Merge pull request #1101 from CHrlS98/cythonization

Cythonization warnings

docs/source/modules/scilpy.tractanalysis.rst

@@ -50,14 +50,6 @@ scilpy.tractanalysis.json\_utils module
    :undoc-members:
    :show-inheritance:
 
-scilpy.tractanalysis.quick\_tools module
-------------------------------------------------------
-
-.. automodule:: scilpy.tractanalysis.quick_tools
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 scilpy.tractanalysis.reproducibility\_measures module
 ------------------------------------------------------
 

scilpy/tractanalysis/streamlines_metrics.pyx

@@ -1,5 +1,5 @@
 # encoding: utf-8
-#cython: profile=False
+# cython: profile=False, language_level=3
 
 # http://www.cse.yorku.ca/~amana/research/grid.pdf
 # http://www.flipcode.com/archives/Raytracing_Topics_Techniques-Part_4_Spatial_Subdivisions.shtml

scilpy/tractanalysis/voxel_boundary_intersection.pyx

@@ -1,5 +1,5 @@
 # encoding: utf-8
-#cython: profile=False
+# cython: profile=False, language_level=3
 
 from libc.math cimport ceil, fabs, floor, sqrt
 from libc.math cimport fmin as cfmin
@@ -27,7 +27,6 @@ cdef struct Pointers:
 
 
 @cython.boundscheck(False)
-@cython.wraparound(False)
 @cython.cdivision(True)
 def subdivide_streamlines_at_voxel_faces(streamlines):
     """
@@ -140,7 +139,6 @@ cdef inline void copypoint_d2f(double * a, float * b) nogil:
 
 
 @cython.boundscheck(False)
-@cython.wraparound(False)
 @cython.cdivision(True)
 cdef cnp.npy_intp _grid_intersections(
         Pointers* pointers,

scilpy/tractograms/streamline_and_mask_operations.py

@@ -13,8 +13,6 @@
 from scilpy.tractograms.streamline_operations import \
     resample_streamlines_step_size
 
-from scilpy.tractanalysis.quick_tools import (get_next_real_point,
-                                              get_previous_real_point)
 from scilpy.tractograms.streamline_operations import \
     filter_streamlines_by_length, _get_point_on_line, _get_streamline_pt_index
 
@@ -596,7 +594,7 @@ def compute_streamline_segment(orig_strl, inter_vox, in_vox_idx, out_vox_idx,
     # If not, find the next real streamline point
     if in_strl_point is None:
         # Find the index of the next real streamline point
-        in_strl_point = get_next_real_point(points_to_indices, in_vox_idx)
+        in_strl_point = np.searchsorted(points_to_indices, in_vox_idx)
         # Generate an artificial point on the line between the previous
         # real point and the next real point
         additional_start_pt = _get_point_on_line(orig_strl[in_strl_point - 1],
@@ -612,8 +610,7 @@ def compute_streamline_segment(orig_strl, inter_vox, in_vox_idx, out_vox_idx,
     # If not, find the previous real streamline point
     if out_strl_point is None:
         # Find the index of the previous real streamline point
-        out_strl_point = get_previous_real_point(points_to_indices,
-                                                 out_vox_idx)
+        out_strl_point = np.searchsorted(points_to_indices, out_vox_idx) - 1
         # Generate an artificial point on the line between the previous
         # real point and the next real point
         additional_exit_pt = _get_point_on_line(orig_strl[out_strl_point],

scilpy/tractograms/uncompress.pyx

@@ -1,6 +1,5 @@
 # encoding: utf-8
-#cython: profile=False
-#cython: language_level=3
+# cython: profile=False, language_level=3
 
 from libc.math cimport ceil, fabs, floor, sqrt
 from libc.math cimport fmin as cfmin
@@ -32,7 +31,6 @@ cdef struct Pointers:
 
 
 @cython.boundscheck(False)
-@cython.wraparound(False)
 @cython.cdivision(True)
 def uncompress(streamlines, return_mapping=False):
     """
@@ -148,7 +146,6 @@ cdef inline void c_get_closest_edge(double *p,
 
 
 @cython.boundscheck(False)
-@cython.wraparound(False)
 @cython.cdivision(True)
 cdef cnp.npy_intp _uncompress(
         Pointers* pointers,

scripts/tests/test_tractogram_cut_streamlines.py

@@ -8,7 +8,8 @@
 from scilpy.io.fetcher import fetch_data, get_testing_files_dict
 
 # If they already exist, this only takes 5 seconds (check md5sum)
-fetch_data(get_testing_files_dict(), keys=['filtering.zip'])
+fetch_data(get_testing_files_dict(),
+           keys=['filtering.zip', 'tractograms.zip', 'connectivity.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
 

setup.py

@@ -16,18 +16,19 @@
 
 
 def get_extensions():
+    define_macros = [('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')]
     uncompress = Extension('scilpy.tractograms.uncompress',
-                           ['scilpy/tractograms/uncompress.pyx'])
-    quick_tools = Extension('scilpy.tractanalysis.quick_tools',
-                            ['scilpy/tractanalysis/quick_tools.pyx'])
+                           ['scilpy/tractograms/uncompress.pyx'],
+                           define_macros=define_macros)
     voxel_boundary_intersection =\
         Extension('scilpy.tractanalysis.voxel_boundary_intersection',
-                  ['scilpy/tractanalysis/voxel_boundary_intersection.pyx'])
+                  ['scilpy/tractanalysis/voxel_boundary_intersection.pyx'],
+                  define_macros=define_macros)
     streamlines_metrics =\
         Extension('scilpy.tractanalysis.streamlines_metrics',
-                  ['scilpy/tractanalysis/streamlines_metrics.pyx'])
-    return [uncompress, quick_tools,
-            voxel_boundary_intersection, streamlines_metrics]
+                  ['scilpy/tractanalysis/streamlines_metrics.pyx'],
+                  define_macros=define_macros)
+    return [uncompress, voxel_boundary_intersection, streamlines_metrics]
 
 
 class CustomBuildExtCommand(build_ext):