Add check for `nodes_0_based'

If not present, the NML is an older 1-based annotation, and each x, y, z
coordinate must be decremented by 1.

treeconvert/__main__.py

@@ -50,12 +50,13 @@
 
 input_file = Path(args.input_file)
 with input_file.open() as f:
-    content = f.read()
-
-nml = nml_to_dict(content, args.from_format == FileFormats.PYKNOSSOS_NML)
+    nml = nml_to_dict(f.read(), args.from_format == FileFormats.PYKNOSSOS_NML)
 
 for i, thing in enumerate(nml['things']):
-    swc = nml_to_swc(nml['things'][i])
+    # <node_0_based /> is an empty tag whose existence determines
+    # whether the coordinates are 0-based. If the tag exists, its value
+    # in <parameters> will be '', otherwise its value is `False'.
+    swc = nml_to_swc(nml['things'][i], nml['parameters']['nodes_0_based'] == '')
 
     if len(nml['things']) == 1:
         output_file = f'{input_file.stem}.swc'

treeconvert/conversion.py

@@ -69,7 +69,7 @@ def nml_to_dict(xml_str: str, is_pyknossos=False) -> dict:
         raise ParseError(str(error))
 
 
-def nml_to_swc(nml: dict) -> SwcData:
+def nml_to_swc(nml: dict, is_zero_based=False) -> SwcData:
     nodes = {node['id']: node for node in nml['nodes']}
     targets = defaultdict(list, {
         target: [edge['source'] for edge in list(edges)]
@@ -92,7 +92,7 @@ def nml_to_swc(nml: dict) -> SwcData:
         first_node = set(nodes).pop()
 
     swc = SwcData()
-    swc.append(Edge.from_nml_entry(nodes[first_node], -1))
+    swc.append(Edge.from_nml_entry(nodes[first_node], -1, is_zero_based))
 
     next_nodes = deque([first_node])
     visited = set()
@@ -105,5 +105,5 @@ def nml_to_swc(nml: dict) -> SwcData:
             if neighbor in visited:
                 continue
             next_nodes.append(neighbor)
-            swc.append(Edge.from_nml_entry(nodes[neighbor], node))
+            swc.append(Edge.from_nml_entry(nodes[neighbor], node, is_zero_based))
     return swc

treeconvert/nml.py

@@ -41,6 +41,7 @@
         declxml.string('.', attribute='path'),
         declxml.integer('.', attribute='overlay')
     ], required=False),
+    declxml.string('nodes_0_based', required=False, default=False)
 ], required=False)
 
 node_processor = declxml.dictionary('node', [

treeconvert/swc.py

@@ -77,13 +77,17 @@ def __str__(self):
         return ' '.join(str(x) for x in vars(self).values())
 
     @classmethod
-    def from_nml_entry(cls, node: dict, parent_id: int):
+    def from_nml_entry(cls, node: dict, parent_id: int, is_zero_based=False):
         # You can dismiss "'IntEnum' object is not callable" because
         # this call gets propagated to `StructureIdentifier_missing_'
         # defined above.
         structure_identifier = StructureIdentifier(node['comment'])
-        return Edge(node['id'], structure_identifier,
-                    node['x'], node['y'], node['z'], node['radius'], parent_id)
+        if is_zero_based:
+            x, y, z = node['x'], node['y'], node['z']
+        else:
+            x, y, z = node['x'] - 1, node['y'] - 1, node['z'] - 1
+        return Edge(node['id'], structure_identifier, x, y, z, node['radius'],
+                    parent_id)
 
 
 class SwcData(collections.abc.MutableSequence):