def ReadWlzTr(): #{ try: #{ errNum = w.enum__WlzErrorNum(w.WLZ_ERR_FILE_OPEN) if args.input== '-': #{ f = libc.stdin else: #}{ f = libc.fopen(args.input, 'rb') #} if not bool(f): #{ raise IOError() #} obj = w.WlzAssignObject( \ w.WlzReadObj(f, c.byref(errNum)), None) if not args.input == '-': #{ libc.fclose(f) #} if not bool(obj): #{ errNum = w.enum__WlzErrorNum(w.WLZ_ERR_OBJECT_NULL) raise WlzError() #} if ((not int(obj.contents.type) == int(w.WLZ_AFFINE_TRANS)) or \ (not int(obj.contents.domain.core.contents.type) == \ int(w.WLZ_TRANSFORM_3D_AFFINE))): #{ errNum = w.enum__WlzErrorNum(w.WLZ_ERR_OBJECT_TYPE) raise WlzError() #} except IOError: #}{ ErrorMsg('Failed to open ' + args.input) except WlzError: #}{ ErrorMsg('Failed to read affine transform from ' + args.input + '(' + w.WlzStringFromErrorNum(errNum, None) + ')') #} mat = WlzTrToMat(obj.contents.domain.t) return(mat)
def setObj2D(self): #{ logging.debug('setObj2D') errnum = c.c_int(w.WLZ_ERR_NONE) t = self.obj.contents.type if t == w.WLZ_2D_DOMAINOBJ: #{ self.obj2d = w.WlzAssignObject(self.obj, None) elif t == w.WLZ_3D_DOMAINOBJ: #}{ logging.debug('cutting section from 3D object') w.WlzInit3DViewStruct(self.view, self.obj) o2d = w.WlzGetSubSectionFromObject( self.obj, None, self.view, c.c_int(w.WLZ_INTERPOLATION_NEAREST), None, c.byref(errnum)) print(o2d) print(errnum) if not bool(errnum): #{ w.WlzFreeObj(self.obj2d) self.obj2d = w.WlzAssignObject(o2d, None) #} #} return (errnum)
def readWlzObj(self, fname): #{ logging.debug('readWlzObj()') obj = None logging.debug('attempting to read object from ' + fname) self.errnum = c.c_int(w.WLZ_ERR_FILE_OPEN) fp = c.cast(libc.fopen(fname, 'rb'), c.POINTER(w.FILE)) if bool(fp): #{ obj = w.WlzAssignObject( \ w.WlzReadObj(fp, c.byref(self.errnum)), None) libc.fclose(fp) if bool(self.errnum): #{ self.warnWlzError('Failed to read object from ' + fname) #} #} return (obj)
def addObj(self, o): #{ logging.debug('addObj()') t = int(o.contents.type) self.errnum = c.c_int(w.WLZ_ERR_OBJECT_TYPE) if (t == int(w.WLZ_2D_DOMAINOBJ)) or (t == int( w.WLZ_3D_DOMAINOBJ)): #{ if t == int(w.WLZ_2D_DOMAINOBJ): #{ self.errnum = c.c_int(w.WLZ_ERR_NONE) else: #}{ logging.debug('making view struct') v = w.WlzMake3DViewStruct(c.c_int(w.WLZ_3D_VIEW_STRUCT), \ c.byref(self.errnum)) if not bool(self.errnum): #{ f = w.WlzDVertex3() v.vtX = c.c_double(0.0) v.vtY = c.c_double(0.0) v.vtZ = c.c_double(0.0) v.contents.theta = self.yaw * m.pi / 180.0 v.contents.phi = self.pitch * m.pi / 180.0 v.contents.zeta = self.roll * m.pi / 180.0 v.contents.dist = self.dist v.contents.fixed = f v.contents.view_mode = c.c_int(w.WLZ_UP_IS_UP_MODE) v.contents.scale = c.c_double(1.0) v.contents.voxelRescaleFlg = c.c_int(0) w.WlzFree3DViewStruct(self.view) self.view = w.WlzAssign3DViewStruct(v, None) #} #} #} if not bool(self.errnum): #{ w.WlzFreeObj(self.obj) self.obj = w.WlzAssignObject(o, None) self.errnum = self.setObj2D() #} if not bool(self.errnum): #{ ary = self.wlz2DToNP() logging.debug('setting image') self.img = ary.astype(np.float64).T self.img_itm.setImage(self.img) self.setROIType('N') #} if bool(self.errnum): #{ self.warnWlzError('Failed to add object.')
import matplotlib.pyplot as pt import numpy as np libc = ctypes.CDLL("libc.so.6") fopen = libc.fopen fclose = libc.fclose errNum = Wlz.enum__WlzErrorNum(Wlz.WLZ_ERR_NONE) fopen.restype = ctypes.POINTER(Wlz.FILE) f = 'test.wlz' print('Read test object from the file ' + f); fp = fopen(f, 'rb') obj = Wlz.WlzAssignObject(Wlz.WlzReadObj(fp, ctypes.byref(errNum)), None) fclose(fp) if(bool(errNum)): print('Failed to read object from ' + f + \ ' (' + Wlz.WlzStringFromErrorNum(errNum, None) + ').') exit(1) if((not bool(obj.contents)) or ((obj.contents.type != Wlz.WlzObjectType(Wlz.WLZ_3D_DOMAINOBJ).value) and (obj.contents.type != Wlz.WlzObjectType(Wlz.WLZ_2D_DOMAINOBJ).value))): print('Either 2 or 3D domain object with values required.') exit(1) print('Computing histogram') hobj = Wlz.WlzAssignObject( \
def ExportDomainsToIndexObj(): #{ # Get domain indices and names from the label description file # adding the domain at each step. cpd_obj = None idx_obj = None max_idx = 0 obj_type = w.WLZ_NULL dom_objs = [] dom_idxs = [] with open(args.ldf) as ldf: #{ for rec in ldf: #{ VerbMsg('rec = ' + rec) if not re.match(r'^[ \t]*#', rec): #{ rec = rec.lstrip() dom_idx = int(re.split('\s+', rec)[0]) dom_name = re.split('"', rec)[1] VerbMsg('idx = ' + str(dom_idx) + ' dom = ' + dom_name) if (dom_idx > 0): #{ try: #{ if dom_idx > max_idx: #{ max_idx = dom_idx #} dom_idxs.append(dom_idx) errNum = w.enum__WlzErrorNum(w.WLZ_ERR_FILE_OPEN) dom_file = args.domaindir + '/' + dom_name + '.wlz' fp = libc.fopen(dom_file, 'rb') if not bool(fp): #{ raise IOError() #} obj = w.WlzAssignObject( \ w.WlzReadObj(fp, c.byref(errNum)), None) if (bool(errNum)): #{ raise WlzError() #} p_lst = w.WlzMakePropertyList(None) p_nam = w.WlzMakeNameProperty(dom_name, c.byref(errNum)) if (bool(errNum)): #{ raise WlzError() #} ft = c.CFUNCTYPE(c.c_void_p, c.c_void_p)\ (w.WlzFreePropertyListEntry) alcerr = w.AlcDLPListEntryAppend(p_lst.contents.list, None, \ p_nam, ft) if (bool(alcerr)): #{ raise WlzError() #} obj.contents.plist = w.WlzAssignPropertyList( p_lst, None) dom_objs.append(obj) libc.fclose(fp) if (bool(errNum)): #{ raise WlzError() #} VerbMsg('domain object type (idx == ' + str(dom_idx) + ') ' + \ str(w.WlzStringFromObjTypeValue( \ obj.contents.type, None))) if (obj_type == w.WLZ_NULL): #{ if((obj.contents.type == w.WLZ_2D_DOMAINOBJ) or \ (obj.contents.type == w.WLZ_3D_DOMAINOBJ)): #{ obj_type = obj.contents.type #} #} except IOError: #}{ ErrorMsg('Failed to read domain from file ' + dom_file + \ ' (' + w.WlzStringFromErrorNum(errNum, None) + ')') except WlzError: #}{ ErrorMsg('Failed to process domain from file ' + dom_file + \ ' (' + w.WlzStringFromErrorNum(errNum, None) + ')') #} #} #} #} #} VerbMsg('Object type ' + str(w.WlzStringFromObjTypeValue(obj_type, None))) if ((max_idx < 1) or ((not obj_type == w.WLZ_2D_DOMAINOBJ) and (not obj_type == w.WLZ_3D_DOMAINOBJ))): #{ ErrorMsg('Require at least one 2 or 3D domain with a positive index.') #} try: #{ VerbMsg('Creating compound array object of domains.') cpd_obj = w.WlzMakeCompoundArray( \ w.enum__WlzObjectType(w.WLZ_COMPOUND_ARR_2), \ 1, max_idx + 1, None, obj_type, c.byref(errNum)) if (bool(errNum)): #{ raise WlzError() #} for i in range(0, len(dom_objs)): #{ obj = dom_objs[i] idx = dom_idxs[i] cpd_obj.contents.o[idx] = obj #} except: #}{ ErrorMsg('Failed to create compound object from domains (' + \ w.WlzStringFromErrorNum(errNum, None) + ')') #} if not args.compound: #{ try: #{ VerbMsg('Creating index object from compound of domains.') idx_obj = w.WlzAssignObject( \ w.WlzIndexObjFromCompound(cpd_obj, c.byref(errNum)), None) if (bool(errNum)): #{ raise WlzError() #} except: #}{ ErrorMsg('Failed to create index object from compound of domains (' + \ w.WlzStringFromErrorNum(errNum, None) + ')') #} #} if bool(args.reference) and (not args.compound): #{ try: #{ VerbMsg('Cutting index object to the same bounding box as the\n' + \ 'reference object (read from ' + args.reference + ').') fp = None errNum = w.enum__WlzErrorNum(w.WLZ_ERR_FILE_OPEN) if args.reference == '-': #{ fp = libc.stdin else: #}{ fp = libc.fopen(args.reference, 'rb') #} if not bool(fp): #{ raise IOError() #} obj = w.WlzAssignObject( \ w.WlzReadObj(fp, c.byref(errNum)), None) if not args.reference == '-': #{ libc.fclose(fp) #} if (bool(errNum)): #{ raise WlzError() #} box = w.WlzBoundingBox3I(obj, c.byref(errNum)) if (not bool(errNum)): #{ gtype = w.WlzGreyTypeFromObj(idx_obj, c.byref(errNum)) #} w.WlzFreeObj(obj) if (bool(errNum)): #{ raise WlzError() #} VerbMsg('Using bounding box ' + \ '(' + str(box.xMin) + ',' + str(box.xMax) + '),' + \ '(' + str(box.yMin) + ',' + str(box.yMax) + '),' + \ '(' + str(box.zMin) + ',' + str(box.zMax) + ')') VerbMsg('Preserving grey type ' + \ w.WlzStringFromGreyType(gtype, None) + \ '.') obj = w.WlzCutObjToBox3D(idx_obj, box, gtype, 0, 0.0, 0.0, \ c.byref(errNum)) if (bool(errNum)): #{ raise WlzError() #} w.WlzFreeObj(idx_obj) idx_obj = obj except IOError: #}{ ErrorMsg('Failed to read the reference object read from ' + \ args.reference + '.') except WlzError: #}{ ErrorMsg('Failed to cut index object to the bounding box of the\n' + \ 'reference object read from (' + args.reference + ') (' + \ w.WlzStringFromErrorNum(errNum, None) + ')') #} #} try: #{ ft = 'index' if args.compound: #{ ft = 'compound' #} VerbMsg('Writing ' + ft + ' object to output file (' + args.output + ').') errNum = w.enum__WlzErrorNum(w.WLZ_ERR_FILE_OPEN) if args.output == '-': #{ fp = libc.stdout else: #}{ fp = libc.fopen(args.output, 'wb') #} if not bool(fp): #{ raise IOError() #} if args.compound: #{ errNum = w.WlzWriteObj(fp, cpd_obj) else: #}{ errNum = w.WlzWriteObj(fp, idx_obj) #} if not args.output == '-': #{ libc.fclose(fp) #} if (bool(errNum)): #{ raise WlzError() #} except: #}{ ErrorMsg('Failed to write ' + ft + ' object to file (' + \ w.WlzStringFromErrorNum(errNum, None) + ')')
rtn = subprocess.call(cmdline) if (bool(rtn)): print(prog + ': MAVTKDomainToSurf failed to create stl file.') CleanExit(1) # Convert the stl file to a Woolz contour object, read it in and then # find the number of faces in the model. cmdline = [WlzExtFFConvert, '-o' + workfile + '0.wlz', \ workfile + '0.stl'] if (args.verbose): print(cmdline) rtn = subprocess.call(cmdline) if (bool(rtn)): print(prog + ': WlzExtFFConvert failed to convert stl file to wlz.') CleanExit(1) obj = Wlz.WlzAssignObject(ReadWoolzFile(workfile + '0.wlz'), None) if (not bool(obj)): print(prog + ': Failed to read Woolz file.') CleanExit(1) model = obj.contents.domain.ctr.contents.model n_faces = model.contents.res.face.numElm if (args.verbose): print('Initial number of faces = ' + str(n_faces)) if (n_faces < 4): print(prog + ': Invalid surface model (n_faces = ' + str(n_faces) + ')') CleanExit(1) # Flip face orientation if required. if (args.flip): if (args.verbose):
'from file\n (url ' + timURL + ').') #} MsgVerbose('Voxel size is ' + str(voxel_sz) + '.') #} # # Copy the grey scale Woolz reference object setting name and # text properties if(not args.nofiles): #{ fple = c.CFUNCTYPE(c.c_void_p, c.c_void_p) \ (w.WlzFreePropertyListEntry) # Read the Woolz grey scale reference object and write it try: #{ MsgVerbose('Reading voxel image from file ' + vox_file) errNum = w.enum__WlzErrorNum(w.WLZ_ERR_FILE_OPEN) fp = libc.fopen(vox_file.encode('utf-8'), 'rb') ref_obj = w.WlzAssignObject( \ w.WlzReadObj(fp, c.byref(errNum)), None) libc.fclose(fp) ChkWoolzError(errNum, 0) MsgVerbose('Setting voxel image voxel size to ' + str(voxel_sz)) w.WlzSetVoxelSize(ref_obj, voxel_sz[0], voxel_sz[1], voxel_sz[2]) MsgVerbose('Creating reference object property list.') p_lst = w.WlzMakePropertyList(None) p_str = stage + '_' + model + '_reference' p_nam = w.WlzMakeNameProperty(p_str.encode('utf-8'), c.byref(errNum)) p_txt = w.WlzMakeTextProperty('Origin'.encode('utf-8'), origin.encode('utf-8'), c.byref(errNum)) alcerr = w.AlcDLPListEntryAppend(p_lst.contents.list, None, p_nam, fple) alcerr = w.AlcDLPListEntryAppend(p_lst.contents.list, None,