def __init__(self, fid_data, procpar, fidheader):
def get_arrayed_AP(p):
"""
check for arrayed acquisition parameters in procpar
return dictionary {par : array_length}
"""
AP_dict = {}
for par in ['tr', 'te', 'fa']:
pass
return AP_dict
self.fid_data = fid_data
self.p = procparReader(procpar).read()
self.fid_header = fidheader
self.rcvrs = str(self.p['rcvrs']).count('y')
self.arrayed_AP = get_arrayed_AP(self.p)
apptype = self.p['apptype']
# decoding skipint parameter
print('Making k-space for '+ str(apptype)+str(self.p['seqfil'])+\
' seqcon: '+str(self.p['seqcon']))
def load_data():
# returns list of data
def ifft(inkdata):
inkdata = np.fft.fftshift(inkdata, axes=(2, 3))
ifft_data = np.fft.ifft2(inkdata, axes=(2, 3), norm='ortho')
ifft_data = np.fft.ifftshift(ifft_data, axes=(2, 3))
return ifft_data
folder = '/home/david/dev/dixon/s_2018080901'
name_list = glob.glob(folder + '/fsems2*img')
#ind = [0,3,6]
ind = [0, 1, 2, 3, 4, 5, 6]
rawre = sorted([i for i in name_list if 'rawRE' in i])
rawim = sorted([i for i in name_list if 'rawIM' in i])
#print('\n'.join(rawim))
#getting only the -pi, 0, pi
combined_names = [[rawre[i], rawim[i]] for i in ind]
data = []
roshift = []
for item in combined_names:
procpar = (item[0] + '/procpar')
#print(procpar)
print(item[0])
ppr = procparReader(item[0] + '/procpar')
roshift.append(float(ppr.read()['roshift']))
hdr, data_re = fdfReader(item[0], 'out').read()
hdr, data_im = fdfReader(item[1], 'out').read()
cdata = np.vectorize(complex)(data_re[0, ...], data_im[0, ...])
data.append(ifft(cdata))
print(data[0].shape)
print(roshift)
return data, roshift, procpar
def __init__(self, data, procpar, fid_path=None):
"""
data = numpy.ndarray(phase, read, slice, echo)
procpar = /path/to/procpar
"""
self.fid = fid_path
self.procpar = procpar
self.p = procparReader(procpar).read()
self.data = data
def __init__(self, data, procpar, fitmethod): self.data = data self.procpar = procpar self.fitmethod = fitmethod ppr = procparReader(procpar) self.ppdict = ppr.read() te = float(self.ppdict['te']) ne = int(self.ppdict['ne']) self.echo_times = [i*te for i in range(1,ne+1)] # echo times in seconds
def __init__(self, kspace, procpar, skiptab=None, skipint=None):
"""
kspace = np.ndarray([receivers, phase, read, slice, echo])
procpar = /procpar/file/path
For CS reconstruction:
skiptab = 'y' or 'n' procpar parameter
skipint = procpar parameter to show which k space lines are excluded
"""
self.skipint = skipint
self.skiptab = skiptab
self.kspace_data = kspace
self.p = procparReader(procpar).read()
def __init__(self, data, procpar, fitmethod, skipfirstecho):
self.procpar = procpar
self.fitmethod = fitmethod
ppr = procparReader(procpar)
self.ppdict = ppr.read()
te = float(self.ppdict['te'])
ne = int(self.ppdict['ne'])
if skipfirstecho == False:
self.data = data
self.echo_times = [i * te for i in range(1, ne + 1)
] # echo times in seconds
elif skipfirstecho == True:
self.data = data[:, :, :, 1:]
self.echo_times = [i * te for i in range(2, ne + 1)
] # echo times in seconds
def fid2nii(indir,
out=None,
saveprocpar=True,
save_kspace=False,
save_imgspace=True):
if not os.path.isdir(indir):
raise (Exception('Please specify input fid directory'))
if out == None:
# if output is not given, take fid as basename for new dir
out = indir[:-4] + '.nifti/'
if not os.path.exists(out):
os.makedirs(out)
fid = indir + '/fid'
procpar = indir + '/procpar'
ppdict = procparReader(procpar).read()
fid_data, fid_header = fidReader(fid, procpar).read()
kspacemaker = kSpaceMaker(fid_data, procpar, fid_header)
kspace = kspacemaker.make()
imgspace = imgSpaceMaker(kspace, procpar).make()
kspace_real = [] # put separate channel data into separate lements of list
kspace_imag = []
for i in range(len(ppdict['rcvrs'])):
kspace_real.append(np.real(kspace[i, ...]))
kspace_imag.append(np.imag(kspace[i, ...]))
writer1 = niftiWriter(procpar, kspace_real[-1])
writer1.write(out + 'kspace_real_ch' + str(i))
writer2 = niftiWriter(procpar, kspace_imag[-1])
writer2.write(out + 'kspace_imag_ch' + str(i))
sumimg = np.sum(np.absolute(imgspace), axis=0)
writer_img = niftiWriter(procpar, sumimg)
writer_img.write(out + 'imgspace_sum')
if saveprocpar == True:
copyfile(procpar, out + '/procpar')
def __init__(self, procpar, kspace_cs, kspace_orig, reconpar=None):
"""
INPUT:
procpar : path to procpar file
kspace_cs : zerofilled cs kspace in numpy array
reconpar: dictionary, ALOHA recon parameters
keys:
filter_size
rcvrs
cs_dim
recontype
"""
def get_recontype(reconpar):
if 'angio' in self.p['pslabel']:
recontype = 'kx-ky_angio'
elif 'mems' in self.p['pslabel']:
recontype = 'k-t'
return recontype
def get_reconpar():
pass
self.p = procparReader(procpar).read()
recontype = get_recontype(reconpar)
rcvrs = self.p['rcvrs'].count('y')
self.rp = {'filter_size' : FILTER_SIZE ,\
'cs_dim' : CS_DIM ,\
'ro_dim' : RO_DIM, \
'rcvrs' : rcvrs , \
'recontype' : recontype,\
'timedim' : 4,\
'stages' : STAGES,\
'virtualcoilboost' : False}
print(self.rp)
self.kspace_cs = np.array(kspace_cs, dtype='complex64')
self.kspace = np.array(kspace_orig, dtype='complex64')
def read(self):
#---------------- auxiliary functions for read method -----------------
def preproc_fdf(fdf):
with open(fdf,'rb') as openFdf:
fdata = bytearray(openFdf.read())
nul = fdata.find(b'\x00')
header = fdata[:nul]
data = fdata[nul+1:]
return (header,data)
# ----------parse fdf header and return into a dictionary --------------
def parse_header(header):
keys_to_parse = sorted(['rank','roi','location','spatial_rank',\
'matrix','orientation',\
'studyid','gap','pe_size','ro_size',\
'pe2_size', 'abscissa',\
'storage'])
to_delete = ('char','float','int')
header = header.decode('ascii').split('\n')
header_dict = {}
for line in header: # some formatting of header
if self.printlines:
print(line)
for item in to_delete:
if line.startswith(item):
line = line.split(item,1)
break
try:
line = line[1].lstrip()
line = line.lstrip('*').rstrip(';')
if '[]' in line:
line = line.replace('[]','')
if '{' in line:
line = line.replace('{','(')
if '}' in line:
line = line.replace('}',')')
if ' ' in line:
line = line.replace(' ','')
line = line.split('=')
header_dict[line[0]] = line[1]
except:
continue
for item in keys_to_parse:
if item in header_dict.keys():
if item == 'abscissa':
tempval = header_dict[item][1:-1];''.join(tempval)
tempval = tempval.replace('"','')
header_dict[item] = tuple([k for k in tempval.split(',')])
if item == 'matrix':
tempval = header_dict[item][1:-1];''.join(tempval)
header_dict[item] = tuple([int(k) for k in tempval.split(',')])
if item == 'roi':
tempval = header_dict[item][1:-1];''.join(tempval)
header_dict[item] = tuple([float(k) for k in tempval.split(',')])
if item == 'ro_size' or item == 'pe_size' or item == 'pe2_size':
header_dict[item] = int(header_dict[item])
if item == 'storage':
tempval = header_dict[item];''.join(tempval)
tempval = tempval.replace('"','')
header_dict[item] = str(tempval)
if item == 'orientation':
tempval = header_dict[item][1:-1];''.join(tempval)
header_dict[item] = tuple([float(k) for k in tempval.split(',')])
if item == 'location':
tempval = header_dict[item][1:-1];''.join(tempval)
header_dict[item] = tuple([float(k) for k in tempval.split(',')])
if item == 'gap':
header_dict[item] = float(header_dict[item])
if item == 'slices':
header_dict[item] = int(header_dict[item])
if item == 'TR':
header_dict[item] = float(header_dict[item])/1000
return header_dict
#----------process bynary data based on header--------------------
def prepare_data(binary_data):
matrix = self.header_dict['matrix']
if self.header_dict['storage'] == 'float' and \
self.header_dict['bits'] == '32':
dt = np.dtype('float32'); dt = dt.newbyteorder('<')
else:
print('')
print('error: data type incorrectly specified in "prepare_data"\n')
return -1
img_data = np.frombuffer(binary_data, dtype=dt)
img_data = np.reshape(img_data,matrix)
return img_data
#--------------------------------------------------------------------------------------
# main read method
#--------------------------------------------------------------------------------------
if os.path.isdir(self.path):
self.procpar = str(self.path)+'/procpar'
fdf_list = sorted(glob.glob(str(self.path)+'/*.fdf'))
(header, data) = preproc_fdf(fdf_list[0]) # run preproc once to get header
ppr = procparReader(self.procpar)
self.ppdict = ppr.read()
else:
try:
ppr = procparReader(self.procpar)
self.ppdict = ppr.read()
except:
print('\nfdfReader.read() warning : Please specify procpar file!\n')
fdf_list =[self.path]
(header, data) = preproc_fdf(self.path)
self.header_dict = parse_header(header)
# ------------------------process if 3d -------------------------
if self.header_dict['spatial_rank'] == '"3dfov"':
full_data = []
time_concat = []
time = len([1 for i in fdf_list if 'slab001' in i])
for i in fdf_list: # only 1 item, but there migh be more in future
(header, data) = preproc_fdf(i)
img_data = prepare_data(data)
full_data.append(img_data) # full data in one list
self.data_array = np.asarray(full_data)
#self.data_array = np.swapaxes(self.data_array, 0,3)
#------- -----------------process if 2d------------------------------------
elif self.header_dict['spatial_rank'] == '"2dfov"':
full_data = []
time_concat = []
time = len([1 for i in fdf_list if 'slice001' in i])
for i in fdf_list:
(header, data) = preproc_fdf(i)
img_data = prepare_data(data)
img_data = np.expand_dims(np.expand_dims(img_data,2),3) # expand 2d to 4d
full_data.append(img_data) # full data in one list
# make sublists
slice_list =[full_data[i:i+time] for i in range(0,len(full_data),time)]
for aslice in slice_list:
time_concat.append(np.concatenate(tuple(aslice),axis=3))
slice_time_concat = np.concatenate(time_concat, axis=2) #slice+time concatenated
self.data_array = slice_time_concat
if str(self.ppdict['orient']) == 'trans90': # vomit inducing method to properly flip data
print('found orientation')
self.data_array = np.swapaxes(self.data_array, 0, 1)
# --------------------process if 1d------------------------ TODO ????
elif self.header_dict['spatial_rank'] == '"1dfov"':
pass
return (self.header_dict, self.data_array)
def __init__(self, procpar, data):
ppr = procparReader(procpar)
self.ppdict = ppr.read()
self.data = data
seqfil = self.ppdict['seqfil']
seqcon = self.ppdict['seqcon']
def run(self):
def make_fieldmap(minus_pi_data, plus_pi_data, procpar):
"""
Make phase correction factor from minus Pi shifted and plus Pi shifted data. Does
unwrapping with prelude in two steps: first step is preliminary field map with output
mask, then this output mask is holefilled and the unwrapping is done again
"""
output_name_fieldmap = self.proc_dir + '/fieldmap_wrapped'
output_name_fieldmap_uw = self.proc_dir + '/fieldmap_unwrapped'
output_name_fieldmap_mask = self.proc_dir + '/fieldmap_premask'
output_name_fieldmap_mask_corr = self.proc_dir + '/fieldmap_mask'
magnitude_name_for_prelude_corr = self.proc_dir + '/masked_abs'
data = np.multiply(plus_pi_data, np.conj(minus_pi_data))
fieldmap = np.arctan2(np.imag(data), np.real(data))
niftiwriter = niftiWriter(procpar, fieldmap)
niftiwriter.write(output_name_fieldmap)
print('Unwrapping fieldmap ...')
# make initial field map
os.system('prelude -p '+output_name_fieldmap+' -a '+magnitude_name_for_prelude+ \
' -u '+output_name_fieldmap_uw+' --savemask='+output_name_fieldmap_mask)
# close gaps in mask
os.system('fslmaths ' + output_name_fieldmap_mask + ' -fillh ' +
output_name_fieldmap_mask_corr)
# make new absolute with mask
os.system('fslmaths '+magnitude_name_for_prelude+' -mul '+output_name_fieldmap_mask_corr+\
' '+magnitude_name_for_prelude_corr)
# make final field map
os.system('prelude -p '+output_name_fieldmap+' -a '+magnitude_name_for_prelude_corr+ \
' -u '+output_name_fieldmap_uw)
print('Fieldmap done!')
return
def inverse_fourier_transform2D(kspace_data):
# changed axes 2,3
print('pproc kdata shape {}'.format(kspace_data.shape))
kspace_data = np.fft.fftshift(kspace_data, axes=(0, 1))
imgspace_data = np.fft.ifft2(kspace_data,
axes=(0, 1),
norm='ortho')
imgspace_data = np.fft.ifftshift(imgspace_data, axes=(0, 1))
return imgspace_data
if not os.path.exists(self.proc_dir):
os.makedirs(self.proc_dir)
if not self.preproc_from_fid:
open(self.preproc_data, 'w').close()
procpar = []
roshift = []
for item in self.combined_names:
# combined_names is a list of lists containing real and imaginary parts
procpar.append(item[0] + '/procpar')
ppr = procparReader(item[0] + '/procpar')
shift = int(float(ppr.read()['roshift']) *
1000000) # write it in microsec for naming
roshift.append(float(ppr.read()['roshift']))
hdr, data_re = fdfReader(item[0], 'out').read()
hdr, data_im = fdfReader(item[1], 'out').read()
kspace_data = np.vectorize(complex)(data_re, data_im)
imgspace_data = inverse_fourier_transform2D(kspace_data)
magnitude_data = np.absolute(imgspace_data)
phase_data = np.arctan2(np.imag(imgspace_data),
np.real(imgspace_data))
niftiwriter = niftiWriter(item[0] + '/procpar', magnitude_data)
output_name_magnitude = self.proc_dir + '/' + self.pslabel + '_' + str(
shift) + 'us_mag'
niftiwriter.write(output_name_magnitude)
niftiwriter = niftiWriter(item[1] + '/procpar', phase_data)
output_name_phase = self.proc_dir + '/' + self.pslabel + '_' + str(
shift) + 'us_ph'
niftiwriter.write(output_name_phase)
output_name_unwrapped = self.proc_dir + '/' + self.pslabel + '_' + str(
shift) + 'us_unwrapped_ph'
if float(ppr.read()['roshift']) == 0.00037:
plus_pi_data = imgspace_data
if float(ppr.read()['roshift']) == -0.00037:
minus_pi_data = imgspace_data
if float(ppr.read()['roshift']) == 0:
magnitude_name_for_prelude = output_name_magnitude
copyfile(item[0] + '/procpar', self.proc_dir + '/procpar')
if self.unwrap_all:
print('Unwrapping phasemaps ...')
os.system('prelude -p '+output_name_phase+' -a '+output_name_magnitude+ \
' -u '+output_name_unwrapped)
with open(self.preproc_data, 'a') as openfile:
line = str(float(ppr.read()['roshift']))+','\
+output_name_magnitude+','\
+output_name_phase+'\n'
openfile.write(line)
if self.preproc_from_fid:
pass
if self.make_fieldmap:
make_fieldmap(minus_pi_data, plus_pi_data, procpar[0])
return