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uvh5_memo.tex
% This is uvh5_memo.tex, a memo on the uvh5 format
% The minted package is used for syntax highlighting of code, and requires the
% pygments package to be installed. pdflatex also needs to be invoked with the
% -shell-escape option. To compile this document:
%   $ pdflatex -shell-escape uvh5_memo.tex
% This should compile the document into uvh5_memo.pdf

\documentclass[11pt, oneside]{article}
\usepackage{geometry}
\geometry{letterpaper}
\usepackage{graphicx}
\usepackage[titletoc,toc,title]{appendix}							
\usepackage{amssymb}

\usepackage{hyperref} 
\hypersetup{
    colorlinks = true
}

\usepackage{cleveref}
\crefformat{footnote}{#2\footnotemark[#1]#3}
\usepackage{minted}

\title{Memo: UVH5 file format}
\author{Paul La Plante, and the pyuvdata team}
\date{November 28, 2018}

\begin{document}
\maketitle
\tableofcontents
\section{Introduction}
\label{sec:intro}
This memo introduces a new HDF5\footnote{\url{https://www.hdfgroup.org/}}-based
file format of a UVData object in
\verb+pyuvdata+\footnote{\url{https://github.com/HERA-Team/pyuvdata}}, a python
package that provides an interface to interferometric data. Here, we describe
the required and optional elements and the structure of this file format, called
\textit{UVH5}.

Note that this file format is specifically designed to represent UVData
objects. Other HDF5-based datasets for radio interferometers, such as
katdal\footnote{\url{https://github.com/ska-sa/katdal}} or
HDFITS\footnote{\url{https://github.com/telegraphic/fits2hdf}} \textit{are not
  compatible} with the standard as defined here. We refer the reader to the
documentation of those other formats to find out more about them.

We assume that the user has a working knowledge of HDF5 and the associated
python bindings in the package \verb+h5py+\footnote{\url{https://www.h5py.org/}}, as
well as UVData objects in pyuvdata. For more information about HDF5, please
visit \url{https://portal.hdfgroup.org/display/HDF5/HDF5}. For more information
about the parameters present in a UVData object, please visit
\url{http://pyuvdata.readthedocs.io/en/latest/uvdata_parameters.html}. An
example for how to interact with UVData objects in pyuvdata is available at
\url{http://pyuvdata.readthedocs.io/en/latest/tutorial.html}.

\section{Overview}
\label{sec:overview}
A UVH5 object contains the interferometric data from a radio telescope, as well
as the associated metadata necessary to interpret it. A UVH5 file contains two
primary HDF5 groups: the \verb+Header+ group, which contains the metadata, and
the \verb+Data+ group, which contains the data itself, the flags, and
information about the number of samples corresponding to the data. Datasets in
the \verb+Data+ group are also typically passed through HDF5's compression
pipeline, to reduce the amount of on-disk space required to store the data.
However, because HDF5 is aware of any compression applied to a dataset, there is
little that the user has to explicitly do when reading data. For users
interested in creating new files, the use of compression is not strictly
required by the UVH5 format, again because the HDF5 file is self-documenting in
this regard. However, be warned that most UVH5 files ``in the wild'' typically
feature compression of datasets in the \verb+Data+ group.

In the disucssion below, we discuss required and optional datasets in the
various groups. We note in parenthesis the corresponding attribute of a UVData
object. Note that in nearly all cases, the names are coincident, to make things
as transparent as possible to the user.

\section{Header}
\label{sec:header}
The \verb+Header+ group of the file contains the metadata necessary to interpret
the data. We begin with the required parameters, then continue to optional
ones. Unless otherwise noted, all datasets are scalars (i.e., not arrays). The
precision of the data type is also not specified as part of the format, because
in general the user is free to set it according to the desired use case (and
HDF5 records the precision and endianness when generating datasets). When using
the standard \verb+h5py+-based implementation in pyuvdata, this typically
results in 32-bit integers and double precision floating point numbers. Each
entry in the list contains \textbf{(1)} the exact name of the dataset in the
HDF5 file, in boldface, \textbf{(2)} the expected datatype of the dataset, in
italics, \textbf{(3)} a brief description of the data, and \textbf{(4)} the name
of the corresponding attribute on a UVData object. Note that unlike in other
formats, names of HDF5 datasets can be quite long, and so in most cases the name
of the dataset corresponds to the name of the UVData attribute.

Note that string datatypes should be handled with care. See
Appendix~\ref{appendix:strings} for appropriately defining them for
interoperability between different HDF5 implementations.

\subsection{Required Parameters}
\label{sec:req_params}
\begin{itemize}
\item \textbf{latitude}: \textit{float} The latitude of the telescope site, in
  degrees. (\textit{latitude})
\item \textbf{longitude}: \textit{float} The longitude of the telescope site, in
  degrees. (\textit{longitude})
\item \textbf{altitude}: \textit{float} The altitude of the telescope site, in
  meters. (\textit{altitude})
\item \textbf{telescope\_name}: \textit{string} The name of the telescope used
  to take the data. The value is used to check that metadata is self-consistent
  for known telescopes in pyuvdata. (\textit{telescope\_name})
\item \textbf{instrument}: \textit{string} The name of the instrument, typically
  the telescope name. (\textit{instrument})
\item \textbf{object\_name}: \textit{string} The name of the object tracked by
  the telescope. For a drift-scan antenna, this is typically
  ``zenith''. (\textit{object\_name})
\item \textbf{history}: \textit{string} The history of the data
  file. (\textit{history})
\item \textbf{phase\_type}: \textit{string} The phase type of the
  observation. Should be ``phased'' or ``drift''. Any other value is treated as
  an unrecognized type. (\textit{phase\_type})
\item \textbf{Nants\_data}: \textit{int} The number of antennas that data in the
  file corresponds to. May be smaller than the number of antennas in the
  array. (\textit{Nants\_data})
\item \textbf{Nants\_telescope}: \textit{int} The number of antennas in the
  array. May be larger than the number of antennas with data corresponding to
  them. (\textit{Nants\_telescope})
\item \textbf{ant\_1\_array}: \textit{int} An array of the first antenna indices
  corresponding to baselines present in the data. This is a one-dimensional
  array of size Nblts. (\textit{ant\_1\_array})
\item \textbf{ant\_2\_array}: \textit{int} An array of the second antenna indices
  corresponding to baselines present in the data. This is a one-dimensional
  array of size Nblts. (\textit{ant\_2\_array})
\item \textbf{antenna\_names}: \textit{string} An array of the names of antennas
  present in the array. This is a one-dimensional array of size
  Nants\_telescope. Note there must be one entry for every unique antenna in
  ant\_1\_array and ant\_2\_array, but there may be additional
  entries. (\textit{antenna\_names})
\item \textbf{Nbls}: \textit{int} the number of baselines present in the
  data. For full cross-correlation data (including auto-correlations), this
  should be Nants\_data$\times$(Nants\_data+1)/2. (\textit{Nbls})
\item \textbf{Nblts}: \textit{int} The number of baseline-times (i.e., the
  number of spectra) present in the data. Note that this value need not be equal
  to Nbls $\times$ Ntimes. (\textit{Nblts})
\item \textbf{Nfreqs}: \textit{int} The number of frequency channels in the
  data. (\textit{Nfreqs})
\item \textbf{Npols}: \textit{int} The number of polarization products in the
  data. (\textit{Npols})
\item \textbf{Ntimes}: \textit{int} The number of time samples present in the
  data. (\textit{Ntimes})
\item \textbf{Nspws}: \textit{int} The number of spectral windows present in the
  data. (\textit{Nspws})
\item \textbf{uvw\_array}: \textit{float} An array of the uvw-coordinates
  corresponding to each observation in the data. This is a two-dimensional array of
  size (Nblts, 3). (\textit{uvw\_array})
\item \textbf{time\_array}: \textit{float} An array of the Julian Date
  corresponding to the center of an integration. This is a one-dimensional array
  of size Nblts. (\textit{time\_array})
\item \textbf{integration\_time}: \textit{float} An array of the length of time
  in seconds of an integration. This is a one-dimensional array of size
  Nblts. (\textit{time\_array})
\item \textbf{freq\_array}: \textit{float} An array of the frequencies stored in
  the file in Hertz. This is a two-dimensional array of size (Nspws,
  Nfreqs). (\textit{freq\_array})
\item \textbf{channel\_width}: \textit{float} The width of frequency channels in
  the file in Hertz. (\textit{channel\_width})
\item \textbf{spw\_array}: \textit{int} An array of the spectral windows in the
  file. This is a one-dimensional array of size Nspws. (\textit{spw\_array})
\item \textbf{polarization\_array}: \textit{int} An array of the polarizations
  contained in the file. This is a one-dimensional array of size Npols. Note
  that the polarizations should be stored as an integer, and use the convention
  defined in AIPS Memo 117. (\textit{polarization\_array})
\item \textbf{antenna\_positions}: \textit{float} An array of the antenna
  coordinates relative to the \textit{telescope\_location} (in the ITRF
  frame). This is a two-dimensional array of size (Nants\_telescope,
  3). (\textit{antenna\_positions})
\end{itemize}

\subsection{Optional Parameters}
\label{sec:opt_params}
\begin{itemize}
\item \textbf{dut1}: \textit{float} DUT1 (google it). AIPS 117 calls it
  ``UT1UTC''. (\textit{dut1})
\item \textbf{earth\_omega}: \textit{float} Earth's rotation rate in degrees per
  day. (\textit{earth\_omega})
\item \textbf{gst0}: \textit{float} Greenwich sidereal time at midnight on
  reference date. (\textit{gst0})
\item \textbf{rdate}: \textit{string} Date for which GST0 (or whichever time
  saved in that field) applies. (\textit{rdate})
\item \textbf{timesys}: \textit{string} Time system. pyuvdata currently only
  supports UTC. (\textit{timesys})
\item \textbf{x\_orientation}: \textit{string} The orientation of the x-arm of a
  dipole antenna. It is assumed to be the same for all antennas in the
  dataset. For instance, ``E'' or ``East'' may be
  used. (\textit{x\_orientation}).
\item \textbf{antenna\_diameters}: \textit{float} An array of the diameters of
  the antennas in meters. This is a one-dimensional array of size
  (Nants\_telescope). (\textit{Nants\_telescope})
\item \textbf{uvplane\_reference\_time}: \textit{int} The time at which the
  phase center is normal to the chosen UV plane for phasing. Used for
  interoperability with the FHD
  package\footnote{\url{https://github.com/EoRImaging/FHD}}.
\item \textbf{phase\_center\_ra}: \textit{float} The right ascension of the
  phase center of the observation in radians. Required if phase\_type is
  ``phased''. (\textit{phase\_center\_ra})
\item \textbf{phase\_center\_dec}: \textit{float} The declination of the phase
  center of the observation in radians. Required if phase\_type is
  ``phased''. (\textit{phase\_center\_dec}).
\item \textbf{phase\_center\_epoch}: \textit{float} The epoch year of the phase
  applied to the data (\textit{e.g.}, 2000.). Required if phase\_type is
  ``phased''. (\textit{phase\_center\_epoch})
\item \textbf{phase\_center\_frame}: \textit{string} The frame the data and
  uvw\_array are phased to. Options are ``gcrs'' and ``icrs'', with default
  ``icrs''. (\textit{phase\_center\_frame})
\item \textbf{lst\_array}: \textit{float} An array corresponding to the local
  sidereal time of the center of each observation in the data in units of
  radians. If it is not specified, it is calculated from the latitude/longitude
  and the time\_array. (\textit{lst\_array})
\end{itemize}

\subsection{Extra Keywords}
\label{sec:extra_keywords}
UVData objects support ``extra keywords'', which are additional bits of
arbitrary metadata useful to carry around with the data but which are not
formally supported as a reserved keyword in the \verb+Header+. In a UVH5 file,
extra keywords are handled by creating a datagroup called \verb+extra_keywords+
inside the \verb+Header+ datagroup. In a UVData object, extra keywords are
expected to be scalars, but UVH5 makes no formal restriction on this. Inside of
the extra\_keywords datagroup, each extra keyword is saved as a key-value pair
using a dataset, where the name of the extra keyword is the name of the dataset
and its corresponding value is saved in the dataset. Though the use of HDF5
attributes can also be used to save additional metadata, it is not recommended,
due to the lack of support inside of pyuvdata for ensuring the attributes are
properly saved when writing out.


\section{Data}
\label{sec:data}
In addition to the \verb+Header+ datagroup in the root namespace, there must be
one called \verb+Data+. This datagroup saves the visibility data, flags, and
number of samples corresponding to each entry. All three datasets must be
present in a valid UVH5 file. They are also all expected to be the same shape:
(Nblts, Nspws, Nfreqs, Npols). Note that due to the intermixing of the baseline
and time axes, it is \textit{not} required for data to exist for every baseline
and time in the file. This behavior is similar to UVFITS and MIRIAD file
formats. Also note that there is no explicit ordering required for the
baseline-time axis. A common ordering is to write the data in ``correlator
order'', and have all baselines for a single time $t_i$, followed by all
baselines for the next time $t_{i+1}$, etc. However, this is merely a
convention, and is not explicitly required for the UVH5 format.

\subsection{Visdata Dataset}
\label{sec:visdata}
The visibility data is saved as a dataset named \verb+visdata+. It should be a
4-dimensional, complex-type dataset with shape (Nblts, Nspws, Nfreqs,
Npols). Most commonly this is saved as an 8-byte complex number (a 4-byte float
for the real and imaginary parts), though some flexibility is possible. 16-byte
complex floating point numbers (composed of two 8-byte floats), as well as
8-byte complex integers (two 4-byte signed integers). In all cases, a compound
datatype is defined, with an \verb+`r'+ field and an \verb+`i'+ field,
corresponding to the real and imaginary parts, respectively. The real and
imaginary types must also be the same datatype. For instance, they should both
be 8-byte floating point numbers, or 32-bit (4-byte) integers. Mixing datatypes
between the real and imaginary parts is not allowed.

Using \verb+h5py+, the datatype for \verb+visdata+ can be specified as
\verb+`c8'+ (8-byte complex numbers, corresponding to the \verb+np.complex64+
datatype) or \verb+`c16'+ (16-byte complex numbers, corresponding to the
\verb+np.complex128+ datatype) out-of-the-box, with no special handling by the
user. \verb+h5py+ transparently handles the definition of the compound
datatype. For examples of how to handle complex integer datatypes in
\verb+h5py+, see Appendix~\ref{appendix:integers}.


\subsection{Flags Dataset}
\label{sec:flags}
The flags corresponding to the data are saved as a dataset named
\verb+flags+. It is a 4-dimensional, boolean-type dataset with shape (Nblts,
Nspws, Nfreqs, Npols). Values of True correspond to instances of flagged data,
and False is non-flagged. Note that the boolean type of the data is \textit{not}
the HDF5-provided \verb+H5T_NATIVE_HBOOL+, and instead is defined to conform to
the \verb+h5py+ implementation of the numpy boolean type. When creating this
dataset from \verb+h5py+, one can specify the datatype as \verb+np.bool+. Behind
the scenes, this defines an HDF5 enum datatype. See
Appendix~\ref{appendix:boolean} for an example of how to write a compatible
dataset from C.

As with the nsamples dataset discussed below, compression is typically applied
to the flags dataset. The LZF filter (included in all HDF5 libraries) provides a
good compromise between speed and compression. In the special cases of
single-valued arrays, the dataset occupies virtually no disk space.

\subsection{Nsamples Dataset}
\label{sec:nsamples}
The number of data points averaged into each data entry is saved as a dataset
named \verb+nsamples+. It is a 4-dimensional, floating-point type dataset with
shape (Nblts, Nspws, Nfreqs, Npols). Note that it is \textit{not} required to be
an integer, and should \textit{not} be saved as an integer type. The product of
the integration\_time array and the data in the nsample array reflects the total
amount of time that went into a visibility. The best practice is for the
nsamples dataset to track flagging within an integration time (leading to a
decrease of the nsamples array value to be less than 1) and LST averaging
(leading to an increase in the nsamples array value). Datasets that have not
been LST averaged should have values in nsamples that are less than or equal to
1. Although this convention is not adhered to by all data formats serviced by
\verb+pyuvdata+, it is recommended to follow it as closely as possible in UVH5
files. What \textit{should} be true is the product of the integration\_time
array and nsamples array corresponding to the total amount of time included in a
visibility.

\newpage

\begin{appendices}
\section{Writing Strings from h5py}
\label{appendix:strings}
String datatypes are finicky, and require special handling to ensure that they
are compatible with the HDF5 bindings in various languages. This is especially
true for files written from \verb+h5py+, which handles strings differently
between python2 and python3. Though python2 is nearing its end-of-life, UVH5
should be backwards compatible with older versions of \verb+h5py+ as much as
possible. To help service this, all string-type metadata in UVH5 files
\textit{must} be fixed-length ASCII type. Not only does this allow for
interoperability between different \verb+h5py+ versions, but it also ensures
that strings can be round-tripped through other HDF5 bindings, such as those in
C, MATLAB, IDL, Fortran\footnote{Strings in Fortran are not null-terminated, so
  these require special handling.}, etc. Note that the string should use one
byte per character, and be null-terminated. This corresponds to the numpy
\verb+S+ datatype in both versions of python2 and python3.

When writing a string-like dataset from \verb+h5py+, scalar data should be
written by casting a string to a \verb+numpy.string_+ object. Array data should
be written as a \verb+S<n>+ dataset, where \verb+<n>+ represents the length of
the strings to be saved. Upon reading, strings can be cast to bytes using the
\verb+tostring()+ method, at which point the data is \verb+<str>+-type (python2)
or can be decoded as UTF-8 to become \verb+<str>+-type (python3).

Below is an example for how to read and write string scalar and array-type
datasets using \verb+h5py+ in python2 and python3.

\subsection{python2}
\begin{minted}{python}
import numpy as np
import h5py
# open file and write string datasets
with h5py.File('test_file.uvh5', 'w') as f:
    header = f.create_group('Header')
    # scalar dataset
    header['scalar_string'] = np.string_('Hello world!')

    # array dataset
    str_array = np.array(['hello', 'world'])
    n_words = len(str_array)
    max_len_words = np.amax([len(n) for n in str_array])
    dtype = "S{:d}".format(max_len_words)
    header.create_dataset('array_string', (n_words,), dtype=dtype,
                          data=str_array)

# read the data back in again
with h5py.File('test_file.uvh5', 'r') as f:
    header = f['Header']
    # read scalar dataset
    scalar_string = header['scalar_string'].value.tostring()
    assert scalar_string == 'Hello world!'

    # read array dataset
    str_array_file = [n.tostring() for n in header['array_string'].value]
    assert np.all(str_array_file == str_array)
\end{minted}

\subsection{python3}
\begin{minted}{python}
import numpy as np
import h5py
# open file and write string datasets
with h5py.File('test_file.uvh5', 'w') as f:
    header = f.create_group('Header')
    # scalar dataset
    header['scalar_string'] = np.string_('Hello world!')

    # array dataset
    str_array = ['hello', 'world']
    header['array_string'] = np.string_(str_array)

# read the data back in again
with h5py.File('test_file.uvh5', 'r') as f:
    header = f['Header']
    # read scalar dataset
    scalar_string = header['scalar_string'].value.tostring().decode('UTF-8')
    assert scalar_string == 'Hello world!'

    # read array dataset
    str_array_file = [n.tostring().decode('UTF-8')
                      for n in header['array_string'].value]
    assert np.all(str_array_file == str_array)
\end{minted}


\section{Integer Datatype Support for Visibility Data}
\label{appendix:integers}
The HERA correlator writes datasets which have 32-bit integer real and imaginary
components. Due to the self-describing nature of HDF5 datasets, this information
is captured by the file format. Nevertheless, special handling must be used to
interpret these datasets as complex numbers. The \verb+astype+ context manager
in \verb+h5py+ is used to convert the datatype on the fly from integers to
complex numbers. Below is an example of how to do this.

\begin{minted}{python}
import numpy as np
import h5py
# define integer datatype
int_dtype = np.dtype([('r', '<i4'), ('i', '<i4')])

# open file and read in the dataset
with h5py.File('test_file.uvh5', 'r') as f:
    visdata = f['Data/visdata']
    dshape = visdata.shape
    data = np.empty(dshape, dtype=np.complex128)
    with visdata.astype(int_dtype):
        data.real = visdata['r'][:, :, :, :]
        data.imag = visdata['i'][:, :, :, :]
\end{minted}


\section{Defining \texttt{numpy} Boolean Arrays in C}
\label{appendix:boolean}
As mentioned in Sec.~\ref{sec:flags}, the flags array in a UVH5 file uses an
HDF5 enum datatype to encode the numpy boolean type. When creating such a
datatype using \verb+h5py+, the user simply needs to ensure the datatype is
\verb+np.bool+. The building of the enum is transparent. When building the enum
from a different language, the precise specification is necessary to ensure
compatibility. The following code is a template for how to build the appropriate
datatype using C. The construction in other languages, such as Fortran, should
follow analogously.
\begin{minted}{c}
#include <hdf5.h>

#define CPTR(VAR,CONST) ((VAR)=(CONST),&(VAR))

typedef enum {
  FALSE,
  TRUE
} bool_t;

int main() {
  bool_t val;
  static hid_t boolenumtype;
  hid_t file_id, dspace_id, flags_id;
  herr_t status;

  /* define enum type */
  boolenumtype = H5Tcreate(H5T_ENUM, sizeof(bool_t));
  H5Tenum_insert(boolenumtype, "FALSE", CPTR(val, FALSE ));
  H5Tenum_insert(boolenumtype, "TRUE" , CPTR(val, TRUE  ));

  /* open a new file */
  file_id = H5Fcreate("test_file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);

  /* define array dimensions */
  int Nblts = 10;
  int Nspws = 1;
  int Nfreqs = 16;
  int Npols = 4;
  hsize_t dims[4] = {Nblts, Nspws, Nfreqs, Npols};

  /* initialize data array with FALSE values */
  bool_t data[Nblts][Nspws][Nfreqs][Npols];
  for (int i=0; i<Nblts; i++) {
    for (int j=0; j<Nspws; j++) {
      for (int k=0; k<Nfreqs; k++) {
        for (int l=0; l<Npols; l++) {
          data[i][j][k][l] = FALSE;
        }
      }
    }
  }

  /* make dataspace and write out data */
  dspace_id = H5Screate_simple(4, dims, dims);
  flags_id = H5Dcreate(file_id, "flags", boolenumtype, dspace_id,
                       H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
  status = H5Dwrite(flags_id, boolenumtype, H5S_ALL, H5S_ALL,
                    H5P_DEFAULT, data);

  /* close down */
  H5Dclose(flags_id);
  H5Sclose(dspace_id);
  H5Fclose(file_id);
  return 0;
}
\end{minted}


\end{appendices}

\end{document}


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