#/*########################################################################## # Copyright (C) 2004-2014 V.A. Sole, European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. # # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU Lesser General Public License as published by the # Free Software Foundation; either version 2 of the License, or (at your option) # any later version. # # This file is distributed in the hope that it will be useful, but WITHOUT ANY # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more # details. # # You should have received a copy of the GNU Lesser General Public # License along with this library; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA # # Please contact the ESRF industrial unit (industry@esrf.fr) if this license # is a problem for you. # #############################################################################*/ __author__ = "V.A. Sole - ESRF Data Analysis" __contact__ = "sole@esrf.fr" __license__ = "LGPL2+" __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France" import os try: import OpenGL.GL as GL import OpenGL.GLU as GLU from OpenGL.GL import glDeleteLists except ImportError: raise ImportError("OpenGL must be installed to use these functionalities") import numpy try: from PyMca5 import spslut except: import spslut try: from PyMca5.Object3D import Object3DBase except ImportError: from Object3D import Object3DBase try: from PyMca5.Object3D import Object3DCTools from PyMca5.Object3D import Object3DQhull except ImportError: try: from Object3D import Object3DCTools from Object3D import Object3DQhull except ImportError: import Object3DCTools import Object3DQhull from PyMca5.PyMcaGui import PyMcaFileDialogs try: from PyMca5.Object3D.Object3DPlugins import Object3DMeshConfig except ImportError: try: from Object3D.Object3DPlugins import Object3DMeshConfig except: import Object3DMeshConfig qt = Object3DMeshConfig.qt import weakref DEBUG = 0 import time DRAW_MODES = ['NONE', 'POINT', 'WIRE', 'SURFACE', 'LIGHT', 'POINT_SELECTION'] COLORMAPLIST = [spslut.GREYSCALE, spslut.REVERSEGREY, spslut.TEMP, spslut.RED, spslut.GREEN, spslut.BLUE, spslut.MANY] class Object3DMesh(Object3DBase.Object3D): def __init__(self, name = "3D-Array"): Object3DBase.Object3D.__init__(self, name) self._alpha = 255 self.drawListDict = {} self._forceListCalculation = {} self.vertices = None self.vertexColors = None self.vertexSelectionColors = None self._selected = False self._vertexSelectionMode = False self.__flat = True self._xyz = False self.facets = None self.drawMode = 'POINT' self._configuration['common']['supportedmodes'] = [1, 1, 1, 1] self._configuration['common']['mode'] = 1 #centered on XY plane and on Z self._configuration['common']['anchor'] = [2, 2, 2] def initPrivateConfiguration(self, name): """ Specific configuration """ self._configuration['private'] = {} if self._privateConfigurationWidget is None: self._privateConfigurationWidget = Object3DMeshConfig.\ Object3DMeshConfig(None, name) self._configuration['private']['widget'] = weakref.proxy(self._privateConfigurationWidget) self._configuration['private']['colorfilter'] = 0 self._configuration['private']['isosurfaces'] = [[0, 10, 'green', 0, 0xFF, 0, 0xFF]] #green self._configuration['private']['useminmax'] = [0, 100, 200] self._configuration['private']['infolabel'] = "Object3DMesh %s" % name def __del__(self): if DEBUG: print("Deleting object %s" % self.name()) for key in self.drawListDict.keys(): if key.upper() != "NONE": if self.drawListDict[key] > 0: glDeleteLists(self.drawListDict[key], 1) del self._privateConfigurationWidget try: Object3DBase.Object3D.__del__(self) except AttributeError: pass def setConfiguration(self, ddict): old_alpha = 1.0 - self._configuration['common']['transparency'] Object3DBase.Object3D.setConfiguration(self, ddict) new_alpha = 1.0 - self._configuration['common']['transparency'] if (new_alpha != old_alpha): self._setAlpha(new_alpha) self.drawMode = DRAW_MODES[self._configuration['common']['mode']] if 'event' in ddict['common']: if ddict['common']['event'] == 'ColormapChanged': self.getColors() def _setAlpha(self, alpha): if alpha < 0: alpha = 0 elif alpha >= 1.0: alpha = 255 else: self._alpha = int(255 * alpha) if self.vertexColors is None: return self.vertexColors[:, 3] = self._alpha def setData(self, data, x=None, y=None, z=None, xyz=None): self.values = data[:] self._configuration['private']['useminmax'] = [0, self.values.min(), self.values.max()] if (xyz is not None) and (x is None) and (y is None): arr = Object3DCTools.getVertexArrayMeshAxes(xyz) if arr is not None: doit = True x = arr[0] if len(x) > 1: if abs(x[1] - xyz[0,0]) > 1.0e-10: #not proper C order #prevent bad plotting of a regular grid doit = False x = None if doit: y = arr[1] z = numpy.zeros(x.shape[0]*y.shape[0], numpy.float) z[:] = xyz[:, 2] xyz = None if (x is None) and (y is None) and (xyz is None): #regular mesh self.xSize, self.ySize = data.shape self.zSize = 1 self._x = numpy.arange(self.xSize).astype(numpy.float32) self._y = numpy.arange(self.ySize).astype(numpy.float32) if z is not None: self._z = numpy.array(z).astype(numpy.float32) if len(self._z.shape) == 0: #assume just a number self._z.shape = 1, 1 self.zSize = 1 else: self._z.shape = -1, 1 self.zSize = self._z.shape[0] self.__flat = False else: self._z = numpy.arange(self.zSize).astype(numpy.float32) self._z.shape = 1, 1 self.zSize = 1 elif xyz is not None: #full irregular mesh self.__setXYZArray(xyz, values=data) self.xSize = self.vertices.shape[0] self.ySize = 1 self._x = self.vertices[:,0] self._y = self.vertices[:,1] self._z = self.vertices[:,2] self._xyz = True elif (x is not None) and (y is not None): #regular mesh self._x = numpy.array(x).astype(numpy.float32) self._y = numpy.array(y).astype(numpy.float32) self._x.shape = -1, 1 self._y.shape = -1, 1 self.xSize = self._x.shape[0] self.ySize = self._y.shape[0] if z is not None: self._z = numpy.array(z).astype(numpy.float32) if len(self._z.shape) == 0: #assume just a number self._z.shape = 1, 1 self.zSize = 1 else: self._z.shape = -1, 1 self.zSize = self._z.shape[0] self.__flat = False else: self._z = numpy.arange(self.zSize).astype(numpy.float32) self._z.shape = 1, 1 self.zSize = 1 else: raise ValueError("Unhandled case") self.nVertices = self.xSize * self.ySize self.values.shape = self.nVertices, 1 self.getColors() self._obtainLimits() def __setXYZArray(self, xyz, values=None): if values is None: #This case could use a 1D texture self.values = xyz[:,2] else: #This case cannot use 1D texture self.values = numpy.array(values, numpy.float32) self.vertices = xyz self.nVertices = self.vertices.shape[0] def getColors(self): if DEBUG: t0 = time.time() self._configuration['common']['colormap'][4]=self.values.min() self._configuration['common']['colormap'][5]=self.values.max() colormap = self._configuration['common']['colormap'] (self.vertexColors,size,minmax)= spslut.transform(self.values, (1,0), (colormap[6],3.0), "RGBX", COLORMAPLIST[int(str(colormap[0]))], colormap[1], (colormap[2], colormap[3]), (0, 255),1) self.vertexColors.shape = self.nVertices, 4 self.vertexColors[:, 3] = self._alpha if DEBUG: print("colors elapsed = ", time.time() - t0) #selection colors # if I have more than pow(2, 24) vertices # the vertex with number pow(2, 24) will never be selected if 0: i = numpy.arange(self.nVertices) self.vertexSelectionColors = numpy.zeros((self.nVertices,4), numpy.uint8) self.vertexSelectionColors[:,0] = (i & 255) self.vertexSelectionColors[:,1] = ((i >> 8) & 255) self.vertexSelectionColors[:,2] = ((i >> 16) & 255) self.vertexSelectionColors[:,3] = 255 - (i >> 24) return def _obtainLimits(self): xmin, ymin, zmin = self._x.min(), self._y.min(), self._z.min() xmax, ymax, zmax = self._x.max(), self._y.max(), self._z.max() self.setLimits(xmin, ymin, zmin, xmax, ymax, zmax) def drawObject(self): if self.values is None: return GL.glPushAttrib(GL.GL_ALL_ATTRIB_BITS) GL.glShadeModel(GL.GL_FLAT) if DEBUG: t0=time.time() if self.drawMode == 'NONE': pass elif (GL.glGetIntegerv(GL.GL_RENDER_MODE) == GL.GL_SELECT) or \ self._vertexSelectionMode: GL.glPointSize(self._configuration['common']['pointsize']) if self._xyz: self.buildPointListXYZ(selection=True) else: self.buildPointList(selection=True) elif self.drawMode == 'POINT': GL.glShadeModel(GL.GL_FLAT) GL.glPointSize(self._configuration['common']['pointsize']) if self._xyz: self.buildPointListXYZ(selection=False) else: self.buildPointList(selection=False) elif self.drawMode == 'POINT_SELECTION': GL.glShadeModel(GL.GL_FLAT) GL.glPointSize(self._configuration['common']['pointsize']) self.buildPointList(selection=True) elif self.drawMode in ['LINES', 'WIRE']: GL.glLineWidth(self._configuration['common']['linewidth']) GL.glShadeModel(GL.GL_SMOOTH) if self._xyz: if self.facets is None: self._getFacets() Object3DCTools.drawXYZLines(self.vertices, self.vertexColors, self.values, self.facets, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) #sys.exit(1) elif self.__flat: Object3DCTools.draw3DGridLines(self._x, self._y, self._z, self.vertexColors, self.values, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) else: Object3DCTools.draw2DGridLines(self._x, self._y, self._z, self.vertexColors, self.values, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) elif self.drawMode == "SURFACE": GL.glShadeModel(GL.GL_SMOOTH) if self._xyz: if self.facets is None: self._getFacets() Object3DCTools.drawXYZTriangles(self.vertices, self.vertexColors, self.values, self.facets, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) elif self.__flat: Object3DCTools.draw3DGridQuads(self._x, self._y, self._z, self.vertexColors, self.values, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) else: Object3DCTools.draw2DGridQuads(self._x, self._y, self._z, self.vertexColors, self.values, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) else: print("UNSUPPORTED MODE") GL.glPopAttrib() if DEBUG: print("Drawing takes ", time.time() - t0) def _getVertexSelectionColors(self): i = numpy.arange(self.nVertices) self.vertexSelectionColors = numpy.zeros((self.nVertices,4), numpy.uint8) self.vertexSelectionColors[:,0] = (i & 255) self.vertexSelectionColors[:,1] = ((i >> 8) & 255) self.vertexSelectionColors[:,2] = ((i >> 16) & 255) self.vertexSelectionColors[:,3] = 255 - (i >> 24) def isVertexSelectionModeSupported(self): return True def _getFacets(self): if self.vertices is None: self.facets = None #if self.vertices.dtype == numpy.float32: # self.facets = Object3DQhullf.delaunay(self.vertices[:,0:2], # "qhull d Qbb QJ Qc Po") #else: if DEBUG: e0 = time.time() self.facets = Object3DQhull.delaunay(self.vertices[:,0:2], "qhull d Qbb QJ Qc") if DEBUG: print("delaunay elapsed = ", time.time() -e0) print("facets 1st= ",self.facets[0,:]) print("vertices 1st =", self.vertices[self.facets[0,0]],\ self.vertices[self.facets[0,1]],\ self.vertices[self.facets[0,2]]) print("COLORS = ", self.vertexColors[self.facets[0,0]],\ self.vertexColors[self.facets[0,1]],\ self.vertexColors[self.facets[0,2]]) print("COLORS = ", self.vertexColors[self.facets[1,0]],\ self.vertexColors[self.facets[1,1]],\ self.vertexColors[self.facets[1,2]]) def buildPointList(self, selection=False): if selection: if self.vertexSelectionColors is None: self._getVertexSelectionColors() if self.__flat: if self._configuration['private']['colorfilter']: tinyNumber = 1.0e-10 minValue = self._configuration['common']['colormap'][2] + tinyNumber maxValue = self._configuration['common']['colormap'][3] - tinyNumber Object3DCTools.draw3DGridPoints(self._x, self._y, self._z, self.vertexSelectionColors, self.values, 0, [1, minValue, maxValue]) else: Object3DCTools.draw3DGridPoints(self._x, self._y, self._z, self.vertexSelectionColors, self.values, 0, self._configuration['private']['useminmax']) else: #if self._configuration['private']['colorfilter'] is selected # I should get the min and max values of the colormap ... if self._configuration['private']['colorfilter']: tinyNumber = 1.0e-10 minValue = self._configuration['common']['colormap'][2] + tinyNumber maxValue = self._configuration['common']['colormap'][3] - tinyNumber Object3DCTools.draw2DGridPoints(self._x, self._y, self._z, self.vertexSelectionColors, self.values, 0, [1, minValue, maxValue]) else: Object3DCTools.draw2DGridPoints(self._x, self._y, self._z, self.vertexSelectionColors, self.values, 0, self._configuration['private']['useminmax']) else: if self.__flat: Object3DCTools.draw3DGridPoints(self._x, self._y, self._z, self.vertexColors, self.values, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) else: Object3DCTools.draw2DGridPoints(self._x, self._y, self._z, self.vertexColors, self.values, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) def buildWireList(self): Object3DCTools.draw3DGridLines(self._x, self._y, self._z, self.vertexColors) def buildPointListXYZ(self, selection=False): if 1: if selection: if self.vertexSelectionColors is None: self._getVertexSelectionColors() if self._configuration['private']['colorfilter']: tinyNumber = 1.0e-10 minValue = self._configuration['common']['colormap'][2] + tinyNumber maxValue = self._configuration['common']['colormap'][3] - tinyNumber Object3DCTools.drawXYZPoints(self.vertices, self.vertexSelectionColors, self.values, None, 0, [1, minValue, maxValue]) else: Object3DCTools.drawXYZPoints(self.vertices, self.vertexSelectionColors, self.values, None, 0, self._configuration['private']['useminmax']) else: Object3DCTools.drawXYZPoints(self.vertices, self.vertexColors, self.values, None, self._configuration['private']['colorfilter'], self._configuration['private']['useminmax']) return GL.glVertexPointerf(self.vertices) if selection: GL.glColorPointerub(self.vertexSelectionColors) else: GL.glColorPointerub(self.vertexColors) GL.glEnableClientState(GL.GL_VERTEX_ARRAY) GL.glEnableClientState(GL.GL_COLOR_ARRAY) GL.glDrawArrays(GL.GL_POINTS, 0, self.nVertices) def buildPointList0(self): """ This is just to test memory and speed """ n1, n2, n3 = 256, 256, 256 zdata = numpy.arange(n1*n2*n3).astype(numpy.float32) zdata.shape= -1, 1 (image,size,minmax)= spslut.transform(zdata, (1,0), (spslut.LINEAR,3.0), "RGBX", spslut.TEMP, 1, (0, 1), (0, 255),1) image.shape = -1, 4 image[:,3] = 255 #self.vertexColors = image.astype(numpy.float32) x = numpy.arange(n1).astype(numpy.float32) y = numpy.arange(n2).astype(numpy.float32) z = numpy.arange(n3).astype(numpy.float32) #Object3DCTools.draw3DGridQuads(x, y, y) #Object3DCTools.draw3DGridLines(x, y, z, image) Object3DCTools.draw3DGridPoints(x, y, z, image) self.zdata = zdata def getIndexValues(self, index): """ x,y,z, I """ if self._xyz: xindex = index yindex = index else: xindex = int(index/self.ySize) yindex = index % (self.ySize) if self.__flat: zindex = 0 else: zindex = index return self._x[xindex], self._y[yindex], self._z[zindex], self.values[index] MENU_TEXT = '3D Mesh' def getObject3DInstance(config=None): #for the time being a former configuration #for serializing purposes is not implemented #I do the import here for the case PyMca is not installed #because the modules could be instanstiated without using #this method try: from PyMca5.PyMcaIO import EdfFile except ImportError: import EdfFile fileTypeList = ['EDF Files (*edf)', 'EDF Files (*ccd)', 'ADSC Files (*img)', 'All Files (*)'] old = PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs * 1 PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = False fileList, filterUsed = PyMcaFileDialogs.getFileList( parent=None, filetypelist=fileTypeList, message="Please select one object data file", mode="OPEN", getfilter=True) PyMcaFileDialogs.PyMcaDirs.nativeFileDialogs = old if not len(fileList): return None if filterUsed == fileTypeList[0]: fileindex = 2 else: fileindex = 1 #file index is irrelevant in case of an actual 3D stack. filename = fileList[0] legend = os.path.basename(filename) edf = EdfFile.EdfFile(filename, access='rb') data = edf.GetData(0).astype(numpy.float32) object3D = Object3DMesh(os.path.basename(filename)) object3D.setData(data, z=data[:]) return object3D if __name__ == "__main__": import sys import os from PyMca5.Object3D import SceneGLWindow try: from PyMca5.PyMcaIO import EdfFile except ImportError: import EdfFile app = qt.QApplication(sys.argv) window = SceneGLWindow.SceneGLWindow() window.show() if len(sys.argv) > 1: flist = [] for i in range(1, len(sys.argv)): flist.append(sys.argv[i]) for f in flist: edf = EdfFile.EdfFile(f, access='rb') data = edf.GetData(0) object3D = Object3DMesh(os.path.basename(f)) else: data = numpy.arange(200.).astype(numpy.float32) data.shape = [40, 5] object3D = Object3DMesh('builtin') #several options: regular grid, irregular grid if len(sys.argv) > 1: #print "IMPOSSING A 1000 OFFSET" #offset = 1000.0 offset = 0 #irregular grid xSize, ySize = data.shape[0:2] zSize = 1 xyz = Object3DCTools.get3DGridFromXYZ(numpy.arange(xSize).astype(numpy.float32)-offset, numpy.arange(xSize).astype(numpy.float32)+offset, numpy.arange(1)+1) a = xyz[:,0] * 1 xyz[:,0] = xyz[:,1] * 1 xyz[:,1] = a[:] #print xyz[0:3,:] #print xyz.shape #print Object3DCTools.getVertexArrayMeshAxes(xyz) #sys.exit(0) data.shape = 1, xSize * ySize xyz[:,2] = data[:] object3D.setData(data, xyz=xyz) elif 0: #flat object3D.setData(data, z=4) else: #not flat object3D.setData(data, z=data) window.addObject(object3D, "Mesh") object3D = None window.glWidget.setZoomFactor(1.0) window.show() app.exec_()