def addObj(self, o): #{
logging.debug('addObj()')
t = int(o.contents.type)
self.errnum = c.c_int(w.WLZ_ERR_OBJECT_TYPE)
if (t == int(w.WLZ_2D_DOMAINOBJ)) or (t == int(
w.WLZ_3D_DOMAINOBJ)): #{
if t == int(w.WLZ_2D_DOMAINOBJ): #{
self.errnum = c.c_int(w.WLZ_ERR_NONE)
else: #}{
logging.debug('making view struct')
v = w.WlzMake3DViewStruct(c.c_int(w.WLZ_3D_VIEW_STRUCT), \
c.byref(self.errnum))
if not bool(self.errnum): #{
f = w.WlzDVertex3()
v.vtX = c.c_double(0.0)
v.vtY = c.c_double(0.0)
v.vtZ = c.c_double(0.0)
v.contents.theta = self.yaw * m.pi / 180.0
v.contents.phi = self.pitch * m.pi / 180.0
v.contents.zeta = self.roll * m.pi / 180.0
v.contents.dist = self.dist
v.contents.fixed = f
v.contents.view_mode = c.c_int(w.WLZ_UP_IS_UP_MODE)
v.contents.scale = c.c_double(1.0)
v.contents.voxelRescaleFlg = c.c_int(0)
w.WlzFree3DViewStruct(self.view)
self.view = w.WlzAssign3DViewStruct(v, None)
#}
#}
#}
if not bool(self.errnum): #{
w.WlzFreeObj(self.obj)
self.obj = w.WlzAssignObject(o, None)
self.errnum = self.setObj2D()
#}
if not bool(self.errnum): #{
ary = self.wlz2DToNP()
logging.debug('setting image')
self.img = ary.astype(np.float64).T
self.img_itm.setImage(self.img)
self.setROIType('N')
#}
if bool(self.errnum): #{
self.warnWlzError('Failed to add object.')
def setObj2D(self): #{
logging.debug('setObj2D')
errnum = c.c_int(w.WLZ_ERR_NONE)
t = self.obj.contents.type
if t == w.WLZ_2D_DOMAINOBJ: #{
self.obj2d = w.WlzAssignObject(self.obj, None)
elif t == w.WLZ_3D_DOMAINOBJ: #}{
logging.debug('cutting section from 3D object')
w.WlzInit3DViewStruct(self.view, self.obj)
o2d = w.WlzGetSubSectionFromObject(
self.obj, None, self.view,
c.c_int(w.WLZ_INTERPOLATION_NEAREST), None, c.byref(errnum))
print(o2d)
print(errnum)
if not bool(errnum): #{
w.WlzFreeObj(self.obj2d)
self.obj2d = w.WlzAssignObject(o2d, None)
#}
#}
return (errnum)
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)
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)):
print('Failed to compute histogram ' + \
'(' + Wlz.WlzStringFromErrorNum(errNum, None) + ').')
exit(1)
print('Plotting histogram')
hist = hobj.contents.domain.hist.contents;
n_bins = hist.nBins
center = np.arange(n_bins) + 0.5;
bins = [0] * n_bins
if(hist.type == Wlz.WLZ_HISTOGRAMDOMAIN_INT):
for i in range(0, n_bins):
bins[i] = hist.binValues.inp[i]
elif(hist.type == Wlz.WLZ_HISTOGRAMDOMAIN_FLOAT):
for i in range(0, n_bins):
bins[i] = hist.binValues.dbp[i]
pt.xlim(0,256)
pt.yscale('log')
pt.bar(center, bins, align='center', width=1.0)
pt.show()
print('Free the objects')
Wlz.WlzFreeObj(hobj)
Wlz.WlzFreeObj(obj)
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.flip):
if (args.verbose):
print('Flipping face orientation.')
errNum = Wlz.WlzGMFilterFlipOrient(model)
if (bool(errNum)):
print(prog + ': Failed to flip face orientation (' +
Wlz.WlzStringFromErrorNum(errNum, None) + ').')
CleanExit(1)
# Write the Woolz object file using the stl file format.
if (args.verbose):
print('Writing working Woolz file.')
if (bool(WriteWoolzObject(workfile + '0.wlz', obj))):
print(prog + ': Failed to write working Woolz file.')
CleanExit(1)
Wlz.WlzFreeObj(obj)
cmdline = [WlzExtFFConvert, '-o' + workfile + '0.stl', \
workfile + '0.wlz']
if (args.verbose):
print(cmdline)
rtn = subprocess.call(cmdline)
if (bool(rtn)):
print(prog +
': WlzExtFFConvert failed to convert working wlz file to stl.')
CleanExit(1)
# Create meshlab filter script to reduce the number of faces and smooth
# the surface
if (args.verbose):
print('Creating MeshLab filter file.')
flt = []
cpd_obj.contents.o[row.index] = w.WlzAssignObject( \
w.WlzReadObj(fp, c.byref(errNum)), None)
libc.fclose(fp)
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)