some optimizations

smparker · Jan 14, 2024 · 3593096 · 3593096
1 parent 6646b56
commit 3593096
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Showing 4 changed files with 8 additions and 11 deletions.
diff --git a/.github/workflows/blender-plugin.yml b/.github/workflows/blender-plugin.yml
@@ -41,7 +41,7 @@ jobs:
       run: |
         mkdir -p ${HOME}/.config/blender/${BLENDER_MAJOR_VERSION}/scripts/addons
         python setup.py build
-        python setup.py install --mode copy
+        python setup.py install
     - name: Test Blender
       run: |
         bash run_test.sh -b blender-${BLENDER_VERSION}-linux-x64/blender
diff --git a/molecular_blender/isosurfaces.py b/molecular_blender/isosurfaces.py
@@ -21,8 +21,8 @@ def transform_triangles(triangles, origin, axes):
     if not triangles:
         return triangles
     coords = np.array(triangles, dtype=DTYPE)
-    out = np.dot(coords, axes)
-    return [out[i, :] + origin for i in range(coords.shape[0])]
+    out = np.dot(coords, axes) + origin
+    return [ out[i,:] for i in range(out.shape[0]) ]
 
 
 def cube_isosurface(data, origin, axes, isovalues, name="cube", wm=None):
@@ -113,16 +113,13 @@ def isosurface_simple(p0, p1, nvoxels, isovalues, box_func, axes, name, wm=None)
     yvals, ystep = np.linspace(p0[1], p1[1], num=nvoxels[1]+1, retstep=True, endpoint=True, dtype=DTYPE)
     zvals, zstep = np.linspace(p0[2], p1[2], num=nvoxels[2]+1, retstep=True, endpoint=True, dtype=DTYPE)
 
-    scaled_axes = np.array(axes, dtype=DTYPE)
-    scaled_axes[:,0] *= xstep
-    scaled_axes[:,1] *= ystep
-    scaled_axes[:,2] *= zstep
+    scaled_axes = np.array(axes, dtype=DTYPE) * np.array([xstep, ystep, zstep], dtype=DTYPE)
 
     box_values = box_func(xvals, yvals, zvals)
     tri_list = marching_cube_box(box_values, isovalues)
 
+    origin = np.array(p0, dtype=DTYPE) * bohr2ang
     for iiso in range(len(isovalues)):
-        origin = np.array(p0, dtype=DTYPE) * bohr2ang
         triangle_sets[iiso]["triangles"] = transform_triangles(
             tri_list[iiso], origin, scaled_axes)
 

diff --git a/molecular_blender/marching_cube_cy.pyx b/molecular_blender/marching_cube_cy.pyx
@@ -331,7 +331,7 @@ ctypedef vector[triangle_vec] iso_triangles
 @cython.nonecheck(CYDEBUG)
 cdef void polygonise(triangle_vec* tri_list, const DTYPE_t* cornervalues,
         const DTYPE_t* cornerpos,
-        float isolevel) nogil:
+        float isolevel) noexcept nogil:
     global edgetable, tritable
 
     cdef point[12] vertlist
@@ -379,7 +379,7 @@ cdef void polygonise(triangle_vec* tri_list, const DTYPE_t* cornervalues,
 @cython.wraparound(CYDEBUG)
 @cython.initializedcheck(CYDEBUG)
 @cython.nonecheck(CYDEBUG)
-cdef void vertex_interp(point* vert_out, float isolevel, const DTYPE_t* p1, const DTYPE_t* p2, const float v1, const float v2) nogil:
+cdef void vertex_interp(point* vert_out, float isolevel, const DTYPE_t* p1, const DTYPE_t* p2, const float v1, const float v2) noexcept nogil:
     cdef float zero = 1e-8
     if (fabs(isolevel-v1) < zero):
         vert_out.x = p1[0]

diff --git a/molecular_blender/orbitals_cy.pyx b/molecular_blender/orbitals_cy.pyx
@@ -430,7 +430,7 @@ cdef void add_box_values(CShell* shell,
         int nz, DTYPE_t* zz,
         DTYPE_t* coeff,
         DTYPE_t* target,
-        float logmxcoeff) nogil:
+        float logmxcoeff) noexcept nogil:
     cdef float X = shell.X
     cdef float Y = shell.Y
     cdef float Z = shell.Z