Expand description
fitsio
- a thin wrapper around the cfitsio
C library.
- File access
- HDU access
- Creating new HDUs
- Header keys
- Reading file data
- Writing file data
- Raw fits file access
- Threadsafe access
This library wraps the low level cfitsio
bindings: fitsio-sys
and provides a more
native experience for rust users.
The main interface to a fits file is FitsFile
. All file manipulation
and reading starts with this class.
§File access
To open an existing file, use the open method.
use fitsio::FitsFile;
// let filename = ...;
let fptr = FitsFile::open(filename)?;
Alternatively a new file can be created on disk with the companion method
create
:
use fitsio::FitsFile;
// let filename = ...;
let fptr = FitsFile::create(filename).open()?;
The create
method returns a NewFitsFile
, which is an
internal representation of a temporary fits file on disk, before the file is fully created.
This representation has two methods: open
and
with_custom_primary
. The open
method actually creates the file on disk, but before calling this method, the
with_custom_primary
method can be used to add a custom
primary HDU. This is mostly useful for images. Otherwise, a default primary HDU is created. An
example of not adding a custom primary HDU is shown above. Below we see an example of
with_custom_primary
:
use fitsio::FitsFile;
use fitsio::images::{ImageType, ImageDescription};
// let filename = ...;
let description = ImageDescription {
data_type: ImageType::Double,
dimensions: &[52, 103],
};
let fptr = FitsFile::create(filename)
.with_custom_primary(&description)
.open()?;
From this point, the current HDU can be queried and changed, or fits header cards can be read or file contents can be read.
To open a fits file in read/write mode (to allow changes to the file), the
edit
must be used. This opens a file which already exists
on disk for editing.
use fitsio::FitsFile;
// let filename = ...;
let fptr = FitsFile::edit(filename)?;
§Pretty printing
Fits files can be pretty-printed with pretty_print
, or its more powerful
cousin pretty_write
.
use fitsio::FitsFile;
let mut fptr = FitsFile::open(filename)?;
fptr.pretty_print()?;
// or
fptr.pretty_write(&mut io::stdout())?;
In the continuing tradition of releasing fits summary programs with each fits library, this
create contains a binary program fitssummary
which can be installed with cargo install
. This
takes fits files on the command line and prints their summaries to stdout.
$ fitssummary ../testdata/full_example.fits
file: ../testdata/full_example.fits
mode: READONLY
extnum hdutype hduname details
0 IMAGE_HDU dimensions: [100, 100], type: Long
1 BINARY_TBL TESTEXT num_cols: 4, num_rows: 50
§HDU access
HDU information belongs to the FitsHdu
object. HDUs can be fetched by
String
/str
or integer (0-indexed), with the hdu
method. The HduInfo
object contains information about the current HDU:
use fitsio::hdu::HduInfo;
let hdu = fptr.hdu(0)?;
// image HDU
if let HduInfo::ImageInfo { shape, .. } = hdu.info {
println!("Image is {}-dimensional", shape.len());
println!("Found image with shape {:?}", shape);
}
// tables
if let HduInfo::TableInfo { column_descriptions, num_rows, .. } = hdu.info {
println!("Table contains {} rows", num_rows);
println!("Table has {} columns", column_descriptions.len());
}
The primary HDU can always be accessed with the FitsFile::primary_hdu
method.
§Creating new HDUs
§Creating a new image
New fits images are created with the create_image
method. This method requires the extension name, and an
ImageDescription
object, which defines the shape and type of
the desired image:
use fitsio::images::{ImageDescription, ImageType};
let image_description = ImageDescription {
data_type: ImageType::Float,
dimensions: &[100, 100],
};
let hdu = fptr.create_image("EXTNAME".to_string(), &image_description)?;
Unlike cfitsio, the order of the dimensions of new_size
follows the C convention, i.e.
row-major order.
§Creating a new table
Similar to creating new images, new tables are created with the
create_table
method. This requires an extension
name, and a slice of ColumnDescription
s:
use fitsio::tables::{ColumnDescription, ColumnDataType};
let first_description = ColumnDescription::new("A")
.with_type(ColumnDataType::Int)
.create()?;
let second_description = ColumnDescription::new("B")
.with_type(ColumnDataType::Long)
.create()?;
let descriptions = [first_description, second_description];
let hdu = fptr.create_table("EXTNAME".to_string(), &descriptions)?;
§Column descriptions
Columns are described with the
ColumnDescription
struct. This
encapsulates: the name of the column, and the data format.
The fits specification allows scalar or vector columns, and the data format is described the
ColumnDataDescription
struct, which in
turn encapsulates the number of elements per row element (typically 1), the width of the
column (for strings), and the data type, which is one of the
ColumnDataType
members
For the common case of a scalar column, a ColumnDataDescription
object can be constructed
with the scalar
method:
use fitsio::tables::{ColumnDescription, ColumnDataDescription, ColumnDataType};
let desc = ColumnDataDescription::scalar(ColumnDataType::Int);
assert_eq!(desc.repeat, 1);
assert_eq!(desc.width, 1);
Vector columns can be constructed with the vector
method:
use fitsio::tables::{ColumnDataDescription, ColumnDescription, ColumnDataType};
let desc = ColumnDataDescription::vector(ColumnDataType::Int, 100);
assert_eq!(desc.repeat, 100);
assert_eq!(desc.width, 1);
These impl From<...> for String
such that the traditional fits column description string can
be obtained:
use fitsio::tables::{ColumnDataDescription, ColumnDescription, ColumnDataType};
let desc = ColumnDataDescription::scalar(ColumnDataType::Int);
assert_eq!(String::from(desc), "1J".to_string());
§Copying HDUs to another file
A HDU can be copied to another open file with the copy_to
method. This
requires another open FitsFile
object to copy to:
hdu.copy_to(&mut src_fptr, &mut dest_fptr)?;
§Deleting a HDU
The current HDU can be deleted using the delete
method. Note: this method
takes ownership of self
, and as such the FitsHdu
object cannot be used after
this is called.
// let fptr = FitsFile::open(...)?;
// let hdu = fptr.hdu(0)?;
hdu.delete(&mut fptr)?;
// Cannot use hdu after this
§Iterating over the HDUs in a file
The iter
method allows for iteration over the HDUs of a fits file.
for hdu in fptr.iter() {
// Do something with hdu
}
§General calling behaviour
All subsequent data acess is performed through the FitsHdu
object. Most methods
take the currently open FitsFile
as the first parameter.
§Header keys
Header keys are read through the read_key
function,
and is generic over types that implement the ReadsKey
trait:
let int_value: i64 = fptr.hdu(0)?.read_key(&mut fptr, "INTTEST")?;
// Alternatively
let int_value = fptr.hdu(0)?.read_key::<i64>(&mut fptr, "INTTEST")?;
// Or let the compiler infer the types (if possible)
HeaderValue
also implements the ReadsKey
trait, and allows the reading of comments:
let int_value_with_comment: HeaderValue<i64> = fptr.hdu(0)?.read_key(&mut fptr, "INTTEST")?;
let HeaderValue { value, comment } = int_value_with_comment;
Header cards can be written through the method write_key
.
It takes a key name and value, or a key name and value-comment tuple.
See the WritesKey
trait for supported data types.
fptr.hdu(0)?.write_key(&mut fptr, "foo", 1i64)?;
assert_eq!(fptr.hdu(0)?.read_key::<i64>(&mut fptr, "foo")?, 1i64);
// with comments
fptr.hdu(0)?.write_key(&mut fptr, "bar", (1i64, "bar comment"))?;
let HeaderValue { value, comment } = fptr.hdu(0)?.read_key::<HeaderValue<i64>>(&mut fptr, "bar")?;
assert_eq!(value, 1i64);
assert_eq!(comment, Some("bar comment".to_string()));
§Reading file data
Methods taking ranges are exclusive of the upper range value, reflecting the nature of Rust’s range type.
§Reading images
Image data can be read through either
read_section
which reads contiguous pixels
between a start index and end index, or
read_region
which reads rectangular chunks from
the image.
// Read the first 100 pixels
let first_row: Vec<i32> = hdu.read_section(&mut fptr, 0, 100)?;
// Read a square section of the image
let xcoord = 0..10;
let ycoord = 0..10;
let chunk: Vec<i32> = hdu.read_region(&mut fptr, &[&ycoord, &xcoord])?;
Unlike cfitsio, the order of the the section ranges follows the C convention, i.e. row-major order.
Some convenience methods are available for reading rows of the image. This is typically useful as it’s an efficient access method:
let start_row = 0;
let num_rows = 10;
let first_few_rows: Vec<f32> = hdu.read_rows(&mut fptr, start_row, num_rows)?;
// 10 rows of 100 columns
assert_eq!(first_few_rows.len(), 1000);
The whole image can also be read into memory:
let image_data: Vec<f32> = hdu.read_image(&mut fptr, )?;
// 100 rows of 100 columns
assert_eq!(image_data.len(), 10_000);
§ndarray
support
When fitsio
is compiled with the array
feature, images can be read into
the ndarray::ArrayD
type:
use fitsio::FitsFile;
use ndarray::ArrayD;
let mut f = FitsFile::open("../testdata/full_example.fits").unwrap();
let hdu = f.primary_hdu().unwrap();
let data: ArrayD<u32> = hdu.read_image(&mut f).unwrap();
let dim = data.dim();
assert_eq!(dim[0], 100);
assert_eq!(dim[1], 100);
assert_eq!(data[[20, 5]], 152);
For more details, see the ndarray_compat
documentation (only
available if compiled with array
feature).
§Reading tables
Columns can be read using the read_col
function,
which can convert data types on the fly. See the ReadsCol
trait for
supported data types.
let integer_data: Vec<i32> = hdu.and_then(|hdu| hdu.read_col(&mut fptr, "intcol"))?;
§Reading cell values
Individual cell values can be read from FITS tables:
let result: i64 = tbl_hdu.read_cell_value(&mut f, "intcol", 4)?;
assert_eq!(result, 16);
let result: String = tbl_hdu.read_cell_value(&mut f, "strcol", 4)?;
assert_eq!(result, "value4".to_string());
§Reading rows
Single rows can be read from a fits table with the row
method. This requires
use of the fitsio-derive
crate.
use fitsio::tables::FitsRow;
use fitsio_derive::FitsRow;
#[derive(Default, FitsRow)]
struct Row {
#[fitsio(colname = "intcol")]
intfoo: i32,
#[fitsio(colname = "strcol")]
foobar: String,
}
// Pick the 4th row
let row: Row = hdu.row(&mut f, 4)?;
assert_eq!(row.intfoo, 16);
assert_eq!(row.foobar, "value4");
§Iterating over columns
Iterate over the columns with columns
.
for column in hdu.columns(&mut fptr) {
// Do something with column
}
§Writing file data
Methods taking ranges are exclusive of the upper range value, reflecting the nature of Rust’s range type.
§Writing images
Image data is written through three methods on the HDU object:
write_section
, write_region
, and
write_image
.
write_section
requires a start index and
end index and data to write. The data parameter needs to be a slice, meaning any contiguous
memory storage method (e.g. Vec
) can be passed.
let data_to_write: Vec<f64> = vec![1.0, 2.0, 3.0];
hdu.write_section(&mut fptr, 0, data_to_write.len(), &data_to_write)?;
write_region
takes a slice of ranges with which
the data is to be written, and the data to write.
let data_to_write: Vec<f64> = vec![1.0, 2.0, 3.0, 4.0];
let ranges = [&(0..1), &(0..1)];
hdu.write_region(&mut fptr, &ranges, &data_to_write)?;
Unlike cfitsio, the order of the ranges follows the C convention, i.e. row-major order.
write_image
writes all of the data passed (if possible) into the
image. If more data is passed than pixels in the image, the method returns with an error.
// Image is 3x1
assert!(hdu.write_image(&mut fptr, &[1.0, 2.0, 3.0]).is_ok());
assert!(hdu.write_image(&mut fptr, &[1.0, 2.0, 3.0, 4.0]).is_err());
§Resizing an image
Images can be resized to a new shape using the resize
method.
The method takes the open FitsFile
, and an slice of usize
values. Note:
currently fitsio
only supports slices with length 2, i.e. a 2D image.
resize
takes ownership self
to force the user to fetch the HDU object
again. This ensures the image changes are reflected in the hew HDU object.
use fitsio::hdu::HduInfo;
hdu.resize(&mut fptr, &[1024, 1024])?;
// Have to get the HDU again, to reflect the latest changes
let hdu = fptr.hdu(0)?;
match hdu.info {
HduInfo::ImageInfo { shape, .. } => {
assert_eq!(shape, [1024, 1024]);
}
_ => panic!("Unexpected hdu type"),
}
Unlike cfitsio, the order of the dimensions of new_size
follows the C convention, i.e.
row-major order.
§Writing tables
§Writing table data
Tablular data can either be written with write_col
or
write_col_range
.
write_col
writes an entire column’s worth of data to the file. It does
not check how many rows are in the file, but extends the table if the length of data is longer
than the table length.
let data_to_write: Vec<i32> = vec![10101; 5];
hdu.write_col(&mut fptr, "bar", &data_to_write)?;
let data: Vec<i32> = hdu.read_col(&mut fptr, "bar")?;
assert_eq!(data, vec![10101, 10101, 10101, 10101, 10101]);
write_col_range
writes data to a range of rows in a table. The
range is inclusive of both the upper and lower bounds, so 0..4
writes 5 elements.
let data_to_write: Vec<i32> = vec![10101; 10];
hdu.write_col_range(&mut fptr, "bar", &data_to_write, &(0..5))?;
let data: Vec<i32> = hdu.read_col(&mut fptr, "bar")?;
assert_eq!(data, vec![10101, 10101, 10101, 10101, 10101]);
§Inserting columns
Two methods on the HDU object allow for adding new columns:
append_column
and insert_column
.
append_column
adds a new column as the last column member, and is
generally
preferred as it does not require shifting of data within the file.
use fitsio::tables::{ColumnDescription, ColumnDataType};
let column_description = ColumnDescription::new("abcdefg")
.with_type(ColumnDataType::Int)
.create()?;
hdu.append_column(&mut fptr, &column_description)?;
§Deleting columns
The HDU object has the method delete_column
which removes a column.
The column can either be accessed by integer or name
let newhdu = hdu.delete_column(&mut fptr, "bar")?;
// or
let newhdu = hdu.delete_column(&mut fptr, 0)?;
§Raw fits file access
§Converting a FitsFile
to a raw fitsio_sys::fitsfile
pointer
If this library does not support the particular use case that is needed, the raw fitsfile
pointer can be accessed:
use fitsio::FitsFile;
let mut fptr = FitsFile::open(filename)?;
/* Find out the number of HDUs in the file */
let mut num_hdus = 0;
let mut status = 0;
unsafe {
let fitsfile = fptr.as_raw();
/* Use the unsafe fitsio-sys low level library to call a function that is possibly not
implemented in this crate */
fitsio_sys::ffthdu(fitsfile, &mut num_hdus, &mut status);
}
assert_eq!(num_hdus, 2);
This (unsafe) pointer can then be used with the underlying fitsio-sys
library directly.
§Creating a FitsFile
from a raw fitsio_sys::fitsfile
pointer
The inverse of the process described above can be performed. Note: calling this FitsFile
constructor is unsafe => it is up to the caller to guarantee that the pointer given was
- created by
cfitsio
(orfitsio_sys
), and - it represents a valid FITS file.
Given these two things, a FitsFile
can be created.
use fitsio::{sys::ffopen, FileOpenMode, FitsFile};
let filename = "../testdata/full_example.fits";
let mut fptr = std::ptr::null_mut();
let mut status = 0;
let c_filename = std::ffi::CString::new(filename).expect("filename is not a valid C-string");
unsafe {
ffopen(
&mut fptr as *mut *mut _,
c_filename.as_ptr(),
0, // readonly
&mut status,
);
}
assert_eq!(status, 0);
let mut f = unsafe { FitsFile::from_raw(fptr, FileOpenMode::READONLY) }.unwrap();
§Threadsafe access
Access to a FitsFile
is not threadsafe. Behind the scenes, fetching a
FitsHdu
changes internal state, and fitsio
does not provide any concurrent access
gauruntees. Therefore, a FitsFile
does not implement Send
or Sync
.
In order to allow for threadsafe access, the FitsFile
struct has a
threadsafe
method, which returns a threadsafe
ThreadsafeFitsFile
struct (a tuple-type wrapper around
Arc<Mutex<FitsFile>>
) which can be shared between threads safely.
The same concerns with Arc<Mutex<T>>
data should be applied here. Additionally, the library is
subject to OS level limits, such as the maximum number of open files.
§Example
let f = fptr.threadsafe();
/* Spawn loads of threads... */
for i in 0..100 {
let mut f1 = f.clone();
/* Send the cloned ThreadsafeFitsFile to another thread */
let handle = thread::spawn(move || {
/* Get the underlyng fits file back */
let mut t = f1.lock().unwrap();
/* Fetch a different HDU per thread */
let hdu_num = i % 2;
let _hdu = t.hdu(hdu_num).unwrap();
});
}
Re-exports§
pub use crate::headers::HeaderValue;
pub use fitsio_sys as sys;
Modules§
- Errors and error handling
- Fits HDU related code
- Header-related code
- Image related code
- Table-related code
- Thread-safe FitsFile struct
Structs§
- Main entry point to the FITS file format
Enums§
- Enumeration of file open modes