Oct 18, 2018 · Oct 18, 2018 · Oct 19, 2018 · Oct 19, 2018 · Oct 19, 2018 · Oct 19, 2018
diff --git a/nibabel/xmlrec.py b/nibabel/xmlrec.py
                 'Date': str,
                 'Time': str}

 # choose appropriate string length for use within the structured array dtype
 str_length_dict = {'Enumeration': '|S32',
                   'String': '|S128',
                   'Date': '|S16',
                   'Time': '|S16'}

 # for use with parrec.py, the Enumeration strings must be converted to ints
 par_type_dict = copy(xml_type_dict)
 par_type_dict['Enumeration'] = int
        a = e.attrib
        if 'Name' in a:
            entry_type = xml_type_dict[a['Type']]
            if entry_type in ['S16', 'S32', 'S128']:
                entry_type = str
            if 'ArraySize' in a:
                val = [entry_type(i) for i in e.text.strip().split()]
            else:
    if not np.all(['Name' in k.attrib for k in img_keys]):
        raise XMLRECError("Expected each Key attribute to have a Name")

    def _get_type(name, type_dict, str_length_dict=str_length_dict):
        t = type_dict[name]
        if t is str:  # convert from str to a specific length such as |S32
            t = str_length_dict[name]
        return t

    dtype_format = dtype_format.lower()
    if dtype_format == 'xml':
        # xml_type_dict keeps enums as their string representation
        key_attributes = [
            (k.get('Name'), xml_type_dict[k.get('Type')]) for k in img_keys]
            (k.get('Name'), _get_type(k.get('Type'), xml_type_dict))
            for k in img_keys]
    elif dtype_format == 'par':
        # par_type_dict converts enums to int as used in PAR/REC
        key_attributes = [
            (image_def_XML_to_PAR[k.get('Name')], par_type_dict[k.get('Type')])
            (image_def_XML_to_PAR[k.get('Name')],
             _get_type(k.get('Type'), par_type_dict))
            for k in img_keys]
    else:
        raise XMLRECError("dtype_format must be 'par' or 'xml'")
            #     print("enum_type = {}".format(enum_type))
            name = a['Name']
            if dtype_format == 'xml':
                entry_type =xml_type_dict[a['Type']]
                entry_type =_get_type(a['Type'], xml_type_dict)
            else:
                entry_type =par_type_dict[a['Type']]
                entry_type =_get_type(a['Type'], par_type_dict)
                if name in image_def_XML_to_PAR:
                    name = image_def_XML_to_PAR[name]
            if 'ArraySize' in a:
        # image_defs based on conversion of types in composite_PAR_keys
        image_def_dtd = _composite_attributes_xml_to_par(image_def_dtd)

    def _get_val(entry_dtype, text):
        if entry_dtype == '|S16':
            val = text[:16]
        elif entry_dtype == '|S32':
            val = text[:32]
        elif entry_dtype == '|S128':
            val = text[:128]
        else:
            val = entry_dtype(text)
        return val

    image_defs = np.zeros(len(image_defs_array), dtype=image_def_dtd)
    already_warned = []
    for i, image_def in enumerate(image_defs_array):
                        already_warned.append((name, key.text))
            else:
                val = key.text
            image_defs[name][i] = dtype_dict[name](val)
            image_defs[name][i] =_get_val(dtype_dict[name],val)

        # for all image properties we know about
        for element in image_def[1:]:
                                # avoid repeated warnings for this enum
                                already_warned.append((name, text))
                    else:
                        val =entry_dtype(text)
                        val =_get_val(entry_dtype,text)
                if dtype_format == 'par' and name in composite_PAR_keys:
                    # conversion of types in composite_PAR_keys
                    name, vec_index = _get_composite_key_index(name)
Original file line number	Diff line number	Diff line change
Expand Up		@@ -52,6 +52,12 @@ class XMLRECError(Exception):
		'Date': str,
		'Time': str}

		# choose appropriate string length for use within the structured array dtype
		str_length_dict = {'Enumeration': '\|S32',
		'String': '\|S128',
		'Date': '\|S16',
		'Time': '\|S16'}

		# for use with parrec.py, the Enumeration strings must be converted to ints
		par_type_dict = copy(xml_type_dict)
		par_type_dict['Enumeration'] = int
Expand DownExpand Up		@@ -276,6 +282,8 @@ def _process_gen_dict_XML(xml_root):
		a = e.attrib
		if 'Name' in a:
		entry_type = xml_type_dict[a['Type']]
		if entry_type in ['S16', 'S32', 'S128']:
		entry_type = str
		if 'ArraySize' in a:
		val = [entry_type(i) for i in e.text.strip().split()]
		else:
Expand DownExpand Up		@@ -320,15 +328,23 @@ def _get_image_def_attributes(xml_root, dtype_format='xml'):
		if not np.all(['Name' in k.attrib for k in img_keys]):
		raise XMLRECError("Expected each Key attribute to have a Name")

		def _get_type(name, type_dict, str_length_dict=str_length_dict):
		t = type_dict[name]
		if t is str: # convert from str to a specific length such as \|S32
		t = str_length_dict[name]
		return t

		dtype_format = dtype_format.lower()
		if dtype_format == 'xml':
		# xml_type_dict keeps enums as their string representation
		key_attributes = [
		(k.get('Name'), xml_type_dict[k.get('Type')]) for k in img_keys]
		(k.get('Name'), _get_type(k.get('Type'), xml_type_dict))
		for k in img_keys]
		elif dtype_format == 'par':
		# par_type_dict converts enums to int as used in PAR/REC
		key_attributes = [
		(image_def_XML_to_PAR[k.get('Name')], par_type_dict[k.get('Type')])
		(image_def_XML_to_PAR[k.get('Name')],
		_get_type(k.get('Type'), par_type_dict))
		for k in img_keys]
		else:
		raise XMLRECError("dtype_format must be 'par' or 'xml'")
Expand All		@@ -343,9 +359,9 @@ def _get_image_def_attributes(xml_root, dtype_format='xml'):
		# print("enum_type = {}".format(enum_type))
		name = a['Name']
		if dtype_format == 'xml':
		entry_type =xml_type_dict[a['Type']]
		entry_type =_get_type(a['Type'], xml_type_dict)
		else:
		entry_type =par_type_dict[a['Type']]
		entry_type =_get_type(a['Type'], par_type_dict)
		if name in image_def_XML_to_PAR:
		name = image_def_XML_to_PAR[name]
		if 'ArraySize' in a:
Expand DownExpand Up		@@ -477,6 +493,17 @@ def _process_image_lines_xml(xml_root, dtype_format='xml'):
		# image_defs based on conversion of types in composite_PAR_keys
		image_def_dtd = _composite_attributes_xml_to_par(image_def_dtd)

		def _get_val(entry_dtype, text):
		if entry_dtype == '\|S16':
		val = text[:16]
		elif entry_dtype == '\|S32':
		val = text[:32]
		elif entry_dtype == '\|S128':
		val = text[:128]
		else:
		val = entry_dtype(text)
		return val

		image_defs = np.zeros(len(image_defs_array), dtype=image_def_dtd)
		already_warned = []
		for i, image_def in enumerate(image_defs_array):
Expand DownExpand Up		@@ -506,7 +533,7 @@ def _process_image_lines_xml(xml_root, dtype_format='xml'):
		already_warned.append((name, key.text))
		else:
		val = key.text
		image_defs[name][i] = dtype_dict[name](val)
		image_defs[name][i] =_get_val(dtype_dict[name],val)

		# for all image properties we know about
		for element in image_def[1:]:
Expand DownExpand Up		@@ -537,7 +564,7 @@ def _process_image_lines_xml(xml_root, dtype_format='xml'):
		# avoid repeated warnings for this enum
		already_warned.append((name, text))
		else:
		val =entry_dtype(text)
		val =_get_val(entry_dtype,text)
		if dtype_format == 'par' and name in composite_PAR_keys:
		# conversion of types in composite_PAR_keys
		name, vec_index = _get_composite_key_index(name)
Expand Down