def embed_nifti(dcmfiles, niftifile, infofile, force=False):
import dcmstack as ds
import nibabel as nb
import os
stack = ds.parse_and_stack(dcmfiles, force=force).values()
if len(stack) > 1:
raise ValueError('Found multiple series')
stack = stack[0]
#Create the nifti image using the data array
if not os.path.exists(niftifile):
nifti_image = stack.to_nifti(embed_meta=True)
nifti_image.to_filename(niftifile)
return ds.NiftiWrapper(nifti_image).meta_ext.to_json()
orig_nii = nb.load(niftifile)
orig_hdr = orig_nii.get_header()
aff = orig_nii.get_affine()
ornt = nb.orientations.io_orientation(aff)
axcodes = nb.orientations.ornt2axcodes(ornt)
new_nii = stack.to_nifti(voxel_order=''.join(axcodes), embed_meta=True)
new_hdr = new_nii.get_header()
#orig_hdr.extensions = new_hdr.extensions
#orig_nii.update_header()
#orig_nii.to_filename(niftifile)
meta = ds.NiftiWrapper(new_nii).meta_ext.to_json()
with open(infofile, 'wt') as fp:
fp.writelines(meta)
return niftifile, infofile
def embed_nifti(dcmfiles, niftifile, infofile, force=False):
import dcmstack as ds
import nibabel as nb
import os
stack = ds.parse_and_stack(dcmfiles, force=force).values()
if len(stack) > 1:
raise ValueError('Found multiple series')
stack = stack[0]
#Create the nifti image using the data array
if not os.path.exists(niftifile):
nifti_image = stack.to_nifti(embed_meta=True)
nifti_image.to_filename(niftifile)
return ds.NiftiWrapper(nifti_image).meta_ext.to_json()
orig_nii = nb.load(niftifile)
orig_hdr = orig_nii.get_header()
aff = orig_nii.get_affine()
ornt = nb.orientations.io_orientation(aff)
axcodes = nb.orientations.ornt2axcodes(ornt)
new_nii = stack.to_nifti(voxel_order=''.join(axcodes), embed_meta=True)
new_hdr = new_nii.get_header()
#orig_hdr.extensions = new_hdr.extensions
#orig_nii.update_header()
#orig_nii.to_filename(niftifile)
meta = ds.NiftiWrapper(new_nii).meta_ext.to_json()
with open(infofile, 'wt') as fp:
fp.writelines(meta)
return niftifile, infofile
def __init__(self, fname):
# A directory containing DICOMs. Convert them to Nifti
print("Converting DICOMS in %s..." % (os.path.basename(fname)))
src_dcms = glob.glob('%s/*' % fname)
nii = None
try:
if HAVE_DCMSTACK:
# Give DCMSTACK a chance to do its thing
stacks = dcmstack.parse_and_stack(src_dcms)
stack = stacks.values()[0]
nii = stack.to_nifti()
except:
warnings.warn("DCMSTACK failed - trying our method")
if nii is None:
# Try our top-secret in-house method
nii = self.fallback_dcmstack(src_dcms)
print("DONE\n")
if len(nii.shape) > 3:
nvols = nii.shape[3]
else:
nvols = 1
grid = DataGrid(nii.shape[:3], nii.header.get_best_affine())
self.dcmdata = nii.get_data()
QpData.__init__(self, fname, grid, nvols, fname=fname)
def dcm_to_nii(dcm, nii_file_name):
try:
stacks = dcmstack.parse_and_stack(dcm)
for stack in stacks.itervalues():
nii = stack.to_nifti()
nii.to_filename(nii_file_name)
break
except:
print 'dcmstack DICOM to NIFTI failed.'
def dcm_to_nii(dcm, nii_file_name):
try:
stacks = dcmstack.parse_and_stack(dcm)
for stack in stacks.itervalues():
nii = stack.to_nifti()
nii.to_filename(nii_file_name)
break
except:
print 'dcmstack DICOM to NIFTI failed.'
def import_dicom(search_path, extension='IMA'):
import dcmstack
from glob import glob
search_string = search_path + '/*.' + extension
src_paths = glob(search_string)
stacks = dcmstack.parse_and_stack(src_paths)
images = []
for key in stacks.keys():
stack = stacks[key]
image = nifti_to_occiput(stack.to_nifti())
images.append(image)
return images
def import_dicom(search_path, extension='IMA'):
import dcmstack
from glob import glob
search_string = search_path + '/*.' + extension
src_paths = glob(search_string)
stacks = dcmstack.parse_and_stack(src_paths)
images = []
for key in stacks.keys():
stack = stacks[key]
image = nifti_to_occiput(stack.to_nifti())
images.append(image)
return images
def import_dicom(search_path, extension='IMA'):
if(not dcmstack_available):
raise ("Pleast install dcmstack from https://github.com/moloney/dcmstack/tags")
else:
search_string = search_path + '/*.' + extension
src_paths = glob(search_string)
stacks = dcmstack.parse_and_stack(src_paths)
images = []
for key in stacks.keys():
stack = stacks[key]
image = nifti_to_occiput(stack.to_nifti())
images.append(image)
return images
def test_default(self):
res = dcmstack.parse_and_stack(self.in_paths)
eq_(len(res), 1)
ds = pydicom.read_file(self.in_paths[0])
group_key = list(res.keys())[0]
for attr_idx, attr in enumerate(dcmstack.default_group_keys):
if attr in dcmstack.default_close_keys:
ok_(np.allclose(group_key[attr_idx], getattr(ds, attr)))
else:
eq_(group_key[attr_idx], getattr(ds, attr))
stack = list(res.values())[0]
ok_(isinstance(stack, dcmstack.DicomStack))
stack_data = stack.get_data()
eq_(stack_data.ndim, 4)
def test_default(self):
res = dcmstack.parse_and_stack(self.in_paths)
eq_(len(res), 1)
ds = pydicom.read_file(self.in_paths[0])
group_key = list(res.keys())[0]
for attr_idx, attr in enumerate(dcmstack.default_group_keys):
if attr in dcmstack.default_close_keys:
ok_(np.allclose(group_key[attr_idx], getattr(ds, attr)))
else:
eq_(group_key[attr_idx], getattr(ds, attr))
stack = list(res.values())[0]
ok_(isinstance(stack, dcmstack.DicomStack))
stack_data = stack.get_data()
eq_(stack_data.ndim, 4)
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
stacks = dcmstack.parse_and_stack(src_paths)
self.out_list = []
for key, stack in stacks.iteritems():
nw = NiftiWrapper(stack.to_nifti(embed_meta=True))
const_meta = nw.meta_ext.get_class_dict(('global', 'const'))
out_path = self._get_out_path(const_meta)
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nw.nii_img, out_path)
self.out_list.append(out_path)
return runtime
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
stacks = dcmstack.parse_and_stack(src_paths)
self.out_list = []
for key, stack in list(stacks.items()):
nw = NiftiWrapper(stack.to_nifti(embed_meta=True))
const_meta = nw.meta_ext.get_class_dict(("global", "const"))
out_path = self._get_out_path(const_meta)
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nw.nii_img, out_path)
self.out_list.append(out_path)
return runtime
def load_dicom_old(search_path, extension='IMA'):
progress_bar = ProgressBar(title='Reading src')
progress_bar.set_percentage(0.1)
if (not dcmstack_available):
progress_bar.set_percentage(100.0)
raise Exception("Pleast install dcmstack from https://github.com/moloney/dcmstack/tags")
else:
search_string = search_path + '/*.' + extension
src_paths = glob(search_string)
stacks = dcmstack.parse_and_stack(src_paths)
images = []
for k, key in enumerate(stacks.keys()):
stack = stacks[key]
img = nipy2occiput(stack.to_nifti(embed_meta=True))
images.append(img)
progress_bar.set_percentage((k + 1) * 100.0 / len(stacks.keys()))
progress_bar.set_percentage(100.0)
return images
def get_dicom_info(dicom_dir, dest):
"""Return a freesurfer style dicom info generator
"""
fl = sorted(glob(os.path.join(dicom_dir, '*.dcm')))
stack = parse_and_stack(fl, force=True, warn_on_except=True)
info = {}
for key in sorted(stack):
key_fields = key.split('-')
idx = int(key_fields[0])
name = key_fields[1]
stack_object = stack[key]
if not stack_object.error:
size = list(stack_object.get_shape())
if len(size) == 3:
size.append(1)
err_status = 'ok'
out_fn = sanitize_path_comp(key) + '.nii.gz'
out_path = os.path.join(dest, out_fn)
nii = stack_object.to_nifti(embed_meta=True)
nii_wrp = NiftiWrapper(nii)
meta_fn = out_fn + '.json'
meta_path = os.path.join(dest, meta_fn)
with open(meta_path, 'w') as fp:
fp.write(nii_wrp.meta_ext.to_json())
nii.to_filename(out_path)
else:
size = [0, 0, 0, 0]
err_status = 'err'
out_fn = None
meta_fn = None
filepath = out_fn
filename = stack_object._files_info[0][2]
info[idx] = dict(idx=idx,
name=name,
err_status=err_status,
size=size,
filename=filename,
filepath=filepath,
metapath=meta_fn)
size = [str(val) for val in size]
print '\t'.join([str(idx), name, err_status] + size + [filename])
return info
def get_dicom_info(dicom_dir, dest):
"""Return a freesurfer style dicom info generator
"""
fl = sorted(glob(os.path.join(dicom_dir, '*.dcm')))
stack = parse_and_stack(fl, force=True, warn_on_except=True)
info = {}
for key in sorted(stack):
key_fields = key.split('-')
idx = int(key_fields[0])
name = key_fields[1]
stack_object = stack[key]
if not stack_object.error:
size = list(stack_object.get_shape())
if len(size) == 3:
size.append(1)
err_status = 'ok'
out_fn = sanitize_path_comp(key) + '.nii.gz'
out_path = os.path.join(dest, out_fn)
nii = stack_object.to_nifti(embed_meta=True)
nii_wrp = NiftiWrapper(nii)
meta_fn = out_fn + '.json'
meta_path = os.path.join(dest, meta_fn)
with open(meta_path, 'w') as fp:
fp.write(nii_wrp.meta_ext.to_json())
nii.to_filename(out_path)
else:
size = [0, 0, 0, 0]
err_status = 'err'
out_fn = None
meta_fn = None
filepath = out_fn
filename = stack_object._files_info[0][2]
info[idx] = dict(idx=idx, name=name, err_status=err_status,
size=size, filename=filename,
filepath=filepath,
metapath=meta_fn)
size = [str(val) for val in size]
print '\t'.join([str(idx), name, err_status] + size + [filename])
return info
"""
import os
os.chdir('/Users/m131199/Downloads/LGG-229/MRI_Hd/axial_T1/')
from nipype.interfaces.dcmstack import DcmStack
stacker = DcmStack()
stacker.inputs.dicom_files = '/Users/m131199/Downloads/LGG-229/MRI_Hd/axial_T1/'
stacker.run()
#result.outputs.out_file
import dcmstack
from glob import glob
src_dcms = glob('/Users/m131199/Downloads/LGG-229/MRI_Hd/axial_T1/*.dcm')
stacks = dcmstack.parse_and_stack(src_dcms)
stack = stacks.values[0]
nii = stack.to_nifti()
nii.to_filename('output.nii.gz')
#import os
#os.chdir('/Users/m131199/Downloads/LGG-229/MRI_Hd/AX_T2_OBL/')
#from nipype.interfaces.freesurfer import DICOMConvert
#cvt = DICOMConvert()
#cvt.inputs.dicom_dir = '/Users/m131199/Downloads/LGG-229/MRI_Hd/AX_T2_OBL/'
#cvt.inputs.file_mapping = [('nifti', '*.nii'), ('info', 'dicom*.txt'), ('dti', '*dti.bv*')]
#
#from nipype.interfaces.dcm2nii import Dcm2nii
#converter = Dcm2nii()
#converter.inputs.source_names = ['/Users/m131199/Downloads/LGG-229/MRI_Hd/AX_T2_OBL/9999.193444720349620986809184775663710556976.dcm']
#converter.inputs.gzip_output = True
def embed_nifti(dcmfiles, niftifile, infofile, bids_info, force, min_meta):
"""
If `niftifile` doesn't exist, it gets created out of the `dcmfiles` stack,
and json representation of its meta_ext is returned (bug since should return
both niftifile and infofile?)
if `niftifile` exists, its affine's orientation information is used while
establishing new `NiftiImage` out of dicom stack and together with `bids_info`
(if provided) is dumped into json `infofile`
Parameters
----------
dcmfiles
niftifile
infofile
bids_info
force
min_meta
Returns
-------
niftifile, infofile
"""
# imports for nipype
import nibabel as nb
import os
import os.path as op
import json
import re
if not min_meta:
import dcmstack as ds
stack = ds.parse_and_stack(dcmfiles, force=force).values()
if len(stack) > 1:
raise ValueError('Found multiple series')
stack = stack[0]
#Create the nifti image using the data array
if not op.exists(niftifile):
nifti_image = stack.to_nifti(embed_meta=True)
nifti_image.to_filename(niftifile)
return ds.NiftiWrapper(nifti_image).meta_ext.to_json()
orig_nii = nb.load(niftifile)
aff = orig_nii.affine
ornt = nb.orientations.io_orientation(aff)
axcodes = nb.orientations.ornt2axcodes(ornt)
new_nii = stack.to_nifti(voxel_order=''.join(axcodes), embed_meta=True)
meta = ds.NiftiWrapper(new_nii).meta_ext.to_json()
meta_info = None if min_meta else json.loads(meta)
if bids_info:
if min_meta:
meta_info = bids_info
else:
# make nice with python 3 - same behavior?
meta_info = meta_info.copy()
meta_info.update(bids_info)
# meta_info = dict(meta_info.items() + bids_info.items())
try:
meta_info['TaskName'] = (re.search(
'(?<=_task-)\w+',
op.basename(infofile)).group(0).split('_')[0])
except AttributeError:
pass
# write to outfile
with open(infofile, 'wt') as fp:
json.dump(meta_info, fp, indent=3, sort_keys=True)
return niftifile, infofile
import dcmstack
from glob import glob
src_paths = glob(
'/media/gregory/Acer2/Users/grego/Documents/CNI/CNI_BOSTON_DATA/WOLFSON_SUBSET_REDUCED2/sub-005/ses-4yr/Rest210_2/*.dcm'
)
stacks = dcmstack.parse_and_stack(src_paths, force=True)
