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 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 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)
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) + ')')
#}
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,
