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 WriteWoolzObject(filename, obj): errNum = Wlz.enum__WlzErrorNum(Wlz.WLZ_ERR_FILE_OPEN) fp = libc.fopen(filename, 'wb') if(bool(fp)): errNum = Wlz.WlzWriteObj(fp, obj) libc.fclose(fp) return(errNum)
def WriteWoolzObject(filename, obj): errNum = Wlz.enum__WlzErrorNum(Wlz.WLZ_ERR_FILE_OPEN) fp = libc.fopen(filename, 'wb') if (bool(fp)): errNum = Wlz.WlzWriteObj(fp, obj) libc.fclose(fp) return (errNum)
def ReadWoolzFile(filename): obj = None errNum = Wlz.enum__WlzErrorNum(Wlz.WLZ_ERR_FILE_OPEN) fp = libc.fopen(filename, 'rb') if(bool(fp)): obj = Wlz.WlzReadObj(fp, ctypes.byref(errNum)) libc.fclose(fp) return(obj)
def ReadWoolzFile(filename): obj = None errNum = Wlz.enum__WlzErrorNum(Wlz.WLZ_ERR_FILE_OPEN) fp = libc.fopen(filename, 'rb') if (bool(fp)): obj = Wlz.WlzReadObj(fp, ctypes.byref(errNum)) libc.fclose(fp) return (obj)
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)
#!/usr/bin/python # Reads a Woolz 2D or 3D domain object and generates a histogram. from __future__ import print_function import sys import ctypes import Wlz 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
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 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 __name__ == '__main__': #{ # Process the command line args = ParseArgs() prog = sys.argv[0] errNum = w.enum__WlzErrorNum(w.WLZ_ERR_NONE) if (args.verbose): #{ print(prog + ': args = ' + str(args)) #} ExportDomainsToIndexObj() #}
def WriteMeshLabFilter(filename, flt): with open(filename, "w") as ff: for fr in flt: print(fr, file=ff) ff.close() def CleanExit(stat): for f in glob.glob(workfile + '[0-1].*'): os.remove(f) exit(stat) if __name__ == '__main__': args = ParseArgs() prog = sys.argv[0]; errNum = Wlz.enum__WlzErrorNum(Wlz.WLZ_ERR_NONE) if(args.verbose): print('Args = ' + str(args)) workfile = tempfile.mktemp(dir=args.tmpdir, prefix='wd2vs') # Use MAVTKDomainToSurf to create an stl file corresponding to the # given Woolz domain. cmdline = [MAVTKDomainToSurf, '-o' + workfile + '0.stl'] if(args.voxelscaling): cmdline.append('-z') cmdline.append(args.infile) if(args.verbose): print(cmdline) rtn = subprocess.call(cmdline)
a_node = False #} #} if(not bool(a_node)): #{ MsgWarn('failed to merge color for EMAPA:' + str(t_EMAPA) + ' ' + row.name) #} #} #} if __name__ == '__main__': #{ # # Process the command line args = ParseArgs() prog = sys.argv[0]; errNum = w.enum__WlzErrorNum(w.WLZ_ERR_NONE) if(args.stage): #{ match = re.match(r'^TS\d\d?$', args.stage.upper()) if(match): #{ single_stage = match.group(0) else: #}{ MsgError('Bad stage, specify using TS[0-9][0-9]? (eg TS07\n' + 'or TS17).', 1) #} #} MsgVerbose('args = ' + str(args)) # # Fetch the EMAP service description file MsgVerbose('Fetching service description file (using url =\n' + emap_srv_desc_url + ').') try: #{
def makeWlzImageObj(slices, rescale): vrbMsg('creating Woolz object') obj = None gvw = None errNum = w.enum__WlzErrorNum(w.WLZ_ERR_NONE) s0 = slices[0] nx = s0.Columns ny = s0.Rows nz = len(slices) sx = float(s0.PixelSpacing[0]) sy = float(s0.PixelSpacing[1]) r_intercept = 0.0 r_slope = 1.0 bgd_v = 0 if rescale: if ('RescaleIntercept' in s0) and ('RescaleSlope' in s0): r_intercept = float(s0.RescaleIntercept) r_slope = float(s0.RescaleSlope) bgd_v = int(r_intercept) else: wrnMsg( 'Unable to rescale image grey values to Hounsfield units as ' + 'rescale parameters not in DICOM metadata.') sz = m.fabs(slices[1].ImagePositionPatient[2] - s0.ImagePositionPatient[2]) if (sz < sys.float_info.epsilon) and ('SpacingBetweenSlices' in s0): sz = m.fabs(s0.SpacingBetweenSlices) if sz < sys.float_info.epsilon: if nz > 1: wrnMsg( 'Multiple slices at same position, slice thickness set to 1.0.' ) sz = 1.0 x1 = int(np.floor(s0.ImagePositionPatient[0] / sx)) y1 = int(np.floor(s0.ImagePositionPatient[1] / sy)) z1 = int(np.floor(s0.ImagePositionPatient[2] / sz)) g_type = w.WlzGreyType(w.WLZ_GREY_ERROR) if s0.BitsAllocated == 8: g_type = int(w.WLZ_GREY_UBYTE) elif s0.BitsAllocated == 16: g_type = int(w.WLZ_GREY_SHORT) else: raise Exception('Unsupported voxel grey type.') err_num = w.enum__WlzErrorNum(w.WLZ_ERR_NONE) obj = w.WlzMakeCuboidI(z1, z1 + nz - 1, y1, y1 + ny - 1, x1, x1 + nx - 1, g_type, bgd_v, None, None, c.byref(err_num)) if not bool(err_num): err_num = w.enum__WlzErrorNum(w.WlzSetVoxelSize(obj, sx, sy, sz)) if not bool(err_num): vvp = obj.contents.values.vox.contents.values for iz in range(0, nz): si = slices[iz] vp = vvp[iz].r.contents.values for iy in range(0, ny): offset = nx * iy for ix in range(0, nx): if g_type == int(w.WLZ_GREY_UBYTE): ubp = vp.ubp[offset + ix] ubp.contents = c.c_char(si.pixel_array[iy, ix]) elif g_type == int(w.WLZ_GREY_SHORT): vp.shp[offset + ix] = c.c_short( int((si.pixel_array[iy, ix] * r_slope) + r_intercept)) else: raise Exception('Unsupported voxel grey type.') return obj