def timeCentroid(data, mask, xyGuess, niter, rad=20):
print "timeCentroid: xyGuess=%3.0f, %3.0f; niter=%2d; rad=%3d;" % \
(xyGuess[0], xyGuess[1], niter, rad),
begTime = time.time()
for ii in range(niter):
PyGuide.centroid(
data=data,
mask=mask,
satMask=None,
xyGuess=xyGuess,
rad=rad,
thresh=Thresh,
ccdInfo=CCDInfo,
)
dTime = time.time() - begTime
print "time/iter=%.3f" % (dTime / niter, )
def centroid(self, xyPos, data):
"""check to see if there is valid signal at xpos, ypos, on image data
if so return the centroid.
"""
# default to 5 px search rad?
return PyGuide.centroid(data, None, None, xyPos, rad = 3, #pixels
ccdInfo = self.config.ccdInfo)
def aligntocat(cube,catalogue):
"""
Take a cube and compare the sources in the field to the positions in the reference
catalogue. Return offsets in ra/dec that can be used for re-projecting the cube
This makes use of pyguide to find stars and centroid on them
"""
import PyGuide
import numpy as np
from astropy import wcs
print("Processing cube {} for offsets".format(cube))
#first project the cube to create a white image with wcs
img, var, wcsimg = cube2img(cube)
#load the reference stars
starcat=np.loadtxt(catalogue,dtype={'names': ('ra','dec'),'formats': ('f4', 'f4')})
#loop on reference stars and centroid
nref=len(starcat['ra'])
#space for offsets
raoffcurrent=[]
decoffcurrent=[]
for sr in range(nref):
#find first guess
pix = wcsimg.wcs_world2pix(starcat['ra'][sr],starcat['dec'][sr],0)
#centroid within 20 pixels
ccd=PyGuide.CCDInfo(0,0,1)
#handle weird errors for bas pixels
usethis=True
try:
centroid=PyGuide.centroid(img,None,None,[pix[0],pix[1]],20,ccd)
except:
usethis=False
#back to ra/dec if centroid is good
if ((centroid.isOK) & (usethis)):
coord = wcsimg.wcs_pix2world(centroid.xyCtr[0],centroid.xyCtr[1],0)
raoffcurrent.append(coord[0]-starcat['ra'][sr])
decoffcurrent.append(coord[1]-starcat['dec'][sr])
#stack offsets
raoff=np.median(np.array(raoffcurrent))
decoff=np.median(np.array(decoffcurrent))
print("Offsets for cube {} RA: {} Dec: {}".format(cube,raoff*3600.,decoff*3600.))
print("Error offsets for cube {} RA: {} Dec: {}".format(cube,np.std(np.array(raoffcurrent))*3600.,
np.std(np.array(decoffcurrent))*3600.))
return raoff,decoff
def aligntocat(cube,catalogue):
"""
Take a cube and compare the sources in the field to the positions in the reference
catalogue. Return offsets in ra/dec that can be used for re-projecting the cube
This makes use of pyguide to find stars and centroid on them
"""
import PyGuide
import numpy as np
from astropy import wcs
print "Processing cube {} for offsets".format(cube)
#first project the cube to create a white image with wcs
img, var, wcsimg = cube2img(cube)
#load the reference stars
starcat=np.loadtxt(catalogue,dtype={'names': ('ra','dec'),'formats': ('f4', 'f4')})
#loop on reference stars and centroid
nref=len(starcat['ra'])
#space for offsets
raoffcurrent=[]
decoffcurrent=[]
for sr in range(nref):
#find first guess
pix = wcsimg.wcs_world2pix(starcat['ra'][sr],starcat['dec'][sr],0)
#centroid within 20 pixels
ccd=PyGuide.CCDInfo(0,0,1)
#handle weird errors for bas pixels
usethis=True
try:
centroid=PyGuide.centroid(img,None,None,[pix[0],pix[1]],20,ccd)
except:
usethis=False
#back to ra/dec if centroid is good
if ((centroid.isOK) & (usethis)):
coord = wcsimg.wcs_pix2world(centroid.xyCtr[0],centroid.xyCtr[1],0)
raoffcurrent.append(coord[0]-starcat['ra'][sr])
decoffcurrent.append(coord[1]-starcat['dec'][sr])
#stack offsets
raoff=np.median(np.array(raoffcurrent))
decoff=np.median(np.array(decoffcurrent))
print "Offsets for cube {} RA: {} Dec: {}".format(cube,raoff*3600.,decoff*3600.)
print "Error offsets for cube {} RA: {} Dec: {}".format(cube,np.std(np.array(raoffcurrent))*3600.,
np.std(np.array(decoffcurrent))*3600.)
return raoff,decoff
def centroidImage(image,xyguess,radiusOfSearch = 6,doDS9=True,usePsfFit=False):
'''
ABW
This function finds the centroid of a star in the image
'''
#remove any undefined values
image[np.invert(np.isfinite(image))]=0.
#Assume anywhere with 0 counts is a dead pixel
deadMask = 1.0*(image==0)
#ignore saturated mask
satMask = np.zeros((len(deadMask),len(deadMask[0])))
# Specify CCDInfo (bias,readNoise,ccdGain,satLevel)
ccd = pg.CCDInfo(0,0.00001,1,2500)
xyguessPyguide = np.subtract(xyguess,(0.5,0.5)) #account for how pyguide puts pixel coordinates
pyguide_output = pg.centroid(image,deadMask,satMask,xyguess,radiusOfSearch,ccd,0,False,verbosity=0, doDS9=doDS9) #Added by JvE May 31 2013
# Use PyGuide centroid positions, if algorithm failed, use xy guess center positions instead
try:
xycenterGuide = [float(pyguide_output.xyCtr[0]),float(pyguide_output.xyCtr[1])]
np.add(xycenterGuide,(0.5,0.5))#account for how pyguide puts pixel coordinates
flag = 0
except TypeError:
xycenterGuide = xyguess
flag = 1
xycenter=xycenterGuide
if usePsfFit:
psfPhot = PSFphotometry(image,centroid=[xycenterGuide],verbose=True)
psfDict = psfPhot.PSFfit(aper_radius=radiusOfSearch)
xycenterPsf = [psfDict['parameters'][2],psfDict['parameters'][3]]
if psfDict['flag'] == 0:
xycenter = xycenterPsf
flag = 0
else:
print 'PSF fit failed with flag: ', psfDict['flag']
#xycenter = xycenterGuide
flag = 1
outDict = {'xycenter':xycenter,'flag':flag}
if usePsfFit:
outDict['xycenterGuide'] = xycenterGuide
outDict['xycenterPsf'] = xycenterPsf
return outDict
def presskey(self, event):
""" Do stuff when press key """
#quit on q
if (event.key == "q"):
self.OnExit()
#centroid on c
elif (event.key == "c"):
ccd = PyGuide.CCDInfo(0, 0, 1)
centroid = PyGuide.centroid(self.fitimg, None, None,
[event.xdata, event.ydata], 20,
ccd)
self.starx.append(centroid.xyCtr[0])
self.stary.append(centroid.xyCtr[1])
thisra, thisdec = self.wcs.wcs_pix2world(
centroid.xyCtr[0], centroid.xyCtr[1], 1)
self.starra.append(thisra)
self.stardec.append(thisdec)
self.starid.append(self.find_id(thisra, thisdec))
self.nstars = self.nstars + 1
self.update_twodimage(update=True)
#store bottom left corner on L
elif (event.key == "n"):
try:
check = float(event.xdata) + float(event.ydata)
self.boxlx.append(event.xdata)
self.boxly.append(event.ydata)
self.warning.set("STATUS: Now mark top/right corner!")
except:
self.boxlx.append(event.xdata)
self.boxly.append(event.ydata)
self.warning.set(
"STATUS: Missed data region... try again!")
elif (event.key == "m"):
try:
check = float(event.xdata) + float(event.ydata)
self.boxrx.append(event.xdata)
self.boxry.append(event.ydata)
self.nbox = self.nbox + 1
self.update_twodimage(update=True)
self.warning.set("STATUS: All good!")
except:
self.warning.set(
"STATUS: Missed data region... try again!")
elif (event.key == "d"):
if (self.nbox > 0):
self.boxlx = self.boxlx[0:-1]
self.boxly = self.boxly[0:-1]
self.boxrx = self.boxrx[0:-1]
self.boxry = self.boxry[0:-1]
self.nbox = self.nbox - 1
if (self.nstars > 0):
self.starra = self.starra[0:-1]
self.stardec = self.stardec[0:-1]
self.starid = self.starid[0:-1]
self.starx = self.starx[0:-1]
self.stary = self.stary[0:-1]
self.nstars = self.nstars - 1
self.update_twodimage(update=True)
rad2.append(float(larr[4]))
elif rtype[i] == 'circle':
xcen.append(float(larr[1]))
ycen.append(float(larr[2]))
rad.append(float(larr[3]))
rad2.append(float(larr[3] * numpy.sqrt(2)))
else:
print "Error: region type is not recognized (or possibly you are specifying an unrecognized coordinate system)"
if float(rad2[i]) > float(rad[i]):
outerrad = rad2[i]
else:
outerrad = float(rad[i])*numpy.sqrt(2)
# subimage = image[:,ycen[i]-rad[i]:ycen[i]+rad[i],xcen[i]-rad[i]:xcen[i]+rad[i]]
subimage = image[:,ycen[i]-outerrad:ycen[i]+outerrad,xcen[i]-outerrad:xcen[i]+outerrad]
# center = PyGuide.centroid(subimage[0],None,None,[outerrad,outerrad],rad[i],ccdinf)
center = PyGuide.centroid(subimage[0],None,None,[rad[i],rad[i]],rad[i],ccdinf,thresh=1,verbosity=0,smooth=0)
innerradius = PyGuide.starShape(subimage[0],None,center.xyCtr,rad[i]).fwhm
outerradius = innerradius * numpy.sqrt(2)
if center.isOK:
(newxcen,newycen)=center.xyCtr
# print "%s %s" % (str(center.xyCtr),str(center.xyErr))
else:
print "Error: %s. Using the point you selected instead of the star center." % str(center.msgStr)
(newxcen,newycen)=[outerrad,outerrad]
inner = core(subimage,newxcen,newycen,innerradius)
equalarea = core(subimage,newxcen,newycen,outerradius) - inner
vspec = inner - equalarea
for j in xrange(1,vspec.shape[0]):
print "%f %f" % (j,vspec[j])
break
i=i+1
actCtr = numpy.random.uniform(
-fwhm / 2.0, fwhm / 2.0, size=(2, )) + nomCtr
cleanData = PyGuide.FakeData.fakeStar(imShape, actCtr, sigma,
ampl)
data = PyGuide.FakeData.addNoise(
data=cleanData,
sky=Sky,
ccdInfo=CCDInfo,
)
ctrData = PyGuide.centroid(
data=data,
mask=mask,
satMask=None,
xyGuess=nomCtr,
rad=fwhm * 3.0,
ccdInfo=CCDInfo,
thresh=Thresh,
doSmooth=DoSmooth,
)
if not ctrData.isOK:
print "%s %s %s NaN NaN NaN NaN NaN NaN NaN %s %r" % (
fwhm,
ampl,
maskWidth,
ctrData.rad,
ctrData.msgStr,
)
nBad += 1
continue
for y in range(grid_height):
for x in range(grid_width):
badMask[y][x] = mask[y][x][t]
for i in range(integration_time):
pltmat[y][x]+=flux_cube[y][x][int(t*integration_time+i)]/integration_time
map.ax = map.fig.add_subplot(111)
map.ax.set_title('Object 1')
map.ax.matshow(pltmat,cmap = plt.cm.gray, origin = 'lower')
map.connect()
plt.show()
try:
xyguess = map.xyguess
except AttributeError:
pass
print 'Guess = ' + str(xyguess)
pyguide_output = pg.centroid(pltmat,badMask,satMask,xyguess,3,ccd,0,False)
try:
xycenter = [float(pyguide_output.xyCtr[0]),float(pyguide_output.xyCtr[1])]
print 'Calculated = ' + str((xycenter))
except TypeError:
print 'Cannot centroid, using guess'
xycenter = xyguess
map = MouseMonitor()
map.fig = plt.figure()
pltmat = np.zeros((grid_height,grid_width))
for y in range(grid_height):
for x in range(grid_width):
for i in range(integration_time):
pltmat[y][x]+=flux_cube[y][x][int(t*integration_time+i)]/integration_time
map.ax = map.fig.add_subplot(111)
def doCentroid(
imName = None,
maskName = None,
satMaskName = None,
xyGuess = None,
invertMask = False,
**kargs
):
"""Centroid and shape-fit a star
Inputs:
- all the arguments for loadFiles plus most values shown by showDef
"""
global im, imFits, mask, maskFits, satMask, satMaskFits, isSat, sd
im, mask, satMask = loadFiles(imName, maskName, satMaskName, invertMask)
if xyGuess is None:
print("xyGuess is required")
return
# check keyword arguments
for paramName in kargs:
if paramName not in CentroidParamNames:
raise RuntimeError("Invalid argument: %s" % (paramName,))
# fill in defaults
globalDict = globals()
for paramName in CentroidParamNames:
if paramName not in kargs:
kargs[paramName] = globalDict[paramName]
# split off ccd info
ccdInfoDict = {}
for paramName in CCDInfoNames:
ccdInfoDict[paramName] = kargs.pop(paramName)
ccdInfo = PyGuide.CCDInfo(**ccdInfoDict)
if kargs["rad"] is None:
print("rad argument is required because the default is presently None")
return
verbosity = kargs["verbosity"]
# centroid
ctrData = PyGuide.centroid(
data = im,
mask = mask,
satMask = satMask,
xyGuess = xyGuess,
ccdInfo = ccdInfo,
**kargs)
if not ctrData.isOK:
print("centroid failed:", ctrData.msgStr)
return
shapeData = PyGuide.starShape(
data = im,
mask = mask,
xyCtr = ctrData.xyCtr,
rad = ctrData.rad,
verbosity = verbosity,
)
# print results
printStarHeader()
printStarData(ctrData, shapeData)
if not shapeData.isOK:
print("starShape failed:", shapeData.msgStr)
for ii in range(NumTries):
xyCtr = numpy.random.uniform(-fwhm/2.0, fwhm/2.0, size=(2,)) + nomCtr
cleanData = PyGuide.FakeData.fakeStar(imShape, xyCtr, sigma, ampl)
data = PyGuide.FakeData.addNoise(
data = cleanData,
sky = Sky,
ccdInfo = CCDInfo,
)
if DoCentroid:
ctrData = PyGuide.centroid(
data = data,
mask = mask,
satMask = None,
xyGuess = nomCtr,
rad = fwhm * 3.0,
ccdInfo = CCDInfo,
thresh = Thresh,
)
if not ctrData.isOK:
print "%.1f %.1f %.1f %.2f %.2f %.2f NaN NaN NaN NaN NaN NaN NaN NaN NaN %r" % (
fwhm, ampl, bkgnd,
xyCtr[0], xyCtr[1], maskWidth,
ctrData.msgStr,
)
nBadCtr += 1
continue
else:
ctrData = PyGuide.CentroidData(
isOK = True,
"""it's a test, ok?
"""
import pyfits
import numpy
import PyGuide
import autoPhot
from autoPhot.config import flareCam
ccdInfo = PyGuide.CCDInfo(0, flareCam.readNoise, flareCam.ccdGain)
img = pyfits.open('/Users/csayres/data/arcsat/GJ1243/gFilter/oneNight/ccs20120520.00001139.LUMINANCE.FIT')
data = img[0].data
img.close()
coord1 = numpy.array([197.66827757, 209.33221882])
coord2 = numpy.array([ 343.39379969, 210.25893067])
cent1 = PyGuide.centroid(data, None, None, coord1, rad = 2, #pixels
ccdInfo = ccdInfo)
cent2 = PyGuide.centroid(data, None, None, coord2, rad = 2, #pixels
ccdInfo = ccdInfo)
diff1 =
def muse_combine(pixtab,cubes,wcslist,lmin=4600,lmax=10000):
"""
Take a list of reduced pixel table and cubes and combine them.
pixtab = reduced pixel table for alignment
wcslist = list of ra dec of bright sources in the field for centroid
that can be used for relative source alignment.
cubes = reduced cubes, which are not directly combined, but they are used to compute alignemnt
lmin,lmax = min max wave interval for combining
Make sure filter list is in working directory
"""
import astropy
from astropy.table import Table
from astropy.io import fits
import PyGuide
import numpy as np
from astropy import wcs
from astropy.coordinates import SkyCoord
import subprocess
#load the wcs
wcstab = Table.read(wcslist,format='ascii')
raoff=[]
decoff=[]
#loop over the pixel table to compute the offsets
for cb in cubes:
print "Processing cube {} for offsets".format(cb)
#project a cube
header=''
fov=project_cube(cb,[4800,8000],False)
#load the wcs
w = wcs.WCS(fov['header'])
raoffcurrent=[]
decoffcurrent=[]
#loop over reference stars
for sr in range(len(wcstab)):
#go to pixels
pix = w.wcs_world2pix(wcstab['col1'][sr],wcstab['col2'][sr],0,1)
#centroid
ccd=PyGuide.CCDInfo(0,0,1)
centroid=PyGuide.centroid(fov["img"],None,None,[pix[0],pix[1]],20,ccd)
#back to ra/dec
if centroid.isOK:
coord = w.wcs_pix2world(centroid.xyCtr[0],centroid.xyCtr[1],0,1)
raoffcurrent.append(coord[0]-wcstab['col1'][sr])
decoffcurrent.append(coord[1]-wcstab['col2'][sr])
#stack offsets
thisdra=np.mean(np.array(raoffcurrent))
thisdde=np.mean(np.array(decoffcurrent))
raoff.append(thisdra)
decoff.append(thisdde)
print "Offsets for this cube RA: {} Dec: {}".format(thisdra,thisdde)
#print offsets
print "All Delta RA ", raoff
print "All Delta Dec ", decoff
rastring = ','.join(str(e) for e in raoff)
decstring = ','.join(str(e) for e in decoff)
#now prepare script for stacking and run the pipeline
sof=open("combine.sof","w")
for pxtb in pixtab:
sof.write(pxtb+' PIXTABLE_REDUCED\n')
sof.write('filter_list.fits FILTER_LIST')
sof.close()
#Write the command file
scr=open("make_combine.sh","w")
scr.write('MUSE_XCOMBINE_RA_OFFSETS="'+rastring+'"\n')
scr.write('MUSE_XCOMBINE_DEC_OFFSETS="'+decstring+'"\n')
scr.write("esorex --log-file=exp_combine.log muse_exp_combine --lambdamin={0:f} --lambdamax={1:f} combine.sof".format(lmin,lmax))
scr.close()
#Run pipeline
subprocess.call(["sh", "make_combine.sh"])
return
cleanData = PyGuide.FakeData.fakeStar(arrShape, actCtr, sigma, ampl)
numpy.random.seed(1)
data = PyGuide.FakeData.addNoise(
cleanData,
sky = Sky,
ccdInfo = CCDInfo,
)
print("\nactual center = %6.2f, %6.2f, sigma = %.2f, scanRad = %d" % (actCtr[0], actCtr[1], sigma, scanRad))
mask = None
ctrData = PyGuide.centroid(
data = data,
mask = mask,
satMask = None,
xyGuess = xyGuess,
rad = scanRad,
ccdInfo = CCDInfo,
doSmooth = DoSmooth,
)
if not ctrData.isOK:
print("centroid failed: %s" % (ctrData.msgStr,))
continue
measCtr = ctrData.xyCtr
nCounts = ctrData.counts
nPts = ctrData.pix
print("meas err = %6.2f, %6.2f; est err = %.2f, %.2f; nCounts = %.0f; nPts = %d" %
(measCtr[0] - actCtr[0], measCtr[1] - actCtr[1], ctrData.xyErr[0], ctrData.xyErr[1], nCounts, nPts))
mask = numpy.zeros(arrShape, numpy.bool)
def performCentroiding(self):
'''
# Function for converting arcseconds to radians.
def arcsec_to_radians(total_arcsec):
total_degrees = total_arcsec/3600.0
total_radians = total_degrees*d2r
return total_radians
# Function for converting radians to arcseconds.
def radians_to_arcsec(total_radians):
total_degrees = total_radians*r2d
total_arcsec = total_degrees*3600.0
return total_arcsec
print 'Not currently implemented...'
d2r = np.pi/180.0
r2d = 180.0/np.pi
# Load data out of display stack h5 file
centroid_RA = self.headerInfo[self.headerTitles.index('RA')]
centroid_DEC = self.headerInfo[self.headerTitles.index('Dec')]
original_lst = self.headerInfo[self.headerTitles.index('lst')]
exptime = self.headerInfo[self.headerTitles.index('exptime')]
integrationTime = self.headerInfo[self.headerTitles.index('integrationTime')]
deadPixelFilename = self.headerInfo[self.headerTitles.index('deadPixFileName')]
HA_offset = self.headerInfo[self.headerTitles.index('HA_offset')]
nRow = self.headerInfo[self.headerTitles.index('nRow')]
nCol = self.headerInfo[self.headerTitles.index('nCol')]
centroid_RA_radians = ephem.hours(centroid_RA).real
centroid_RA_arcsec = radians_to_arcsec(centroid_RA_radians)
centroid_DEC_radians = ephem.degrees(centroid_DEC).real
centroid_DEC_arcsec = radians_to_arcsec(centroid_DEC_radians)
original_lst_radians = ephem.hours(original_lst).real
original_lst_seconds = radians_to_arcsec(original_lst_radians)/15.0
'''
# Load up dead pixel mask. Invert for PyGuide format.
#deadFile = np.load(self.deadPixelFilename)
#deadMask = deadFile['deadMask']
#deadMask = -1*deadMask + 1
# Saturated pixels already taken care of by hot pixel code.
satMask = np.zeros((46,44))
# Specify CCDInfo (bias,readNoise,ccdGain,satLevel)
ccd = pg.CCDInfo(0,0.00001,1,2500)
# Initialize arrays that will be saved in h5 file. 1 array element per centroid frame.
timeList=[]
xPositionList=[]
yPositionList=[]
hourAngleList=[]
flagList=[]
flag=0
print 'Centroiding a total of ' + str(self.totalFrames) + ' frames...'
for iFrame in range(self.totalFrames):
apertureRadius = self.apertureRadii[iFrame]
image = np.array(self.stackData[:,:,iFrame])
nanMask = np.isnan(image)
image[nanMask] = 0.
deadMask = np.zeros((self.nRow,self.nCol))
deadMask[np.where(image==0)] = 1
xyguess = np.array(self.centerPositions[iFrame])
pyguide_output = pg.centroid(image,deadMask,satMask,xyguess,apertureRadius,ccd,0,False,verbosity=2, doDS9=True)
# Use PyGuide centroid positions, if algorithm failed, use xy guess center positions instead
print pyguide_output
try:
xycenter = [float(pyguide_output.xyCtr[0]),float(pyguide_output.xyCtr[1])]
print 'Frame ' + str(iFrame) +': Calculated [x,y] center = ' + str((xycenter)) + '.'
flag = 0
except TypeError:
print 'Cannot centroid frame' + str(iFrame) + ', using guess instead'
xycenter = xyguess
flag = 1
# Calculate lst for a given frame, at midpoint of frame
current_lst_seconds = self.original_lst_seconds + (iFrame+0.5)*self.integrationTime
current_lst_radians = self.arcsec_to_radians(current_lst_seconds*15.0)
# Calculate hour angle for a given frame. Include a constant offset for instrumental rotation.
HA_variable = current_lst_radians - self.centroid_RA_radians
HA_static = self.HA_offset*self.d2r
HA_current = HA_variable + HA_static
# Make lists to save to h5 file
timeList.append((iFrame+0.5)*self.integrationTime)
xPositionList.append(xycenter[0])
yPositionList.append(xycenter[1])
hourAngleList.append(HA_current)
flagList.append(flag)
self.objectIdentifier = self.loadStackName[0:self.loadStackName.index('ImageStacks/ImageStack_')]
self.obsIdentifier = self.loadStackName[self.loadStackName.rindex('ImageStacks/ImageStack_') + len('ImageStacks/ImageStack_'):-3]
fullCentroidListFileName = self.objectIdentifier + 'CentroidLists/Centroid_' + self.obsIdentifier + '.h5'
print 'Saving to ' + fullCentroidListFileName
# Write data to new h5 file
centroidListFile = tables.openFile(fullCentroidListFileName,mode='w')
centroidHeaderGroupName = 'header'
centroidHeaderTableName = 'header'
centroidDataGroupName = 'centroidlist'
centroidDataGroup = centroidListFile.createGroup(centroidListFile.root,centroidDataGroupName,'Table of times, x positions, y positions, hour angles, and flags')
#paramstable = tables.Array(centroidgroup,'params', object=paramsList, title = 'Object and array params')
timestable = tables.Array(centroidDataGroup,'times',object=timeList,title='Times at which centroids were calculated')
xpostable = tables.Array(centroidDataGroup,'xPositions',object=xPositionList,title='X centroid positions')
ypostable = tables.Array(centroidDataGroup,'yPositions',object=yPositionList,title='Y centroid positions')
hatable = tables.Array(centroidDataGroup,'hourAngles',object=hourAngleList,title='Hour angles at specified times')
flagtable = tables.Array(centroidDataGroup,'flags',object=flagList,title='Flags whether or not guess had to be used, 1 for guess used')
# Should probably just copy original header information over, more info this way!!!
centroidHeaderGroup = centroidListFile.createGroup("/", centroidHeaderGroupName, 'Header')
centroidHeaderTable = centroidListFile.createTable(centroidHeaderGroup, centroidHeaderTableName, DisplayStack.DisplayStack.headerDescription,
'Header Info')
centroidHeader = centroidHeaderTable.row
for iItem in range(len(self.headerInfo)):
centroidHeader[self.headerTitles[iItem]] = self.headerInfo[iItem]
centroidHeader.append()
centroidListFile.flush()
centroidListFile.close()
print 'Done performing centroiding...'
def doCentroid(imName=None,
maskName=None,
satMaskName=None,
xyGuess=None,
invertMask=False,
**kargs):
"""Centroid and shape-fit a star
Inputs:
- all the arguments for loadFiles plus most values shown by showDef
"""
global im, imFits, mask, maskFits, satMask, satMaskFits, isSat, sd
im, mask, satMask = loadFiles(imName, maskName, satMaskName, invertMask)
if xyGuess is None:
print("xyGuess is required")
return
# check keyword arguments
for paramName in kargs:
if paramName not in CentroidParamNames:
raise RuntimeError("Invalid argument: %s" % (paramName, ))
# fill in defaults
globalDict = globals()
for paramName in CentroidParamNames:
if paramName not in kargs:
kargs[paramName] = globalDict[paramName]
# split off ccd info
ccdInfoDict = {}
for paramName in CCDInfoNames:
ccdInfoDict[paramName] = kargs.pop(paramName)
ccdInfo = PyGuide.CCDInfo(**ccdInfoDict)
if kargs["rad"] is None:
print("rad argument is required because the default is presently None")
return
verbosity = kargs["verbosity"]
# centroid
ctrData = PyGuide.centroid(data=im,
mask=mask,
satMask=satMask,
xyGuess=xyGuess,
ccdInfo=ccdInfo,
**kargs)
if not ctrData.isOK:
print("centroid failed:", ctrData.msgStr)
return
shapeData = PyGuide.starShape(
data=im,
mask=mask,
xyCtr=ctrData.xyCtr,
rad=ctrData.rad,
verbosity=verbosity,
)
# print results
printStarHeader()
printStarData(ctrData, shapeData)
if not shapeData.isOK:
print("starShape failed:", shapeData.msgStr)