def tab1_update_addStrID():
global dftmp
if tab1_selected_dspec_square:
time0, time1 = dftmp['time'].min() + timestart, dftmp['time'].max() + timestart
freq0, freq1 = dftmp['freq'].min(), dftmp['freq'].max()
date_char = Time(timestart / 3600. / 24., format='jd', scale='utc', precision=3, out_subfmt='date').iso
t0_char = Time(time0 / 3600. / 24., format='jd', scale='utc', precision=3, out_subfmt='date_hms').iso
t0_char = t0_char.split(' ')[1]
t1_char = Time(time1 / 3600. / 24., format='jd', scale='utc', precision=3, out_subfmt='date_hms').iso
t1_char = t1_char.split(' ')[1]
time0, time1 = (time0 / 86400. - 2400000.5) * 24. * 3600., (time1 / 86400. - 2400000.5) * 24. * 3600.
StrID = pd.DataFrame(dict(time=[[time0, time1, time1, time0]], freq=[[freq0, freq0, freq1, freq1]],
str_id=[[tab1_input_StrID.value]], date=[[date_char]],
timeran=[[t0_char + '~' + t1_char]],
freqran=[["{:.3f}~{:.3f} GHz".format(freq0, freq1)]]))
StrIDList = pd.read_json(event_dir + 'StrID_list_tmp.json')
StrIDList = pd.concat([StrIDList, StrID])
StrIDList = StrIDList.sort_values(by='timeran', ascending=1)
StrIDList.index = range(StrIDList.index.size)
StrIDList.to_json(event_dir + 'StrID_list_tmp.json')
StrIDList['time'] = [ll - tab1_tim[0] for ll in StrIDList['time']]
tab1_render_patch.data_source.data = ColumnDataSource(StrIDList).data
tab1_Div_Tb.text = """<p>added <b>""" + tab1_input_StrID.value + """</b> to the list</p>"""
else:
tab1_Div_Tb.text = """<p><b>Warning: No time & freq range selected.
def tab2_BUT_tCLN_param_default():
global tab2_tCLN_Param_dict, dspecDF0
tab2_tCLN_Param_dict = OrderedDict()
time0, time1 = dspecDF0['time'].min() + timestart, dspecDF0['time'].max(
) + timestart
t0_char = Time(time0 / 3600. / 24.,
format='jd',
scale='utc',
precision=3,
out_subfmt='date_hms').iso
date0_char = t0_char.split(' ')[0].replace('-', '/')
time0_char = t0_char.split(' ')[1]
t1_char = Time(time1 / 3600. / 24.,
format='jd',
scale='utc',
precision=3,
out_subfmt='date_hms').iso
date1_char = t1_char.split(' ')[0].replace('-', '/')
time1_char = t1_char.split(' ')[1]
freq0, freq1 = dspecDF0['freq'].min(), dspecDF0['freq'].max()
freqrange = "'{:.3f}~{:.3f} GHz'".format(freq0, freq1)
tab2_tCLN_Param_dict['freqrange'] = freqrange
tab2_tCLN_Param_dict['workdir'] = "'./'"
tab2_tCLN_Param_dict['vis'] = "''"
tab2_tCLN_Param_dict['imageprefix'] = "'slfcal/{}{}'".format(
struct_id, CleanID)
tab2_tCLN_Param_dict['ncpu'] = "10"
tab2_tCLN_Param_dict['twidth'] = "1"
tab2_tCLN_Param_dict['doreg'] = "False"
tab2_tCLN_Param_dict['timerange'] = "''"
tab2_tCLN_Param_dict['uvrange'] = "''"
tab2_tCLN_Param_dict['antenna'] = "''"
tab2_tCLN_Param_dict['ephemfile'] = "'horizons_sun_20141101.radecp'"
tab2_tCLN_Param_dict[
'msinfofile'] = "'SUN01_20141101.T163940-164700.50ms.cal.msinfo.npz'"
tab2_tCLN_Param_dict['event_id'] = "'{}'".format(event_id.replace("/", ""))
tab2_tCLN_Param_dict['struct_id'] = "'{}'".format(
struct_id.replace("/", ""))
tab2_tCLN_Param_dict['clean_id'] = "'{}'".format(CleanID.replace("/", ""))
tab2_tCLN_Param_dict['mode'] = "'channel'"
tab2_tCLN_Param_dict['imagermode'] = "'csclean'"
tab2_tCLN_Param_dict['weighting'] = "'natural'"
tab2_tCLN_Param_dict['gain'] = '0.1'
tab2_tCLN_Param_dict['psfmode'] = "'clark'"
tab2_tCLN_Param_dict['imsize'] = "" '[256, 256]' ""
tab2_tCLN_Param_dict['cell'] = "['3.0arcsec', '3.0arcsec']"
tab2_tCLN_Param_dict['phasecenter'] = "'J2000 14h26m22.7351 -14d29m29.801'"
tab2_tCLN_Param_dict['mask'] = "''"
tab2_tCLN_Param_dict['stokes'] = "'RRLL'"
tab2_tCLN_Param_dict['uvrange'] = "''"
tab2_tCLN_Param_dict['niter'] = "500"
tab2_tCLN_Param_dict['usescratch'] = "False"
tab2_tCLN_Param_dict['interactive'] = "False"
tab2_Div_tCLN_text = '<p><b># ptclean :: Parallelized clean in consecutive time steps</b></p>' + ' '.join(
"<p><b>{}</b> = {}</p>".format(key, val)
for (key, val) in tab2_tCLN_Param_dict.items())
tab2_Div_tCLN.text = tab2_Div_tCLN_text
tab2_Div_tCLN2.text = '<p><b>Default parameter Restored.</b></p>'
def onTimer(self):
timeStr = Time(datetime.utcnow(), scale='utc').iso.split('.')[0]
self.curTime.setText(timeStr.split(" ")[1])
#print('write ' + timeStr.split(" ")[1])
dateStr = Time(datetime.utcnow(), scale='utc').iso.split(' ')[0]
self.curDate.setText(dateStr)
if (self.cmd < 200):
self.cmd = 200
else:
self.cmd = 100
self.SendTimePacket()
self.SrhAntSocket.writeDatagram(
QtCore.QByteArray(
struct.pack('!16sHHHLL', b'_Srh_Net_Packet_', 0,
self.cmd, 0, 0, 0)),
QtNetwork.QHostAddress('192.168.0.168'), 9998)
testSocket = QtNetwork.QTcpSocket()
testSocket.connectToHost('192.168.0.1', 80)
if testSocket.waitForConnected() == True:
self.Network.setPixmap(self.greenBox)
else:
self.Network.setPixmap(self.redBox)
testSocket.close()
def epoch_time_array(
epoch_range,
index_epoch=None,
cadence=None,
):
"""Create a Skyfield :class:`~skyfield.timelib.Timescale` object at which to evaluate satellite positions.
Begins by downloading up-to-date time files, using the skyfield :class:`~skyfield.iokit.Loader` class,
needed to accurate converted between various time formats. See `Dates and Time
<https://rhodesmill.org/skyfield/time.html>`_ for more info. The files are saved to
:samp:`./embers_out/sat_utils/skyfield-data`.
For a particular time inverval in :samp:`epoch_range`, chosen by :samp:`index_epoch`, a
Skyfield :class:`~skyfield.timelib.Timescale` array object is generated, at a given time :samp:`cadence`. This time array will be used by :func:`~embers.sat_utils.sat_ephemeris.sat_pass` to compute the position of satellites at each time.
.. code-block:: python
from embers.sat_utils.sat_ephemeris import load_tle, epoch_ranges, epoch_time_array
sats, epochs = load_tle('~/embers-data/TLE/21576.txt')
epoch_range = epoch_ranges(epochs)
index_epoch = 0 # select first time interval from epoch_range
cadence = 10 # evaluate satellite position every 10 seconds
t_arr, index_epoch = epoch_time_array(epoch_range, index_epoch, cadence)
:param index_epoch: Index of :samp:`epoch_range` to be converted to time array :class:`~int`
:param epoch_range: List of time intervals where an epoch is most accurate, from :func:`embers.sat_utils.sat_ephemeris.epoch_ranges`
:param cadence: Time cadence at which to evaluate sat position, in seconds :class:`~int`
:returns:
A :class:`~tuple` of (t_arr, index_epoch)
- t_arr: Skyfield :class:`~skyfield.timelib.Timescale` object with array of times at given :samp:`cadence`
- index_epoch: Index of :samp:`epoch_range` to be converted to time array :class:`~int`
"""
# Skyfield Timescale
ts = load.timescale(builtin=True)
# find time between epochs/ midpoints in seconds, using Astropy Time
t1 = Time(epoch_range[index_epoch], scale="tt", format="jd").gps
t2 = Time(epoch_range[index_epoch + 1], scale="tt", format="jd").gps
dt = round(t2 - t1)
t3 = Time(epoch_range[index_epoch], scale="tt", format="jd").iso
date, time = t3.split()
year, month, day = date.split("-")
hour, minute, _ = time.split(":")
# Create a time array, every 2[cadence] seconds, starting at the first epoch, approximately
seconds = np.arange(0, dt, cadence)
t_arr = ts.tt(int(year), int(month), int(day), int(hour), int(minute),
seconds)
return (t_arr, index_epoch)
def SolarSystem(t_jd):
t_iso = Time(t_jd, format='jd', scale='utc').iso
date = ':'.join(t_iso.split(':')[:-1])
sim = rebound.Simulation()
sim.units = ('yr', 'AU', 'Msun')
sim.add("Sun", date=date)
sim.add("Mercury", date=date)
sim.add("Venus", date=date)
sim.add("399", date=date) # Earth
sim.add("301", date=date) # Moon
sim.add("Mars", date=date)
sim.add("Jupiter", date=date)
sim.add("Saturn", date=date)
sim.add("Uranus", date=date)
sim.add("Neptune", date=date)
sim.particles[0].hash = 'sun'
sim.particles[3].hash = 'earth'
# sim.convert_particle_units('AU', 'yr', 'Msun')
sim.move_to_com()
return sim
def launch_ds9(dir, tree, overwrite):
#LOAD CONFIG
try:
with open(root_path + "/obsconfig.txt", "r") as obsf:
for line in obsf:
if "Observatory Code" in line:
obscode = line.split(":")[-1].strip()
if "Name" in line:
obsname = line.split(":")[-1].strip()
if "Observer" in line:
observer = line.split(":")[-1].strip()
if "Measurer" in line:
measurer = line.split(":")[-1].strip()
if "Telescope" in line:
telescope = line.split(":")[-1].strip()
if "Email" in line:
email = line.split(":")[-1].strip()
if "Initials" in line:
initials = line.split(":")[-1].strip()
if "DS9 Text Color" in line:
ds9Color = line.split(":")[-1].strip()
if "DS9 Font Size" in line:
ds9FontSize = line.split(":")[-1].strip()
if "Invert images?" in line:
invertImages = False
if line.split(":")[-1].strip() == "yes":
invertImages = True
if "Blink Inverval" in line:
ds9BlinkInterval = line.split(":")[-1].strip()
except:
print("\nConfiguration file obsconfig.txt not found, exiting..\n")
return
try:
with open(dir + '/asteroids', 'rb') as fp:
asteroids = pickle.load(fp)
with open(dir + '/midpoints', 'rb') as fp:
midpoints = pickle.load(fp)
with open(dir + '/totaltime', 'rb') as fp:
totalTime = pickle.load(fp)
except:
print("\nAsteroids file or Midpoints file missing\n")
return
findDesig = True
reportClosed = False
##### ADD REPORT DATE #####
ut = Time(datetime.utcnow(), scale='utc')
ut = str(ut)
yymmdd = ut.split(" ")[0]
hhmmss = ut.split(" ")[-1]
yy = yymmdd.split("-")[0]
mo = yymmdd.split("-")[1]
dd = yymmdd.split("-")[2]
hh = hhmmss.split(":")[0]
mm = hhmmss.split(":")[1]
ss = hhmmss.split(":")[2]
ss = ss.split(".")[0]
reportDate = yy + "." + mo + "." + dd + " " + hh + ":" + mm + ":" + ss
#### CHECK FOR REPORT FILE AND ASK TO REPLACE? ###
replacereport = overwrite
if (replacereport):
reportfile = open(dir + "/report.txt", "w")
reportfile.write("COD " + obscode + "\n")
reportfile.write("CON " + obsname + " [" + email + "]\n")
reportfile.write("OBS " + observer + "\n")
reportfile.write("MEA " + measurer + "\n")
reportfile.write("TEL " + telescope + "\n")
reportfile.write("ACK MPCReport file updated " + reportDate +
"\n") #ADD UTC DATE TIME
reportfile.write("AC2 " + email + "\n")
reportfile.write("NET Gaia DR1\n")
#Output to user
print("\nLaunching DS9 to confirm asteroids..\nAnswer y or n\n")
#Initiate DS9
d = pyds9.DS9(target='DS9:*', start=True, wait=15, verify=False)
#Clear out any previous runs in DS9
d.set("blink no")
d.set("frame delete all")
fitsfiles = glob.glob(dir + "/*.fits")
#Check for only "Stack" fits
for file in fitsfiles:
if "Stack" in file:
continue
else:
fitsfiles.remove(file)
#Sort by name
fitsfiles.sort()
#Load frames into DS9
for i in range(len(fitsfiles)):
#print(fitsfiles[i])
d.set("frame " + str(i + 1))
d.set("fits " + fitsfiles[i])
if (invertImages):
d.set("cmap invert yes")
#set locks and scale
d.set("scale squared")
d.set("scale zscale")
d.set("scale match yes")
d.set("frame lock wcs")
d.set("lock colorbar yes")
d.set("lock scalelimits yes")
d.set("blink interval " + ds9BlinkInterval)
d.set("zoom 4")
astnum = 0
astLength = len(asteroids)
def close_out():
print("\nFinished processing asteroids for this sequence.\n")
if (replacereport):
reportfile.write("----- end -----")
reportfile.close()
d.set("blink no")
#tree.destroy()
# CLEAR OUT TREE
tree.delete(*tree.get_children())
#for asteroid in asteroids:
def show_asteroid(event):
curItem = tree.focus()
if tree.item(curItem)["text"] == "END":
print("Enter to close sequence")
d.set("blink no")
return
astindex = int(tree.item(curItem)["text"])
asteroid = asteroids[astindex]
print("Asteroid ", astindex + 1, "/", astLength)
def displayAst(ast):
d.set("blink no")
if ast[0][0] == 'dummy':
d.set("frame 1")
d.set("regions delete all")
#pass
else:
d.set("frame 1")
d.set("regions delete all")
d.set(
'regions', 'image; circle(' + ast[0][4] + ' ' + ast[0][5] +
' 9")# color=' + ds9Color + ' font="times' + ds9FontSize +
'" text={' + ast[0][2] + 'V ' + ast[0][3] + ' FWHM }')
d.set("frame 2")
d.set("regions delete all")
d.set(
'regions', 'image; circle(' + ast[1][4] + ' ' + ast[1][5] +
' 9")# color=' + ds9Color + ' font="times' + ds9FontSize +
'" text={' + ast[1][2] + 'V ' + ast[1][3] + ' FWHM }')
d.set("frame 3")
d.set("regions delete all")
d.set(
'regions', 'image; circle(' + ast[2][4] + ' ' + ast[2][5] +
' 9")# color=' + ds9Color + ' font="times' + ds9FontSize +
'" text={' + ast[2][2] + 'V ' + ast[2][3] + ' FWHM }')
if ast[3][0] == 'dummy':
d.set("frame 4")
d.set("regions delete all")
#pass
else:
d.set("frame 4")
d.set("regions delete all")
d.set(
'regions', 'image; circle(' + ast[3][4] + ' ' + ast[3][5] +
' 9")# color=' + ds9Color + ' font="times' + ds9FontSize +
'" text={' + ast[3][2] + 'V ' + ast[3][3] + ' FWHM }')
d.set("pan to " + str(ast[1][0]) + ' ' + str(ast[1][1]) + " wcs")
#d.set("regions save foo.reg")
#print(d.get('regions'))
d.set("blink yes")
### INITIAL DISPLAY ###
displayAst(asteroid)
### DISPLAY 1-3 or 2-4 ###
if asteroid[0][0] == 'dummy':
print("Images 2-4")
elif asteroid[3][0] == "dummy":
print("Images 1-3")
else:
print("Images 1-4")
### SHOW LOCATION ####
dispRA = asteroid[1][0]
dispDEC = asteroid[1][1]
dispT = SkyCoord(ra=dispRA * u.degree, dec=dispDEC * u.degree)
dispcoordsT = dispT.to_string('hmsdms')
dispCOORDS = clean_coords(dispcoordsT)
print("Location: ", dispCOORDS, " Copied to Clipboard")
pyperclip.copy(dispCOORDS)
print("\n")
#print("Resid: ",asteroid[4][0] )
#ENTER Q/A RESP
## CONFIM WITH ENTER
def just_desig(event):
curItem = tree.focus()
if tree.item(curItem)["text"] == "END":
close_out()
return
astindex = int(tree.item(curItem)["text"])
asteroid = asteroids[astindex]
print("Asteroid ", astindex + 1, "/", astLength)
print("\n")
if astindex == astLength + 1:
print("\n close out")
return
#print("Resid: ",asteroid[4][0] )
#ENTER Q/A RESP
#DESIG IS SET HERE FIRST
desig = "TMP001"
# AST #PLOT #CONFIRM
resids = solve_residuals(asteroid, False, True)
resids = "{:.2f}".format(resids)
print("\n", resids, " Asteroid mean residual")
#Temp file for scoring asteroids
tempfile = open(dir + "/digest2temp.txt", "w")
raT = asteroid[1][0]
decT = asteroid[1][1]
magT = round(float(asteroid[1][2]), 1)
magT = str(magT) + " V"
cT = SkyCoord(ra=raT * u.degree, dec=decT * u.degree)
coordsT = cT.to_string('hmsdms')
coordsCleanT = clean_coords(coordsT)
# Get designation of first measurement, parse MPC
if (findDesig):
# Only need 1 pos to search for desig
obsT = " " + desig + " KC" + midpoints[
1] + coordsCleanT + " " + magT + " " + obscode
# find designation
solveddesig = find_desig(obsT)
print("Information for " + desig)
print("##########################################")
print("##### MPC SEARCH RESULTS BELOW #####")
print("##########################################")
print("\n", solveddesig)
if (solveddesig is not None):
desig = solveddesig.split()[1]
print("MPC desig: ", desig + "\n")
else:
print("No MPC designation found.\n")
for i in range(len(asteroid)):
#convert radec
if asteroid[i][0] == 'dummy':
continue
ra = asteroid[i][0]
dec = asteroid[i][1]
mag = round(float(asteroid[i][2]), 1)
#Catch bad mags
if (mag > 21.2):
mag = " "
else:
mag = str(mag) + " V"
c = SkyCoord(ra=ra * u.degree, dec=dec * u.degree)
coords = c.to_string('hmsdms')
coordsClean = clean_coords(coords)
desig = desig.rjust(11)
blankSP = " "
tempfile.write(desig + blankSP + "KC" + midpoints[i] +
coordsClean + " " + mag + " " +
obscode + "\n")
tempfile.close()
#Score the rock and print out
score_rock(dir)
print("\n Finished searching and scoring object. \n")
def confirm_asteroid(event):
curItem = tree.focus()
if tree.item(curItem)["text"] == "END":
close_out()
return
astindex = int(tree.item(curItem)["text"])
asteroid = asteroids[astindex]
print("Asteroid ", astindex + 1, "/", astLength)
print("\n")
if astindex == astLength + 1:
print("\n close out")
return
#print("Resid: ",asteroid[4][0] )
#ENTER Q/A RESP
#DESIG IS SET HERE FIRST
desig = "TMP001"
desigFromMPC = False
# AST #PLOT #CONFIRM
resids = solve_residuals(asteroid, False, True)
resids = "{:.2f}".format(resids)
print("\n", resids, " Asteroid mean residual")
#Temp file for scoring asteroids
tempfile = open(dir + "/digest2temp.txt", "w")
raT = asteroid[1][0]
decT = asteroid[1][1]
magT = round(float(asteroid[1][2]), 1)
magT = str(magT) + " V"
cT = SkyCoord(ra=raT * u.degree, dec=decT * u.degree)
coordsT = cT.to_string('hmsdms')
coordsCleanT = clean_coords(coordsT)
# Get designation of first measurement, parse MPC
if (findDesig):
# Only need 1 pos to search for desig
obsT = " " + desig + " KC" + midpoints[
1] + coordsCleanT + " " + magT + " " + obscode
# find designation
solveddesig = find_desig(obsT)
print("Information for " + desig)
print("##########################################")
print("##### MPC SEARCH RESULTS BELOW #####")
print("##########################################")
print("\n", solveddesig)
if (solveddesig is not None):
useMPCdesig = True
if (useMPCdesig):
desig = solveddesig.split()[1]
print("Assigned MPC desig: ", desig + "\n")
desigFromMPC = True
else:
print("No MPC designation found.")
#OVERWRITE REPORT?
if (replacereport and not desigFromMPC):
desig = id_generator()
print("Assigned temp designation: " + desig + "\n")
for i in range(len(asteroid)):
#convert radec
if asteroid[i][0] == 'dummy':
continue
ra = asteroid[i][0]
dec = asteroid[i][1]
mag = round(float(asteroid[i][2]), 1)
#Catch bad mags
if (mag > 21.2):
mag = " "
else:
mag = str(mag) + " V"
c = SkyCoord(ra=ra * u.degree, dec=dec * u.degree)
coords = c.to_string('hmsdms')
coordsClean = clean_coords(coords)
if (desigFromMPC):
#Capture provisional designation
if len(desig) == 7:
desig = desig.rjust(12)
blankSP = " "
if len(desig) < 7:
blankSP = " "
desig = desig.ljust(11)
else:
desig = desig.rjust(11)
blankSP = " "
# IF WE REPLACE REPORT
if (replacereport):
reportfile.write(desig + blankSP + "KC" + midpoints[i] +
coordsClean + " " + mag + " " +
obscode + "\n")
tempfile.write(desig + blankSP + "KC" + midpoints[i] +
coordsClean + " " + mag + " " +
obscode + "\n")
tempfile.close()
#Score the rock and print out
score_rock(dir)
print("\n Finished processing object. \n")
#CLEAR OUT TREE
tree.delete(*tree.get_children())
# TREE COLUMNS CREATE
# tree.config(columns=('fwhm','astloc','astresid', 'astmag'))
tree['columns'] = ('fwhm', 'astloc', 'astresid', 'astmag', 'velocity')
tree.column('#0', width=70)
tree.column('fwhm', width=70, anchor='center')
tree.column('astloc', width=180, anchor='center')
tree.column('astresid', width=70, anchor='center')
tree.column('astmag', width=70, anchor='center')
tree.column('velocity', width=150, anchor='center')
tree.heading('#0', text='Ast Num')
tree.heading('fwhm', text='Ast FWHM')
tree.heading('astloc', text='Ast Location')
tree.heading('astresid', text='Ast Resid')
tree.heading('astmag', text='Ast Mag')
tree.heading('velocity', text='Ast Vel Arcsec/min')
tree.config(selectmode='browse')
tree.bind('<<TreeviewSelect>>', show_asteroid)
tree.bind("<Return>", confirm_asteroid)
tree.bind("<c>", just_desig)
astnum2 = 0
#Convert total time to float
totalTime = float(totalTime)
for ast in asteroids:
astT = []
#REMOVE DUMMY
for k in range(len(ast)):
if ast[k][0] == "dummy":
continue
else:
astT.append(ast[k])
#SOLVE AVE FWHM
fwhm = sum(float(astT[i][3]) for i in range(len(astT))) / len(astT)
fwhm = round(fwhm, 2)
#SOLVE AVE MAG
mag = sum(float(astT[i][2]) for i in range(len(astT))) / len(astT)
mag = round(mag, 2)
#SOLVE RESID
resid = solve_residuals(astT, False, False)
### SHOW LOCATION ####
ra = astT[2][0]
dec = astT[2][1]
dispT = SkyCoord(ra=ra * u.degree, dec=dec * u.degree)
dispcoordsT = dispT.to_string('hmsdms')
dispCOORDS = clean_coords(dispcoordsT)
#### SOLVE SPEED ####
x1 = astT[0][0]
y1 = astT[0][1]
x2 = astT[-1][0]
y2 = astT[-1][1]
astDist = math.sqrt((x2 - x1)**2 + (y2 - y1)**2)
astDist = astDist * 3600 # CONVERT TO ARCSEC
vel = round(astDist / totalTime, 2)
# parent id name text #fwhm #loc #resid #mag
tree.insert('',
str(astnum2),
text=str(astnum2),
values=(fwhm, dispCOORDS, resid, mag, vel))
astnum2 += 1
#INSERT END LINE
if astnum2 == len(asteroids):
tree.insert('', str(len(asteroids) + 1), text="END")
tree.update()
#MODULE TESTING PURPOSES, UNCOMMENT
# myTree = Toplevel()
# tree1 = ttk.Treeview(myTree)
# tree1.pack(fill="both")
#launch_ds9("/home/david/Desktop/C4", tree1, False)
def shownightobs(observable, meteo, obs_night=None, savefig=False, dirpath=None, verbose=False):
"""
Plot the observability of one observable along the night
#todo: add the option to be returned in an Axes object instead of plotting
"""
logger.debug("Creating night observability plot for {}".format(observable.name))
if not obs_night:
meteo.time.format = 'iso'
hour = int(meteo.time.value.split()[1][:2])
if hour < 12:
obs_night = Time(meteo.time.mjd - 1, format='mjd', scale='utc')
else:
obs_night = Time(meteo.time.mjd, format='mjd', scale='utc')
obs_night.format = 'iso'
obs_night = obs_night.value.split()[0]
# list of times between nautical twilights
times = meteo.get_nighthours(obs_night)
#mymeteo = pythoncopy.deepcopy(meteo) # as we don't want to affect the current meteo, we make a copy that we update with the time
mymeteo = meteo
obss = []
moonseps = []
airmasses = []
for time in times:
mymeteo.update(obs_time=time, minimal=True)
observable.compute_observability(meteo=mymeteo, displayall=True, cloudscheck=False, verbose=verbose)
observable.compute_airmass(mymeteo)
obss.append(observable.observability)
moonseps.append(observable.angletomoon.degree)
airmasses.append(observable.airmass)
# create the x ticks labels every hour
Time('%s 05:00:00' % obs_night, format='iso', scale='utc')
hstart=22
hend=12
nhbm = 24-hstart # number of hours before midnight...
myhours = []
for hour in np.arange(nhbm)[::-1]:
myhours.append(24-(hour+1))
for hour in np.arange(hend+1):
myhours.append(hour)
myhours = ["%02i:00:00" % h for h in myhours]
mytimes = [Time('%s %s' % (obs_night, h), format='iso', scale='utc') for h in myhours[:nhbm]]
for h in myhours[nhbm:]:
t = Time('%s %s' % (obs_night, h), format='iso', scale='utc')
t = Time(t.mjd + 1, format='mjd', scale='utc')
mytimes.append(t)
tmin, tmax = times[0].mjd, times[-1].mjd
xmax=len(obss)
xs = [(t.mjd-tmin)*xmax/(tmax-tmin) for t in mytimes]
labels = [str(h[:5]) for h in myhours]
starttimes = []
stoptimes = []
# todo: this needs to be improved.
if 1 in obss:
starttimes.append(times[obss.index(1)])
stoptimes.append(times[::-1][obss[::-1].index(1)])
if 0.8 in obss:
starttimes.append(times[obss.index(0.8)])
stoptimes.append(times[::-1][obss[::-1].index(0.8)])
if 0.7 in obss:
starttimes.append(times[obss.index(0.7)])
stoptimes.append(times[::-1][obss[::-1].index(0.7)])
if 0.56 in obss:
starttimes.append(times[obss.index(0.56)])
stoptimes.append(times[::-1][obss[::-1].index(0.56)])
if not 1 in obss and not 0.8 in obss and not 0.7 in obss and not 0.56 in obss:
print(("%s is not observable tonight !" % observable.name))
return
starttime = min(starttimes)
stoptime = max(stoptimes)
# shift the start and stoptime if needed
if starttime.mjd > stoptime.mjd - (observable.exptime/60./1440.):
starttime = Time(stoptime.mjd - (observable.exptime/60./1440.), format='mjd', scale='utc')
if stoptime.mjd < starttime.mjd + (observable.exptime/60./1440.):
stoptime = Time(starttime.mjd + (observable.exptime/60./1440.), format='mjd', scale='utc')
starttime = starttime.iso
stoptime = stoptime.iso
plt.figure(figsize=(8,1.3))
plt.subplots_adjust(left=0.02, right=0.98, bottom=0.45, top=0.7)
ax = plt.subplot(1, 1, 1)
xticks = np.arange(len(obss))
plt.xticks(xs, labels, fontsize=16)
# green, everything is fine
if 1 in obss:
plt.axvspan(obss.index(1), len(obss)-obss[::-1].index(1), color='chartreuse')
# blue, problem with moon sep, airmass or both. #todo: code that better
if 0.8 in obss:
color = "royalblue"
plt.axvspan(obss.index(0.8), len(obss)-obss[::-1].index(0.8), color=color)
msg = "Moonsep = %i" % int(min(moonseps))
plt.annotate(msg, xy=(0, -1.5), xycoords='axes fraction', fontsize=14, color=color)
if 0.7 in obss:
color = "royalblue"
plt.axvspan(obss.index(0.7), len(obss)-obss[::-1].index(0.7), color=color)
msg = "Airmass > 1.5"
plt.annotate(msg, xy=(0, -1.5), xycoords='axes fraction', fontsize=14, color=color)
if 0.56 in obss:
color = "indianred"
plt.axvspan(obss.index(0.5), len(obss)-obss[::-1].index(0.5), color='indianred')
msg = "Moonsep = %i, Airmass > 1.5" % int(min(moonseps))
plt.annotate(msg, xy=(1.0, -1.5), ha="right", xycoords='axes fraction', fontsize=14, color=color)
plt.axis([min(xticks), max(xticks), 0.0, 1.0])
ax.get_yaxis().set_visible(False)
plt.xlabel('UT', fontsize=18)
plt.suptitle(observable.name+" ("+starttime.split(" ")[1][:5]+" --> "+stoptime.split(" ")[1][:5]+")", fontsize=25, y=0.93)
if savefig:
assert dirpath != None
if not os.path.isdir(os.path.join(dirpath, obs_night)):
os.mkdir(os.path.join(dirpath, obs_night))
path = os.path.join(dirpath, obs_night, observable.name+'.png')
plt.savefig(path)
print(("Plot saved on %s" % path))
else:
plt.show()
logger.info("Night observability plot for {} done".format(observable.name))
def readsdofile(datadir=None, wavelength=None, jdtime=None, isexists=False, timtol=1):
'''
read sdo file from local database
:param datadir:
:param wavelength:
:param jdtime: the timestamp or timerange in Julian days. if is timerange, return a list of files in the timerange
:param isexists: check if file exist. if files exist, return file name
:param timtol: time difference tolerance in days for considering data as the same timestamp
:return:
'''
from astropy.time import Time
import sunpy.map
from datetime import date
from datetime import timedelta as td
wavelength = str(wavelength)
wavelength = wavelength.lower()
if timtol < 12. / 3600 / 24:
timtol = 12. / 3600 / 24
if isinstance(jdtime, list) or isinstance(jdtime, tuple) or type(jdtime) == np.ndarray:
if len(jdtime) != 2:
raise ValueError('jdtime must be a number or a two elements array/list/tuple')
else:
if jdtime[1] < jdtime[0]:
raise ValueError('start time must be occur earlier than end time!')
else:
sdofitspath = []
jdtimestr = [Time(ll, format='jd').iso for ll in jdtime]
ymd = [ll.split(' ')[0].split('-') for ll in jdtimestr]
d1 = date(int(ymd[0][0]), int(ymd[0][1]), int(ymd[0][2]))
d2 = date(int(ymd[1][0]), int(ymd[1][1]), int(ymd[1][2]))
delta = d2 - d1
for i in xrange(delta.days + 1):
ymd = d1 + td(days=i)
sdofitspathtmp = glob.glob(
datadir + '/{:04d}/{:02d}/{:02d}/aia.lev1_*Z.{}.image_lev1.fits'.format(ymd.year, ymd.month,
ymd.day, wavelength))
if len(sdofitspathtmp) > 0:
sdofitspath = sdofitspath + sdofitspathtmp
if len(sdofitspath) == 0:
if isexists:
return sdofitspath
else:
raise ValueError(
'No SDO file found under {} at the time range of {} to {}. Download the data with EvtBrowser first.'.format(
datadir, jdtimestr[0], jdtimestr[1]))
sdofits = [os.path.basename(ll) for ll in sdofitspath]
sdotimeline = Time(
[insertchar(insertchar(ll.split('.')[2].replace('T', ' ').replace('Z', ''), ':', -4), ':', -2) for
ll in sdofits], format='iso', scale='utc')
sdofitspathnew = [x for (y, x) in sorted(zip(sdotimeline.jd, sdofitspath))]
sdofitsnew = [os.path.basename(ll) for ll in sdofitspathnew]
sdotimelinenew = Time(
[insertchar(insertchar(ll.split('.')[2].replace('T', ' ').replace('Z', ''), ':', -4), ':', -2) for
ll in sdofitsnew], format='iso', scale='utc')
sdofile = list(np.array(sdofitspathnew)[np.where(
np.logical_and(jdtime[0] < sdotimelinenew.jd, sdotimelinenew.jd < jdtime[1]))[0]])
return sdofile
else:
jdtimstr = Time(jdtime, format='jd').iso
ymd = jdtimstr.split(' ')[0].split('-')
sdofitspath = glob.glob(
datadir + '/{}/{}/{}/aia.lev1_*Z.{}.image_lev1.fits'.format(ymd[0], ymd[1], ymd[2], wavelength))
if len(sdofitspath) == 0:
raise ValueError('No SDO file found under {}.'.format(datadir))
sdofits = [os.path.basename(ll) for ll in sdofitspath]
sdotimeline = Time(
[insertchar(insertchar(ll.split('.')[2].replace('T', ' ').replace('Z', ''), ':', -4), ':', -2) for ll in
sdofits], format='iso', scale='utc')
if timtol < np.min(np.abs(sdotimeline.jd - jdtime)):
raise ValueError('No SDO file found at the select timestamp. Download the data with EvtBrowser first.')
idxaia = np.argmin(np.abs(sdotimeline.jd - jdtime))
sdofile = sdofitspath[idxaia]
if isexists:
return sdofile
else:
try:
sdomap = sunpy.map.Map(sdofile)
return sdomap
except:
raise ValueError('File not found or invalid input')
def generate_polycos(
self,
model,
mjdStart,
mjdEnd,
obs,
segLength,
ncoeff,
obsFreq,
maxha=12.0,
method="TEMPO",
numNodes=20,
):
"""
Generate the polyco data.
Parameters
----------
model : TimingModel
TimingModel to generate the Polycos with parameters
setup.
mjdStart : float / numpy longdouble
Start time of polycos in mjd
mjdEnd : float / numpy longdouble
Ending time of polycos in mjd
obs : str
Observatory code
segLength : int
Length of polyco segement [minutes]
ncoeff : int
Number of coefficents
obsFreq : float
Observing frequency [MHz]
maxha : float optional. Default 12.0
Maximum hour angle. Only 12.0 is supported for now.
method : string optional ["TEMPO", "TEMPO2", ...] Default TEMPO
Method to generate polycos. Only the TEMPO method is supported for now.
numNodes : int optional. Default 20
Number of nodes for fitting. It cannot be less then the number of
coefficents.
Return
---------
A polyco table.
"""
mjdStart = data2longdouble(mjdStart)
mjdEnd = data2longdouble(mjdEnd)
segLength = int(segLength)
obsFreq = float(obsFreq)
# Use the planetary ephemeris specified in the model, if available.
if model.EPHEM.value is not None:
ephem = model.EPHEM.value
else:
log.info(
"No ephemeris specified in model, using DE421 to generate polycos"
)
ephem = "DE421"
if maxha != 12.0:
raise ValueError("Maximum hour angle != 12.0 is not supported.")
# Make sure the number of nodes is bigger than number of coeffs.
if numNodes < ncoeff:
numNodes = ncoeff + 1
mjdSpan = data2longdouble(segLength / MIN_PER_DAY)
# Generate "nice" MJDs for consistency with what tempo2 does
tmids = np.arange(
int(mjdStart * 24) * 60,
int(mjdEnd * 24) * 60 + segLength, segLength)
tmids = data2longdouble(tmids) / MIN_PER_DAY
# generate the ploynomial coefficents
if method == "TEMPO":
entryList = []
# Using tempo1 method to create polycos
# If you want to disable the progress bar, add disable=True to the tqdm() call.
for tmid in tqdm(tmids):
tStart = tmid - mjdSpan / 2
tStop = tmid + mjdSpan / 2
nodes = np.linspace(tStart, tStop, numNodes)
toaMid = toa.get_TOAs_list(
[
toa.TOA((np.modf(tmid)[1], np.modf(tmid)[0]),
obs=obs,
freq=obsFreq)
],
ephem=ephem,
)
refPhase = model.phase(toaMid, abs_phase=True)
# Create node toas(Time sample using TOA class)
toaList = [
toa.TOA(
(np.modf(toaNode)[1], np.modf(toaNode)[0]),
obs=obs,
freq=obsFreq,
) for toaNode in nodes
]
toas = toa.get_TOAs_list(toaList, ephem=ephem)
ph = model.phase(toas, abs_phase=True)
dt = (nodes - tmid) * MIN_PER_DAY
rdcPhase = ph - refPhase
rdcPhase = rdcPhase.int - (dt * model.F0.value *
60.0) + rdcPhase.frac
dtd = dt.astype(float) # Truncate to double
rdcPhased = rdcPhase.astype(float)
coeffs = np.polyfit(dtd, rdcPhased, ncoeff - 1)[::-1]
date, hms = Time(tmid, format="mjd", scale="utc").iso.split()
yy, mm, dd = date.split("-")
date = dd + "-" + MONTHS[int(mm) - 1] + "-" + yy[-2:]
hms = float(hms.replace(":", ""))
entry = PolycoEntry(
tmid,
segLength,
refPhase.int,
refPhase.frac,
model.F0.value,
ncoeff,
coeffs,
)
entry_dict = OrderedDict()
entry_dict["psr"] = model.PSR.value
entry_dict["date"] = date
entry_dict["utc"] = hms
entry_dict["tmid"] = tmid
entry_dict["dm"] = model.DM.value
entry_dict["doppler"] = 0.0
entry_dict["logrms"] = 0.0
entry_dict["mjd_span"] = segLength
entry_dict["t_start"] = entry.tstart
entry_dict["t_stop"] = entry.tstop
entry_dict["obs"] = obs
entry_dict["obsfreq"] = obsFreq
if model.is_binary:
binphase = model.orbital_phase(toaMid, radians=False)[0]
entry_dict["binary_phase"] = binphase
b = model.get_components_by_category()["pulsar_system"][0]
entry_dict["f_orbit"] = 1 / b.PB.value
entry_dict["entry"] = entry
entryList.append(entry_dict)
pTable = table.Table(entryList, meta={"name": "Polyco Data Table"})
self.polycoTable = pTable
if len(self.polycoTable) == 0:
raise ValueError("Zero polycos found for table")
else:
raise NotImplementedError(
"Only TEMPO method has been implemented.")
def patchAndDenoise(x_values,
orders,
waves,
x_errors=None,
times=None,
file_list=None,
K=2,
num_iters=50,
running_window=9,
line_cutoff=0.5,
file_cutoff=0.5,
outlier_cut=0,
verbose=False):
"""
- Vet for bad lines/exposures
- Initial patch of bad data with running mean
- Iterative patch with PCA for specified number of iterations
- Optional second round of interative PCA patching to catch outliers
Parameters
----------
x_values, x_errors : 2D ndarray
Array of line positions for all lines for each exposure and errors
orders : 1D ndarray
Array of orders for each line
waves : 1D ndarray
Array of wavelengths for each line
times : 1D ndarray, optional
Time stamps for each exposure
Just written into the returned patch dictionary
(not explicitely used for this code, but helps with evalWaveSol)
K : int, optional (default: 2)
Number of principal components used for denoising
num_iters : int, optional (default: 50)
Number of iterations to run iterative PCA patching
running_window ; int, optional (default: 9)
Window size of running mean used to initialize pixel values
for lines missing measured pixel values
line_cutoff, file_cutoff : float [0,1], optional (default: 0.5)
Cutoff for bad lines or files, respectively.
i.e. defaults cut lines that show up in less than 50% of exposure
and files that contain less than 50% of all lines
outlier_cut : float, optional (default: 0)
Sigma cut used to identify outliers following first round of
iterative PCA.
Note: 0 means this process isn't done.
Returns
-------
patch : dict
Dictionary containing all the useful information from this process
(among, very many uselss information!)
Needed for evalWaveSol function
"""
# Arrays that aren't needed, but are helpful to have in returned dictionary
if times is None:
times = np.zeros_like(file_list)
if x_errors is None:
x_errors = np.zeros_like(x_errors)
if file_list is None:
file_list = np.zeros_like(times)
### Vetting
# Find where there is no line information
x_values[np.nan_to_num(x_values) < 1] = np.nan
# Mask out of order lines
out_of_order = np.zeros_like(x_values, dtype=bool)
for m in np.unique(orders):
I = orders == m
wave_sort = np.argsort(waves[I])
for i, exp in enumerate(x_values):
exp_sort = exp[I][wave_sort]
exp_diff = np.diff(exp_sort)
left_diff = np.insert(exp_diff < 0, 0, False)
right_diff = np.append(exp_diff < 0, False)
exp_mask = np.logical_or(left_diff, right_diff)
out_of_order[i, I] = exp_mask.copy()
x_values[out_of_order] = np.nan
if verbose:
num_bad = np.sum(out_of_order)
num_total = out_of_order.size
print('{:.3}% of lines masked'.format((num_bad) / num_total * 100))
# Get rid of bad lines
good_lines = np.mean(np.isnan(x_values), axis=0) < line_cutoff
# Trim everything
orders = orders[good_lines]
waves = waves[good_lines]
x_values = x_values[:, good_lines]
x_errors = x_errors[:, good_lines]
if verbose:
num_good = np.sum(good_lines)
num_total = good_lines.size
print('{} of {} lines cut ({:.3}%)'.format(
(num_total - num_good), num_total,
(num_total - num_good) / num_total * 100))
# Get rid of bad files
good_files = np.mean(np.isnan(x_values), axis=1) < file_cutoff
# Trim everything
x_values = x_values[good_files]
x_errors = x_errors[good_files]
file_names = file_list[good_files]
file_times = times[good_files]
if verbose:
num_good = np.sum(good_files)
num_total = good_files.size
print('{} of {} files cut ({:.3}%)'.format(
(num_total - num_good), num_total,
(num_total - num_good) / num_total * 100))
print('Files that were cut:')
print(file_list[~good_files])
### Patching
# Initial patch of bad data with mean
bad_mask = np.isnan(x_values) # mask to identify patched x_values
if running_window > 0:
half_size = int(running_window // 2)
counter = 6
while np.sum(np.isnan(x_values)) > 0:
for i in range(x_values.shape[0]):
# Identify files in window
file_range = [
max((i - half_size, 0)),
min((i + half_size + 1, x_values.shape[1]))
]
# Find mean of non-NaN values
run_med = np.nanmean(x_values[file_range[0]:file_range[1], :],
axis=0)
# Patch NaN values with mean for center file
x_values[i][bad_mask[i, :]] = run_med[bad_mask[i, :]]
counter -= 1
if counter < 0:
print("Persistant NaNs with running mean.")
print("Replacing remaining NaNs with global mean.")
tot_mean = np.nanmean(
x_values, axis=0)[None, ...] * np.ones_like(x_values)
x_values[np.isnan(x_values)] = tot_mean[np.isnan(x_values)]
break
else: # don't bother with running mean
mean_values = np.nanmean(x_values, axis=0)
mean_patch = np.array([mean_values for _ in range(x_values.shape[0])])
x_values[bad_mask] = mean_patch[bad_mask]
# Iterative PCA
pca_results = pcaPatch(x_values, bad_mask, K=K, num_iters=num_iters)
x_values, mean_x_values, denoised_xs, uu, ss, vv = pca_results
# Mask line center outliers
if outlier_cut > 0:
x_resids = x_values - denoised_xs
out_mask = abs(x_resids - np.mean(x_resids)) > (outlier_cut *
np.nanstd(x_resids))
if verbose:
num_out = np.sum(out_mask)
num_total = out_mask.size
num_bad = np.sum(np.logical_and(out_mask, bad_mask))
print('{:.3}% of lines marked as Outliers'.format(
(num_out) / num_total * 100))
print('{:.3}% of lines marked as Outliers that were PCA Patched'.
format((num_bad) / num_total * 100))
pca_results = pcaPatch(x_values,
np.logical_or(bad_mask, out_mask),
K=K,
num_iters=num_iters)
x_values, mean_x_values, denoised_xs, uu, ss, vv = pca_results
# Load in all relevant information into dictionary
patch_dict = {}
patch_dict['K'] = K
# Exposure Information
patch_dict['files'] = file_names.copy()
patch_dict['times'] = file_times.copy()
min_date = Time(file_times.min(), format='mjd').isot.split('T')[0]
yr, mn, dy = min_date.split('-')
patch_dict['min_date'] = yr[2:] + mn + dy
min_date = Time(file_times.max(), format='mjd').isot.split('T')[0]
yr, mn, dy = min_date.split('-')
patch_dict['max_date'] = yr[2:] + mn + dy
# Line Information
patch_dict['orders'] = orders.copy()
patch_dict['waves'] = waves.copy()
# Line Measurement Information
patch_dict['x_values'] = x_values.copy()
patch_dict['x_errors'] = x_errors.copy()
patch_dict['denoised_xs'] = denoised_xs.copy()
patch_dict['mean_xs'] = mean_x_values.copy()
patch_dict['bad_mask'] = bad_mask.copy()
# PCA Information
patch_dict['u'] = uu.copy()
patch_dict['s'] = ss.copy()
patch_dict['v'] = vv.copy()
patch_dict['ec'] = (uu * ss)[:, :K]
# Outlier Information
if outlier_cut > 0:
patch_dict['out_mask'] = out_mask.copy()
return patch_dict
Photo_Log = Photo_Log.round({
'HWPANG': 2,
'JD': 6,
'FWHM_o': 2,
'FWHM_e': 2,
'Aper [pix]': 2,
'EXP [s]': 2,
'Ann': 2,
'Ann_out': 2,
'Flux_o': 4,
'eFLux_o': 4,
'Flux_e': 4,
'eFLux_e': 4,
'SNR_o': 2,
'SNR_e': 2,
'Sky_o': 4,
'eSky_o': 4,
'Sky_e': 4,
'eSky_e': 4
})
Pol_Log.to_csv(
os.path.join(path, 'result_Pol_{}.csv'.format(time_.split(' ')[0])))
Photo_Log.to_csv(
os.path.join(path, 'result_Photo_{}.csv'.format(time_.split(' ')[0])))
print(
os.path.join(path, 'result_Pol_{}.csv'.format(time_.split(' ')[0])) +
' is created.')
print(
os.path.join(path, 'result_Photo_{}.csv'.format(time_.split(' ')[0])) +
' is created.')
import yaml
from astropy.time import Time
import os
with open('recycler.yaml', 'r') as f:
recy = yaml.load(f)
propid = recy["propid"]
MJDnite = recy["start_of_season"]
nite = Time(MJDnite, format="mjd").iso
nite = nite.split(' ')[0].split('-')[0] + nite.split(' ')[0].split(
'-')[1] + nite.split(' ')[0].split('-')[2]
os.system('. ./getExpWPropIDandNite.sh -n ' + nite + ' -p ' + propid)
def tab2_BUT_tCLN_param_save():
with open(CleanID_dir + 'CASA_CLN_args.json', 'w') as fp:
json.dump(tab2_tCLN_Param_dict, fp)
tab2_Div_tCLN2.text = '<p>CASA script and arguments config file saved to <b>{}</b>.</p>'.format(
CleanID_dir)
timestrs = []
fits_local = []
fits_global = []
if 'twidth' in tab2_tCLN_Param_dict.keys():
val = tab2_tCLN_Param_dict['twidth']
exec('twidth = int({})'.format(val))
else:
twidth = 1
if 'workdir' in tab2_tCLN_Param_dict.keys():
val = tab2_tCLN_Param_dict['workdir']
exec('workdir = {}'.format(val))
else:
workdir = './'
# os.system('cp {} {}'.format(CleanID_dir + 'CASA_CLN_args.json', workdir))
os.system('cp {}/DataBrowser/ToClean/script_clean.py {}'.format(
suncasa_dir, CleanID_dir))
for ii in range(tab2_ntim):
iit = int(ii) / twidth * twidth
t0 = xx[iit] - tab2_dt / 2
datestr = Time(t0 / 3600. / 24.,
format='jd',
scale='utc',
precision=3,
out_subfmt='date').iso
timestr0 = Time(t0 / 3600. / 24.,
format='jd',
scale='utc',
precision=3,
out_subfmt='date_hms').iso
timestr0 = timestr0.split(' ')[1]
timestr = datestr.replace("-", "") + 'T' + timestr0.replace(":", "")
timestrs.append(timestr0)
fits_local.append(timestr + '.fits')
fits_global.append(timestr + '.fits')
timestrs = timestrs * int(tab2_nfreq)
fits_local = fits_local * int(tab2_nfreq)
fits_global = fits_global * int(tab2_nfreq)
freqstrs = ['{:.3f}'.format(ll) for ll in yy]
dspecDFout = pd.DataFrame({
'time': xx - xx[0],
'freq': yy,
'timestr': timestrs,
'freqstr': freqstrs,
'dspec': tab2_spec_plt.flatten(),
'fits_local': fits_local,
'fits_global': fits_global
})
with open(FS_dspecDF, 'wb') as fp:
pickle.dump(dspecDFout, fp)
tab2_Div_tCLN2.text = '<p>CASA script, arguments config file and dspecDF-base saved to <b>{}</b>. '.format(
CleanID_dir
) + 'Click the <b>clean</b> button to clean. When finished, \
go back to <b>QLook</b> window, select StrID <b>{}</b> and \
click <b>FSview</b> button again.</p>'.format(CleanID_dir,
struct_id[0:-1])
def tab2_dspec_selection_change(attrname, old, new):
global tapPointDF_dspec, dspecDF_select
global SRC_dspec_quadselround
if clickmode == 'singleclick':
tab2_r_dspec_patch.data_source.data = {'xx': [], 'yy': []}
tab2_SRC_dspec_quadx_selected = tab2_SRC_dspec_quadx.selected['1d'][
'indices']
tab2_SRC_dspec_quady_selected = tab2_SRC_dspec_quady.selected['1d'][
'indices']
if len(tab2_SRC_dspec_quadx_selected) > 0 and len(
tab2_SRC_dspec_quady_selected) > 0:
quadx_selected = tab2_SRC_dspec_quadx_selected[0]
quady_selected = tab2_SRC_dspec_quady_selected[0]
idx = quady_selected * tab2_ntim + quadx_selected
tmp = tab2_r_dspec.data_source.data['image'][0]
timstr = dspecDF0['timestr'].iloc[idx]
freqstr = '{:.3f} [GHz]'.format(dspecDF0['freq'].iloc[idx])
tooltips = ['{} {}'.format(timstr, freqstr)]
tab2_dspec_xPro_data = {
'x': tab2_dtim,
'y': tmp[quady_selected, :]
}
r_dspec_xPro.data_source.data = tab2_dspec_xPro_data
tab2_dspec_xPro_hover_data = {
'x': [tab2_dtim[quadx_selected]],
'y': [tmp[quady_selected, quadx_selected]],
'tooltips': tooltips
}
r_dspec_xPro_hover.data_source.data = tab2_dspec_xPro_hover_data
tab2_dspec_yPro_data = {
'x': tmp[:, quadx_selected],
'y': tab2_freq
}
r_dspec_yPro.data_source.data = tab2_dspec_yPro_data
tab2_dspec_yPro_hover_data = {
'x': [tmp[quady_selected, quadx_selected]],
'y': [tab2_freq[quady_selected]],
'tooltips': tooltips
}
r_dspec_yPro_hover.data_source.data = tab2_dspec_yPro_hover_data
tab2_r_dspec_line_x.data_source.data = {
'time': [tab2_dtim[0], tab2_dtim[-1]],
'freq': [tab2_freq[quady_selected]] * 2
}
tab2_r_dspec_line_y.data_source.data = {
'time': [tab2_dtim[quadx_selected]] * 2,
'freq': [tab2_freq[0], tab2_freq[-1]]
}
elif len(tab2_SRC_dspec_quadx_selected) == 0 and len(
tab2_SRC_dspec_quady_selected) == 0:
r_dspec_xPro.data_source.data = {'x': [], 'y': []}
r_dspec_xPro_hover.data_source.data = {
'x': [],
'y': [],
'tooltips': []
}
r_dspec_yPro.data_source.data = {'x': [], 'y': []}
r_dspec_yPro_hover.data_source.data = {
'x': [],
'y': [],
'tooltips': []
}
tab2_r_dspec_line_x.data_source.data = {'time': [], 'freq': []}
tab2_r_dspec_line_y.data_source.data = {'time': [], 'freq': []}
elif clickmode == 'doubleclick':
SRC_dspec_quadselround += 1
if SRC_dspec_quadselround == 2:
SRC_dspec_quadselround = 0
tab2_SRC_dspec_quadx_selected = tab2_SRC_dspec_quadx.selected[
'1d']['indices']
tab2_SRC_dspec_quady_selected = tab2_SRC_dspec_quady.selected[
'1d']['indices']
tab2_SRC_dspec_quadx.selected = {
'0d': {
'glyph': None,
'indices': []
},
'1d': {
'indices': []
},
'2d': {}
}
tab2_SRC_dspec_quady.selected = {
'0d': {
'glyph': None,
'indices': []
},
'1d': {
'indices': []
},
'2d': {}
}
if len(tab2_SRC_dspec_quadx_selected) > 0 and len(
tab2_SRC_dspec_quady_selected) > 0:
quadx_selected = tab2_SRC_dspec_quadx_selected[0]
quady_selected = tab2_SRC_dspec_quady_selected[0]
tapPointDF_dspec = tapPointDF_dspec.append(pd.Series({
'xx':
tab2_dtim[quadx_selected],
'yy':
tab2_freq[quady_selected]
}),
ignore_index=True)
if len(tapPointDF_dspec.index) == 1:
tab2_r_dspec_lines.data_source.data = {
'xs': [[tab2_dtim[quadx_selected]] * 2,
[tab2_dtim[0], tab2_dtim[-1]]],
'ys': [[tab2_freq[0], tab2_freq[-1]],
[tab2_freq[quady_selected]] * 2]
}
tab2_r_dspec_patch.data_source.data = {'xx': [], 'yy': []}
elif len(tapPointDF_dspec.index) == 2:
x0, x1 = tapPointDF_dspec['xx'].min(
), tapPointDF_dspec['xx'].max()
y0, y1 = tapPointDF_dspec['yy'].min(
), tapPointDF_dspec['yy'].max()
tab2_r_dspec_patch.data_source.data = {
'xx': [x0, x1, x1, x0],
'yy': [y0, y0, y1, y1]
}
tab2_r_dspec_lines.data_source.data = {'xs': [], 'ys': []}
dspecDF_select = \
dspecDF0_rs[dspecDF0_rs['time'] >= x0][dspecDF0_rs['time'] <= x1][
dspecDF0_rs['freq'] >= y0][
dspecDF0_rs['freq'] <= y1]
tapPointDF_dspec = pd.DataFrame({'xx': [], 'yy': []})
time0, time1 = dspecDF_select['time'].min(
) + timestart, dspecDF_select['time'].max() + timestart
t0_char = Time(time0 / 3600. / 24.,
format='jd',
scale='utc',
precision=3,
out_subfmt='date_hms').iso
date0_char = t0_char.split(' ')[0].replace('-', '/')
time0_char = t0_char.split(' ')[1]
t1_char = Time(time1 / 3600. / 24.,
format='jd',
scale='utc',
precision=3,
out_subfmt='date_hms').iso
date1_char = t1_char.split(' ')[0].replace('-', '/')
time1_char = t1_char.split(' ')[1]
tab2_tCLN_Param_dict['timerange'] = "'{}/{}~{}/{}'".format(
date0_char, time0_char, date1_char, time1_char)
freq0, freq1 = dspecDF_select['freq'].min(
), dspecDF_select['freq'].max()
freqrange = "'{:.3f}~{:.3f} GHz'".format(freq0, freq1)
tab2_tCLN_Param_dict['freqrange'] = freqrange
tab2_Div_tCLN_text = ' '.join(
"<p><b>{}</b> = {}</p>".format(key, val)
for (key, val) in tab2_tCLN_Param_dict.items())
tab2_Div_tCLN.text = tab2_Div_tCLN_text
xx = tim_map.flatten()
yy = freq_map.flatten()
timestart = xx[0]
tab2_panel_Div_exit = Div(
text="""<p><b>Warning</b>: Click the <b>Exit ToClean</b>
first before closing the tab</p></b>""",
width=config_main['plot_config']['tab_ToClean']['widgetbox_wdth1'])
timestrs = []
for ll in tab2_tim:
timestr = Time(ll / 3600. / 24.,
format='mjd',
scale='utc',
precision=3,
out_subfmt='date_hms').iso
timestrs.append(timestr.split(' ')[1])
timestrs = timestrs * tab2_nfreq
dspecDF0 = pd.DataFrame({
'time': xx - xx[0],
'freq': yy,
'dspec': tab2_spec_plt.flatten(),
'timestr': timestrs
})
rmax, rmin = tab2_spec_plt.max(), tab2_spec_plt.min()
# timestart = xx[0]
TOOLS = "crosshair,pan,wheel_zoom,box_zoom,reset,save"
# downsample_dspecDF(spec_square_rs_tmax=spec_square_rs_tmax, spec_square_rs_fmax=spec_square_rs_fmax)
# tab2_SRC_dspec_square = ColumnDataSource(dspecDF0_rs)
dspecDF0_rs = dspecDF0.copy()
'''create the dynamic spectrum plot'''
ignore_index=True)
Pol_name = ['filename', 'JD', 'alpha [deg]', 'PsANG [deg]',
'q', 'u', 'ran_q', 'ran_u', 'sys_q', 'sys_u',
'P', 'eP', 'Pr', 'theta', 'theta_r', 'eTheta',
'Aper_radius [pix]']
Phot_name = ['Object', 'Filename', 'set', 'TIME', 'JD',
'HWPANG', 'FWHM_o', 'FWHM_e', 'EXP [s]',
'Aper [pix]', 'Ann', 'Ann_out', 'Flux_o',
'eFLux_o', 'Flux_e', 'eFLux_e', 'Sky_o',
'eSky_o', 'Sky_e', 'eSky_e', 'SNR_o',
'SNR_e']
Pol_Log = Pol_Log.reindex(columns=Pol_name)
Photo_Log = Photo_Log.reindex(columns=Phot_name)
Pol_Log = Pol_Log.round({'JD': 6, 'alpha [deg]': 2, 'PsANG [deg]': 2,
'q': 4, 'u': 4, 'ran_q': 4, 'ran_u': 4,
'sys_q': 4, 'sys_u': 4, 'theta': 2, 'theta_r': 2,
'P': 4, 'eP': 4, 'Aper_radius [pix]': 2, 'Pr': 4,
'eTheta': 2})
Photo_Log = Photo_Log.round({'HWPANG': 2, 'JD': 6, 'FWHM_o': 2, 'FWHM_e': 2,
'Aper [pix]': 2, 'EXP [s]': 2, 'Ann': 2,
'Ann_out': 2, 'Flux_o': 4, 'eFLux_o': 4,
'Flux_e': 4, 'eFLux_e': 4, 'SNR_o': 2,
'SNR_e': 2, 'Sky_o': 4, 'eSky_o': 4,
'Sky_e': 4, 'eSky_e': 4})
Pol_Log.to_csv(os.path.join(path, 'result_Pol_{}.csv'.format(time_.split(' ')[0])))
Photo_Log.to_csv(os.path.join(path, 'result_Photo_{}.csv'.format(time_.split(' ')[0])))
print(os.path.join(path, 'result_Pol_{}.csv'.format(time_.split(' ')[0])) + ' is created.')
print(os.path.join(path, 'result_Photo_{}.csv'.format(time_.split(' ')[0])) + ' is created.')
