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)
Exemplo n.º 2
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def outputFiles(out_dir, img_series, rescale, nowrite):
    for i in img_series:
        vrbMsg('Encoding ' + img_series[i][0].ProtocolName + '_' + str(i))
        obj = makeWlzImageObj(img_series[i], rescale)
        file_base = out_dir + '/' + img_series[i][0].ProtocolName + '_' + str(
            i)
        wlz_file_nm = file_base + '.wlz'
        txt_file_nm = file_base + '.txt'
        if not nowrite:
            fp = c.cast(fopen(wlz_file_nm.encode('utf-8'), b'wb'),
                        c.POINTER(w.FILE))
            err_num = w.WlzWriteObj(fp, obj)
            if bool(err_num):
                raise WlzError()
            fclose(fp)
            vrbMsg('Woolz object written to ' + wlz_file_nm)
        w.WlzFreeObj(obj)
        obj = None
        if not nowrite:
            f = open(txt_file_nm, 'wt')
            f.write(str(img_series[i][0]))
            f.close()
            vrbMsg('Text written to ' + txt_file_nm)
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) + ')')
     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,
                                      p_txt, fple)
     if(bool(alcerr)): #{
       errNum = w.enum__WlzErrorNum(w.WLZ_ERR_MEM_ALLOC)
     #}
     ChkWoolzError(errNum, 0)
     ref_obj.contents.plist = w.WlzAssignPropertyList(p_lst, None)
     out_file_ref = file_base + '_reference.wlz'
     MsgVerbose('Writing voxel image to file ' + out_file_ref)
     fp = libc.fopen(out_file_ref.encode('utf-8'), 'wb')
     errNum = w.WlzWriteObj(fp, ref_obj)
     libc.fclose(fp)
     ChkWoolzError(errNum, 0)
   except: #}{
     MsgError('Failed to copy grey scale Woolz voxel object (' +
              vox_file + ')', 1)
   #}
 #}
 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( \