Save dicom series is done

medio/backends/itk_io.py

@@ -2,6 +2,7 @@
 import numpy as np
 from pathlib import Path
 from typing import Union
+import uuid
 from medio.metadata.affine import Affine
 from medio.metadata.metadata import MetaData
 from medio.metadata.itk_orientation import itk_orientation_code, codes_str_dict
@@ -83,6 +84,7 @@ def prepare_dcm_image(image_np):
 
  @staticmethod
  def read_img_file(filename, pixel_type=pixel_type, fallback_only=False):
+ """Common pixel types: itk.SS (int16), itk.US (uint16), itk.UC (uint8)"""
  image = itk.imread(filename, pixel_type, fallback_only=fallback_only)
  return image
 
@@ -200,47 +202,52 @@ def read_dcm_dir(dirname, image_type=image_type):
  return itk_img
 
  @staticmethod
- def save_dcm_dir(dirname, image_np, metadata, use_original_ornt=True, dtype='int16'):
+ def save_dcm_dir(dirname, image_np, metadata, use_original_ornt=True, dtype='int16', **kwargs):
  """Save a 3d numpy array image_np as a dicom series of 2d dicom slices in the directory dirname"""
  image = ItkIO.prepare_image(image_np, metadata, use_original_ornt, dtype)
  image_type = type(image)
  _, (pixel_type, _) = itk.template(image)
  image2d_type = itk.Image[pixel_type, 2]
  writer = itk.ImageSeriesWriter[image_type, image2d_type].New()
  make_empty_dir(dirname)
- # the number of slices:
- n = image.GetLargestPossibleRegion().GetSize().GetElement(2)
- filenames = [str(Path(dirname) / f'IM{i}.dcm') for i in range(1, n + 1)]
+ # Generate necessary metadata and filenames per slice:
+ mdict_list, filenames = ItkIO.dcm_metadata(image, dirname, **kwargs)
+ metadict_vec = itk.vector[itk.MetaDataDictionary](mdict_list)
+ writer.SetMetaDataDictionaryArray(metadict_vec)
  writer.SetFileNames(filenames)
- # necessary metadata:
- metadicts = ItkIO.dcm_metadata(image, n)
- # image.SetMetaDataDictionary(mdict)
- # writer.SetMetaDataDictionary(mdict) # shared properties. TODO: add more
- metadict_vec = itk.vector[itk.MetaDataDictionary](metadicts)
- writer.SetMetaDataDictionaryArray(metadict_vec) # TODO: add per slice metadata (position, instance number, ...)
  dicom_io = itk.GDCMImageIO.New()
  dicom_io.KeepOriginalUIDOn()
  writer.SetImageIO(dicom_io)
  writer.SetInput(image)
  writer.Update()
 
  @staticmethod
- def dcm_metadata(image, n):
+ def dcm_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: pattern for the filenames, 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()
 
- # Shared properties for all the slices:
- # TODO: use better UIDs...
  # Series Instance UID
- mdict['0020|000e'] = '1.3.6.1.4.1.5962.99.1.3721201789.257940085.1558499395709.4.0'
+ mdict['0020|000e'] = str(uuid.uuid1())
  # Study Instance UID
- mdict['0020|000d'] = '1.2.826.0.1.3680043.2.1125.1.56230505590330521811301239661751799'
+ mdict['0020|000d'] = str(uuid.uuid1())
 
- # Pixel Spacing
- mdict['0028|0030'] = f'{image.GetSpacing()[0]}\\{image.GetSpacing()[1]}' # TODO: is this tag necessary?
+ # Pixel Spacing - TODO: maybe not necessary? automatically saved
+ mdict['0028|0030'] = f'{image.GetSpacing()[0]}\\{image.GetSpacing()[1]}'
  # Slice Thickness
  mdict['0018|0050'] = str(image.GetSpacing()[2])
- # Spacing Between Slices
- # TODO: duplicate slice thickness
+ # Spacing Between Slices - TODO: it duplicates slice thickness
  mdict['0018|0088'] = str(image.GetSpacing()[2])
  # Image Orientation (Patient)
  orientation_str = '\\'.join([str(image.GetDirection().GetVnlMatrix().get(i, j))
@@ -251,9 +258,17 @@ def dcm_metadata(image, n):
  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
 
- mdict_list = []
  # Per slice properties:
+ mdict_list = []
+ filenames = []
+
  for i in range(n):
  # copy the shared properties dict:
  mdict_i = itk.MetaDataDictionary(mdict)
@@ -265,6 +280,6 @@ def dcm_metadata(image, n):
  mdict_i['0020|0032'] = position_str
 
  mdict_list += [mdict_i]
+ filenames += [str(Path(dirname) / pattern.format(i + 1))]
 
- return mdict_list
-
+ return mdict_list, filenames

medio/read_save.py

@@ -71,6 +71,6 @@ def save_img(filename, np_image, metadata, use_original_ornt=True, backend=None,
  writer(filename, np_image, metadata, use_original_ornt, **kwargs)
 
 
-def save_dir(dirname, np_image, metadata, use_original_ornt=True):
+def save_dir(dirname, np_image, metadata, use_original_ornt=True, **kwargs):
  """Save image as a dicom directory"""
- ItkIO.save_dcm_dir(dirname, np_image, metadata, use_original_ornt)
+ ItkIO.save_dcm_dir(dirname, np_image, metadata, use_original_ornt, **kwargs)