Merge pull request #39 from haddocking/19-unused-code

Remove dead code/tests

Author: BSchilperoort

src/powerfit_em/correlators/clkernels.py

@@ -1,6 +1,4 @@
-import numpy as np
 import pyopencl as cl
-from pyopencl.array import Array as ClArray
 from pyopencl.elementwise import ElementwiseKernel
 
 
@@ -45,17 +43,6 @@ def __init__(self, ctx, values):
         self._rotate_image3d = self._program.rotate_image3d
         self._gws_rotate_grid3d = (96, 64, 1)
 
-    def rotate_grid3d(
-        self,
-        queue: cl.CommandQueue,
-        grid:ClArray,
-        rotmat: np.ndarray,
-        out: ClArray,
-        nearest: bool = False
-    ):
-        args = (grid.data, rotmat, out.data, np.int32(nearest))
-        self._program.rotate_grid3d(queue, self._gws_rotate_grid3d, None, *args)
-
     def rotate_image3d(self, queue: cl.CommandQueue, image, rotmat, out, nearest=False):
         if nearest:
             args = (image, self.sampler_nearest, rotmat, out.data)

src/powerfit_em/correlators/cpu.py

@@ -6,7 +6,7 @@
 
 from tqdm import tqdm
 
-from powerfit_em.correlators.shared import Correlator, Vars, VarsFT, get_ft_shape, get_lcc_mask, get_normalization_factor, f32, i32
+from powerfit_em.correlators.shared import Correlator, Vars, VarsFT, get_ft_shape, get_lcc_mask, f32, i32
 
 try:
     from pyfftw.builders import rfftn as rfftn_builder, irfftn as irfftn_builder

src/powerfit_em/correlators/gpu.py

@@ -10,7 +10,7 @@
 
 
 from powerfit_em.correlators.clkernels import CLKernels
-from powerfit_em.correlators.shared import Correlator, Vars, VarsFT, get_ft_shape, get_lcc_mask, get_normalization_factor, f32, i32
+from powerfit_em.correlators.shared import Correlator, Vars, VarsFT, get_ft_shape, get_lcc_mask, f32, i32
 
 
 def init_gpu_vars(

src/powerfit_em/correlators/kernels.cl

@@ -12,153 +12,6 @@
 #define SIZE ((SHAPE_Z * SLICE))
 
 
-kernel
-void rotate_grid3d(
-        global float *grid, float16 rotmat, global float *out, int nearest
-        )
-{
-    // Rotate grid around the origin. Only grid points within LLENGTH of the
-    // origin are rotated.
-
-    int zid = get_global_id(0);
-    int yid = get_global_id(1);
-    int xid = get_global_id(2);
-    int zstride = get_global_size(0);
-    int ystride = get_global_size(1);
-    int xstride = get_global_size(2);
-
-    int z, y, x, x0, y0, z0, x1, y1, z1, offset0, offset1, grid_ind;
-    float dx, dy, dz, dx1, dy1, dz1, c00, c10, c01, c11, c0, c1, c;
-    float4 dist2, coor_z, coor_zy, coor_zyx;
-    int4 out_ind;
-
-    for (z = zid - LLENGTH; z <= LLENGTH; z += zstride) {
-        dist2.s2 = SQUARE(z);
-
-        coor_z.s0 = rotmat.s6 * z;
-        coor_z.s1 = rotmat.s7 * z;
-        coor_z.s2 = rotmat.s8 * z;
-
-        out_ind.s0 = z * SLICE;
-        if (z < 0)
-            out_ind.s0 += SIZE;
-
-        for (y = yid - LLENGTH; y <= LLENGTH; y += ystride) {
-            dist2.s1 = SQUARE(y) + dist2.s2;
-            if (dist2.s1 > LLENGTH2)
-                continue;
-
-            coor_zy.s0 = rotmat.s3 * y + coor_z.s0;
-            coor_zy.s1 = rotmat.s4 * y + coor_z.s1;
-            coor_zy.s2 = rotmat.s5 * y + coor_z.s2;
-
-            out_ind.s1 = out_ind.s0 + y * SHAPE_X;
-            if (y < 0)
-                out_ind.s1 += SLICE;
-
-            for (x = xid - LLENGTH; x <= LLENGTH; x += xstride) {
-                dist2.s0 = SQUARE(x) + dist2.s1;
-                if (dist2.s0 > LLENGTH2)
-                    continue;
-                coor_zyx.s0 = rotmat.s0 * x + coor_zy.s0;
-                coor_zyx.s1 = rotmat.s1 * x + coor_zy.s1;
-                coor_zyx.s2 = rotmat.s2 * x + coor_zy.s2;
-
-                out_ind.s2 = out_ind.s1 + x;
-                if (x < 0)
-                    out_ind.s2 += SHAPE_X;
-
-                if (nearest > 0) {
-
-                    x0 = (int) round(coor_zyx.s0);
-                    y0 = (int) round(coor_zyx.s1);
-                    z0 = (int) round(coor_zyx.s2);
-
-                    grid_ind = z0 * SLICE + y0 * SHAPE_X + x0;
-                    if (x0 < 0)
-                        grid_ind += SHAPE_X;
-                    if (y0 < 0)
-                        grid_ind += SLICE;
-                    if (z0 < 0)
-                        grid_ind += SIZE;
-
-                    out[out_ind.s2] = grid[grid_ind];
-
-                } else {
-                    x0 = (int) floor(coor_zyx.s0);
-                    y0 = (int) floor(coor_zyx.s1);
-                    z0 = (int) floor(coor_zyx.s2);
-                    x1 = x0 + 1;
-                    y1 = y0 + 1;
-                    z1 = z0 + 1;
-
-                    // Grid index
-                    grid_ind = z0 * SLICE + y0 * SHAPE_X + x0;
-                    if (x0 < 0)
-                        grid_ind += SHAPE_X;
-                    if (y0 < 0)
-                        grid_ind += SLICE;
-                    if (z0 < 0)
-                        grid_ind += SIZE;
-
-                    dx = coor_zyx.s0 - x0;
-                    dy = coor_zyx.s1 - y0;
-                    dz = coor_zyx.s2 - z0;
-                    dx1 = 1 - dx;
-                    dy1 = 1 - dx;
-                    dz1 = 1 - dx;
-
-                    offset1 = 1;
-                    if (x1 == 0)
-                        offset1 -= SHAPE_X;
-                    c00 = grid[grid_ind] * dx1 +
-                          grid[grid_ind + offset1] * dx;
-
-                    offset0 = SHAPE_X;
-                    if (y1 == 0)
-                        offset0 -= SLICE;
-                    offset1 = offset0 + 1;
-                    if (x1 == 0)
-                        offset1 -= SHAPE_X;
-                    c10 = grid[grid_ind + offset0] * dx1 +
-                          grid[grid_ind + offset1] * dx;
-
-                    offset0 = SLICE;
-                    if (z1 == 0)
-                        offset0 -= SIZE;
-                    offset1 = offset0 + 1;
-                    if (x1 == 0)
-                        offset1 -= SHAPE_X;
-                    c01 = grid[grid_ind + offset0] * dx1 +
-                          grid[grid_ind + offset1] * dx;
-
-                    offset0 = SLICE + SHAPE_X;
-                    if (z1 == 0)
-                        offset0 -= SIZE;
-                    if (y1 == 0)
-                        offset0 -= SLICE;
-                    offset1 = offset0 + 1;
-                    if (x1 == 0)
-                        offset1 -= SHAPE_X;
-                    c01 = grid[grid_ind + offset0] * dx1 +
-                          grid[grid_ind + offset1] * dx;
-
-                    c0 = c00 * dy1 + c10 * dy;
-                    c1 = c01 * dy1 + c11 * dy;
-                    // TODO fix why nan = 1 * 1 + 0 * 0, instead of 1
-                    printf("c1 = c01 * dy1 + c11 * dy: %f = %f * %f + %f * %f\n", c1, c01, dy1, c11, dy);
-
-                    c = c0 * dz1 + c1 * dz;
-
-                    //printf("c = c0 * dz1 + c1 * dz: %f = %f * %f + %f * %f\n", c, c0, dz1, c1, dz);
-                    out[out_ind.s2] = c;
-                }
-            }
-        }
-    }
-}
-
-
 kernel
 void rotate_image3d(
         read_only image3d_t image, sampler_t sampler, float16 rotmat, 

src/powerfit_em/helpers.py

@@ -1,7 +1,5 @@
 
-import os
-import errno
-from math import sqrt, pi
+from math import sqrt
 
 import numpy as np
 from scipy.ndimage import binary_erosion
@@ -10,8 +8,6 @@
 except ImportError:
     pass
 
-from . import volume
-
 
 def determine_core_indices(mask):
     """Calculate the core indices of a shape"""

src/powerfit_em/report.py

@@ -642,7 +642,6 @@ def generate_report(
 
 if __name__ == "__main__":
     import argparse
-    from argparse import FileType
 
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawTextHelpFormatter,