User's guide

nom.tam.fits is a full-featured, fast, 100% pure Java 8+ library for reading, writing, and modifying FITS files. The library owes its origins to Tom A. McGlynn (hence the nom.tam prefix) at NASA Goddard Space Flight Center. Currently it is maintained by Attila Kovacs at the Center for Astrophysics | Harvard & Smithsonian.

This document has been updated for 1.20 and/or later 1.x releases.

FITS (Flexible Image Transport System) is a binary format of many astronomical datasets and images.

The library requires a level of familiarity with FITS and its common standards and conventions for effective use. For example, while the library will automatically interpret and populate the mandatory minimum data description in FITS headers, it will not automatically process many optional standard or conventional header entries. It is mostly up to the users to extract or complete the description of data to its full extent, for example to include FITS world coordinate systems (WCS), physical units, etc. Users are encouraged to familiarize themselves with the FITS standard and conventions described therein to be effective users of this library.

This is an open-source, community maintained, project hosted on github as nom-tam-fits. Further information and documentation, including API docs, can be found on the project site.

FITS data (HDU) types

A FITS file is composed of one or more Header-Data Units (HDUs). Each HDU consists of a header, which describes the data and possibly contain extra metadata (as key-value pairs) or comments, and a data section.

The current FITS standard (4.0) recognizes the following principal HDU / data types:

Image can store a regular array of 1-999 dimensions with a type corresponding to Java numerical primitives, such as a one-dimensional time series of samples (e.g. int[]), or a three-dimensional cube of voxels (e.g. float[][][]). (Note, that Java supports images up to 255 dimensions only but it's unlikely you'll find that limiting for your application.)
Binary Table can store rows and columns of assorted of elements. Each column entry may be either a single value, or a fixed-sized (multidimensional) array, or else a variable-length 1D arrays of a given type. All Java primitive numerical types are supported, but also String, Boolean (logical), boolean (bits), and ComplexValue types.
ASCII Table (discouraged) is a simpler, less capable table format with support for storing singular primitive numerical types, and strings only -- in human-readable format. You should probably use the more flexible (and more compact) binary tables instead for your application, and reserve use of ASCII tables for reading data that may still contain these.
Random Groups (discouraged) can contain a set of images of the same type and dimensions along with a set of parameters of the same type (for example an int[][] image, along with a set of int parameters). They were never widely used and the FITS 4.0 standard discourages them going forward, given that binary tables provide far superior capabilities for storing the same type of data. Support for these type of HDUs is basic, and aimed mainly at providing a way to access data that was already written in this format.
Foreign File can encapsulate various other files within the FITS. Foreign file HDUs are a recognised convention, but not (yet) officially part of the FITS standard. We do not explicitly support foreign file encapsulation yet, but it is something that we are considering for a future release.

In addition to the basic HDU types, there are extension of table HDUs that serve specific purposes, such as:

Compressed Images / Tables are an extension of the binary table HDUs for storing an image or a binary table in a compressed format, with tiling support to make parts easily accessible from the whole. We provide full support for compressing and decompressing images and tables, and for accessing specific regions of compressed data stored in this format.
The Hierarchical Grouping convention is an extension of table HDUs (ASCII or binary) for storing information on the hierarchical relation of HDUs contained within (or external to) the FITS. The hierarchical grouping is a recognized convention, but not (yet) officially part of the FITS standard. We do not explicitly support this convention yet, but it is something that we are considering for a future release.

FITS vs Java data types

Signed vs unsigned bytes

Java bytes are signed, but FITS bytes are not. If any arithmetic processing is to be done on byte valued data, users may need to be careful of Java’s automated conversion of signed bytes to widened integers. Thus, a value of 0xFFwould signify 255 in FITS, but has a Java value of -1. To preserve the FITS meaning, we may upconvert it to short as:

  short shortValue = (byteValue & 0xFF);

This idiom of AND-ing the byte values with 0xFF before a widening conversion is generally the way to prevent undesired sign extension of bytes.

Strings

FITS generally represents character strings as byte arrays of ASCII characters, with legal values between 0x20 and 0x7E (inclusive). The library automatically converts between Java Strings and their FITS representations, by the appropriate narrowing conversion of 16-bit Unicode char to byte. Therefore, you should be careful to avoid using extended Unicode characters (and also ASCII beyond the 0x20 -- 0x7E range) in Strings, when including these in FITS.

Compatibility with prior releases

The current version of the nom.tam.fits library requires Java 8 (or later).

We strive to maintain API compatibility with earlier releases of this library, and to an overwhelming extent we continue to deliver on that. However, in a few corner cases we had no choice but to change the API and/or behavior slightly to fix bugs, nagging inconsistencies, or non-compliance to the FITS standard. Such changes are generally rare, and typically affect some of the more obscure features of the library -- often classes and methods that probably should never have been expossed to users in the first place. Most typical users (and use cases) of this library will never see a difference, but some of the more advanced users may find changes that would require some small modifications to their application in how they use nom-tam-fits with recent releases. If you find yourself to be one of the ones affected, please know that the decision to 'break' previously existing functionality was not taken lightly, and was done only because it was inavoidable in order to make the library function better overall.

Note, that as of 1.16 we offer only API compatibility to earlier releases, but not binary compatilibility. In practical terms it means that you cannot simply drop-in replace you JAR file, from say version 1.15.2 to 1.19.0. Instead, you are expected to (re)compile your application with the JAR version of this library that you intend to use. This is because some method signatures have changed to use an encompassing argument type, such as Number instead of the previously separate byte, short, int, long, float, double methods. (These otherwise harmless API changes improve consistency across numerical types.)

Starting with version 1.16, we also started deprecating some of the older API, either because methods were ill-conceived, confusing, or generaly unsafe to use; or because they were internals of the library that should never have been exposed to users in the first place. Rest assured, the deprecations do not cripple the intended functionality of the library. If anything they make the library less confusing and safer to use. The Javadoc API documentation mentions alternatives for the methods that were deprecated, as appropriate. And, if nothing else works, you should still be able to compile your old code with deprecations enabled in the compiler options. Rest assured, all deprecated methods, no matter how ill-conceived or dodgy they may be, will be supported in all future releases prior to version 2.0 of the library.

Reading FITS files

Deferred reading
Tolerance to standard violations in 3rd party FITS files
Reading images
Reading tables

Deferred reading

When FITS data are being read from a non-compressed random accessible input (such as a FitsFile), the read() call will parse all HDU headers but will typically skip over the data segments (noting their position in the file however). Only when the user tries to access data from an HDU, will the library load that data from the previously noted file position. The behavior allows to inspect the contents of a FITS file very quickly even when the file is large, and reduces the need for IO when only parts of the whole are of interest to the user. Deferred input, however, is not possible when the input is compressed or if it is uses an stream rather than a random-access FitsFile.

One thing to keep in mind with deferred reading is that you should not close your Fits or its random-accessible input file before all the required data has been loaded. For example, the following will cause an error:

  Fits fits = new Fits("somedata.fits");
   
  // Scans the FITS, but defers loading data until we need it
  fits.read();
   
  // We close the FITS prematurely.
  fits.close();
   
  // !!!BAD!!! now if  we try to access data
  //           we'll get and exception...
  float[][] image = (float[][]) fits.getHDU(0).getKernel();

In the above, the getKernel() method will try to load the deferred data from the input that we closed just before it. That's not going to work. The correct order is of course:

  // Scans the FITS, but defers loading data until we need it
  fits.read();
 
  // Good, the FITS is still open so we can get the deferred data
  float[][] image = (float[][]) fits.getHDU(0).getKernel(); 

  // We close only after we grabbed all the data we needed.
  fits.close();

As of version 1.18, all data classes of the library support deferred reading.

Tolerance to standard violations in 3rd party FITS files.

By default the library will be tolerant to FITS standard violations when parsing 3rd-party FITS files. We believe that if you use this library to read a FITS produced by other software, you are mainly interested to find out what's inside it, rather than know if it was written properly. However, problems such as missing padding at the end of the file, or an unexpected end-of-file before content was fully parsed, will be logged so they can be inspected. Soft violations of header standards (those that can be overcome with educated guesses) are also tolerared when reading, but logging for these is not enabled by default (since they may be many, and likely you don't care). You can enable logging standard violations in 3rd-party headers by Header.setParserWarningsEnabled(true). You can also enforce stricter compliance to the standard when reading FITS files via FitsFactory.setAllowHeaderRepairs(false) and FitsFactory.setAllowTerminalJunk(false). When violations are not tolerated, appropriate exceptions will be thrown during reading.

Reading Images

Reading whole images
Reading selected parts of images only (cutouts)
Streaming image cutouts
Low-level reading of image data

Reading whole images

The simplest example of reading an image contained in the first HDU is given below:

  Fits f = new Fits("myfile.fits");
  ImageHDU hdu = (ImageHDU) f.readHDU();
  int[][] image = (int[][]) hdu.getKernel();

First we create a new instance of Fits with the filename. Then we can get first HDU using the getHDU() method.

Note the casting into an ImageHDU. When reading FITS data using the nom.tam library the user will often need to cast the results to the appropriate type. Given that the FITS file may contain many different kinds of data and that Java provides us with no class that can point to different kinds of primitive arrays other than Object, such explicit casting is inevitable if you want to use the data from the FITS files.

Converting images to a different type

As of version 1.20, the library provides the means for converting images between numerical types. Let's say the FITS stored the images as integer, but we want them as double-precision values.

  double[][] darray = (double[][]) hdu.getData().convertTo(double.class).getKernel();

Things get somewhat interesting at this point, because the FITS standard also allows for the integer representation of floating-point values as integers, via quantization. The quantization has the following parameters:

A scaling factor, i.e. the separation of discrete levels in the floating point data (defaults to 1.0)
an offset, i.e. the floating point value that corresponds to an integer value of 0 (defaults to 0.0).
a blanking value, i.e. the integer that corresponds to NaN (not used by default).

The quantization of images is defined by the BSCALE, BZERO, and BLANK keywords accordingly in the FITS header. Thus, when these keywords are present, the integer to decimal conversion will automatically apply the integer-to-decimal conversion as:

  <decimal-value> = <scaling> * <integer-value> + <offset>

or else set NaN values when the integer value matches the designated blanking value. In the absense of the above header keywords defining quantization, the integer-to-decimal conversion is effectively just a widening conversion.

The reverse conversion, from decimal images to integer images, involves rounding, i.e.:

  <integer-value> = round((<decimal-value> - <offset>) / <scaling>)

If you want to convert the image without quantization, you may call ImageData.setQuantizer(null) prior to the conversions, or else use the static low-level ArrayFuncs.convertArray(Object, Class) method instead.

Complex valued images

While the original FITS standard designated images for scalar numerical types only, the current standard (version 4.0) also specifies a convention to represent complex valued data as images. Complex arrays are recorded as any scalar numerical type, but with an extra dimension of 2 containing the real and imaginary components. E.g. a 4x3 complex array can thus be represented as any primitive type array with 4x3x2 dimensions. The convention is that the axis containing the complex pair of values has is CTYPEn header keyword named as 'COMPLEX'. Note, that complex values can be recorded as integers also, and use quantization just like decimals.

As of version 1.20, this library recognises when the convention is used when reading FITS image HDUs. (The library can only handle the convention if the 'COMPLEX' axis is the first or last image axis -- which should cover all but some very pathological use cases.)

However, images recorded this way will continue to read back as their storage type (e.g. float[4][3][2]) for back compatibility with previous releases. But, you can check if the data is meant to be complex (or not) and convert it to complex values in a second step after loading the data:

  // Get the data in the stored data format as some primitive array...
  ImageData data = hdu.getData();
  
  // If the complex array convention was used in the header, we can convert the image data
  // to complex-valued as the second step...
  if (data.isComplexValued()) {
     ComplexValue[][] z = (ComplexValue[][]) data.convertTo(ComplexValue.class).getKernel();
     ...
  }

Reading selected parts of an image only (cutouts)

Since version 1.18, it is possible to read select cutouts of large images, including sparse sampling of specific image regions. When reading image data users may not want to read an entire array especially if the data is very large. An ImageTiler can be used to read in only a portion of an array. The user can specify a box (or a sequence of boxes) within the image and extract the desired subsets. ImageTiler can be used for any image. The library will try to only read the subsets requested if the FITS data is being read from an uncompressed file but in many cases it will need to read in the entire image before subsetting.

Suppose the image we retrieve above has 2000x2000 pixels, but we only want to see the innermost 100x100 pixels. This can be achieved with

  ImageTiler tiler = hdu.getTiler();
  short[] center = (short[]) tiler.getTile(new int[] {950, 950}, new int[] {100, 100});

The tiler needs to know the corners and size of the tile we want. Note that we can tile an image of any dimensionality. getTile() returns a one-dimensional array with the flattened 1D image. You can convert it to a 2D image afterwards using ArrayFuncs.curl(), e.g.:

  short[][] center2D = (short[][]) ArrayFuncs.curl(center, 100, 100);

And you can convert to other numerical types, e.g. via one of the ArrayFuncs.convertArray() methods, e.g.:

  double[][] dCenter2D = (double[][]) ArrayFuncs.convertArray(center2D, double.class, hdu.getData().getQuantizer());

Streaming image cutouts

Since version 1.18 it is also possible to stream cutouts, using the StreamingTileImageData class. The streaming can be used with any source that implements the RandomAccessFileIO interface, which provides file-like random access, for example for a resource on the Amazon S3 cloud:

  import nom.tam.util.RandomAccessFileIO;

  public final class S3RandomAccessFileIO implements RandomAccessFileIO {
      // ...
  }

Below is an example code sketch for streaming image cutouts from a very large image residing on Amazon S3:

  Fits source = new Fits(new S3RandomAccessFileIO(...));
  ImageHDU imageHDU = source.getHDU(...);
  
  // Manually set up the header for the cutout image as necessary
  Header cutoutHeader = ...
  
  // Define the image cutout region we want 
  int[] tileStarts, tileLengths, tileSteps;
  ...

  // Create the cutout with the specified parameters
  StreamingTileImageData streamingTileImageData = new StreamingTileImageData(
      cutoutHeader, imageHDU.getTiler(), tileStarts, tileLengths, tileSteps
  );
      
  // Add the cutout region to a new FITS object
  Fits output = new Fits();
  output.addHDU(FitsFactory.hduFactory(cutoutHeader, streamingTileImageData));
      
  // The cutout is processed at write time!
  output.write(outputStream);

As of version 1.18 it is also possible to stream cutouts from compressed images using the CompressedImageTiler class. Whereas the asImageHDU() method decompresses the entire image in memory, the CompressedImageTiler will decompress only the tiles necessary for obtaining the desired cutout. For example, consider writing the cutout from a compressed image as a regular non-compressed ImageHDU. This can be achieved much the same way as in the above example, replacing imageHDU.getTiler() with a CompressedImageTiler step, such as:

  ...
  CompressedImageTiler compressedImageTiler = new CompressedImageTiler(compressedImageHDU);
  StreamingTileImageData streamingTileImageData = new StreamingTileImageData(
      cutoutHeader, compressedImageTiler, corners, lengths, steps
  );
  ...

Low-level reading of image data

Suppose we want to get the average value of a 100,000 x 40,000 pixel image. If the pixels are 32-bit integers, that would be an 16 GB file. However, we do not need to load the entire image into memory at once. Instead we can analyze it via bite-sized chunks. For example, we start by finding the beginning of the relevant data segment in the file:

  Fits fits = new Fits("bigimg.fits");
  ImageHDU img = fits.getHDU(0);
  
  // Rewind the stream to the beginning of the data segment
  if (!img.getData().reset()) {
      // Uh-oh...
      throw new IllegalStateException("Unable to seek to data start”);
  }

The reset() method causes the internal stream to seek to the beginning of the data area. If that’s not possible it returns false. Next, we obtain the input file or stream for reading, query the image size, and set up our chunk-sized storage (e.g. by image row):

  // Get the input associated to the FITS
  ArrayDataInput in = fits.getStream();
  
  int[] dims = img.getAxes();      // the image dimensions
  int[] chunk = new int[dims[1]];  // a buffer for a row of data

Now we can cycle through the image rows (or chunks) and collect the statistics as we go, e.g.:

  long sum = 0;

  for (int row = 0; row < dims[0]; row++) {
      in.readLArrayFully(chunk); 
      for (int i = 0; i < chunk.length; i++) {
          sum += line[i];
      }
  }
      
  // Return the average value
  return (double) sum / (dims[0] * dims[1]);

Reading Tables

The easiest and safest way to access data in tables, is by individual entries. Typically, we start by identifying our table HDU in the FITS:

  Fits f = new Fits("mytable.fits");

  // Say, our table is the first extension HDU...
  TableHDU hdu = (TableHDU) f.getHDU(1);

If we are using a random-accessible input (like the file above), we have the option (for binary tables) to load the entire table into memory first. This may be a good idea for small tables, and/or if we plan to access all the data contained in the table -- or not such a good idea if we deal with huge tables from which we need only a selection of the entries. To load the entire HDU into memory:

  // This will load the main table and the heap area into memory (if we want to...)
  hdu.getKernel();

Next, we might want to find which columns store the data we need, using column names if appropriate. (We can of course rely on hard-coded column indices too when we know we are dealing with tables of known fixed format).

  // Find column indices by name and check that they exist...
  int colUTC = hdu.findColumn("UTC");
  if (colUTC < 0) {
      // uh-oh, there is no such column...
  }

Now we can loop through the rows of interest and pick out the entries we need. For example, to loop through all table rows to get only the scalar values from the column named UTC (see above), a phase value in the 4th column (Java index 3), and a spectrum stored in the fifth column (i.e. Java index 4):

  // Loop through rows, accessing the relevant column data
  for(int row = 0; row < tab.getNRows(); row++) {
  
      // Retrieve scalar entries with convenient getters... 
      double utc  = tab.getDouble(row, colUTC);
           
      // We can also access by fixed column index...
      ComplexValue phase = (ComplexValue) tab.get(row, 3);
      ComplexValue[] spectrum = (ComplexValue[]) tab.get(row, 4);
      
      // process the data...
      ...
  }

The old getElement() / setElement() methods supported access as arrays only. While this is still a viable alternative (though slightly less elegant), we recommend against it going forward. Nevetheless, the equivalent to the above using this approach would be:

  // Loop through rows, accessing the relevant column data
  for(int row = 0; row < tab.getNRows(); row++) {
  
      // Retrieve scalar entries by casting the element to the correct array 
      // type, and returning the first (and only) element from that array...
      double utc  = ((double[]) tab.getElement(row, colUTC))[0];
      
      // We can also access by fixed column index...
      float[] phase = ((float[]) tab.getElement(row, 3));
      float[][] spectrum = (float[][]) tab.getElement(row, 4);
      
      // process the data...
      ...
  }

These older methods (getElement(), getRow() and getColumn()) always return table data as arrays, even for scalar types, so a single integer entry will be returned as int[1], a single string as String[1]. Complex values are stored as float[2] or double[2] depending on the precision (FITS type C or M). So, a double-precision FITS complex array of size [5][7] will be returned a double[5][7][2]. Logicals return boolean[], which means that while FITS supports null logical values, we don't and these will default to false. (However, the get() method introduced in version 1.18 will return these as Boolean arrays instead, retaining null values appropriately!).

Note that for best performance you should access elements in monotonically increasing order when in deferred mode -- at least for the rows, but it does not hurt to follow the same principle for columns inside the loops also. This will help avoid excess buffering that way be required at times for backward jumps.

The library provides methods for accessing entire rows and columns also via the TableData.getRow(int) and TableData.getColumn(int) or BinaryTable.getColumn(String) methods. However, we recommend against using these going forward because these methods return data that may be confounding to interpret, with non-trivial data types and/or dimensions.

Converting array elements

As of version 1.20, the library also support converting array elements to a different numerical type than the stored data. Like in the case for images (further above) the integer-decimal conversions will use the columns qunatization parameters if they are defined. Otherwise narrowing conversions of decimal-to-integer types will use simple rounding. You can convert array elements via the BinaryTable.getArrayElementAs() method. E.g.:

  BinaryTable tab = ...;

  // Assuming that the column contains 2D numerical entries of some type...
  // Get a table entry as an array of doubles, regardless of its (numerical) storage type...
  double[][] e = tab.getArrayElementAs(1, 3, double.class);

The quantization of columns is automatically digested based on the TSCALn, TZEROn, and TNULLn keywords in the table's header, but can be (re)set to a different quantization using the ColumnDesc.setQuantizer() method, if need be.

Because binary tables already have designated complex-valued column types, the conversions apply only between scalar numerical types, such as byte.class, short.class, int.class, long.class, float.class, and double.class.

Writing FITS data

Writing complete FITS files
Writing one HDU at a time
Low-level writes

Writing complete FITS files

When creating FITS files from data we have at hand, the easiest is to start with a Fits object. We can add to it image and/or table HDUs we create. When everything is assembled, we write the FITS to a file or stream:

  Fits fits = new Fits();

  fits.addHDU(...);
  ...
 
  fits.write("myfits.fits");

Images can be added to the FITS at any point. For example, consider a 2D float[][] image we want to add to a FITS:

  float[][] image ...
  
  ImageHDU imageHDU = Fits.makeHDU(image);
  fits.addHDU(imageHDU);

The makeHDU() method only populates the essential descriptions of the image in the HDU's header. We may want to complete that description (e.g. add WCS information, various other data descriptions) to the new HDU's header, e.g.:

  Header header = imageHDU.getHeader();
  
  header.addValue(Standard.BUNIT, "Jy/beam");
  ...

After that we can add further images or table(s), such as binary tables (preferred) or ASCII tables. Once all HDUs have been assembled this way, we write the FITS as usual:

  fits.write("myfits.fits");
  fits.close();

An important thing to remember is that while images can be anywhere in the FITS files, tables are extensions, and so, they may not reside in the first HDU in a file. Thus, if a table is the first HDU we add to a FITS container, it will be automatically prepended by a dummy primary HDU, and our data will actually be written as the second HDU (Java index 1).

Binary versus ASCII tables

When writing simple tables it may be possible to write the tables in either binary or ASCII format, provided all columns are scalar types. By default, the library will create and write binary tables for such data. To create ASCII tables instead the user should call FitsFactory.setUseAsciiTables(true) first. Given the superiority and compactness of binary tables, we recommend against using ASCII tables, unless you have to for a compelling reason.

Writing one HDU at a time

Sometimes you do not want to add all your HDUs to a Fits object before writing them out to a file or stream. Maybe because they use up too much RAM, or you are recording from a live stream and want to add HDUs to the file as they come in. As of version 1.17 of the library, you can write FITS files one HDU at a time without having to place them in a Fits container first, or having to worry about the mandatory keywords having been set for primary or extension HDUs. Or, you can write a Fits object with some number of HDUs, but then keep appending further HDUs after, worry-free. The FitsFile or FitsOutputStream object will keep track of where things go in the file or stream, and set the required header keywords for the appended HDUs as appropriate for a primary or extension HDU automatically.

Here is an example of how ro create a FITS file HDU-by-HDU without the need for a Fits object as a holding container:

  // Create the file to which to write the HDUs as they come
  FitsFile out = new FitsFile("my-incremental.fits", "rw");
  ...

  // you can append 'hdu' objects to the FITS file (stream) as:
  // The first HDU will be set primary (if possible), and following HDUs will be extensions. 
  hdu.write(out);
  ...

  // When you are all done you can close the FITS file/stream
  out.close();

In the above case the FitsFile output is random accessible, which means you can go back and re-write HDUs (or their headers) in place later. If you do go all the way back to the head of the file, and re-write the first HDU, you can be assured that it will contain the necessary header entries for a primary HDU, even if you did not set them yourself. Easy as pie.

Of course, you can use a FitsOutputStream as opposed to a file as the output also, e.g.:

  FitsOutputStream out = new FitsOutputStream(new FileOutputStream("my-incremental.fits"));
  ...

in which case going back ro re-write what was already written before is not an option.

Low-level writes

When a large table or image is to be written, the user may wish to stream the write. This is possible but rather more difficult than in the case of reads.

There are two main issues:

The header for the HDU must written to show the size of the entire file when we are done. Thus the user may need to modify the header data appropriately.
After writing the data, a valid FITS file may need to be padded to an appropriate length.

It's not hard to address these requirements, but the user needs some familiarity with the internals of the FITS representation.

Images

We can write images one subarray at a time, if we want to. Here is an example of how you could go about it. First, create storage for the contiguous chunk we want to write at a time. For example, same we want to write a 32-bit floating-point image with [nRows][nCols] pixels, and we want to write these one row at a time:

First let's create storage for the chunk:

  // An array to hold data for a chunk of the image...
  float[] chunk = new float[nCols];

Next create a header. It's easiest to create it from the chunk, and then just modify the dimensions for the full image, e.g. as:

  // Create an image HDU with the row 
  BasicHDU hdu = Fits.makeHDU(row);
  Header header = hdu.getHeader();

  // Override the image dimensions in the header to describe the full image
  ImageData.overrideHeaderAxes(header, nRow, nCol);

Next, we can complete the header description adding whatever information we desire. Once complete, we'll write the image header to the output:

  // Create a FITS and write to the image to it
  FitsFile out = new FitsFile("image.fits", "rw");
  header.write(out);

Now, we can start writing the image data, iterating over the rows, populating our chunk data in turn, and writing it out as we go.

  // Iterate over the image rows
  for (int i = 0; i < nRows; i++) {
     // fill up the chunk with one row's worth of data
     ...

     // Write the row to the output
     out.writeArray(chunk);
  }

Finally, add the requisite padding to complete the FITS block of 2880 bytes after the end of the image data:

  FitsUtil.pad(out, out.position());
  out.close();

Tables

We can do something pretty similar for tables so long as we don't have variable length columns, but it requires a little more work.

First we have to make sure we are not trying to write tables into the primary HDU of a FITS. Tables can only reside in extensions, and so we might need to create and write a dummy primary HDU to the FITS before we can write the table itself:

  FitsFile out = new FitsFile("table.fits", "rw");

  // Binary tables cannot be in the primary HDU of a FITS file
  // So we must add a dummy primary HDU to the FITS first if necessary
  new NullDataHDU().write(out);

Next, assume we have a binary table that we either read from an input, or else assembled ourselves (see further below on how to build binary tables):

  BinaryTable table = ...

Next, we will need to create an appropriate FITS header for the table:

  Header header = new Header();
  table.fillHeader(header);

We can now complete the header descriprtion as we see fit, with whatever optional entries. We can also save space for future additions, e.g. for values we will have only after we start writing the table data itself:

   // Make space for at least 200 more header lines to be added later
   header.ensureCardSpace(200);

Now, we can write out the header:

   header.write(out);

Next, we can finally write regular table rows (without variable-length entries) in a loop. Assuming that our row is something like { { double[1] }, { byte[10] }, { float[256] }, ... }:

  for (...) {
     // Write data one element at the time into the buffer via the 
     // rowStream. These must match the column structure of the table, 
     // in terms of order, data types, and element counts. 

     out.writeDouble(ra);
     out.write(fixedLengthNameBytes);
     out.witeArray(spectrum);
     ...
  }

We want to keep count of the rows we write (e.g. nRowsWritten). Once we finish writing the table data, we must add the requisite padding to complete the FITS block of 2880 bytes after the table data ends.

  // Add padding to the file to complete the FITS block
  FitsUtil.pad(out, nRowsWritten * table.getRegularRowSize());

After the table has been thus written to the output, we should make sure that the header has the correct number of table rows in in NAXIS2 entry:

  header.addValue(Standard.NAXISn.n(2), nRowsWritten);

We can also complete the header with any other information that became available since the start (using the space we reserved for additions earlier). Once the header is all in ship-shape, we can re-write in the file at its original location:

   // Re-write the header with the new information we added since we began writing 
   // the table data
   header.rewrite();

Modifying existing FITS files

An existing FITS file can be modified in place in some circumstances. The file must be an uncompressed (random-accessible) file, with permissions to read and write. The user can then modify elements either by directly modifying the kernel data object for image data, or by using the setElement or similar methods for tables.

Suppose we have just a couple of specific elements we know we need to change in a given file:

  Fits f = new Fits("mod.fits");
     
  ImageHDU hdu = (ImageHDU) f.getHDU(0);
  int[][] img = (int[][]) hdu.getKernel();
     
  // modify the image as needed...
  img[i][j] = ...
  ...
  
  // write the new data back in the place of the old
  hdu.rewrite();

Same goes for a table HDU:

  BinaryTableHDU hdu = (BinaryTableHDU) f.getHDU(1);
  
  // Modify the table as necessary
  hdu.set(3, 0, 3.14159265);
  ...
  
  // Make sure the file contains the changes made above
  hdu.rewrite();

Note, that in the above table example, the rewrite() call may be superfluous since BinaryTable.set() may be editing the file in situ if the data has been left in deferred-read mode (random accessible file, without data loaded to memory). Nevertheless, it is best practice to call rewrite() anyway to ensure that the updates are synched to the output under all circumstances. And, you should also close the output (e.g. via Fits.close()) after done editing the FITS file to ensure that any pending file changes are fully flushed to the output.

Defragmenting binary tables allows to reclaim heap space that is no longer used in the heap area. When deleting variable-length columns, or when replacing entries inside variable-length columns, some or all of the space occupied by old entries on the heap may become orphaned, needlessly bloating the heap storage. Also, changed entries may be placed on the heap out of order, which can slow down caching effectiveness for sequential table acces. Thus when modifying tables with variable-length columns, it may be a good idea to defragment the heap before writing in to the output. For the above example, this would be adding an extra step before rewrite).

  ...
  
  // If we changed variable-length data, it may be a good
  // idea to defragment the heap before writing...
  hdu.defragment();

  hdu.rewrite();

Defragmenting might also be a good idea when building tables with variable-length data column by column (as opposed to row-by-row).

And, headers can also be updated in place also -- you don't even need to access the data, which can be left in deferred state:

  BasicHDU<?> hdu = f.getHDU(1);
  Header header = hdu.getHeader();
  
  header.addValue(Standard.TELESCOP, "SMA").comment("The Submillimeter Array");
  header.addValue(Standard.DATE-OBS, FitsDate.now());
  ...
  
  header.rewrite();

Generally rewrites can be made as long as the only change is to the data content, but not to the data size (and the FITS file meets the criteria mentioned above). An exception will be thrown if the data has been added or deleted or too many changes have been made to the header. Some additions to the header may be allowed as long as the header still fits in the same number of FITS blocks (of 2880 bytes) as before. (Hint, you can always reserve space in headers for later additions using Header.ensureCardSpace(int) prior to writing the header or HDU originally.)

FITS headers

What is in a header
Accessing header values
Standard and conventional FITS header keywords
Hierarchical and long header keywords
Long string values
Checksums
Preallocated header space
Standard compliance
Migrating header data between HDUs

What is in a header

The FITS header consists of a list of 80-byte records at the beginning of each HDU. They contain key/value pairs and comments and serve three distinct purposes:

First and foremost, the header provides an essential description of the HDU's data segment with a set of reserved FITS keywords and associated values. These must appear in a specific place and order order in all FITS headers. The keywords SIMPLE or XTENSION, BITPIX, NAXIS, NAXISn, PCOUNT, GCOUNT, GROUPS, THEAP, TFIELDS, TTYPEn, TBCOLn, TFORMn, and END form the set of essential keywords. The library automatically takes care of adding these header entries in the required order, and users of the library should never attempt to set or modify the essential data description manually.
FITS standard also reserves further header keywords to provide optional standardized descriptions of the data, such as HDU names or versions, physical units, World Coordinate Systems (WCS), column names etc. It is up to the user to familiarize themselves with the standard keywords and their usage, and use these to describe their data as fully as appropriate, or to extract information from 3rd party FITS headers.
Finally, the FITS headers may also store a user dictionary of key/value pairs and/or comments. You may store whatever further information you like (within the constraints of what FITS allows) as long as they stay clear of the set of reserved FITS keywords mentioned above.

It is a bit unfortunate that FITS was designed to mix the essential, standard, and user-defined keys in a single shared space of the same FITS header. It is therefore best practice for all creators of FITS files to:

Avoid setting or modifying the essential data description (which could result in corrupted or unreadable FITS files). Let the library handle these appropriately.
Keep standard (reserved) keywords separated from user-defined keywords in the header if possible. It is recommended for users to add the standardized header entries first, and then add any/all user-defined entries after. It is also recommended that users add a comment line (or lines) in-between to cleary demark where the standard FITS description ends, and where the user dictionary begins after.
Use comment cards to make headers self explanatory and easy for other humans to understand and digest. The header is also in a sense the self-contained documentation of your FITS data.

Note, that originally, header keywords were limited to a maximum of 8 upper-case alphanumeric characters (A to Z and 0 to 9), plus hyphens (-) and underscores (_), and string values may not exceed 68 characters in length. However, the HIERARCH keyword convention allows for longer and/or more extended set of keywords that may utilize the ASCII range from 0x21 through 0x7E, and which can contain hierarchies. And string values of arbitrary length may be added to headers via the CONTINUE long keyword convention, which is now an integral part of the standard as of FITS version 4.0. See more about these conventions, and their usage within this library, further below.

Accessing header entries

There are two basic ways to access data contained in FITS headers: direct (by keyword) or ordered (iterator-based).

A. Direct access header entries

You can retrieve keyed values by their associated keyword from the header using the get...Value() methods. To set values use one of the addValue(...) methods. These methods define a standard dictionary lookup access to key/value pair stored in the FITS headers.

For example, to find out the telescope or observatory was used to obtain the data you might want to know the value of the TELESCOP key.

  Fits f = new Fits("img.fits")
  Header header = f.getHDU(0).getHeader();
  String telescope =  header.getStringValue("TELESCOP");

Note, that as of version 1.19 you might want to use one of the Fits.getCompleteHeader(...) methods when inspecting headers of HDUs stored in the FITS file, since the header returned by these methods would also contain keywords indirectly inherited from the primary HDU, when the INHERIT keywords is used and set to T (true) in the header of the specified HDU extension.

You can also use header.getStringValue(Standard.TELESCOPE) instead of the string constant to retrieve the same value with less chance of a typo spoiling your intent. See more on the use of standard keywords in the section below).

Or if we want to know the right ascension (R.A.) coordinate of the reference position in the image:

  double ra = header.getDoubleValue("CRVAL1");

or, equivalently

  double ra = header.getDoubleValue(WCS.CRVALna.n(1));

[Note, that the FITS WCS convention is being used here. For typical 2D images the reference coordinates are in the pair of keys, CRVAL1 and CRVAL2 and our example assumes an equatorial coordinate system.]

To add or change the R.A. coordinate value, you can use:

  header.addValue("CRVAL1", ra, "[deg] R.A. coordinate");

or, similarly

  header.addValue(WCS.CRVALna.n(1), ra);

The second argument is our new right ascension coordinate (in degrees). The third is a comment field that will also be written to that header in the space remaining. (When using the standard keyword, the netry is created with the the standard comment belonging to the keyword, and you may change that by adding .comment(...) if you want it to be something more specific).

The addValue(...) methods will update existing matching header entries in situ with the newly defined value and comment, while it will add/insert new header entries at the current mark position. By default, this means that new entries will be appended at the end of the header, unless you have called Header.findCard(...) earlier to change the mark position at which new card are added to that immediately before the specified other card, or else you called Header.seekHead() to add new cards at the start of the (non-essential) header space. Note, that you can always restore the default behavior of adding new entries at the end by calling Header.seekTail(), if desired. (This may be a little confusing at first, but the origins of the position marking behavior go a long way back in the history of the library, and therefore it is here to stay until at least version 2.0.)

Note, that the mark position also applies to adding comment cards via Header.insertComment(), .insertHistory(), .insertCommentStyle() and related methods.

Thus, Header.findCard(), .seekHead() and/or .seekTail() methods will allow you to surgically control header order when adding new cards to headers using the direct access methods.

Table HDUs may contain several standard kewords to describe individual columns, and the TableHDU.setColumnMeta(...) methods can help you add these optional descriptor for your data while keeping column-specific keywords organized into header blocks around the mandatory TFORMn keywords. Notem that the .setColumnMeta(...) methods also change the mark position at which new header entries are added.

B. Iterator-based access of header values

For ordered access of header values you can also use the nom.tam.util.Cursor interface to step through header cards in the order they are stored in the FITS.

  Cursor<String, HeaderCard> c = header.iterator();

returns a cursor object that points to the first card of the header. The Cursor.prev() and .next() methods allow to step through the header, and .add() and .delete() methods can add/remove records at specific locations. The methods of HeaderCard allow us to manipulate the contents of the current card as desired. Comment and history header cards can be created and added to the header, e.g. via HeaderCard.createCommentCard() or .createHistoryCard() respectively.

Note, that the iterator-based approach is the only way to extract comment cards from a header (if you are so inclined), since dictionary lookup will not work for these -- as comment cards are by definition not key/value pairs.

Standard and conventional FITS header keywords

The FITS standard defines a set of reserved keywords. You can find a collection of these under the nom.tam.fits.header package:

Standard -- The core keywords of the FITS standard.
WCS -- Standard FITS Word coordinate system (WCS) keywords
DateTime -- Standard date-time related FITS keywords
Compression -- Standard keywords used for describing compressed data
Checksum -- Standard keywords used for data checksumming

In addition to the keywords defined by the FITS standard, the library also recognizes further conventional and commonly used keyword, which as also collected in the nom.tam.fits.header package:

HierarchicalGrouping -- Keywords for the Hierarchical Grouping Convention
NonStandard -- A few commonly used and recognized keywords that are not strictly part of the FITS standard
DataDescription -- Conventional keywords for describing the data content
InstrumentDescription -- Conventional keywords for describing the instrumentation used for observing
ObservationDescription -- Commonly used keywords that describe the observation
ObservationDurationDescription -- Commonly used keywords for the timing of observations

Finally, many organisations (or groups of organisations) have defined their own sets of FITS keywords. Some of these can be found under the nom.tam.fits-header.extra package, such as:

NOAOExt -- keywords used by the National Optical Astronomy Observatory (no longer available since the IRAF project is no longer supported)
SBFitsExt -- Santa Barbara Instrument Group FITS Extension (SBFITSEXT)
- MaxImDLExt -- MaxIm DL Astronomy and Scientific Imaging Solutions
CXCExt -- keywords defined for the Chandra X-ray Observatory
STScIExt -- keywords used by the Space Telescope Science Institute

You can use the standardized keywords contained in these enums to populate headers or access header values. For example,

  hdr.addValue(Standard.INSTRUME, "My super-duper camera");
  hdr.addValue(InstrumentDescription.FILTER, "Meade #25A Red");
  ...

The advantage of using these standardized keywords, as opposed to strings, is that they help avoid keyword typos, since the compiler (or your IDE) will warn you if the keyword name is not recognised.

Some keywords contain indices that must be specified via the n() method. You must spececify one integer (one-based index) for each 'n' appearing in the keyword name. For example, to set the value of the WAT9_234 keyword to the string value of "50":

  hdr.addValue(NOAOExt.WATn_nnn.n(9, 2, 3, 4), "50");

For best practice, try rely on the standard keywords, or those in registered conventions, when possible.

Keyword checking

Another advantage of using the standardized keywords implementing the IFitsHeader interface is that the library can check (since 1.19) automatically that (a) the keyword is appropriate for the type of HDU it is used in, and (b) if the keyword is one of the essential keywords that should be set by the library alone without users tinkering with them. If the keyword should not be used in the header belonging to a specific type of HDU under the current checking policy, the library will throw an IllegalArgumentException.

You can use Header.setKeywordChecking() to adjust the type of checking to be applied on a per header instance basis, or use the static Header.setDefaultKeywordChecking() to change the default policy for all newly created headers.

The Header.KeywordCheck enum defines the following policies that may be used:

NONE -- no keyword checking will be applied. You can do whatever you want without consequences. This policy is the most backward compatible one, since we have not done checking before.
DATA_TYPE -- Checks that the keyword is supported by the data type that the header is meant to describe. This is the default policy since version 1.19 of the library.
STRICT -- In addition to checking if the keyword is suitable for the data type, the library will also prevent users from setting essential keywords that really should be handled by the library alone (such as SIMPLE or XTENSION, BITPIX, NAXIS etc.).

Value checking

The standardized keywords that implement the IFitsHeader interface can also specify the type of acceptable values to use. As of 1.19 we will throw an appropriate exception (IllegalArgumentException or ValueTypeException, depending on the method) if the user attempt to set a value of unsupported type. For example trying to set the value of the Standard.TELESCOP keyword (which expects a string value) to a boolean will throw an exception.

The keyword checking policy can be adjusted via the HeaderCard.setValueCheckingPolicy() method. HeaderCard.ValueCheck defines the following policies:

NONE -- no value type checking will be performed. You can do whatever you want without consequences. This policy is the most backward compatible one, since we have not done checking before.
LOGGING -- Attempting to set values of the wrong type for IFitsHeader keywords will be allowed but a warning will be logged each time.
EXCEPTION -- Attempting to set values of the wrong type for IFitsHeader keywords will throw an appropriate exception, such as ValueTypeException or IllegalArgumentException depending on the method used. This is the default policy since version 1.19 of the library.

Hierarchical and long header keywords

The standard FITS header keywords consists of maximum 8 upper case letters (A through Z) or numbers (0 through 9) and/or dashes (-) and underscores (_). The HIERARCH keyword convention allows for storing longer and/or hierarchical sets of FITS keywords, and can support a somewhat more extended set of ASCII characters (in the range of 0x21 to 0x7E). Support for HIERARCH-style keywords is enabled by default as of version 1.16. HIERARCH support can be toggled if needed via FitsFactory.setUseHierarch(boolean). By default, HIERARCH keywords are converted to upper-case only (cfitsio convention), so

  HeaderCard hc = new HeaderCard(Hierarch.key("my.lower.case.keyword[!]"), "value", "comment");

will write the header entry to FITS as:

  HIERARCH MY LOWER CASE KEYWORD[!] = 'value' / comment

You can use FitsFactory.getHierarchFormater().setCaseSensitive(true) to allow the use of lower-case characters, and hence enable case-sensitive keywords also. After the setting, the same card will be written to FITS as:

  HIERARCH my lower case keyword[!] = 'value' / comment

You may note a few other properties of HIERARCH keywords as implemented by this library:

The case sensitive setting (above) also determines whether or not HIERARCH keywords are converted to upper-case upon parsing also. As such, the header entry in last example above may be referred as HIERARCH.my.lower.case.keyword[!] or as HIERARCH.MY.LOWER.CASE.KEYWORD[!] internally after parsing, depending on whether case-sensitive mode is enabled or not, respectively.
If FitsFactory has HIERARCH support disabled, any attempt to define a HIERARCH-style long keyword will throw a HierarchNotEnabledException runtime exception. (However, just HIERARCH by itself will still be allowed as a standard 8-character FITS keyword on its own).
The convention of the library is to refer to HIERARCH keywords internally as a dot-separated hierarchy, preceded by HIERARCH., e.g. HIERARCH.my.keyword. (The static methods of the Hierarch class can make it easier to create such keywords).
The HIERARCH keywords may contain all printable standard ASCII characters that are allowed in FITS headers (0x20 thru 0x7E). As such, we take a liberal reading of the ESO convention, which designated only upper-case letters, numbers, dashes (-) and underscores (_). If you want to conform to the ESO convention more closely, you should avoid using characters outside of the set of the original convention.
The library adds a space between the keywords and the = sign, as prescribed by the cfitsio convention. The original ESO convention does not require such a space (but certainly allows for it). We add the extra space to offer better compatibility with cfitsio.
The HIERARCH parsing is tolerant, and does not care about extra space (or spaces) between the hierarchical components or before =. It also recognises . as a separator of hierarchy besides the conventional white space. As such the following may all appear in a FITS header to define the same two-component keyword:

  HIERARCH MY KEYWORD

  HIERARCH MY.KEYWORD

  HIERARCH MY .. KEYWORD

Long string values

The standard maximum length for string values in the header is 68 characters. As of FITS 4.0, the CONTINUE long string convention is part of the standard. And, as of version 1.16 of this library, it is supported by default. Support for long strings can be turned off (or on again) via FitsFactory.setLongStringEnabled(boolean) if necessary. If the settings is disabled, any attempt to set a header value to a string longer than the space available for it in a single 80-character header record will throw a LongStringsNotEnabledException runtime exception.

Checksums

Checksums can be added to (and updated in) the headers of HDUs, and can be used to check the integrity of the FITS data after. Fits, BasicHDU, and Data classes provide methods both for setting / updating or for verifying checksums. The checksums will be calculated directly from the file (as of 1.17) for all data in deferred read mode. Thus, it is possible to checksum or verify huge FITS files without having to load large volumes of data into RAM at any point.

Setting the checksums (CHECKSUM and DATASUM keywords) should be the last modification to the FITS object or HDU before writing. Here is an example of settting a checksum for an HDU before you write it to disk:

  BasicHDU<?> hdu;
         
  // ... prepare the HDU and header ...
   
  hdu.setChecksum();
  hdu.write(...);

Or you can set checksums for all HDUs in your Fits in one go before writing the entire Fits object out to disk:

  Fits f;
  
  // ... Compose the FITS with the HDUs ...
  
  f.setChecksum();
  f.write(...);

Then later, as of version 1.18.1, you can verify the integrity of FITS files using the stored checksums (or data sums) just as easily too:

  try (Fits f = new Fits("huge-file.fits")) {
      f.verifyIntegrity();
  } catch (FitsIntegrityException e) {
      // Failed integrity check
  } catch (...)
      // some other error...
  }

The above will calculate checksums for each HDU directly from the file without reading the potentially large data into memory, and compare HDU checksums and/or data checksums to those stored in the FITS headers. The verification can also be performed on stream inputs but, unlike for files, data will be invariable loaded into memory (at least temporarily).

You can also verify the integrity of HDUs or their data segments individually, via BasicHDU.verifyIntegrity() or BasicHDU.verifyDataIntegrity() calls on specific HDUs.

Finally, you might want to update the checksums for a FITS you modify in place:

  Fits f = new Fits("my.fits");
  
  // We'll modify the fist HDU...
  ImageHDU im = (ImageHDU) f.readHDU();
  float[][] data = (float[][]) im.getData():
  
  // Offset the data by 1.12
  for (int i = 0; i < data.length; i++) 
      for (int j = 0; i < data[0].length; j++)
          data[i][j] += 1.12;
    
  // Calculate new checksums for the HDU
  im.setChecksum();
  im.rewrite();

Or, (re)calculate and set checksums for all HDUs in a FITS file, once again leaving deferred data in unloaded state and computing the checksums for these directly from disk:

  Fits f = new Fits("my.fits");
  f.setChecksum();
  f.rewrite();

The above will work as expected provided the original FITS already had CHECKSUM and DATASUM keys in the HDUs, or else the headers had enough unused space for adding these without growing the size of the headers. If any of the headers or data in the Fits have changed size, the Fits.rewrite() call will throw a FitsException without modifying any of the records. In such cases You may proceed re-writing a selection of the HDUs, or else write the Fits to a new file with a different size.

Preallocated header space

Many FITS files are created by live-recording of data, e.g. from astronomical instruments. As such not all header values may be defined when one begins writing the data segment of the HDU that follows the header. For example, we do not know in advance how many rows the binary table will contain, which will depend on when the recording will stop. Other metadata may simply not be available until a later time. For this reason version 4.0 of the FITS standard has specified preallocating header space as some number of blank header records between the last defined header entry and the END keyword.

As of version 1.16, this library supports preallocated header space via Header.ensureCardSpace(int), which can be used to ensure that the header can contain at least the specified number of 80-character records when written to the output. (In reality it may accommodate somewhat more than that because of the required padding to multiples of 2880 bytes or 36 records -- and you can use Header.getMinimumSize() to find out just how many bytes are reserved / used by any header object at any point).

Once the space has been reserved, the header can be written to the output, and one may begin recording data after it. The header can be completed later, up to the number of additional card specified (and sometimes beyond), and the updated header can be rewritten place at a later time with the additional entries.

For example,

  FitsFile out = new FitsFile("mydata.fits", "rw");
  
  Header h = new Header();
  
  // We want to keep room for 200 80-character records in total
  // to be filled later
  h.ensureCardSpace(200);

  // We can now write the header, knowing we can fill it with up to
  // 200 records in total at a later point
  h.write(out);

Now you can proceed to recording the data, such as a binary table row-by-row. Once you are done with it, you can go back and make edits to the header, adding more header cards, in the space you reserved earlier, and rewrite the header in front of the data without issues:

  // Once the data has been recorded we can proceed to fill in 
  // the additional header values, such as the end time of observation
  h.addValue("DATE-END", FitsDate.getFitsDateString(), "end of observation");
  
  // And we can re-write the header in place
  h.rewrite();

Preallocated header space is also preserved when reading the data in. When parsing headers trailing blank header records (before the END key) are counted as reserved card space. (Internal blank cards, between two regular keyword entries, are however preserved as blank comment cards and their space will not be reusable unless these cards are explicitly removed first). After reading a header with preallocated space, the user can add at least as many new cards into that header as trailing blank records were found, and still call rewrite() on that header without any problems.

Standard compliance

As of version 1.16, the library offers a two-pronged approach to ensure header compliance to the FITS standard.

First, we fully enforce the standards when creating FITS headers using this library, and we do it in a way that is compliant with earlier FITS specifications (prior to 4.0) also. We will prevent the creation of non-standard header entries (cards) by throwing appropriate runtime exceptions (such as IllegalArgumentException, LongValueException, LongStringsNotEnabledException, HierarchNotEnabledException) as soon as one attempts to set a header component that is not supported by FITS or by the set of standards selected in the current FitsFactory settings.
Second, we offer the choice between tolerant and strict interpretation of 3rd-party FITS headers when parsing these. In tolerant mode (default), the parser will do its best to overcome standard violations as much as possible, such that the header can be parsed as fully as possible, even if some entries may have malformed content. The user may enable Header.setParserWarningsEnabled(true) to log each violation detected by the parser as warnings, so these can be inspected if the user cares to know. Stricter parsing can be enabled by FitsFactory.setAllowHeaderRepairs(false). In this mode, the parser will throw an exception when it encounters a severely corrupted header entry, such as a string value with no closing quote (UnclosedQuoteException) or a complex value without a closing bracket (IllegalArgumentException). Lesser violations can still be logged, the same way as in tolerant mode.

Additionally, we provide HeaderCard.sanitize(String) method that the user can call to ensure that a Java String can be used in FITS headers. The method will replace illegal FITS characters (outside of the range of 0x20 thru 0x7E) with ?.

Migrating header data between HDUs

Sometimes we want to create a new HDU based on an existing HDU, such as a cropped image, or a table segment, in which we want to reuse much of the information contained in the original header. The best way to go about it is via the following steps:

Start by creating the new HDU from the data it will hold. It ensures that the new HDU will have the correct essential data description (type and size) in its header.
Merge distict (non-conflicting) header entries from the original HDU into the header of the new HDU, using the Header.mergeDistinct(Header source) method. It will migrate the header entries from the original HDU to the new one, without overriding the proper essential data description.
Update the header entries as necessary, such as WCS, in the new HDU. Pay attention to removing obsoleted entries also, such as descriptions of table columns that no longer exist in the new data.
If the header contains checksums, make sure you update these before writing the header or HDU to an output.

For example:

  // Some image HDU whose header we want to reuse for another...
  ImageHDU origHDU = ...
  
  // 1. create the new image HDU with the new data
  float[][] newImage = ...
  ImageHDU newHDU = ImageData.from(newImage).toHDU();
  
  // 2. copy over non-conflicting header entries from the original
  Header newHeader = newHDU.getHeader();
  newHeader.mergeDistinct(origHDU.getHeader());

  // 3. Update the WCS for the cropped data...
  newHeader.addValue(Standard.CRPIXn.n(1), ...);
  ...
  
  // 4. Update checksums, if necessary
  newHDU.setChecksum();

Creating tables

Buiding tables row-by-row
Buiding tables column-by-column
Creating ASCII tables (discouraged)

Building tables row-by-row

As of version 1.18 building tables one row at a time is both easy and efficient -- and may be the least confusing way to get tables done right. (In prior releases, adding rows to existing tables was painfully slow, and much more constrained).

You may want to start by defining the types and dimensions of the data (or whether variable-length) that will be contained in each table column:

   BinaryTable table = new BinaryTable();
   
   // A column containing 64-bit floating point scalar values, 1 per row...
   table.addColumn(ColumnDesc.createForScalars(double.class));
   
   // A column containing 5x4 arrays of single-precision complex values...
   table.addColumn(ColumnDesc.createForArrays(ComplexValue.Float.class, 5, 4));
   
   // A column containing Strings of variable length using 32-bit heap pointers...
   table.addColumn(ColumnDesc.createForVariableLength(String.class));
   
   ...

Defining columns this way is not always necessary before adding rows to the table. However, it is necessary if you will have data that needs variable-length storage row-after-row; or if you want more control over specifics of the column format. As such, it is best practice to define the columns explictly even if not strictly required for your particular application.

Now you can populate the table with your data, one row at a time, using the addRow() method as many times over as necessary:

   for (...) {
       // prepare the row data, making sure each row is compatible with prior rows...
       ...
   	
       // Add the row to the table
       table.addRow(...);
   }

As of version 1.18, you may use Java boxed types (as an alternative to primitive arrays-of-one) to specify primitive scalar table elements, including auto-boxing of literals or variables. You may also use vararg syntax for adding rows if that is more convenient in your application. Thus, you may simply write:

   table.addRowEntries(1, 3.14159265);

to add a row consisting of an 32-bit integer, a double-precision floating point value (presuming your table has those two types of columns). Prior to 1.18, the same would have to have been written as:

  table.addRow(new Object[] { new int[] {1}, new double[] {3.14159265} };

Tables built entirely row-by-row are naturally defragmented, as long as they are not modified subsequently.

Once the table is complete, you can make a HDU from it:

  BinaryTableHDU hdu = table.toHDU();

which will populate the header with the requisite entries that describe the table. You can then edit the new header to add any extra information (while being careful to not modify the essential table description). Note, that once the table is encompassed in an HDU, it is generally not safe to edit the table data, since the library has no foolproof way to keep the header description of the table perfectly in sync. Thus it is recommended that you create table HDUs only after the table data has been fully populated.

A few rules to remember when building tables by rows:

All rows must contain the same number of entries (the number of columns)
Entries in the same column must match in their column type in every row.
Entries must be of the following supported types:
- A supported Java type (String or ComplexValue), or
- primitive arrays (e.g. int[], float[][]), or
- Arrays of Boolean (logicals), String or ComplexValue (such as Boolean[][] or String[]), or
- Scalar primitives stored as arrays of 1 (e.g. short[1]).
If entries are multi-dimensional arrays, they must have the same dimensionality and shape in every row. (Otherwise, they will be stored as variable-length arrays in flattened 1D format, where the shape may be lost).
If entries are one-dimensional, they can vary in size from row to row freely.
Java null entries are allowed for String and Boolean (logical) types, but not for the other data types. (these will map to empty strings or undefined logical values respectively)

Building tables column-by-column

Sometimes we might want to assemble a table from a selection of data which will readily consitute columns in the table. We can add these as columns to an existing table (empty or not) using the BinaryTable.addColumn(Object) method. For example, say we have two arrays, one a time-series of spectra, and a matching array of corresponding timestamps. We can create a table with these (or add them to an existing table with a matching number of rows) as:

   double[] timestamps = new double[nRows]; 
   ComplexValue[][] spectra = new ComplexValue[nRows][];
   ...
   
   BinaryTable tab = new BinaryTable();
   
   table.addColumn(timestamps);
   table.addColumn(spectra);

There are just a few rules to keep in mind when constructing tables in this way:

All columns added this way must contain the same number of elements (number of rows).
In column data, scalars entries are simply elements in a 1D primitive array (e.g. double[]), in which each element (e.g. a double) is the scalar value for a given row. (I.e. unlike in the row-major table format required to create entire tables at once, we do not have to wrap scalar values in self-contained arrays of 1)
Other than the above, the same rules apply as for creating HDUs row-by-row (above).
If setting complex columns with arrays of float[2] or double[2] (the old way), you will want to call setComplexColumn(int) afterwards for that column to make sure they are labeled properly in the FITS header (rather than as real-valued arrays of float or double).
Similarly, if adding arrays of boolean values, you might consider calling convertToBits(int) on that column for a more compact storage option of the true/false values, rather than as 1-byte FITS logicals (default).

Defragmenting might also be a good idea before writing binary tables with variable-length data built column by column (as opposed to row-by-row):

  table.defragment();

before calling write() on the encompassing HDU.

Creating ASCII tables (discouraged)

While the library also supports ASCII tables for storing a more limited assortment of scalar entries, binary tables should always be your choice for storing table data. ASCII tables are far less capable overall. And while they may be readable from a console without the need for other tools, there is no compelling reason for using ASCII tables today. Binary tables are simply better, because they:

Support arrays (including multidim and variable-length).
Support more data types (such as logical, and complex values).
Offer additional flexibility, such as variable sized and multi-dimensional array entries.
Take up less space on disk
Can be compressed to an even smaller size

However, if you insist on creating ASCII tables (provided the data allows for it) you may:

Build them column by column using one of the AsciiTable.addColumn(...) method, or
Build all at once, from a set of readily available columns via AsciiTable.fromColumnMajor(Object[]) (since 1.19), or else
Set FitsFactory.setUseAsciiTables(true) prior to calling Fits.makeHDU() or one of the factory methods to encapsulate a column-major table data objects automatically as ASCII tables whenever it is possible.

(Note that while the AsciiTable class also provides an .addRow(Object[]) method, we strongly recommend against it because it is extremely inefficient, i.e. painfully slow). Either way, you should keep in mind the inherent limitations of ASCII tables:

Only scalar entries are allowed (no arrays whatsoever!)
Only int, long, float, double and String entries are supported.

Compression support

File level compression
Image compression
Table compression

Starting with version 1.15 we include support for compressing images and tables. The compression algorithms have been ported to Java from cfitsio to provide a pure 100% Java implementation. However, versions prior to 1.19.1 had a number of lingering compression related bugs of varying severity, which may have prevented realiable use.

File level compression

It is common practice to compress FITS files using gzip (.gz extension) so they can be exchanged in a more compact form. Java 8+ supports the creation of gzipped FITS out of the box, by wrapping the file's output stream into a GZIPOutputStream or , such as:

  Fits f = ...
  
  FitsOutputStream out = new FitsOutputStream(new GZIPOutputStream(
  	new FileOutputStream(new File("mydata.fits.gz"))));
  f.write(out);

While we only support GZIP compression for writing compressed files (thanks to Java's support out of the box), we can read more compressed formats using Apaches commons-compress library. We support reading compressed files produced via gzip (.gz), the Linux compress tools (.Z), and via bzip2 (.bz2). The decompression happens automatically when we construct a Fits object with an input stream:

  new FileInputStream compressedStream = new FileInputStream(new File("image.fits.bz2"));
 
  // The input stream will be filtered through a decompression algorithm
  // All read access to the FITS will pass through that decompression...
  Fits fits = new Fits(compressedStream);
  ...

Image compression

Image compression and tiling are fully supported by nom-tam-fits as of 1.18, including images of any dimensionality and rectangular morphologies. (Releases between 1.15 and 1.17 had partial image compression support for 2D square images only, while some quantization support for compression was lacking prior to 1.18).

The tiling of non-2D images follows the CFITSIO convention with 2D tiles, where the tile size is set to 1 in the higher dimensions.

Compressing an image HDU is typically a multi-step process:

Create a CompressedImageHDU, e.g. with fromImageHDU(ImageHDU, int...):

  ImageHDU image = ...
 
  CompressedImageHDU compressed = CompressedImageHDU.fromImageHDU(image, 60, 40);

Set up the compression algorithm, including quantization (if desired) via setCompressAlgorithm(String) and setQuantAlgorithm(String), and optionally the compressiomn method used for preserving the blank values via preserveNulls(String):

  compressed.setCompressAlgorithm(Compression.ZCMPTYPE_RICE_1)
            .setQuantAlgorithm(Compression.ZQUANTIZ_SUBTRACTIVE_DITHER_1)
            .preserveNulls(Compression.ZCMPTYPE_HCOMPRESS_1);

Set compression (and quantization) options, via calling on getCompressOption(Class):

  compressed.getCompressOption(RiceCompressOption.class).setBlockSize(32);
  compressed.getCompressOption(QuantizeOption.class).setBZero(3.0).setBScale(0.1).setBNull(-999);

Finally, perform the actual compression via compress():

  compressed.compress();

After the compression, the compressed image HDU can be handled just like any other HDU, and written to a file or stream, for example (just not as the first HDU in a FITS...).

The reverse process is simply via the asImageHDU() method. E.g.:

  CompressedImageHDU compressed = ...
  ImageHDU image = compressed.asImageHDU();

When compressing or decompression images, all available CPUs are automatically utilized.

Accessing image header values without decompressing:

You don't need to decompress the image to see what the decompressed image header is. You can simply call CompressedImageHDU.getImageHeader() to peek into the reconstructed header of the image before it was compressed:

  CompressedImageHDU compressed = ...
  Header imageHeader = compressed.getImageHeader();

Accessing specific parts of a compressed image

Often compressed images can be very large, and we are interested in specific areas of it only. As such, we do not want to decompress the entire image. In these cases we can use the getTileHDU() method of CompressedImageHDU class to decompress only the selected image area. As of version 1.18, this is really easy also:

  CompressedImageHDU compressed = ...
   
  int[] fromPixels = ...
  int[] cutoutSize = ...
   
  ImageHDU cutout = compressed.getTileHDU(fromPixels, cutoutSize);

Table compression

Table compression is also supported in nom-tam-fits from version 1.15, and more completely since 1.19.1. When compressing a table, the 'tiles' are sets of contiguous rows within a column. Each column may use a different compression algorithm. As for FITS version 4.0 only lossless compression is supported for tables, and hence only GZIP_1, GZIP_2 (default), RICE_1 (with default options), and NOCOMPRESS are admissible. The default compression is with GZIP_2, unless explicitly defined otherwise.

Tile compression mimics image compression, and is typically a 2-step process:

Create a CompressedTableHDU, e.g. with fromBinaryTableHDU(BinaryTableHDU, int, String...), using the specified number of table rows per compressed block, and compression algorithm(s), e.g. RICE_1 for the first column, and GZIP_2 for the rest:

   BinaryTableHDU table = ...
   CompressedTableHDU compressed = CompressedTableHDU.fromBinaryTableHDU(table, 4, Compression.RICE_1);

Perform the compression via compress():

   compressed.compress();

The two step process (as opposed to a single-step one) was probably chosen because it mimics that of CompressedImageHDU, where further configuration steps may be inserted in-between (which might become possible in a future FITS standard). But, of course we can combine the steps into a single line:

   CompressedTableHDU compressed = CompressedTableHDU.fromBinaryTableHDU(table, 4, Compression.RICE_1).compress();

After the compression, the compressed table HDU can be handled just like any other HDU, and written to a file or stream, for example.

The reverse process is simply via the asBinaryTableHDU() method. E.g.:

    CompressedTableHDU compressed = ...
    BinaryTableHDU table = compressed.asBinaryTableHDU();

Accessing image header values without decompressing

You don't need to decompress the table to see what the decompressed table header is. You can simply call CompressedTableHDU.getTableHeader() to peek into the reconstructed header of the original table before it was compressed:

   CompressedTableHDU compressed = ...
   Header origHeader = compressed.getTableHeader();

Decompressing select parts of a compressed binary table

Sometimes we are interested in a section of the compressed table only. As of version 1.18, this is really easy also. If you just want to uncompress a range of the compressed tiles, you can

   CompressedTableHDU compressed = ...
   TableHDU section = compressed.asTableHDU(fromTile, toTile);

The resulting HDU will contain all columns but on only the uncompressed rows for the selected tiles.

And, if you want to surgically access a range of data from select columns (and tiles) only:

   CompressedTableHDU compressed = ...
   Object[] colData = compressed.getColumnData(colIndex, fromTile, toTile);

The methods CompressedTableHDU.getTileRows() and .getTileCount() can be used to help determined which tile(s) to decompress to get access to specific table rows.

Note on compressing variable-length arrays (VLAs)

The compression of variable-length table columns is a fair bit more involved process than that for fixed-sized table entries, and we only started properly supporting it in 1.19.1. When compressing/decompressing tables containing VLAs, you should be aware of the very limited interoperability with other tools, including (C)FITSIO and its fpack / funpack (more on these below). In fact, we are not aware of any tool other than nom.tam.fits that offers a truly complete and accurate implementation of this part of the standard.

Note, that the (C)FITSIO implementation of VLA compression diverges from the documented standard (FITS 4.0 and the original Pence et al. 2013 convention) by storing the adjoint desciptors in reversed order, w.r.t. the standard, on the heap. Our understanding, based on communication with the maintainers of the FITS standard, is that this discrepacy will be resolved by changing the documentation (the standard) to conform to the (C)FITSIO implementation. Therefore, our implementation for the compression of VLAs is generally compliant to that of (C)FITSIO, and not to the current prescription of the standard. However, we wish to support reading files produced either way via the static CompressedTableHDU.useOldStandardVLAIndexing(boolean) method selecting the convention according to which the adjoint table descriptors are stored in the file: either in the format described by the original FITS 4.0 standard / Pence+2013 convention (true), or else in the (C)FITSIO compatible format (false; default).

Interoperability with (C)FITSIO's `fpack` / `funpack`

The table compression implementation of nom.tam.fits is now both more standard(!) and more reliable(!) than that of (C)FITSIO and fpack / funpack. Issues of interoperability are not due to a fault of our own. Specifically, the current (4.4.0) and earlier (C)FITSIO releases are affected by a slew of table-compression related bugs, quirks, and oddities -- which severely limit its interoperability with other tools. Some of the bugs in fpack may result in entirely corrupted FITS files, while others limit what standard compressed data funpack is able to decompress:

(C)FITSIO and fpack version <= 4.4.0 do not properly handle the THEAP keyword (if present). If the keyword is present, fpack will use it incorrectly, resulting in a bloated compressed FITS that is also unreadable because of an incorrect PCOUNT value in the compressed header. Therefore, we will skip adding THEAP to the table headers when not necessary (that is when the heap follows immediately after the main table), in order to provide better interoperability with (C)FITSIO and fpack.
(C)FITSIO and fpack version <= 4.4.0 do not handle byte-type and short-type VLA columns properly. In the fpack-compressed headers these are indicated as compressed via GZIP_1 and GZIP_2 respectively (regardless of the user-specified compression option), whereas the data on the heap is not actually GZIP compressed for either (in fact, they appear uncompressed, actually). Note, that fpack does compress int type VLAs properly, albeit always with RICE_1, regardless of the user selection for the compression option; whereas fixed-sized byte[] and short[] array columns they are in fact compressed with GZIP_1 and GZIP_2 respectively, as indicated.
(C)FITSIO and funpack version <= 4.4.0 do not handle uncompressed data columns (with ZCTYPn = 'NOCOMPRESS') in compressed tables, despite these being standard.

Release schedule

A predictable release schedule and process can help manage expectations and reduce stress on adopters and developers alike.

Releases of the library follow a quarterly release schedule since version 1.16. You may expect upcoming releases to be published around March 15, June 15, September 15, and/or December 15 each year, on an as needed basis. That means that if there are outstanding bugs, or new pull requests (PRs), you may expect a release that addresses these in the upcoming quarter. The dates are placeholders only, with no guarantee that a release will actually be available every quarter. If nothing of note comes up, a potential release date may pass without a release being published.

Feature releases (1.x.0 version bumps), which may include significant API changes, are provided at least 6 months apart, to reduce stress on adopters who may need/want to tweak their code to integrate these. Between feature releases, bug fix releases (without significant API changes) may be provided as needed to address issues. New features are generally reserved for the feature releases, although they may also be rolled out in bug-fix releases as long as they do not affect the existing API -- in line with the desire to keep bug-fix releases fully backwards compatible with their parent versions.

In the month(s) preceding releases one or more release candidates (e.g. 1.19.1-rc3) will be available on github briefly, under Releases, so that changes can be tested by adopters before the releases are finalized. Please use due diligence to test such release candidates with your code when they become available to avoid unexpected suprises when the finalized release is published. Release candidates are typically available for one week only before they are superseded either by another, or by the finalized release.

How to contribute

The nom-tam-fits library is a community-maintained project. We absolutely rely on developers like you to make it better and to keep it going. Whether there is a nagging issue you would like to fix, or a new feature you'd like to see, you can make a difference yourself. We welcome you as a contributor. You became part of our community the moment you landed on this page. We very much encourange you to make this project a little bit your own, by submitting pull requests with fixes and enhancement. When you are ready, here are the typical steps for contributing to the project:

Old or new Issue? Whether you just found a bug, or you are missing a much needed feature, start by checking open (and closed) Issues. If an existing issue seems like a good match to yours, feel free to comment on it, and/or to offer help in resolving it. If you find no issues that match, go ahead and create a new one.
Fork. Is it something you'd like to help resolve? Great! You should start by creating your own fork of the repository so you can work freely on your solution. We also recommend that you place your work on a branch of your fork, which is named either after the issue number, e.g. issue-192, or some other descriptive name, such as implement-foreign-hdu.
Develop. Feel free to experiment on your fork/branch. If you run into a dead-end, you can always abandon it (which is why branches are great) and start anew. You can run your own test builds locally using mvn clean test before committing your changes. If the tests pass, you should also try running mvn clean package and mvn site stage to ensure that the package and javadoc are also in order. Remember to synchronize your master branch by fetching changes from upstream every once in a while, and rebasing your development branch. Don't forget to:
- Add Javadoc your new code. You can keep it sweet and simple, but make sure it properly explains your methods, their arguments and return values, and why and what exceptions may be thrown. You should also cross-reference other methods that are similar, related, or relevant to what you just added.
- Add Unit Tests. Make sure your new code has as close to full unit test coverage as possible. You should aim for 100% diff coverage. When pushing changes to your fork, you can get a coverage report by checking the Github Actions result of your commit (click the Codecov link), and you can analyze what line(s) of code need to have tests added. Try to create tests that are simple but meaningful (i.e. check for valid results, rather than just confirm existing behavior), and try to cover as many realistic scenarios as appropriate. Write lots of tests if you need to. It's OK to write 100 lines of test code for 5 lines of change. Go for it! And, you will get extra kudos for filling unit testing holes outside of your area of development!
Pull Request. Once you feel your work can be integrated, create a pull request from your fork/branch. You can do that easily from the github page of your fork/branch directly. In the pull request, provide a concise description of what you added or changed. Your pull request will be reviewed. You may get some feedback at this point, and maybe there will be discussions about possible improvements or regressions etc. It's a good thing too, and your changes will likely end up with added polish as a result. You can be all the more proud of it in the end!
If all goes well, your pull-request will get merged, and will be included in the upcoming release of nom-tam-fits. Congratulations for your excellent work, and many thanks for dedicating some of your time for making this library a little bit better. There will be many who will appreciate it. :-)

If at any point you have questions, or need feedback, don't be afraid to ask. You can put your questions into the issue you found or created, or your pull-request, or as a Q&A in Discussions.

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