suspect.io.load_twix() to accept binary stream input

suspect/io/dicom.py

@@ -56,7 +56,7 @@ def load_dicom(filename):
 
     # versions of pydicom >2.0.0 require explicit conversion from bytestring to list
     if type(dataset[0x5600, 0x0020].value) == bytes:
-        data_iter = iter(np.fromstring(dataset[0x5600, 0x0020].value, dtype=np.float32))
+        data_iter = iter(np.frombuffer(dataset[0x5600, 0x0020].value, dtype=np.float32))
 
     elif type(dataset[0x5600, 0x0020].value) == list:
         data_iter = iter(dataset[0x5600, 0x0020].value)

suspect/io/twix.py

@@ -1,9 +1,12 @@
+from contextlib import contextmanager
 from suspect import MRSData, transformation_matrix, rotation_matrix
 
 import struct
 import numpy
 #import quaternion
 import re
+import io
+import os
 
 # This file largely relies on information from Siemens regarding the structure
 # of the TWIX file formats. Most of the parameters that are read use the same
@@ -97,10 +100,14 @@ def get_meta_regex(regex_list, header_string, convert=1, default=None):
 
     Parameters
     ----------
-    regex_list : List of regex string
-    header_string : TWIX header string
-    convert : Unit convertion, if value is number. Defaults to 1 (means no convertion)
-    default : Default value if match found, but value is empty. Defaults to None.
+    regex_list : list
+        List of regex string
+    header_string : string
+        TWIX header string
+    convert : int, optional
+        Unit convertion, if value is number. Defaults to 1 (means no convertion)
+    default
+        Default value if match found, but value is empty. Defaults to None.
 
     Returns
     -------
@@ -502,10 +509,33 @@ def load_twix_vd(fin, builder):
         # move the file pointer to the start of the next scan
         fin.seek(initial_position + DMA_length)
 
+def load_twix(source_file, buffering=io.DEFAULT_BUFFER_SIZE):
+    """
+    Load TWIX data. 
 
-def load_twix(filename):
-    with open(filename, 'rb') as fin:
+    Parameters
+    ----------
+    source_file : str or file-like
+        File path of TWIX file
+
+    Returns
+    -------
+    suspect.MRSData
+
+    """
+    @contextmanager
+    def open_if_filepath(file_or_path, mode='r', **kwargs):
+        """Context manager to open a file if argument is string"""
+        if isinstance(file_or_path, (str, os.PathLike)):
+            f = open(file_or_path, mode, **kwargs)
+            try:
+                yield f
+            finally:
+                f.close()
+        else:
+            yield file_or_path
 
+    with open_if_filepath(source_file, 'rb') as fin:
         # we can tell the type of file from the first two uints in the header
         first_uint, second_uint = struct.unpack("II", fin.read(8))
 

tests/test_mrs/test_twix.py

@@ -39,6 +39,10 @@ def test_veriofile():
          [0, 0, 0, 1]]
     ))
 
+    # Test loading via file-like object and ensure same result
+    with open("tests/test_data/siemens/twix_vd.dat", "rb") as f:
+        data_from_binary_stream = suspect.io.load_twix(f)
+        assert numpy.all(data == data_from_binary_stream)
 #def test_skyra():
 #    data = suspect.io.load_twix("tests/test_data/twix_vd_csi.dat")
 #    assert data.np == 2048