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 warnWlzError(self, msg): #{ logging.debug('warnWlzError') logging.debug('error message is: ' + msg) err = str(w.WlzStringFromErrorNum(self.errnum, None)) logging.debug('error code is: ' + err) QtGui.QMessageBox.critical(self, 'Warning', msg + ' (' + err + ')', QtGui.QMessageBox.Close) self.errnum = c.c_int(w.WLZ_ERR_NONE)
def ChkWoolzError(errNum, status): #{ if(bool(errNum)): #{ msg = 'Woolz error ' + w.WlzStringFromErrorNum(errNum, None) if(status < 1): #{ MsgWarn(msg) else: #}{ MsgError(msg, status) #} raise WlzError()
def ReadLmkTr(): #{ sv = [] tv = [] try: #{ if args.input == '-': #{ f = sys.stdin else: #}{ f = open(args.input, 'r') #} doc = et.parse(f) idx = 0 for lm in doc.findall('Landmark'): #{ s = lm.find('Source') t = lm.find('Target') sv.append(GetLmkVertex(s)) tv.append(GetLmkVertex(t)) VerbMsg('{:d} {:g} {:g} {:g} {:g} {:g} {:g}'. \ format( \ idx, \ sv[idx].vtX, sv[idx].vtY, sv[idx].vtZ, \ tv[idx].vtX, tv[idx].vtY, tv[idx].vtZ)) idx = idx + 1 #} if not args.input == '-': #{ f.close() #} if ((not len(sv) == len(tv)) or (len(sv) < 3)): #{ raise IOError() #} except IOError: #}{ ErrorMsg('Failed to read ITK affine transform from file ' + args.input) #} try: #{ n = len(sv) svtx = (w.WlzDVertex3 * n)() tvtx = (w.WlzDVertex3 * n)() errNum = w.enum__WlzErrorNum(w.WLZ_ERR_NONE) for i in range(0, n): #{ svtx[i] = sv[i] tvtx[i] = tv[i] #} tr = w.WlzAffineTransformLSq3D(n, tvtx, n, svtx, 0, None, \ w.enum__WlzTransformType(w.WLZ_TRANSFORM_3D_AFFINE), \ c.byref(errNum)) if bool(errNum) or \ (not int(tr.contents.type) == int(w.WLZ_TRANSFORM_3D_AFFINE)): #{ raise WlzError() #} except WlzError: #}{ ErrorMsg('Failed to compute LSq affine transform from landmarks (' + w.WlzStringFromErrorNum(errNum, None) + ')') #} mat = WlzTrToMat(tr) return(mat)
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( \ Wlz.WlzHistogramObj(obj, \ ctypes.c_int(0), ctypes.c_double(0.0), ctypes.c_double(1.0), \ ctypes.byref(errNum)), None) if(bool(errNum)):
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) + ')')
if(model_has_anat): #{ # # Create compound object from the anatomy domains. if(not (args.nofiles or args.noindex)): #{ try: #{ nullValues = w.WlzValues(None) errNum = w.enum__WlzErrorNum(w.WLZ_ERR_NONE) cpd_obj = w.WlzMakeCompoundArray( \ w.enum__WlzObjectType(w.WLZ_COMPOUND_ARR_2), \ 1, idx_max + 1, None, ref_obj.contents.type, c.byref(errNum)) ChkWoolzError(errNum, 0) except: #}{ MsgError('Failed to create compound object for ' + stage + ' ' + model + ' (' + w.WlzStringFromErrorNum(errNum, None) + ')', 1) #} for idx in range(0, len(anat_table)): #{ row = anat_table[idx] domfile = glob.glob(db_image_area + stage.lower() +'/' + model +'/' + '/anatomy/EMAPA_' + str(row.accession) + '/*.wlz') if(len(domfile) == 0): #{ domfile = None MsgWarn('Anatomy domain file not found for ' + stage + ' ' + model + ' EMAPA_' + str(row.accession)) elif(len(domfile) > 1): #}{ MsgError('Multiple domain files found for ' + stage + ' ' + model + ' EMAPA_' + str(row.accession), 1) else: #}{