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 doFindStars(imName=None,
maskName=None,
satMaskName=None,
invertMask=False,
**kargs):
"""Find stars and centroid and shape-fit them.
Inputs:
- all the arguments for loadFiles plus values shown by showDef
"""
global isSat, sd
im, mask, satMask = loadFiles(imName, maskName, satMaskName, invertMask)
# check keyword arguments
for paramName in kargs:
if paramName not in FindParamNames:
raise RuntimeError("Invalid argument: %s" % (paramName, ))
# fill in defaults
globalDict = globals()
for paramName in FindParamNames:
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)
# find stars and centroid
print("Calling PyGuide.findStars")
ctrDataList, imStats = PyGuide.findStars(data=im,
mask=mask,
satMask=satMask,
ccdInfo=ccdInfo,
**kargs)
print("%s stars found:" % (len(ctrDataList), ))
printStarHeader()
for ctrData in ctrDataList:
# measure star shape
try:
shapeData = PyGuide.starShape(
data=im,
mask=mask,
xyCtr=ctrData.xyCtr,
rad=ctrData.rad,
)
except RuntimeError as e:
print("starShape failed: %s" % (e, ))
shapeData = PyGuide.StarShapeData()
printStarData(ctrData, shapeData)
def centeredcentroids(data, mask=None):
"""Finds centroids in an image, with (0,0) at the center of the image
Parameters:
data (ndarray):
a 2d numpy array containing image data, assumed to be x row major
mask (ndarray):
a 2d numpy array containing binary image data (0 for do process and 1 for don't)
Returns:
xys (list):
a list of interleaved xy positions
these are the positions of the centroids in the image
"""
centroids, stats = PyGuide.findStars(data, mask, None, PyGuide.CCDInfo(2176, 19, 2.1), thresh=10, radMult=1.0, rad=None, verbosity=0, doDS9=False)
out = []
for centroid in centroids:
out.append(centroid.xyCtr[0]-data.shape[1]/2)
out.append(centroid.xyCtr[1]-data.shape[0]/2)
return out
def unitdiskcentroids(data, mask=None):
"""Finds centroids in an image, with (0,0) at the center of the image and the largest possible circle around this (0,0) having magnitude 1
Parameters:
data (ndarray):
a 2d numpy array containing image data, assumed to be x row major
mask (ndarray):
a 2d numpy array containing binary image data (0 for do process and 1 for don't)
Returns:
xys (list):
a list of interleaved xy positions
these are the positions of the centroids in the image
"""
centroids, stats = PyGuide.findStars(data, mask, None, PyGuide.CCDInfo(2176, 19, 2.1), thresh=10, radMult=1.0, rad=None, verbosity=0, doDS9=False)
out = []
scale = min(data.shape[0],data.shape[1])/2
for centroid in centroids:
out.append((centroid.xyCtr[0]-data.shape[1]/2)/scale)
out.append((centroid.xyCtr[1]-data.shape[0]/2)/scale)
return out
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)
import calendar
import time
import timeit
import cv2
DEBUG = True
#add path to PyGuide, I think it is some weirdness going on with using
#Anaconda and what paths are set.
sys.path.append("/usr/local/lib/python2.7/dist-packages")
import PyGuide
# Default Parameters
# these settings will need to be updated once we have the real guide camera
# in order, bias (ADU), readnoise (e-), gain (e-/ADU), saturation level (ADU)
ccdInfo = PyGuide.CCDInfo(10.0, 4.01, 1.5, 256)
# these are general settings
thresh = 5.0
radMult = 3.0
rad = 20
satLevel = (2**8) - 1
verbosity = 0
doDS9 = False
mask = None
satMask = None
def imageList(fpath):
"""Find all images with a given extention and return their names as
a list"""
flist = raw_input("What is the file identifier? (*.?) >")
2005-10-14 ROwen Supply null satMask for PyGuide 2.1.
2008-01-02 ROwen Added DoSmooth constant.
2009-11-20 ROwen Modified to use numpy.
"""
import numpy
import PyGuide
from Stats import Stats
# settings
DoSmooth = True
ImWidth = 64
Sky = 1000, # sky level, in ADU
CCDInfo = PyGuide.CCDInfo(
bias=2176, # image bias, in ADU
readNoise=19, # read noise, in e-
ccdGain=2.1, # inverse ccd gain, in e-/ADU
)
Thresh = 2.5
imShape = (ImWidth, ImWidth)
nomCtr = (ImWidth // 2, ImWidth // 2)
mask = numpy.zeros(imShape, numpy.bool)
NaN = float("NaN")
# settings
AmplValues = (100, 1000, 10000)
FWHMValues = (2.0, 3.0, 4.0)
MaskWidthsPerFWHM = (0.0, 0.5, 1.0, 1.5, 2.0) # fractions of a FWHM
NumTries = 20
#filePath = input("Enter path to file (eg. ~/Pictures/SX_CCD): ")
#dataFile = input("Enter desired output file (eg. data.csv): ")
if filePath[0] == '~':
filePath = os.path.expanduser('~') + filePath[1:]
if dataFile[0] == '~':
dataFile = os.path.expanduser('~') + dataFile[1:]
#print(filePath)
#print(dataFile)
CCDInfo = PyGuide.CCDInfo(
bias=BIAS_LEVEL, # image bias, in ADU
readNoise=READ_NOISE, # read noise, in e-
ccdGain=GAIN, # inverse ccd gain, in e-/ADU
)
if filePath[len(filePath) - 5:] == '.fits':
dataListTemp = single_image(filePath)
dataList = []
dataList.append(dataListTemp)
write_to_csv(dataFile, dataList)
else:
if filePath[len(filePath) - 1] != '/':
filePath = filePath + '/'
if not os.path.exists(filePath):
print("ERROR: That file path does not exist.")
2004-08-04 ROwen Modified to work with 2004-08-03 findStars.
2004-08-06 ROwen Modified to work with 2004-08-06 findStars.
2005-02-07 ROwen Modified for PyGuide 1.2.
Modified to show shape info for all found stars.
2005-04-19 ROwen Modified for PyGuide 2.0
2005-10-14 ROwen Supply null satMask for PyGuide 2.1.
"""
import os.path
import sys
import PyGuide
import pyfits
# these values are probably wrong for the given test image
CCDInfo = PyGuide.CCDInfo(
bias=200, # image bias, in ADU
readNoise=21.391, # read noise, in e-
ccdGain=1.643, # ccd gain, in e-/pixel
)
UseDS9 = True
if len(sys.argv) > 1:
filename = sys.argv[1]
else:
testDir = os.path.dirname(__file__)
filename = os.path.join(testDir, "test.fits")
testimg = pyfits.open(filename)
data = testimg[0].data
if UseDS9:
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)
