# 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,
p_txt, fple)
if(bool(alcerr)): #{
errNum = w.enum__WlzErrorNum(w.WLZ_ERR_MEM_ALLOC)
#}
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
