forgot a dicom wrapper

Author: jonasteuwen

examples/dicom_wrapper.py

@@ -0,0 +1,37 @@
+# encoding: utf-8
+import SimpleITK as sitk
+import logging
+import dicom
+
+logger = logging.getLogger(__name__)
+
+def read_dicom_series(folder):
+    """Read a folder with DICOM files and outputs a SimpleITK image.
+    Assumes that there is only one DICOM series in the folder.
+
+    Parameters
+    ----------
+    folder : string
+      Full path to folder with dicom files.
+
+    Returns
+    -------
+    SimpleITK image.
+    """
+    reader = sitk.ImageSeriesReader()
+    series_ids = reader.GetGDCMSeriesIDs(folder.encode('ascii'))
+
+    assert len(series_ids) == 1, 'Assuming only one series per folder.'
+
+    filenames = reader.GetGDCMSeriesFileNames(folder, series_ids[0],
+                                              False,  # useSeriesDetails
+                                              False,  # recursive
+                                              True)  # load sequences
+    reader.SetFileNames(filenames)
+    image = reader.Execute()
+
+    logger.info('Read DICOM series from {} ({} files).\nSize: {}\n'
+                'Spacing: {}'.format(folder, len(filenames),
+                                     image.GetSize(), image.GetSpacing()))
+
+    return image

examples/resample_isotropically.py

@@ -1,5 +1,5 @@
 # encoding: utf-8
-"""A an example to read in a image file, and resample the image to a new grid.
+"""An example to read in a image file, and resample the image to a new grid.
 """
 
 import SimpleITK as sitk
@@ -23,7 +23,6 @@
 }
 
 
-
 def resample_sitk_image(sitk_image, spacing=None, interpolator=None,
                         fill_value=0):
     """Resamples an ITK image to a new grid. If no spacing is given,

examples/resample_tests.py

@@ -21,7 +21,7 @@
 import os
 from glob import glob
 import dicom
-from dicom import read_dicom_series
+from dicom_wrapper import read_dicom_series
 from resample_isotropically import resample_sitk_image
 
 import logging