Added (optional) paths to blender & inkscape binaries in config file …

…to make the inkscape / blender dependencies on macos work better.

cortex/blender/__init__.py

@@ -6,10 +6,13 @@
 
 import numpy as np
 
+from .. import options
 from .. import freesurfer
 from .. import dataset
 from .. import utils 
 
+default_blender = options.config.get('dependency_paths', 'blender')
+
 _base_imports = """import sys
 sys.path.insert(0, '{path}')
 import xdrlib
@@ -19,18 +22,18 @@
 from bpy import data as D
 """.format(path=os.path.split(os.path.abspath(__file__))[0])
 
-def _call_blender(filename, code):
+def _call_blender(filename, code, blender_path=default_blender):
     """Call blender, while running the given code. If the filename doesn't exist, save a new file in that location.
     New files will be initially cleared by deleting all objects.
     """
     with tempfile.NamedTemporaryFile() as tf:
         print("In new named temp file: %s"%tf.name)
         startcode=_base_imports
         endcode = "\nbpy.ops.wm.save_mainfile(filepath='{fname}')".format(fname=filename)
-        cmd = "blender -b {fname} -P {tfname}".format(fname=filename, tfname=tf.name)
+        cmd = "{blender_path} -b {fname} -P {tfname}".format(blender_path=blender_path, fname=filename, tfname=tf.name)
         if not os.path.exists(filename):
             startcode += "blendlib.clear_all()\n"
-            cmd = "blender -b -P {tfname}".format(tfname=tf.name)
+            cmd = "{blender_path} -b -P {tfname}".format(blender_path=blender_path, tfname=tf.name)
 
         tf.write((startcode+code+endcode).encode())
         tf.flush()
@@ -131,6 +134,11 @@ def gii_cut(fname, subject, hemi):
 def fs_cut(fname, subject, hemi, freesurfer_subject_dir=None):
     """Cut freesurfer surface using blender interface
 
+    Parameters
+    ----------
+    fname : str
+        file path for new .blend file (must end in ".blend")
+
     if `freesurfer_subject_dir` is None, it defaults to SUBJECTS_DIR environment variable
     """
     wpts, polys, curv = freesurfer.get_surf(subject, hemi, 'smoothwm', freesurfer_subject_dir=freesurfer_subject_dir)

cortex/blender/blendlib.py

@@ -14,7 +14,7 @@ def _repack(linear, n=3):
     For example, _repack([1, 2, 3, 4, 5, 6], n=3) -> [[1, 2, 3], [4, 5, 6]]
     Good for unravelling ravelled data
     """
-    return list(zip(*[iter(linear)]*3))
+    return list(zip(*[iter(linear)] * n))
 
 def clear_all():
     bpy.ops.object.select_all(action='SELECT')
@@ -112,6 +112,7 @@ def write_patch(filename, pts, edges=None):
                 fp.write(struct.pack('>i3f', i+1, *pt))
 
 def save_patch(fname, mesh='hemi'):
+    """Saves patch to file that can be read by pycortex"""
     if isinstance(mesh, str):
         mesh = D.meshes[mesh]
 

cortex/defaults.cfg

@@ -3,6 +3,19 @@ default_cmap = RdBu_r
 default_cmap2D = RdBu_covar
 fsl_prefix = fsl5.0-
 
+[dependency_paths]
+# The following specify paths to the binary executable files
+# for blender and inkscape (which are external dependencies of
+# pycortex). "inkscape" and "blender" alone should work on Linux,
+# since the binaries should already be on the system path.
+# For MacOS, unless you have done some manual configuration on
+# your own, these will need to be something like:
+# blender = /Applications/Blender/blender.app/Contents/MacOS/blender
+# inkscape = /Applications/Inkscape.app/Contents/MacOS/Inkscape
+# Windows is not currently supported.  
+inkscape = inkscape
+blender = blender
+
 [mayavi_aligner]
 line_width = 1
 point_size = 2