if "plot limits" in arcdata[image_name]:
# Use previously stored value if present
vmin = arcdata[image_name]["plot limits"]["min"]
else:
minfactor = MINFACTOR_DEFAULT
else:
minfactor = cmd_args.minfactor
if vmin is None:
vmin = avbg - minfactor*dbg
plot_limits_modified = True
# Now update the db if necessary
if plot_limits_modified:
arcdata[image_name]["plot limits"] = {"max": vmax, "min": vmin}
arcdata["info"]["history"].append(
"Plot limits modified for " + image_name + " " + run_info())
arcdata["help"]["brightness"]["plot limits"] \
= "Minimum and maximum brightness for *-images.pdf"
update_json_file(arcdata, dbfile)
instrument = " ".join([arcdata[image_name][k]
for k in ["camera", "filter", "date"]
if k in arcdata[image_name]])
# Plot image of the FITS array of this object
#
plt.clf()
f = plt.figure(figsize=(18,9))
ax1 = aplpy.FITSFigure(hdu, figure=f, subplot=(1, 2, 1), north=True)
ax1.recenter(ra0, dec0, 2*Rc)
ax1.show_grayscale(invert=True, vmin=vmin, vmax=vmax)
ymin = avbg - 2*wbg
ymax = avsh + 2*wsh
print("BG trimean = {:.2f}, iqr = {:.2f}".format(avbg, wbg))
print("Shell trimean = {:.2f}, iqr = {:.2f}".format(avsh, wsh))
print("Adopting plot range of {:.2f} to {:.2f}".format(ymin, ymax))
# Save brightness statistics to a new JSON file
arcdata[image_name]["background"] = {"value": float(avbg), "delta": float(wbg),
"N": int(nbg)}
arcdata[image_name]["shell"] = {"value": float(avsh), "delta": float(wsh),
"N": int(nsh)}
arcdata[image_name]["shell center"] = {"value": float(avshc), "delta": float(wshc),
"N": int(nshc)}
arcdata["info"]["history"].append("Shell data for " + image_name + " added/modified by " + run_info())
# Save brightness statistics in the help section
help_brightness = {"shell":"Trimean brightness and interquartile (difference between quartiles) of shell",
"shell center":"Trimean brightness and interquartile (difference between quartiles) of shell center",
"background":"Trimean brightness and interquartile (difference between quartiles) of background"}
arcdata["help"].update(brightness=help_brightness)
# Calculate average binned profiles versus theta
NTH = 25
need_to_bin_profiles = True
while need_to_bin_profiles:
th_edges = np.linspace(-60.0, 60.0, NTH)
th_centers = 0.5*(th_edges[:-1] + th_edges[1:])
print("Unknown shell type")
sys.exit()
shell = Shell(beta,cmd_args.type)
R = shell.radius(theta)
R[R<0]=np.nan
R_in = inner(R,theta,cmd_args.mach)
R_com,theta_com = mirror(R_in,theta)
arcdata = {
"info":{
"Description": "CRW theoretical stationary bowshocks",
"history":["Initially created by "+ run_info()],
"beta": beta,
"inner wind type": cmd_args.type
},
"help":{
"M": "Mach number of inner wind",
"beta":"Two-winds momentum ratio",
"i": "Rotation angle between proplyd reference frame and observer reference frame",
"inner wind type": "Angular variation of density's inner wind",
"x": "(list) x-coordinates of the outer shell normalized with distance",
"y": "(list) y-coordinates of the outer shell normalized with distance"
},
"inner":{}
}
for inc in [0.0,15.0,30.0,45.0,60.0]:
xp,yp = rotate(np.radians(inc),R_com,theta_com)
print("Fixing EQUINOX from string or zero value")
outhdu.header["EQUINOX"] = 2000.0
hdu.header["EQUINOX"] = 2000.0
## TODO: copy over more keywords from the original FITS header
## E.g., filter, camera, etc
##
## Save the small image
##
outfile = "-".join([cmd_args.source, image_name, "extract.fits"])
outhdu.writeto(outfile, output_verify="fix", clobber=True)
##
## Update the JSON database with information about the image
##
# Always overwrite an existing section with the same name
db[image_name] = {
"original FITS file": misc_utils.contract_fits_path(fits_path),
"extracted FITS file": outfile,
}
db[image_name].update(fits_utils.get_instrument_configuration(hdu))
db["info"]["history"].append("Image " + image_name + " added by " + misc_utils.run_info())
misc_utils.update_json_file(db, dbfile)
help="Name of source")
parser.add_argument("--savefig", action="store_true",
help="Save a figure showing the fit")
parser.add_argument("--debug", action="store_true",
help="Print out verbose debugging info")
cmd_args = parser.parse_args()
dbfile = cmd_args.source + "-arcdata.json"
db = json.load(open(dbfile))
for arc in "inner", "outer":
if arc in db:
update_arc_data(db[arc])
db["info"]["history"].append("Circle fits added by " + run_info())
update_json_file(db, dbfile)
region_file = dbfile.replace("-arcdata.json", "-arcfits.reg")
with open(region_file, "w") as f:
f.writelines([s + "\n" for s in create_arc_regions(db)])
if cmd_args.savefig:
plotfile = dbfile.replace("-arcdata.json", "-arcfits.pdf")
plt.plot(0.0, 0.0, 'o')
plt.axis("equal")
plt.savefig(plotfile)
db = json.load(open(infile))
if "beta" in infile:
f = plt.figure()
for i,inc in enumerate([0.0,15.0,30.0,45.0,60.0]):
try:
ax = f.add_subplot(2,3,i+1)
update_arc_data(db["outer"]["i="+str(inc)],teo=True)
except KeyError:
#print "inclination not available",inc
break
else:
for arc in "inner", "outer":
update_arc_data(db[arc])
db["info"]["history"].append("Conic fits added by " + run_info())
# save database to the same name: *-arcdata.json
outfile = infile
with tempfile.NamedTemporaryFile(
'w', dir=os.path.dirname(outfile), delete=False) as tf:
json.dump(db, tf, indent=4)
tempname = tf.name
os.rename(tempname, outfile)
if cmd_args.savefig:
plotfile = infile.replace("-arcdata.json", "-conic-fits.pdf")
if "beta" in infile:
f.tight_layout()
f.set_size_inches(2*5,3*5)
f.savefig(plotfile)
default="angel@crya",
help="User@system ID use for guessing paths")
parser.add_argument("--debug", action="store_true",
help="Print out verbose debugging info")
cmd_args = parser.parse_args()
dbfile = cmd_args.source + "-arcdata.json"
db = json.load(open(dbfile))
for secname, section in db.items():
if "original FITS file" in section:
oldpath = section["original FITS file"]
newpath = misc_utils.contract_fits_path(oldpath, user=cmd_args.user)
if cmd_args.debug:
print("Contracting full paths in", secname)
print("From", oldpath, "to", newpath)
section["original FITS file"] = newpath
db["info"]["history"].append("Paths corrected by " + misc_utils.run_info())
misc_utils.update_json_file(db, dbfile)
