Merge pull request #61 from jjhelmus/nmrml

Initial support for reading nmrML files

doc/source/reference/index.rst

@@ -14,6 +14,7 @@ fileio modules
     bruker
     convert
     fileiobase
+    nmrml
     pipe
     rnmrtk
     simpson

doc/source/reference/nmrml.rst

@@ -0,0 +1,32 @@
+.. _nmrml_module:
+
+nmrglue.nmrml
+=============
+
+.. automodule:: nmrglue.fileio.nmrml
+
+This modules is imported as nmrglue.nmrml and can be called as such.
+
+User Information
+----------------
+
+User Functions
+^^^^^^^^^^^^^^
+
+.. autosummary::
+    :toctree: generated/
+
+    read
+
+Developer Infomation
+--------------------
+
+Developer Functions
+^^^^^^^^^^^^^^^^^^^
+
+These functions are typically not used directly by users.
+
+.. autosummary::
+    :toctree: generated/
+
+    _get_nmrml_data

nmrglue/fileio/__init__.py

@@ -1,6 +1,6 @@
 from . import bruker
 from . import convert
-# from . import glue
+from . import nmrml
 from . import pipe
 from . import rnmrtk
 from . import simpson

nmrglue/fileio/nmrml.py

@@ -0,0 +1,76 @@
+"""
+Functions for reading `nmrML <http://nmrml.org/>`_ files.
+"""
+
+import base64
+import zlib
+from warnings import warn
+
+import numpy as np
+
+
+def read(filename, data_dtype=None):
+    """
+    Read a nmrML file.
+
+    Parameters
+    ----------
+    filename : str
+        Name of nmrML file to read.
+    data_dtype : str, optional
+        NumPy data type of the data. None, the default, will determine this
+        data type from the infomation in the file. Occasionally this
+        information is incorrect and this argument can be used to explicitly
+        supply this information.
+
+    Returns
+    -------
+    dic : dict
+        Dictionary of spectra parameters.
+    data : ndarray, 1D
+        Array of spectral data.
+
+    """
+    import xmltodict  # delay import so that xmltodict is optional
+    with open(filename, 'rb') as nmrml_file:
+        doc = xmltodict.parse(nmrml_file.read())
+
+    fid_dict = doc['nmrML']['acquisition']['acquisition1D']['fidData']
+    data = _get_nmrml_data(fid_dict, data_dtype)
+
+    dic = doc['nmrML']
+    return dic, data
+
+
+BYTE_FORMAT_TO_DTYPE = {
+    'float32': '<f4',
+    'float64': '<f8',
+    'complex64': '<c8',
+    'complex128': '<c16',
+}
+
+
+def _get_nmrml_data(fid_dict, data_dtype):
+    """ Return a NumPy array for spectral data in a nmrML data file. """
+    # read required parameters from dictionary
+    byte_format = fid_dict['@byteFormat'].lower()
+    compressed = fid_dict['@compressed'].lower() == 'true'
+    encoded_length = int(fid_dict['@encodedLength'])
+    base64_text = fid_dict['#text']
+    if len(base64_text) != encoded_length:
+        warn("Size of encoded text (%i) does not match stated length (%i)"
+             % (len(base64_text), encoded_length))
+
+    # decode and uncompress
+    compressed_bytes = base64.b64decode(base64_text)
+    if compressed:
+        uncompressed_bytes = zlib.decompress(compressed_bytes)
+    else:
+        uncompressed_bytes = compressed_bytes
+
+    # convert to ndarray
+    if data_dtype is None:
+        data_dtype = BYTE_FORMAT_TO_DTYPE[byte_format]
+    data = np.fromstring(uncompressed_bytes, dtype=data_dtype)
+
+    return data