def _make_one_example(features_filepath, labels_filepath):
"""Create a `tf.train.Example` instance of the given arrays of volumetric features and labels."""
dtype = _TFRECORDS_FEATURES_DTYPE
x = nib.load(features_filepath)
if to_ras:
x = nib.as_closest_canonical(x)
xdata = x.get_fdata(caching='unchanged', dtype=dtype)
y = nib.load(labels_filepath)
if to_ras:
y = nib.as_closest_canonical(y)
ydata = y.get_fdata(caching='unchanged', dtype=dtype)
def bytes_feature(value):
return tf.train.Feature(bytes_list=tf.train.BytesList(
value=[value]))
feature = {
'volume':
bytes_feature(xdata.ravel().tostring()),
'volume_affine':
bytes_feature(x.affine.astype(dtype).ravel().tostring()),
'label':
bytes_feature(ydata.ravel().tostring()),
'label_affine':
bytes_feature(y.affine.astype(dtype).ravel().tostring()),
}
return tf.train.Example(features=tf.train.Features(feature=feature))
def reorient_images(self):
if (self.reorient_flag):
print(
"Reorient flag is set to true, Hence reorienting both images to Right Anterior Superior"
)
canonical_img_1 = nb.as_closest_canonical(self.orig_nii_stationary)
print(" ============= ============== ===================")
print("orientation changed t1 affine: {}".format(
canonical_img_1.affine))
print(" ============= ============== ===================")
print("orientation changed t1 : {}".format(
nb.aff2axcodes(canonical_img_1.affine)))
print(" ============= ============== ===================")
canonical_img_2 = nb.as_closest_canonical(self.orig_nii_moving)
print(" ============= ============== ===================")
print("orientation changed t2 affine: {}".format(
canonical_img_2.affine))
print(" ============= ============== ===================")
print("orientation changed t1 : {}".format(
nb.aff2axcodes(canonical_img_2.affine)))
print(" ============= ============== ===================")
self.canonical_img_1 = canonical_img_1
self.canonical_img_2 = canonical_img_2
return self.canonical_img_1, self.canonical_img_2
else:
print(" ============= ============== ===================")
print("Not reorienting the images as reorient flag is false")
print(" ============= ============== ===================")
self.canonical_img_1 = orig_nii_stationary
self.canonical_img_2 = orig_nii_moving
return self.canonical_img_1, self.canonical_img_2
def get_nii_nii(volpath,segpath):
vol = nib.as_closest_canonical(nib.load(volpath))
vol = vol.get_data().astype(np.int16)
seg = nib.as_closest_canonical(nib.load(segpath))
seg = seg.get_data().astype(np.int16)
return vol, seg
def reorient(imgloc, segloc=None):
imagedata = nib.load(imgloc)
orig_affine = imagedata.affine
orig_header = imagedata.header
imagedata = nib.as_closest_canonical(imagedata)
img_affine = imagedata.affine
numpyimage = imagedata.get_data().astype(IMG_DTYPE)
numpyseg = None
print('image : ', nib.orientations.aff2axcodes(orig_affine), ' to ',
nib.orientations.aff2axcodes(img_affine))
if segloc is not None:
segdata = nib.load(segloc)
old_affine = segdata.affine
segdata = nib.as_closest_canonical(segdata)
seg_affine = segdata.affine
if not np.allclose(seg_affine, img_affine):
segcopy = nib.load(segloc).get_data()
copy_header = orig_header.copy()
segdata = nib.nifti1.Nifti1Image(segcopy,
orig_affine,
header=copy_header)
segdata = nib.as_closest_canonical(segdata)
seg_affine = segdata.affine
print('seg : ', nib.orientations.aff2axcodes(old_affine), ' to ',
nib.orientations.aff2axcodes(seg_affine))
numpyseg = segdata.get_data().astype(SEG_DTYPE)
return numpyimage, orig_header, numpyseg
def load(filename,
gradients_file=None,
b0_file=None,
brainmask_file=None,
fmap_file=None):
"""Load DWI data."""
filename = Path(filename)
if filename.name.endswith(".h5"):
return DWI.from_filename(filename)
if not gradients_file:
raise RuntimeError("A gradients file is necessary")
img = nb.as_closest_canonical(nb.load(filename))
retval = DWI(affine=img.affine, )
grad = np.loadtxt(gradients_file, dtype="float32").T
gradmsk = grad[-1] > 50
retval.gradients = grad[..., gradmsk]
retval.dataobj = img.get_fdata(dtype="float32")[..., gradmsk]
if b0_file:
b0img = nb.as_closest_canonical(nb.load(b0_file))
retval.bzero = np.asanyarray(b0img.dataobj)
if brainmask_file:
mask = nb.as_closest_canonical(nb.load(brainmask_file))
retval.brainmask = np.asanyarray(mask.dataobj)
if fmap_file:
fmapimg = nb.as_closest_canonical(nb.load(fmap_file))
retval.fieldmap = fmapimg.get_fdata(fmapimg, dtype="float32")
return retval
def reorient(imgloc, segloc=None):
imagedata = nib.load(imgloc)
orig_affine = imagedata.affine
orig_header = imagedata.header
imagedata = nib.as_closest_canonical(imagedata)
img_affine = imagedata.affine
numpyimage = imagedata.get_data().astype(np.int16)
numpyseg = None
if segloc is not None:
segdata = nib.load(segloc)
old_affine = segdata.affine
segdata = nib.as_closest_canonical(segdata)
seg_affine = segdata.affine
if not np.allclose(seg_affine, img_affine):
segcopy = nib.load(segloc).get_data()
copy_header = orig_header.copy()
segdata = nib.nifti1.Nifti1Image(segcopy,
orig_affine,
header=copy_header)
segdata = nib.as_closest_canonical(segdata)
seg_affine = segdata.affine
numpyseg = segdata.get_data().astype(np.uint8)
return numpyimage, orig_header, numpyseg
def __init__(self,
input_filename,
gt_filename,
cache=True,
canonical=False):
self.input_filename = input_filename
self.gt_filename = gt_filename
self.canonical = canonical
self.cache = cache
self.input_handle = nib.load(self.input_filename)
# Unlabeled data (inference time)
if self.gt_filename is None:
self.gt_handle = None
else:
self.gt_handle = nib.load(self.gt_filename)
if len(self.input_handle.shape) > 3:
raise RuntimeError("4-dimensional volumes not supported.")
# Sanity check for dimensions, should be the same
input_shape, gt_shape = self.get_pair_shapes()
if self.gt_handle is not None:
if not np.allclose(input_shape, gt_shape):
raise RuntimeError(
'Input and ground truth with different dimensions.')
if self.canonical:
self.input_handle = nib.as_closest_canonical(self.input_handle)
# Unlabeled data
if self.gt_handle is not None:
self.gt_handle = nib.as_closest_canonical(self.gt_handle)
def extract_mid_slice_and_convert_coordinates_to_heatmaps(
path, suffix, aim=-1):
"""
This function takes as input a path to a dataset and generates a set of images:
(i) mid-sagittal image and
(ii) heatmap of disc labels associated with the mid-sagittal image.
Example::
ivadomed_prepare_dataset_vertebral_labeling -p path/to/bids -s _T2w -a 0
Args:
path (string): path to BIDS dataset form which images will be generated. Flag: ``--path``, ``-p``
suffix (string): suffix of image that will be processed (e.g., T2w). Flag: ``--suffix``, ``-s``
aim (int): If aim is not 0, retrieves only labels with value = aim, else create heatmap with all labels.
Flag: ``--aim``, ``-a``
Returns:
None. Images are saved in BIDS folder
"""
t = os.listdir(path)
t.remove('derivatives')
for i in range(len(t)):
sub = t[i]
path_image = os.path.join(path, t[i], 'anat',
t[i] + suffix + '.nii.gz')
if os.path.isfile(path_image):
path_label = os.path.join(
path, 'derivatives', 'labels', t[i], 'anat',
t[i] + suffix + '_labels-disc-manual.nii.gz')
list_points = mask2label(path_label, aim=aim)
image_ref = nib.load(path_image)
nib_ref_can = nib.as_closest_canonical(image_ref)
imsh = np.array(nib_ref_can.dataobj).shape
mid_nifti = imed_preprocessing.get_midslice_average(
path_image, list_points[0][0], slice_axis=0)
nib.save(
mid_nifti,
os.path.join(path, t[i], 'anat',
t[i] + suffix + '_mid.nii.gz'))
lab = nib.load(path_label)
nib_ref_can = nib.as_closest_canonical(lab)
label_array = np.zeros(imsh[1:])
for j in range(len(list_points)):
label_array[list_points[j][1], list_points[j][2]] = 1
heatmap = imed_maths.heatmap_generation(label_array[:, :], 10)
arr_pred_ref_space = imed_utils.reorient_image(
np.expand_dims(heatmap[:, :], axis=0), 2, lab, nib_ref_can)
nib_pred = nib.Nifti1Image(arr_pred_ref_space, lab.affine)
nib.save(
nib_pred,
os.path.join(
path, 'derivatives', 'labels', t[i], 'anat',
t[i] + suffix + '_mid_heatmap' + str(aim) + '.nii.gz'))
else:
pass
def orient_correctly(img_nii):
orientation = nibabel.io_orientation(img_nii.affine)
try:
img_new = nibabel.as_closest_canonical(img_nii,
True).get_data().astype(float)
except:
img_new = nibabel.as_closest_canonical(img_nii,
False).get_data().astype(float)
img_trans = np.transpose(img_new, (0, 2, 1))
img_flip = np.flip(img_trans, 0)
img_flip = np.flip(img_flip, 1)
return img_flip, orientation
def __init__(self, input_filenames, gt_filenames, metadata=None, cache=True, canonical=False):
self.input_filenames = input_filenames
self.gt_filenames = gt_filenames
self.metadata = metadata
self.canonical = canonical
self.cache = cache
# list of the images
self.input_handle = []
# loop over the filenames (list)
for input_file in self.input_filenames:
input_img = nib.load(input_file)
self.input_handle.append(input_img)
if len(input_img.shape) > 3:
raise RuntimeError("4-dimensional volumes not supported.")
# list of GT for multiclass segmentation
self.gt_handle = []
# Unlabeled data (inference time)
if self.gt_filenames is not None:
for gt in self.gt_filenames:
if gt is not None:
self.gt_handle.append(nib.load(gt))
else:
self.gt_handle.append(None)
# Sanity check for dimensions, should be the same
input_shape, gt_shape = self.get_pair_shapes()
if self.gt_filenames is not None:
if not np.allclose(input_shape, gt_shape):
raise RuntimeError('Input and ground truth with different dimensions.')
if self.canonical:
for idx, handle in enumerate(self.input_handle):
self.input_handle[idx] = nib.as_closest_canonical(handle)
# Unlabeled data
if self.gt_filenames is not None:
for idx, gt in enumerate(self.gt_handle):
if gt is not None:
self.gt_handle[idx] = nib.as_closest_canonical(gt)
if self.metadata:
self.metadata = []
for data, input_filename in zip(metadata, input_filenames):
data["input_filenames"] = input_filename
data["gt_filenames"] = gt_filenames
self.metadata.append(data)
def OnOpenOverlay(self, pubsub_evt):
dirpath = dialog.ShowOpenNiftiDialog()
nifti_image = nifti.ReadNifti(dirpath)
if nifti_image:
# Rearranges the axes of the image to be closest to RAS+ orientation,
# so the slices of the image (axial, coronal, sagittal) are shown correctly.
# See http://nipy.org/nibabel/image_orientation.html
nifti_image = as_closest_canonical(nifti_image)
imagedata = nifti_image.get_data()
# Conversion of type of numpy array (to unsigned char)
imagedata = imagedata.astype('f')
slc = sl.Slice()
y, x = slc.buffer_slices["AXIAL"].image.shape
z = slc.buffer_slices["SAGITAL"].image.shape[0]
# Add borders (with zero values) to overlay array to fit the dimensions of the 3D image
pad_x = numpy.abs( (x/2.0) - (imagedata.shape[0]/2.0) )
pad_y = numpy.abs( (y/2.0) - (imagedata.shape[1]/2.0) )
pad_z = numpy.abs( (z/2.0) - (imagedata.shape[2]/2.0) )
final_overlay = numpy.pad(imagedata, ((pad_x,pad_x),(pad_y,pad_y),(pad_z,pad_z)), mode='constant', constant_values=0)
# Modifications to work with Invesalius (Z,Y,X)
final_overlay = numpy.swapaxes(final_overlay, 0, 2)
final_overlay = numpy.fliplr(final_overlay)
Publisher.sendMessage('Set slice overlay', final_overlay)
def flipAndSaveToRAS(filename):
#Recover the image object
imageObj = nib.load(filename)
#Get the current orientation
CurrentOrientation = nib.aff2axcodes(imageObj.affine)
print("The current orientation is : ", CurrentOrientation)
#Check if the current orientation is already RAS+
if CurrentOrientation == ('R', 'A', 'S'):
print(
"Image already recorded into the RAS+ orientation, nothing to do")
return filename
else:
#Flip the image to RAS
flippedImage = nib.as_closest_canonical(imageObj)
##Check the new orientation
NewOrientation = nib.aff2axcodes(flippedImage.affine)
#Set Qcode to 1 that the Qform matrix can be used into the further processing
flippedImage.header['qform_code'] = 1
#Save the flipped image
nib.save(flippedImage, RASFile)
print("The new orientation is now : ", NewOrientation)
return RASFile
def load_medical_image(path,
crop_size=(0, 0, 0),
crop=(0, 0, 0),
type=None,
normalization="mean",
resample=None,
viz3d=False,
to_canonical=False):
slices_crop, w_crop, h_crop = crop
img_nii = nib.load(path)
img_np = np.squeeze(img_nii.get_fdata(dtype=np.float32))
if viz3d:
return torch.from_numpy(img_np)
if to_canonical:
img_nii = nib.as_closest_canonical(img_nii)
img_np = img_nii.get_fdata(dtype=np.float32)
if crop_size[0] != 0:
img_np = img_np[slices_crop:slices_crop + crop_size[0],
w_crop:w_crop + crop_size[1],
h_crop:h_crop + crop_size[2]]
if resample is not None:
img_nii = resample_to_output(img_nii, voxel_sizes=resample)
img_np = np.squeeze(img_nii.get_fdata(dtype=np.float32))
img_tensor = torch.from_numpy(img_np) # slice , width, height
#print('final tensor shape', img_tensor.shape)
if type != "label":
img_tensor = normalize(img_tensor, normalization=normalization)
return img_tensor
def transform_input_images(image_path, scan_names):
"""
Transform input input images for processing
+ n4 normalization between scans
+ move t1 to the canonical space
Images are stored in the tmp/ folder
"""
# check if tmp folder is available
tmp_folder = os.path.join(image_path, 'tmp')
if os.path.exists(tmp_folder) is False:
os.mkdir(tmp_folder)
# normalize images
for s in scan_names:
current_scan = os.path.join(image_path, s)
nifti_orig = nib.load(current_scan)
im_ = nifti_orig.get_data()
processed_scan = nib.Nifti1Image(im_.astype('<f4'),
affine=nifti_orig.affine)
# check for extra dims
if len(nifti_orig.get_data().shape) > 3:
processed_scan = nib.Nifti1Image(np.squeeze(
processed_scan.get_data()),
affine=nifti_orig.affine)
processed_scan.get_data()[:] = normalize_data(
processed_scan.get_data(), norm_type='zero_one')
t1_nifti_canonical = nib.as_closest_canonical(processed_scan)
t1_nifti_canonical.to_filename(os.path.join(tmp_folder, s))
def reorient(in_file):
import nibabel as nb
import os
_, outfile = os.path.split(in_file)
nii = nb.as_closest_canonical(nb.load(in_file))
nii.to_filename(outfile)
return os.path.abspath(outfile)
def main(self, niifile, slicerange, labelinclude, labelexclude, labelrange,
bottompx, strokepx):
nii = nibabel.load(niifile)
nii = nibabel.as_closest_canonical(nii)
hdr = nii.get_header()
img = nii.get_data()
pngdir = self.tempdir('png')
svgdir = self.tempdir('svg')
svxdir = self.tempdir('svx')
densdir = self.tempdir('svx/dens')
# autodetect slicerange if not specified
if slicerange == []:
mask = applyMask(img, labelrange, labelinclude, labelexclude)
select = numpy.flatnonzero(mask.max(axis=0).max(axis=1))
slicerange = [select[0], select[-1]]
srange = range(slicerange[0], slicerange[1])
mask = img[:, srange, :]
mask = applyMask(mask, labelrange, labelinclude,
labelexclude).astype(float)
if strokepx:
if bottompx:
bottompx = range(0, bottompx) if bottompx > 0 else range(
mask.shape[1] + bottompx, mask.shape[1])
solidmask = mask[:, bottompx, :]
mask = binaryContour(mask)
if bottompx:
mask[:, bottompx, :] = solidmask
radius = strokepx * math.pi / 3
ball = ball3d(radius) - 1
mask = ndimage.grey_dilation(mask, structure=ball)
mask = (mask * 255.999).astype(numpy.uint8)
return FancyOutput(mask=mask, slicerange=slicerange)
def read_image(img_spec, error_msg='image', num_dims=3):
"""Image reader. Removes stray values close to zero (smaller than 5 %ile)."""
if isinstance(img_spec, str):
if pexists(realpath(img_spec)):
hdr = nib.load(img_spec)
# trying to stick to an orientation
hdr = nib.as_closest_canonical(hdr)
img = hdr.get_data()
else:
raise IOError('Given path to {} does not exist!\n\t{}'.format(
error_msg, img_spec))
elif isinstance(img_spec, np.ndarray):
img = img_spec
else:
raise ValueError(
'Invalid input specified! '
'Input either a path to image data, or provide 3d Matrix directly.'
)
if num_dims == 3:
img = check_image_is_3d(img)
elif num_dims == 4:
check_image_is_4d(img)
else:
raise ValueError('Requested check for {} dims - allowed: 3 or 4!')
if not np.issubdtype(img.dtype, np.float64):
img = img.astype('float32')
return img
def buildAnat(self, parFiles):
""" Build a 3D structural/anatomical Nifti image from the par/rec file
On Philip's scanner, entire anat image is assumed to be contained in
single par/rec file pair. Open the par file, extract the image data,
realign to RAS+ and build a nifti object
Parameters
----------
parFiles : list
list containing the file names (file names ONLY, no path) of all
par files in a the series directory. If this is an anatomical image
there should only be a single file in the list
Returns
-------
anatImage_RAS : Nifti1Image
nifti-1 formated image of the 3D anatomical data, oriented in
RAS+
See Also
--------
nibabel.nifti1.Nifti1Image()
"""
# should only be a single parFile in the list
anatImage = nib.load(join(self.seriesDir, parFiles[0]), strict_sort=True)
# convert to RAS+
anatImage_RAS = nib.as_closest_canonical(anatImage)
print('Nifti image dims: {}'.format(anatImage_RAS.shape))
return anatImage_RAS
def reorient_t1w(img: str, anat_preproc_dir: Path):
"""Reorients input image to RAS+. Essentially a wrapper on `nib.as_closest_canonical` and `normalize_xform`.
Parameters
----------
img : str
Path to image being reoriented
anat_preproc_dir : Path
Location of preproc directory for anatomical files.
Returns
-------
str
Path to reoriented image
"""
# Load image, orient as RAS
orig_img = nib.load(img)
reoriented = nib.as_closest_canonical(orig_img)
normalized = normalize_xform(reoriented)
# Image may be reoriented
out_name = anat_preproc_dir / f"{get_filename(img)}"
if normalized is not orig_img:
print(f"Reorienting {img} to RAS+...")
out_name = str(out_name) + "_reor_RAS.nii.gz"
else:
out_name = str(out_name) + "_RAS.nii.gz"
normalized.to_filename(out_name)
return out_name
def map(self, func_name, data, thresh=None, **kwargs):
"""Map a dataset across the mosaic of axes.
Parameters
----------
func_name : str
Name of a pyplot function.
data : filename, nibabel image, or array
Dataset to plot.
thresh : float
Don't map voxels in ``data`` below this threshold.
kwargs : key, value mappings
Other keyword arguments are passed to the plotting function.
"""
if isinstance(data, string_types):
data_img = nib.load(data)
elif isinstance(data, np.ndarray):
data_img = nib.Nifti1Image(data, np.eye(4))
else:
data_img = data
data_img = nib.as_closest_canonical(data_img)
data = data_img.get_data()
data = data.astype(np.float)
if thresh is not None:
data[data < thresh] = np.nan
data = data[self.x_slice, self.y_slice, self.z_slice]
self._map(func_name, data, **kwargs)
def mask2label(path_label, aim=0):
"""
Retrieve points coordinates and value from a label file containing singl voxel label
Args:
path_label (str): path of nifti image
aim (int): -1 will return all points with label between 3 and 30 , any other int > 0 will return
only the coordinates of points with label defined by aim.
Returns:
ndarray: array containing the asked point in the format [x,y,z,value] in the RAS orientation.
"""
image = nib.load(path_label)
image = nib.as_closest_canonical(image)
arr = np.array(image.dataobj)
list_label_image = []
# Arr non zero used since these are single voxel label
for i in range(len(arr.nonzero()[0])):
x = arr.nonzero()[0][i]
y = arr.nonzero()[1][i]
z = arr.nonzero()[2][i]
# need to check every points
if aim == 0:
# we don't want to account for pmj (label 49) nor C1/C2 which is hard to distinguish.
if arr[x, y, z] < 30 and arr[x, y, z] != 1:
list_label_image.append([x, y, z, arr[x, y, z]])
elif aim > 0:
if arr[x, y, z] == aim:
list_label_image.append([x, y, z, arr[x, y, z]])
list_label_image.sort(key=lambda x: x[3])
return list_label_image
def buildAnat(self, parFiles):
""" Build a 3D structural/anatomical Nifti image from the par/rec file
On Philip's scanner, entire anat image is assumed to be contained in
single par/rec file pair. Open the par file, extract the image data,
realign to RAS+ and build a nifti object
Parameters
----------
parFiles : list
list containing the file names (file names ONLY, no path) of all
par files in a the series directory. If this is an anatomical image
there should only be a single file in the list
Returns
-------
anatImage_RAS : Nifti1Image
nifti-1 formated image of the 3D anatomical data, oriented in
RAS+
See Also
--------
nibabel.nifti1.Nifti1Image()
"""
# should only be a single parFile in the list
anatImage = nib.load(join(self.seriesDir, parFiles[0]),
strict_sort=True)
# convert to RAS+
anatImage_RAS = nib.as_closest_canonical(anatImage)
print('Nifti image dims: {}'.format(anatImage_RAS.shape))
return anatImage_RAS
def _run_interface(self, runtime):
# Load image, orient as RAS
fname = self.inputs.in_file
orig_img = nb.load(fname)
reoriented = nb.as_closest_canonical(orig_img)
# Reconstruct transform from orig to reoriented image
ornt_xfm = nb.orientations.inv_ornt_aff(
nb.io_orientation(orig_img.affine), orig_img.shape)
normalized = normalize_xform(reoriented)
# Image may be reoriented
if normalized is not orig_img:
out_name = fname_presuffix(fname,
suffix='_ras',
newpath=runtime.cwd)
normalized.to_filename(out_name)
else:
out_name = fname
mat_name = fname_presuffix(fname,
suffix='.mat',
newpath=runtime.cwd,
use_ext=False)
np.savetxt(mat_name, ornt_xfm, fmt='%.08f')
self._results['out_file'] = out_name
self._results['transform'] = mat_name
return runtime
def reorient_and_discard_non_steady(in_file, float32=False):
import nibabel as nb
import os
import numpy as np
import nibabel as nb
from statsmodels.robust.scale import mad
_, outfile = os.path.split(in_file)
nii = nb.as_closest_canonical(nb.load(in_file))
in_data = nii.get_data()
# downcast to reduce space consumption and improve performance
if float32 and np.dtype(in_data.dtype).itemsize > 4:
in_data = in_data.astype(np.float32)
data = in_data[:, :, :, :50]
timeseries = data.max(axis=0).max(axis=0).max(axis=0)
outlier_timecourse = (timeseries - np.median(timeseries)) / mad(
timeseries)
exclude_index = 0
for i in range(10):
if outlier_timecourse[i] > 10:
exclude_index += 1
else:
break
nb.Nifti1Image(in_data[:, :, :, exclude_index:], nii.affine, nii.header).to_filename(outfile)
nii.uncache()
return exclude_index, os.path.abspath(outfile)
def weights_to_nifti(weights, image, output_filename):
"""
Args:
weights:
image:
output_filename:
Returns:
"""
# Normalize with 2-norm
# features = 2 * weights / np.power(norm(weights.flatten(), 2), 2)
# Normalize inf-norm
features = weights / abs(weights).max()
img = nib.load(image)
canonical_img = nib.as_closest_canonical(img)
hd = canonical_img.header
qform = np.zeros((4, 4))
for i in range(1, 4):
qform[i-1, i-1] = hd['pixdim'][i]
qform[i-1, 3] = -1.0 * hd['pixdim'][i] * hd['dim'][i] / 2.0
output_image = nib.Nifti1Image(features, qform)
nib.save(output_image, output_filename)
def get_midslice_average(path_im, ind, slice_axis=0):
"""
Extract an average 2D slice out of a 3D volume. This image is generated by
averaging the 7 slices in the middle of the volume
Args:
path_im (string): path to image
ind (int): index of the slice around which we will average
slice_axis (int): Slice axis according to RAS convention
Returns:
nifti: a single slice nifti object containing the average image in the image space.
"""
image = nib.load(path_im)
image_can = nib.as_closest_canonical(image)
arr_can = np.array(image_can.dataobj)
numb_of_slice = 3
# Avoid out of bound error by changing the number of slice taken if needed
if ind + 3 > arr_can.shape[slice_axis]:
numb_of_slice = arr_can.shape[slice_axis] - ind
if ind - numb_of_slice < 0:
numb_of_slice = ind
slc = [slice(None)] * len(arr_can.shape)
slc[slice_axis] = slice(ind - numb_of_slice, ind + numb_of_slice)
mid = np.mean(arr_can[tuple(slc)], slice_axis)
arr_pred_ref_space = imed_utils.reorient_image(
np.expand_dims(mid[:, :], axis=slice_axis), 2, image,
image_can).astype('float32')
nib_pred = nib.Nifti1Image(arr_pred_ref_space, image.affine)
return nib_pred
def ReadOthers(dir_):
"""
Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,
remove singleton image dimensions and convert image orientation to
RAS+ canonical coordinate system. Analyze header does not support
affine transformation matrix, though cannot be converted automatically
to canonical orientation.
:param dir_: file path
:return: imagedata object
"""
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
try:
imagedata = nib.squeeze_image(nib.load(dir_))
imagedata = nib.as_closest_canonical(imagedata)
imagedata.update_header()
except (nib.filebasedimages.ImageFileError):
return False
return imagedata
def main(self,niifile,slicerange,labelinclude,labelexclude,labelrange,bottompx,strokepx):
nii = nibabel.load(niifile)
nii = nibabel.as_closest_canonical(nii)
hdr = nii.get_header()
img = nii.get_data()
pngdir = self.tempdir('png')
svgdir = self.tempdir('svg')
svxdir = self.tempdir('svx')
densdir = self.tempdir('svx/dens')
# autodetect slicerange if not specified
if slicerange == []:
mask = applyMask(img,labelrange,labelinclude,labelexclude)
select = numpy.flatnonzero(mask.max(axis=0).max(axis=1))
slicerange = [select[0],select[-1]]
srange = range(slicerange[0],slicerange[1])
mask = img[:,srange,:]
mask = applyMask(mask,labelrange,labelinclude,labelexclude).astype(float)
if strokepx:
if bottompx:
bottompx = range(0,bottompx) if bottompx>0 else range(mask.shape[1]+bottompx,mask.shape[1])
solidmask = mask[:,bottompx,:]
mask = binaryContour(mask)
if bottompx:
mask[:,bottompx,:] = solidmask
radius = strokepx*math.pi/3
ball = ball3d(radius)-1
mask = ndimage.grey_dilation(mask,structure=ball)
mask = (mask*255.999).astype(numpy.uint8)
return FancyOutput(
mask = mask,
slicerange = slicerange
)
def ReadOthers(dir_):
"""
Read the given Analyze, NIfTI, Compressed NIfTI or PAR/REC file,
remove singleton image dimensions and convert image orientation to
RAS+ canonical coordinate system. Analyze header does not support
affine transformation matrix, though cannot be converted automatically
to canonical orientation.
:param dir_: file path
:return: imagedata object
"""
if not const.VTK_WARNING:
log_path = os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt')
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path.encode(const.FS_ENCODE))
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
try:
imagedata = nib.squeeze_image(nib.load(dir_))
imagedata = nib.as_closest_canonical(imagedata)
imagedata.update_header()
except(nib.filebasedimages.ImageFileError):
return False
return imagedata
def get_data(self, img):
"""
Extract data array and meta data from loaded image and return them.
This function returns 2 objects, first is numpy array of image data, second is dict of meta data.
It constructs `affine`, `original_affine`, and `spatial_shape` and stores in meta dict.
If loading a list of files, stack them together and add a new dimension as first dimension,
and use the meta data of the first image to represent the stacked result.
Args:
img: a Nibabel image object loaded from a image file or a list of Nibabel image objects.
"""
img_array: List[np.ndarray] = list()
compatible_meta: Dict = {}
for i in ensure_tuple(img):
header = self._get_meta_dict(i)
header["affine"] = self._get_affine(i)
header["original_affine"] = self._get_affine(i)
header["as_closest_canonical"] = self.as_closest_canonical
if self.as_closest_canonical:
i = nib.as_closest_canonical(i)
header["affine"] = self._get_affine(i)
header["spatial_shape"] = self._get_spatial_shape(i)
img_array.append(self._get_array_data(i))
_copy_compatible_dict(header, compatible_meta)
img_array_ = np.stack(img_array,
axis=0) if len(img_array) > 1 else img_array[0]
return img_array_, compatible_meta
def load_image(file):
image = nib.load(file)
image = nib.as_closest_canonical(image)
# print(nib.aff2axcodes(image.affine))
image_np = image_to_np(image)
return image, image_np
def plot_spikes(in_file, in_fft, spikes_list, cols=3,
labelfmt='t={0:.3f}s (z={1:d})',
out_file=None):
from mpl_toolkits.axes_grid1 import make_axes_locatable
nii = nb.as_closest_canonical(nb.load(in_file))
fft = nb.load(in_fft).get_data()
data = nii.get_data()
zooms = nii.header.get_zooms()[:2]
tstep = nii.header.get_zooms()[-1]
ntpoints = data.shape[-1]
if len(spikes_list) > cols * 7:
cols += 1
nspikes = len(spikes_list)
rows = 1
if nspikes > cols:
rows = math.ceil(nspikes / cols)
fig = plt.figure(figsize=(7 * cols, 5 * rows))
for i, (t, z) in enumerate(spikes_list):
prev = None
pvft = None
if t > 0:
prev = data[..., z, t - 1]
pvft = fft[..., z, t - 1]
post = None
psft = None
if t < (ntpoints - 1):
post = data[..., z, t + 1]
psft = fft[..., z, t + 1]
ax1 = fig.add_subplot(rows, cols, i + 1)
divider = make_axes_locatable(ax1)
ax2 = divider.new_vertical(size="100%", pad=0.1)
fig.add_axes(ax2)
plot_slice_tern(data[..., z, t], prev=prev, post=post, spacing=zooms,
ax=ax2,
label=labelfmt.format(t * tstep, z))
plot_slice_tern(fft[..., z, t], prev=pvft, post=psft, vmin=-5, vmax=5,
cmap=get_parula(), ax=ax1)
plt.tight_layout()
if out_file is None:
fname, ext = op.splitext(op.basename(in_file))
if ext == '.gz':
fname, _ = op.splitext(fname)
out_file = op.abspath('%s.svg' % fname)
fig.savefig(out_file, format='svg', dpi=300, bbox_inches='tight')
return out_file
def center_nifti_origin(input_image, output_image):
"""
Put the origin of the coordinate system at the center of the image
Args:
input_image: path to the input image
output_image: path to the output image (where the result will be stored)
Returns:
"""
import nibabel as nib
import numpy as np
img = nib.load(input_image)
canonical_img = nib.as_closest_canonical(img)
hd = canonical_img.header
# if hd['quatern_b'] != 0 or hd['quatern_c'] != 0 or hd['quatern_d'] != 0:
# print('Warning: Not all values in quatern are equal to zero')
qform = np.zeros((4, 4))
for i in range(1, 4):
qform[i - 1, i - 1] = hd['pixdim'][i]
qform[i - 1, 3] = -1.0 * hd['pixdim'][i] * hd['dim'][i] / 2.0
new_img = nib.Nifti1Image(canonical_img.get_data(caching='unchanged'), qform)
nib.save(new_img, output_image)
def sanitize(input_fname):
im = nb.as_closest_canonical(nb.squeeze_image(nb.load(str(input_fname))))
hdr = im.header.copy()
dtype = 'int16'
data = None
if str(input_fname).endswith('_mask.nii.gz'):
dtype = 'uint8'
data = im.get_fdata() > 0
if str(input_fname).endswith('_probseg.nii.gz'):
dtype = 'float32'
hdr['cal_max'] = 1.0
hdr['cal_min'] = 0.0
data = im.get_fdata()
data[data < 0] = 0
if input_fname.name.split('_')[-1].split('.')[0] in ('T1w', 'T2w', 'PD'):
data = im.get_fdata()
data[data < 0] = 0
hdr.set_data_dtype(dtype)
nii = nb.Nifti1Image(
data if data is not None else im.get_fdata().astype(dtype), im.affine,
hdr)
sform = nii.header.get_sform()
nii.header.set_sform(sform, 4)
nii.header.set_qform(sform, 4)
nii.header.set_xyzt_units(xyz='mm')
nii.to_filename(str(input_fname))
def processVolume(self, volIdx):
""" Process a single 3D timepoint from the series
Extract the 3D numpy array of voxel data for the current volume (set by
self.volCounter attribute). Reorder the voxel data so that it is RAS+,
build a header JSON object, and then send both the header and the voxel
data out over the socket connection to Pyneal
Parameters
----------
volIdx : int
index (0-based) of the volume you want to process
"""
self.logger.info('Volume {} processing'.format(volIdx))
### Prep the voxel data by extracting this vol from the imageMatrix,
# and then converting to a Nifti1 object in order to set the voxel
# order to RAS+, then get the voxel data as contiguous numpy array
thisVol = self.imageMatrix[:, :, :, volIdx]
thisVol_nii = nib.Nifti1Image(thisVol, self.affine)
thisVol_RAS = nib.as_closest_canonical(thisVol_nii) # make RAS+
thisVol_RAS_data = np.ascontiguousarray(thisVol_RAS.get_fdata())
### Create a header with metadata info
volHeader = {
'volIdx': volIdx,
'TR': str(self.tr),
'dtype': str(thisVol_RAS_data.dtype),
'shape': thisVol_RAS_data.shape,
'affine': json.dumps(thisVol_RAS.affine.tolist())
}
### Send the voxel array and header to the pynealSocket
self.sendVolToPynealSocket(volHeader, thisVol_RAS_data)
def __call__(self, data):
"""
:param data: Data dictionary to be processed by this transform
:type data: dict
:return: Updated data dictionary
:rtype: dict
"""
for field in self.fields:
complete_file_path = os.path.join(self.data_dir, data[field])
assert complete_file_path[0:5] == 's3://'
filename = get_file_from_s3(self.s3_client, complete_file_path, self.cache)
img = nib.load(filename)
if self.canonical:
img = nib.as_closest_canonical(img)
data[field] = img
data[field + '_affines'] = img.affine
data[field + '_orientations'] = nib.aff2axcodes(img.affine)
return data
def __init__(self, fmapnii, weights=None, knots_zooms=None, padding=3,
pe_dir=1, njobs=-1):
self._pedir = pe_dir
if knots_zooms is None:
knots_zooms = [40., 40., 18.]
knots_zooms[pe_dir] = 60.
if not isinstance(knots_zooms, (list, tuple)):
knots_zooms = [knots_zooms] * 3
self._knots_zooms = np.array(knots_zooms)
if isinstance(fmapnii, str):
fmapnii = nb.as_closest_canonical(nb.load(fmapnii))
self._fmapnii = fmapnii
self._padding = padding
# Pad data with zeros
self._data = np.zeros(tuple(np.array(
self._fmapnii.get_data().shape) + 2 * padding))
# The list of ijk coordinates
self._fmapijk = get_ijk(self._data)
# Find padding coordinates
self._data[padding:-padding,
padding:-padding,
padding:-padding] = 1
self._frameijk = self._data[tuple(self._fmapijk.T)] > 0
# Set data
self._data[padding:-padding,
padding:-padding,
padding:-padding] = fmapnii.get_data()
# Get ijk in homogeneous coords
ijk_h = np.hstack((self._fmapijk, np.array([1.0] * len(self._fmapijk))[..., np.newaxis]))
# The list of xyz coordinates
self._fmapaff = compute_affine(self._data, self._fmapnii.header.get_zooms())
self._fmapxyz = self._fmapaff.dot(ijk_h.T)[:3, :].T
# Mask coordinates
self._weights = self._set_weights(weights)
# Generate control points
self._generate_knots()
self._X = None
self._coeff = None
self._smoothed = None
self._Xinv = None
self._inverted = None
self._invcoeff = None
self._njobs = njobs
def load_nifti(fname, reorient=True):
"""
Loads a nifti image,
returns a ndarray()
"""
img = nib.load(fname)
if reorient:
img = nib.as_closest_canonical(img)
return(img.get_data())
def niiToArray(niiImg, c_contiguos=True, canonical=False):
if canonical:
rough_data = nib.as_closest_canonical(niiImg).get_data()
else:
rough_data = niiImg.get_data()
print np.isfortran(rough_data)
#if c_contiguos and np.isfortran(rough_data):
# rough_data = rough_data.T
if c_contiguos and not rough_data.flags['C_CONTIGUOUS']:
rough_data = rough_data.T
return rough_data
def main(self,mncfile,niifile):
mnc = nibabel.load(mncfile)
hdr = mnc.get_header()
q = hdr.get_best_affine()
print('Affine transformation matrix: {}'.format(q))
img = mnc.get_data()
print('Some data... {}'.format(img[:10,:10,:10]))
print('Niifile {}'.format(niifile))
nii = nibabel.Nifti1Image(img,q)
nii = nibabel.as_closest_canonical(nii)
nibabel.save(nii,niifile)
return FancyOutput( niifile )
def reorient(in_file, out_file=None):
import nibabel as nb
from fmriprep.utils.misc import genfname
from builtins import (str, bytes)
if out_file is None:
out_file = genfname(in_file, suffix='ras')
if isinstance(in_file, (str, bytes)):
nii = nb.load(in_file)
nii = nb.as_closest_canonical(nii)
nii.to_filename(out_file)
return out_file
def OnShowNiftiFile(self, pubsub_evt):
dirpath = dialog.ShowOpenNiftiDialog()
nifti_image = nifti.ReadNifti(dirpath)
if nifti_image:
# Rearranges the axes of the image to be closest to RAS+ orientation,
# so the slices of the image (axial, coronal, sagittal) are shown correctly.
# See http://nipy.org/nibabel/image_orientation.html
nifti_image = as_closest_canonical(nifti_image)
self.CreateNiftiProject(nifti_image)
self.LoadProject()
Publisher.sendMessage("Enable state project", True)
def main(self,inp,out):
nii = nibabel.load(inp)
nii = nibabel.as_closest_canonical(nii)
# remove trailing singleton dimension
hdr = nii.get_header()
shape = hdr.get_data_shape()
if shape[-1] == 1:
img = nii.get_data()
img = img.squeeze(-1)
nii = nibabel.nifti1.Nifti1Image(img,hdr.get_best_affine())
nibabel.nifti1.save(nii, out)
return FancyDict(
out = out,
dtype = nii.get_data_dtype()
)
def _run_interface(self, runtime):
# load image
nii = nb.load(self.inputs.in_file)
hdr = nii.get_header().copy()
if self.inputs.check_ras:
nii = nb.as_closest_canonical(nii)
if self.inputs.check_dtype:
changed = True
datatype = int(hdr['datatype'])
if datatype == 1:
IFLOGGER.warn('Input image %s has a suspicious data type "%s"',
self.inputs.in_file, hdr.get_data_dtype())
# signed char and bool to uint8
if datatype == 1 or datatype == 2 or datatype == 256:
dtype = np.uint8
# int16 to uint16
elif datatype == 4:
dtype = np.uint16
# Signed long, long long, etc to uint32
elif datatype == 8 or datatype == 1024 or datatype == 1280:
dtype = np.uint32
# Floats over 32 bits
elif datatype == 64 or datatype == 1536:
dtype = np.float32
else:
changed = False
if changed:
hdr.set_data_dtype(dtype)
nii = nb.Nifti1Image(nii.get_data().astype(dtype),
nii.get_affine(), hdr)
# Generate name
out_file, ext = op.splitext(op.basename(self.inputs.in_file))
if ext == '.gz':
out_file, ext2 = op.splitext(out_file)
ext = ext2 + ext
self._results['out_file'] = op.abspath('{}_conformed{}'.format(out_file, ext))
nii.to_filename(self._results['out_file'])
return runtime
def processParFile(self, par_fname):
""" Process a given par header file
Read the par header file and corresponding rec image file. Read in as
a nifti object that will provide the 3D voxel array for this volume.
Reorder to RAS+, and then send to the pynealSocket
Parameters
----------
par_fname : string
full path to the par file that you want to process
"""
# make sure the corresponding rec file exists
while not os.path.isfile(par_fname.replace('.par', '.rec')):
time.sleep(.01)
### Build the 3D voxel array and reorder to RAS+
# nibabel will load the par/rec, but there can be multiple images (mag,
# phase, etc...) concatenated into the 4th dimension. Loading with the
# strict_sort option (I think) will make sure the first image is the
# data we want. Extract this data, then reorder the voxel array to RAS+
thisVol = nib.load(par_fname, strict_sort=True)
# get the volume index from the acq_nr field of the header (1-based index)
volIdx = int(thisVol.header.general_info['acq_nr']) - 1
self.logger.info('Volume {} processing'.format(volIdx))
# convert to RAS+
thisVol_RAS = nib.as_closest_canonical(thisVol)
# grab the data for the first volume along the 4th dimension
# and store as contiguous array (required for ZMQ)
thisVol_RAS_data = np.ascontiguousarray(thisVol_RAS.get_data()[:, :, :, 0].astype('uint16'))
### Create a header with metadata info
volHeader = {
'volIdx': volIdx,
'dtype': str(thisVol_RAS_data.dtype),
'shape': thisVol_RAS_data.shape,
'affine': json.dumps(thisVol_RAS.affine.tolist()),
'TR': str(thisVol.header.general_info['repetition_time'][0])
}
### Send the voxel array and header to the pynealSocket
self.sendVolToPynealSocket(volHeader, thisVol_RAS_data)
def _get_limits(nifti_file, only_plot_noise=False):
if isinstance(nifti_file, str):
nii = nb.as_closest_canonical(nb.load(nifti_file))
data = nii.get_data()
else:
data = nifti_file
data_mask = np.logical_not(np.isnan(data))
if only_plot_noise:
data_mask = np.logical_and(data_mask, data != 0)
vmin = np.percentile(data[data_mask], 0)
vmax = np.percentile(data[data_mask], 61)
else:
vmin = np.percentile(data[data_mask], 0.5)
vmax = np.percentile(data[data_mask], 99.5)
return vmin, vmax
def niiToArray(niiImg, canonical, c_contiguos):
dataType = getNumpyDataFormat(niiImg)
sizeof_hdr = niiImg.header['sizeof_hdr']
scl_slope = niiImg.header['scl_slope']
scl_inter = niiImg.header['scl_inter']
if math.isnan(sizeof_hdr):
sizeof_hdr = 1
if math.isnan(scl_slope):
scl_slope = 1
if math.isnan(scl_inter):
scl_inter = 0
if canonical:
aligendImage = nib.as_closest_canonical(niiImg)
else:
aligendImage = niiImg
INroughData = aligendImage.get_data()
if c_contiguos and not INroughData.flags['C_CONTIGUOUS']:
INroughData = INroughData.T
return INroughData * scl_slope + scl_inter
def _get_limits(nifti_file, only_plot_noise=False):
from builtins import bytes, str # pylint: disable=W0622
if isinstance(nifti_file, (str, bytes)):
nii = nb.as_closest_canonical(nb.load(nifti_file))
data = nii.get_data()
else:
data = nifti_file
data_mask = np.logical_not(np.isnan(data))
if only_plot_noise:
data_mask = np.logical_and(data_mask, data != 0)
vmin = np.percentile(data[data_mask], 0)
vmax = np.percentile(data[data_mask], 61)
else:
vmin = np.percentile(data[data_mask], 0.5)
vmax = np.percentile(data[data_mask], 99.5)
return vmin, vmax
def prepRealDataset(image_path):
""" Prepare a real, existing dataset for use with the simulator
Read in the supplied 4d image file, set orientation to RAS+
Parameters
----------
image_path : string
full path to the dataset you want to use
Returns
-------
ds_RAS : nibabel-like image
Nibabel dataset with orientation set to RAS+
"""
print('Prepping dataset: {}'.format(image_path))
ds = nib.load(image_path)
# make sure it's RAS+
ds_RAS = nib.as_closest_canonical(ds)
print('Dimensions: {}'.format(ds_RAS.shape))
return ds_RAS
def reorient(in_file, newpath=None):
"""Reorient Nifti files to RAS"""
out_file = fname_presuffix(in_file, suffix='_ras', newpath=newpath)
nb.as_closest_canonical(nb.load(in_file)).to_filename(out_file)
return out_file
def _run_interface(self, runtime):
# Load image, orient as RAS
fname = self.inputs.in_file
orig_img = nb.load(fname)
reoriented = nb.as_closest_canonical(orig_img)
# Set target shape information
target_zooms = np.array(self.inputs.target_zooms)
target_shape = np.array(self.inputs.target_shape)
target_span = target_shape * target_zooms
zooms = np.array(reoriented.header.get_zooms()[:3])
shape = np.array(reoriented.shape[:3])
# Reconstruct transform from orig to reoriented image
ornt_xfm = nb.orientations.inv_ornt_aff(
nb.io_orientation(orig_img.affine), orig_img.shape)
# Identity unless proven otherwise
target_affine = reoriented.affine.copy()
conform_xfm = np.eye(4)
xyz_unit = reoriented.header.get_xyzt_units()[0]
if xyz_unit == 'unknown':
# Common assumption; if we're wrong, unlikely to be the only thing that breaks
xyz_unit = 'mm'
# Set a 0.05mm threshold to performing rescaling
atol = {'meter': 1e-5, 'mm': 0.01, 'micron': 10}[xyz_unit]
# Rescale => change zooms
# Resize => update image dimensions
rescale = not np.allclose(zooms, target_zooms, atol=atol)
resize = not np.all(shape == target_shape)
if rescale or resize:
if rescale:
scale_factor = target_zooms / zooms
target_affine[:3, :3] = reoriented.affine[:3, :3].dot(np.diag(scale_factor))
if resize:
# The shift is applied after scaling.
# Use a proportional shift to maintain relative position in dataset
size_factor = target_span / (zooms * shape)
# Use integer shifts to avoid unnecessary interpolation
offset = (reoriented.affine[:3, 3] * size_factor - reoriented.affine[:3, 3])
target_affine[:3, 3] = reoriented.affine[:3, 3] + offset.astype(int)
data = nli.resample_img(reoriented, target_affine, target_shape).get_data()
conform_xfm = np.linalg.inv(reoriented.affine).dot(target_affine)
reoriented = reoriented.__class__(data, target_affine, reoriented.header)
# Image may be reoriented, rescaled, and/or resized
if reoriented is not orig_img:
out_name = fname_presuffix(fname, suffix='_ras', newpath=runtime.cwd)
reoriented.to_filename(out_name)
else:
out_name = fname
transform = ornt_xfm.dot(conform_xfm)
assert np.allclose(orig_img.affine.dot(transform), target_affine)
mat_name = fname_presuffix(fname, suffix='.mat', newpath=runtime.cwd, use_ext=False)
np.savetxt(mat_name, transform, fmt='%.08f')
self._results['out_file'] = out_name
self._results['transform'] = mat_name
return runtime
def __init__(self, anat, stat=None, mask=None, n_col=9, step=2,
tight=True, show_mask=True, slice_dir="axial",
anat_lims=None, title=None):
"""Plot a mosaic of axial slices through an MRI volume.
Parameters
----------
anat : filename, nibabel image, or array
The anatomical image that will form the background of the mosaic.
If only an array is passed, an identity matrix will be used as
the affine and orientation could be incorrect.
stat : filename, nibabel image, or array
A statistical map to plot as an overlay (which happens by calling
one of the methods). If only an array is passed, it is assumed
to have the same orientation as the anatomy.
mask : filename, nibabel image, or array
A binary image where voxels included in the statistical analysis
are True. This will be used to gray-out voxels in the anatomical
image that are outside the field of view. If you want to overlay
the mask itself, pass it to ``stat``.
n_col : int
Number of columns in the mosaic. This will also determine the size
of the figure (1 inch per column).
step : int
Show every ``step`` slice along the slice_dir in the mosaic.
tight : bool
If True, try to crop panes to focus on the brain volume.
show_mask : bool
If True, gray-out voxels in the anat image that are outside
of the mask image.
slice_dir : axial | coronal | sagital
Direction to slice the mosaic on.
anat_lims : pair of floats
Limits for the anatomical (background) image colormap
"""
# -- Load and reorient the anatomical image
if isinstance(anat, string_types):
anat_img = nib.load(anat)
have_orientation = True
elif isinstance(anat, nib.spatialimages.SpatialImage):
anat_img = anat
have_orientation = True
elif isinstance(anat, np.ndarray):
anat_img = nib.Nifti1Image(anat, np.eye(4))
have_orientation = False
else:
raise TypeError("anat type {} not understood".format(type(anat)))
self.anat_img = nib.as_closest_canonical(anat_img)
self.anat_data = self.anat_img.get_data()
# -- Load and reorient the statistical image
if isinstance(stat, string_types):
stat_img = nib.load(stat)
elif isinstance(stat, nib.spatialimages.SpatialImage):
stat_img = stat
elif isinstance(stat, np.ndarray):
if stat.dtype is np.dtype("bool"):
stat = stat.astype(np.int)
stat_img = nib.Nifti1Image(stat, anat_img.affine, anat_img.header)
elif stat is not None:
raise TypeError("stat type {} not understood".format(type(stat)))
else:
stat_img = None
if stat_img is not None:
self.stat_img = nib.as_closest_canonical(stat_img)
# -- Load and reorient the mask image
if isinstance(mask, string_types):
mask_img = nib.load(mask)
elif isinstance(mask, nib.spatialimages.SpatialImage):
mask_img = mask
elif isinstance(mask, np.ndarray):
if mask.dtype is np.dtype("bool"):
mask = mask.astype(np.int)
mask_img = nib.Nifti1Image(mask, anat_img.affine, anat_img.header)
elif mask is not None:
raise TypeError("mask type {} not understood".format(type(mask)))
else:
mask_img = None
mask_data = None
if mask is not None:
self.mask_img = nib.as_closest_canonical(mask_img)
mask_data = self.mask_img.get_data().astype(bool)
if slice_dir[0] not in "sca":
err = "Slice direction {} not understood".format(slice_dir)
raise ValueError(err)
# Find a field of view that tries to eliminate empty voxels
anat_fov = self.anat_img.get_data() > 1e-5
if tight:
self.fov = anat_fov
if mask is not None:
self.fov &= mask_data
else:
self.fov = np.ones_like(anat_fov, np.bool)
# Save the mosaic parameters
self.n_col = n_col
self.step = step
self.slice_dir = slice_dir
self.title = title
# Define slice objects to crop to the volume
slices, = ndimage.find_objects(self.fov.astype(np.int))
self.x_slice, self.y_slice, self.z_slice = slices
# Update the slice on the mosiac axis with steps
slice_ax = dict(s="x", c="y", a="z")[slice_dir[0]]
ms = getattr(self, slice_ax + "_slice")
mosaic_slice = slice(ms.start, ms.stop, step)
setattr(self, slice_ax + "_slice", mosaic_slice)
self.n_slices = (ms.stop - ms.start) // step
# Initialize the figure and plot the constant info
self._setup_figure()
self._plot_anat(anat_lims)
if mask is not None and show_mask:
self._plot_inverse_mask()
# Label the anatomy
if have_orientation:
l_label, r_label = dict(s="PA", c="LR", a="LR")[self.slice_dir[0]]
self.fig.text(.01, .03, l_label, size=14, color="w",
ha="left", va="center")
self.fig.text(.99, .03, r_label, size=14, color="w",
ha="right", va="center")
def _gen_reference(fixed_image, moving_image, fov_mask=None, out_file=None,
message=None, force_xform_code=None):
"""
Generates a sampling reference, and makes sure xform matrices/codes are
correct
"""
if out_file is None:
out_file = fname_presuffix(fixed_image,
suffix='_reference',
newpath=os.getcwd())
# Moving images may not be RAS/LPS (more generally, transverse-longitudinal-axial)
reoriented_moving_img = nb.as_closest_canonical(nb.load(moving_image))
new_zooms = reoriented_moving_img.header.get_zooms()[:3]
# Avoid small differences in reported resolution to cause changes to
# FOV. See https://github.com/poldracklab/fmriprep/issues/512
# A positive diagonal affine is RAS, hence the need to reorient above.
new_affine = np.diag(np.round(new_zooms, 3))
resampled = nli.resample_img(fixed_image,
target_affine=new_affine,
interpolation='nearest')
if fov_mask is not None:
# If we have a mask, resample again dropping (empty) samples
# out of the FoV.
fixednii = nb.load(fixed_image)
masknii = nb.load(fov_mask)
if np.all(masknii.shape[:3] != fixednii.shape[:3]):
raise RuntimeError(
'Fixed image and mask do not have the same dimensions.')
if not np.allclose(masknii.affine, fixednii.affine, atol=1e-5):
raise RuntimeError(
'Fixed image and mask have different affines')
# Get mask into reference space
masknii = nli.resample_img(fixed_image,
target_affine=new_affine,
interpolation='nearest')
res_shape = np.array(masknii.shape[:3])
# Calculate a bounding box for the input mask
# with an offset of 2 voxels per face
bbox = np.argwhere(masknii.get_data() > 0)
new_origin = np.clip(bbox.min(0) - 2, a_min=0, a_max=None)
new_end = np.clip(bbox.max(0) + 2, a_min=0,
a_max=res_shape - 1)
# Find new origin, and set into new affine
new_affine_4 = resampled.affine.copy()
new_affine_4[:3, 3] = new_affine_4[:3, :3].dot(
new_origin) + new_affine_4[:3, 3]
# Calculate new shapes
new_shape = new_end - new_origin + 1
resampled = nli.resample_img(fixed_image,
target_affine=new_affine_4,
target_shape=new_shape.tolist(),
interpolation='nearest')
xform = resampled.affine # nibabel will pick the best affine
_, qform_code = resampled.header.get_qform(coded=True)
_, sform_code = resampled.header.get_sform(coded=True)
xform_code = sform_code if sform_code > 0 else qform_code
if xform_code == 1:
xform_code = 2
if force_xform_code is not None:
xform_code = force_xform_code
# Keep 0, 2, 3, 4 unchanged
resampled.header.set_qform(xform, int(xform_code))
resampled.header.set_sform(xform, int(xform_code))
resampled.header['descrip'] = 'reference image generated by %s.' % (
message or '(unknown software)')
resampled.to_filename(out_file)
return out_file
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
def plot_mosaic(img, out_file=None, ncols=8, title=None, overlay_mask=None,
bbox_mask_file=None, only_plot_noise=False, annotate=True,
vmin=None, vmax=None, cmap='Greys_r', plot_sagittal=True,
fig=None, zmax=128):
if isinstance(img, (str, bytes)):
nii = nb.as_closest_canonical(nb.load(img))
img_data = nii.get_data()
zooms = nii.header.get_zooms()
else:
img_data = img
zooms = [1.0, 1.0, 1.0]
out_file = 'mosaic.svg'
# Remove extra dimensions
img_data = np.squeeze(img_data)
if img_data.shape[2] > zmax and bbox_mask_file is None:
lowthres = np.percentile(img_data, 5)
mask_file = np.ones_like(img_data)
mask_file[img_data <= lowthres] = 0
img_data = _bbox(img_data, mask_file)
if bbox_mask_file is not None:
bbox_data = nb.as_closest_canonical(
nb.load(bbox_mask_file)).get_data()
img_data = _bbox(img_data, bbox_data)
z_vals = np.array(list(range(0, img_data.shape[2])))
# Reduce the number of slices shown
if len(z_vals) > zmax:
rem = 15
# Crop inferior and posterior
if not bbox_mask_file:
# img_data = img_data[..., rem:-rem]
z_vals = z_vals[rem:-rem]
else:
# img_data = img_data[..., 2 * rem:]
z_vals = z_vals[2 * rem:]
while len(z_vals) > zmax:
# Discard one every two slices
# img_data = img_data[..., ::2]
z_vals = z_vals[::2]
n_images = len(z_vals)
nrows = math.ceil(n_images / ncols)
if plot_sagittal:
nrows += 1
if overlay_mask:
overlay_data = nb.as_closest_canonical(
nb.load(overlay_mask)).get_data()
# create figures
if fig is None:
fig = plt.figure(figsize=(22, nrows * 3))
est_vmin, est_vmax = _get_limits(img_data,
only_plot_noise=only_plot_noise)
if not vmin:
vmin = est_vmin
if not vmax:
vmax = est_vmax
naxis = 1
for z_val in z_vals:
ax = fig.add_subplot(nrows, ncols, naxis)
if overlay_mask:
ax.set_rasterized(True)
plot_slice(img_data[:, :, z_val], vmin=vmin, vmax=vmax,
cmap=cmap, ax=ax, spacing=zooms[:2],
label='%d' % z_val, annotate=annotate)
if overlay_mask:
from matplotlib import cm
msk_cmap = cm.Reds # @UndefinedVariable
msk_cmap._init()
alphas = np.linspace(0, 0.75, msk_cmap.N + 3)
msk_cmap._lut[:, -1] = alphas
plot_slice(overlay_data[:, :, z_val], vmin=0, vmax=1,
cmap=msk_cmap, ax=ax, spacing=zooms[:2])
naxis += 1
if plot_sagittal:
naxis = ncols * (nrows - 1) + 1
step = int(img_data.shape[0] / (ncols + 1))
start = step
stop = img_data.shape[0] - step
if step == 0:
step = 1
for x_val in list(range(start, stop, step))[:ncols]:
ax = fig.add_subplot(nrows, ncols, naxis)
plot_slice(img_data[x_val, ...], vmin=vmin, vmax=vmax,
cmap=cmap, ax=ax, label='%d' % x_val,
spacing=[zooms[0], zooms[2]])
naxis += 1
fig.subplots_adjust(
left=0.05, right=0.95, bottom=0.05, top=0.95, wspace=0.05,
hspace=0.05)
if title:
fig.suptitle(title, fontsize='10')
fig.subplots_adjust(wspace=0.002, hspace=0.002)
if out_file is None:
fname, ext = op.splitext(op.basename(img))
if ext == ".gz":
fname, _ = op.splitext(fname)
out_file = op.abspath(fname + '_mosaic.svg')
fig.savefig(out_file, format='svg', dpi=300, bbox_inches='tight')
return out_file
def buildFunc(self, parFiles):
""" Build a 4D functional image from list of par files
Given a list of `parFiles`, build a 4D functional image from them. For
Philips scanners, there should be a par header file and corresponding
rec image file for each volume in the series. This function will read
each header/image pair and construct a 4D nifti object. The 4D nifti
object contain a voxel array ordered like RAS+ as well the affine
transformation to map between vox and mm space
Parameters
----------
parFiles : list
list containing the file names (file names ONLY, no path) of all
par files to be used in constructing the final nifti image
Returns
-------
funcImage_RAS : Nifti1Image
nifti-1 formated image of the 4D functional data, oriented in
RAS+
See Also
--------
nibabel.nifti1.Nifti1Image()
"""
imageMatrix = None
affine = None
TR = None
### Loop over all of the par files
nVols = len(parFiles)
for par_fname in parFiles:
# build full path to this par file
par_fname = join(self.seriesDir, par_fname)
# make sure there is a corresponding .rec file
if not os.path.isfile(par_fname.replace('.par', '.rec')):
print('No REC file found to match par: {}', par_fname)
### Build the 3d voxel array for this volume and reorder to RAS+
# nibabel will load the par/rec, but there can be multiple images
# (mag, phase, etc...) concatenated into the 4th dimension. Loading
# with the strict_sort option (I think) will make sure the first
# image is the data we want. Extract this data, then reorder the
# voxel array to RAS+
thisVol = nib.load(par_fname, strict_sort=True)
# get the vol index (0-based index) from the acq_nr field of the
# header (1-based index)
volIdx = int(thisVol.header.general_info['acq_nr']) - 1
# set TR
if TR is None:
TR = thisVol.header.general_info['repetition_time'][0]
# convert to RAS+
thisVol_RAS = nib.as_closest_canonical(thisVol)
# construct the imageMatrix if it hasn't been made yet
if imageMatrix is None:
imageMatrix = np.zeros(shape=(thisVol_RAS.shape[0],
thisVol_RAS.shape[1],
thisVol_RAS.shape[2],
nVols), dtype=np.uint16)
# construct the affine if it isn't made yet
if affine is None:
affine = thisVol_RAS.affine
# Add this data to the image matrix
imageMatrix[:, :, :, volIdx] = thisVol_RAS.get_data()[:, :, :, 0].astype('uint16')
### Build a Nifti object
funcImage = nib.Nifti1Image(imageMatrix, affine=affine)
# add the correct TR to the header
pixDims = np.array(funcImage.header.get_zooms())
pixDims[3] = TR
funcImage.header.set_zooms(pixDims)
return funcImage
def _run_interface(self, runtime):
import nibabel as nb
import nilearn.image as nli
from nipype.utils.filemanip import fname_presuffix, copyfile
in_names = self.inputs.t1w_list
orig_imgs = [nb.load(fname) for fname in in_names]
reoriented = [nb.as_closest_canonical(img) for img in orig_imgs]
target_shape = np.max([img.shape for img in reoriented], axis=0)
target_zooms = np.min([img.header.get_zooms()[:3]
for img in reoriented], axis=0)
resampled_imgs = []
for img in reoriented:
zooms = np.array(img.header.get_zooms()[:3])
shape = np.array(img.shape)
xyz_unit = img.header.get_xyzt_units()[0]
if xyz_unit == 'unknown':
# Common assumption; if we're wrong, unlikely to be the only thing that breaks
xyz_unit = 'mm'
# Set a 0.05mm threshold to performing rescaling
atol = {'meter': 5e-5, 'mm': 0.05, 'micron': 50}[xyz_unit]
# Rescale => change zooms
# Resize => update image dimensions
rescale = not np.allclose(zooms, target_zooms, atol=atol)
resize = not np.all(shape == target_shape)
if rescale or resize:
target_affine = np.eye(4, dtype=img.affine.dtype)
if rescale:
scale_factor = target_zooms / zooms
target_affine[:3, :3] = np.diag(scale_factor).dot(img.affine[:3, :3])
else:
target_affine[:3, :3] = img.affine[:3, :3]
if resize:
# The shift is applied after scaling.
# Use a proportional shift to maintain relative position in dataset
size_factor = (target_shape.astype(float) + shape) / (2 * shape)
# Use integer shifts to avoid unnecessary interpolation
offset = (img.affine[:3, 3] * size_factor - img.affine[:3, 3]).astype(int)
target_affine[:3, 3] = img.affine[:3, 3] + offset
else:
target_affine[:3, 3] = img.affine[:3, 3]
data = nli.resample_img(img, target_affine, target_shape).get_data()
img = img.__class__(data, target_affine, img.header)
resampled_imgs.append(img)
out_names = [fname_presuffix(fname, suffix='_ras', newpath=runtime.cwd)
for fname in in_names]
for orig, final, in_name, out_name in zip(orig_imgs, resampled_imgs,
in_names, out_names):
if final is orig:
copyfile(in_name, out_name, copy=True, use_hardlink=True)
else:
final.to_filename(out_name)
self._results['t1w_list'] = out_names
return runtime
def plot_mosaic(nifti_file, title=None, overlay_mask=None,
fig=None, bbox_mask_file=None, only_plot_noise=False,
figsize=DINA4_LANDSCAPE):
from six import string_types
from pylab import cm
if isinstance(nifti_file, string_types):
nii = nb.as_closest_canonical(nb.load(nifti_file))
mean_data = nii.get_data()
else:
mean_data = nifti_file
if bbox_mask_file:
bbox_data = nb.as_closest_canonical(nb.load(bbox_mask_file)).get_data()
B = np.argwhere(bbox_data)
(ystart, xstart, zstart), (ystop, xstop, zstop) = B.min(0), B.max(
0) + 1
mean_data = mean_data[ystart:ystop, xstart:xstop, zstart:zstop]
z_vals = np.array(list(range(0, mean_data.shape[2])))
# Reduce the number of slices shown
if mean_data.shape[2] > 70:
rem = 15
# Crop inferior and posterior
if not bbox_mask_file:
mean_data = mean_data[..., rem:-rem]
z_vals = z_vals[rem:-rem]
else:
mean_data = mean_data[..., 2 * rem:]
z_vals = z_vals[2 * rem:]
if mean_data.shape[2] > 70:
# Discard one every two slices
mean_data = mean_data[..., ::2]
z_vals = z_vals[::2]
n_images = mean_data.shape[2]
row, col = _calc_rows_columns((figsize[0] / figsize[1]), n_images)
if overlay_mask:
overlay_data = nb.as_closest_canonical(
nb.load(overlay_mask)).get_data()
# create figures
if fig is None:
fig = plt.Figure(figsize=figsize)
FigureCanvas(fig)
fig.subplots_adjust(top=0.85)
for image, z_val in enumerate(z_vals):
ax = fig.add_subplot(row, col, image + 1)
data_mask = np.logical_not(np.isnan(mean_data))
if only_plot_noise:
data_mask = np.logical_and(data_mask, mean_data != 0)
if overlay_mask:
ax.set_rasterized(True)
if only_plot_noise:
vmin = np.percentile(mean_data[data_mask], 0)
vmax = np.percentile(mean_data[data_mask], 61)
else:
vmin = np.percentile(mean_data[data_mask], 0.5)
vmax = np.percentile(mean_data[data_mask], 99.5)
ax.imshow(np.fliplr(mean_data[:, :, image].T), vmin=vmin,
vmax=vmax,
cmap=cm.Greys_r, interpolation='nearest', origin='lower')
if overlay_mask:
cmap = cm.Reds # @UndefinedVariable
cmap._init()
alphas = np.linspace(0, 0.75, cmap.N + 3)
cmap._lut[:, -1] = alphas
ax.imshow(np.fliplr(overlay_data[:, :, image].T), vmin=0, vmax=1,
cmap=cmap, interpolation='nearest', origin='lower')
ax.annotate(
str(z_val), xy=(.99, .99), xycoords='axes fraction',
fontsize=8, color='white', horizontalalignment='right',
verticalalignment='top')
ax.axis('off')
fig.subplots_adjust(
left=0.05, right=0.95, bottom=0.05, top=0.95, wspace=0.01, hspace=0.1)
if not title:
_, title = op.split(nifti_file)
title += " (last modified: {})".format(
time.ctime(op.getmtime(nifti_file)))
fig.suptitle(title, fontsize='10')
fig.subplots_adjust(wspace=0.002, hspace=0.002)
return fig