")
+        #remove_action.triggered.connect(self.changedata)
+
+        self.menu1 = QMenu('BG Color')
+        self.painting = QMenu('Painting')
+        self.menuSeg = QMenu('Show Seg.')
+        self.image_action = QMenu("Image Render")
+
+        gis_rainbow = QAction("RainBow")
+        gis_rainbow.triggered.connect(partial(self.cmap_image, 'gist_rainbow_r'))
+
+        gray = QAction("Gray")
+        gray.triggered.connect(partial(self.cmap_image, 'gray_r'))
+
+        original = QAction("Original")
+        original.triggered.connect(partial(self.cmap_image, 'original'))
+
+        jet = QAction("JET")
+        jet.triggered.connect(partial(self.cmap_image, 'jet_r'))
+
+        CMRmap = QAction("gnuplot")
+        CMRmap.triggered.connect(partial(self.cmap_image, 'gnuplot2'))
+
+        gnuplot_r = QAction("gnuplot2")
+        gnuplot_r.triggered.connect(partial(self.cmap_image, 'gnuplot_r'))
+        self.image_action.addAction(gis_rainbow)
+        self.image_action.addAction(gray)
+        self.image_action.addAction(jet)
+        self.image_action.addAction(CMRmap)
+        self.image_action.addAction(gnuplot_r)
+        self.image_action.addAction(original)
+        grc = QAction('Gray')
+        gc = QAction("Green")
+        oc = QAction("Orange")
+        pc = QAction("Pink")
+        vc = QAction("Violet")
+        rc = QAction("Red")
+        bc = QAction("Blue")
+        wc = QAction("White")
+        yc = QAction("Yellow")
+        blc = QAction("Black")
+        """
+
+        dict_color = {
+            "Green":[0.1, 1, 0.7,1],
+            "Yellow":[1, 0.7, 0.1, 1],
+            "Violet":[0.7, 0.1, 1, 1],
+            "Red":[1, 1, 1.0,1],
+            "Blue":[1, 0.1, 0.1, 1],
+            "White":[0.0, 0.1, 1, 1]
+
+        }
+        for key in dict_color:
+            act = QAction(key)
+            act.triggered.connect(partial(self.changeBG, dict_color[key]))
+            self.menu1.addAction(act)
+        """
+
+        gc.triggered.connect(partial(self.changeBG, [0.5, 1, 0.0, 1]))
+        oc.triggered.connect(partial(self.changeBG, [1, 0.7, 0.1, 1]))
+        pc.triggered.connect(partial(self.changeBG, [1, 0.41, 0.79, 1]))
+
+        vc.triggered.connect(partial(self.changeBG, [0.93, 0.51, 0.93, 1]))
+        wc.triggered.connect(partial(self.changeBG, [0.96, 0.96, 0.86, 1]))
+        rc.triggered.connect(partial(self.changeBG, [0.98, 0.5, 0.44, 1]))
+        bc.triggered.connect(partial(self.changeBG, [0.25, 0.87, 0.82, 1]))
+        yc.triggered.connect(partial(self.changeBG, [1, 0.87, 0.0, 1]))
+        blc.triggered.connect(partial(self.changeBG, [0.05, 0.05, 0.05, 1]))
+        grc.triggered.connect(partial(self.changeBG, [0.3, 0.3, 0.3, 1]))
+        self.menu1.addAction(gc)
+        self.menu1.addAction(grc)
+        self.menu1.addAction(rc)
+        self.menu1.addAction(bc)
+        self.menu1.addAction(vc)
+        self.menu1.addAction(wc)
+        self.menu1.addAction(oc)
+        self.menu1.addAction(pc)
+        self.menu1.addAction(yc)
+        self.menu1.addAction(blc)
+
+        #cb = QtGui.QGuiApplication.clipboard()
+        #cb.clear(mode=cb.Clipboard)
+        #cb.setText("Clipboard Text", mode=cb.Clipboard)
+        #menu.addAction(remove_action)
+        menu.addAction(self.goto_action)
+        #menu.addAction(self.draw_action)
+
+
+        self.menuSeg.addSeparator()
+        self.menuSeg.addAction(self.im_seg_action)
+        self.menuSeg.addAction(self.seg_action)
+        menu.addMenu(self.menuSeg)
+
+        menu.addMenu(self.menu1)
+        menu.addMenu(self.painting)
+
+
+
+        self.painting.addAction(self.draw_action)
+        self.painting.addAction(self.draw_art)
+        self.painting.addAction(self.clear_action)
+        self.painting.addMenu(self.image_action)
+
+
+        menu.addAction(self.axis_action)
+        menu.addAction(self.grid_action)
+        menu.addAction(self.one_third_action)
+        menu.addAction(self.screenshot_action)
+        menu.exec_(self.mapToGlobal(pos))
+
+    def changeAxis(self, polygon, axis):
+        if axis == 'coronal':
+            polygon = polygon[:, [0, 2, 1]]
+            # polygon = np.flipud(polygon)
+            polygon[:, 0] = self.maxXYZ[2] - polygon[:, 0]
+            polygon[:, 2] = self.maxXYZ[0] - polygon[:, 2]
+        elif axis == 'sagittal':
+            polygon = polygon[:, [2, 0, 1]]
+            #polygon[:, 1] = self.maxXYZ[2] - polygon[:, 1]
+            polygon[:, 2] = self.maxXYZ[0] - polygon[:, 2]
+            #polygon[:,0] = -polygon[:,0]
+            #polygon[:,2] = -polygon[:,2]
+        elif axis == 'axial':
+            polygon = polygon[:, [0, 1, 2]]
+            polygon[:, 0] = self.maxXYZ[2] - polygon[:, 0]
+            #polygon[:, 2] = self.maxXYZ[2] - polygon[:, 2]
+        return polygon
+
+
+    def updateSegSlice(self, imSeg, edges, currentWidnowName, sliceNum):
+        """
+        :param totalPs: keys of total points
+        :param changedIndice: indices of key name
+        :return:
+        """
+        minimum_area = 2
+        if currentWidnowName.lower() == 'coronal':
+            subim = imSeg[:,sliceNum,:]
+            d = np.where(subim > 0)
+            contours, hierarchy = cv2.findContours(image=subim.astype(np.uint8), mode=cv2.RETR_TREE,
+                                                   method=cv2.CHAIN_APPROX_NONE)
+            if len(contours)==0:
+                item = GLScatterPlotItem(pos=np.empty(shape=(0,3), dtype=np.int64), color=np.empty(shape=(0,4), dtype=np.float64), pxMode=True, size=5)
+                self.addItem(item, 'scatter_{}_{}'.format(currentWidnowName, sliceNum))
+                return
+            else:
+                cnts = []
+                i = 0
+                for contour in contours:
+                    if cv2.contourArea(contour)<minimum_area:
+                        continue
+                    cnt = contour.squeeze()
+                    val = subim[cnt[0, 1], cnt[0, 0]]
+                    if val > 150:
+                        val -= 150
+                        subc = subim[cnt[:, 1], cnt[:, 0]]
+                        if sum(subc>150)>0:
+                            subc[subc>150] = subc[subc>150] - 150
+                            subim[cnt[:, 1], cnt[:, 0]] = subc
+                    cnts.append([cnt, val])
+                    subim[cnt[:, 1], cnt[:, 0]] = 150+subim[cnt[0, 1], cnt[0, 0]]
+                    print(np.unique(subim))
+                    print(i)
+                    i+=1
+                    print('')
+            #cnt = contours[0].squeeze()
+
+            #subim[cnt[:, 1], cnt[:, 0]] = 150+subim[cnt[0, 1], cnt[0, 0]]
+            points = np.vstack((d[0], np.repeat(sliceNum,len(d[0])), d[1])).transpose([1,0])[:,[2,1,0]]
+            #cnts = np.vstack((cnt[:, 1], np.repeat(sliceNum, cnt.shape[0]), cnt[:, 0] )).transpose([1, 0])[:, [2, 1, 0]]
+        elif currentWidnowName.lower() == 'sagittal':
+            subim = imSeg[:,:,sliceNum]
+            d = np.where(subim > 0)
+            contours, hierarchy = cv2.findContours(image=subim.astype(np.uint8), mode=cv2.RETR_TREE,
+                                                   method=cv2.CHAIN_APPROX_NONE)
+            if len(contours)==0:
+                item = GLScatterPlotItem(pos=np.empty(shape=(0,3), dtype=np.int64), color=np.empty(shape=(0,4), dtype=np.float64), pxMode=True, size=5)
+                self.addItem(item, 'scatter_{}_{}'.format(currentWidnowName, sliceNum))
+                return
+            else:
+                cnts = []
+                for contour in contours:
+                    if cv2.contourArea(contour)<minimum_area:
+                        continue
+                    cnt = contour.squeeze()
+                    val = subim[cnt[0, 1], cnt[0, 0]]
+                    if val>150:
+                        val -= 150
+                        d = subim[cnt[:, 1], cnt[:, 0]]
+                        if sum(d>150)>0:
+                            d[d>150] = d[d>150] - 150
+                            subim[cnt[:, 1], cnt[:, 0]] = d
+                    cnts.append([cnt, val] )
+                    subim[cnt[:, 1], cnt[:, 0]] = 150+subim[cnt[0, 1], cnt[0, 0]]
+            points = np.vstack((d[0], d[1],np.repeat(sliceNum,len(d[0])))).transpose([1,0])[:,[2,1,0]]
+            #cnts = np.vstack((cnt[:, 1], cnt[:, 0], np.repeat(sliceNum, cnt.shape[0]))).transpose([1, 0])[:, [2, 1, 0]]
+        elif currentWidnowName.lower() == 'axial':
+            subim = imSeg[sliceNum,:,:]
+            d = np.where(subim > 0)
+            contours, hierarchy = cv2.findContours(image=subim.astype(np.uint8), mode=cv2.RETR_TREE,
+                                                   method=cv2.CHAIN_APPROX_NONE)
+            if len(contours)==0:
+                item = GLScatterPlotItem(pos=np.empty(shape=(0,3), dtype=np.int64), color=np.empty(shape=(0,4), dtype=np.float64), pxMode=True, size=5)
+                self.addItem(item, 'scatter_{}_{}'.format(currentWidnowName, sliceNum))
+                return
+            else:
+                cnts = []
+                for contour in contours:
+                    if cv2.contourArea(contour)<minimum_area:
+                        continue
+                    cnt = contour.squeeze()
+                    val = subim[cnt[0, 1], cnt[0, 0]]
+                    if val > 150:
+                        val -= 150
+                        d = subim[cnt[:, 1], cnt[:, 0]]
+                        if sum(d>150)>0:
+                            d[d>150] = d[d>150] - 150
+                            subim[cnt[:, 1], cnt[:, 0]] = d
+                    cnts.append([cnt, val])
+                    subim[cnt[:, 1], cnt[:, 0]] = 150+subim[cnt[0, 1], cnt[0, 0]]
+            #cnt = contours[0].squeeze()
+            #subim[cnt[:, 1], cnt[:, 0]] = 150+subim[cnt[0, 1], cnt[0, 0]]
+            points = np.vstack((np.repeat(sliceNum,len(d[0])),d[0], d[1])).transpose([1,0])[:,[2,1,0]]
+            #cnts = np.vstack((np.repeat(sliceNum, cnt.shape[0]), cnt[:, 1], cnt[:, 0] )).transpose([1, 0])[:, [2, 1, 0]]
+
+
+        #d = np.where(imSeg>0)
+        #if d[0].shape[0]<=1:
+            #return
+        #points = np.vstack((d[0], d[1], d[2])).transpose([1, 0])[:,[2,1,0]]
+
+        points[:, 0] = self.maxXYZ[2] - points[:, 0]
+        points[:, 2] = self.maxXYZ[0] - points[:, 2]
+
+        #cnts[:, 0] = self.maxXYZ[2] - cnts[:, 0]
+        #cnts[:, 2] = self.maxXYZ[0] - cnts[:, 2]
+
+
+        """
+        if windowName == 'coronal':
+            points[:, 0] = self.maxXYZ[2] - points[:, 0]
+            points[:, 2] = self.maxXYZ[0] - points[:, 2]
+        elif windowName == 'sagittal':
+            points[:, 2] = self.maxXYZ[0] - points[:, 2]
+        elif windowName == 'axial':
+            points[:, 0] = self.maxXYZ[2] - points[:, 0]
+        """
+        colors = np.zeros((points.shape[0], 4))
+        #colors[:, 3] = imSeg[tuple(zip(d))].squeeze()
+        #colors[:, 2] = data[tuple(zip(d))].squeeze()
+        #colors[:, 1] = data[tuple(zip(d))].squeeze()
+        colorsInd =  subim[tuple(zip(d))].transpose().squeeze()
+        for cl in np.unique(colorsInd[colorsInd<=150]):
+            if cl == 0:
+                continue
+            ind = colorsInd == cl
+            colorval = self.colorsCombinations[int(cl)]
+            colors[ind,:] =colorval
+
+            ind_edge = colorsInd == cl+150
+            colorval_edge = (0.,0.,0.,1.0)
+            colors[ind_edge, :] = colorval_edge
+            for cnt0 in cnts:
+                cnt, cl = cnt0
+                subim[cnt[:, 1], cnt[:, 0]] = cl
+        #colors[:,0] = 255.0
+        #colors = colors/255.0
+        item = GLScatterPlotItem(pos=points, color = colors, pxMode=True, size=5)
+        self.addItem(item, 'scatter_{}_{}'.format(currentWidnowName, sliceNum))
+
+        return
+
+
+    def updateSegVolItem(self, imSeg = None, imOrg = None, currentWidnowName=None, sliceNum = None):
+        """
+        :param totalPs: keys of total points
+        :param changedIndice: indices of key name
+        :return:
+        """
+        self.removeItem('scatter_total')
+        d = np.where(imSeg>0)
+        if d[0].shape[0]<=1:
+            return
+        self.maxXYZ_current = [d[0].max(),d[1].max(),d[2].max()]
+
+        self.minXYZ_current = [d[0].min(),d[1].min(),d[2].min()]
+        if d[0].shape[0]<=1:
+            self.removeItem('scatter_total')
+            return
+
+
+        """
+        if windowName == 'coronal':
+            points[:, 0] = self.maxXYZ[2] - points[:, 0]
+            points[:, 2] = self.maxXYZ[0] - points[:, 2]
+        elif windowName == 'sagittal':
+            points[:, 2] = self.maxXYZ[0] - points[:, 2]
+        elif windowName == 'axial':
+            points[:, 0] = self.maxXYZ[2] - points[:, 0]
+        """
+
+        #colors[:, 3] = imSeg[tuple(zip(d))].squeeze()
+        #colors[:, 2] = data[tuple(zip(d))].squeeze()
+        #colors[:, 1] = data[tuple(zip(d))].squeeze()
+        colorsInd =  imSeg[tuple(zip(d))].squeeze()
+        uq = np.unique(colorsInd)
+        if 9876 not in self.colorInds:  # len(self.colorsCombinations):
+            selected_ud = self.colorInds
+        else:
+            selected_ud = uq
+        _seg_im = np.zeros((*imSeg.shape, 4))
+        indics = 0
+        for cl in uq:
+            if cl in selected_ud:
+                ind = imSeg == cl
+                indics += ind
+                try:
+                    colorval = self.colorsCombinations[int(cl)]
+                    _seg_im[ind, :] = colorval
+                except:
+                    print('Index {} does not have a representative color.'.format(int(cl)))
+        #colors[:,0] = 255.0
+        #colors = colors/255.0
+        #if self._indices is None:
+        self._indices = indics>self._threshold
+        self._rendered = 'seg'
+        self._verticalSlider_1.setVisible(False)
+        _seg_im *= 255
+        _seg_im[self._excluded_inds,:]=0
+        #im_or = np.repeat(imOrg[..., None], [4], axis=-1)
+        #im_or[indics<=0,:]=0
+        #a = self.intensitySeg * _seg_im + (1 - self.intensitySeg) * im_or
+
+        if self.im_seg_action.isChecked():
+            cm = np.repeat(self._image[..., None], 4, -1)
+            mask = self._image <= (self._image.max() * self._threshold / 100)
+
+            cm_rgb = cm[...,:3]/255.0
+            #cm_rgb[imSeg>0,:]=0 # remove segmented ROIs from the original image
+            cm_alpha = cm[...,3]/255.0
+
+            seg_rgb = _seg_im[...,:3]/255.0
+            seg_alpha = _seg_im[..., 3]/ 255.0
+
+            cm_alpha *=0.02
+            #seg_alpha *= 0.98 # linear
+            seg_alpha = np.sqrt(seg_alpha) # non linear
+
+            composite_alpha = cm_alpha + seg_alpha *(1-cm_alpha)
+
+            composite_alpha_clipped = np.clip(composite_alpha, a_min=1e-10, a_max=None)
+            composite_rgb = (cm_rgb * cm_alpha[..., np.newaxis] + seg_rgb * seg_alpha[..., np.newaxis] * (
+                        1 - cm_alpha[..., np.newaxis])) / composite_alpha_clipped[..., np.newaxis]
+            composite_rgb[composite_alpha == 0] = 0
+            composite_alpha[composite_alpha == 0] = 1
+            _seg_im = np.concatenate((composite_rgb*255.0, composite_alpha[..., np.newaxis] * 255), axis=-1)
+            _seg_im[mask,:] = 0
+            #self._seg_im = _seg_im
+            #self.GLV.setData(_seg_im, self._artistic)
+
+        self._seg_im = _seg_im
+        self.GLV.setData(_seg_im, self._artistic)
+
+        self.GLV.setDepthValue(20)
+        self.addItem(self.GLV, 'vol_total')
+
+        return
+
+
+
+    def SubUpdateSegScatterItem(self):
+        if self._seg_im is None:
+            return
+        if self._indices is None:
+            self._indices = self._image>0
+        self.removeItem('vol_total')
+        d = np.where(self._indices)
+        if d[0].shape[0]<=1:
+            return
+        points = np.vstack((d[0], d[1], d[2])).transpose([1, 0])  # [:,[2,1,0]]
+
+        points[:, 0] = self.maxXYZ[0] - points[:, 0]  # axial
+        points[:, 2] = self.maxXYZ[2] - points[:, 2]  # sagittal
+        # points[:, 1] = self.maxXYZ[1] - points[:, 1]#coronal
+        points = points[:, [2, 1, 0]]
+        colors = self._seg_im[self._indices]/255.0
+
+        self.GLSC.setData(pos=points, color = colors, pxMode=True, size=5)
+        self.addItem(self.GLSC, 'scatter_total')
+
+    def updateSegScatterItem(self, imSeg, windowName):
+        """
+        :param totalPs: keys of total points
+        :param changedIndice: indices of key name
+        :return:
+        """
+        self.removeItem('vol_total')
+
+        d = np.where(imSeg>0)
+        if d[0].shape[0]<=1:
+            self.removeItem('scatter_total')
+            return
+        points = np.vstack((d[0], d[1], d[2])).transpose([1, 0])#[:,[2,1,0]]
+
+        points[:, 0] = self.maxXYZ[0] - points[:, 0]#axial
+        points[:, 2] = self.maxXYZ[2] - points[:, 2]#sagittal
+        #points[:, 1] = self.maxXYZ[1] - points[:, 1]#coronal
+        points = points[:,[2,1,0]]
+
+        """
+        if windowName == 'coronal':
+            points[:, 0] = self.maxXYZ[2] - points[:, 0]
+            points[:, 2] = self.maxXYZ[0] - points[:, 2]
+        elif windowName == 'sagittal':
+            points[:, 2] = self.maxXYZ[0] - points[:, 2]
+        elif windowName == 'axial':
+            points[:, 0] = self.maxXYZ[2] - points[:, 0]
+        """
+        colors = np.ones((points.shape[0], 4))*10000
+        #colors[:, 3] = imSeg[tuple(zip(d))].squeeze()
+        #colors[:, 2] = data[tuple(zip(d))].squeeze()
+        #colors[:, 1] = data[tuple(zip(d))].squeeze()
+        colorsInd =  imSeg[tuple(zip(d))].squeeze()
+        uq = np.unique(colorsInd)
+        if 9876 not in self.colorInds:  # len(self.colorsCombinations):
+            selected_ud = self.colorInds
+        else:
+            selected_ud = uq
+
+        for cl in uq:
+            if cl == 0:
+                continue
+            if cl in selected_ud:
+                ind = colorsInd == cl
+                try:
+                    colorval = self.colorsCombinations[int(cl)]
+                    colors[ind,:] =colorval
+                except:
+                    print('Index {} does not have a representative color.'.format(int(cl)))
+        #colors[:,0] = 255.0
+        #colors = colors/255.0
+        ind_non_zero = colors.sum(1)!=10000*4
+        self.GLSC.setData(pos=points[ind_non_zero, :], color = colors[ind_non_zero, :], pxMode=True, size=5)
+        self.addItem(self.GLSC, 'scatter_total')
+        return
+        if len(changedIndice)== 0:
+            return
+
+        for axis in totalPs.keys():
+            for Pls in totalPs[axis].keys():
+                for key in totalPs[axis][Pls].keys():
+                    keyName = str(axis) + '_' + str(Pls) + '_' + str(key)
+                    if keyName in changedIndice:
+                        ind = changedIndice.index(keyName)
+                        self.removeItem(keyName)
+                        polyg, color = totalPs[axis][Pls][key]
+                        polygon = np.array(list(polyg.exterior.coords))
+                        polygon = self.changeAxis(polygon, axis)
+                        keyName = str(axis) + '_' + str(Pls) + '_' + str(key)
+                        polygon = np.array(PolygonTessellator().tessellate(polygon))
+                        self.addSegItem(polygon, keyName, color)
+                        changedIndice.pop(ind)
+        if len(changedIndice) != 0:
+            for keyName in changedIndice:
+                self.removeItem(keyName)
+
+
+
+
+    #def paint(self, imSeg = None, edges = None, currentWidnowName=None, sliceNum = None):
+    def paint(self, imSeg = None, im = None, currentWidnowName=None, sliceNum = None):
+        if not self._updatePaint:
+            return
+        if not self._renderMode.lower()=='seg':
+            return
+        #self._seg_im = imSeg
+        #if imSeg is not None:
+            #if currentWidnowName is None:
+        #if self._UseScatter:
+        #    self.updateSegScatterItem(imSeg, currentWidnowName)
+        #else:
+
+        self.updateSegVolItem(imSeg, currentWidnowName)
+            #else:
+            #    self.updateSegSlice(imSeg, edges, currentWidnowName, sliceNum)
+
+        if self.isVisible():
+            self.show()
+
+
+    def load_paint(self, imSeg):
+
+        if hasattr(self,'items_names'):
+            if len(self.items_names)>3:
+                try:
+                    total_items = list(set(self.items_names) - set(['scatter_total', 'xyz', 'ax']))
+                    for item in total_items:
+                        _, currentWidnowName, sliceNum = item.split('_')
+                        sliceNum = int(sliceNum)
+                        self.updateSegSlice(imSeg, [], currentWidnowName, sliceNum)
+                    delattr(self, 'items_names')
+                    self.update()
+                except:
+                    self.paint(imSeg, None)
+            else:
+                self.paint(imSeg, None)
+        if hasattr(self, 'items_names'):
+            delattr(self, 'items_names')
+
+
+    def createGridAxis(self, maxcoord):
+        self.removeItem('vol_total')
+        #maxcoord = self.testTest()
+        ############# create the background grids #############
+        self.setMaxCoords(maxcoord)
+
+        #self._seg_im = np.zeros((*maxcoord,1)).squeeze()
+        if len(self.totalItems['axis']) != 0:
+            self.removeItem(self.totalItems['axis'][0])
+            self.removeItem(self.totalItems['axis'][1])
+            #self.removeItem(self.totalItems['axis'][2])
+            #self.removeItem(self.totalItems['axis'][3])
+            del self.totalItems['axis']
+        zmax, ymax, xmax = maxcoord
+        self.maxXYZ = [zmax, ymax, xmax]
+        self._excluded_inds = np.zeros((self.maxXYZ[0],self.maxXYZ[1],self.maxXYZ[2]), bool)
+        self._excluded_inds[:]=False
+        xvals = np.arange(0, xmax + xmax/10, xmax/5).astype(np.int64)
+        yvals = np.arange(0, ymax + ymax/10, ymax/5).astype(np.int64)
+        zvals = np.arange(0, zmax + zmax/10, zmax/5).astype(np.int64)
+
+        self.maxXYZ = [zmax, ymax, xmax]
+        self.maxXYZ_current = [zmax, ymax, xmax]
+        self.minXYZ_current = [0, 0, 0]
+        #xvals = -np.arange(0, xmax + xmax/5, xmax/5).astype("int")[::-1]
+        #yvals = -np.arange(0, ymax + ymax/5, ymax/5).astype("int")[::-1]
+        #zvals = -np.arange(0, zmax + zmax/5, zmax/5).astype("int")[::-1]
+
+        zmax = zvals[-1]; ymax = yvals[-1]; xmax=xvals[-1]
+        zmin = zvals[0];ymin = yvals[0];xmin = xvals[0]
+        self.gx = GLGridItem(glOptions='translucent', color=[0,0,0,1])
+        self.gx.setGrid(xvals, yvals, zvals )
+        self.gx.setDepthValue(0)
+
+
+
+
+
+        #gx.translate(-zmax, 0,  0)
+        #gx.rotate(90, 0, 1, 0)
+        #gx.translate(0, 0, zmax)
+        self.totalItems['axis'].append('xyz')
+        self.addItem(self.gx, 'xyz')
+
+        #imxz = np.zeros((xmax, zmax,3))
+        #Imxz = GLImageItem(imxz, color=[1,1,0,1], program=self.program)
+        #Imxz.rotate(90,0,1,0)
+        #self.addItem(Imxz, 'imxz')
+
+        #gy = gl.GLGridItem(glOptions='opaque', program=self.program)
+        #gy.rotate(90, 1, 0, 0)
+        #gy.setGrid(xvals, zvals)
+        #self.totalItems['axis'].append('y')
+        #self.addItem(gy, 'y')
+
+        #gz = gl.GLGridItem(glOptions='opaque', program=self.program)
+        #gz.setGrid(xvals, yvals)
+        #self.totalItems['axis'].append('z')
+        #self.addItem(gz, 'z')
+
+        ############# axis #############
+        self.ax = GLAxisItem(antialias=True, glOptions='translucent')
+        self.ax.setDepthValue(0)
+        self.ax.setGLViewWidget(self)
+        #ax.setSize(0, xmax, 0, ymax, 0, zmax)
+        self.ax.setSize(xmin, xmax, ymin,ymax, zmin, zmax)
+        self.ax.setOriging(maxcoord[2]/2,maxcoord[1]/2,maxcoord[0]/2)
+        self.totalItems['axis'].append('ax')
+        self.addItem(self.ax, 'ax')
+
+        # Switch to 'nearly' orthographic projection.
+        #self.opts['distance'] = 40000
+        self.opts['fov'] = 45
+        self.opts['elevation'] = 45
+        self.opts['azimuth'] = 45
+
+        self.setCameraPosition(pos=QVector3D(maxcoord[2]/2,maxcoord[1]/2,maxcoord[0]/2), rotation=(0,0,1,1),
+                               distance= max(xmax, ymax, zmax))
+                               #distance=np.sqrt(maxcoord[0]**2+maxcoord[1]**2+maxcoord[2]**2),
+                               #)
+        self.totalPolyItems = []
+
+        self._enabledPolygon = False
+        self._indices = None
+        self._rendered = 'seg'
+        self._numPolys = 0
+        self.totalpolys = defaultdict(list)
+        self.totalpolys_camer = defaultdict(list)
+
+
+
+
+
+
+# Start Qt event loop unless running in interactive mode.
+class Ui_Main0():
+    NumRows = 2
+    NumColumns = 3
+
+    def __init__(self):
+        super(Ui_Main0, self).__init__()
+
+        self.glWidgets = []
+
+    def setupUi(self, Main):
+        Main.resize(2000, 1800)
+        self.centralwidget = QWidget(Main)
+        self.centralwidget.setEnabled(True)
+        self.v = glScientific(self.centralwidget)
+
+
+        import pickle
+        #with open('dictionary', 'wb') as output:
+        #    pickle.dump(self.colorsCombinations, output, pickle.HIGHEST_PROTOCOL)
+        with open('dictionary', 'rb') as output:
+            r = pickle.load(output)
+
+        self.v.colorsCombinations = r
+        self.v.colorInds = [85,45]
+        #v.animation()
+
+class MainWindow0(QWidget, Ui_Main0):
+    def __init__(self, *args, obj=None, **kwargs):
+        super(MainWindow0, self).__init__(*args, **kwargs)
+        #QtGui.QWidget.__init__(self)
+        self.setupUi(self)
+        from nibabel import load
+        #nii = load('inp.nii')
+        #data = np.squeeze(nii.get_data())
+
+        data = np.load('aa.npy')
+        data = data.astype("float")  # Typecast to float
+        #data = data[:, :, ::-1]
+        self.v._renderMode = 'seg'
+        self.v._excluded_inds = np.zeros_like(data).astype('bool')
+        self.v._excluded_inds[:] = False
+        self.v.createGridAxis(list(data.shape))
+        self.v.paint(data)
+        self.v.show()
+
+        data = np.rot90(data, axes=(1, 2))# x
+        data = np.rot90(data, axes=(0, 2)) #y
+        data = np.rot90(data, axes=(0, 1))  # z
+
+        #data = np.load('ab.npy')
+        #data = data.astype("float")  # Typecast to float
+
+
+
+
+
+if __name__ == '__main__':
+    app = QApplication(sys.argv)
+
+    window = MainWindow0()
+
+    #window.show()
+    sys.exit(app.exec_())
+
+
+