def nii_save(volume,path,filename):
output = nib.Nifti1Image(volume,np.eye(4))
nib.save(output,os.path.join(path,filename))
def _run_interface(self, runtime):
from scipy import ndimage as sim
fmap_nii = nb.load(self.inputs.in_file)
data = np.squeeze(fmap_nii.get_fdata(dtype='float32'))
# Despike / denoise (no-mask)
if self.inputs.despike:
data = _despike2d(data, self.inputs.despike_threshold)
mask = None
if isdefined(self.inputs.in_mask):
masknii = nb.load(self.inputs.in_mask)
mask = np.asanyarray(masknii.dataobj).astype('uint8')
# Dilate mask
if self.inputs.mask_erode > 0:
struc = sim.iterate_structure(sim.generate_binary_structure(3, 2), 1)
mask = sim.binary_erosion(
mask, struc,
iterations=self.inputs.mask_erode
).astype(np.uint8) # pylint: disable=no-member
self._results['out_file'] = fname_presuffix(
self.inputs.in_file, suffix='_enh', newpath=runtime.cwd)
datanii = nb.Nifti1Image(data, fmap_nii.affine, fmap_nii.header)
if self.inputs.unwrap:
data = _unwrap(data, self.inputs.in_magnitude, mask)
self._results['out_unwrapped'] = fname_presuffix(
self.inputs.in_file, suffix='_unwrap', newpath=runtime.cwd)
nb.Nifti1Image(data, fmap_nii.affine, fmap_nii.header).to_filename(
self._results['out_unwrapped'])
if not self.inputs.bspline_smooth:
datanii.to_filename(self._results['out_file'])
return runtime
else:
from ..utils import bspline as fbsp
from statsmodels.robust.scale import mad
# Fit BSplines (coarse)
bspobj = fbsp.BSplineFieldmap(datanii, weights=mask,
njobs=self.inputs.num_threads)
bspobj.fit()
smoothed1 = bspobj.get_smoothed()
# Manipulate the difference map
diffmap = data - smoothed1.get_fdata(dtype='float32')
sderror = mad(diffmap[mask > 0])
LOGGER.info('SD of error after B-Spline fitting is %f', sderror)
errormask = np.zeros_like(diffmap)
errormask[np.abs(diffmap) > (10 * sderror)] = 1
errormask *= mask
nslices = 0
try:
errorslice = np.squeeze(np.argwhere(errormask.sum(0).sum(0) > 0))
nslices = errorslice[-1] - errorslice[0]
except IndexError: # mask is empty, do not refine
pass
if nslices > 1:
diffmapmsk = mask[..., errorslice[0]:errorslice[-1]]
diffmapnii = nb.Nifti1Image(
diffmap[..., errorslice[0]:errorslice[-1]] * diffmapmsk,
datanii.affine, datanii.header)
bspobj2 = fbsp.BSplineFieldmap(diffmapnii, knots_zooms=[24., 24., 4.],
njobs=self.inputs.num_threads)
bspobj2.fit()
smoothed2 = bspobj2.get_smoothed().get_fdata(dtype='float32')
final = smoothed1.get_fdata(dtype='float32').copy()
final[..., errorslice[0]:errorslice[-1]] += smoothed2
else:
final = smoothed1.get_fdata(dtype='float32')
nb.Nifti1Image(final, datanii.affine, datanii.header).to_filename(
self._results['out_file'])
return runtime
def plot_brainrsa_montage(img,
threshold=None,
slice=[6, 6, 6],
background=get_bg_ch2bet()):
"""
Plot the RSA-result by different cuts
Parameters
----------
img : string
The file path of the .nii file of the RSA results.
threshold : None or int. Default is None.
The threshold of the number of voxels used in correction.
If threshold=n, only the similarity clusters consisting more than threshold voxels will be visible. If it is
None, the threshold-correction will not work.
slice : array
The point where the cut is performed.
If slice=[slice_x, slice_y, slice_z], slice_x, slice_y, slice_z represent the coordinates of each cut in the x,
y, z direction. If slice=[[slice_x1, slice_x2], [slice_y1, slice_y2], [slice_z1, slice_z2]], slice_x1 & slice_x2
represent the coordinates of each cut in the x direction, slice_y1 & slice_y2 represent the coordinates of each
cut in the y direction, slice_z1 & slice_z2 represent the coordinates of each cut in the z direction.
background : Niimg-like object or string. Default is stuff.get_bg_ch2bet()
The background image that the RSA results will be plotted on top of.
"""
imgarray = nib.load(img).get_data()
if (imgarray == np.nan).all() == True:
print("No Valid Results")
else:
if threshold != None:
imgarray = nib.load(img).get_data()
affine = get_affine(img)
imgarray = correct_by_threshold(imgarray, threshold)
img = nib.Nifti1Image(imgarray, affine)
slice_x = slice[0]
slice_y = slice[1]
slice_z = slice[2]
if slice_x != 0:
plotting.plot_stat_map(stat_map_img=img,
bg_img=background,
display_mode='x',
cut_coords=slice_x,
title="Similarity -sagittal",
draw_cross=True,
vmax=1)
if slice_y != 0:
plotting.plot_stat_map(stat_map_img=img,
bg_img=background,
display_mode='y',
cut_coords=slice_y,
title="Similarity -coronal",
draw_cross=True,
vmax=1)
if slice_z != 0:
plotting.plot_stat_map(stat_map_img=img,
bg_img=background,
display_mode='z',
cut_coords=slice_z,
title="Similarity -axial",
draw_cross=True,
vmax=1)
plt.show()
objmask = np.zeros( numpypredict.shape, dtype='uint8' )
scoreimg = np.zeros( numpypredict.shape, dtype='float16' )
# In[ ]:
# FIXME - vectorize this
for iii in range(nslice):
print(iii,)
myimage = numpypredict[:,:,iii]
results = model.detect([myimage[:,:,np.newaxis] ], verbose=1)
myoutput = results[0]
for jjj,idclass in enumerate(myoutput['class_ids']):
scoreimg[myoutput['rois'][jjj][0]:myoutput['rois'][jjj][2], myoutput['rois'][jjj][1]:myoutput['rois'][jjj][3], iii ] = myoutput['scores'][jjj]
objmask[myoutput['rois'][jjj][0]:myoutput['rois'][jjj][2], myoutput['rois'][jjj][1]:myoutput['rois'][jjj][3], iii ] = 1
objmask[:,:,iii] = objmask[:,:,iii] + idclass*myoutput['masks'][:,:,jjj].astype('uint8')
# write out
segout_img = nib.Nifti1Image(objmask , None, header=imageheader)
segout_img.to_filename( options.segmentation )
scrout_img = nib.Nifti1Image(scoreimg, None, header=imageheader)
scrout_img.to_filename( '/'.join(options.segmentation.split('/')[:-1]) + '/objscore.nii.gz' )
##########################
# print help
##########################
else:
import keras; import tensorflow as tf
print("keras version: ",keras.__version__, 'TF version:',tf.__version__)
print("debug: /opt/apps/miniconda/maskrcnn/lib/python3.6/site-packages/keras/engine/training.py(1450)train_on_batch()->[566.86456, 114.579956, 168.20625, 284.07834, 0.0, 0.0]")
print("debug: /opt/apps/miniconda/maskrcnn/lib/python3.6/site-packages/keras/engine/training_generator.py(174)fit_generator()")
dataset_test = LoadDataset()
parser.print_help()
def colorize(self, col_out_dir, final_out_dir):
"""
Transforms the individual channels from Pipeline.color_split using the
affine/nonlinear transformation parameters from Pipeline.slice_by_slice_alignment()
and the nonlinear volumetric transformation parameters from Pipeline.blockface_to_MRI_alignment()
Because each transformation is independent of the others, the script will utilize all
threads provided by the user to transform multiple slices simultaneously.
See Transform_Wrapper for more information and the transformation code.
"""
#Feed transformation information to sub-processes through Transform_Wrapper
out_suf_list = ['Blue', 'Green', 'Red']
skip_flag = False
for i, col_vol in enumerate([
self.hist_NIFTI.Blue_vol, self.hist_NIFTI.Green_vol,
self.hist_NIFTI.Red_vol
]):
for j in range(len(self.hist_NIFTI.slices)):
if not os.path.isfile(self.orig_slice_by_slice_loc +
'/color/' + out_suf_list[i] + '/' +
col_vol.slices[j].name):
break
else:
continue
break
else:
print(
' - All Color Channel Split Transformed Files Exist. Utilizing currently existing data.'
)
skip_flag = True
if skip_flag == False:
print(
'====================================ATTEMPTING TO MULTITHREAD===================================='
)
pool = Pool(processes=self.threads)
self.hist_NIFTI.Blue_vol.col = 'Blue'
self.hist_NIFTI.Green_vol.col = 'Green'
self.hist_NIFTI.Red_vol.col = 'Red'
for col_vol in enumerate([
self.hist_NIFTI.Blue_vol, self.hist_NIFTI.Green_vol,
self.hist_NIFTI.Red_vol
]):
pool.map(
Transform_Wrapper(
col_vol, self.hist_transform, self.BF_NIFTI,
self.orig_slice_by_slice_loc + '/color/'),
list(range(len(self.hist_transform.slices))))
pool.close()
pool.join()
#Load output color channel split Stacks and convert to volume/
tmp = self.BF_NIFTI
r = Stacks.NIFTI_Stack(self.orig_slice_by_slice_loc + '/color/Red/')
r.affine_3D = tmp.affine_3D
r.volumize(self.orig_slice_by_slice_loc +
'/color/volumes/r_vol.nii.gz')
g = Stacks.NIFTI_Stack(self.orig_slice_by_slice_loc + '/color/Green/')
g.affine_3D = tmp.affine_3Dblockface_to_MRI_alignment.nii.gz
g.volumize(self.orig_slice_by_slice_loc +
'/color/volumes/g_vol.nii.gz')
b = Stacks.NIFTI_Stack(self.orig_slice_by_slice_loc + '/color/Blue/')
b.affine_3D = tmp.affine_3D
b.volumize(self.orig_slice_by_slice_loc +
'/color/volumes/b_vol.nii.gz')
#Transform color-split volumes to the MRI space
self.final_apply_transform(
self.orig_slice_by_slice_loc + '/color/volumes/b_vol.nii.gz',
self.orig_slice_by_slice_loc + '/color/volumes/final_b_vol.nii.gz')
self.final_apply_transform(
self.orig_slice_by_slice_loc + '/color/volumes/g_vol.nii.gz',
self.orig_slice_by_slice_loc + '/color/volumes/final_g_vol.nii.gz')
self.final_apply_transform(
self.orig_slice_by_slice_loc + '/color/volumes/r_vol.nii.gz',
self.orig_slice_by_slice_loc + '/color/volumes/final_r_vol.nii.gz')
#Load transformed and color-split volumes. Merge the channels to create and RGB volume.
print('Loading RGB')
r_data = nib.load(self.orig_slice_by_slice_loc +
'/color/volumes/final_r_vol.nii.gz').get_data()
g_data = nib.load(self.orig_slice_by_slice_loc +
'/color/volumes/final_g_vol.nii.gz').get_data()
b_data = nib.load(self.orig_slice_by_slice_loc +
'/color/volumes/final_b_vol.nii.gz').get_data()
print('Merging Channels')
rgb = np.empty((r_data.shape[0], r_data.shape[1], r_data.shape[2], 3))
rgb[:, :, :, 0] = b_data
rgb[:, :, :, 1] = g_data
rgb[:, :, :, 2] = r_data
rgb = rgb.astype('u1')
#Save the RGB Volume
print('Saving Volume')
shape_3d = rgb.shape[0:3]
rgb_dtype = np.dtype([('R', 'u1'), ('G', 'u1'), ('B', 'u1')])
rgb_typed = rgb.view(rgb_dtype).reshape(shape_3d)
tmp = nib.load(self.MRI)
volume = nib.Nifti1Image(rgb_typed, affine=tmp.affine)
nib.save(volume, final_out_dir + '/RGB_aligned_histology_vol.nii.gz')
def calc_pve(self):
if self.bt_ok.text() == ("Operate" or "计算"):
try:
if self.lan == 0:
self.bt_ok.setText("Cancel")
elif self.lan == 1:
self.bt_ok.setText("取消")
if self.index_method == 0:
for idx in range(len(self.path_cbf)):
nii_cbf = ni.load(self.path_cbf[idx])
nii_gm = ni.load(self.path_gm[idx])
nii_wm = ni.load(self.path_wm[idx])
if nii_cbf.shape != nii_gm.shape:
if self.bul_autoreg == 1:
# 预留将结构像与CBF自动配准的功能,用resample代替
nii_cbf = resample_to_img(nii_cbf, nii_gm)
else:
if self.lan == 0:
warn_msg(self, "Shape of CBF and T1 are different.")
elif self.lan == 1:
warn_msg(self, "CBF与结构像大小不一致")
continue
data_cbf = nii_cbf.get_fdata()
data_gm = nii_gm.get_fdata()
data_wm = nii_wm.get_fdata()
data_temp = (data_cbf * ((data_gm + data_wm) > 0.1)) / (((data_gm) + 0.4 * (data_wm)) * ((data_gm + 0.4 * data_wm) > 0.1))
data_temp[np.isnan(data_temp)] = 0
data_temp[np.isinf(data_temp)] = 0
self.data_temp.append(ni.Nifti1Image(data_temp, nii_gm.affine, nii_gm.header))
self.temp.set_nii(self.data_temp)
if self.lan == 0:
self.bt_ok.setText("Operate")
elif self.lan == 1:
self.bt_ok.setText("计算")
self.temp.fname = [item.replace(".nii", "_pve.nii") for item in self.path_cbf]
if self.checkbox_autosave == 1:
ni.save(ni.Nifti1Image(data_temp, nii_gm.affine, nii_gm.header), item.replace(".nii", "_pve.nii"))
self.close()
elif self.index_method == 1:
data_temp = 0
self.lr_thread = LRThread(self, self.lan)
self.lr_thread.start()
self.lr_thread.progress.connect(self.update_progress)
self.lr_thread.trigger.connect(self.get_data_thread)
self.lr_thread.file.connect(self.get_data_each)
else:
pass # 预留其他方法
except FileNotFoundError:
if self.lan == 0:
warn_msg(self, "File not existed.")
elif self.lan == 1:
warn_msg(self, "选择的文件不存在")
except ni.filebasedimages.ImageFileError:
if self.lan == 0:
warn_msg(self, "Selected file is not an nii file.")
elif self.lan == 1:
warn_msg(self, "选择的文件格式错误")
elif self.bt_ok.text() == ("Cancel" or "取消"):
self.lr_thread.stop()
self.lr_thread.quit()
self.lr_thread.wait()
del self.lr_thread
if self.lan == 0:
self.bt_ok.setText("Operate")
elif self.lan == 1:
self.bt_ok.setText("计算")
def test(model, limit, save, bbox):
"""Test the model.
model: the model to test.
limit: the images to be used.
save: whether to save the masks.
limit: whether to draw the bboxes.
"""
per_class_ious = []
info = json.load(open(args.data + "dataset.json"))
info = list(info['train_and_test'])
detect_time = 0
for path in info[:limit]:
path_image = path['image']
path_label = path['label']
image = nib.load(path_image).get_data().copy()
label = nib.load(path_label) # load the gt-masks
affine = label.affine # prepared to save the predicted mask later
label = label.get_data().copy()
image = np.expand_dims(image, -1)
start_time = time.time()
result = model.detect([image])[0]
detect_time += time.time() - start_time
print("detect_time:", time.time() - start_time)
"""The shape of result: a dict containing
{
"rois": final_rois, [N, (y1, x1, z1, y2, x2, z2)] in real coordinates
"class_ids": final_class_ids, [N]
"scores": final_scores, [N]
"mask": final_mask, [mask_shape[0], mask_shape[1], mask_shape[2]]
}"""
rois = result["rois"]
class_ids = result["class_ids"]
scores = result["scores"]
mask = result["mask"]
# Prepare the gt-masks and pred-masks to calculate the ious.
gt_masks = np.zeros((image.shape[0], image.shape[1], image.shape[2],
model.config.NUM_CLASSES - 1))
pred_masks = np.zeros((image.shape[0], image.shape[1], image.shape[2],
model.config.NUM_CLASSES - 1))
# Generate the per instance gt masks.
for j in range(model.config.NUM_CLASSES - 1):
gt_masks[:, :, :, j][label == j + 1] = 1
# Generate the per instance predicted masks.
for j in range(model.config.NUM_CLASSES - 1):
pred_masks[:, :, :, j][mask == j + 1] = 1
# calculate different kind of ious
per_class_iou = utils.compute_per_class_mask_iou(gt_masks, pred_masks)
per_class_ious.append(per_class_iou)
# Save the results
if save == "true":
# Draw bboxes
if bbox == "true":
y1, x1, z1, y2, x2, z2 = rois[0, :]
mask[y1, x1:x2, z1] = 10
mask[y1, x1:x2, z2] = 10
mask[y2, x1:x2, z1] = 10
mask[y2, x1:x2, z2] = 10
mask[y1:y2, x1, z1] = 10
mask[y1:y2, x2, z1] = 10
mask[y1:y2, x1, z2] = 10
mask[y1:y2, x2, z2] = 10
mask[y1, x1, z1:z2] = 10
mask[y1, x2, z1:z2] = 10
mask[y2, x1, z1:z2] = 10
mask[y2, x2, z1:z2] = 10
vol = nib.Nifti1Image(mask.astype(np.int32), affine)
if not os.path.exists("./results"):
os.makedirs("./results")
nib.save(
vol, "./results/" + str(per_class_iou.mean()) + "_" +
path_image[-17:])
print(path_image[-17:] + " detected done. iou = " + str(per_class_iou))
print("Test completed.")
# Print the iou results.
per_class_ious = np.array(per_class_ious)
print("per class iou mean:", np.mean(per_class_ious, axis=0))
print("std:", np.std(per_class_ious, axis=0))
print("Total ious mean:", per_class_ious.mean())
print("Total detect time:", detect_time)
])
#raw_img = '/gsfs0/data/poskanzc/Sherlock/preproc/fmriprep/sub-01/func/sub-01_task-sherlockPart1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'
mask = '/gsfs0/data/poskanzc/Sherlock/preproc/fmriprep/gm_bin_mask.nii.gz'
#raw = nib.load(raw_img)
#raw_hdr = raw.header
mfn = nib.load(mask)
#masker = NiftiMasker()
#masker.fit(mfn)
for sub in subjects:
masker = NiftiMasker()
masker.fit(mfn)
run1 = np.load(data_dir + sub + '/' + sub + '_compcorr/' + sub +
'_GM_run_1_compcorr_TRedit.npy')
raw_img = '/gsfs0/data/poskanzc/Sherlock/preproc/fmriprep/' + sub + '/func/' + sub + '_task-sherlockPart1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'
raw = nib.load(raw_img)
#raw_hdr = raw.header
localizer_data = run1[0:204, :]
nifti = masker.inverse_transform(localizer_data)
nifti_data = nifti.get_data()
nifti_array = np.array(nifti_data)
final_img = nib.Nifti1Image(nifti_array, mfn.affine, raw.header)
#print(nifti.header.get_zooms())
#nib.Nifti1Header.from_header(header = hdr, check = True)
#final_img = nib.Nifti1Image(nifti,affine)
nib.save(
final_img, data_dir + sub + '/' + sub + '_compcorr/' + sub +
'_GM_run_1_compcorr_localizer.nii.gz')
def __getitem__(self, index):
item = self.data_list[index]
input_data = self.data_file.root.data[
item] # data shape:(4, 128, 128, 128)
label_data = self.data_file.root.truth[
item] # truth shape:(1, 128, 128, 128)
seg_label = get_target_label(label_data, self.config)
affine = self.data_file.root.affine[item]
# dimessions of data
n_dim = len(seg_label[0].shape)
if self.phase == "train":
if self.config["random_offset"] is not None:
offset_factor = -0.25 + np.random.random(n_dim)
else:
offset_factor = None
if self.config["random_flip"] is not None:
flip_axis = random_flip_dimensions(n_dim)
else:
flip_axis = None
# Apply random offset and flip to each channel according to randomly generated offset factor and flip axis respectively.
data_list = list()
for data_channel in range(input_data.shape[0]):
# Transform ndarray data to Nifti1Image
channel_image = nib.Nifti1Image(
dataobj=input_data[data_channel], affine=affine)
data_list.append(
resample_to_img(augment_image(channel_image,
flip_axis=flip_axis,
offset_factor=offset_factor),
channel_image,
interpolation="continuous").get_data())
input_data = np.asarray(data_list)
# Transform ndarray segmentation label to Nifti1Image
seg_image = nib.Nifti1Image(dataobj=seg_label[0], affine=affine)
seg_label = resample_to_img(augment_image(
seg_image, flip_axis=flip_axis, offset_factor=offset_factor),
seg_image,
interpolation="nearest").get_data()
seg_label = seg_label[np.newaxis]
elif self.phase == "validate":
data_list = list()
offset_factor = None
flip_axis = None
for data_channel in range(input_data.shape[0]):
# Transform ndarray data to Nifti1Image
channel_image = nib.Nifti1Image(
dataobj=input_data[data_channel], affine=affine)
data_list.append(
resample_to_img(augment_image(channel_image,
flip_axis=flip_axis,
offset_factor=offset_factor),
channel_image,
interpolation="continuous").get_data())
input_data = np.asarray(data_list)
# Transform ndarray segmentation label to Nifti1Image
seg_image = nib.Nifti1Image(dataobj=seg_label[0], affine=affine)
seg_label = resample_to_img(augment_image(
seg_image, flip_axis=flip_axis, offset_factor=offset_factor),
seg_image,
interpolation="nearest").get_data()
if len(seg_label.shape) == 3:
seg_label = seg_label[np.newaxis]
elif self.phase == "test":
pass
if self.config["VAE_enable"]:
# Concatenate to (5, 128, 128, 128) as network output
final_label = np.concatenate((seg_label, input_data), axis=0)
else:
final_label = seg_label
return input_data, final_label
def create_cfm(in_file, lesion_mask=None, global_mask=True, out_path=None):
"""
Create a mask to constrain registration.
Parameters
----------
in_file : str
Path to an existing image (usually a mask).
If global_mask = True, this is used as a size/dimension reference.
out_path : str
Path/filename for the new cost function mask.
lesion_mask : str, optional
Path to an existing binary lesion mask.
global_mask : bool
Create a whole-image mask (True) or limit to reference mask (False)
A whole image-mask is 1 everywhere
Returns
-------
str
Absolute path of the new cost function mask.
Notes
-----
in_file and lesion_mask must be in the same
image space and have the same dimensions
"""
import os
import numpy as np
import nibabel as nb
from nipype.utils.filemanip import fname_presuffix
if out_path is None:
out_path = fname_presuffix(in_file, suffix='_cfm', newpath=os.getcwd())
else:
out_path = os.path.abspath(out_path)
if not global_mask and not lesion_mask:
NIWORKFLOWS_LOG.warning(
'No lesion mask was provided and global_mask not requested, '
'therefore the original mask will not be modified.')
# Load the input image
in_img = nb.load(in_file)
# If we want a global mask, create one based on the input image.
data = np.ones(in_img.shape,
dtype=np.uint8) if global_mask else in_img.get_data()
if set(np.unique(data)) - {0, 1}:
raise ValueError(
"`global_mask` must be true if `in_file` is not a binary mask")
# If a lesion mask was provided, combine it with the secondary mask.
if lesion_mask is not None:
# Reorient the lesion mask and get the data.
lm_img = nb.as_closest_canonical(nb.load(lesion_mask))
# Subtract lesion mask from secondary mask, set negatives to 0
data = np.fmax(data - lm_img.get_data(), 0)
# Cost function mask will be created from subtraction
# Otherwise, CFM will be created from global mask
cfm_img = nb.Nifti1Image(data, in_img.affine, in_img.header)
# Save the cost function mask.
cfm_img.set_data_dtype(np.uint8)
cfm_img.to_filename(out_path)
return out_path
mri_data = {}
for runii, fname in enumerate(nifti_files):
for ROI in rois:
# Get all cortex data and task orders
lh_mask = np.array(nib.load(
os.path.join(ROI_dir, 'lh.%s_vol_dil.nii.gz' % ROI)).get_data(),
dtype=bool)
rh_mask = np.array(nib.load(
os.path.join(ROI_dir, 'rh.%s_vol_dil.nii.gz' % ROI)).get_data(),
dtype=bool)
# mri_data[ROI] = np.array([np.vstack([nib.load(nf).get_data()[lh_mask,:], nib.load(nf).get_data()[rh_mask,:]]) for nf in nifti_files])
old_img = nib.load(nifti_files[runii])
new_img = nib.Nifti1Image(old_img.get_data()[lh_mask + rh_mask, :],
old_img.affine)
new_img.to_filename(
os.path.join(deriv_dir, '%s-%s-%i.nii.gz' % (subid, ROI, runii)))
# Load trial data
task_data = {'trial_order': [], 'trial_stimuli': [], 'trial_params': []}
# for ti,par in zip(trialinfo_files, params_files):
[
trial_array, trial_indices, trial_params, per_trial_parameters,
per_trial_phase_durations, staircase
] = pickle.load(open(trialinfo_files[runii], 'rb'))
trial_times = np.vstack(per_trial_phase_durations)[:, 0] + np.arange(
len(per_trial_phase_durations)) * TR
os.path.join(path_to_images, "OAS1_*_MR1/mwc1OAS1_*dim.nii")))
images = images[:39]
### Mask data
print "Nifti masker"
nifti_masker = NiftiMasker(
smoothing_fwhm=FWHM,
memory='nilearn_cache',
memory_level=1) # cache options
# remove NaNs from images
ref_affine = np.asarray(nibabel.load(images[0]).get_affine())
images_ = [np.asarray(nibabel.load(img).get_data()) for img in images]
nonnan_images = []
for img in images_:
img[np.isnan(img)] = 0.
nonnan_images.append(nibabel.Nifti1Image(img, ref_affine))
# remove features with zero between-subject variance
images_masked = nifti_masker.fit_transform(images)
images_masked[:, images_masked.var(0) < 0.01] = 0.
# final masking
new_images = nifti_masker.inverse_transform(images_masked)
images_masked = nifti_masker.fit_transform(new_images)
n_samples, n_features = images_masked.shape
print n_samples, "subjects, ", n_features, "features"
### Euclidean distance between subjects
print "Compute Euclidean distances"
>>>>>>> 7127fbafc1c48de982482a106d48dcc6ac422172
dist = euclidean_distances(images_masked)
mahalanobis_dist = np.mean(dist, 0) - np.median(dist)
threshold = stats.chi2(n_samples).isf(0.1 / float(n_samples))
save_c = click.confirm('\nSave masks? ', default=True)
print('Finding MUs:')
for x in progressbar.progressbar(range(1, n_points)):
dims = objs[x]
roi = regs == x
roi_sig = np.nansum(np.ma.masked_array(stir_slice, ~roi), axis=(0, 1))
c = np.corrcoef(global_sig, roi_sig)[1, 0]
corr_sig.append(c)
map_2d = (np.sum(roi, axis=2) > 0) * x
mu_map += map_2d
if save_c:
volumes.append(np.sum(np.sum(np.sum(roi, axis=0), axis=0), axis=0))
spat_size.append(
np.sqrt((dims[1].stop - dims[1].start) ^ 2 +
(dims[0].stop - dims[0].start) ^ 2))
mask = nib.Nifti1Image(roi.astype(int), n1_img.affine)
direc = "/".join(filename.split('/')[:-1])
direc += '/mask_{}.nii'.format(x)
nib.save(mask, direc)
masked = np.ma.masked_where(mu_map == 0, mu_map)
plt.imshow(stir_slice[:, :, 1].T, origin="upper", cmap="gray")
plt.imshow(masked.T, cmap="jet", origin="upper", alpha=0.9)
plt.suptitle('MU maps')
plt.show()
repeat = click.confirm('\nRedo analysis?', default=False)
sorted_indices = np.argsort(corr_sig)[::-1]
def save_to_video(filename):
"""If we want to export the variances as a video, this is how we save it out."""
if bvals[index] < 100:
attenuatedBrainData = segmentedBrainData
else:
#Convert bvecs to angles
x = bvecRotated[0]
y = bvecRotated[1]
z = bvecRotated[2]
r, theta, phi = shm.cart2sphere(x, y, z)
#Make design matrix
B, m, n = shm.real_sym_sh_basis(order, theta, phi)
#Get attenuated data
print('Attenuating volume ' + str(index))
if bvals[index] < 1500:
attenuatedBrainData = pl.attenuateImageSphericalHarmonics (segmentedBrainData, B, coefficientsb1000, bvals[index], 1000)
elif bvals[index] > 1500 and bvals[index] < 2500:
attenuatedBrainData = pl.attenuateImageSphericalHarmonics (segmentedBrainData, B, coefficientsb2000, bvals[index], 2000)
attenuatedBrainNii = nib.Nifti1Image(attenuatedBrainData, segmentedBrain.get_affine(),segmentedBrain.get_header())
attenuatedBrainNii.to_filename(os.path.join(codeDir,'attenuatedBrainPy.nii.gz'))
shutil.move(codeDir + "/attenuatedBrainPy.nii.gz", outputDir+ "/brain"+str(index)+".nii.gz")
#Register to reference brain to get sizes right
print('Registering volume ' + str(index))
call(["flirt","-in",outputDir+ "/brain"+str(index)+".nii.gz","-ref",outputDir+ "/brainref.nii.gz","-applyxfm","-out",outputDir+ "/brain"+str(index)+".nii.gz"])
def nifti_image_files(outdir, filelist, shape):
for f in ensure_list(filelist):
img = np.random.random(shape)
nb.Nifti1Image(img, np.eye(4),
None).to_filename(os.path.join(outdir, f))
if os.path.exists(clone_path): shutil.rmtree(clone_path)
os.makedirs(clone_path)
# create each clone channel
for j in range(len(channels)):
channel_img = nib.load(channels[j])
channel_data = channel_img.get_data().copy()
# get data withing roi (label)
roi_data = channel_data[np.nonzero(label_data)]
# new data follows gaussian distribution
mean_value, std_value = [np.mean(roi_data), np.std(roi_data)]
channel_data[np.nonzero(label_data)] = np.array([
random.gauss(mean_value, std_value)
for _ in range(roi_data.shape[0])
])
# create modified channel for clone
modified_channel = nib.Nifti1Image(channel_data,
channel_img.affine)
#TODO: Normalize image?
# save clone channel
channel_name = os.path.basename(channels[j])
nib.save(
modified_channel,
os.path.join(clone_path,
'clone_V2_' + str(i) + '.' + channel_name))
# save unaltered label for clone
label_name = os.path.basename(label[0])
nib.save(
label_img,
os.path.join(clone_path, 'clone_V2_' + str(i) + '.' + label_name))
#save unaltered mask for clone
mask_img = nib.load(mask[0])
# make new_brainsuite_head_label_volume
# new_brainsuite_head_label_volume = np.zeros(brainsuite_head_label_volume.shape)
# for label_index in label_index_brainsuite_head:
# mylabel_value = find_subdict_index(inputdict_brainsuite, label_index, mylabel_value=3)
# boolwhich1 = brainsuite_head_label_volume == label_index
# new_brainsuite_head_label_volume[boolwhich1] = mylabel_value
new_brainsuite_head_label_volume = label_index_replace(
brainsuite_head_label_volume, inputdict_brainsuite, mylabel_value=3)
# combine freesurfer label and brainsuite label
boolwhich2 = new_freesurfer_label_volume > 0
# brainsuite_label_volume_flip[boolwhich2] = 0 # test for joint label !!
# brainsuite_head_label_volume_flip[boolwhich2] = 0
# label_joint = brainsuite_head_label_volume_flip + new_freesurfer_label_volume
new_brainsuite_head_label_volume[boolwhich2] = 0
label_joint = new_brainsuite_head_label_volume + new_freesurfer_label_volume
# combine joint label with Lesions
for l in lesion_label_path:
lesion_label = nib.load(l)
lesion_label = lesion_label.get_fdata()
lesion_type = sample_info.loc[sample_info['INDI Subject ID'] ==
int(subjectID[1:]), ['Stroke type']]
label_index = 14 if lesion_type.values == 'Embolic' else 15
boolwhich3 = lesion_label > 0
label_joint[boolwhich3] = label_index
img = nib.Nifti1Image(label_joint, raw_affine)
img.header.get_xyzt_units()
nib.save(
img,
output_path + os.path.basename(one_sample).split('.')[0] + sample_ext)
vmax = image.max()
source_affine = np.eye(4)
# Use canonical vectors for affine
# Give the affine an offset
source_affine[:2, 3] = np.array([96, 64])
# Rotate it slightly
angle = np.pi / 180 * 15
rotation_matrix = np.array([[np.cos(angle), -np.sin(angle)],
[np.sin(angle), np.cos(angle)]])
source_affine[:2, :2] = rotation_matrix * 2.0 # 2.0mm voxel size
# We need to turn this data into a nibabel image
import nibabel
img = nibabel.Nifti1Image(image[:, :, np.newaxis], affine=source_affine)
#############################################################################
# Now resample the image
from nilearn.image import resample_img
img_in_mm_space = resample_img(img,
target_affine=np.eye(4),
target_shape=(512, 512, 1))
target_affine_3x3 = np.eye(3) * 2
target_affine_4x4 = np.eye(4) * 2
target_affine_4x4[3, 3] = 1.
img_3d_affine = resample_img(img, target_affine=target_affine_3x3)
img_4d_affine = resample_img(img, target_affine=target_affine_4x4)
target_affine_mm_space_offset_changed = np.eye(4)
target_affine_mm_space_offset_changed[:3, 3] = \
def get_data_each(self, int_file):
self.idx_file = int_file
data_temp = self.lr_thread.data_result
self.data_temp.append(ni.Nifti1Image(data_temp, ni.load(self.path_cbf[self.idx_file]).affine, ni.load(self.path_cbf[self.idx_file]).header))
CCA_classes = np.zeros([pred.shape[0], pred.shape[1], pred.shape[2], 8])
error = np.zeros([pred.shape[0], pred.shape[1], pred.shape[2], 8])
for m in range(CCA_classes.shape[-1]):
labelled_mask, num_labels = ndimage.label(sep_classes[:, :, :, m])
largest_cc_mask = (labelled_mask == (
np.bincount(labelled_mask.flat)[1:].argmax() + 1))
CCA_classes[:, :, :, m] = largest_cc_mask
labelled_mask[largest_cc_mask] = 0
labelled_mask[labelled_mask > 0] = 1
error[:, :, :, m] = labelled_mask
classes = CCA_classes.argmax(axis=3)
all_errors = error.argmax(axis=3)
all_errors[all_errors > 0] = 1
classes = classes.astype(np.float64)
all_errors = all_errors.astype(np.float64)
classes[all_errors == 1] = np.nan
invalid = np.isnan(classes)
ind = ndimage.distance_transform_edt(invalid,
return_distances=False,
return_indices=True)
postproc = classes[tuple(ind)].astype('uint32')
postproc[postproc == 1] = 500
postproc[postproc == 2] = 600
postproc[postproc == 3] = 420
postproc[postproc == 4] = 550
postproc[postproc == 5] = 205
postproc[postproc == 6] = 820
postproc[postproc == 7] = 850
labBox = nib.Nifti1Image(postproc, b0.affine, new_header_b)
index = n + 1
nib.save(labBox, 'WHS/Results/nii/ct_test_20{}_label.nii.gz'.format(index))
def map_to_brain(image_3d,brain_mask,axis="axial",rotations=3):
'''map_to_brain
map 3d data matrix onto a brain_mask, specified by axis. If axis is not valid, will return False. If valid, will return nibabel.Nifti1Image
:param image_3d: numpy array read in from read_png. Usually of shape (512, 512, N), where N is 3 for 3D image, and 4 for png with alpha. If an alpha channel is found, pixels with 0 alpha will be rendered as transparent (0).
'''
R = image_3d[:,:,0]
G = image_3d[:,:,1]
B = image_3d[:,:,2]
axis = axis.lower()
# Convert to integer value
rgb = R;
rgb = (rgb << 8) + G
rgb = (rgb << 8) + B
# Normalize
rgb = (rgb - rgb.mean()) / rgb.std()
rgb = numpy.rot90(rgb, k=rotations)
# Houston, we have alpha!
alpha_channel = False
if image_3d.shape[2] == 4:
alpha_channel = True
if axis == "axial":
width = brain_mask.shape[0]
height = brain_mask.shape[1]
else:
print "Invalid specification of atlas, %s. Currently only supported is axial." %axis
return False
# Only square images, sorry
if rgb.shape[0] != rgb.shape[1]:
print "Sorry, only square images are currently supported."
return False
# We will interpolate down the largest dimension of the image
if rgb.shape[0] >= rgb.shape[1]:
scale = float(width)/rgb.shape[0]
else:
scale = float(height)/rgb.shape[1]
# order 0 means nearest interpolation
scaled = scipy.ndimage.zoom(rgb, scale, order=0)
if alpha_channel:
scaled_alpha = scipy.ndimage.zoom(image_3d[:,:,3], scale, order=0)
scaled[scaled_alpha==0] = 0
# Calculate left and right padding, keep as ints to take floor
padding_width = (width - scaled.shape[0]) /2
padding_height = (height - scaled.shape[1]) /2
padded = numpy.pad(scaled, ((padding_width,padding_width), # Default value is 0
(padding_height,padding_height)),mode="constant")
# Create array of same size as brainmap, just in case we are off a bit
array = numpy.zeros((width,height))
# This is slow and stupid, but it will work
for x in range(width):
for y in range(height):
try:
array[x,y] = padded[x,y]
except:
pass
# Let's write the image to all slices
empty_brain = numpy.zeros(brain_mask.shape)
mask = brain_mask.get_data()
# Add support for other axis?
if axis == "axial":
for z in range(brain_mask.shape[2]):
zslice = mask[:,:,z]
empty_brain[zslice!=0,z] = array[zslice!=0]
nii = nibabel.Nifti1Image(empty_brain,affine=brain_mask.get_affine())
return nii
def _create_image(image_shape):
data = np.asarray(np.arange(np.prod(image_shape)).reshape(image_shape),
dtype=np.float)
affine = np.zeros((4, 4))
np.fill_diagonal(affine, 1)
return nib.Nifti1Image(data, affine)
def TrainODModel():
# load database
print('loading memory map db for large dataset')
#npdatabase = np.load(options.globalnpfile,mmap_mode='r')
npdatabase = np.load(options.globalnpfile)
# Training dataset
dataset_train = ShapesDataset()
dataset_train.load_shapes('train',npdatabase )
dataset_train.prepare()
# Validation dataset
dataset_val = ShapesDataset()
dataset_val.load_shapes('validate',npdatabase )
dataset_val.prepare()
# ensure we get the same results each time we run the code
np.random.seed(seed=0)
#np.random.shuffle(dataset_train.dbsubset )
#np.random.shuffle(dataset_val.dbsubset)
## # subset within bounding box that has liver
## totnslice = len(dataset_train.dbsubset ) + len(dataset_val.dbsubset)
## slicesplit = len(dataset_train.dbsubset )
## print("nslice: ",totnslice ," split: " ,slicesplit )
## # FIXME - Verify stacking indicies
## x_train=np.vstack((dataset_train.dbsubset ['imagedata'],dataset_val.dbsubset['imagedata']))
## y_train=np.vstack((dataset_train.dbsubset ['truthdata'],dataset_val.dbsubset['truthdata']))
## TRAINING_SLICES = slice(0,slicesplit)
## VALIDATION_SLICES = slice(slicesplit,totnslice)
# In[6]:
# Load and display random samples
image_ids = np.random.choice(dataset_train.image_ids, 20)
print(image_ids)
import nibabel as nib
for image2did in image_ids:
image = dataset_train.load_image(image2did)
imageinfo = dataset_train.image_reference(image2did)
mask, class_ids = dataset_train.load_mask(image2did)
print(imageinfo,image2did,image.shape, mask.shape, class_ids, dataset_train.class_names)
#visualize.display_top_masks(np.squeeze(image), mask, class_ids, dataset_train.class_names,image2did)
original_image, image_meta, gt_class_id, gt_bbox, gt_mask = modellib.load_image_gt(dataset_train, config, image2did, use_mini_mask=False)
#visualize.display_instances(np.repeat(original_image,3,axis=2), gt_bbox, gt_mask, gt_class_id, dataset_train.class_names, figsize=(8, 8))
objmask = np.zeros( gt_mask.shape[0:2], dtype='uint8' )
for iii,idclass in enumerate(gt_class_id):
objmask[gt_bbox[iii][0]:gt_bbox[iii][2], gt_bbox[iii][1]:gt_bbox[iii][3] ] = 1
objmask = objmask + idclass*gt_mask[:,:,iii].astype('uint8')
segnii = nib.Nifti1Image(objmask.astype('uint8') , None )
segnii.to_filename( 'tmp/mask.%05d.nii.gz' % image2did )
imgnii = nib.Nifti1Image(image , None )
imgnii.to_filename( 'tmp/image.%05d.nii.gz' % image2did )
# ## Create Model
# In[ ]:
# Create model in training mode
model = modellib.MaskRCNN(mode="training", config=config,
model_dir=MODEL_DIR)
# In[7]:
# Which weights to start with?
init_with = "coco" # imagenet, coco, or last
init_with = "last" # imagenet, coco, or last
# ## Training
#
# Train in two stages:
# 1. Only the heads. Here we're freezing all the backbone layers and training only the randomly initialized layers (i.e. the ones that we didn't use pre-trained weights from MS COCO). To train only the head layers, pass `layers='heads'` to the `train()` function.
#
# 2. Fine-tune all layers. For this simple example it's not necessary, but we're including it to show the process. Simply pass `layers="all` to train all layers.
if init_with == "imagenet":
model.load_weights(model.get_imagenet_weights(), by_name=True)
raise(" freeze backbone ? input error")
elif init_with == "coco":
# Load weights trained on MS COCO, but skip layers that
# are different due to the different number of classes
# See README for instructions to download the COCO weights
model.load_weights(COCO_MODEL_PATH, by_name=True,
exclude=["mrcnn_class_logits", "mrcnn_bbox_fc",
"mrcnn_bbox", "mrcnn_mask","conv1"])
# Train the head branches
# Passing layers="heads" freezes all layers except the head
# layers. You can also pass a regular expression to select
# which layers to train by name pattern.
model.train(dataset_train, dataset_val,
learning_rate=config.LEARNING_RATE,
epochs=100,
layers='heads')
elif init_with == "last":
# Load the last model you trained and continue training
model.load_weights(model.find_last(), by_name=True)
# Fine tune all layers
# Passing layers="all" trains all layers. You can also
# pass a regular expression to select which layers to
# train by name pattern.
model.train(dataset_train, dataset_val,
learning_rate=config.LEARNING_RATE/10.,
epochs=500,
layers="all")
# Save weights
# Typically not needed because callbacks save after every epoch
# Uncomment to save manually
model_path = os.path.join(MODEL_DIR, "mask_rcnn_tumor.h5")
model.keras_model.save_weights(model_path)
def save_nifti(fname, data, affine):
result_img = nib.Nifti1Image(data, affine)
result_img.to_filename(fname)
def fit(self, niimgs, y):
"""Fit the searchlight
Parameters
----------
niimg : niimg
4D image.
y : 1D array-like
Target variable to predict. Must have exactly as many elements as
3D images in niimg.
Attributes
----------
`scores_` : numpy.ndarray
search_light scores. Same shape as input parameter
process_mask_img.
"""
# Compute world coordinates of all in-mask voxels.
mask, mask_affine = masking._load_mask_img(self.mask_img)
mask_coords = np.where(mask != 0)
mask_coords = np.asarray(
mask_coords + (np.ones(len(mask_coords[0]), dtype=np.int), ))
mask_coords = np.dot(mask_affine, mask_coords)[:3].T
# Compute world coordinates of all in-process mask voxels
if self.process_mask_img is None:
process_mask = mask
process_mask_coords = mask_coords
else:
process_mask, process_mask_affine = \
masking._load_mask_img(self.process_mask_img)
process_mask_coords = np.where(process_mask != 0)
process_mask_coords = \
np.asarray(process_mask_coords
+ (np.ones(len(process_mask_coords[0]),
dtype=np.int),))
process_mask_coords = np.dot(process_mask_affine,
process_mask_coords)[:3].T
clf = neighbors.NearestNeighbors(radius=self.radius)
A = clf.fit(mask_coords).radius_neighbors_graph(process_mask_coords)
del process_mask_coords, mask_coords
A = A.tolil()
# scores is an 1D array of CV scores with length equals to the number
# of voxels in processing mask (columns in process_mask)
X = masking._apply_mask_fmri(
niimgs,
nibabel.Nifti1Image(as_ndarray(mask, dtype=np.int8), mask_affine))
estimator = self.estimator
if isinstance(estimator, basestring):
estimator = ESTIMATOR_CATALOG[estimator]()
scores = search_light(X, y, estimator, A, self.scoring, self.cv,
self.n_jobs, self.verbose)
scores_3D = np.zeros(process_mask.shape)
scores_3D[process_mask] = scores
self.scores_ = scores_3D
return self
def saveNifti(dataIn, fileName, affMatrix=None):
if affMatrix is None:
affMatrix = np.eye(4)
img = nib.Nifti1Image(dataIn, affMatrix)
nib.save(img, fileName)
def pred_to_nib(data_lst: List[np.ndarray],
z_lst: List[int],
fname_ref: str,
fname_out: str,
slice_axis: int,
debug: bool = False,
kernel_dim: str = '2d',
bin_thr: float = 0.5,
discard_noise: bool = True,
postprocessing: dict = None) -> nib.Nifti1Image:
"""Save the network predictions as nibabel object.
Based on the header of `fname_ref` image, it creates a nibabel object from the Network predictions (`data_lst`).
Args:
data_lst (list of np arrays): Predictions, either 2D slices either 3D patches.
z_lst (list of ints): Slice indexes to reconstruct a 3D volume for 2D slices.
fname_ref (str): Filename of the input image: its header is copied to the output nibabel object.
fname_out (str): If not None, then the generated nibabel object is saved with this filename.
slice_axis (int): Indicates the axis used for the 2D slice extraction: Sagittal: 0, Coronal: 1, Axial: 2.
debug (bool): If True, extended verbosity and intermediate outputs.
kernel_dim (str): Indicates whether the predictions were done on 2D or 3D patches. Choices: '2d', '3d'.
bin_thr (float): If positive, then the segmentation is binarized with this given threshold. Otherwise, a soft
segmentation is output.
discard_noise (bool): If True, predictions that are lower than 0.01 are set to zero.
postprocessing (dict): Contains postprocessing steps to be applied.
Returns:
nibabel.Nifti1Image: NiBabel object containing the Network prediction.
"""
# Check fname_ref extention and update path if not NifTI
fname_ref = imed_loader_utils.update_filename_to_nifti(fname_ref)
# Load reference nibabel object
nib_ref = nib.load(fname_ref)
nib_ref_can = nib.as_closest_canonical(nib_ref)
if kernel_dim == '2d':
# complete missing z with zeros
tmp_lst = []
for z in range(nib_ref_can.header.get_data_shape()[slice_axis]):
if z not in z_lst:
tmp_lst.append(np.zeros(data_lst[0].shape))
else:
tmp_lst.append(data_lst[z_lst.index(z)])
if debug:
logger.debug(f"Len {len(tmp_lst)}")
for arr in tmp_lst:
logger.debug(f"Shape element lst {arr.shape}")
# create data and stack on depth dimension
arr_pred_ref_space = np.stack(tmp_lst, axis=-1)
else:
arr_pred_ref_space = data_lst[0]
n_channel = arr_pred_ref_space.shape[0]
oriented_volumes = []
if len(arr_pred_ref_space.shape) == 4:
for i in range(n_channel):
oriented_volumes.append(
imed_loader_utils.reorient_image(arr_pred_ref_space[i, ],
slice_axis, nib_ref,
nib_ref_can))
# transpose to locate the channel dimension at the end to properly see image on viewer
arr_pred_ref_space = np.asarray(oriented_volumes).transpose(
(1, 2, 3, 0))
else:
arr_pred_ref_space = imed_loader_utils.reorient_image(
arr_pred_ref_space, slice_axis, nib_ref, nib_ref_can)
if bin_thr >= 0:
arr_pred_ref_space = imed_postpro.threshold_predictions(
arr_pred_ref_space, thr=bin_thr)
elif discard_noise: # discard noise
arr_pred_ref_space[arr_pred_ref_space <= 1e-2] = 0
# create nibabel object
if postprocessing:
fname_prefix = fname_out.split(
"_pred.nii.gz")[0] if fname_out is not None else None
postpro = imed_postpro.Postprocessing(postprocessing,
arr_pred_ref_space,
nib_ref.header['pixdim'][1:4],
fname_prefix)
arr_pred_ref_space = postpro.apply()
# Here we prefer to copy the header (rather than just the affine matrix), in order to preserve the qform_code.
# See: https://github.com/ivadomed/ivadomed/issues/711
nib_pred = nib.Nifti1Image(dataobj=arr_pred_ref_space,
affine=nib_ref.header.get_best_affine(),
header=nib_ref.header.copy())
# save as NifTI file
if fname_out is not None:
nib.save(nib_pred, fname_out)
return nib_pred
def main():
cleanup=True
verbose=False
scriptdir=os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) # script directory
template=resource_filename(Requirement.parse("pydeface"), 'data/mean_reg2mean.nii.gz')
facemask=resource_filename(Requirement.parse("pydeface"), "data/facemask.nii.gz")
try:
assert os.path.exists(facemask)
except:
raise Exception('missing facemask: %s'%facemask)
try:
assert os.path.exists(template)
except:
raise Exception('missing template: %s'%template)
if len(sys.argv)<2:
usage()
sys.exit(2)
else:
infile=sys.argv[1]
if len(sys.argv)>2:
outfile=sys.argv[2]
else:
outfile=infile.replace('.nii.gz','_defaced.nii.gz')
try:
assert not os.path.exists(outfile)
except:
raise Exception('%s already exists, remove it first'%outfile)
if os.environ.has_key('FSLDIR'):
FSLDIR=os.environ['FSLDIR']
else:
print 'FSL must be installed and FSLDIR environment variable must be defined'
sys.exit(2)
foo,tmpmat=tempfile.mkstemp()
tmpmat=tmpmat+'.mat'
foo,tmpfile=tempfile.mkstemp()
tmpfile=tmpfile+'.nii.gz'
if verbose:
print tmpmat
print tmpfile
foo,tmpfile2=tempfile.mkstemp()
foo,tmpmat2=tempfile.mkstemp()
print 'defacing',infile
# register template to infile
flirt=fsl.FLIRT()
flirt.inputs.cost_func='mutualinfo'
flirt.inputs.in_file=template
flirt.inputs.out_matrix_file=tmpmat
flirt.inputs.out_file=tmpfile2
flirt.inputs.reference=infile
flirt.run()
# warp facemask to infile
flirt=fsl.FLIRT()
flirt.inputs.in_file=facemask
flirt.inputs.in_matrix_file=tmpmat
flirt.inputs.apply_xfm=True
flirt.inputs.reference=infile
flirt.inputs.out_file=tmpfile
flirt.inputs.out_matrix_file=tmpmat2
flirt.run()
# multiply mask by infile and save
infile_img=nibabel.load(infile)
tmpfile_img=nibabel.load(tmpfile)
outdata=infile_img.get_data()*tmpfile_img.get_data()
outfile_img=nibabel.Nifti1Image(outdata,infile_img.get_affine(),infile_img.get_header())
outfile_img.to_filename(outfile)
if cleanup:
os.remove(tmpfile)
os.remove(tmpfile2)
os.remove(tmpmat)
def plot_brainrsa_surface(img, threshold=None):
"""
Plot the RSA-result into a brain surface
Parameters
----------
img : string
The file path of the .nii file of the RSA results.
threshold : None or int. Default is None.
The threshold of the number of voxels used in correction.
If threshold=n, only the similarity clusters consisting more than threshold voxels will be visible. If it is
None, the threshold-correction will not work.
"""
imgarray = nib.load(img).get_data()
if (imgarray == np.nan).all() == True:
print("No Valid Results")
else:
if threshold != None:
imgarray = nib.load(img).get_data()
affine = get_affine(img)
imgarray = correct_by_threshold(imgarray, threshold)
img = nib.Nifti1Image(imgarray, affine)
fsaverage = datasets.fetch_surf_fsaverage(mesh='fsaverage')
texture_left = surface.vol_to_surf(img, fsaverage.pial_left)
texture_right = surface.vol_to_surf(img, fsaverage.pial_right)
plotting.plot_surf_stat_map(fsaverage.pial_left,
texture_left,
hemi='left',
threshold=0.1,
bg_map=fsaverage.sulc_right,
colorbar=False,
vmax=0.8,
darkness=0.7)
plotting.plot_surf_stat_map(fsaverage.pial_right,
texture_right,
hemi='right',
threshold=0.1,
bg_map=fsaverage.sulc_right,
colorbar=True,
vmax=0.8,
darkness=0.7)
plotting.plot_surf_stat_map(fsaverage.pial_right,
texture_left,
hemi='left',
threshold=0.1,
bg_map=fsaverage.sulc_right,
colorbar=False,
vmax=0.8,
darkness=0.7)
plotting.plot_surf_stat_map(fsaverage.pial_left,
texture_right,
hemi='right',
threshold=0.1,
bg_map=fsaverage.sulc_right,
colorbar=True,
vmax=0.8,
darkness=0.7)
plt.show()
#Load data
img = nib.load('./data.nii.gz')
data = img.get_data()
#build mask
gtab = dpg.gradient_table('./bvals', './bvecs', b0_threshold=10)
mean_b0 = np.mean(data[..., gtab.b0s_mask], -1)
_, mask = median_otsu(mean_b0,
4,
2,
False,
vol_idx=np.where(gtab.b0s_mask),
dilate=1)
if not op.exists('./mask.nii.gz'):
nib.save(nib.Nifti1Image(mask.astype(int), img.affine), 'mask.nii.gz')
# denoise
from dipy.denoise import nlmeans
from dipy.denoise.noise_estimate import estimate_sigma
sigma = estimate_sigma(data)
denoised_data = nlmeans.nlmeans(data, sigma=sigma, mask=mask)
if not op.exists('./denoised_data.nii.gz'):
nib.save(nib.Nifti1Image(denoised_data, img.affine),
'denoised_data.nii.gz')
#tensor model
import dipy.reconst.dti as dti