From de28d6e7802518760155d7b70fbc8d40bc36115d Mon Sep 17 00:00:00 2001
From: Philipp Schlegel <observing@web.de>
Date: Fri, 16 Oct 2020 10:32:03 +0100
Subject: [PATCH] in_volume: allow using any mesh-like objects

---
 navis/intersection/intersect.py | 16 +++++++++++-----
 navis/utils/__init__.py         |  2 +-
 navis/utils/misc.py             | 24 ++++++++++++++++++++----
 3 files changed, 32 insertions(+), 10 deletions(-)

diff --git a/navis/intersection/intersect.py b/navis/intersection/intersect.py
index e484cbcf..e5500e12 100644
--- a/navis/intersection/intersect.py
+++ b/navis/intersection/intersect.py
@@ -161,9 +161,9 @@ def in_volume(x: Union['core.NeuronObject', Sequence, pd.DataFrame],
                         - ``pandas.DataFrame`` needs to have ``x, y, z``
                           columns
 
-    volume :            navis.Volume | dict or list of navis.Volume
-                        :class:`navis.Volume` to test. Multiple volumes can
-                        be given as list (``[volume1, volume2, ...]``) or dict
+    volume :            navis.Volume | navis.MeshNeuron | any mesh-like object
+                        Multiple volumes can be given as list
+                        (``[volume1, volume2, ...]``) or dict
                         (``{'label1': volume1, ...}``).
     mode :              'IN' | 'OUT', optional
                         If 'IN', parts of the neuron that are within the volume
@@ -242,14 +242,17 @@ def in_volume(x: Union['core.NeuronObject', Sequence, pd.DataFrame],
         # Force into dict
         if not isinstance(volume, dict):
             # Make sure all Volumes can be uniquely indexed
-            vnames = [v.name for v in volume if isinstance(v, core.Volume)]
+            vnames = [getattr(v, 'name', i) for i, v in enumerate(volume)]
             dupli = [v for v in set(vnames) if vnames.count(v) > 1]
             if dupli:
                 raise ValueError('Duplicate Volume names detected: '
                                  f'{",".join(dupli)}. Volume.name must be '
                                  'unique.')
 
-            volume = {v.name: v for v in volume if isinstance(v, core.Volume)}
+            volume = {getattr(v, 'name', i): v for i, v in enumerate(volume)}
+
+        # Make sure everything is a volume
+        volume = {k: utils.make_volume(v) for k, v in enumerate(volume)}
 
         # Validate now - this might safe us troubles later
         if validate:
@@ -278,6 +281,9 @@ def in_volume(x: Union['core.NeuronObject', Sequence, pd.DataFrame],
                                 backend=backend)
         return data
 
+    # Coerce volume into navis.Volume
+    volume = utils.make_volume(volume)
+
     if not isinstance(volume, core.Volume):
         raise TypeError(f'Expected navis.Volume, got "{type(volume)}"')
 
diff --git a/navis/utils/__init__.py b/navis/utils/__init__.py
index 551db6fb..423883cc 100644
--- a/navis/utils/__init__.py
+++ b/navis/utils/__init__.py
@@ -1,7 +1,7 @@
 from .iterables import make_iterable, make_non_iterable, is_iterable
 from .misc import (is_jupyter, set_loggers, set_pbars, unpack_neurons,
                    set_default_connector_colors, parse_objects,
-                   is_url, make_url, lock_neuron)
+                   is_url, make_url, lock_neuron, make_volume)
 from .validate import validate_options, validate_table
 from .eval import (eval_node_ids, eval_neurons, eval_id, eval_conditions,
                    is_mesh)
diff --git a/navis/utils/misc.py b/navis/utils/misc.py
index 2325eb34..c3a764fa 100644
--- a/navis/utils/misc.py
+++ b/navis/utils/misc.py
@@ -11,13 +11,15 @@
 #    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #    GNU General Public License for more details.
 
-import pandas as pd
-import numpy as np
 import requests
 import urllib
 
+import numpy as np
+import pandas as pd
+import trimesh as tm
+
 from functools import wraps
-from typing import Optional, Union, List, Iterable, Dict, Tuple
+from typing import Optional, Union, List, Iterable, Dict, Tuple, Any
 
 from .. import config, core
 from .eval import is_mesh
@@ -26,6 +28,20 @@
 logger = config.logger
 
 
+def make_volume(x: Any) -> 'core.Volume':
+    """Try making a navis.Volume from input object."""
+    if isinstance(x, core.Volume):
+        return x
+    if is_mesh(x):
+        inits = dict(vertices=x.vertices, faces=x.faces)
+        for p in ['name', 'id', 'color']:
+            if hasattr(x, p):
+                inits[p] = getattr(x, p, None)
+        return core.Volume(**inits)
+
+    raise TypeError(f'Unable to coerce input of type "{type(x)}" to navis.Volume')
+
+
 def lock_neuron(function):
     """Lock neuron while function is executed.
 
@@ -237,7 +253,7 @@ def parse_objects(x) -> Tuple['core.NeuronList',
     -------
     Neurons :       navis.NeuronList
     Dotprops :      pd.DataFrame
-    Volume :        list of navis.Volume
+    Volume :        list of navis.Volume (trimesh.Trimesh will be converted)
     Points :        list of arrays
     Visuals :       list of vispy visuals