Пример #1
0
 def wlz2DToNP(self):  #{
     ary = None
     logging.debug('wlz2DToNP()')
     try:  #{
         box = w.WlzBoundingBox3I(self.obj2d, c.byref(self.errnum))
         if (bool(self.errnum)):  #{
             raise WlzError()
         #}
         sz = w.WlzIVertex2()
         sz.vtX = box.xMax - box.xMin + 1
         sz.vtY = box.yMax - box.yMin + 1
         org = w.WlzIVertex2()
         org.vtX = box.xMin
         org.vtY = box.yMin
         gtype = w.WlzGreyTypeFromObj(self.obj2d, c.byref(self.errnum))
         if (bool(self.errnum)):  #{
             raise WlzError()
         #}
         if gtype == w.WLZ_GREY_INT:  #{
             vtype = c.c_int
         elif gtype == w.WLZ_GREY_SHORT:  #}{
             vtype = c.c_short
         elif gtype == w.WLZ_GREY_UBYTE:  #}{
             vtype = c.c_ubyte
         elif gtype == w.WLZ_GREY_FLOAT:  #}{
             vtype = c.c_float
         elif gtype == w.WLZ_GREY_DOUBLE:  #}{
             vtype = c.c_double
         else:  #}{
             self.errnum = c.c_int(w.WLZ_ERR_GREY_TYPE)
             raise WlzError()
         #}
         UPP = c.POINTER(c.POINTER(vtype))
         UPV = c.POINTER(c.c_void_p)
         aryc = c.cast(0, UPV)
         self.errnum = w.WlzToArray2D(c.byref(aryc), self.obj2d, sz, org, 0, \
                                      c.c_int(gtype))
         if (bool(self.errnum)):  #{
             raise WlzError()
         #}
         aryc = c.cast(aryc, UPP)
         ary = np.ctypeslib.as_array(aryc.contents, (sz.vtY, sz.vtX))
         self.obj_gtype = gtype
         self.obj2d_sz = [sz.vtX, sz.vtY]
         self.obj2d_org = [org.vtX, org.vtY]
         w.AlcFree(aryc)
     except WlzError:  #}{
         self.warnWlzError('Failed to extract numeric data from object.')
     #}
     return (ary)
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) + ')')
     ChkWoolzError(errNum, 0)
   except: #}{
     MsgError('Failed to read anatomy domain from' + domfile, 1)
   #}
 #}
 try: #{
   alcerr = [None, None, None]
   MsgVerbose('Creating index object from compound of domains.')
   errNum = w.enum__WlzErrorNum(w.WLZ_ERR_NONE)
   tmp_obj = w.WlzAssignObject(
             w.WlzIndexObjFromCompound(cpd_obj, 
                                       c.byref(errNum)), None)
   w.WlzFreeObj(cpd_obj)
   ChkWoolzError(errNum, 0)
   MsgVerbose('Cutting index image to a cuboid.')
   box = w.WlzBoundingBox3I(ref_obj, c.byref(errNum))
   ChkWoolzError(errNum, 0)
   idx_obj_grey_type = w.WLZ_GREY_INT
   if (idx_max < 255): #{
     idx_obj_grey_type = w.WLZ_GREY_UBYTE
   elif (idx_max < 32768): #}{
     idx_obj_grey_type = w.WLZ_GREY_SHORT
   #}
   idx_obj = w.WlzAssignObject(
             w.WlzCutObjToValBox3D(tmp_obj, box,
                w.enum__WlzGreyType(idx_obj_grey_type), None,
                0, 0.0, 0.0, c.byref(errNum)), None)
   ChkWoolzError(errNum, 0)
   w.WlzFreeObj(tmp_obj)
   MsgVerbose('Setting index image voxel size to ' + str(voxel_sz))
   w.WlzSetVoxelSize(idx_obj,