# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""This class supports communication with DS9 through the XPA
Some code in this class was adapted from pysao, which can be found at https://github.com/leejjoon/pysao.
Specifically this package used the existing Cython implementation to the XPA and extended the calls to
the other available XPA executables so that more functionality is added. The same information is available
here: http://hea-www.harvard.edu/RD/xpa/client.html#xpaopen
Using Cython will allow for broader development of the code and produce faster runtimes for large datasets
with repeated calls to the display manager.
XPA is licensed under LGPL, help can be found here: http://hea-www.cfa.harvard.edu/saord/xpa/help.html
The current XPA can be downloaded from here: http://hea-www.harvard.edu/saord/xpa/
DS9 also supports the SAMP protocol, but that has not been fully implemented in this package. http://ds9.si.edu/doc/ref/samp.html
"""
from __future__ import print_function, division, absolute_import
import os
import shutil
import numpy as np
from subprocess import Popen
import time
import warnings
import logging
from tempfile import mkdtemp
import imexam.xpa_wrap as xpa
from imexam.xpa import XpaException
from . import util
from astropy.io import fits
class UnsupportedDatatypeException(Exception):
pass
class UnsupportedImageShapeException(Exception):
pass
__all__ = ['ds9']
# make a new object for every window you want to create
[docs]class ds9(object):
""" A class which controls all interactions between the user and the ds9 window
The ds9() contructor takes a ds9 target as its main argument. If none is given,
then a new window will be opened.
DS9's xpa access points are documented in the reference manual, but the can also
be returned to the user with a call to xpaset.
http://hea-www.harvard.edu/saord/ds9/ref/xpa.html
Parameters
----------
target: string, optional
the ds9 target name or id (default is to start a new instance)
path : string, optional
path of the ds9
wait_time : float, optional
waiting time before error is raised
quit_ds9_on_del : boolean, optional
If True, try to quit ds9 when this instance is deleted.
Attributes
----------
wait_time: float
The waiting time before error is raised
path: string
The path to the DS9 executable
_xpa_name: string
The value in XPA_METHOD, the name of the DS9 window
_quit_ds9_on_del: boolean
Determine whether to quit ds9 when object goes out of scope.
_ds9_unix_name: string
The full path filename to the unix socket, only if unix sockets are being used with local
_need_to_purge: boolean
whenever there are unix socket directories which need to be purged when the object goes out of scope
_tmpd_name: string
The full path name to the unix socket file on the local system
_filename: string
The name of the image that's currently loaded into DS9
_ext: int
Extension of the current image that is loaded. If one extension of an MEF file is loaded this will be 1
regarless of the extension that was specified (because DS9 and the XPA now see it as a single image and header)
_extname: string
If available, the EXTNAME of the MEF extension that is loaded, taken from the current data header
_extver: int
If available, the EXTVER of the MEF extension that is loaded, taken from the current data header
_ds9_process: pointer
Points to the ds9 process id on the system, returned by Popen, whenever this module starts DS9
_mef_file: boolean
The file is a multi-extension fits file
_iscube: bookean
The file is a multiextension fits file, and one of the extensions contains at least 1 additional extension (3D or more)
_numaxis: int
number of image planes, this is NAXIS
_naxis: tuple
specific image plane displayed, defaulted to 1 image plane, most relevant to cube fits files
"""
# _ImgCode : copied from fits, used for displaying arrays straight to DS9
_ImgCode = {'float32': -32,
'float64': -64,
'float16': -16,
'int16': 16,
'int32': 32,
'int64': 64,
'uint8': 8}
_tmp_dir = ""
_process_list = list()
def __init__(self, target=None, path=None, wait_time=5,
quit_ds9_on_del=True):
"""
Notes
-----
I think this is a quirk in the XPA communication. The xpans, and XPA prefer to have all connections
be of the same type. DS9 defaults to creating an INET connection. In some cases, if no IP address can be
found for the computer, the startup can hang. In these cases, a local connection is preferred, which
uses a unix filename for the socket.
The problem arises that if the user already has DS9 windows running, that were started by default, the nameserver
is only listening for the default socket type (inet) and not local. There are also cases where the machine
running this code does not have xpa installed, so there is no xpans (nameserver) to run and keep track of the
open connections. In that case, the user needs to provide this init with the name of the socket in their
window (in XPA_METHOD) in order to create the connection.
"""
self._quit_ds9_on_del = quit_ds9_on_del # determine whether to quit ds9 also when object deleted.
self.wait_time = wait_time
self._need_to_purge = False
self._tmpd_name = None
# dictionary where each key is a frame number, and the values are a dictionary of details
# about the image loaded in that frame
self._viewer = dict()
self._current_frame = None
self._current_slice = None
# default starting socket type to local in order get around user xpa
# installation issues
self._xpa_method = "local"
self._xpa_name = ""
# only used for DS9 windows started from this module
self._ds9_process = None
self._ds9_path = None
if path is None:
self._ds9_path = util.find_ds9()
if not self._ds9_path:
raise OSError("Could not find ds9 executable on your path")
else:
self._ds9_path = path
if not target:
# Check to see if the user has chosen a preference first
if 'XPA_METHOD' in os.environ:
self._xpa_method = os.environ['XPA_METHOD'].lower()
if 'inet' in self._xpa_method:
self._xpa_name = self.run_inet_ds9()
# xpa_name is the title of the window, the xpa can be referenced
# with either the socket address or name of the window
elif 'local' in self._xpa_method:
self._xpa_name, self._ds9_unix_name = self._run_unixonly_ds9()
# tells xpa where to find sockets
os.environ['XPA_METHOD'] = self._xpa_method
else:
# just register with the target the user provided
self._xpa_name = target
# xpa_name sets the template for the get and set commands
self.xpa = xpa.XPA(self._xpa_name)
if 'local' in self._xpa_method:
self._set_frameinfo() # initial load
self._define_cmaps() # dictionary of color maps
def __str__(self):
pass
def __del__(self):
if self._quit_ds9_on_del:
if 'local' in self._xpa_method:
self._purge_local()
else:
self._stop_process()
def _set_frameinfo(self):
"""Set the name and extension information for the data displayed in the current frame
and gather header information
Notes
-----
The absolute path reference is stored to make XPA happy in all cases, wherever the user
started the DS9 process.
The only consistant way to return which cube and slice that is displayed is with the call
to "file" which has the full plane=x:y information, but only when looking at something
other than the first extension for each plane. In this case, you have to look at the header
information to see it's a cube image, and assume the first image plane is displayed.
If you load a single extension from an MEF into DS9, XPA references the extension as 1 afterwards for access points
you need to look in the header of the displayed image to find out what the actual extension that is loaded is
"""
# check the current frame, if none exists, then don't continue
frame = self.frame()
if frame:
if frame not in self._viewer:
self._viewer[frame] = dict()
try:
user_array = self._viewer[frame]['user_array']
except KeyError:
user_array = None
extver = None # extension number
extname = None # name of extension
filename = None # filename of image
numaxis = 2 # number of image planes, this is NAXIS
# tuple of each image plane, defaulted to 1 image plane
naxis = (0)
# data has more than 2 dimensions and loads in cube/slice frame
iscube = False
mef_file = False # used to check misleading headers in fits files
load_header = False # not used for in memory arrays
self._current_frame = frame
# see if any file is currently loaded into ds9, xpa returns '\n' for nothing loaded
# get the current frame
try:
filename_string = self.get('file')
if len(filename_string) > 1:
filename = str(filename_string.strip().split('[')[0])
self._viewer[frame]['filename'] = os.path.abspath(filename)
load_header = True
except XpaException:
filename_string = ""
try:
if "plane" in filename_string:
iscube = True
if ":" in filename_string:
naxis = filename_string.strip().split(']')[
1].split("=")[1].split(":")
else:
naxis = filename_string.strip().split(']')[
1].split('=')[1].split()
if len(naxis) == 1:
naxis.append("0")
naxis.reverse() # for astropy.fits row-major ordering
naxis = map(int, naxis)
naxis = [
axis -
1 if axis > 0 else 0 for axis in naxis] # zero index fits
naxis = tuple(naxis)
except ValueError:
raise ValueError("Problem parsing filename")
if load_header:
# set the extension from the header information returned from DS9
# this is the best way to get the information if the user changes
# the loaded file using the gui
header_cards = fits.Header.fromstring(
self.get_header(),
sep='\n')
mef_file = util.check_filetype(filename)
if mef_file:
try:
extver = int(header_cards['EXTVER'])
except KeyError:
# fits doesn't require extver if there is only 1
# extension
extver = 1
try:
extname = str(header_cards['EXTNAME'])
except KeyError:
extname = None
try:
numaxis = int(header_cards['NAXIS'])
except KeyError:
raise KeyError("Problem getting NAXIS from header")
if not iscube:
if numaxis > 2:
iscube = True
naxis = list()
# assume the first axis in each extension is displayed
for axis in range(numaxis, 2, -1):
naxis.append(0)
naxis = tuple(naxis)
# update the viewer dictionary, if the user changes what's displayed in a frame this should update correctly
# this dictionary will be referenced in the other parts of the code. This enables tracking user arrays through
# frame changes
self._viewer[frame] = {'filename': filename,
'extver': extver,
'extname': extname,
'naxis': naxis,
'numaxis': numaxis,
'iscube': iscube,
'user_array': user_array,
'mef': mef_file}
else:
warnings.warn("No frame loaded in viewer")
[docs] def valid_data_in_viewer(self):
"""return bool if valid file or array is loaded into the viewer"""
frame = self.frame()
if frame:
self._set_frameinfo()
if self._viewer[frame]['filename']:
return True
else:
try:
if self._viewer[frame]['user_array'].any():
return True
except AttributeError as ValueError:
print("error in array")
return False
[docs] def get_filename(self):
"""return the filename currently on display
This function will check if there is already a filename saved. It's possible that the user can
connect to a ds9 window with no file loaded and then ask for the data file name after loading one through
the ds9 menu options. This will poll the private filename and then try and set one if it's empty.
"""
# see if the user has loaded a file by hand or changed frames in the
# gui
frame = self.frame()
if frame != self._current_frame:
self._set_frameinfo()
else:
return self._viewer[frame]['filename']
[docs] def get_frame_info(self):
"""return more explicit information about the data displayed in the current frame"""
self._set_frameinfo()
return self._viewer[self.frame()]
[docs] def get_viewer_info(self):
"""Return a dictionary of information about all frames which are loaded with data
Notes
-----
Consider adding a loop to verify that all the frames still exist and the user
has not deleted any through the gui.
"""
self._set_frameinfo()
return self._viewer
@classmethod
def _purge_tmp_dirs(cls):
"""Delete temporary directories made for the unix socket
When used with ipython (pylab mode), it seems that the objects
are not properly deleted, i.e., temporary directories are not
deleted. This is a work around for that.
"""
if cls._tmp_dir:
shutil.rmtree(cls._tmp_dir)
@classmethod
def _stop_running_process(cls):
"""stop self generated DS9 windows when user quits python window"""
while cls._process_list:
process = cls._process_list.pop()
if process.poll() is None:
process.terminate()
def _stop_process(self):
"""stop the ds9 window process nicely, only if this package started it"""
try:
if self._ds9_process:
# none means not yet terminated
if self._ds9_process.poll() is None:
self.set("exit")
if self._ds9_process in self._process_list:
self._process_list.remove(self._ds9_process)
except XpaException as e:
print("XPA Exception: {0}".format(e))
def _purge_local(self):
"""remove temporary directories from the unix socket"""
if not self._need_to_purge:
return
if not self._quit_ds9_on_del:
warnings.warn(
"You need to manually delete tmp. dir ({0:s})".format(
self._tmpd_name))
return
self._stop_process()
# add a wait for the process to terminate before trying to delete the
# tree
time.sleep(0.5)
try:
shutil.rmtree(self._tmpd_name)
except OSError:
warnings.warn(
"Warning : couldn't delete the temporary directory ({0:s})".format(self._tmpd_name,))
self._need_to_purge = False
[docs] def close(self):
""" close the window and end connection"""
# make sure we clean up the object and quit_ds9 local files
if 'local' in self._xpa_method or 'tmp' in self._xpa_method:
self._purge_local()
else:
self._stop_process()
[docs] def run_inet_ds9(self):
"""start a new ds9 window using an inet socket connection
Notes
-----
It is given a unique title so it can be identified later.
"""
env = os.environ
# this is the title of the window, without a nameserver connection
# is there a way to get the inet x:x address?
# that should be unique enough, something better?
xpaname = "imexam" + str(time.time())
try:
p = Popen([self._ds9_path,
"-xpa", "inet",
"-title", xpaname],
shell=False, env=env)
self._ds9_process = p
self._process_list.append(p)
self._need_to_purge = False
return xpaname
except Exception as e: # refine error class
warnings.warn("Opening ds9 failed")
print("Exception: {}".format(repr(e)))
from signal import SIGTERM
os.kill(p.pid, SIGTERM)
raise Exception
def _run_unixonly_ds9(self):
""" start new ds9 window and connect to object using a unix socket
Notes
-----
When the xpa method in libxpa parses given template as an unix socket, it checks if the template string starts with tmpdir (from env["XPA_TMPDIR"]
or default to /tmp/.xpa). This can make having multiple instances of ds9 a bit difficult, but if you give it unique names or use the inet address
you should be fine
For unix only, we run ds9 with XPA_TMPDIR set to temporary directory whose prefix start with /tmp/xpa
(eg, /tmp/xpa_sf23f), them set os.environ["XPA_TMPDIR"] (which affect xpa set and/or get command from python) to /tmp/xpa.
"""
env = os.environ
wait_time = self.wait_time
self._tmpd_name = mkdtemp(
prefix="xpa_" +
env.get(
"USER",
""),
dir="/tmp")
# this is the first directory the servers looks for on the path
env["XPA_TMPDIR"] = self._tmpd_name
iraf_unix = "{0:s}/.IMT".format(self._tmpd_name)
# that should be unique enough, something better?
title = str(time.time())
try:
# unix only flag disables the fifos and inet connections
p = Popen([self._ds9_path,
"-xpa", "local",
"-unix_only", "-title", title,
"-unix", "%s" % iraf_unix],
shell=False, env=env)
# wait until ds9 starts and the .IMT socket exists
while wait_time > 0:
file_list = os.listdir(self._tmpd_name)
if ".IMT" in file_list:
break
time.sleep(0.5)
wait_time -= 0.5
if wait_time == 0:
from signal import SIGTERM
os.kill(p.pid, SIGTERM)
print(
"Connection timeout with the ds9. Try to increase the *wait_time* parameter (current value is {0:d} s)".format(self.wait_time,))
except (OSError, ValueError, AttributeError) as e:
warnings.warn("Starting ds9 failed")
shutil.rmtree(self._tmpd_name)
else:
self._tmp_dir = self._tmpd_name
self._ds9_process = p
self._process_list.append(p)
# this might be sketchy
try:
file_list.remove(".IMT") # should be in the directory, if not
except (ValueError, IOError):
warnings.warn("IMT not found in tmp, using first thing in list")
if len(file_list) > 0:
xpaname = os.path.join(self._tmpd_name, file_list[0])
else:
shutil.rmtree(self._tmpd_name)
raise ValueError("Problem starting ds9 local socket connection")
env["XPA_TMPDIR"] = "/tmp/xpa" # for all local connections
self._need_to_purge = True
self._xpa_method = 'local'
return xpaname, iraf_unix
[docs] def set_iraf_display(self):
""" Set the environemnt variable IMTDEV to the socket address of the current imexam.ds9 instance.
Notes
-----
For example, your pyraf commands will use this ds9 for display.
TODO: Not sure this is still needed.
"""
os.environ["IMTDEV"] = "unix:%s" % (self._ds9_unix_name)
def _check_ds9_process(self):
"""Check to see if the ds9 process is still running
Notes
-----
If you start a ds9 window from the shell and then connect to imexam, imexam
will not have a reference for the process, so this method ignores that state.
"""
if self._ds9_process:
ret = self._ds9_process.poll()
if ret is not None:
raise RuntimeError("The ds9 process is externally killed.")
self._purge_local()
[docs] def set(self, param, buf=None):
"""XPA set method to ds9 instance
Notes
-----
This function is linked with the Cython implementation
set(param, buf=None)
param : parameter string (eg. "fits" "regions")
buf : aux data string (sometime string needed to be ended with CR)
"""
self._check_ds9_process()
self.xpa.set(param, buf)
[docs] def get(self, param):
"""XPA get method to ds9 instance which returns received string
Parameters
----------
param : parameter string (eg. "fits" "regions")
Notes
-----
This function is linked with the Cython implementation
get(param)
"""
self._check_ds9_process()
return self.xpa.get(param)
[docs] def readcursor(self):
"""returns image coordinate postion and key pressed,
Notes
-----
XPA returns strings of the form: u a 257.5 239 \n
"""
try:
xpa_string = self.get("imexam any coordinate image")
except XpaException as e:
print("Xpa problem reading cursor: {0}".format(str(e)))
raise KeyError
except ValueError:
raise ValueError("Outside of data range")
k, x, y = xpa_string.split()
# ds9 is returning 1 based array
return float(x), float(y), str(k)
[docs] def alignwcs(self, on=True):
"""align wcs
Parameters
----------
on: bool
Align the images using the WCS in their headers
"""
self.set("align %s" % (str(on)))
[docs] def blink(self, blink=True, interval=None):
"""Blink frames
Parameters
----------
blink: bool, optional
Set to True to start blinking the frames which are open
interval: int
Set interval equal to the length of pause for blinking
Notes
-----
blink_syntax=
Syntax:
blink
[true|false]
[interval <value>]
"""
cstring = "blink "
if blink:
cstring += "yes "
else:
cstring += "no "
if interval:
cstring += (" %d") % (interval)
self.set(cstring)
[docs] def clear_contour(self):
"""clear contours from the screen"""
self.set("contour clear")
def _define_cmaps(self):
"""setup the default color maps which are available"""
self._cmap_syntax = """
Syntax:
cmap [<colormap>]
[file]
[load <filename>]
[save <filename>]
[invert true|false]
[value <constrast> <bias>]
[tag [load|save] <filename>]
[tag delete]
[match]
[lock [true|false]]
[open|close]
Example:
>obj.cmap(map="Heat")
>obj.cmap(invert=True)
"""
# is there a list I can pull automatically from ds9?
self._cmap_colors = [
"heat",
"grey",
"cool",
"aips0",
"a",
"b",
"bb",
"he",
"i8"]
[docs] def cmap(self, color=None, load=None, invert=False, save=False,
filename='colormap.ds9'):
""" Set the color map table to something else, using a defined list of options
Parameters
----------
color: string
color must be set to one of the available DS9 color map names
load: string, optional
set to the filename which is a valid colormap lookup table
valid contrast values are from 0 to 10, and valid bias values are from 0 to 1
invert: bool, optional
invert the colormap
save: bool, optional
save the current colormap as a file
filename: string, optional
the name of the file to save the colormap to
"""
if color:
color = color.lower()
if color in self._cmap_colors:
cstring = "cmap %s" % (color)
self.set(cstring)
else:
print("Unrecognized color map, choose one of these:")
print(self._cmap_colors)
if invert:
invert = 'yes'
cstring = ('cmap invert %s') % (invert)
self.set(cstring)
if load:
cstring = ('cmap load %s') % (load) # where load is the filename
self.set(cstring)
if save:
cstring = ('cmap save %s') % (filename)
self.set(cstring)
[docs] def colorbar(self, on=True):
"""turn the colorbar on the bottom of the window on and off
Parameters
----------
on: bool
Set to True to turn on the colorbar, False to turn it off
"""
self.set("colorbar %s".format(str(on)))
[docs] def contour(self, on=True, construct=True):
"""show contours on the window
Parameters
----------
on: bool
Set to true to turn on contours
construct: bool, optional
Will open the contour dialog box which has more options
"""
self.set("contour {0:s}".format(str(on)))
if construct:
self.set("contour levels")
[docs] def contour_load(self, filename):
"""load a contour file into the window
Parameters
----------
filename: string
The name of the file with the contour level defined
"""
if filename:
self.set("contour loadlevels {0:s}".format(str(filename)))
else:
warnings.warn("No filename provided for contours")
[docs] def crosshair(self, x=None, y=None, coordsys="physical",
skyframe="wcs", skyformat="fk5", match=False, lock=False):
"""Control the position of the crosshair in the current frame, crosshair mode is turned on automatically
Parameters
----------
x: string or int
The value of x is converted to a string for the call to XPA, use a value here appropriate for the skyformat you choose
y: string or int
The value of y is converted to a string for the call to XPA, use a value here appropriate for the skyformat you choose
coordsys: string, optional
The coordinate system your x and y are defined in
skyframe: string, optional
If skyframe has "wcs" in it then skyformat is also sent to the XPA
skyformat: string, optional
Used with skyframe, specifies the format of the coordinate which were given in x and y
match: bool, optional
If set to True, then the wcs is matched for the frames
lock: bool, optional
If set to True, then the frame is locked in wcs
"""
if x and y:
if "wcs" in skyframe:
format = skyformat
else:
format = ""
self.window.set("crosshair {0:s} {1:s} {2:s} {3:s}".format(
str(x), str(y), str(coordsys), format))
if match:
self.window.set("crosshair match wcs")
if lock:
self.window.set("crosshair lock wcs")
[docs] def cursor(self, x=None, y=None):
"""move the cursor in the current frame to the specified image pixel; selected regions will also be moved
Parameters
----------
x: int
pixel location x coordinate to move to
y: int
pixel location y coordinate to move to
x and y are converted to strings for the call
"""
if x and y:
self.set("cursor {0:s} {1:s}".format(str(x), str(y)))
else:
warnings.warn(
"You need to supply both an x and y location for the cursor")
[docs] def frame(self, n=None):
"""convenience function to change or report frames
Parameters
----------
n: int, string, optional
The frame number to open or change to. If the number specified doesn't exist, a new frame will be opened
If nothing is specified, then the current frame number will be returned. The value of n is converted to
a string before passing to the XPA
Examples
--------
frame(1) sets the current frame to 1
frame("last") set the current frame to the last frame
frame() returns the number of the current frame
frame("new") opens a new frame
frame(3) opens frame 3 if it doesn't exist already, otherwise goes to frame 3
"""
frame = self.get("frame").strip() # xpa returns '\n' for no frame
if frame:
if n:
if "delete" in str(n):
if frame in self._viewer:
del self._viewer[frame]
self.set("frame {0:s}".format(str(n)))
else:
try:
if len(frame) < 1:
self.set("frame 1")
# the user can delete frame 1, but ds9 defaults to 1,
# so set it
return '1'
else:
return str(frame)
except XpaException as e:
raise XpaException(
"XPA Exception getting frame: {0}".format(e))
else:
if len(frame) < 1:
self.set("frame 1")
# the user can delete frame 1, but ds9 defaults to 1, so set it
return '1'
[docs] def iscube(self):
"""return information on whether a cube image is displayed in the current frame"""
frame = self.frame()
if frame != self._current_frame:
self._set_frameinfo()
else:
return self._viewer[frame]['iscube']
[docs] def get_slice_info(self):
"""return the slice tuple that is currently displayed"""
self._set_frameinfo()
frame = self.frame()
if self._viewer[frame]['iscube']:
image_slice = self._viewer[frame]['naxis']
else:
image_slice = None
return image_slice
[docs] def get_data(self):
""" return a numpy array of the data displayed in the current frame
Notes
-----
This is the data array that the imexam() function from connect() uses for analysis
astropy.io.fits stores data in row-major format. So a 4d image would be [NAXIS4, NAXIS3, NAXIS2, NAXIS1]
just the one image is retured in the case of multidimensional data, not the cube
"""
# make sure the filename and extension info are correct for the current
# frame in DS9, users can change this in the gui
# users can change frame and slice before calling this, best to check
self._set_frameinfo()
frame = self.frame()
if frame:
if isinstance(self._viewer[frame]['user_array'], np.ndarray):
return self._viewer[frame]['user_array']
else:
filename = self._viewer[frame]['filename']
extver = self._viewer[frame]['extver']
extname = self._viewer[frame]['extname']
naxis = self._viewer[frame]['naxis']
if self._viewer[frame]['mef']:
with fits.open(filename) as filedata:
if self._viewer[frame]['iscube']:
data = filedata[extname, extver].section[naxis]
else:
data = filedata[extname, extver].data
return data
else:
with fits.open(filename) as filedata:
data = filedata[0].data
return data
[docs] def grid(self, on=True, param=False):
"""convenience to turn the grid on and off, grid can be flushed with many more options
Parameters
----------
on: bool, optional
Will turn the grid overlay on in the current frame
param: bool, optional
Will open the parameter dialog in DS9
"""
self.set("grid %s" % (str(on)))
if param:
self.set("grid open")
[docs] def hideme(self):
"""lower the ds9 window"""
self.set("lower")
[docs] def load_fits(self, fname="", extver=1, extname=None):
"""convenience function to load fits image to current frame
Parameters
----------
fname: string, optional
The name of the file to be loaded. You can specify the full extension in the name, such as
filename_flt.fits[sci,1] or filename_flt.fits[1]
extver: int, optional
The extension to load (EXTVER in the header)
extname: string, optional
The name (EXTNAME in the header) of the image to load
Notes
-----
To tell ds9 to open a file whose name or path includes spaces,
surround the path with "{...}", e.g.
% xpaset -p ds9 file "{foo bar/my image.fits}"
This is assuming that the image loads into the current or next new frame, watch the internal
file and ext values because the user can switch frames through DS9 app itself
XPA needs to have the absolute path to the filename so that if the DS9 window was started
in another directory it can still find the file to load. arg.
"""
frame = self.frame()
if not frame:
frame = 1 # load into first frame
if fname:
# see if the image is MEF or Simple
fname = os.path.abspath(fname)
# strip the extensions for now
shortname = fname.split("[")[0]
cstring = util.verify_filename(shortname, extver, extname)
self.set(cstring)
self._set_frameinfo()
# make sure any previous reference is reset
self._viewer[frame]['user_array'] = None
else:
print("No filename provided")
[docs] def load_region(self, filename):
"""Load regions from a file which uses ds9 standard formatting
Parameters
----------
filename: string
The file containing the DS9 style region description
"""
if os.access(filename, os.F_OK):
self.set("regions load %s" % filename)
else:
warnings.warn("No such file:{0:s}".format(filename))
[docs] def load_rgb(self, red, green, blue, scale=False, lockwcs=False):
"""load 3 images into an RGBimage frame
Parameters
----------
red: string
The name of the fits file which will be loaded into the red channel
green: string
The name of the fits file which will be loaded into the green channel
blue: string
The name of the fits file which will be loaded into the blue channel
scale: bool
If True, then each image will be scale with zscale() after loading
lockwcs: bool
If True, then the image positions will be locked to each other using the WCS
information in their headers
"""
self.set("rgb new")
self.set("rgb channel red")
self.load_fits(red)
if scale:
self.scale()
self.set("rgb channel green")
self.load_fits(green)
if scale:
self.scale()
self.set("rgb channel blue")
self.load_fits(blue)
if scale:
self.scale()
if lockwcs:
self.set("rgb wcs yes")
[docs] def load_mef_as_cube(self, filename=None):
"""Load a Mult-Extension-Fits image into one frame as an image cube"""
if not filename:
print("No filename specified")
else:
self.set("file mecube new {0:s}".format(filename))
[docs] def load_mef_as_multi(self, filename=None):
"""Load a Mult-Extension-Fits image into multiple frames"""
if not filename:
print("No filename specified")
else:
self.set("file multiframe {0:s}".format(filename))
[docs] def mark_region_from_array(
self, input_points, ptype="image", textoff=10, size=5):
"""mark ds9 regions regions given an input list of tuples, a convienence function, you can also use set_region
Parameters
----------
input_points: a tuple, or list of tuples, or a string: (x,y,comment),
ptype: string
the reference system for the point locations, image|physical|fk5
size: int
the size of the region marker
textoff: string
the offset for the comment text, if comment is empty it will not show
Notes
-----
only circular regions are supported currently
"""
if isinstance(input_points, tuple):
input_points = [input_points]
elif isinstance(input_points, str):
input_points = [tuple(input_points.split())]
X = 0
Y = 1
COMMENT = 2
rtype = "circle" # only one supported right now
for location in input_points:
if rtype == "circle":
pline = rtype + " " + \
str(location[X]) + " " + str(location[Y]) + " " + str(size)
print(pline)
self.set_region(pline)
try:
if(len(str(location[COMMENT])) > 0):
pline = "text " + str(float(location[X]) + textoff) + " " + \
str(float(location[Y]) + textoff) + " '" + \
str(location[COMMENT]) + "' #font=times"
print(pline)
self.set_region(pline)
except IndexError:
pass
[docs] def make_region(self, infile, labels=False, header=0, textoff=10, size=5):
"""make an input reg file with [x,y,comment] to a DS9 reg file, the input file should contains lines with x,y,comment
Parameters
----------
infile: str
input filename
labels: bool
add labels to the regions
header: int
number of header lines in text file to skip
textoff: int
offset in pixels for labels
size: int
size of the region type
Notes
-----
only circular regions are supported currently
"""
try:
f = open(infile, 'r')
lines = f.readlines()
f.close()
except IOError as e:
warnings.warn("Unable to open input file")
print("{0}".format(e))
raise ValueError
# assumed defaults for simple regions file
point = rtype
delta = textoff # pixels to offset text
lines = lines[header:]
numCols = len(lines[0])
text = list()
x = list()
y = list()
for i in range(0, len(lines), 1):
words = lines[i].split(',')
x.append(words[0].strip())
y.append(words[1].strip())
if(len(words) > 2 and labels):
text.append(words[2].strip())
# now write out to a reg file
out = infile + ".reg"
f = open(out, 'w')
for i in range(0, len(lines), 1):
pline = "image; " + point + \
"(" + x[i] + "," + y[i] + "," + str(size) + ")\n"
f.write(pline)
if(len(text) > 0):
pline = "image;text(" + str(float(x[i]) + delta) + "," + \
str(float(y[i]) + delta) + \
"{ " + text[i] + " })# font=\"time 12 bold\"\n"
f.write(pline)
f.close()
print("output reg file saved to: {0:s}".format(out))
[docs] def match(self, coordsys="wcs", frame=True, crop=False, fslice=False,
scale=False, bin=False, colorbar=False, smooth=False, crosshair=False):
"""match all other frames to the current frame
Parameters
----------
coordsys: string, optional
The coordinate system to use
frame: bool, optional
Match all other frames to the current frame, using the set coordsys
crop: bool, optional
Set the current image display area, using the set coordsys
fslice: bool, optional
Match current slice in all frames
scale: bool, optional
Match to the current scale for all frames
bin: bool, optional
Match to the current binning for all frames
colorbar: bool, optional
Match to the current colorbar for all frames
smooth: bool, optional
Match to the current smoothing for all frames
crosshair: bool, optional
Match the crosshair in all frames, using the current coordsys
Notes
-----
You can only choose one of the options at a time, and the logic will select the first True option
so set frame=False and something else in addition to your choice if you don't want the default option.
"""
cstring = "match "
if frame:
cstring += "frame {0:s}".format(corrdsys)
elif crosshair:
cstring += "crosshair {0:s}".format(corrdsys)
elif crop:
cstring += "crop {0:s}".format(corrdsys)
elif fslice:
cstring += "slice"
elif bin:
cstring += "bin"
elif scale:
cstring += "scale"
elif colorbar:
cstring += "colorbar"
elif smooth:
cstring += "smooth"
self.set(cstring)
[docs] def nancolor(self, color="red"):
"""set the not-a-number color, default is red
Parameters
----------
color: string
The color to use for NAN pixels
"""
self.set("nan {0:s}".format(color))
[docs] def panto_image(self, x, y):
"""convenience function to change to x,y physical image coordinates
Parameters
----------
x: float
X location in physical coords to pan to
y: float
Y location in physical coords to pan to
"""
self.set("pan to {0:f} {0:f} image".format(x, y))
[docs] def panto_wcs(self, x, y, system='fk5'):
"""pan to wcs location coordinates in image
Parameters
----------
x: string
The x location to move to, specified using the given system
y: string
The y location to move to
system: string
The reference system that x and y were specified in, they should be understood by DS9
"""
self.set("pan to {0:s} {1:s} wcs %s".format(x, y, system))
[docs] def rotate(self, value=None, to=False):
"""rotate the current frame (in degrees), the current rotation is printed with no params
Parameters
----------
value: float [degrees]
Rotate the current frame {value} degrees
If value is 0, then the current rotation is printed
to: bool
Rotate the current frame to the specified value
"""
if value is None:
print("Image rotated at {0:s}".format(self.get("rotate")))
elif to and value >= 0:
cstring = "rotate to {0:s}".format(str(value))
self.set(cstring)
elif value > 0:
cstring = "rotate {0:s}".format(str(value))
self.set(cstring)
cstring = "Image rotated at {0:s}".format(self.get("rotate"))
print(cstring)
logging.info(cstring)
[docs] def save_regions(self, filename=None):
"""save the regions in the current window to a DS9 style regions file
Parameters
----------
filename: string
The nameof th file to which the regions displayed in the current window are saved
If no filename is provided then it will try and save the regions to the name of the
file in the current display with _regions.txt appended
If a file of that name already exists on disk it will no attempt to overwrite it
"""
regions = self.get("regions save")
frame = self.frame()
if frame and not filename:
filename = self._viewer[frame]['filename'] + "_regions.txt"
# check if the file already exists
if not os.access(filename, os.F_OK):
with open(filename, "w") as region_file:
region_file.write(regions)
else:
warnings.warn(
"File already exists: {0} try again".format(filename))
[docs] def save_rgb(self, filename=None):
"""save an rgbimage frame as an MEF fits file
Parameters
----------
filename: string
The name of the output fits image
"""
if not filename:
print("No filename specified, try again")
else:
self.set("save rgbimage {0:s}".format(filename))
[docs] def scale(self, scale='zscale'):
""" The default zscale is the most widely used option
Parameters
----------
scale: string
The scale for ds9 to use, these are set strings of
[linear|log|pow|sqrt|squared|asinh|sinh|histequ]
Notes
-----
The xpa doesn't return an error if you set an unknown scale,
it just doesn't do anything, this is true for all the xpa calls
"""
_help = """Syntax:
scales available: [linear|log|pow|sqrt|squared|asinh|sinh|histequ]
[log exp <value>]
[datasec yes|no]
[limits <minvalue> <maxvalue>]
[mode minmax|<value>|zscale|zmax]
[scope local|global]
[match]
[lock [yes|no]]
[open|close]
"""
mode_scale = ["zscale", "zmax", "minmax"]
cstring = ("scale %s") % (scale)
if scale in mode_scale:
cstring = ("scale mode %s") % (scale)
try:
self.set(cstring)
except (XpaException, ValueError):
print("{0:s} not valid".format(cstring))
print(_help)
[docs] def set_region(self, region_string=""):
"""display a region using the specifications in region_string
Parameters
----------
region_string: string
Should take the form of a region string that DS9 is expecting
Examples
--------
set_region("physical ruler 200 300 200 400")
set_region("line 0 400 3 400 #color=red")
"""
command = "regions command {{ {0:s} }}\n".format(region_string)
self.set(command)
[docs] def showme(self):
"""raise the ds9 window"""
self.set("raise")
[docs] def showpix(self, close=False):
"""display the pixel value table, close window when done
Parameters
----------
close: bool, optional
If set to True, then the pixel table dialog window is closed
"""
self.get("pixeltable")
if close:
self.set("pixeltable close")
[docs] def snapsave(self, filename=None, format=None, resolution=100):
"""create a snap shot of the current window and save in specified format.
Parameters
----------
filename: str, optional
filename of output image, the extension in the filename can also be used to specify the format
If no filename is specified, then the filename will be constructed from the name of the
currently displayed image with _snap.jpg appended.
format: str, optional
available formats are fits, eps, gif, tiff, jpeg, png
If no format is specified the filename extension is used
resolution: int, optional
1 to 100, for jpeg images
"""
frame = self.frame()
if not filename:
filename = self._viewer[frame]['filename'] + "_snap.jpg"
cstring = "saveimage "
name = filename
if format:
name = filename + format
cstring += name
if "jpeg" in name:
cstring += (" " + str(resolution))
self.set(cstring)
print("Image saved to {0:s}".format(filename))
logging.info("Image saved to {0:s}".format(filename))
[docs] def view(self, img):
""" Display numpy image array to current frame
Parameters
----------
img: numpy array
The array containing data, it will be forced to numpy.array()
"""
frame = self.frame()
if not frame:
print("No valid frame")
else:
img = np.array(img)
if img.dtype.type == np.bool8:
img = img.astype(np.uint8)
try:
img.shape = img.shape[-2:]
except:
raise UnsupportedImageShapeException(repr(img.shape))
if img.dtype.byteorder in ["=", "|"]:
dt = img.dtype.newbyteorder(">")
img = np.array(img, dtype=dt)
byteorder = ">"
else:
byteorder = img.dtype.byteorder
endianness = {">": ",arch=bigendian",
"<": ",arch=littleendian"}[byteorder]
(ydim, xdim) = img.shape
arr_str = img.tostring()
itemsize = img.itemsize * 8
try:
bitpix = self._ImgCode[img.dtype.name]
except KeyError as e:
raise UnsupportedDatatypeException(e)
option = "[xdim=%d,ydim=%d,bitpix=%d%s]" % (xdim, ydim,
bitpix, endianness)
try:
self.set("array " + option, arr_str)
self._set_frameinfo()
self._viewer[frame]['user_array'] = img
except XpaException as e:
raise XpaException(
"XPA: {0} : Problem loading array into frame {1}".format(e, frame))
[docs] def zoomtofit(self):
"""convenience function for zoom"""
self.zoom("to fit")
[docs] def zoom(self, par="to fit"):
""" zoom using the specified command in par
Parameters
----------
par: string
it can be a number (ranging 0 to 8 effectively), and successive calls continue zooming in the same direction
it can be two numbers '4 2', which specify zoom on different axis
if can be to a specific value 'to 8' or 'to fit'
it can be 'open' to open the dialog box
it can be 'close' to close the dialog box (only valid if the box is already open)
Examples
--------
zoom("0.1")
"""
try:
self.set("zoom %s" % (str(par)))
except XpaException:
print(
"XPA problem with zoom (probably your zoom window is already closed)")
[docs] def show_commands(self):
"""print the available XPA commands"""
print(self.get()) # with no arguments supplied, XPA returns options
import atexit
atexit.register(ds9._purge_tmp_dirs)
atexit.register(ds9._stop_running_process)