def resample_niftyreg(fref,
fflo,
faff,
outpath='',
fimout='',
fcomment='',
pickname='ref',
intrp=1,
executable='',
verbose=True):
# check if the executable exists:
# if executable=='' and 'RESPATH' in Cnt and os.path.isfile(Cnt['RESPATH']):
# executable = Cnt['RESPATH']
if not os.path.isfile(executable):
raise IOError('Incorrect path to executable file for registration.')
#> output path
if outpath == '' and fimout != '':
opth = os.path.dirname(fimout)
if opth == '':
opth = os.path.dirname(fflo)
elif outpath == '':
opth = os.path.dirname(fflo)
else:
opth = outpath
imio.create_dir(opth)
#> the output naming
if '/' in fimout:
fout = fimout
elif fimout != '' and not os.path.isfile(fimout):
fout = os.path.join(opth, fimout)
elif pickname == 'ref':
fout = os.path.join(opth, 'affine_ref-' \
+ os.path.basename(fref).split('.nii')[0]+fcomment+'.nii.gz')
elif pickname == 'flo':
fout = os.path.join(opth, 'affine_flo-' \
+ os.path.basename(fflo).split('.nii')[0]+fcomment+'.nii.gz')
if isinstance(intrp, (int, long)): intrp = str(intrp)
cmd = [
executable, '-ref', fref, '-flo', fflo, '-trans', faff, '-res', fout,
'-inter', intrp
]
if not verbose:
cmd.append('-voff')
call(cmd)
return fout
def resample_vinci(
fref,
fflo,
faff,
intrp=0,
fimout='',
fcomment='',
outpath='',
pickname='ref',
vc='',
con='',
vincipy_path='',
atlas_resample=False,
atlas_ref_make=False,
atlas_ref_del=False,
close_vinci=False,
close_buff=True,
):
''' Resample the floating image <fflo> into the geometry of <fref>,
using the Vinci transformation output <faff> (an *.xml file).
Output the NIfTI file path of the resampled/resliced image.
'''
#---------------------------------------------------------------------------
#> output path
if outpath == '' and fimout != '' and '/' in fimout:
opth = os.path.dirname(fimout)
if opth == '':
opth = os.path.dirname(fflo)
fimout = os.path.basename(fimout)
elif outpath == '':
opth = os.path.dirname(fflo)
else:
opth = outpath
imio.create_dir(opth)
#> output floating and affine file names
if fimout == '':
if pickname == 'ref':
fout = os.path.join(
opth,
'affine-ref-' \
+os.path.basename(fref).split('.nii')[0]+fcomment+'.nii.gz')
else:
fout = os.path.join(
opth,
'affine-flo-' \
+os.path.basename(fflo).split('.nii')[0]+fcomment+'.nii.gz')
else:
fout = os.path.join(opth, fimout.split('.nii')[0] + '.nii.gz')
#---------------------------------------------------------------------------
if vincipy_path == '':
try:
import resources
vincipy_path = resources.VINCIPATH
except:
raise NameError('e> could not import resources \
or find variable VINCIPATH in resources.py')
sys.path.append(vincipy_path)
try:
from VinciPy import Vinci_Bin, Vinci_Connect, Vinci_Core, Vinci_XML, Vinci_ImageT
except ImportError:
raise ImportError('e> could not import Vinci:\n \
check the variable VINCIPATH (path to Vinci) in resources.py')
#---------------------------------------------------------------------------
#> start Vinci core engine if it is not running/given
if vc == '' or con == '':
#> adopted from the Vinci's example RunMMMJob.py
bin = Vinci_Bin.Vinci_Bin()
con = Vinci_Connect.Vinci_Connect(bin)
vinci_binpath = con.StartMyVinci()
vc = Vinci_Core.Vinci_CoreCalc(con)
vc.StdProject()
#---------------------------------------------------------------------------
if int(intrp) == 0:
interp_nn = True
else:
interp_nn = False
#---------------------------------------------------------------------------
#> change the reference image to be loaded as atlas
if atlas_resample and atlas_ref_make:
#> output file name for the extra reference image
fextref = os.path.join(opth, 'reference-as-atlas.nii.gz')
prc.nii_modify(fref, fimout=fextref, voxel_range=[0., 255.])
ref = Vinci_ImageT.newTemporary(vc,
szFileName=fextref,
bLoadAsAtlas=atlas_resample)
if atlas_ref_del:
os.remove(fextref)
else:
ref = Vinci_ImageT.newTemporary(vc,
szFileName=fref,
bLoadAsAtlas=atlas_resample)
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
#> reapply rigid transformation to new image
flo = Vinci_ImageT.newTemporary(vc,
szFileName=fflo,
bLoadAsAtlas=atlas_resample)
rsl = flo.reapplyMMMTransform(faff, refImage=ref, IsComputed=True)
rsl.saveYourselfAs(bUseOffsetRotation=True,
bUseNextNeighbourInterp=interp_nn,
szFullFileName=fout)
#---------------------------------------------------------------------------
#> close image buffers for reference and floating
if close_buff:
ref.killYourself()
flo.killYourself()
rsl.killYourself()
if close_vinci: con.CloseVinci(True)
return fout
def coreg_vinci(
fref,
fflo,
vc='',
con='',
vincipy_path='',
scheme_xml='',
outpath='',
fname_aff='',
pickname='ref',
fcomment='',
flo_colourmap='Green',
close_vinci=False,
close_buff=True,
cleanup=True,
save_res=False,
):
if scheme_xml == '':
raise IOError('e> the Vinci schema *.xml file is not provided. \n \
i> please add the schema file in the call: scheme_xml=...')
#---------------------------------------------------------------------------
#> output path
if outpath == '' and fname_aff != '' and '/' in fname_aff:
opth = os.path.dirname(fname_aff)
if opth == '':
opth = os.path.dirname(fflo)
fname_aff = os.path.basename(fname_aff)
elif outpath == '':
opth = os.path.dirname(fflo)
else:
opth = outpath
imio.create_dir(opth)
imio.create_dir(os.path.join(opth, 'affine-vinci'))
#> output floating and affine file names
if fname_aff == '':
if pickname == 'ref':
faff = os.path.join(
opth,
'affine-vinci',
'affine-ref-' \
+os.path.basename(fref).split('.nii')[0]+fcomment+'.xml')
fout = os.path.join(
opth,
'affine-vinci',
'affine-ref-' \
+os.path.basename(fref).split('.nii')[0]+fcomment+'.nii.gz')
else:
faff = os.path.join(
opth,
'affine-vinci',
'affine-flo-' \
+os.path.basename(fflo).split('.nii')[0]+fcomment+'.xml')
fout = os.path.join(
opth,
'affine-vinci',
'affine-flo-' \
+os.path.basename(fflo).split('.nii')[0]+fcomment+'.nii.gz')
else:
#> add '.xml' extension if not in the affine output file name
if not fname_aff.endswith('.xml'):
fname_aff += '.xml'
faff = os.path.join(opth, 'affine-vinci', fname_aff)
fout = os.path.join(opth, fname_aff.split('.')[0] + '.nii.gz')
#---------------------------------------------------------------------------
if vincipy_path == '':
try:
import resources
vincipy_path = resources.VINCIPATH
except:
raise NameError('e> could not import resources \
or find variable VINCIPATH in resources.py')
sys.path.append(vincipy_path)
try:
from VinciPy import Vinci_Bin, Vinci_Connect, Vinci_Core, Vinci_XML, Vinci_ImageT
except ImportError:
raise ImportError('e> could not import Vinci:\n \
check the variable VINCIPATH (path to Vinci) in resources.py')
#> start Vinci core engine if it is not running/given
if vc == '' or con == '':
#> adopted from the Vinci's example RunMMMJob.py
bin = Vinci_Bin.Vinci_Bin()
con = Vinci_Connect.Vinci_Connect(bin)
vinci_binpath = con.StartMyVinci()
vc = Vinci_Core.Vinci_CoreCalc(con)
vc.StdProject()
#> read the registration schema file
f = open(scheme_xml, 'rb')
reg_scheme = f.read()
f.close()
#> check scheme data file and remove possible XML comments at its beginning
root = Vinci_XML.ElementTree.fromstring(reg_scheme)
if root.tag != "MMM":
sys.exit("scheme data file %s does not contain tag MMM\n" % scheme_xml)
reg_scheme = Vinci_XML.ElementTree.tostring(root)
# bytes -> str
reg_scheme = reg_scheme.decode("utf-8")
#> pick reference and floating images
ref = Vinci_ImageT.newTemporary(vc, szFileName=fref)
rsl = Vinci_ImageT.newTemporary(vc, szFileName=fflo)
#> set the colour map for the floating image
rsl.setColorSettings(CTable=flo_colourmap)
#---------------------------------------------------------------------------
#> perform the registration
rsl.alignToRef(ref, reg_scheme, szRegistrationSummaryFile=faff)
#---------------------------------------------------------------------------
#> find the weird folder name created and to be disposed of.
if cleanup:
#> get the folder name (going to rubbish)
del_dir = os.path.normpath(faff).split(os.sep)[1]
fflo_dir = os.path.split(fflo)[0]
del_dir = os.path.join(
os.path.split(fflo)[0],
os.path.normpath(faff).split(os.sep)[1])
if os.path.isdir(del_dir):
shutil.rmtree(del_dir)
#> save the registered image
if save_res:
rsl.saveYourselfAs(bUseOffsetRotation=True, szFullFileName=fout)
#> close image buffers for reference and floating
if close_buff:
rsl.killYourself()
ref.killYourself()
if close_vinci: con.CloseVinci(True)
#else: con.CloseSockets()
return {'faff': faff, 'fim': fout, 'vinci_con': con, 'vinci_vc': vc}
def resample_mltp_spm(fims,
ftr,
interp=1.,
which=1,
mask=0,
mean=0,
graph=0,
niisort=False,
prefix='r_',
outpath='',
fcomment='',
pickname='ref',
copy_input=False,
del_in_uncmpr=False,
del_out_uncmpr=False):
'''
fims: has to be a list of at least two files with the first one acting
as a reference.
'''
if not isinstance(fims, list) and not isinstance(fims[0], basestring):
raise ValueError('e> unrecognised list of input images')
if not os.path.isfile(ftr):
raise IOError(
'e> cannot open the file with translations and rotations')
#> output path
if outpath == '':
opth = os.path.dirname(fims[0])
else:
opth = outpath
imio.create_dir(opth)
#> working file names (not touching the original ones)
_fims = []
#> decompress if necessary
for f in fims:
if not os.path.isfile(f) and not (f.endswith('nii')
or f.endswith('nii.gz')):
raise IOError('e> could not open file:', f)
if f[-3:] == '.gz':
fugz = imio.nii_ugzip(f, outpath=os.path.join(opth, 'copy'))
elif copy_input:
fnm = os.path.basename(f).split('.nii')[0] + '_copy.nii'
fugz = os.path.join(opth, 'copy', fnm)
shutil.copyfile(f, fugz)
else:
fugz = f
_fims.append(fugz)
if niisort:
niisrt = imio.niisort(_fims)
_fims = niisrt['files']
#> maximal number of characters per line (for Matlab array)
Pinmx = max([len(f) for f in _fims])
#> equalise the input char array
Pineq = [f.ljust(Pinmx) for f in _fims]
#---------------------------------------------------------------------------
#> SPM reslicing (resampling) flags
flgs = []
flgs.append('flgs.mask = ' + str(mask))
flgs.append('flgs.mean = ' + str(mean))
flgs.append('flgs.which = ' + str(which))
flgs.append('flgs.interp = ' + str(interp))
flgs.append('flgs.graphics = ' + str(graph))
flgs.append('flgs.wrap = [0 0 0]')
flgs.append('flgs.prefix = ' + "'" + prefix + "'")
flgs.append('disp(flgs)')
#---------------------------------------------------------------------------
fsrpt = os.path.join(opth, 'pyauto_script_resampling.m')
with open(fsrpt, 'w') as f:
f.write(
'% AUTOMATICALLY GENERATED MATLAB SCRIPT FOR SPM RESAMPLING PET IMAGES\n\n'
)
f.write('%> the following flags for image reslicing are used:\n')
f.write("disp('m> SPM reslicing flags:');\n")
for item in flgs:
f.write("%s;\n" % item)
f.write('\n%> the following PET images will be aligned:\n')
f.write("disp('m> PET images for SPM reslicing:');\n")
f.write('P{1,1} = [...\n')
for item in Pineq:
f.write("'%s'\n" % item)
f.write('];\n\n')
f.write('disp(P{1,1});\n')
# f.write('\n%> the following PET images will be aligned using the translations and rotations in X:\n')
# f.write("X = dlmread('"+ftr+"');\n")
# f.write('for fi = 2:'+str(len(fims))+'\n')
# f.write(" VF = strcat(P{1,1}(fi,:),',1');\n")
# f.write(' M_ = zeros(4,4);\n')
# f.write(' M_(:,:) = spm_get_space(VF);\n')
# f.write(' M = spm_matrix(X(fi,:));\n')
# f.write(' spm_get_space(VF, M\M_(:,:));\n')
# f.write('end\n\n')
f.write('spm_reslice(P, flgs);\n')
cmd = [
'matlab', '-nodisplay', '-nodesktop', '-r',
'run(' + '\'' + fsrpt + '\'' + '); exit'
]
call(cmd)
if del_in_uncmpr:
for fpth in _fims:
os.remove(fpth)
def realign_mltp_spm(fims,
quality=1.0,
fwhm=6,
sep=4,
rtm=1,
interp=2,
graph=0,
outpath='',
fcomment='',
niicopy=False,
niisort=False):
'''
fims: has to be a list of at least two files with the first one acting
as a reference.
'''
#> input folder
inpath = os.path.dirname(fims[0])
#> output folder
if outpath == '':
outpath = os.path.join(inpath, 'align')
else:
outpath = os.path.join(outpath, 'align')
if fims[0][-3:] == '.gz' or niicopy:
tmpth = outpath #os.path.join(outpath, 'tmp')
rpth = tmpth
else:
tmpth = outpath
rpth = inpath
imio.create_dir(tmpth)
#> uncompress for SPM
fungz = []
for f in fims:
if f[-3:] == '.gz':
fun = imio.nii_ugzip(f, outpath=tmpth)
elif os.path.isfile(f) and f.endswith('nii'):
if niicopy:
fun = os.path.join(
tmpth,
os.path.basename(f).split('.nii')[0] + '_copy.nii')
shutil.copyfile(f, fun)
else:
fun = f
else:
print 'w> omitting file/folder:', f
fungz.append(fun)
if niisort:
niisrt = imio.niisort([os.path.join(tmpth,f) for f in os.listdir(tmpth) \
if os.path.isfile(os.path.join(tmpth,f))])
fsrt = niisrt['files']
else:
fsrt = fungz
P_input = [f+',1' for f in fsrt\
if f.endswith('nii') and f[0]!='r' and 'mean' not in f]
#> maximal number of characters per line (for Matlab array)
Pinmx = max([len(f) for f in P_input])
#> equalise the input char array
Pineq = [f.ljust(Pinmx) for f in P_input]
#---------------------------------------------------------------------------
#> MATLAB realign flags for SPM
flgs = []
pw = '\'\''
flgs.append('flgs.quality = ' + str(quality))
flgs.append('flgs.fwhm = ' + str(fwhm))
flgs.append('flgs.sep = ' + str(sep))
flgs.append('flgs.rtm = ' + str(rtm))
flgs.append('flgs.pw = ' + str(pw))
flgs.append('flgs.interp = ' + str(interp))
flgs.append('flgs.graphics = ' + str(graph))
flgs.append('flgs.wrap = [0 0 0]')
flgs.append('disp(flgs)')
#---------------------------------------------------------------------------
fscript = os.path.join(outpath, 'pyauto_script_realign.m')
with open(fscript, 'w') as f:
f.write(
'% AUTOMATICALLY GENERATED MATLAB SCRIPT FOR SPM PET REALIGNMENT\n\n'
)
f.write('%> the following flags for PET image alignment are used:\n')
f.write("disp('m> SPM realign flags:');\n")
for item in flgs:
f.write("%s;\n" % item)
f.write('\n%> the following PET images will be aligned:\n')
f.write("disp('m> PET images for SPM realignment:');\n")
f.write('P{1,1} = [...\n')
for item in Pineq:
f.write("'%s'\n" % item)
f.write('];\n\n')
f.write('disp(P{1,1});\n')
f.write('spm_realign(P, flgs);')
cmd = [
'matlab', '-nodisplay', '-nodesktop', '-r',
'run(' + '\'' + fscript + '\'' + '); exit'
]
call(cmd)
fres = glob.glob(os.path.join(rpth, 'rp*.txt'))[0]
res = np.loadtxt(fres)
return {'fout': fres, 'outarray': res, 'P': Pineq, 'fims': fsrt}
def resample_spm(imref,
imflo,
M,
matlab_eng='',
intrp=1.,
which=1,
mask=0,
mean=0,
outpath='',
fimout='',
fcomment='',
prefix='r_',
pickname='ref',
del_ref_uncmpr=False,
del_flo_uncmpr=False,
del_out_uncmpr=False):
print '====================================================================='
print ' S P M inputs:'
print '> ref:', imref
print '> flo:', imflo
print '====================================================================='
import matlab
from pkg_resources import resource_filename
#-start Matlab engine if not given
if matlab_eng == '':
import matlab.engine
eng = matlab.engine.start_matlab()
else:
eng = matlab_eng
# add path to SPM matlab file
spmpth = resource_filename(__name__, 'spm')
eng.addpath(spmpth, nargout=0)
#> output path
if outpath == '' and fimout != '':
opth = os.path.dirname(fimout)
if opth == '':
opth = os.path.dirname(imflo)
elif outpath == '':
opth = os.path.dirname(imflo)
else:
opth = outpath
imio.create_dir(opth)
#> decompress if necessary
if imref[-3:] == '.gz':
imrefu = imio.nii_ugzip(imref, outpath=opth)
else:
fnm = os.path.basename(imref).split('.nii')[0] + '_copy.nii'
imrefu = os.path.join(opth, fnm)
shutil.copyfile(imref, imrefu)
#> floating
if imflo[-3:] == '.gz':
imflou = imio.nii_ugzip(imflo, outpath=opth)
else:
fnm = os.path.basename(imflo).split('.nii')[0] + '_copy.nii'
imflou = os.path.join(opth, fnm)
shutil.copyfile(imflo, imflou)
if isinstance(M, basestring):
if os.path.basename(M).endswith('.txt'):
M = np.loadtxt(M)
print 'i> matrix M given in the form of text file'
elif os.path.basename(M).endswith('.npy'):
M = np.load(M)
print 'i> matrix M given in the form of NumPy file'
else:
raise IOError('e> unrecognised file extension for the affine.')
elif isinstance(M, (np.ndarray, np.generic)):
print 'i> matrix M given in the form of Numpy array'
else:
raise IOError('The form of affine matrix not recognised.')
# run the Matlab SPM resampling
r = eng.resample_spm_m(imrefu, imflou, matlab.double(M.tolist()), mask,
mean, intrp, which, prefix)
#-compress the output
split = os.path.split(imflou)
fim = os.path.join(split[0], prefix + split[1])
imio.nii_gzip(fim, outpath=opth)
# delete the uncompressed
if del_ref_uncmpr: os.remove(imrefu)
if del_flo_uncmpr and os.path.isfile(imflou): os.remove(imflou)
if del_out_uncmpr: os.remove(fim)
#> the compressed output naming
if fimout != '':
fout = os.path.join(opth, fimout)
elif pickname == 'ref':
fout = os.path.join(opth, 'affine_ref-' \
+ os.path.basename(imrefu).split('.nii')[0]+fcomment+'.nii.gz')
elif pickname == 'flo':
fout = os.path.join(opth, 'affine_flo-' \
+ os.path.basename(imflo).split('.nii')[0]+fcomment+'.nii.gz')
# change the file name
os.rename(fim + '.gz', fout)
return fout
def coreg_spm(
imref,
imflo,
matlab_eng='',
outpath='',
fname_aff='',
fcomment='',
pickname='ref',
costfun='nmi',
sep=[4, 2],
tol=[
0.0200, 0.0200, 0.0200, 0.0010, 0.0010, 0.0010, 0.0100, 0.0100, 0.0100,
0.0010, 0.0010, 0.0010
],
fwhm=[7, 7],
params=[0, 0, 0, 0, 0, 0],
graphics=1,
visual=0,
del_uncmpr=True,
save_arr=True,
save_txt=True,
):
import matlab
from pkg_resources import resource_filename
#-start Matlab engine if not given
if matlab_eng == '':
import matlab.engine
eng = matlab.engine.start_matlab()
else:
eng = matlab_eng
# add path to SPM matlab file
spmpth = resource_filename(__name__, 'spm')
print 'PATH: ' + spmpth
eng.addpath(spmpth, nargout=0)
#> output path
if outpath == '' and fname_aff != '' and '/' in fname_aff:
opth = os.path.dirname(fname_aff)
if opth == '':
opth = os.path.dirname(imflo)
fname_aff = os.path.basename(fname_aff)
elif outpath == '':
opth = os.path.dirname(imflo)
else:
opth = outpath
imio.create_dir(opth)
#> decompress ref image as necessary
if imref[-3:] == '.gz':
imrefu = imio.nii_ugzip(imref, outpath=opth)
else:
fnm = os.path.basename(imref).split('.nii')[0] + '_copy.nii'
imrefu = os.path.join(opth, fnm)
shutil.copyfile(imref, imrefu)
#> floating
if imflo[-3:] == '.gz':
imflou = imio.nii_ugzip(imflo, outpath=opth)
else:
fnm = os.path.basename(imflo).split('.nii')[0] + '_copy.nii'
imflou = os.path.join(opth, fnm)
shutil.copyfile(imflo, imflou)
# run the matlab SPM coregistration
Mm, xm = eng.coreg_spm_m(imrefu,
imflou,
costfun,
matlab.double(sep),
matlab.double(tol),
matlab.double(fwhm),
matlab.double(params),
graphics,
visual,
nargout=2)
# get the affine matrix
M = np.array(Mm._data.tolist())
M = M.reshape(4, 4).T
# get the translation and rotation parameters in a vector
x = np.array(xm._data.tolist())
# delete the uncompressed files
if del_uncmpr:
if imref[-3:] == '.gz': os.remove(imrefu)
if imflo[-3:] == '.gz': os.remove(imflou)
imio.create_dir(os.path.join(opth, 'affine-spm'))
#---------------------------------------------------------------------------
if fname_aff == '':
if pickname == 'ref':
faff = os.path.join(
opth, 'affine-spm', 'affine-ref-' +
os.path.basename(imref).split('.nii')[0] + fcomment + '.npy')
else:
faff = os.path.join(
opth, 'affine-spm', 'affine-flo-' +
os.path.basename(imflo).split('.nii')[0] + fcomment + '.npy')
else:
#> add '.npy' extension if not in the affine output file name
if not fname_aff.endswith('.npy'):
fname_aff += '.npy'
faff = os.path.join(opth, 'affine-spm', fname_aff)
#---------------------------------------------------------------------------
#> safe the affine transformation
if save_arr:
np.save(faff, M)
if save_txt:
np.savetxt(faff.split('.npy')[0] + '.txt', M)
return {
'affine': M,
'faff': faff,
'rotations': x[3:],
'translations': x[:3],
'matlab_eng': eng
}
def resample_fsl(imref,
imflo,
faff,
outpath='',
fimout='',
pickname='ref',
fcomment='',
intrp=1,
executable=''):
if executable == '':
if 'FSLDIR' not in os.environ:
raise IOError('e> no FSL executable provided!')
else:
executable = os.path.join(os.environ['FSLDIR'], 'bin', 'flirt')
if not os.path.isfile(executable) or not call([executable, '-version'
]) == 0:
raise IOError('e> no valid FSL executable provided!')
print '==================================================================='
print ' F S L resampling'
#> output path
if outpath == '' and fimout != '':
opth = os.path.dirname(fimout)
if opth == '':
opth = os.path.dirname(imflo)
elif outpath == '':
opth = os.path.dirname(imflo)
elif outpath != '':
opth = outpath
imio.create_dir(opth)
#> the output naming
if '/' in fimout:
fout = fimout
elif fimout != '' and not os.path.isfile(fimout):
fout = os.path.join(opth, fimout)
elif pickname == 'ref':
fout = os.path.join(opth, 'affine_ref-' \
+ os.path.basename(imref).split('.nii')[0]+fcomment+'.nii.gz')
elif pickname == 'flo':
fout = os.path.join(opth, 'affine_flo-' \
+ os.path.basename(imflo).split('.nii')[0]+fcomment+'.nii.gz')
intrp = int(intrp)
if isinstance(intrp, (int, long)): intrp = str(intrp)
if intrp == '1':
interpolation = 'trilinear'
elif intrp == '0':
interpolation = 'nearestneighbour'
cmd = [
executable, '-in', imflo, '-ref', imref, '-out', fout, '-init', faff,
'-applyxfm', '-interp', interpolation
]
call(cmd)
print 'D O N E'
print '==================================================================='
return fout
def affine_niftyreg(fref,
fflo,
outpath='',
fname_aff='',
pickname='ref',
fcomment='',
executable='',
omp=1,
rigOnly=False,
affDirect=False,
maxit=5,
speed=True,
pi=50,
pv=50,
smof=0,
smor=0,
rmsk=True,
fmsk=True,
rfwhm=15.,
rthrsh=0.05,
ffwhm=15.,
fthrsh=0.05,
verbose=True):
# check if the executable exists:
if not os.path.isfile(executable):
raise IOError('Incorrect path to executable file for registration.')
#create a folder for images registered to ref
if outpath != '':
odir = os.path.join(outpath, 'affine-niftyreg')
fimdir = os.path.join(outpath, os.path.join('affine-niftyreg', 'mask'))
else:
odir = os.path.join(os.path.dirname(fflo), 'affine-niftyreg')
fimdir = os.path.join(os.path.dirname(fflo), 'affine-niftyreg', 'mask')
imio.create_dir(odir)
imio.create_dir(fimdir)
if rmsk:
f_rmsk = os.path.join(
fimdir,
'rmask_' + os.path.basename(fref).split('.nii')[0] + '.nii.gz')
create_mask(fref, fimout=f_rmsk, thrsh=rthrsh, fwhm=rfwhm)
if fmsk:
f_fmsk = os.path.join(
fimdir,
'fmask_' + os.path.basename(fflo).split('.nii')[0] + '.nii.gz')
create_mask(fflo, fimout=f_fmsk, thrsh=fthrsh, fwhm=ffwhm)
# output in register with ref and text file for the affine transform
if fname_aff != '':
fout = os.path.join(odir, fname_aff.split('.')[0] + '.nii.gz')
faff = os.path.join(odir, fname_aff)
else:
if pickname == 'ref':
fout = os.path.join(odir, 'affine_ref-' \
+os.path.basename(fref).split('.nii')[0]+fcomment+'.nii.gz')
faff = os.path.join(odir, 'affine_ref-' \
+os.path.basename(fref).split('.nii')[0]+fcomment+'.txt')
elif pickname == 'flo':
fout = os.path.join(odir, 'affine_flo-' \
+os.path.basename(fflo).split('.nii')[0]+fcomment+'.nii.gz')
faff = os.path.join(odir, 'affine_flo-' \
+os.path.basename(fflo).split('.nii')[0]+fcomment+'.txt')
# call the registration routine
cmd = [
executable, '-ref', fref, '-flo', fflo, '-aff', faff, '-pi',
str(pi), '-pv',
str(pv), '-smooF',
str(smof), '-smooR',
str(smor), '-maxit', '10', '-omp',
str(omp), '-res', fout
]
if speed:
cmd.append('-speeeeed')
if rigOnly:
cmd.append('-rigOnly')
if affDirect:
cmd.append('affDirect')
if rmsk:
cmd.append('-rmask')
cmd.append(f_rmsk)
if fmsk:
cmd.append('-fmask')
cmd.append(f_fmsk)
if not verbose:
cmd.append('-voff')
call(cmd)
#> affine to Numpy array
aff = np.loadtxt(faff)
return {'affine': aff, 'faff': faff, 'fim': fout} #faff, fout
def affine_fsl(fref,
fflo,
outpath='',
fname_aff='',
pickname='ref',
fcomment='',
executable='',
costfun='normmi',
dof=6,
hstbins=256,
verbose=True):
if executable == '':
if 'FSLDIR' not in os.environ:
raise IOError('e> no FSL executable provided!')
else:
executable = os.path.join(os.environ['FSLDIR'], 'bin', 'flirt')
if not os.path.isfile(executable) or not call([executable, '-version'
]) == 0:
raise IOError('e> no valid FSL executable provided!')
#---------------------------------------------------------------------------
#> output path
if outpath == '' and fname_aff != '' and os.path.isfile(fname_aff):
opth = os.path.dirname(fname_aff)
if opth == '':
opth = os.path.dirname(fflo)
fname_aff = os.path.basename(fname_aff)
elif outpath == '':
opth = os.path.dirname(fflo)
else:
opth = outpath
imio.create_dir(opth)
imio.create_dir(os.path.join(opth, 'affine-fsl'))
#> output floating and affine file names
if fname_aff == '':
if pickname == 'ref':
faff = os.path.join(
opth,
'affine-fsl',
'affine-ref-' \
+os.path.basename(fref).split('.nii')[0]+fcomment+'.txt')
else:
faff = os.path.join(
opth,
'affine-fsl',
'affine-flo-' \
+os.path.basename(fflo).split('.nii')[0]+fcomment+'.txt')
else:
#> add '.xml' extension if not in the affine output file name
if not fname_aff.endswith('.txt'):
fname_aff += '.txt'
faff = os.path.join(opth, 'affine-vinci', fname_aff)
#---------------------------------------------------------------------------
#> command with options for FSL-FLIRT registration
cmd = [
executable, '-cost', costfun, '-dof',
str(dof), '-omat', faff, '-in', fflo, '-ref', fref, '-bins',
str(hstbins)
]
#> add verbose mode if requested
if isinstance(verbose, bool): verbose = int(verbose)
if verbose > 0: cmd.extend(['-verbose', str(verbose)])
#> execute FSL-FLIRT command with the above options
call(cmd)
# convert to Numpy float
aff = np.loadtxt(faff)
return {'affine': aff, 'faff': faff}