ENH: Add parser for Siemens "ASCCONV" text format

Author: moloney

nibabel/nicom/ascconv.py

@@ -0,0 +1,207 @@
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""
+Parse the "ASCCONV" meta data format found in a variety of Siemens MR files.
+"""
+import re
+import ast
+from ..externals import OrderedDict
+
+
+ASCCONV_RE = re.compile(
+    r'### ASCCONV BEGIN((?:\s*[^=\s]+=[^=\s]+)*) ###\n(.*?)\n### ASCCONV END ###',
+    flags=re.M | re.S)
+
+
+class AscconvParseError(Exception):
+    """ Error parsing ascconv file """
+
+
+class Atom(object):
+    """ Object to hold operation, object type and object identifier
+
+    An atom represents an element in an expression.  For example::
+
+        a.b[0].c
+
+    has four elements.  We call these elements "atoms".
+
+    We represent objects (like ``a``) as dicts for convenience.
+
+    The last element (``.c``) is an ``op = ast.Attribute`` operation where the
+    object type (`obj_type`) of ``c`` is not constrained (we can't tell from
+    the operation what type it is).  The `obj_id` is the name of the object --
+    "c".
+
+    The second to last element ``[0]``, is ``op = ast.Subscript``, with object type
+    dict (we know from the subsequent operation ``.c`` that this must be an
+    object, we represent the object by a dict).  The `obj_id` is the index 0.
+
+    Parameters
+    ----------
+    op : {'name', 'attr', 'list'}
+        Assignment type.  Assignment to name (root namespace), attribute or
+        list element.
+    obj_type : {list, dict, other}
+        Object type being assigned to.
+    obj_id : str or int
+        Key (``obj_type is dict``) or index (``obj_type is list``)
+    """
+
+    def __init__(self, op, obj_type, obj_id):
+        self.op = op
+        self.obj_type = obj_type
+        self.obj_id = obj_id
+
+
+class NoValue(object):
+    """ Signals no value present """
+
+
+def assign2atoms(assign_ast, default_class=int):
+    """ Parse single assignment ast from ascconv line into atoms
+
+    Parameters
+    ----------
+    assign_ast : assignment statement ast
+        ast derived from single line of ascconv file.
+    default_class : class, optional
+        Class that will create an object where we cannot yet know the object
+        type in the assignment.
+
+    Returns
+    -------
+    atoms : list
+        List of :class:`atoms`.  See docstring for :class:`atoms`.  Defines
+        left to right sequence of assignment in `line_ast`.
+    """
+    if not len(assign_ast.targets) == 1:
+        raise AscconvParseError('Too many targets in assign')
+    target = assign_ast.targets[0]
+    atoms = []
+    prev_target_type = default_class  # Placeholder for any scalar value
+    while True:
+        if isinstance(target, ast.Name):
+            atoms.append(Atom(target, prev_target_type, target.id))
+            break
+        if isinstance(target, ast.Attribute):
+            atoms.append(Atom(target, prev_target_type, target.attr))
+            target = target.value
+            prev_target_type = OrderedDict
+        elif isinstance(target, ast.Subscript):
+            index = target.slice.value.n
+            atoms.append(Atom(target, prev_target_type, index))
+            target = target.value
+            prev_target_type = list
+        else:
+            raise AscconvParseError(
+                'Unexpected LHS element {0}'.format(target))
+    return reversed(atoms)
+
+
+def _create_obj_in(atom, root):
+    """ Create object defined in `atom` in dict-like given by `root`
+
+    Return defined object.
+    """
+    name = atom.obj_id
+    obj = root.get(name, NoValue)
+    if obj is not NoValue:
+        return obj
+    obj = atom.obj_type()
+    root[name] = obj
+    return obj
+
+
+def _create_subscript_in(atom, root):
+    """ Create object defined in `atom` at index ``atom.obj_id`` in list `root`
+
+    Return defined object.
+    """
+    curr_n = len(root)
+    index = atom.obj_id
+    if curr_n > index:
+        return root[index]
+    obj = atom.obj_type()
+    root += [None] * (index - curr_n) + [obj]
+    return obj
+
+
+def obj_from_atoms(atoms, namespace):
+    """ Return object defined by list `atoms` in dict-like `namespace`
+
+    Parameters
+    ----------
+    atoms : list
+        List of :class:`atoms`
+    namespace : dict-like
+        Namespace in which object will be defined.
+
+    Returns
+    -------
+    obj_root : object
+        Namespace such that we can set a desired value to the object defined in
+        `atoms` with ``obj_root[obj_key] = value``.
+    obj_key : str or int
+        Index into list or key into dictionary for `obj_root`.
+    """
+    root_obj = namespace
+    for el in atoms:
+        prev_root = root_obj
+        if isinstance(el.op, (ast.Attribute, ast.Name)):
+            root_obj = _create_obj_in(el, root_obj)
+        else:
+            root_obj = _create_subscript_in(el, root_obj)
+        if not isinstance(root_obj, el.obj_type):
+            raise AscconvParseError(
+                'Unexpected type for {0} in {1}'.format(el.obj_id, prev_root))
+    return prev_root, el.obj_id
+
+
+def _get_value(assign):
+    value = assign.value
+    if isinstance(value, ast.Num):
+        return value.n
+    if isinstance(value, ast.Str):
+        return value.s
+    if isinstance(value, ast.UnaryOp) and isinstance(value.op, ast.USub):
+        return -value.operand.n
+    raise AscconvParseError('Unexpected RHS of assignment: {0}'.format(value))
+
+
+def parse_ascconv(ascconv_str, str_delim='"'):
+    '''Parse the 'ASCCONV' format from `input_str`.
+
+    Parameters
+    ----------
+    ascconv_str : str
+        The string we are parsing
+    str_delim : str, optional
+        String delimiter.  Typically '"' or '""'
+
+    Returns
+    -------
+    prot_dict : OrderedDict
+        Meta data pulled from the ASCCONV section.
+    attrs : OrderedDict
+        Any attributes stored in the 'ASCCONV BEGIN' line
+
+    Raises
+    ------
+    AsconvParseError
+        A line of the ASCCONV section could not be parsed.
+    '''
+    attrs, content = ASCCONV_RE.match(ascconv_str).groups()
+    attrs = OrderedDict((tuple(x.split('=')) for x in attrs.split()))
+    # Normalize string start / end markers to something Python understands
+    content = content.replace(str_delim, '"""')
+    # Use Python's own parser to parse modified ASCCONV assignments
+    tree = ast.parse(content)
+
+    prot_dict = OrderedDict()
+    for assign in tree.body:
+        atoms = assign2atoms(assign)
+        obj_to_index, key = obj_from_atoms(atoms, prot_dict)
+        obj_to_index[key] = _get_value(assign)
+
+    return prot_dict, attrs