def annotate_image(fits_file, reg_file=None):
print(f"You are going to give an annotation for {fits_file}")
input("You will be prompted from the command line, keep it open \n\
Press enter to continue")
with fits.open(fits_file) as f:
try:
dim=pyds9.DS9(FITS_XPA_METHOD)
except:
print("Looks like your SAO DS9 is not connected")
xpa_method = input("Please input you XPA METHOD \n\
This can be found in your version of ds9:\n\
\tFile > XPA > Information > XPA METHOD")
dim = pyds9.DS9(xpa_method)
# get the pixel-image coordinate representation of region
outf=fits.HDUList(f[0])
dim.set("frame new")
showtest=dim.set_pyfits(outf)
if reg_file is not None:
region_string = utils.get_text_in_file(reg_file)
dim.set('regions', region_string)
dim.set("regions -system image")
dim.set("regions shape box")
for key, val in config.color_key.items():
dim.set(f"regions color {val}")
print(f"Now, annotate all {key}")
input("When you are done, press return")
region_string = dim.get("regions -system image")
dim.set("frame delete")
return region_string
def ds9(self):
if not self._ds9:
# start xpans if needed
logger.debug("Starting XPANS")
ds9.ds9_xpans()
logger.debug("Starting DS9")
# start ds9 if need, or connect to existing
try:
self._ds9 = ds9.DS9(target='gui', start=False)
except ValueError as ve:
cnt = 0
while cnt < 10:
cnt += 1
try:
self._ds9 = ds9.DS9(target='gui',
start=True,
wait=30,
verify=True)
self.set_ds9(level="INIT")
self.set_ds9(level="PREF")
break
except ValueError as ve:
logger.debug(f"DS9 not started yet: {ve}")
pass
finally:
self._ds9.set("frame delete all")
logger.debug(f"DS9 Operational")
self._ds9.reset_preferences = self.set_ds9
self._ds9.new_frame = self._new_frame
return self._ds9
def ds9(*instance):
'''
Attach to a given ds9 instance or create a new one.
'''
if not instance:
targets = pyds9.ds9_targets()
else:
targets = [str(instance[0])]
dsn = pyds9.DS9(targets[0]) if targets else pyds9.DS9()
return dsn
def cmap(self, value=None):
""" Controls the colormap for the current frame. The colormap name is
not case sensitive. A valid contrast value is from 0 to 10 and bias
value from 0 to 1.
Parameters
----------
value : str, optional
Value to be passed to the cmap command.
Notes
-----
syntax:
.. code-block:: none
cmap [<colormap>]
[file]
[load <filename>]
[save <filename>]
[invert yes|no]
[value <constrast> <bias>]
[tag [load|save] <filename>]
[tag delete]
[match]
[lock [yes|no]]
[open|close]
"""
self.window = pyds9.DS9(self.window_name)
self.window.set('cmap ' + str(value))
def set_region_type_to_image(reg_file, fits_file):
with fits.open(fits_file) as f:
region_string = utils.get_text_in_file(reg_file)
# get the format of the coordinates in the reg file
region_string_split = region_string.split("\n")
if len(region_string_split) > 2:
region_type = region_string_split[2]
else:
region_type = None
if region_type != "image" and region_type != None:
###
# hacky code:
# If you are getting an error here:
# FITS_XPA_METHOD needs to be set above
# in your version of ds9:
# File > XPA > Information > XPA METHOD
# This is necessary because the pyregions library has bugs
###
dim=pyds9.DS9(FITS_XPA_METHOD)
# get the pixel-image coordinate representation of region
outf=fits.HDUList(f[0])
showtest=dim.set_pyfits(outf)
dim.set("regions", region_string)
region_string = dim.get("regions -system image")
# rewrite region file to be in image coordinates
with open(reg_file, "w") as reg_file:
reg_file.write(region_string)
def __init__(self, **kwargs):
self.hi_res_map_list = kwargs['hi_res_map_list']
self.hi_res_cat_list = kwargs['hi_res_cat_list']
self.hi_res_label = kwargs['hi_res_label']
self.hi_res_coord_index = kwargs['hi_res_coord_index']
self.low_res_map_list = kwargs['low_res_map_list']
self.low_res_noise_list = kwargs['low_res_noise_list']
self.low_res_cat = np.loadtxt(
kwargs['low_res_cat'],
dtype=zip(*utils.get_ascii_table_header(kwargs['low_res_cat'])),
ndmin=1)
self.low_res_label = kwargs['low_res_label']
self.low_res_beamsize = kwargs['low_res_beamsize']
self.low_res_coord_index = kwargs['low_res_coord_index']
self.low_res_ps = kwargs['low_res_ps']
self.low_res_psf = os.path.abspath(kwargs['low_res_psf'])
self.galfit_workroot = os.path.abspath(kwargs['galfit_workroot'])
self.galfit_bin = os.path.abspath(kwargs['galfit_bin'])
self.xclip_bin = os.path.abspath(kwargs['xclip_bin'])
self._validate_bin()
self.xpa_extracmd = kwargs['xpa_extracmd']
self.lastwarning = ""
self._result_loaded = False
self.ds9 = pyds9.DS9("DS9-GalFit")
self.clean_display()
def tile(self, mode='column'):
""" Controls the tile display mode.
Parameters
----------
mode : str, optional
The mode used for tiling the frames.
Notes
-----
Syntax:
.. code-block:: none
tile []
[yes|no]
[mode grid|column|row]
[grid]
[grid mode automatic|manual]
[grid direction x|y]
[grid layout <col> <row>]
[grid gap <pixels>]
[row]
[column]
"""
self.window = pyds9.DS9(self.window_name)
if mode == 'off':
self.window.set('tile off')
else:
self.window.set('tile on')
self.window.set('tile mode ' + mode)
def zoom(self, value='to fit'):
""" Controls the current zoom value for the current frame.
Parameters
----------
value : str or int
Parameters of the zoom command.
Notes
-----
syntax:
.. code-block:: none
zoom [<value>]
[<value> <value>]
[to <value>]
[to <value> <value>]
[in]
[out]
[to fit]
[open|close]
"""
self.window = pyds9.DS9(self.window_name)
self.window.set('zoom ' + str(value))
def load_pyds9(self, image, angunit=None, wait=10, overwrite=True):
'''
Load DS9 region to IMRegion.
This method uses pyds9.DS9().
Args:
image (IMFITS)
angunit (str, default = None):
The angular unit of region. If None, it will take from
the default angunit of the input image
wait (float, default = 10):
seconds to wait for ds9 to start.
overwrite (boolean, default = True):
If overwrite=True, previous region is removed.
Returns:
IMRegion.
'''
if angunit is None:
angunit = image.angunit
try:
d = pyds9.DS9(wait=wait)
except ValueError:
print("ValueError: try longer 'wait' time or installation of XPA.")
except:
print("Unexpected Error!")
raise
else:
ds9reg = d.get("regions -system image")
region = ds9reg_to_reg(ds9reg=ds9reg, image=image, angunit=angunit)
if overwrite:
return region
else:
return self + region
def ds9view(fitsfile, regfile=None, width=750, height=750, mecube=False):
"""
View image with our without regions in ds9.
Parameters
----------
fitsfile : string
Fits file of image
regfile : string, optional
ds9 regions file. If None, no regions will be drawn.
width : float, optional
Width of window
height : float, optional
height of window
mecube : bool, optional
If True, open file as multiple extension cube.
"""
import pyds9
ds9 = pyds9.DS9(start='-view layout vertical '+\
'-width '+str(width)+' '+\
'-height '+str(height)+' '+\
'-scale zscale '+\
'-wcs skyformat degrees '+\
'-cmap invert yes ')
cmd = 'file mecube ' + fitsfile if mecube else 'file ' + fitsfile
ds9.set(cmd)
if regfile is not None:
ds9.set('regions load ' + regfile)
ds9.set('zoom to fit')
def display(self, *arrays, **kwargs):
""" Displays one or multiple arrays (listed in ``*arrays``).
Parameters
----------
*arrays : list of arrays
The arrays to be displayed.
**kwargs : dictionary, optional
Only one parameter is admitted: ``keep_frames``. When
``keep_frames`` is passed and is set to True, the new arrays are
displayed in the existing window (creating new ds9 frames). If no
``keep_frames`` is given or if it is set to False, then the existing
ds9 frames are not preserved.
"""
self.window = pyds9.DS9(self.window_name)
if 'keep_frames' in kwargs:
if not kwargs['keep_frames']:
self.delete_frame(all_frames=True)
else:
self.delete_frame(all_frames=True)
self.tile()
for i, array in enumerate(arrays):
if i == 0:
self.create_frame()
self.window.set_np2arr(array)
else:
self.window.set('frame new')
self.window.set_np2arr(array)
def ds9():
import pyds9
import os
import time
PWD = os.getcwd()
new_dir_path = PWD + "/" + 'jpeg'
dir_name = "fits"
file_list = os.listdir(PWD + "/" + dir_name)
if not os.path.exists(new_dir_path):
os.mkdir(new_dir_path)
d = pyds9.DS9()
time.sleep(5)
d.set("cmap value 1 .5")
d.set("smooth")
d.set("smooth radius 10")
d.set("smooth sigma 5")
time.sleep(5)
d.set("view colorbar no")
d.set("cmap aips0")
d.set("scale squared")
for i in file_list:
root, ext = os.path.splitext(i)
d.set("file %s/%s" % (dir_name, i))
d.set("saveimage png %s/%s.png" % (new_dir_path, root))
d.set("exit")
else:
print("jpeg directory exist!!")
def display_gal(fname):
"""Open a DS9 window for the cutout being classified.
Parameters
----------
fname : string
Full path to the cutout being classified.
"""
print "==========================================================="
print "Displaying cutout {}".format(fname)
ds9window = ds9.DS9()
ds9window.set("tile yes")
ds9window.set("tile mode column")
ds9window.set("frame 1")
ds9window.set("file " + fname)
ds9window.set("zoom to fit")
ds9window.set("scale log")
#ds9window.set("scale limits -0.1 2")
ds9window.set("frame 2")
ds9window.set("file " + fname)
ds9window.set("zoom to fit")
ds9window.set("scale log")
ds9window.set("scale limits -0.1 25")
return
def show_ds9_list(imgList,instanceName='default'):
''' display a list of images in a DS9 instance '''
#Setup the DS9 instance
disp = pyds9.DS9(instanceName)
disp.set("frame delete all")
disp.set("view image no")
disp.set("view colorbar no")
disp.set("view panner no")
disp.set("view info yes")
disp.set("view magnifier no")
disp.set("view buttons no")
disp.set("tile yes")
disp.set("tile column")
disp.set("width 1200")
disp.set("height 275")
#Display the images
for i,img in enumerate(imgList):
disp.set("frame {}".format(i))
ds9cmd = "file fits {}".format(img)
disp.set(ds9cmd)
disp.set("scale mode minmax")
disp.set("regions delete all")
disp.set("scale log")
disp.set("cmap invert yes")
disp.set(ds9cmd)
return disp
def scale(self, value=None):
""" Controls the limits and color scale distribution.
Parameters
----------
value : str, optional
Controls the scaling.
Notes
-----
Syntax:
.. code-block:: none
scale [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]
[match limits]
[lock [yes|no]]
[lock limits [yes|no]]
[open|close]
"""
self.window = pyds9.DS9(self.window_name)
if value:
self.window.set('scale ' + str(value))
else:
self.window.set('scale open')
def get_comps_fwhm(comparisons, xpapoint):
# requires fwhm_from_star, namesplit
# create a ds9 object linked with an XPA point
win = pyds9.DS9(xpapoint)
# load the image from ds9 (not from disk!)
hdu_link = win.get_pyfits()
image = hdu_link[0].data
nc = len(comparisons)
tot_fwhm = 0.
# comparisons is alist of tuples, in each tuple first element has x,y,r
print "* I will use", nc, "star(s) to get an estimate of the FWHM:"
for i in range(0,nc):
xt = comparisons[i][0][0]
yt = comparisons[i][0][1]
r = comparisons[i][0][2]
x1 = int(xt - r)
x2 = int(xt + r)
y1 = int(yt - r)
y2 = int(yt + r)
# caution - I don't know why order of x and y is inverted here
crop_image = image[y1:y2,x1:x2]
# hdu=pyfits.PrimaryHDU(crop_image)
# hdu.writeto("test.fits")
fwhm = fwhm_from_star(crop_image)
cname = (comparisons[i][1])
print i+1, cname, fwhm
tot_fwhm = tot_fwhm + abs(fwhm)
mean_fwhm = tot_fwhm / nc
print "* Calculated a mean FWHM of:", ("%.2f" % abs(mean_fwhm)),"pixels"
print
return mean_fwhm
def start_ds9(name=DS9_NAME):
"""
START a DS9 viewer with name 'name' if one with that name isn't already running.
:param name: name to give the ds9 server.
:return: ds9 server object.
:rtype DS9
"""
c = 0
while True:
try:
ds9 = pyds9.DS9(target=name)
time.sleep(2)
break
except Exception as ex:
if c > 10:
raise ex
c += 1
logging.debug("Trying again to connect to ds9 after 5s wait")
time.sleep(5)
levels = ['INIT', 'PREF']
for level in levels:
setting = config.read(f"DS9.{level}")
for key in list(setting.keys()):
ds9.set(f"{key.replace('_', ' ')} {setting[key]}")
ds9.set("view panner yes")
ds9.set("view magnifier yes")
ds9.set('cmap 1.4 0.5')
ds9.set("frame delete all")
return ds9
def __init__(self,
name='general',
wait=10,
minimal=True,
xsize=300, ysize=300,
rotate=None, **kwargs):
'''initialize the ds9 display object
name = an identifier so you can point back to this
ds9 display, e.g. to refresh it later
wait = how many seconds to wait when trying to open ds9
minimial = hide all the bells and whistles
rotate = should images be rotated by default
'''
# pass kw on to Display
Display.__init__(self, **kwargs)
# make sure the name is valid
self.name = name.replace(' ','_')
# attempt to open, but don't freak out
try:
self.speak('trying to open a new ds9 window called "{0}"'.format(
self.name))
self.speak(' (will wait up to {0:.0f} seconds)'.format(wait))
self.window = pyds9.DS9(self.name,start=True,wait=wait,verify=True)
except IOError:
self.speak(' :( failed to open ds9 window "{0}"'.format(self.name))
if minimal:
self.sparse()
self.resize(xsize, ysize)
self.rotate=rotate
def setup_ds9_connection(reconnect):
""" Open a DS9 window. If DS9 already opened spawn a new instance """
# ds9_targets returns None if no ds9 window is opened
ds9_running = pyds9.ds9_targets()
if ds9_running:
if reconnect and len(ds9_running) == 1:
connectionstring = (ds9_running[0]).replace("DS9:ds9 ", "")
d = pyds9.DS9(connectionstring)
time.sleep(0.5)
return d, connectionstring
elif reconnect and len(ds9_running) != 1:
print "Error: multiple ds9 instances running. Unknown which to connect to."
exit(1)
print "We see that ds9 is already running."
sys.stdout.write("Opening a new ds9 window...")
sys.stdout.flush()
import os
launch = os.system(
"/Applications/SAOImage\ DS9.app/Contents/MacOS/ds9 &")
del (os)
time.sleep(3)
if launch is 0:
print " done"
ds9_running_new = pyds9.ds9_targets()
unique_entries = list(set(ds9_running_new) - set(ds9_running))
if len(unique_entries) == 1:
connectionstring = unique_entries[0]
connectionstring = connectionstring.replace("DS9:ds9 ", "")
d = pyds9.DS9(connectionstring)
time.sleep(0.5)
else:
exit(1)
else:
exit(1)
else:
print "No ds9 instance is running."
sys.stdout.write("Opening a new ds9 window ...")
sys.stdout.flush()
d = pyds9.DS9()
time.sleep(0.5)
connectionstring = (pyds9.ds9_targets()[0]).replace("DS9:ds9 ", "")
print " done"
return d, connectionstring
def get_ds9(name):
"""
Get a connection to 'name' DS9 server, don't start one if it isn't already going.
:param name: name of the server to connect to.
:return: ds9 server connection
:rtype DS9
"""
return pyds9.DS9(target=name, start=False)
def main(argv=None):
''' Main Function '''
# Call initial parser from init_utils
parser = ap.ArgumentParser(description="""Create HDF5 file.""",
add_help=True)
parser.add_argument("hdf5_file", type=str, help='''Name of h5/hdf5 file''')
parser.add_argument("-e",
"--extension",
help='''Extension or extensions''',
type=str,
default=None)
parser.add_argument("-q",
"--query",
help='''Query to be applied''',
type=str,
default=None)
parser.add_argument('-s',
'--show',
help='''Show tables/extensions within file''',
action="count",
default=0)
args = parser.parse_args(argv)
args.log = setup_logging()
try:
h5file = open_file(args.hdf5_file, mode='r')
except:
if not op.exists(args.hdf5_file):
args.log.error('%s does not exist' % args.hdf5_file)
return None
else:
args.log.error('File exists but could not open %s' %
args.hdf5_file)
return None
if args.show:
table_names = ['Shot', 'Fibers', 'Images']
for kind in table_names:
print('%s column names:' % kind)
b = getattr(h5file.root.Info, kind)
for name in b.colnames:
base = getattr(b.cols, name)
shape = str(base.shape)
print('\t%s: %s %s' % (name, base.type, shape))
return None
if args.extension is None:
args.log.error('No extension provided to display in ds9')
return None
table = h5file.root.Info.Fibers
spec = np.array(table.cols.spectrum[:])
ds9 = pyds9.DS9()
ds9.set_np2arr(spec)
h5file.close()
def start_ds9(name):
ds9 = pyds9.DS9(target=name)
levels = ['INIT', 'PREF']
for level in levels:
setting = config.read(f"DS9.{level}")
for key in list(setting.keys()):
ds9.set(f"{key.replace('_', ' ')} {setting[key]}")
ds9.set("frame delete all")
return ds9
def annotate_composite(fits_files, reg_file=None, size=IMSIZE):
fits_files = [f for f in fits_files if f != ""]
if len(fits_files) > 3:
fits_files = fits_files[-3:]
elif len(fits_files) == 2:
fits_files = fits_files + [fits_files[1]]
elif len(fits_files) == 1:
fits_files = fits_files * 3
print(fits_files)
imarrays = [get_image_data(f)[0] for f in fits_files]
imarrays = [preprocess(im, resize=False) for im in imarrays]
imarrays = [resize_image(im, size) for im in imarrays]
opened_files = [fits.PrimaryHDU(data=im) for im in imarrays]
try:
dim=pyds9.DS9(FITS_XPA_METHOD)
except:
print("Looks like your SAO DS9 is not connected")
xpa_method = input("Please input you XPA METHOD \n\
This can be found in your version of ds9:\n\
\tFile > XPA > Information > XPA METHOD")
dim = pyds9.DS9(xpa_method)
outfiles = [fits.HDUList(f) for f in opened_files]
dim.set("frame new rgb")
for outf, color in zip(outfiles, ["red", "green", "blue"]):
dim.set(f"rgb channel {color}")
dim.set_pyfits(outf)
if reg_file is not None:
region_string = utils.get_text_in_file(reg_file)
dim.set('regions', region_string)
dim.set("regions -system image")
dim.set("regions shape box")
for key, val in config.color_key.items():
dim.set(f"regions color {val}")
print(f"Now, annotate all {key}s")
input("When you are done, press return")
region_string = dim.get("regions -system image")
dim.set("frame delete")
return region_string
def display_regions(imgname, coordsys, reg_dict_list, flag_counts_list, n_sources_list):
"""
Display the input input image overplot the positions of flagged sources
parameters
----------
imgname : string
input image name
coordsys : string
coordinate system to use
reg_dict_list : list
list of dictionaries containing region info keyed by flag bit for both sourcelists
flag_counts_list : list
list of overall flag population stats broken down by individual flag bit for both sourcelists
n_sources_list : list
list total number of sources in each sourcelist
returns
-------
nothing.
"""
imghdu = fits.open(imgname)
d = pyds9.DS9()
print("{}Catalog #1{}Catalog #2".format(" " * 56, " " * 10))
for ctr in range(0, len(bit_list)):
bit_val = bit_list[ctr]
padding1 = 6 - len(str(bit_val))
padding2 = 27 - len(flag_meanings[ctr])
text_stuff = "Frame {}: Bit value {}{}{}{}".format(ctr+1,bit_val,"."*padding1,flag_meanings[ctr],padding2*".")
pct_1 = (float(flag_counts_list[0][ctr])/float(n_sources_list[0]))*100.0
pct_2 = (float(flag_counts_list[1][ctr]) / float(n_sources_list[1])) * 100.0
out_string = "{:9d} {:8.3f}% {:9d} {:8.3f}%".format(flag_counts_list[0][ctr],pct_1,flag_counts_list[1][ctr],pct_2)
print("{}{}".format(text_stuff,out_string.replace(" ",".")))
if ctr != 0:
d.set("frame new")
d.set_fits(imghdu)
d.set("scale zscale")
if coordsys == "radec":
d.set("wcs fk5")
d.set("wcs degrees")
for reg_dict in reg_dict_list:
if reg_dict[bit_val]:
if coordsys == "xy":
d.set('regions', 'physical; {}'.format(reg_dict[bit_val]))
if coordsys == "radec":
d.set('regions', 'fk5; {}'.format(reg_dict[bit_val]))
out_string = ".......{:9d}{}{:9d}".format(n_sources_list[0], "." * 11 , n_sources_list[1])
print("{}TOTAL CATALOG LENGTH{}".format(" " * 25,out_string.replace(" ",".")))
d.set("lock frame image")
def openDS9(self):
# Opens DS9 or points to existing window if already open.
pyds9.DS9()
# If called after taking an exposure open that exposure.
#print("> Opening image in ds9...")
os.system(
'xpaset -p ds9 fits ' +
str('/home/fhire/Desktop/FHiRE_GAM/RefractorImage_temp-G.fits'))
os.system('xpaset -p ds9 zoom to fit')
os.system('xpaset -p ds9 zscale')
def open():
#call('xpans &', shell=True) #Load XPA immediately, so XPA commands can be sent to ds9, commented out for now, apparently doesn't work
#call('ds9 &', shell=True) #Load DS9
#if check_output('xpaaccess ds9 &', shell=True) == 'no\n':
# call(['/bin/bash', '-i', '-c', 'ds9 &']) #Load DS9 with bash, change bash to whatever shell you use if you are having issues
#while check_output('xpaaccess ds9 &', shell=True) == 'no\n': #While loop that checks every second or so if DS9 is open before continuing
# time.sleep(1) #Wait one second than check if DS9 is open again
global d
if d == None: #Is DS9 not open yet...
d = pyds9.DS9() #Open a DS9 object with pyds9
else: #If DS9 is already open...
print('WARNING: DS9 is already open.')
def unlock(self, scale=True, colorbar=True, crosshair=True, slices=True):
""" The opposite of the ``lock`` method.
"""
self.window = pyds9.DS9(self.window_name)
if scale:
self.window.set('lock scale no')
if colorbar:
self.window.set('lock colorbar no')
if crosshair:
self.window.set('lock crosshair none')
if slices:
self.window.set('lock slice none')
def main( fits, ext="png" ):
d = pyd.DS9()
#d.set("height 750")
#d.set("width 1150")
d.set("file %s" % fits)
d.set("scale zscale")
d.set("zoom to fit")
img = fits[0:fits.rfind(".")] + ".%s"%ext
d.set("saveimage %s %s" % (ext,img))
d.set("exit")
def lock(self, scale=True, colorbar=True, crosshair=True, slices=True):
""" Locks the scaling, colorbar, crosshair position, or slice in cube
for all existing ds9 frames (wrt the active one). """
self.window = pyds9.DS9(self.window_name)
if scale:
self.window.set('lock scale yes')
if colorbar:
self.window.set('lock colorbar yes')
if crosshair:
self.window.set('lock crosshair image')
if slices:
self.window.set('lock slice image')
def rotate(self, value=None):
""" Rotates with a given angle.
Parameters
----------
value : float, optional
Angle.
"""
self.window = pyds9.DS9(self.window_name)
if value:
self.window.set('rotate ' + str(value))
else:
self.window.set('rotate open')