def Volume3DToDicom(imgObj, MetadataObj = None, outdir = "", format_templ = "%03d.dcm"):
format_templ = os.path.join(outdir, format_templ)
entire_region = imgObj.GetLargestPossibleRegion()
fngen = itk.NumericSeriesFileNames.New()
fngen.SetSeriesFormat(format_templ)
fngen.SetStartIndex( entire_region.GetIndex()[2] )
fngen.SetEndIndex( entire_region.GetIndex()[2] + entire_region.GetSize()[2] - 1 )
fngen.SetIncrementIndex(1)
if not MetadataObj is None:
metadata_array_copy = itk.vector.itkMetaDataDictionary()
# I had to create a set of metadata to avoid pointers issues
metadata_list_objs = [ itk.MetaDataDictionary() for metadata_list in MetadataObj ]
for metadata_list, temp_metadata in zip(MetadataObj, metadata_list_objs):
for k,v in metadata_list.items():
temp_metadata[k] = v
metadata_array_copy.append(temp_metadata)
s,d = itk.template(imgObj)[1]
dicom_io = itk.GDCMImageIO.New()
writer_type = itk.Image[s,d]
writer_otype = itk.Image[s,d-1]
writer = itk.ImageSeriesWriter[writer_type, writer_otype].New()
writer.SetInput(imgObj)
writer.SetImageIO(dicom_io)
writer.SetFileNames(fngen.GetFileNames())
if not MetadataObj is None:
writer.SetMetaDataDictionaryArray(metadata_array_copy)
writer.Update()
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# ==========================================================================*/
import itk
md = itk.MetaDataDictionary()
# one way of setting and retrieving double value in the dictionary
dv = itk.MetaDataObject.D.New()
dv.SetMetaDataObjectValue(10.0)
md.Set("double", dv)
print(md.Get("double"))
# other way of setting and retrieving double value (leverages Python's
# weak type system)
md["double"] = 10.0
print(md["double"])
# Required for "NRRD_measurement frame"
itk.MetaDataObject[itk.vector[itk.vector[itk.D]]].New()
def dcm_series_metadata(image,
dirname,
pattern='IM{}.dcm',
metadata_dict=None):
"""
Return dicom series metadata per slice and filenames
:param image: the full itk image to be saved as dicom series
:param dirname: the directory name
:param pattern: str pattern for the filenames to save, including a placeholder ('{}') for the slice number
:param metadata_dict: dictionary of metadata for adding tags or overriding the default values. For example,
metadata_dict={'0008|0060': 'US'} will override the default 'CT' modality and set it to 'US' (ultrasound)
:return: metadata dictionaries per slice, slice filenames
"""
# The number of slices
n = image.GetLargestPossibleRegion().GetSize().GetElement(2)
# Shared properties for all the n slices:
mdict = itk.MetaDataDictionary()
# Series Instance UID
mdict['0020|000e'] = generate_uid()
# Study Instance UID
mdict['0020|000d'] = generate_uid()
# Pixel Spacing - TODO: not necessary - automatically saved
spacing = image.GetSpacing()
mdict['0028|0030'] = f'{spacing[0]}\\{spacing[1]}'
# Spacing Between Slices
mdict['0018|0088'] = str(spacing[2])
# Image Orientation (Patient)
orientation_str = '\\'.join([
str(image.GetDirection().GetVnlMatrix().get(i, j))
for j in range(2) for i in range(3)
])
mdict['0020|0037'] = orientation_str
# Number of Frames
mdict['0028|0008'] = '1'
# Number of Slices
mdict['0054|0081'] = str(n)
# Modality
mdict['0008|0060'] = 'CT'
if metadata_dict is not None:
for key, val in metadata_dict.items():
mdict[key] = val
# Per slice properties:
mdict_list = []
filenames = []
for i in range(n):
# copy the shared properties dict:
mdict_i = itk.MetaDataDictionary(mdict)
# Instance Number
mdict_i['0020|0013'] = str(i + 1)
# Image Position (Patient)
position = image.TransformIndexToPhysicalPoint([0, 0, i])
position_str = '\\'.join([str(position[i]) for i in range(3)])
mdict_i['0020|0032'] = position_str
mdict_list += [mdict_i]
filenames += [str(Path(dirname) / pattern.format(i + 1))]
return mdict_list, filenames
