Marius Isken 3 months ago
parent
commit
1db49e3ae2
  1. 9
      lightguide/goldstein.py
  2. 103
      src/lib.rs
  3. 2
      tests/conftest.py
  4. 23
      tests/test_goldstein.py

9
lightguide/goldstein.py

@ -29,7 +29,7 @@ def triangular_taper(size: int, plateau: int):
raise ValueError("Size and plateau have to be even.")
ramp_size = int((size - plateau) / 2)
ramp = num.linspace(0.0, 1.0, ramp_size)
ramp = num.linspace(0.0, 1.0, ramp_size + 2)[1:-1]
window = num.ones(size)
window[:ramp_size] = ramp
window[size - ramp_size :] = ramp[::-1]
@ -139,8 +139,11 @@ def plot_goldstein(data):
)
data_filtered = goldstein_filter_rust(
data, window_size=window_size, exponent=val, overlap=overlap,
adaptive_weights=adaptive_weights
data,
window_size=window_size,
exponent=val,
overlap=overlap,
adaptive_weights=adaptive_weights,
)
image_python.set_data(data_filtered_py)

103
src/lib.rs

@ -1,7 +1,7 @@
use ndarray::prelude::*;
use std::collections::HashMap;
use ndarray::{Array, Array2, ArrayView2};
use ndarray::{Array2, ArrayView2};
use numpy::{IntoPyArray, PyArray2, PyReadonlyArray2};
use pyo3::prelude::*;
@ -14,20 +14,41 @@ use rayon::prelude::*;
use std::cmp;
#[derive(Hash)]
struct Tile {
px_x: (usize, usize),
px_y: (usize, usize),
ix: usize,
iy: usize,
}
impl PartialEq for Tile {
fn eq(&self, other: &Self) -> bool {
self.ix == other.ix && self.iy == other.iy
}
}
impl Eq for Tile {}
fn triangular_taper(window_size: usize, plateau: usize) -> Array2<f32> {
assert!(plateau < window_size, "Plateau cannot be larger than size.");
assert!(window_size as f32 % 2.0 == 0., "Size has to be even");
let ramp_size = (window_size - plateau) / 2;
let ramp = Array::<f32, _>::linspace(0., 1., ramp_size);
let mut taper = Array::<f32, _>::ones(window_size);
// Crop 0.0 and 1.0
let ramp = Array1::<f32>::linspace(0., 1., ramp_size + 2)
.slice(s![1..-1])
.to_owned();
taper.slice_mut(s![..ramp_size]).assign(&ramp);
taper
let mut taper_both = Array1::<f32>::ones(window_size);
taper_both.slice_mut(s![..ramp_size]).assign(&ramp);
taper_both
.slice_mut(s![window_size - ramp_size..])
.assign(&ramp.slice(s![..;-1]));
let window = &taper * &taper.slice(s![.., NewAxis]);
window
let taper = &taper_both * &taper_both.slice(s![.., NewAxis]);
taper
}
fn goldstein_filter(
@ -41,17 +62,28 @@ fn goldstein_filter(
((window_size as f64).log2() % 1.0 == 0.) && window_size > 4,
"window_size has to be pow(2) and > 4."
);
assert!(
overlap < (window_size / 2 - 1),
"Overlap is too large. Maximum overlap: window_size / 2 - 1."
overlap < (window_size / 2),
"overlap {} is too large. Maximum overlap: {}",
overlap,
window_size / 2 - 1
);
let window_stride = window_size - overlap;
let window_non_overlap = window_size - 2 * overlap;
let window_px = window_size * window_size;
let npx_x = data.nrows();
let npx_y = data.ncols();
let mut data_padded = Array2::<f32>::zeros((
data.nrows() + 2 * window_stride,
data.ncols() + 2 * window_stride,
));
data_padded
.slice_mut(s![
window_stride..data.nrows() + window_stride,
window_stride..data.ncols() + window_stride
])
.assign(&data);
let npx_x = data_padded.nrows();
let npx_y = data_padded.ncols();
let nx = npx_x / window_stride;
let ny = npx_y / window_stride;
@ -63,19 +95,27 @@ fn goldstein_filter(
for ix in 0..nx {
let px_x_beg = cmp::min(ix * window_stride, npx_x);
let px_x_end = cmp::min(px_x_beg + window_size, npx_x);
for ny in 0..ny {
let px_y_beg = cmp::min(ny * window_stride, npx_y);
for iy in 0..ny {
let px_y_beg = cmp::min(iy * window_stride, npx_y);
let px_y_end = cmp::min(px_y_beg + window_size, npx_y);
let window_data = data
let tile = Tile {
px_x: (px_x_beg, px_x_end),
px_y: (px_y_beg, px_y_end),
ix: ix,
iy: iy,
};
let window_data = data_padded
.slice(s![px_x_beg..px_x_end, px_y_beg..px_y_end])
.to_owned();
frames.insert((px_x_beg, px_x_end, px_y_beg, px_y_end), window_data);
frames.insert(tile, window_data);
}
}
let fft2_r2c = R2CPlan32::aligned(&[window_size, window_size], Flag::MEASURE).unwrap();
let fft2_c2r = C2RPlan32::aligned(&[window_size, window_size], Flag::MEASURE).unwrap();
frames.par_iter_mut().for_each(|(_frame, window_data)| {
frames.par_iter_mut().for_each(|(_tile, window_data)| {
let frame_shape = [window_data.shape()[0], window_data.shape()[1]];
let mut window_data_fft = AlignedVec::new((window_size / 2 + 1) * window_size);
@ -94,17 +134,16 @@ fn goldstein_filter(
// Scale the spectrum
let mut weight: f32;
let mut weight_sum = 0.;
let mut window_power = 0.;
for px in window_data_fft.iter_mut() {
weight = px.norm().powf(exponent);
weight_sum += px.norm();
window_power += px.norm().powf(2.);
*px *= weight;
}
if adaptive_weights {
for px in window_data_fft.iter_mut() {
*px *= weight_sum.powf(2);
*px /= window_power / window_px as f32;
}
}
@ -112,7 +151,7 @@ fn goldstein_filter(
.c2r(&mut window_data_fft, &mut window_data_slice)
.unwrap();
//Apply the taper
// Normalize fft
*window_data /= window_px as f32;
*window_data *= &taper;
@ -123,14 +162,18 @@ fn goldstein_filter(
}
});
let mut filtered_data = Array2::<f32>::zeros(data.raw_dim());
for (frame, window_data) in frames.iter() {
let &(px_x_beg, px_x_end, px_y_beg, px_y_end) = frame;
let mut filtered_data = Array2::<f32>::zeros(data_padded.raw_dim());
for (tile, window_data) in frames.iter() {
let mut filtered_slice =
filtered_data.slice_mut(s![px_x_beg..px_x_end, px_y_beg..px_y_end]);
filtered_data.slice_mut(s![tile.px_x.0..tile.px_x.1, tile.px_y.0..tile.px_y.1]);
filtered_slice += window_data;
}
filtered_data
.slice(s![
window_stride..data.nrows() + window_stride,
window_stride..data.ncols() + window_stride
])
.to_owned()
}
/// A Python module implemented in Rust.
@ -142,9 +185,9 @@ fn rust(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
py: Python<'py>,
window_size: usize,
plateau: usize,
) -> PyResult<&'py PyArray2<f32>> {
) -> &'py PyArray2<f32> {
let taper = triangular_taper(window_size, plateau).into_pyarray(py);
Ok(taper)
taper
}
#[pyfn(m)]
@ -156,11 +199,11 @@ fn rust(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
overlap: usize,
exponent: f32,
adaptive_weights: bool,
) -> PyResult<&'py PyArray2<f32>> {
) -> &'py PyArray2<f32> {
let data_array = data.as_array();
let result = goldstein_filter(data_array, window_size, overlap, exponent, adaptive_weights)
.into_pyarray(py);
Ok(result)
result
}
Ok(())
}

2
tests/conftest.py

@ -1,5 +1,5 @@
import pytest
from pyrocko_das import gf
from lightguide import gf
km = 1e3

23
tests/test_goldstein.py

@ -24,10 +24,23 @@ def test_taper():
assert window[32 // 2, 32 // 2] == 1.0
assert window.shape == (32, 32)
window_rust = rust.triangular_taper(32, 4)
taper_rust = rust.triangular_taper(32, 4)
window_rust = taper_rust["full"]
num.testing.assert_almost_equal(window, window_rust)
def test_plot_taper():
import matplotlib.pyplot as plt
taper_rust = rust.triangular_taper(32, 4)
fig = plt.figure()
ax = fig.gca()
ax.imshow(taper_rust)
plt.show()
@pytest.mark.skip
def test_benchmark_goldstein(benchmark, data_big):
benchmark(goldstein.goldstein_filter, data_big, 32, 14, 0.5)
@ -38,9 +51,13 @@ def test_benchmark_goldstein_rust(benchmark, data_big):
benchmark(rust.goldstein_filter, data_big, 32, 14, 0.5, False)
@pytest.mark.skip
def test_goldstein(data):
import matplotlib.pyplot as plt
filtered_data = goldstein.goldstein_filter(data, 32, 14, 0.5)
filtered_data_rust = rust.goldstein_filter(data, 32, 14, 0.5, False)
num.testing.assert_allclose(filtered_data_rust, filtered_data)
plt.imshow(filtered_data_rust)
plt.show()
# num.testing.assert_allclose(filtered_data_rust, filtered_data)

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