from __future__ import (print_function, absolute_import, division, unicode_literals) import contextlib import shutil import sys import subprocess import shlex import os import time import array import platform import textwrap as tw import warnings import xpa from io import BytesIO """ ds9.py connects python and ds9 via the xpa messaging system: - The ds9 class constructor connects to a single instance of a running ds9. - The ds9 object supports 'set' and 'get' methods to communicate with ds9. - Send/retrieve numpy arrays and pyfits (or astropy) hdulists to/from ds9. - The ds9_targets() function lists ds9 programs running on your system. - The ds9_openlist() function connects to a list of running ds9 instances. """ # pyds9 version __version__ = '1.8.1' # try to be a little bit neat with global parameters ds9Globals = {} # platform-specific parameters ds9Globals["ulist"] = platform.uname() def get_xpans_ds9(): """Look for xpans and ds9 executable or app Returns ------- xpans : string full path to the xpans executable ds9 : list of strings path to the ds9 executable or, on OSX, ``["open", "-a" to call the Aqua version. """ # create the path there to look for xpans executable xpans_path = os.environ['PATH'] pyds9_dir = os.path.dirname(__file__) # it could be the development version, then the executable is in the # ``xpa`` directory containing the c code xpa_dir = os.path.join(os.path.dirname(__file__), 'xpa') xpans_path = os.pathsep.join([pyds9_dir, xpa_dir, xpans_path]) # find the executables xpans = shutil.which('xpans', path=xpans_path) ds9 = [shutil.which('ds9')] # warning message in case ds9 and/or xpans is not found ds9_warning = ("Can't locate DS9 executable. Please add the DS9 directory" " to your PATH and try again.") xpans_warning = ("Can't locate xpans executable.") if ds9Globals["ulist"][0] == 'Darwin' and not ds9[0]: # on mac OSX the Aqua version can be installed. If this is the case, # look for a "SAOImage DS9.app" directory in ``/Applications``, # ``$HOME`` and ``$HOME/Applications``. If it's found use the mac # ``open`` command ds9_app = "SAOImage DS9.app" user_dir = os.path.expanduser('~') for p in ['/Applications', user_dir, os.path.join(user_dir, 'Applications'), os.path.join(user_dir, 'Desktop')]: ds9_app_dir = os.path.join(p, ds9_app) if os.path.exists(ds9_app_dir): ds9 = ['open', '-a', ds9_app_dir, '--args'] break ds9_warning = ("Can't locate the X11 DS9 executable in your PATH or" " the Aqua SAOImage DS9 app in /Applications, $HOME" " or $HOME/Applications. Please configure your PATH or" " make SAOImage DS9 available in a known location.") # warn the user if xpans or ds9 is not found if not xpans: warnings.warn(xpans_warning) if not ds9[0]: warnings.warn(ds9_warning) return xpans, ds9 ds9Globals["progs"] = get_xpans_ds9() # default list of commands that returns binary data that should not be decoded ds9Globals['bin_cmd'] = ["array", "fits", "fits image", "fits table", "fits slice", "gif", "jpeg", "mecube", "mosaic", "mosaicimage", "nrrd", "png", "rgbarray", "rgbcube", "rgbimage", "tiff"] # load pyfits, if available try: from astropy.io import fits as pyfits ds9Globals["pyfits"] = 1 except: try: import pyfits if pyfits.__version__ >= '2.2': ds9Globals["pyfits"] = 2 else: ds9Globals["pyfits"] = 0 except: ds9Globals["pyfits"] = 0 # load numpy, if available try: import numpy ds9Globals["numpy"] = 1 except: ds9Globals["numpy"] = 0 # numpy-dependent routines if ds9Globals["numpy"]: def _bp2np(bitpix): """ Convert FITS bitpix to numpy datatype """ if bitpix == 8: return numpy.uint8 elif bitpix == 16: return numpy.int16 elif bitpix == 32: return numpy.int32 elif bitpix == 64: return numpy.int64 elif bitpix == -32: return numpy.float32 elif bitpix == -64: return numpy.float64 elif bitpix == -16: return numpy.uint16 else: raise ValueError('unsupported bitpix: %d' % bitpix) def _np2bp(dtype): """ Convert numpy datatype to FITS bitpix """ if dtype.kind == 'u': # unsigned ints if dtype.itemsize == 1: return 8 if dtype.itemsize == 2: # this is not in the FITS standard? return -16 elif dtype.kind == 'i': # integers if dtype.itemsize == 2: return 16 elif dtype.itemsize == 4: return 32 elif dtype.itemsize == 8: return 64 elif dtype.kind == 'f': # floating point if dtype.itemsize == 4: return -32 elif dtype.itemsize == 8: return -64 raise ValueError('unsupported dtype: %s' % dtype) def string_to_bytes(string): """Converts the input (list of) string(s) into (a list of) bytes :param string: string or list of strings to encode :rtypes: (list of) byte string(s) """ if True: if isinstance(string, str): return string.encode() elif isinstance(string, bytes): return string else: try: out = [] for s in string: if isinstance(s, str): out.append(s.decode()) else: out.append(s) return out except TypeError: # non iterable return string else: return string def bytes_to_string(byte): """Converts the input (list of) byte string(s) into (a list of) string(s) :param byte: (list of) byte string(s) to decode :rtypes: string or list of strings """ if True: if isinstance(byte, bytes): return byte.decode() elif isinstance(byte, str): return byte else: try: out = [] for b in byte: if isinstance(b, bytes): out.append(b.decode()) else: out.append(b) return out except TypeError: # non iterable return byte else: return byte # if xpans is not running, start it up def ds9_xpans(): """ :rtype: 0 => xpans already running, 1 => xpans started by this routine ds9_xpans() starts the xpans name server, if its not already running. If xpans was not running (and so was started by this routine) while ds9 was already running, an explanation on how to connect to that instance of ds9 is displayed. """ if xpa.xpaaccess(b"xpans", None, 1) is None: _fname = ds9Globals["progs"][0] if _fname: # start up xpans subprocess.Popen([_fname, "-e"]) # if ds9 is already running, issue a warning p = subprocess.Popen(['ps', '-A'], stdout=subprocess.PIPE, universal_newlines=True) pslist = p.communicate()[0] # get the std out if 'ds9' in pslist: print(tw.dedent(""" An instance of ds9 was found to be running before we could start the 'xpans' name server. You will need to perform a bit of manual intervention in order to connect this existing ds9 to Python. For ds9 version 5.7 and beyond, simply register the existing ds9 with the xpans name server by selecting the ds9 File->XPA->Connect menu option. Your ds9 will now be fully accessible to pyds9 (e.g., it appear in the list returned by the ds9_targets() routine). For ds9 versions prior to 5.7, you cannot (easily) register with xpans, but you can view ds9's File->XPA Information menu option and pass the value associated with XPA_METHOD directly to the Python DS9() constructor, e.g.: d = DS9('a000101:12345') The good news is that new instances of ds9 will be registered with xpans, and will be known to ds9_targets() and the DS9() constructor. """)) return 1 else: raise ValueError("xpans is not running and cannot be located. You" " will not be able to communicate with ds9") else: return 0 def ds9_targets(target='DS9:*'): """ :param target: ds9 target template (default: all ds9 instances) :rtype: list of available targets matching template (name and id) To see all actively running ds9 instances for a given target, use the ds9_targets() routine:: >>> ds9_targets() ['DS9:foo1 838e29d4:42873', 'DS9:foo2 838e29d4:35739'] You then can pass one of the ids (or names) to the DS9() constructor. """ targets = xpa.xpaaccess(string_to_bytes(target), None, 1024) return bytes_to_string(targets) def ds9_openlist(target='DS9:*', n=1024): """ :param target: the ds9 target template (default: all ds9 instances) :param n: maximum number of targets to connect to (default: 1024) :rtype: list of connected ds9 objects To open multiple instances of ds9, use the ds9_openlist() routine. Specify the target template and an (optional) max target count, and the routine returns a list of ds9 objects. For example, assuming 3 instances of ds9 are running with names foo1, foo2, foo3:: >>> ds9list = ds9_openlist("foo*") >>> for d in ds9list: ... print d.target, d.id ... DS9:foo1 a000104:56249 DS9:foo2 a000104:56254 DS9:foo3 a000104:56256 >>> ds9list[1].set("file test.fits") """ tlist = xpa.xpaaccess(string_to_bytes(target), None, n) if not tlist: raise ValueError('no active ds9 found for target: %s' % target) else: ds9list = [] for item in bytes_to_string(tlist): ds9list.append(DS9(item.split()[0])) return ds9list class DS9(object): """ The DS9 class supports communication with a running ds9 program via the xpa messaging system. All of ds9's xpa access points are available via the DS9.get() and DS9.set() methods: - str = get(paramlist): get data or info from ds9 - n = set(paramlist, [buf, [blen]]): send data or commands to ds9 The get method returns the data as a string, while the set method returns the number of targets successfully processed (i.e., 1 means success, while 0 probably means the ds9 is no longer running). DS9's xpa access points are documented in the reference manual: - http://hea-www.harvard.edu/saord/ds9/ref/xpa.html In addition, a number of special methods are implemented to facilitate data access to/from python objects: - get_arr2np: retrieve a FITS image or an array into a numpy array - get_np2arr: send a numpy array to ds9 for display - get_pyfits: retrieve a FITS image into a pyfits (or astropy) hdu list - set_pyfits: send a pyfits (or astropy) hdu list to ds9 for display """ # access points that do not get trailing cr stripped from them _nostrip = ['array', 'fits', 'regions'] # private attributes that cannot be changed _privates = ['target', 'id', 'method'] # ds9 constructor args: # target => XPA template (only one target per object is allowed) # verify => use xpaaccess to check target before each method call def __init__(self, target='DS9:*', start=True, wait=10, verify=True): """ :param target: the ds9 target name or id (default is all ds9 instances) :param start: start ds9 if its not already running (optional: instead of True, you can specify a string or a list of ds9 command line args) :param wait: seconds to wait for ds9 to start :param verify: perform xpaaccess check before each set or get? :rtype: DS9 object connected to a single instance of ds9 The DS9() contructor takes a ds9 target as its main argument. If start is True (default), the ds9 program will be started automatically if its not already running. The default target matches all ds9 instances. (Note that ds9 instances are given unique names using the -title switch on the command line). In general, this is the correct way to find ds9 if only one instance of the program is running. However, this default target will throw an error if more than one ds9 instance is running. In this case, you will be shown a list of the actively running programs and will be asked to use one of them to specify which ds9 is wanted:: >>> DS9() More than one ds9 is running for target DS9:*: DS9:foo1 838e29d4:42873 DS9:foo2 838e29d4:35739 Use a specific name or id to construct a ds9 object, e.g.: d = ds9('foo1') d = ds9('DS9:foo1') d = ds9('838e29d4:42873') The 'ip:port' id (3rd example) will always be unique. ... ValueError: too many ds9 instances running for target: DS9:* You then can choose one of these to pass to the contructor:: d = DS9('838e29d4:35739') Of course, you can always specify a name for this instance of ds9. A unique target name is especially appropriate if you want to start up ds9 with a specified command line. This is because pyds9 will start up ds9 only if a ds9 with the target name is not already running. If the verify flag is turned on, each ds9 method call will check whether ds9 is still running, and will throw an exception if this is not the case. Otherwise, the method return value can be used to detect failure. Using verification allows ds9 methods to used in try/except constructs, at the expense of a slight decrease in performance. """ tlist = xpa.xpaaccess(string_to_bytes(target), None, 1024) # no need to convert, as tlist content is not used if not tlist and start: if '?' in target or '*' in target: target = "ds9" try: args = shlex.split(start) except AttributeError: # Not a parsable string-like object try: args = list(start) except TypeError: # Not an iterable object args = [] self.pid = subprocess.Popen(ds9Globals["progs"][1] + ['-title', target] + args) for i in range(wait): tlist = xpa.xpaaccess(string_to_bytes(target), None, 1024) if tlist: break time.sleep(1) tlist = bytes_to_string(tlist) if not tlist: raise ValueError('no active ds9 running for target: %s' % target) elif len(tlist) > 1: if 'XPA_METHOD' in os.environ.keys(): method = os.environ['XPA_METHOD'] else: method = 'inet' if method == 'local' or method == 'unix': s = 'local file' else: s = 'ip:port' print('More than one ds9 is running for target %s:' % target) for l in tlist: print(" %s" % l) a = tlist[0].split() print('Use a specific name or id to construct a DS9 object, e.g.:') print(" d = DS9('%s')" % a[0].split()[0].split(':')[1]) print(" d = DS9('%s')" % a[0]) print(" d = DS9('%s')" % a[1]) print("The '%s' id (3rd example) will always be unique.\n" % s) raise ValueError('too many ds9 instances for target: %s' % target) else: a = tlist[0].split() self.__dict__['target'] = target self.__dict__['id'] = a[1] self.verify = verify def __setattr__(self, attrname, value): """ An internal routine to guard read-only attributes. """ if attrname in self._privates: raise AttributeError('attribute modification is not permitted: %s' % attrname) else: self.__dict__[attrname] = value def _selftest(self): """ An internal test to make sure that ds9 is still running." """ if self.verify and not xpa.xpaaccess(string_to_bytes(self.id), None, 1): raise ValueError('ds9 is no longer running (%s)' % self.id) def get(self, paramlist=None, decode=None): """ :param paramlist: command parameters (documented in the ds9 ref manual) :param decode: decode the output; if ``None`` decodes the output if ``paramlist`` is not present in the list ``ds9Globals['bin_cmd']`` :rtype: returned data or info (as a string or byte string) Once a DS9 object has been initialized, use 'get' to retrieve data from ds9 by specifying the standard xpa paramlist:: >>> d.get("file") '/home/eric/python/ds9/test.fits' >>> d.get("fits height") '15' >>> d.get("fits width") '15' >>> d.get("fits bitpix") '32' Note that all access points return data as python strings. """ self._selftest() # convert to byte string in python3 x = xpa.xpaget(string_to_bytes(self.id), string_to_bytes(paramlist), 1) if decode is None: decode = paramlist not in ds9Globals['bin_cmd'] if decode: x = bytes_to_string(x) if len(x) > 0: if paramlist not in self._nostrip: x[0] = x[0].strip() return x[0] else: return x def set(self, paramlist, buf=None, blen=-1): """ :param paramlist: command parameters (documented in the ds9 ref manual) :rtype: 1 for success, 0 for failure Once a DS9 object has been initialized, use 'set' to send data and commands to ds9:: >>> d.set("file /home/eric/data/casa.fits") 1 A return value of 1 indicates that ds9 was contacted successfully, while a return value of 0 indicates a failure. To send data (as well as the paramlist) to ds9, specify the data buffer in the argument list. The data buffer must either be a string, a numpy.ndarray, or an array.array:: >>> d.set("array [xdim=1024 ydim=1024 bitpix=-32]", arr) Sending both a paramlist and data is the canonical way to send a region to ds9:: >>> d.set('regions', 'fk5; circle(345.29,58.87,212.58")'); 1 This is equivalent to the Unix xpaset command: echo 'fk5; circle(345.29,58.87,212.58")' | xpaset ds9 regions Indeed, if you are having problems with ds9.set() or ds9.get(), it often is helpful to try the equivalent command using the Unix xpaset and xpaget programs. """ self._selftest() if ds9Globals["numpy"] and type(buf) == numpy.ndarray: s = buf.tostring() elif type(buf) == array.array: try: # Python >= 3.2 s = buf.tobytes() except AttributeError: s = buf.tostring() else: s = string_to_bytes(buf) return xpa.xpaset(string_to_bytes(self.id), string_to_bytes(paramlist), s, blen, 1) def info(self, paramlist): """ :rtype: 1 for success, 0 for failure Once a DS9 object has been initialized, use 'info' to send xpa info messages to ds9. (NB: ds9 currently does not support info messages.) """ self._selftest() return xpa.xpainfo(string_to_bytes(self.id), string_to_bytes(paramlist), 1) def access(self): """ :rtype: xpa target name and id The 'access' method returns the xpa id of the current instance of ds9, by making a direct contact with ds9 itself. """ self._selftest() x = xpa.xpaaccess(string_to_bytes(self.id), None, 1) return bytes_to_string(x[0]) if ds9Globals["pyfits"]: def get_pyfits(self): """ :rtype: pyfits hdulist To read FITS data or a raw array from ds9 into pyfits, use the 'get_pyfits' method. It takes no args and returns an hdu list:: >>> hdul = d.get_pyfits() >>> hdul.info() Filename: StringIO No. Name Type Cards Dimensions Format 0 PRIMARY PrimaryHDU 24 (1024, 1024) float32 >>> data = hdul[0].data >>> data.shape (1024, 1024) """ self._selftest() imgData = self.get('fits') imgString = BytesIO(string_to_bytes(imgData)) return pyfits.open(imgString) def set_pyfits(self, hdul): """ :param hdul: pyfits hdulist :rtype: 1 for success, 0 for failure After manipulating or otherwise modifying a pyfits hdulist (or making a new one), you can display it in ds9 using the 'set_pyfits' method, which takes the hdulist as its sole argument:: >>> d.set_pyfits(nhdul) 1 A return value of 1 indicates that ds9 was contacted successfully, while a return value of 0 indicates a failure. """ self._selftest() if not ds9Globals["pyfits"]: raise ValueError('set_pyfits not defined (pyfits not found)') if type(hdul) != pyfits.HDUList: if ds9Globals["pyfits"] == 1: raise ValueError('requires pyfits.HDUList as input') else: raise ValueError('requires astropy.HDUList as input') # for python2 BytesIO and StringIO are the same with contextlib.closing(BytesIO()) as newFitsFile: hdul.writeto(newFitsFile) newfits = newFitsFile.getvalue() got = self.set('fits', newfits, len(newfits)) return got else: def get_pyfits(self): """ This method is not defined because pyfits in not installed. """ raise ValueError('get_pyfits not defined (pyfits not found)') def set_pyfits(self): """ This method is not defined because pyfits in not installed. """ raise ValueError('set_pyfits not defined (pyfits not found)') if ds9Globals["numpy"]: def get_arr2np(self): """ :rtype: numpy array To read a FITS file or an array from ds9 into a numpy array, use the 'get_arr2np' method. It takes no arguments and returns the np array:: >>> d.get("file") '/home/eric/data/casa.fits[EVENTS]' >>> arr = d.get_arr2np() >>> arr.shape (1024, 1024) >>> arr.dtype dtype('float32') >>> arr.max() 51.0 """ self._selftest() w = int(self.get('fits width')) h = int(self.get('fits height')) d = int(self.get('fits depth')) bp = int(self.get('fits bitpix')) s = self.get('array') if d > 1: arr = numpy.fromstring(s, dtype=_bp2np(bp)).reshape((d, h, w)) else: arr = numpy.fromstring(s, dtype=_bp2np(bp)).reshape((h, w)) # if sys.byteorder != 'big': arr.byteswap(True) return arr def set_np2arr(self, arr, dtype=None): """ :param arr: numpy array :param dtype: data type into which to convert array before sending :rtype: 1 for success, 0 for failure After manipulating or otherwise modifying a numpy array (or making a new one), you can display it in ds9 using the 'set_np2arr' method, which takes the array as its first argument:: >>> d.set_np2arr(arr) 1 A return value of 1 indicates that ds9 was contacted successfully, while a return value of 0 indicates a failure. An optional second argument specifies a datatype into which the array will be converted before being sent to ds9. This is important in the case where the array has datatype np.uint64, which is not recognized by ds9:: >>> d.set_np2arr(arru64) ... ValueError: uint64 is unsupported by DS9 (or FITS) >>> d.set_np2arr(arru64,dtype=np.float64) 1 Also note that np.int8 is sent to ds9 as int16 data, np.uint32 is sent as int64 data, and np.float16 is sent as float32 data. """ self._selftest() if type(arr) != numpy.ndarray: raise ValueError('requires numpy.ndarray as input') if dtype and dtype != arr.dtype: narr = arr.astype(dtype) else: if arr.dtype == numpy.int8: narr = arr.astype(numpy.int16) elif arr.dtype == numpy.uint32: narr = arr.astype(numpy.int64) elif hasattr(numpy, "float16") and arr.dtype == numpy.float16: narr = arr.astype(numpy.float32) else: narr = arr if not narr.flags['C_CONTIGUOUS']: narr = numpy.ascontiguousarray(narr) bp = _np2bp(narr.dtype) buf = narr.tostring('C') blen = len(buf) (w, h) = narr.shape # note that this needs the "endian=" part because sometimes it's # left out completely endianness = '' if narr.dtype.byteorder == '=': endianness = ',endian=' + sys.byteorder elif narr.dtype.byteorder == '<': endianness = ',endian=little' elif narr.dtype.byteorder == '>': endianness = ',endian=big' paramlist = 'array [xdim={0},ydim={1},bitpix={2}{3}]' return self.set(paramlist.format(h, w, bp, endianness), buf, blen+1) else: def get_arr2np(self): """ This method is not defined because numpy in not installed. """ raise ValueError('get_arr2np not defined (numpy not found)') def set_np2arr(self): """ This method is not defined because numpy in not installed. """ raise ValueError('set_np2arr not defined (numpy not found)') class ds9(DS9): """ This is a backwards-compatibility "shell" class that acts like the DS9 class but has the old name. In the future, you should switch to using the new name (``DS9``). """ def __init__(self, *args, **kwargs): from warnings import warn warn('The class name "ds9" is deprecated. In the future, use "DS9" ' 'instead.') super(ds9, self).__init__(*args, **kwargs) # start xpans, if necessary # it seems that this must be done at import time, so that we can sense the # case where xpa is not installed, and ds9 is started before python if "PYDS9_NOXPANS" not in os.environ.keys(): ds9_xpans() def test(): print("starting quick test for pyds9 version " + __version__) # start ds9 if necessary tries = 0 print("looking for our 'pytest' ds9 ...") while ds9_targets("pytest") == None: if tries == 0: print("starting ds9 ...") subprocess.Popen(ds9Globals["progs"][1] + ['-title', 'pytest']) print("\nwaiting for ds9 to be available ",) elif tries == 10: raise ValueError("tired of waiting for ds9!") print(".",) time.sleep(1) tries += 1 print(" ds9 is running!") print("\ntesting ds9 support ...") l = ds9_targets("pytest") print("target list:\n", l) d = DS9(l[0].split()[1]) print("connected to ds9 with id %s" % d.id) print("connected to ds9 with id %s" % d.id) tfits = os.path.join(os.getcwd(), "test.fits") if os.path.exists(tfits): cmd = "file " + tfits d.set(cmd) print("sent file=%s dims=(%s,%s) bitpix=%s" % (d.get("file"), d.get("fits width"), d.get("fits height"), d.get("fits bitpix"))) if ds9Globals["numpy"]: print("\ntesting numpy support ...") a = d.get_arr2np() print("reading nparray: shape=%s dtype=%s" % (a.shape, a.dtype)) print(a) print("writing modified nparray ...") a[0:3, 0:3] = 8 a[12:15, 12:15] = 9 d.set_np2arr(a) a = d.get_arr2np() print("re-reading nparray: shape=%s dtype=%s" % (a.shape, a.dtype)) print(a) else: print("\nskipping numpy test ...") if ds9Globals["pyfits"]: print("\ntesting pyfits support (%d) ..." % ds9Globals["pyfits"]) hdul = d.get_pyfits() print(hdul.info()) i = hdul[0].data print("reading back pyfits: shape=%s dtype=%s" % (i.shape, i.dtype)) print(i) else: print("\nskipping pyfits test ...") else: print("could not find " + tfits + " ... skipping numpy,pyfits tests") stime = 7 print("sleeping for " + str(stime) + " seconds ...") time.sleep(stime) print("stopping ds9 ...") d.set("exit") casa = os.path.join(os.getcwd(), "casa.fits") if os.path.exists(casa): print("starting ds9 (no args) ...") d2 = DS9('pytest2') d2.set("file " + casa) print("starting ds9 (string args) ...") d3 = DS9('pytest3', start=["-grid", "-cmap", "sls", casa]) print("starting ds9 (list args) ...") d4 = DS9('pytest4', start=["-grid", "-cmap", "heat", casa]) print("testing ds9_targets ... ") print(ds9_targets()) ds = ds9_openlist("pytest*") for d in ds: print(d.id + ": file: " + d.get("file") + " cmap: " + d.get("cmap")) time.sleep(stime) for d in ds: print("stopping ds9: " + d.id + " ...") d.set("exit") else: print("could not find " + casa + " ... skipping casa tests") if __name__ == '__main__': test()