Cian-H/read_aconity_layers
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First commit. Separated project out from MTPy.

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Cian Hughes
2024-05-01 17:46:03 +01:00
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# Generated by Cargo
# will have compiled files and executables
debug/
target/
# Remove Cargo.lock from gitignore if creating an executable, leave it for libraries
# More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html
Cargo.lock
# These are backup files generated by rustfmt
**/*.rs.bk
# MSVC Windows builds of rustc generate these, which store debugging information
*.pdb
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
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MANIFEST
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
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[package]
name = "read_aconity_layers"
version = "0.1.0"
edition = "2021"
[lib]
path = "src/lib.rs"
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MIT License
Copyright (c) 2021 Cian-H
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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A utility for fast reading of layer data from the aconity mini powder bed fusion machine

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[[package]]
name = "ruff"
version = "0.4.2"
description = "An extremely fast Python linter and code formatter, written in Rust."
optional = false
python-versions = ">=3.7"
files = [
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[[package]]
name = "typing-extensions"
version = "4.11.0"
description = "Backported and Experimental Type Hints for Python 3.8+"
optional = false
python-versions = ">=3.8"
files = [
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[metadata]
lock-version = "2.0"
python-versions = "^3.11"
content-hash = "d42c1045a4073be06cbdd6380b01cb3da87f4a970e2f7dd5128652d96f79481c"

204
pyproject.toml Normal file
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@@ -0,0 +1,204 @@
[tool.poetry]
name = "read-aconity-layers"
version = "0.1.0"
description = "A utility for fast reading of layer data from the aconity mini powder bed fusion machine"
authors = ["Cian Hughes <chughes000@gmail.com>"]
license = "MIT"
readme = "README.md"
[tool.poetry.dependencies]
python = "^3.11"
maturin = "^1.5.1"
numpy = "^1.26.4"
[tool.poetry.group.dev.dependencies]
ruff = "^0.4.2"
mypy = "^1.10.0"
[build-system]
requires = ["poetry-core"]
build-backend = "mason"
[tool.maturin]
# Bindings type
bindings = "pyo3"
# Don't check for manylinux compliance
skip-auditwheel = false
# Python source directory
# python-source = "src/mtpy"
# Strip the library for minimum file size
strip = true
# Source distribution generator,
# supports cargo (default) and git.
sdist-generator = "cargo"
[tool.ruff]
# Same as Black.
line-length = 100
# Assume Python 3.11
target-version = "py311"
exclude = ["docs/", "tests/"]
[tool.ruff.lint]
# Configure ruff to be *heavily* opinionated. We want to enforce a consistent style across all code.
# Enable checks for pydocstyle (`D`), pycodestyle (`E`, `W`), Pyflakes (`F`), McCabe Complexity (C90)
# isort (`I`), pep8 naming (`N`), flake8 (`A`, `ANN`, `B`, `C4`, `EM`, `FBT`, `ICN`, `INT`, `ISC`, `PT`,
# `PTH`, `RET`, `SIM`, `TCH`, and `TID`), perflint (`PERF`), numpy rules (`NPY`), pandas
# rules (`PD`), pylint (`PL`), ruff rules (`RUF`).
select = [
"D",
"E",
"W",
"F",
"C90",
"I",
"N",
"A",
"ANN",
"B",
"C4",
"EM",
"FBT",
"ICN",
"INT",
"ISC",
"PT",
"PTH",
"RET",
"SIM",
"TCH",
"TID",
"PERF",
"NPY",
"PD",
"PL",
"RUF",
]
# Reasons for disabling certain rules:
# - PD002: despite its problems we need to use inplace operations for performance reasons.
# - ANN002: as much as i'd like to enforce this using `TypedDict`s and a `__kwargs__`
# dunder, it would tightly couple us to external libraries.
# - ANN003: same as above.
# - PLR0913: as nice as smaller functions are for maintenance and readability, this rule
# is unenforceable in such a data-heavy library.
# - PLR0914: same as above.
# - PLR0917: same as above.
# - TCH001: the `TYPE_CHECKING` blocks either don't work or i'm too stupid to get them to work.
# - TCH002: same as above.
# - TCH003: same as above.
# - ISC001: Personally, i really like this rule but apparently it can cause issues with the ruff formatter.
ignore = [
"PD002",
"ANN002",
"ANN003",
"PLR0913",
# "PLR0914",
# "PLR0917",
"TCH001",
"TCH002",
"TCH003",
"ISC001",
]
# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = [
"A",
"B",
"C",
"D",
"E",
"F",
"G",
"I",
"N",
"Q",
"S",
"T",
"W",
"ANN",
"ARG",
"BLE",
"COM",
"DJ",
"DTZ",
"EM",
"ERA",
"EXE",
"FBT",
"ICN",
"INP",
"ISC",
"NPY",
"PD",
"PGH",
"PIE",
"PL",
"PT",
"PTH",
"PYI",
"RET",
"RSE",
"RUF",
"SIM",
"SLF",
"TCH",
"TID",
"TRY",
"UP",
"YTT",
]
unfixable = []
exclude = [
".bzr",
".direnv",
".eggs",
".git",
".hg",
".mypy_cache",
".nox",
".pants.d",
".pytype",
".ruff_cache",
".svn",
".tox",
".venv",
"__pypackages__",
"_build",
"buck-out",
"build",
"dist",
"node_modules",
"venv",
".vscode",
"docs",
]
# Allow unused variables when underscore-prefixed.
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
extend-select = ["I"]
[tool.ruff.lint.isort]
force-sort-within-sections = true
lines-after-imports = -1
[tool.ruff.lint.pydocstyle]
convention = "google"
[tool.ruff.format]
quote-style = "double"
indent-style = "space"
line-ending = "auto"
[tool.ruff.lint.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 10
[tool.ruff.lint.flake8-annotations]
mypy-init-return = true
[tool.mypy]
check_untyped_defs = true
ignore_missing_imports = true
exclude = ["docs/", "tests/"]
[[tool.mypy.overrides]]
module = ["flet.*", "flet_core.*", "fsspec.*"]
ignore_missing_imports = true

11
read_layers.pyi Normal file
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@@ -0,0 +1,11 @@
from pathlib import Path
from typing import List, Tuple
from numpy import ndarray
def read_selected_layers(file_list: List[Path]) -> ndarray: ...
def read_layer(file: str) -> ndarray: ...
def read_file(filepath: Path) -> Tuple[ndarray, float, int]: ...
def get_z(filepath: Path) -> float: ...
def correct_x(x: float) -> None: ...
def correct_y(y: float) -> None: ...

195
src/lib.rs Normal file
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@@ -0,0 +1,195 @@
use numpy::{IntoPyArray, PyArray2};
use pyo3::prelude::{pymodule, PyModule, PyResult, Python};
use pyo3::types::{PyList, PyString};
use std::path::Path;
#[pymodule]
fn read_aconity_layers(_py: Python<'_>, m: &PyModule) -> PyResult<()> {
#[pyfn(m)]
fn read_layers<'py>(py: Python<'py>, folder: &PyString) -> &'py PyArray2<f64> {
rust_fn::read_layers(folder.to_str().unwrap()).into_pyarray(py)
}
#[pyfn(m)]
fn read_selected_layers<'py>(py: Python<'py>, file_list: &PyList) -> &'py PyArray2<f64> {
rust_fn::read_selected_layers(
file_list
.iter()
.map(|x| Path::new(&(*x).str().unwrap().to_string()).to_path_buf())
.collect(),
)
.into_pyarray(py)
}
#[pyfn(m)]
fn read_layer<'py>(py: Python<'py>, file: &PyString) -> &'py PyArray2<f64> {
rust_fn::read_layer(file.to_str().unwrap()).into_pyarray(py)
}
Ok(())
}
mod rust_fn {
use csv::ReaderBuilder;
use glob::{glob, GlobError};
use indicatif::ProgressBar;
use ndarray::{concatenate, Array2, ArrayView2, Axis, Slice};
use ndarray_csv::Array2Reader;
use rayon::prelude::*;
use std::error::Error;
use std::fs::File;
use std::path::{Path, PathBuf};
pub fn read_layers(folder: &str) -> Array2<f64> {
let glob_string: String = folder.to_owned() + "/*.pcd";
let mut glob_iterator: Vec<PathBuf> = glob(glob_string.as_str())
.expect("Files not found!")
.collect::<Result<Vec<PathBuf>, GlobError>>()
.unwrap();
glob_iterator.par_sort_unstable_by(|a, b| get_z(a).partial_cmp(&get_z(b)).unwrap());
let len: usize = glob_iterator.len();
let bar = ProgressBar::new(len as u64);
let mut arrays: Vec<Array2<f64>> = vec![Array2::<f64>::zeros((0, 0)); len];
let mut z_vals: Vec<f64> = vec![0.; len];
let mut z_lens: Vec<usize> = vec![0; len];
glob_iterator
.par_iter()
.zip(arrays.par_iter_mut())
.zip(z_vals.par_iter_mut())
.zip(z_lens.par_iter_mut())
.for_each(
|(((filepath, array_element), z_vals_element), z_lens_element)| {
let (array, z, z_len) = read_file(filepath.to_path_buf()).unwrap();
*array_element = array;
*z_vals_element = z;
*z_lens_element = z_len;
bar.inc(1)
},
);
let mut padding_arrays: Vec<Array2<f64>> = Vec::<Array2<f64>>::new();
for (z, z_len) in z_vals.iter().zip(z_lens) {
let z_array: Array2<f64> = Array2::from_elem((z_len, 1), *z);
padding_arrays.push(z_array);
}
let padding_array_views: Vec<ArrayView2<f64>> =
padding_arrays.iter().map(|x| x.view()).collect();
let array_views: Vec<ArrayView2<f64>> = arrays.iter().map(|x| x.view()).collect();
let mut out_array = concatenate(
Axis(1),
&[
concatenate(Axis(0), &array_views)
.unwrap()
.slice_axis(Axis(1), Slice::from(0..2)),
concatenate(Axis(0), &padding_array_views).unwrap().view(),
concatenate(Axis(0), &array_views)
.unwrap()
.slice_axis(Axis(1), Slice::from(2..4)),
],
)
.unwrap();
out_array.column_mut(0).par_map_inplace(correct_x);
out_array.column_mut(1).par_map_inplace(correct_y);
out_array
}
pub fn read_selected_layers(file_list: Vec<PathBuf>) -> Array2<f64> {
let len: usize = file_list.len();
let bar = ProgressBar::new(len as u64);
let mut arrays: Vec<Array2<f64>> = vec![Array2::<f64>::zeros((0, 0)); len];
let mut z_vals: Vec<f64> = vec![0.; len];
let mut z_lens: Vec<usize> = vec![0; len];
file_list
.par_iter()
.zip(arrays.par_iter_mut())
.zip(z_vals.par_iter_mut())
.zip(z_lens.par_iter_mut())
.for_each(
|(((filepath, array_element), z_vals_element), z_lens_element)| {
let (array, z, z_len) = read_file(filepath.to_path_buf()).unwrap();
*array_element = array;
*z_vals_element = z;
*z_lens_element = z_len;
bar.inc(1)
},
);
let mut padding_arrays: Vec<Array2<f64>> = Vec::<Array2<f64>>::new();
for (z, z_len) in z_vals.iter().zip(z_lens) {
let z_array: Array2<f64> = Array2::from_elem((z_len, 1), *z);
padding_arrays.push(z_array);
}
let padding_array_views: Vec<ArrayView2<f64>> =
padding_arrays.iter().map(|x| x.view()).collect();
let array_views: Vec<ArrayView2<f64>> = arrays.iter().map(|x| x.view()).collect();
let mut out_array = concatenate(
Axis(1),
&[
concatenate(Axis(0), &array_views)
.unwrap()
.slice_axis(Axis(1), Slice::from(0..2)),
concatenate(Axis(0), &padding_array_views).unwrap().view(),
concatenate(Axis(0), &array_views)
.unwrap()
.slice_axis(Axis(1), Slice::from(2..4)),
],
)
.unwrap();
out_array.column_mut(0).par_map_inplace(correct_x);
out_array.column_mut(1).par_map_inplace(correct_y);
out_array
}
pub fn read_layer(file: &str) -> Array2<f64> {
let (array, z, z_len) = read_file(Path::new(file).to_path_buf()).unwrap();
let z_array: Array2<f64> = Array2::from_elem((z_len, 1), z);
let z_array_view: ArrayView2<f64> = z_array.view();
let array_view: ArrayView2<f64> = array.view();
let mut out_array = concatenate(Axis(1), &[array_view, z_array_view]).unwrap();
out_array.column_mut(0).par_map_inplace(correct_x);
out_array.column_mut(1).par_map_inplace(correct_y);
out_array
}
fn read_file(filepath: PathBuf) -> Result<(Array2<f64>, f64, usize), Box<dyn Error>> {
let z: f64 = get_z(&filepath);
let file = File::open(filepath)?;
let mut rdr = ReaderBuilder::new()
.has_headers(false)
.delimiter(b' ')
.from_reader(file);
let array_read: Array2<f64> = rdr.deserialize_array2_dynamic()?;
let z_len: usize = array_read.shape()[0];
Ok((array_read, z, z_len))
}
fn get_z(filepath: &PathBuf) -> f64 {
filepath
.file_stem()
.unwrap()
.to_str()
.unwrap()
.parse::<f64>()
.unwrap()
}
fn correct_x(x: &mut f64) -> () {
*x = -((((*x + 16384.) * 0.009155273) - 87.) / 1.01);
}
fn correct_y(y: &mut f64) -> () {
*y = (((*y + 16384.) * 0.009155273) - 91.) / 1.02;
}
}