def testGetPixelCountImage(bins=250, integrationTime=1):
'''
Do two runs of getPixelCountImage and compare the results
to check the repeatability (i.e., test the degree of
effect of the random dithering in the wavelength handling.)
INPUTS:
bins - set the number of bins for the output histogram
OUTPUTS:
Displays the two images in ds9, as well as image1 divided
by image2. Also shows the latter in a regular plot, as well
as a histogram of the image1/image2 ratios over all pixels.
'''
obsfile = loadTestObsFile.loadTestObsFile()
obsfile.setWvlCutoffs(4000,8000)
#Get first image
im1 = obsfile.getPixelCountImage(firstSec=0, integrationTime=30, weighted=True,
fluxWeighted=False, getRawCount=False,
scaleByEffInt=False)['image']
#Get supposedly identical image
im2 = obsfile.getPixelCountImage(firstSec=0, integrationTime=30, weighted=True,
fluxWeighted=False, getRawCount=False,
scaleByEffInt=False)['image']
utils.ds9Array(im1,frame=1)
utils.ds9Array(im2,frame=2)
divim = im1/im2
utils.ds9Array(divim,frame=3)
utils.plotArray(divim, colormap=pl.cm.hot, cbar=True, normMax=np.mean(divim)+2*np.std(divim))
toHist = divim.flatten()
toHist = toHist[np.isfinite(toHist)]
pl.figure()
pl.hist(toHist,bins=bins)
pl.title('Ratio of image1/image2, wavelength range '+str(obsfile.wvlLowerLimit)
+'-'+str(obsfile.wvlUpperLimit)+'Ang')
pl.xlabel('Ratio')
pl.ylabel('Number of pixels')
print 'Mean image1/image2: ',np.mean(toHist)
print 'Std. dev image1/image2: ',np.std(toHist)
def display(
self,
normMin=None,
normMax=None,
expWeight=True,
pclip=None,
colormap=mpl.cm.hot,
image=None,
logScale=False,
fileName=None,
ds9=False,
cbar=False,
noAxis=False,
):
"""
Display the current image. Currently just a short-cut to utils.plotArray,
but needs updating to mark RA and Dec on the axes.
NOTE: FOR NOW, PLOTTING AGAINST RA/DEC IS SWITCHED OFF, SINCE IT LOOKS LIKE THE IMAGE FLIP/ROTATION
ASSUMED BY CALCULATERADEC.PY MAY BE WRONG. NEEDS SORTING OUT, BUT IN THE MEANTIME, JUST SHOW THE IMAGE
THE RIGHT WAY ROUND, AND DON'T LABEL THE AXES.
INPUTS:
normMin, normMax: Minimum and maximum values for the color-scale stretch
expWeight: if True, scale each virtual pixel by its exposure time
pclip: Apply a percentile clip to the image at the lower [pclip] and upper [100-pclip]'th
percentiles (where pclip is in percent). Overrides normMin and normMax.
colorMap: as for plotArray, can specify the matplotlib color map to use.
image: if set to a 2D array, displays that array instead of the default image.
logScale: if True, display the intensities on a log scale.
fileName: if a string, save the plot to this filename. If anything else (inc. None),
display to screen.
ds9: if True, send image to DS9 (in which case pretty much all the other parameters
are ignored).
cbar: if True, add a colour bar (note you can end up with multiple color bars if you
call this repeatedly though.)
noAxis: if True, don't mark or label the axes.
"""
showCoordsOnAxes = (
False
) # For now, don't try, since it looks like image flip/rotation assumed by CalculateRaDec may be wrong.
assert np.all(self.image[self.effIntTimes == 0] == 0)
if expWeight:
toDisplay = np.copy(self.image * self.expTimeWeights)
else:
toDisplay = np.copy(self.image)
if ds9 is True:
utils.ds9Array(toDisplay)
return # Don't need to do anything else in this case.
if logScale is True:
toDisplay = np.log10(toDisplay)
if image is not None:
toDisplay = np.copy(image)
#####################
# Rotate by 180deg so north is up and east is left - just a fudge for now, need to
# sort this out properly.
if showCoordsOnAxes is False:
toDisplay = np.rot90(np.rot90(toDisplay))
#####################
if pclip:
normMin = np.percentile(toDisplay[np.isfinite(toDisplay)], q=pclip)
normMax = np.percentile(toDisplay[np.isfinite(toDisplay)], q=100.0 - pclip)
# Display NaNs as zeros so it looks better
toDisplay[np.isnan(toDisplay)] = 0
# Find the coordinates of the centers of the virtual pixels in degrees
# raMin = (self.gridRA[0:-1] + self.gridRA[1:])/2.0 / np.pi * 180.
# dec = (self.gridDec[0:-1] + self.gridDec[1:])/2.0 / np.pi * 180.
# utils.plotArray(toDisplay,cbar=True,normMin=normMin,normMax=normMax,
# colormap=colormap,plotFileName=fileName,
# showMe=(type(fileName) is not str))
# fig = mpl.figure()
# ax = fig.add_subplot(111)
# ax.set_xticklabels(ax.get_xticklabels(),rotation=90)
mpl.ticklabel_format(style="plain", useOffset=False)
mpl.tick_params(direction="out")
### Use until we get image rotation/flip sorted out properly
if showCoordsOnAxes is True:
origin = "lower"
extent = (180.0 / np.pi) * np.array([self.gridRA[0], self.gridRA[-1], self.gridDec[0], self.gridDec[-1]])
else:
origin = "lower"
extent = None
###
if noAxis is True:
mpl.axis("off") # Hopefully overrides any axis labeling that comes later. But haven't checked...
mpl.imshow(toDisplay, vmin=normMin, vmax=normMax, extent=extent, origin=origin, cmap=colormap)
# mpl.ticklabel_format(style='plain',useOffset=False)
if showCoordsOnAxes is True:
ax = mpl.gca()
xtickBase = 10 ** (np.round(np.log10((self.gridRA[-1] - self.gridRA[0]) * 180.0 / np.pi / 10.0)))
ytickBase = 10 ** (np.round(np.log10((self.gridDec[-1] - self.gridDec[0]) * 180.0 / np.pi / 10.0)))
ax.xaxis.set_major_locator(mpl.MultipleLocator(base=xtickBase))
ax.yaxis.set_major_locator(mpl.MultipleLocator(base=ytickBase))
mpl.xticks(rotation=90)
mpl.xlabel("R.A. (deg)")
mpl.ylabel("Dec. (deg)")
if cbar is True:
mpl.colorbar()
utils.showzcoord()
def divideObsFiles(fileName1='/Users/vaneyken/Data/UCSB/ARCONS/turkDataCopy/ScienceData/PAL2012/20121211/flat_20121212-134024.h5',
fileName2='/Users/vaneyken/Data/UCSB/ARCONS/turkDataCopy/ScienceData/PAL2012/20121211/flat_20121212-134637.h5',
firstSec=0, integrationTime=10., nbins=None):
'''
Divide the raw image from one obs file by another, and display and return the result.
This works with raw counts, so the obs file need not be calibrated.
INPUTS:
fileName1, fileName2 -- names of two obs files to divide by each other, OR two ObsFile
objects can be passed directly.
firstSec - time during the obs files at which to start integration of images (sec)
integrationTime - time to integrate for to make the images (sec)
nbins - number of bins for histogram plot (if None, makes a semi-reasonable guess)
OUTPUTS:
Displays the divided result to the screen and to ds9.
Returs a tuple of image arrays:
divided image, input image 1, input image 2, obsFile 1, obsFile 2
'''
if type(fileName1) is str:
obsf1 = ObsFile.ObsFile(fileName1)
fn1 = fileName1
else:
obsf1=fileName1 #Otherwise just assume it's an ObsFile instance.
fn1=obsf1.fileName
if type(fileName2) is str:
obsf2 = ObsFile.ObsFile(fileName2)
fn2 = fileName2
else:
obsf2=fileName2
fn2=obsf2.fileName
print 'Reading '+os.path.basename(fn1)
pci1 = obsf1.getPixelCountImage(firstSec=firstSec,integrationTime=integrationTime,getRawCount=True)
print 'Reading '+os.path.basename(fn2)
pci2 = obsf2.getPixelCountImage(firstSec=firstSec,integrationTime=integrationTime,getRawCount=True)
im1 = pci1['image']
im2 = pci2['image']
divIm = im1/im2
med = np.median(divIm[~np.isnan(divIm)])
#Approximate std. dev from median abs. dev. (more robust)
sdev = astropy.stats.median_absolute_deviation(divIm[~np.isnan(divIm)]) *1.4826
badFlag = np.abs(divIm - med) > 3.0*sdev
print 'Displaying'
toDisplay = np.copy(divIm)
toDisplay[np.isnan(toDisplay)]=0
utils.plotArray(toDisplay, cbar=True, normMin=med-4.*sdev, normMax=med+4.*sdev, colormap=mpl.cm.hot, fignum=None)
yy,xx = np.indices(np.shape(divIm))
mpl.scatter(xx[badFlag], yy[badFlag], marker='o', c='r')
utils.ds9Array(divIm)
mpl.figure()
if nbins is None: nbins=np.sqrt(np.sum(np.isfinite(divIm)))
mpl.hist(divIm[np.isfinite(divIm)].flatten(),bins=nbins)
print 'Median: ',med
print 'Approx std. dev. (M.A.D * 1.4826): ',sdev
print 'Done.'
return divIm,im1,im2,obsf1,obsf2,badFlag