def bart_cs(bart_dir, ks, sensemap, l1=0.01):
cfl_ks = np.squeeze(ks)
cfl_ks = np.expand_dims(cfl_ks, -2)
cfl_sensemap = np.squeeze(sensemap)
cfl_sensemap = np.expand_dims(cfl_sensemap, -2)
ks_dir = os.path.join(bart_dir, "file_ks")
sense_dir = os.path.join(bart_dir, "file_sensemap")
img_dir = os.path.join(bart_dir, "file_img")
cfl.write(ks_dir, cfl_ks, "R")
cfl.write(sense_dir, cfl_sensemap, "R")
# L1-wavelet regularized
cmd_flags = "-S -e -R W:3:0:%f -i 100" % l1
cmd = "%s pics %s %s %s %s" % (
BIN_BART,
cmd_flags,
ks_dir,
sense_dir,
img_dir,
)
subprocess.check_call(["bash", "-c", cmd])
bart_recon = load_recon(img_dir, sense_dir)
return bart_recon
def bart_pics(
ks_input,
verbose=False,
sensemap=None,
shape_e=2,
do_cs=True,
do_imag_reg=False,
filename_ks_tmp="ks.tmp",
filename_map_tmp="map.tmp",
filename_im_tmp="im.tmp",
filename_ks_out_tmp="ks_out.tmp",
):
"""BART PICS reconstruction."""
if verbose:
print("PICS (l1-ESPIRiT) reconstruction...")
cfl.write(filename_ks_tmp, ks_input)
if sensemap is None:
cmd = "bart ecalib -m %d -c 1e-9 %s %s" % (
shape_e,
filename_ks_tmp,
filename_map_tmp,
)
if verbose:
print(" %s" % cmd)
subprocess.check_output(["bash", "-c", cmd])
else:
cfl.write(filename_map_tmp, sensemap)
if do_cs:
flags = "-l1 -r 1e-2"
else:
flags = "-l2 -r 1e-2"
if do_imag_reg:
flags = flags + " -R R1:7:1e-1"
cmd = "bart pics %s -S %s %s %s" % (
flags,
filename_ks_tmp,
filename_map_tmp,
filename_im_tmp,
)
if verbose:
print(" %s" % cmd)
subprocess.check_output(["bash", "-c", cmd])
cmd = "bart fakeksp -r %s %s %s %s" % (
filename_im_tmp,
filename_ks_tmp,
filename_map_tmp,
filename_ks_out_tmp,
)
if verbose:
print(" %s" % cmd)
subprocess.check_output(["bash", "-c", cmd])
ks_pics = np.squeeze(cfl.read(filename_ks_out_tmp))
ks_pics = np.expand_dims(ks_pics, axis=0)
return ks_pics
def bart_cs(self, ks, sensemap, l1=0.01):
if self.data_type is "knee" or "DCE_2D":
cfl_ks = np.squeeze(ks)
cfl_ks = np.expand_dims(cfl_ks, -2)
cfl_sensemap = np.squeeze(sensemap)
cfl_sensemap = np.expand_dims(cfl_sensemap, -2)
ks_dir = os.path.join(self.bart_dir, "file_ks")
sense_dir = os.path.join(self.bart_dir, "file_sensemap")
img_dir = os.path.join(self.bart_dir, "file_img")
cfl.write(ks_dir, cfl_ks, "R")
cfl.write(sense_dir, cfl_sensemap, "R")
# L1-wavelet regularized
cmd_flags = "-S -e -R W:3:0:%f -i 100" % l1
# cmd_flags = "-S -e -R W:0:0:%f -i 100" % l1
cmd = "%s pics %s %s %s %s" % (
BIN_BART,
cmd_flags,
ks_dir,
sense_dir,
img_dir,
)
subprocess.check_call(["bash", "-c", cmd])
bart_recon = self.load_recon(img_dir, sense_dir)
elif self.data_type is "DCE":
cfl_ks = np.squeeze(ks)
cfl_sensemap = np.squeeze(sensemap)
cfl_ks = np.transpose(cfl_ks, [0, 1, 3, 2])
cfl_ks = np.expand_dims(cfl_ks, -2)
cfl_ks = np.expand_dims(cfl_ks, 2)
cfl_sensemap = np.expand_dims(cfl_sensemap, axis=-2)
ks_dir = os.path.join(self.bart_dir, "file_ks")
sense_dir = os.path.join(self.bart_dir, "file_sensemap")
img_dir = os.path.join(self.bart_dir, "file_img")
cfl.write(ks_dir, cfl_ks, "R")
cfl.write(sense_dir, cfl_sensemap, "R")
# Low-rank
# might be 3:3
cmd_flags = "-S -e -R L:7:7:%f -i 100" % l1
cmd = "%s pics %s %s %s %s" % (
BIN_BART,
cmd_flags,
ks_dir,
sense_dir,
img_dir,
)
subprocess.check_call(["bash", "-c", cmd])
bart_recon = self.load_recon(img_dir, sense_dir)
else:
print("implement bart for this data type")
exit()
return bart_recon
def bart_espirit(
ks_input,
shape=None,
verbose=False,
shape_e=2,
crop_value=None,
cal_size=None,
smooth=False,
filename_ks_tmp="ks.tmp",
filename_map_tmp="map.tmp",
):
"""Estimate sensitivity maps using BART ESPIRiT.
ks_input dimensions: [emaps, channels, kz, ky, kx]
"""
if verbose:
print("Estimating sensitivity maps...")
if shape is not None:
ks_input = recon.crop(ks_input, [-1, -1, shape[0], shape[1], -1])
ks_input = recon.zeropad(ks_input, [-1, -1, shape[0], shape[1], -1])
flags = ""
if crop_value is not None:
flags = flags + "-c %f " % crop_value
if cal_size is not None:
flags = flags + "-r %d " % cal_size
if smooth:
flags = flags + "-S "
cfl.write(filename_ks_tmp, ks_input)
cmd = "bart ecalib -m %d %s %s %s" % (
shape_e,
flags,
filename_ks_tmp,
filename_map_tmp,
)
if verbose:
print(" %s" % cmd)
time_start = timer()
subprocess.check_output(["bash", "-c", cmd])
time_end = timer()
sensemap = cfl.read(filename_map_tmp)
return sensemap, time_end - time_start
def setup_data_tfrecords_MFAST(
dir_in_root,
dir_out,
data_divide=(0.75, 0.05, 0.2),
min_shape=[80, 180],
num_maps=1,
crop_maps=False,
verbose=False,
):
"""Setups training data as tfrecords.
prep_data.setup_data('/mnt/raid3/data/Studies_DCE/recon-ccomp6/',
'/mnt/raid3/jycheng/Project/deepspirit/data/train/', verbose=True)
"""
if verbose:
print("Directory names:")
print(" Input root: %s" % dir_in_root)
print(" Output root: %s" % dir_out)
file_kspace = "kspace"
file_sensemap = "sensemap"
case_list = os.listdir(dir_in_root)
random.shuffle(case_list)
num_cases = len(case_list)
i_train_1 = np.round(data_divide[0] * num_cases).astype(int)
i_validate_0 = i_train_1 + 1
i_validate_1 = np.round(
data_divide[1] * num_cases).astype(int) + i_validate_0
if not os.path.exists(dir_out):
os.mkdir(dir_out)
if not os.path.exists(os.path.join(dir_out, "train")):
os.mkdir(os.path.join(dir_out, "train"))
if not os.path.exists(os.path.join(dir_out, "validate")):
os.mkdir(os.path.join(dir_out, "validate"))
if not os.path.exists(os.path.join(dir_out, "test")):
os.mkdir(os.path.join(dir_out, "test"))
i_case = 0
for case_name in case_list:
file_kspace_i = os.path.join(dir_in_root, case_name, file_kspace)
file_sensemap_i = os.path.join(dir_in_root, case_name, file_sensemap)
if not os.path.exists(file_kspace_i + ".hdr"):
print("skipping due to kspace not existing in this folder")
continue
if i_case < i_train_1:
dir_out_i = os.path.join(dir_out, "train")
elif i_case < i_validate_1:
dir_out_i = os.path.join(dir_out, "validate")
else:
dir_out_i = os.path.join(dir_out, "test")
if verbose:
print("Processing [%d] %s..." % (i_case, case_name))
i_case = i_case + 1
kspace = np.squeeze(cfl.read(file_kspace_i))
num_coils = kspace.shape[0]
if num_coils is not 32:
print("skipping due to incorrect number of coils")
continue
if verbose:
print(" Slice shape: (%d, %d)" %
(kspace.shape[1], kspace.shape[2]))
print(" Num channels: %d" % kspace.shape[0])
shape_x = kspace.shape[-1]
# for n in range(shape_x):
# modulation = (-1) ** n
# kspace[:, :, :, n] = kspace[:, :, :, n] * [
# 1,
# 1,
# 1,
# np.exp(-1j * modulation),
# ]
# print("kspace shape after modulation")
# should this be here?
kspace = fftc.ifftc(kspace, axis=-1)
print("original kspace shape")
print(kspace.shape)
# x,y,z,coils
# crop or zero pad to the correct size
# if (kspace.shape[0] is not min_shape[0]) or (kspace_shape[1] is not min_shape[1]):
# print("resizing")
# image = fftc.ifft2c(kspace, do_orthonorm=True, order='C')
# new_shape = (kspace.shape[0], min_shape[0], min_shape[1], kspace.shape[-1])
# resized_im = image.copy()
# resized_im.resize(new_shape, refcheck=False)
# kspace = fftc.fft2c(resized_im, do_orthonorm=True, order='C')
kspace = kspace.astype(np.complex64)
print("new kspace shape")
print(kspace.shape)
file_kspace_i = file_kspace_i + "_resized"
cfl.write(file_kspace_i, kspace)
cmd_flags = ""
if crop_maps:
cmd_flags = cmd_flags + " -c 1e-9"
cmd_flags = cmd_flags + (" -m %d" % num_maps)
cmd = "%s ecalib %s %s %s" % (
BIN_BART,
cmd_flags,
file_kspace_i,
file_sensemap_i,
)
if verbose:
print(" Estimating sensitivity maps (bart espirit)...")
print(" %s" % cmd)
subprocess.check_call(["bash", "-c", cmd])
sensemap = np.squeeze(cfl.read(file_sensemap_i))
sensemap = np.expand_dims(sensemap, axis=0)
sensemap = sensemap.astype(np.complex64)
if verbose:
print(" Creating tfrecords (%d)..." % shape_x)
for i_x in range(shape_x):
file_out = os.path.join(dir_out_i,
"%s_x%03d.tfrecords" % (case_name, i_x))
kspace_x = kspace[:, :, :, i_x]
sensemap_x = sensemap[:, :, :, :, i_x]
example = tf.train.Example(features=tf.train.Features(
feature={
"name": _bytes_feature(str.encode(case_name)),
"xslice": _int64_feature(i_x),
"ks_shape_x": _int64_feature(kspace.shape[3]),
"ks_shape_y": _int64_feature(kspace.shape[2]),
"ks_shape_z": _int64_feature(kspace.shape[1]),
"ks_shape_c": _int64_feature(kspace.shape[0]),
"map_shape_x": _int64_feature(sensemap.shape[4]),
"map_shape_y": _int64_feature(sensemap.shape[3]),
"map_shape_z": _int64_feature(sensemap.shape[2]),
"map_shape_c": _int64_feature(sensemap.shape[1]),
"map_shape_m": _int64_feature(sensemap.shape[0]),
"ks": _bytes_feature(kspace_x.tostring()),
"map": _bytes_feature(sensemap_x.tostring()),
}))
tf_writer = tf.python_io.TFRecordWriter(file_out)
tf_writer.write(example.SerializeToString())
tf_writer.close()
def test(self):
print("testing")
# read in a correct test dicom file to change it later
dicom_filename = pydicom.data.get_testdata_files("MR_small.dcm")[0]
self.ds = pydicom.dcmread(dicom_filename)
# 18 time frames in each DICOM
max_frame = self.max_frames
frame = 0
x_slice = 0
case = 1
gif = []
print("number of test cases", self.input_files)
total_acc = []
mask_input = tf_util.kspace_mask(self.ks, dtype=tf.complex64)
numel = tf.cast(tf.size(mask_input), tf.float32)
acc = numel / tf.reduce_sum(tf.abs(mask_input))
input_psnr = []
input_nrmse = []
input_ssim = []
output_psnr = []
output_nrmse = []
output_ssim = []
cs_psnr = []
cs_nrmse = []
cs_ssim = []
input_volume = np.zeros((self.max_frames, 192, 80, 180))
output_volume = np.zeros((self.max_frames, 192, 80, 180))
cs_volume = np.zeros((self.max_frames, 192, 80, 180))
model_time = []
cs_time = []
for step in range(self.input_files // 2):
# for step in range(20):
# DCE_2D: iterator will see each slice followed by 18 time frames
# then the next slice
print("test file #", step)
acc_run = self.sess.run(acc)
total_acc.append(acc_run)
print(
"total test acc:",
np.round(np.mean(total_acc), decimals=2),
np.round(np.std(total_acc), decimals=2),
)
if self.data_type is "knee":
# l1 = 0.015
l1 = 0.0035
if self.data_type is "DCE":
# l1 = 0.05
l1 = 0.01
if self.data_type is "DCE_2D":
l1 = 0.05
model_start_time = time.time()
(
input_image,
output_image,
complex_truth,
ks_run,
sensemap_run,
) = self.sess.run([
self.im_in,
self.output_image,
self.complex_truth,
self.ks,
self.sensemap,
])
runtime = time.time() - model_start_time
if step is not 1:
model_time.append(runtime)
print("GAN: %s seconds" % np.mean(model_time),
"+/- %s" % np.std(model_time))
# bart_test = np.zeros_like(output_image)
cs_start_time = time.time()
bart_test = self.bart_cs(ks_run, sensemap_run, l1=l1)
runtime = time.time() - cs_start_time
if step is not 1:
cs_time.append(runtime)
print("CS: %s seconds" % np.mean(cs_time),
"+/- %s" % np.std(cs_time))
if self.data_type is "knee":
input_image = np.squeeze(input_image)
output_image = np.squeeze(output_image)
truth_image = np.squeeze(complex_truth)
cs_image = np.squeeze(bart_test)
psnr, nrmse, ssim = metrics.compute_all(truth_image,
cs_image,
sos_axis=-1)
cs_psnr.append(psnr)
cs_nrmse.append(nrmse)
cs_ssim.append(ssim)
print("cs psnr, nrmse, ssim")
print(
np.round(np.mean(cs_psnr), decimals=2),
np.round(np.mean(cs_nrmse), decimals=2),
np.round(np.mean(cs_ssim), decimals=2),
)
psnr, nrmse, ssim = metrics.compute_all(truth_image,
output_image,
sos_axis=-1)
output_psnr.append(psnr)
output_nrmse.append(nrmse)
output_ssim.append(ssim)
print("output psnr, nrmse, ssim")
print(
np.round(np.mean(output_psnr), decimals=2),
np.round(np.mean(output_nrmse), decimals=2),
np.round(np.mean(output_ssim), decimals=2),
)
psnr, nrmse, ssim = metrics.compute_all(truth_image,
input_image,
sos_axis=-1)
input_psnr.append(psnr)
input_nrmse.append(nrmse)
input_ssim.append(ssim)
print("input psnr, nrmse, ssim")
print(
np.round(np.mean(input_psnr), decimals=2),
np.round(np.mean(input_nrmse), decimals=2),
np.round(np.mean(input_ssim), decimals=2),
)
def rotate_image(img):
img = np.squeeze(np.absolute(img))
if self.data_type is "DCE":
img = np.transpose(img, axes=(1, 0, 2))
img = np.flip(img, axis=2) # flip the time
if self.data_type is "DCE_2D":
img = np.transpose(img, axes=(1, 0))
return img
mag_input = rotate_image(input_image)
mag_output = rotate_image(output_image)
mag_cs = rotate_image(bart_test)
# x, y, z, time
if self.data_type is "DCE":
input_volume[step, :, :, :] = mag_input
output_volume[step, :, :, :] = mag_output
cs_volume[step, :, :, :] = mag_cs
if self.data_type is "DCE_2D":
input_volume[frame, x_slice, :, :] = mag_input
output_volume[frame, x_slice, :, :] = mag_output
cs_volume[frame, x_slice, :, :] = mag_cs
new_filename = (self.log_dir + "/dicoms/" + "output_slice_" +
str(x_slice) + "_f" + str(frame) + ".dcm")
self.write_dicom(mag_input, new_filename, x_slice, frame)
# increment frame
# if frame is 17, go back to next slice
if frame == self.max_frames - 1:
frame = 0
x_slice += 1
else:
frame += 1
print("slice", x_slice, "time frame", frame)
in_sl = np.abs(input_volume[2, 0, :, :])
filename = os.path.join(self.log_dir,
os.path.basename(self.search_str[:-11]))
input_dir = filename + "_input" + ".npy"
output_dir = filename + "_output" + ".npy"
cs_dir = filename + "_cs" + ".npy"
print("saving numpy volumes")
np.save(input_dir, input_volume)
np.save(output_dir, output_volume)
np.save(cs_dir, cs_volume)
print(output_dir)
print("saving cfl volumes")
cfl.write(input_dir, input_volume, "R")
cfl.write(output_dir, output_volume, "R")
cfl.write(cs_dir, cs_volume, "R")
if self.data_type is "knee":
print("output psnr = " + str(np.mean(output_psnr)) + " +\- " +
str(np.std(output_psnr)) + "\n" + "output nrmse = " +
str(np.mean(output_nrmse)) + " +\- " +
str(np.std(output_nrmse)) + "\n" + "output ssim = " +
str(np.mean(output_ssim)) + " +\- " +
str(np.std(output_ssim)) + "\n" + "test acc = " +
str(np.mean(total_acc)) + " +\-" + str(np.std(total_acc)))
txt_path = os.path.join(self.log_dir, "output_metrics.txt")
f = open(txt_path, "w")
f.write("output psnr = " + str(np.mean(output_psnr)) + " +\- " +
str(np.std(output_psnr)) + "\n" + "output nrmse = " +
str(np.mean(output_nrmse)) + " +\- " +
str(np.std(output_nrmse)) + "\n" + "output ssim = " +
str(np.mean(output_ssim)) + " +\- " +
str(np.std(output_ssim)) + "\n" + "input psnr = " +
str(np.mean(input_psnr)) + " +\- " +
str(np.std(input_psnr)) + "\n" + "input nrmse = " +
str(np.mean(input_nrmse)) + " +\- " +
str(np.std(input_nrmse)) + "\n" + "input ssim = " +
str(np.mean(input_ssim)) + " +\- " +
str(np.std(input_ssim)) + "\n" + "test acc = " +
str(np.mean(total_acc)) + " +\-" + str(np.std(total_acc)))
f.close()
txt_path = os.path.join(self.log_dir, "cs_metrics.txt")
f = open(txt_path, "w")
f.write("cs psnr = " + str(np.mean(cs_psnr)) + " +\- " +
str(np.std(cs_psnr)) + "\n" + "output nrmse = " +
str(np.mean(cs_nrmse)) + " +\- " + str(np.std(cs_nrmse)) +
"\n" + "output ssim = " + str(np.mean(cs_ssim)) + " +\- " +
str(np.std(cs_ssim)))
f.close()
