1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686
// This Source Code Form is subject to the terms of the Mozilla Public
// License, v. 2.0. If a copy of the MPL was not distributed with this
// file, You can obtain one at http://mozilla.org/MPL/2.0/.
/*!
Helper functions for reading FITS files.
*/
pub mod error;
pub use error::FitsError;
use fitsio::{hdu::*, FitsFile};
use fitsio_sys::{ffgkls, fitsfile};
use libc::c_char;
use log::trace;
use std::ffi::*;
use std::ptr;
#[cfg(test)]
mod test;
/// Open a fits file.
///
/// # Examples
///
/// ```
/// # use mwalib::*;
/// # fn main() -> Result<(), FitsError> {
/// let metafits = "test_files/1101503312_1_timestep/1101503312.metafits";
/// let mut fptr = fits_open!(&metafits)?;
/// # Ok(())
/// # }
/// ```
#[macro_export]
macro_rules! fits_open {
($fptr:expr) => {
_open_fits($fptr, file!(), line!())
};
}
/// Open a fits file's HDU.
///
/// # Examples
///
/// ```
/// # use mwalib::*;
/// # fn main() -> Result<(), FitsError> {
/// // Open a fits file
/// let metafits = "test_files/1101503312_1_timestep/1101503312.metafits";
/// let mut fptr = fits_open!(&metafits)?;
/// // Open HDU 1 (index 0).
/// let hdu = fits_open_hdu!(&mut fptr, 0)?;
/// # Ok(())
/// # }
/// ```
#[macro_export]
macro_rules! fits_open_hdu {
($fptr:expr, $hdu_num:expr) => {
_open_hdu($fptr, $hdu_num, file!(), line!())
};
}
/// Given a FITS file pointer, a HDU that belongs to it, and a keyword that may
/// or may not exist, pull out the value of the keyword, parsing it into the
/// desired type.
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `hdu` - A reference to the HDU you want to find `keyword` in the header of.
///
/// * `keyword` - String containing the keyword to read.
///
///
/// # Returns
///
/// * A Result containing an Option containing the value read or None if the key did not exist, or an error.
///
/// # Examples
///
/// ```
/// # use mwalib::*;
/// # fn main() -> Result<(), FitsError> {
/// let metafits = "test_files/1101503312_1_timestep/1101503312.metafits";
/// let mut fptr = fits_open!(&metafits)?;
/// let hdu = fits_open_hdu!(&mut fptr, 0)?;
/// let freq_centre: Option<f64> = get_optional_fits_key!(&mut fptr, &hdu, "FREQCENT")?;
/// assert_eq!(freq_centre, Some(154.24));
/// let not_real: Option<f64> = get_optional_fits_key!(&mut fptr, &hdu, "NOTREAL")?;
/// assert_eq!(not_real, None);
/// # Ok(())
/// # }
/// ```
#[macro_export]
macro_rules! get_optional_fits_key {
($fptr:expr, $hdu:expr, $keyword:expr) => {
_get_optional_fits_key($fptr, $hdu, $keyword, file!(), line!())
};
}
/// Given a FITS file pointer, a HDU that belongs to it, and a keyword, pull out
/// the value of the keyword, parsing it into the desired type.
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `hdu` - A reference to the HDU you want to find `keyword` in the header of.
///
/// * `keyword` - String containing the keyword to read.
///
///
/// # Returns
///
/// * A Result containing the value read or an error.
///
/// # Examples
///
/// ```
/// # use mwalib::*;
/// # fn main() -> Result<(), FitsError> {
/// let metafits = "test_files/1101503312_1_timestep/1101503312.metafits";
/// let mut fptr = fits_open!(&metafits)?;
/// let hdu = fits_open_hdu!(&mut fptr, 0)?;
/// let freq_centre: f64 = get_required_fits_key!(&mut fptr, &hdu, "FREQCENT")?;
/// assert_eq!(freq_centre, 154.24);
/// # Ok(())
/// # }
/// ```
#[macro_export]
macro_rules! get_required_fits_key {
($fptr:expr, $hdu:expr, $keyword:expr) => {
_get_required_fits_key($fptr, $hdu, $keyword, file!(), line!())
};
}
/// Get a column from a fits file's HDU.
///
/// # Examples
///
/// ```
/// # use mwalib::*;
/// # fn main() -> Result<(), FitsError> {
/// let metafits = "test_files/1101503312_1_timestep/1101503312.metafits";
/// let mut fptr = fits_open!(&metafits)?;
/// let hdu = fits_open_hdu!(&mut fptr, 1)?;
/// let east: Vec<f32> = get_fits_col!(&mut fptr, &hdu, "East")?;
/// assert_eq!(east[0], -585.675);
/// # Ok(())
/// # }
/// ```
#[macro_export]
macro_rules! get_fits_col {
($fptr:expr, $hdu:expr, $keyword:expr) => {
_get_fits_col($fptr, $hdu, $keyword, file!(), line!())
};
}
/// Get the size of the image on the supplied FITS file pointer and HDU.
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `hdu` - A reference to the HDU you want to find the image dimensions of.
///
///
/// # Returns
///
/// * A Result containing a vector of the size of each dimension, if Ok.
///
#[macro_export]
macro_rules! get_hdu_image_size {
($fptr:expr, $hdu:expr) => {
_get_hdu_image_size($fptr, $hdu, file!(), line!())
};
}
/// Given a FITS file pointer, and a keyword to a long string keyword that may
/// or may not exist, pull out the long string of the keyword. This deals with
/// FITSs CONTINUE mechanism by calling a low level fits function.
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `hdu` - A reference to the HDU you want to find `keyword` in the header
/// of.
///
/// * `keyword` - String containing the keyword to read.
///
///
/// # Returns
///
/// * A Result containing an Option containing the value read or None if the key
/// did not exist, or an error.
///
#[macro_export]
macro_rules! get_optional_fits_key_long_string {
($fptr:expr, $hdu:expr, $keyword:expr) => {
_get_optional_fits_key_long_string($fptr, $hdu, $keyword, file!(), line!())
};
}
/// Given a FITS file pointer, and a keyword to a long string keyword, pull out
/// the long string of the keyword. This deals with FITSs CONTINUE mechanism by
/// calling a low level fits function.
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `hdu` - A reference to the HDU you want to find `keyword` in the header
/// of.
///
/// * `keyword` - String containing the keyword to read.
///
///
/// # Returns
///
/// * A Result containing the value read or an error.
///
#[macro_export]
macro_rules! get_required_fits_key_long_string {
($fptr:expr, $hdu:expr, $keyword:expr) => {
_get_required_fits_key_long_string($fptr, $hdu, $keyword, file!(), line!())
};
}
/// Given a FITS file pointer and a HDU, read the associated image.
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `hdu` - A reference to the HDU you want to find `keyword` in the header
/// of.
///
///
/// # Returns
///
/// * A Result containing the vector of data or an error.
///
#[macro_export]
macro_rules! get_fits_image {
($fptr:expr, $hdu:expr) => {
_get_fits_image($fptr, $hdu, file!(), line!())
};
}
/// Given a FITS file pointer and a HDU, read the associated float image.
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `hdu` - A reference to the HDU you want to find `keyword` in the header
/// of.
///
/// * `buffer` - Buffer of floats (as a slice) to fill with data from the HDU.
///
///
/// # Returns
///
/// * A Result of Ok on success, Err on error.
///
#[macro_export]
macro_rules! get_fits_float_image_into_buffer {
($fptr:expr, $hdu:expr, $buffer:expr) => {
_get_fits_float_img_into_buf($fptr, $hdu, $buffer, file!(), line!())
};
}
/// Open a fits file.
///
/// To only be used internally; use the `fits_open!` macro instead.
#[doc(hidden)]
pub fn _open_fits<T: AsRef<std::path::Path>>(
file: &T,
source_file: &'static str,
source_line: u32,
) -> Result<FitsFile, FitsError> {
match FitsFile::open(file) {
Ok(f) => {
trace!(
"_open_fits() filename: '{}'",
file.as_ref().to_str().unwrap().to_string()
);
Ok(f)
}
Err(e) => Err(FitsError::Open {
fits_error: e,
fits_filename: file.as_ref().to_str().unwrap().to_string(),
source_file,
source_line,
}),
}
}
/// Open a fits file's HDU.
///
/// To only be used internally; use the `fits_open_hdu!` macro instead.
#[doc(hidden)]
pub fn _open_hdu(
fits_fptr: &mut FitsFile,
hdu_num: usize,
source_file: &'static str,
source_line: u32,
) -> Result<FitsHdu, FitsError> {
match fits_fptr.hdu(hdu_num) {
Ok(f) => {
trace!(
"_open_hdu() filename: '{}' hdu: {}",
fits_fptr.filename,
hdu_num
);
Ok(f)
}
Err(e) => Err(FitsError::Fitsio {
fits_error: e,
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu_num + 1,
source_file,
source_line,
}),
}
}
/// Get an optional key from a fits file's HDU.
///
/// To only be used internally; use the `get_optional_fits_key!` macro instead.
// Benchmarks show that, for pulling out an i64, this function is *slightly*
// slower than just using the hdu with `read_key::<i64>` (by ~100ns on my Ryzen
// 9 3900X). But, even for small FITS values (e.g. BITPIX = -32), using an i32
// gives the wrong result (consistent with cfitsio in C), forcing the use of
// i64 for even these kinds of values. Thus, this function is nice because is
// lets rust parse the string it extracts.
//
#[doc(hidden)]
pub fn _get_optional_fits_key<T: std::str::FromStr>(
fits_fptr: &mut FitsFile,
hdu: &FitsHdu,
keyword: &str,
source_file: &'static str,
source_line: u32,
) -> Result<Option<T>, FitsError> {
let unparsed_value: String = match hdu.read_key(fits_fptr, keyword) {
Ok(key_value) => key_value,
Err(e) => match &e {
fitsio::errors::Error::Fits(fe) => match fe.status {
202 | 204 => return Ok(None),
_ => {
return Err(FitsError::Fitsio {
fits_error: e,
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
})
}
},
_ => {
return Err(FitsError::Fitsio {
fits_error: e,
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
})
}
},
};
trace!(
"_get_optional_fits_key() filename: '{}' hdu: {} keyword: '{}' value: '{}'",
&fits_fptr.filename,
hdu.number,
String::from(keyword),
unparsed_value
);
match unparsed_value.parse() {
Ok(parsed_value) => Ok(Some(parsed_value)),
Err(_) => Err(FitsError::Parse {
key: keyword.to_string(),
fits_filename: fits_fptr.filename.to_string(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
}
}
/// Get a required key from a fits file's HDU.
///
/// To only be used internally; use the `get_required_fits_key!` macro instead.
#[doc(hidden)]
pub fn _get_required_fits_key<T: std::str::FromStr>(
fits_fptr: &mut FitsFile,
hdu: &FitsHdu,
keyword: &str,
source_file: &'static str,
source_line: u32,
) -> Result<T, FitsError> {
match _get_optional_fits_key(fits_fptr, hdu, keyword, source_file, source_line) {
Ok(Some(value)) => Ok(value),
Ok(None) => Err(FitsError::MissingKey {
key: keyword.to_string(),
fits_filename: fits_fptr.filename.to_string(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
Err(error) => Err(error),
}
}
/// Get a column from a fits file's HDU.
///
/// To only be used internally; use the `fits_get_col!` macro instead.
#[doc(hidden)]
pub fn _get_fits_col<T: fitsio::tables::ReadsCol>(
fits_fptr: &mut FitsFile,
hdu: &FitsHdu,
keyword: &str,
source_file: &'static str,
source_line: u32,
) -> Result<Vec<T>, FitsError> {
match hdu.read_col(fits_fptr, keyword) {
Ok(c) => {
trace!(
"_get_fits_col() filename: '{}' hdu: {} keyword: '{}' values: {}",
fits_fptr.filename,
hdu.number,
keyword,
c.len()
);
Ok(c)
}
Err(fits_error) => Err(FitsError::Fitsio {
fits_error,
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
}
}
/// Get an optional long string out of a FITS file.
///
/// The HDU is actually not needed in this function. We supply it to this
/// function *only* because it forces the caller to open the intended HDU first,
/// so that when cfitsio is called directly, it tries to get the string from the
/// right place.
///
/// To only be used internally; use the `get_optional_fits_key_long_string!`
/// macro instead.
#[doc(hidden)]
pub fn _get_optional_fits_key_long_string(
fits_fptr: &mut fitsio::FitsFile,
hdu: &FitsHdu,
keyword: &str,
source_file: &'static str,
source_line: u32,
) -> Result<Option<String>, FitsError> {
// Read the long string.
let (status, long_string) = unsafe { get_fits_long_string(fits_fptr.as_raw(), keyword) };
match status {
0 => {
trace!(
"_get_optional_fits_key_long_string() filename: {} keyword: '{}' value: '{}'",
&fits_fptr.filename,
keyword,
long_string
);
Ok(Some(long_string))
}
202 => Ok(None),
_ => Err(FitsError::LongString {
key: keyword.to_string(),
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
}
}
/// Get a required long string out of a FITS file.
///
/// The HDU is actually not needed in this function. We supply it to this
/// function *only* because it forces the caller to open the intended HDU first,
/// so that when cfitsio is called directly, it tries to get the string from the
/// right place.
///
/// To only be used internally; use the `get_required_fits_key_long_string!`
/// macro instead.
#[doc(hidden)]
pub fn _get_required_fits_key_long_string(
fits_fptr: &mut FitsFile,
hdu: &FitsHdu,
keyword: &str,
source_file: &'static str,
source_line: u32,
) -> Result<String, FitsError> {
match _get_optional_fits_key_long_string(fits_fptr, hdu, keyword, source_file, source_line) {
Ok(Some(value)) => Ok(value),
Ok(None) => Err(FitsError::MissingKey {
key: keyword.to_string(),
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
Err(error) => Err(error),
}
}
/// Get the size of an image from the supplied HDU.
///
/// To only be used internally; use the `get_hdu_image_size!` macro instead.
#[doc(hidden)]
pub fn _get_hdu_image_size(
fits_fptr: &mut FitsFile,
hdu: &FitsHdu,
source_file: &'static str,
source_line: u32,
) -> Result<Vec<usize>, FitsError> {
match &hdu.info {
HduInfo::ImageInfo { shape, .. } => {
trace!(
"_get_hdu_image_size() filename: '{}' hdu: {} shape: {:?}",
fits_fptr.filename,
hdu.number,
shape
);
Ok(shape.clone())
}
_ => Err(FitsError::NotImage {
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
}
}
/// Get the data out of a HDU's image.
///
/// To only be used internally; use the `get_fits_image!` macro instead.
#[doc(hidden)]
pub fn _get_fits_image<T: fitsio::images::ReadImage>(
fits_fptr: &mut FitsFile,
hdu: &FitsHdu,
source_file: &'static str,
source_line: u32,
) -> Result<T, FitsError> {
match &hdu.info {
HduInfo::ImageInfo { .. } => match hdu.read_image(fits_fptr) {
Ok(img) => {
trace!(
"_get_fits_image() filename: '{}' hdu: {}",
fits_fptr.filename,
hdu.number
);
Ok(img)
}
Err(e) => Err(FitsError::Fitsio {
fits_error: e,
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
},
_ => Err(FitsError::NotImage {
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
}),
}
}
/// Direct read of FITS HDU
#[doc(hidden)]
pub fn _get_fits_float_img_into_buf(
fits_fptr: &mut FitsFile,
hdu: &FitsHdu,
buffer: &mut [f32],
source_file: &'static str,
source_line: u32,
) -> Result<(), FitsError> {
unsafe {
// Get raw ptr and length to user supplied buffer
let buffer_len = buffer.len() as i64;
let buffer_ptr = buffer.as_mut_ptr();
// Call the underlying cfitsio read function for floats
let mut status = 0;
fitsio_sys::ffgpv(
fits_fptr.as_raw(),
fitsio_sys::TFLOAT as _,
1,
buffer_len,
ptr::null_mut(),
buffer_ptr as *mut _,
ptr::null_mut(),
&mut status,
);
// Check fits call status
match fitsio::errors::check_status(status) {
Ok(_) => {}
Err(e) => {
return Err(FitsError::Fitsio {
fits_error: e,
fits_filename: fits_fptr.filename.clone(),
hdu_num: hdu.number + 1,
source_file,
source_line,
});
}
}
}
trace!(
"_get_fits_float_img_into_buf() filename: '{}' hdu: {}",
fits_fptr.filename,
hdu.number
);
Ok(())
}
/// Get a long string from a FITS file. The supplied FITS file pointer *must* be
/// using the appropriate HDU already, or this function will fail.
///
/// This function exists because the rust library `fitsio` does not support
/// reading in long strings (i.e. those that have CONTINUE statements).
///
///
/// # Arguments
///
/// * `fits_fptr` - A reference to the `FITSFile` object.
///
/// * `keyword` - String containing the keyword to read.
///
///
/// # Returns
///
/// * A FITS status code and the long string
///
///
/// # Safety
///
/// This function is no less safe than calling cfitsio itself.
///
unsafe fn get_fits_long_string(fptr: *mut fitsfile, keyword: &str) -> (i32, String) {
let keyword_ffi =
CString::new(keyword).expect("get_fits_long_string: CString::new() failed for keyword");
// For reasons I cannot fathom, ffgkls expects `value` to be a malloc'd
// char** in C, but will only use a single char* inside it, and that doesn't
// need to be allocated. Anyway, Vec<*mut c_char> works for me in rust.
let mut value: [*mut c_char; 1] = [ptr::null_mut()];
let mut status = 0;
ffgkls(
fptr,
keyword_ffi.as_ptr(),
value.as_mut_ptr(),
ptr::null_mut(),
&mut status,
);
// Check the call worked!
let long_string = match status {
0 => CString::from_raw(value[0])
.into_string()
.expect("get_fits_long_string: converting string_ptr failed"),
_ => String::from(""),
};
(status, long_string)
}