def movie(data,aslice,plen,loop=1,direc='z',cmax=None,cmin=None):
"movie(data,slice,pause,loop=1,direc='z')"
gist.animate(1)
if type(aslice) is types.IntType:
num = aslice
aslice = [slice(None)]*3
aslice[ord('x')-ord(direc)-1] = num
for num in range(loop):
for k in range(data.shape[0]):
gist.fma()
gist.pli(data[k][aslice],cmax=cmax,cmin=cmin)
gist.pause(plen)
gist.animate(0)
def movie(data,aslice,plen,loop=1,direc='z',cmax=None,cmin=None):
"movie(data,slice,pause,loop=1,direc='z')"
gist.animate(1)
if type(aslice) is types.IntType:
num = aslice
aslice = [slice(None)]*3
aslice[ord('x')-ord(direc)-1] = num
for num in range(loop):
for k in range(data.shape[0]):
gist.fma()
gist.pli(data[k][aslice],cmax=cmax,cmin=cmin)
gist.pause(plen)
gist.animate(0)
def imagesc(z,cmin=None,cmax=None,xryr=None,_style='default', palette=None,
color='black',colormap=None):
"""Plot an image on axes.
z -- The data
cmin -- Value to map to lowest color in palette (min(z) if None)
cmax -- Value to map to highest color in palette (max(z) if None)
xryr -- (xmin, ymin, xmax, ymax) coordinates to print
(0, 0, z.shape[1], z.shape[0]) if None
_style -- A 'style-sheet' to use if desired (a default one will be used
if 'default'). If None, then no style will be imposed.
palette -- A string for a palette previously saved in a file (see write_palette)
or an array specifying the red-green-blue values (2-d array N x 3) or
gray-scale values (2-d array N x 1 or 1-d array).
color -- The color to use for the axes.
"""
if xryr is None:
xryr = (0,0,z.shape[1],z.shape[0])
try:
_style = None
saveval = gist.plsys(2)
gist.plsys(saveval)
except:
_style = 'default'
if not _hold:
gist.fma()
gist.animate(0)
if _style is not None:
if _style == "default":
_style=os.path.join(_user_path,'image.gs')
system = write_style.getsys(hticpos='below',vticpos='left',frame=1,
color=color)
fid = open(_style,'w')
fid.write(write_style.style2string(system))
fid.close()
gist.window(style=_style)
_current_style=_style
if cmax is None:
cmax = max(ravel(z))
if cmin is None:
cmin = min(ravel(z))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(z,cmin=cmin,cmax=cmax)
if (colormap is not None): palette=colormap
change_palette(palette)
gist.pli(byteimage,xryr[0],xryr[1],xryr[2],xryr[3])
return
def imagesc(z,cmin=None,cmax=None,xryr=None,_style='default', palette=None,
color='black',colormap=None):
"""Plot an image on axes.
z -- The data
cmin -- Value to map to lowest color in palette (min(z) if None)
cmax -- Value to map to highest color in palette (max(z) if None)
xryr -- (xmin, ymin, xmax, ymax) coordinates to print
(0, 0, z.shape[1], z.shape[0]) if None
_style -- A 'style-sheet' to use if desired (a default one will be used
if 'default'). If None, then no style will be imposed.
palette -- A string for a palette previously saved in a file (see write_palette)
or an array specifying the red-green-blue values (2-d array N x 3) or
gray-scale values (2-d array N x 1 or 1-d array).
color -- The color to use for the axes.
"""
if xryr is None:
xryr = (0,0,z.shape[1],z.shape[0])
try:
_style = None
saveval = gist.plsys(2)
gist.plsys(saveval)
except:
_style = 'default'
if not _hold:
gist.fma()
gist.animate(0)
if _style is not None:
if _style == "default":
_style=os.path.join(_user_path,'image.gs')
system = write_style.getsys(hticpos='below',vticpos='left',frame=1,
color=color)
fid = open(_style,'w')
fid.write(write_style.style2string(system))
fid.close()
gist.window(style=_style)
_current_style=_style
if cmax is None:
cmax = max(ravel(z))
if cmin is None:
cmin = min(ravel(z))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(z,cmin=cmin,cmax=cmax)
if (colormap is not None): palette=colormap
change_palette(palette)
gist.pli(byteimage,xryr[0],xryr[1],xryr[2],xryr[3])
return
def imagesc_cb(z,cmin=None,cmax=None,xryr=None,_style='default',
zlabel=None,font='helvetica',fontsize=16,color='black',
palette=None):
"""Plot an image on axes with a colorbar on the side.
z -- The data
cmin -- Value to map to lowest color in palette (min(z) if None)
cmax -- Value to map to highest color in palette (max(z) if None)
xryr -- (xmin, ymin, xmax, ymax) coordinates to print
(0, 0, z.shape[1], z.shape[0]) if None
_style -- A 'style-sheet' to use if desired (a default one will be used
if 'default'). If None, then no style will be imposed.
palette -- A string for a palette previously saved in a file (see write_palette)
or an array specifying the red-green-blue values (2-d array N x 3) or
gray-scale values (2-d array N x 1 or 1-d array).
zlabel -- The label to attach to the colorbar (font, fontsize, and color
match this).
color -- The color to use for the ticks and frame.
"""
if xryr is None:
xryr = (0,0,z.shape[1],z.shape[0])
if not _hold:
gist.fma()
gist.animate(0)
if _style is not None:
if _style == 'default':
_style=os.path.join(_user_path,"colorbar.gs")
system = write_style.getsys(hticpos='below',vticpos='left',frame=1,color=color)
fid = open(_style,'w')
fid.write(write_style.style2string(system))
fid.close()
gist.window(style=_style)
_current_style=_style
if cmax is None:
cmax = max(ravel(z))
if cmin is None:
cmin = min(ravel(z))
cmax = float(cmax)
cmin = float(cmin)
change_palette(palette)
byteimage = gist.bytscl(z,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xryr[0],xryr[1],xryr[2],xryr[3])
colorbar.color_bar(cmin,cmax,ncol=240,zlabel=zlabel,font=font,fontsize=fontsize,color=color)
def imagesc_cb(z,cmin=None,cmax=None,xryr=None,_style='default',
zlabel=None,font='helvetica',fontsize=16,color='black',
palette=None):
"""Plot an image on axes with a colorbar on the side.
z -- The data
cmin -- Value to map to lowest color in palette (min(z) if None)
cmax -- Value to map to highest color in palette (max(z) if None)
xryr -- (xmin, ymin, xmax, ymax) coordinates to print
(0, 0, z.shape[1], z.shape[0]) if None
_style -- A 'style-sheet' to use if desired (a default one will be used
if 'default'). If None, then no style will be imposed.
palette -- A string for a palette previously saved in a file (see write_palette)
or an array specifying the red-green-blue values (2-d array N x 3) or
gray-scale values (2-d array N x 1 or 1-d array).
zlabel -- The label to attach to the colorbar (font, fontsize, and color
match this).
color -- The color to use for the ticks and frame.
"""
if xryr is None:
xryr = (0,0,z.shape[1],z.shape[0])
if not _hold:
gist.fma()
gist.animate(0)
if _style is not None:
if _style == 'default':
_style=os.path.join(_user_path,"colorbar.gs")
system = write_style.getsys(hticpos='below',vticpos='left',frame=1,color=color)
fid = open(_style,'w')
fid.write(write_style.style2string(system))
fid.close()
gist.window(style=_style)
_current_style=_style
if cmax is None:
cmax = max(ravel(z))
if cmin is None:
cmin = min(ravel(z))
cmax = float(cmax)
cmin = float(cmin)
change_palette(palette)
byteimage = gist.bytscl(z,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xryr[0],xryr[1],xryr[2],xryr[3])
colorbar.color_bar(cmin,cmax,ncol=240,zlabel=zlabel,font=font,fontsize=fontsize,color=color)
def getFocusCents(zernlist={3: 1.},
nact=9,
readnoise=10.,
usePoisson=1,
sig=500. / 64,
plot=0,
fullpupil=0):
"""Compute centroids that would be obtained for a focus zernike term.
zernlist can also be a phasescreen...
"""
import util.zernikeMod, util.centroid, util.tel
nphs = (nact - 1) * 8
pupil = util.tel.Pupil(nphs, nphs / 2, 0)
if fullpupil:
pupil.fn[:] = 1
avphase = numpy.zeros((nact - 1, nact - 1), numpy.float64)
if type(zernlist) == numpy.ndarray:
phase = zernlist
else:
zern = util.zernikeMod.Zernike(pupil, max(zernlist.keys()) + 1)
phase = numpy.zeros((nphs, nphs), "d")
for key in zernlist.keys():
phase += zernlist[key] * zern.zern[key] #focus zernike
for i in range(nact - 1):
for j in range(nact - 1):
avphase[i, j] = numpy.average(
numpy.array(phase[i * 8:i * 8 + 8, j * 8:j * 8 + 8].flat))
c = util.centroid.centroid(nact - 1,
pupil.fn,
readnoise=readnoise,
addPoisson=usePoisson,
readbg=0.,
sig=sig)
c.printmax = 1
cents = c.calc(phase)
if plot:
print "Max counts: %g, max, min per subap %g %g, plotting SHS image..." % (
max(c.tile.flat), max(c.photPerSubap.flat), min(
c.photPerSubap.flat))
gist.fma()
gist.pli(c.tile)
#cents=util.centroid.calc(phase,8,pupil.fn)
return c, phase, avphase
def matview(A,cmax=None,cmin=None,palette=None,color='black'):
"""Plot an image of a matrix.
"""
A = Numeric.asarray(A)
if A.dtype.char in ['D','F']:
print "Warning: complex array given, plotting magnitude."
A = abs(A)
M,N = A.shape
A = A[::-1,:]
if cmax is None:
cmax = max(ravel(A))
if cmin is None:
cmin = min(ravel(A))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(A,cmin=cmin,cmax=cmax)
change_palette(palette)
gist.window(style='nobox.gs')
_current_style='nobox.gs'
gist.pli(byteimage)
old_vals = gist.limits(square=1)
vals = gist.limits(square=1)
if color is None:
return
vp = gist.viewport()
axv,bxv,ayv,byv = vp
axs,bxs,ays,bys = vals[:4]
# bottom left corner column
posy = -ays*(byv-ayv)/(bys-ays) + ayv
posx = -axs*(bxv-axv)/(bxs-axs) + axv
gist.plt('b',posx,posy-0.005,justify='LT',color=color)
# bottom left corner row
gist.plt(str(M),posx-0.005,posy,justify='RB',color=color)
# top left corner row
posy = (M-ays)*(byv-ayv)/(bys-ays) + ayv
gist.plt('b',posx-0.005,posy,justify='RT',color=color)
# bottom right column
posy = -ays*(byv-ayv)/(bys-ays) + ayv
posx = (N-axs)*(bxv-axv)/(bxs-axs) + axv
gist.plt(str(N),posx,posy-0.005,justify='RT',color=color)
def matview(A,cmax=None,cmin=None,palette=None,color='black'):
"""Plot an image of a matrix.
"""
A = numpy.asarray(A)
if A.dtype.char in ['D','F']:
print "Warning: complex array given, plotting magnitude."
A = abs(A)
M,N = A.shape
A = A[::-1,:]
if cmax is None:
cmax = max(ravel(A))
if cmin is None:
cmin = min(ravel(A))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(A,cmin=cmin,cmax=cmax)
change_palette(palette)
gist.window(style='nobox.gs')
_current_style='nobox.gs'
gist.pli(byteimage)
old_vals = gist.limits(square=1)
vals = gist.limits(square=1)
if color is None:
return
vp = gist.viewport()
axv,bxv,ayv,byv = vp
axs,bxs,ays,bys = vals[:4]
# bottom left corner column
posy = -ays*(byv-ayv)/(bys-ays) + ayv
posx = -axs*(bxv-axv)/(bxs-axs) + axv
gist.plt('b',posx,posy-0.005,justify='LT',color=color)
# bottom left corner row
gist.plt(str(M),posx-0.005,posy,justify='RB',color=color)
# top left corner row
posy = (M-ays)*(byv-ayv)/(bys-ays) + ayv
gist.plt('b',posx-0.005,posy,justify='RT',color=color)
# bottom right column
posy = -ays*(byv-ayv)/(bys-ays) + ayv
posx = (N-axs)*(bxv-axv)/(bxs-axs) + axv
gist.plt(str(N),posx,posy-0.005,justify='RT',color=color)
def handle(self, data):
"""Handle data returned from the simulation"""
if data[1] == "warning" or data[1] == "error":
print "Error retrieving data", data[1:], data[0]
elif len(self.gettype()) == 0: #not doing anything with it...
pass
else:
if self.when[:3] != "rpt" or self.repeating == 1: #still expecting data
if self.ret != None and data[3].has_key(self.ret):
data = data[3][self.ret]
else:
data = None
ret = self.ret
if ret == None:
ret = "None"
if self.button == None:
d = {ret: data, "button": None}
else:
d = {ret: data, "button": self.button[0]}
try:
exec self.preprocess in d
except:
pass
if self.button != None:
self.button[0] = d["button"]
data = d[ret]
dim = self.dim
xaxis = self.xaxis
if dim == None:
if type(data) == numpy.ndarray:
if len(data.shape) > 1:
dim = 2
elif len(data.shape) == 1:
dim = 1
else:
dim = 0
else:
dim = 0
if dim == 1:
if type(self.xaxis) == types.NoneType:
if len(data.shape) > 1:
xaxis = data[0]
data = data[1:]
else:
xaxis = numpy.arange(data.shape[0])
data = data
else:
if type(self.xaxis) == types.StringType:
xaxis = eval(self.xaxis)
if self.gisttype:
if type(data) == numpy.ndarray:
if not self.info.has_key("window"):
self.info["window"] = 0
if not self.info.has_key("palette"):
self.info["palette"] = "gray.gp"
if not self.info.has_key("gistdpi"):
self.info["gistdpi"] = 75
if self.gistWindow == None:
self.gistWindow = gist.window(
self.info["window"],
wait=1,
dpi=self.info["gistdpi"])
gist.animate(0)
gist.animate(1)
gist.palette(self.info["palette"])
else:
gist.window(self.gistWindow)
#gist.fma()
if dim == 1:
for i in range(data.shape[0]):
gist.plg(data[i], xaxis)
else:
gist.pli(data)
gist.fma()
else:
print "Cannot display type %s with gist" % str(
type(data))
if self.pylabtype:
if type(data) == numpy.ndarray:
if not self.info.has_key("palette"):
self.info["palette"] = "gray"
if not self.info.has_key("interp"):
self.info["interp"] = "nearest"
if not self.info.has_key("plotwin"):
self.info["plotwin"] = mypylab.plot()
p = self.info["plotwin"]
p.win.set_title(self.title)
p.newPalette(self.info["palette"])
p.newInterpolation(self.info["interp"])
p.deactivatefn = self.cancel #deactivate
p = self.info["plotwin"]
if dim == 1:
p.dims = 1
axis = xaxis
else:
p.dims = 2
axis = None
if p.active:
p.plot(data, axis=axis)
else:
if self.button != None:
self.button[0] = 0
#print "Not expecting this data any more... (simdata.handle, type=pylab)"
self.repeating = 0
else:
print "Cannot display type %s with pylab" % str(
type(data))
if self.texttype:
#self.info["texttype"]=="ownwindow, mainwindow", default own
#self.info["replace"]==1 or 0, default 0
if not self.info.has_key("wintype"):
self.info["wintype"] = "ownwindow"
if not self.info.has_key("textreplace"):
self.info["textreplace"] = 0
if self.info["wintype"] == "ownwindow":
if self.textWindow == None:
self.textWindow = textbox(self.title)
self.textWindow.closeFunc = self.cancel #deactivate
if self.textWindow.destroyed == 0:
#print "adding text",str(data)
self.textWindow.addText(
str(data) + "\n",
replace=self.info["textreplace"])
else: #tell simulation not to send...
print "Not expecting this data any more... (simdata.handle, type=text)"
self.textWindow = None
self.repeating = 0
else:
print str(data)
if self.savetype:
if not self.info.has_key("filetype"):
self.info["filetype"] = "fits"
if not self.info.has_key("filename"):
self.info["filename"] = "tmp.fits"
if not self.info.has_key("filereplace"):
self.info["filereplace"] = 0
if self.info["filetype"] == "fits":
if type(data) == numpy.ndarray:
print "WARNING - depreciated - use util.FITS instead (code needs updating)"
if self.info["filereplace"]:
imghdu = util.pyfits.PrimaryHDU(
numarray.array(data))
imghdu.header.update("DATE", time.asctime())
imghdu.header.update("USER",
os.environ["USER"])
imghdu.header.update(
"CREATOR", "simctrl.py simulation control")
imghdu.header.update("TITLE", str(self.title))
imghdu.header.update("COMMAND", str(self.cmd))
imghdu.header.update("RETURN", str(self.ret))
imghdu.header.update("TYPE", self.gettype())
imghdu.header.update("PREPROC",
str(self.preprocess))
imghdu.header.update("DIMS", str(self.dim))
imghdu.header.update("XAXIS", str(self.xaxis))
imghdu.header.update("WHEN", str(self.when))
imghdu.header.update("INFO", str(self.info))
hdulist = util.pyfits.HDUList([imghdu])
hdulist.writeto(self.info["filename"],
clobber=True)
else:
f = util.pyfits.open(self.info["filename"],
mode="update")
imghdu = util.pyfits.ImageHDU(
numarray.array(data))
imghdu.header.update("DATE", time.asctime())
imghdu.header.update("USER",
os.environ["USER"])
imghdu.header.update(
"CREATOR", "simctrl.py simulation control")
imghdu.header.update("TITLE", str(self.title))
imghdu.header.update("COMMAND", str(self.cmd))
imghdu.header.update("RETURN", str(self.ret))
imghdu.header.update("TYPE", self.gettype())
imghdu.header.update("PREPROC",
str(self.preprocess))
imghdu.header.update("DIMS", str(self.dim))
imghdu.header.update("XAXIS", str(self.xaxis))
imghdu.header.update("WHEN", str(self.when))
imghdu.header.update("INFO", str(self.info))
f.append(imghdu)
f.close()
else:
print "Cannot save fits data of this format:", type(
data)
elif self.info["filetype"] == "csv":
if self.info["filereplace"]:
mode = "w"
else:
mode = "a"
f = open(self.info["filename"], mode)
f.write(
"#Date\t%s\n#User\t%s\n#Creator\tsimctrl.py simulation control\n#Title\t%s\n#Command\t%s\n#Return\t%s\n#Type\t%s\n#Preprocess\t%s\n#Dims\t%s\n#Xaxis\t%s\n#When\t%s\n#Info\t%s\n"
% (time.asctime(), os.environ["USER"],
str(self.title), str(self.cmd), str(self.ret),
self.gettype(), str(self.preprocess),
str(self.dim), str(self.xaxis), str(
self.when), str(self.info)))
if dim == 1:
try:
for i in range(xaxis.shape[0]):
f.write("%g" % float(xaxis[i]))
for j in range(data.shape[0]):
f.write("\t%g" % float(data[j][i]))
f.write("\n")
f.write("\n")
except:
print "Data not in correct 1D format - can't save as csv"
f.write(str(data))
f.write("\n\n")
else:
print "Can't save 2D data as csv... using text instead"
f.write(str(data))
f.write("\n\n")
f.close()
elif self.info["filetype"] == "text":
if self.info["filereplace"]:
mode = "w"
else:
mode = "a"
f = open(self.info["filename"], mode)
f.write(
"#Date\t%s\n#User\t%s\n#Creator\tsimctrl.py simulation control\n#Title\t%s\n#Command\t%s\n#Return\t%s\n#Type\t%s\n#Preprocess\t%s\n#Dims\t%s\n#Xaxis\t%s\n#When\t%s\n#Info\t%s\n"
% (time.asctime(), os.environ["USER"],
str(self.title), str(self.cmd), str(self.ret),
self.gettype(), str(self.preprocess),
str(self.dim), str(self.xaxis), str(
self.when), str(self.info)))
f.write(str(data))
f.write("\n\n")
f.close()
else:
print "Unrecognised filetype - not saving"
if self.feedbacktype:
try:
d = {"feedback": data}
exec self.info["feedbackmsg"] in d
msg = d["msg"]
except:
msg = "Feedback data:" + str(data)
print msg
exec self.post
else:
print "Warning: No longer expecting data for", self.cmd
def plotImg(img):
import gist
im=img[256*256:]
im.shape=128,128
gist.fma()
gist.pli(im)
spotpsf=numpy.zeros((fftsize,fftsize),"f")
spotpsf[fftsize/2-5:fftsize/2+5,fftsize/2-5:fftsize/2+5]=1
spotpsf[fftsize/2-7:fftsize/2-3,fftsize/2-7:fftsize/2-3]=1
spotpsf[fftsize/2+3:fftsize/2+7,fftsize/2+3:fftsize/2+7]=1
elif spotpsfdim==4:
spotpsf=numpy.zeros((nsubx,nsubx,fftsize,fftsize),"f")
spotpsf[:,:,fftsize/2-5:fftsize/2+5,fftsize/2-5:fftsize/2+5]=1
spotpsf[:,:,fftsize/2-7:fftsize/2-3,fftsize/2-7:fftsize/2-3]=1
spotpsf[:,:,fftsize/2+3:fftsize/2+7,fftsize/2+3:fftsize/2+7]=1
spotpsf[2,2,fftsize/2-4:fftsize/2+4,fftsize/2-4:fftsize/2+4]=0
#spotpsf[2,2]=0.
else:
spotpsf=None
if type(sig)==numpy.ArrayType:
sig=sig.flat
bimg=numpy.zeros((nsubx,nsubx,nimg,nimg),numpy.float32)
print "Initialising"
cc=util.centcmod.centcmod(nthreads,nsubx,ncen,fftsize,nimg,phasesize,readnoise,readbg,addPoisson,noiseFloor,sig,skybrightness,calsource,pxlPower,nintegrations,seed,reorderedPhs,pup,spotpsf,cents,bimg)
print "Running"
t=cc.run(calsource)
print "Time taken",t
def makeImage(bimg):
img=numpy.zeros((nsubx*nimg,nsubx*nimg),numpy.float32)
for i in range(nsubx):
for j in range(nsubx):
img[i*nimg:(i+1)*nimg,j*nimg:(j+1)*nimg]=bimg[i,j]
return img
gist.fma();gist.pli(makeImage(bimg))
import gist def plot_cross(x,y,sz=1,color='red'): gist.pldj([x],[y-sz],[x],[y+sz],color=color) gist.pldj([x-sz],[y],[x+sz],[y],color=color) file=os.path.join(os.path.dirname(__file__),'ascam1_20080710T230802.fits') data=pyfits.open(file)[0].data z=data[686-4-1-5-5:686+4-1+5-5,711-4-1-1-5:711+4-1-1+5] ##z=numpy.flipud(z) ana=iqe(z) gist.fma() gist.pli(z) plot_cross(ana[0]+.5,ana[1]+.5) ## sub-image Z = z[10:18,6:14].copy() ana=iqe(Z) gist.fma() gist.pli(Z) plot_cross(ana[0]+.5,ana[1]+.5) ## add hotspot Z = z[10:18,6:14].copy() Z[3,2]=10.*Z.max() anah=iqe(Z) gist.fma() gist.pli(Z)
def doit(zernlist=None,
nact=9,
cents=None,
avphase=None,
readnoise=10.,
usePoisson=1,
sig=1000.,
fullpupil=0,
monteNoiseCovariance=0,
phaseCov="bccb",
diagonaliseinvChatReordered=1,
diagonaliseA=0.5,
useChatFromDiagonalisedA=1,
oversampleFFT=0,
fft2d=1,
oversampleAndBinFFTofr=0,
removeHiFreqZ=0,
removeHiFreqP=0,
removeHiFreqX=0,
convToPxl=1):
"""Create a zernike mode and get the centroids for this. Put these centroids into the PCG algorithm, and recreate the phase, and then compare with the original input phase
defaultOptions are:
diagonaliseinvChatReordered:1#should we diagonlise C-1, or use whole MX?
diagonaliseA:0#should we diagonalise A or use the whole MX.
useChatFromDiagonalisedA:1#should we compute invChat using a diagonalised chat or not?
zernlist can be a dict of zernikes eg {3:1} would be focus, amplitude 1...
or it can be the phase, or it can be none (in which case a phasescreen is
created).
This now seems to be working fairly well, iterates to an exact solution after about 10 iters, and 4-5 should be sufficient for a good solution.
"""
options = {
"diagonaliseinvChatReordered": diagonaliseinvChatReordered,
"diagonaliseA": diagonaliseA,
"useChatFromDiagonalisedA": useChatFromDiagonalisedA,
"oversampleFFT": oversampleFFT,
"2dfft": fft2d,
"oversampleAndBinFFTofr": oversampleAndBinFFTofr,
"removeHiFreqZ": removeHiFreqZ,
"removeHiFreqP": removeHiFreqP,
"removeHiFreqX": removeHiFreqX
}
gist.window(0)
gist.palette("gray.gp")
pupfn = util.tel.Pupil(nact - 1, (nact - 1) / 2., 0).fn
actfn = util.tel.Pupil(nact, nact / 2., 0).fn
noiseCov = None
if type(cents) == type(None):
if type(zernlist) in [type(1), type(1.)]:
zernlist = {zernlist: 1.}
elif type(zernlist) == type([]):
tmp = {}
for i in zernlist:
tmp[i] = 1.
zernlist = tmp
elif type(zernlist) == type(None):
zernlist = science.infScrn.makeInitialScreen(dpix=(nact - 1) * 8,
Dtel=4.2,
L0=30.,
scrnXPxls=None,
scrnYPxls=None,
seed=None,
tstep=0.05,
globR0=0.2,
strLayer=1.,
natype=numpy.float64,
windDirection=0.,
vWind=10.)[:-1,
1:].copy()
c, phase, avphase = getFocusCents(zernlist,
nact=nact,
readnoise=readnoise,
usePoisson=usePoisson,
sig=sig,
plot=1,
fullpupil=fullpupil)
print phase.shape
cents = c.cent
if monteNoiseCovariance:
noiseCov = c.computeNoiseCovariance(20, convertToRad=1)
if convToPxl: #convert from radians to pixel values for the noises...
radToPxlFactor = 1. / c.convFactor**2
else:
radToPxlFactor = 1.
Pcg = testfull(fromdisk=0,
nact=nact,
pupfn=pupfn,
actfn=actfn,
fullpmx=1,
noiseCov=noiseCov,
phaseCov=phaseCov,
options=options,
radToPxlFactor=radToPxlFactor) #agbhome
Pcg.newCentroids(cents)
Pcg.initialise()
#now inverse A, multiply with b, to get the MVM reconstructed phase...
invA = numpy.linalg.inv(Pcg.A)
gist.fma()
gist.pli(invA)
raw_input("Displaying inverse of A... press return")
gist.fma()
gist.pli(phase)
raw_input("The phase... press a key")
recphase = quick.dot(invA, Pcg.b)
print "Reconstructed phase min/max:", min(recphase.flat), max(
recphase.flat)
recphase.shape = (9, 9)
gist.window(4)
gist.palette("gray.gp")
gist.fma()
gist.pli(recphase)
gist.palette("gray.gp")
gist.window(0)
chires = numpy.zeros((100, ), "d")
#also compute what a traditional MVM with pokemx would give...
#invpokemx=numpy.linalg.pinv(Pcg.pokemx)#same as generalised_inverse
#pmphase=quick.dot(invpokemx,cents)
print "Press return for next iteration or key+return to quit"
#gist.fma()
#gist.pli(numpy.reshape(pmphase,(nact,nact)))
if type(avphase) != type(None):
print "press a key"
raw_input()
gist.fma()
gist.pli(avphase)
actphase = phase2acts(avphase)
actphase -= numpy.average(actphase.flat) #remove piston
smallpupfn = util.tel.Pupil(nact, nact / 2. - 2, 0).fn
raw_input("press return (min, max actphase is %g %g" %
(min(actphase.flat), max(actphase.flat)))
gist.fma()
gist.pli(actphase)
gist.window(1)
gist.palette("gray.gp")
gist.window(2)
gist.palette("gray.gp")
niter = 0
while len(raw_input()) == 0:
niter += 1
gist.window(1)
gist.fma()
img = numpy.reshape(Pcg.x.real, (nact, nact))
gist.pli(img)
gist.window(2)
gist.fma()
img = smallpupfn * img
#gist.pli(numpy.where(img==0,min(img.flat),img))
gist.pli(numpy.reshape(Pcg.p, (nact, nact)))
gist.window(3)
gist.fma()
fftimg = numpy.fft.fft2(numpy.reshape(Pcg.x, (nact, nact)))
gist.pli(fftimg.real)
Pcg.nextIter()
chirespos = niter - 1
if chirespos > 99:
chirespos = 99
chires[chirespos] = chi2(Pcg.x, recphase,
scale=0) #changed from actphase
Pcg.alphaHist[chirespos] = Pcg.alpha
Pcg.betaHist[chirespos] = Pcg.beta
Pcg.tolerance[chirespos] = max(numpy.fabs(Pcg.xprev - Pcg.x))
print niter, Pcg.tolerance[chirespos], chires[chirespos], min(
Pcg.x.real), max(Pcg.x.real), min(Pcg.p), max(
Pcg.p), Pcg.alphaHist[chirespos], Pcg.betaHist[chirespos]
print "Press return for next iteration or key+return to quit"
gist.fma()
gist.plg(chires[:chirespos])
gist.window(2)
gist.fma()
gist.plg(Pcg.tolerance[:niter])
gist.window(0)
return Pcg, actphase, phase, recphase, c
def twoplane(DATA,slice1,slice2,dx=[1,1,1],cmin=None,cmax=None,xb=None,xe=None,
xlab="",ylab="",zlab="",clab="",titl="",
totalheight=0.5,space=0.02, medfilt=5,
font='helvetica',fontsize=16,color='black',lcolor='white',
fcolor='black', cb=1, line=1, palette=None):
""" Visualize a 3d volume as a two connected slices. The slices are
given in the 2-tuple slice1 and slice2.
These give the dimension and corresponding slice numbers to plot.
The unchosen slice is the common dimension in the images.
twoplane(img3d,(0,12),(2,60)) plots two images with a common "x"-axis
as the first dimension. The lower plot is img3d[12,:,:] with a line
through row 60 corresponding to the slice transpose(img3d[:,:,60])
plotted above this first plot.
"""
if xb is None:
xb = [0,0,0]
if xe is None:
xe = DATA.shape
# get two image slices
# make special style file so that pixels are square
getdx = array([1,1,1])
imgsl1 = [slice(None,None),slice(None,None),slice(None,None)]
imgsl1[slice1[0]] = slice1[1]
img1 = DATA[imgsl1]
getdx1 = getdx.__copy__()
getdx1[slice1[0]] = 0
dx1 = compress(getdx1,dx,axis=-1)
xb1 = compress(getdx1,xb,axis=-1)
xe1 = compress(getdx1,xe,axis=-1)
imgsl2 = [slice(None,None),slice(None,None),slice(None,None)]
imgsl2[slice2[0]] = slice2[1]
img2 = DATA[imgsl2]
getdx2 = getdx.__copy__()
getdx2[slice2[0]] = 0
dx2 = compress(getdx2,dx,axis=-1)
xb2 = compress(getdx2,xb,axis=-1)
xe2 = compress(getdx2,xe,axis=-1)
if (slice1[0] == slice2[0]):
raise ValueError, "Same slice dimension.."
for k in range(3):
if k not in [slice1[0],slice2[0]]:
samedim = k
break
if samedim == 2:
pass
elif samedim == 1:
if samedim > slice1[0]:
img1 = transpose(img1)
dx1 = dx1[::-1]
xb1 = xb1[::-1]
xe1 = xe1[::-1]
if samedim > slice2[0]:
img2 = transpose(img2)
dx2 = dx2[::-1]
xb2 = xb2[::-1]
xe2 = xe2[::-1]
else:
img1 = transpose(img1)
dx1 = dx1[::-1]
xb1 = xb1[::-1]
xe1 = xe1[::-1]
img2 = transpose(img2)
dx2 = dx2[::-1]
xb2 = xb2[::-1]
xe2 = xe2[::-1]
assert(img1.shape[1] == img2.shape[1])
units = totalheight - space
totaldist = img1.shape[0]*dx1[0] + img2.shape[0]*dx2[0]
convfactor = units / float(totaldist)
height1 = img1.shape[0]*dx1[0] * convfactor
xwidth = img1.shape[1]*dx1[1]*convfactor
if xwidth > 0.6:
rescale = 0.6 / xwidth
xwidth = rescale * xwidth
height1 = rescale * height1
totalheight = totalheight * rescale
print xwidth, height1
else:
print xwidth
ystart = 0.5 - totalheight / 2
ypos1 = [ystart, ystart+height1]
ypos2 = [ystart+height1+space,ystart+totalheight]
xpos = [0.395-xwidth/2.0, 0.395+xwidth/2.0]
systems = []
system = write_style.getsys(hticpos='', vticpos='left')
system['viewport'] = [xpos[0],xpos[1],ypos2[0],ypos2[1]]
if fcolor not in ['black',None]:
_add_color(system, _colornum[color])
systems.append(system)
system = write_style.getsys(hticpos='below', vticpos='left')
system['viewport'] = [xpos[0],xpos[1],ypos1[0],ypos1[1]]
if fcolor not in ['black',None]:
_add_color(system, _colornum[color])
systems.append(system)
the_style = os.path.join(_user_path,"two-plane.gs")
write_style.writestyle(the_style,systems)
gist.window(style=the_style)
_current_style = the_style
change_palette(palette)
gist.plsys(1)
if medfilt > 1:
img1 = signal.medfilt(img1,[medfilt,medfilt])
img2 = signal.medfilt(img2,[medfilt,medfilt])
if cmax is None:
cmax = max(max(ravel(img1)),max(ravel(img2)))
if cmin is None:
cmin = min(min(ravel(img1)),min(ravel(img2)))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(img2,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xb2[1],xb2[0],xe2[1],xe2[0])
ylabel(zlab,color=color)
if titl != "":
title(titl,color=color)
if line:
xstart = xb2[1]
xstop = xe2[1]
yval = slice1[1]*(xe2[0] - xb2[0])/(img2.shape[0]) + xb2[0]
gist.pldj([xstart],[yval],[xstop],[yval],type='dash',width=2,color='white')
gist.plsys(2)
ylabel(ylab,color=color)
xlabel(xlab,color=color)
byteimage = gist.bytscl(img1,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xb1[1],xb1[0],xe1[1],xe1[0])
if line:
xstart = xb1[1]
xstop = xe1[1]
yval = slice2[1]*(xe1[0] - xb1[0])/(img1.shape[0]) + xb1[0]
gist.pldj([xstart],[yval],[xstop],[yval],type='dash',width=2,color='white')
if cb:
colorbar.color_bar(cmin,cmax,ncol=240,zlabel=clab,font=font,fontsize=fontsize,color=color,ymin=ystart,ymax=ystart+totalheight,xmin0=xpos[1]+0.02,xmax0=xpos[1]+0.04)
def twoplane(DATA,slice1,slice2,dx=[1,1,1],cmin=None,cmax=None,xb=None,xe=None,
xlab="",ylab="",zlab="",clab="",titl="",
totalheight=0.5,space=0.02, medfilt=5,
font='helvetica',fontsize=16,color='black',lcolor='white',
fcolor='black', cb=1, line=1, palette=None):
""" Visualize a 3d volume as a two connected slices. The slices are
given in the 2-tuple slice1 and slice2.
These give the dimension and corresponding slice numbers to plot.
The unchosen slice is the common dimension in the images.
twoplane(img3d,(0,12),(2,60)) plots two images with a common "x"-axis
as the first dimension. The lower plot is img3d[12,:,:] with a line
through row 60 corresponding to the slice transpose(img3d[:,:,60])
plotted above this first plot.
"""
if xb is None:
xb = [0,0,0]
if xe is None:
xe = DATA.shape
# get two image slices
# make special style file so that pixels are square
getdx = array([1,1,1])
imgsl1 = [slice(None,None),slice(None,None),slice(None,None)]
imgsl1[slice1[0]] = slice1[1]
img1 = DATA[imgsl1]
getdx1 = getdx.__copy__()
getdx1[slice1[0]] = 0
dx1 = compress(getdx1,dx,axis=-1)
xb1 = compress(getdx1,xb,axis=-1)
xe1 = compress(getdx1,xe,axis=-1)
imgsl2 = [slice(None,None),slice(None,None),slice(None,None)]
imgsl2[slice2[0]] = slice2[1]
img2 = DATA[imgsl2]
getdx2 = getdx.__copy__()
getdx2[slice2[0]] = 0
dx2 = compress(getdx2,dx,axis=-1)
xb2 = compress(getdx2,xb,axis=-1)
xe2 = compress(getdx2,xe,axis=-1)
if (slice1[0] == slice2[0]):
raise ValueError, "Same slice dimension.."
for k in range(3):
if k not in [slice1[0],slice2[0]]:
samedim = k
break
if samedim == 2:
pass
elif samedim == 1:
if samedim > slice1[0]:
img1 = transpose(img1)
dx1 = dx1[::-1]
xb1 = xb1[::-1]
xe1 = xe1[::-1]
if samedim > slice2[0]:
img2 = transpose(img2)
dx2 = dx2[::-1]
xb2 = xb2[::-1]
xe2 = xe2[::-1]
else:
img1 = transpose(img1)
dx1 = dx1[::-1]
xb1 = xb1[::-1]
xe1 = xe1[::-1]
img2 = transpose(img2)
dx2 = dx2[::-1]
xb2 = xb2[::-1]
xe2 = xe2[::-1]
assert(img1.shape[1] == img2.shape[1])
units = totalheight - space
totaldist = img1.shape[0]*dx1[0] + img2.shape[0]*dx2[0]
convfactor = units / float(totaldist)
height1 = img1.shape[0]*dx1[0] * convfactor
xwidth = img1.shape[1]*dx1[1]*convfactor
if xwidth > 0.6:
rescale = 0.6 / xwidth
xwidth = rescale * xwidth
height1 = rescale * height1
totalheight = totalheight * rescale
print xwidth, height1
else:
print xwidth
ystart = 0.5 - totalheight / 2
ypos1 = [ystart, ystart+height1]
ypos2 = [ystart+height1+space,ystart+totalheight]
xpos = [0.395-xwidth/2.0, 0.395+xwidth/2.0]
systems = []
system = write_style.getsys(hticpos='', vticpos='left')
system['viewport'] = [xpos[0],xpos[1],ypos2[0],ypos2[1]]
if fcolor not in ['black',None]:
_add_color(system, _colornum[color])
systems.append(system)
system = write_style.getsys(hticpos='below', vticpos='left')
system['viewport'] = [xpos[0],xpos[1],ypos1[0],ypos1[1]]
if fcolor not in ['black',None]:
_add_color(system, _colornum[color])
systems.append(system)
the_style = os.path.join(_user_path,"two-plane.gs")
write_style.writestyle(the_style,systems)
gist.window(style=the_style)
_current_style = the_style
change_palette(palette)
gist.plsys(1)
if medfilt > 1:
import scipy.signal
img1 = scipy.signal.medfilt(img1,[medfilt,medfilt])
img2 = scipy.signal.medfilt(img2,[medfilt,medfilt])
if cmax is None:
cmax = max(max(ravel(img1)),max(ravel(img2)))
if cmin is None:
cmin = min(min(ravel(img1)),min(ravel(img2)))
cmax = float(cmax)
cmin = float(cmin)
byteimage = gist.bytscl(img2,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xb2[1],xb2[0],xe2[1],xe2[0])
ylabel(zlab,color=color)
if titl != "":
title(titl,color=color)
if line:
xstart = xb2[1]
xstop = xe2[1]
yval = slice1[1]*(xe2[0] - xb2[0])/(img2.shape[0]) + xb2[0]
gist.pldj([xstart],[yval],[xstop],[yval],type='dash',width=2,color='white')
gist.plsys(2)
ylabel(ylab,color=color)
xlabel(xlab,color=color)
byteimage = gist.bytscl(img1,cmin=cmin,cmax=cmax)
gist.pli(byteimage,xb1[1],xb1[0],xe1[1],xe1[0])
if line:
xstart = xb1[1]
xstop = xe1[1]
yval = slice2[1]*(xe1[0] - xb1[0])/(img1.shape[0]) + xb1[0]
gist.pldj([xstart],[yval],[xstop],[yval],type='dash',width=2,color='white')
if cb:
colorbar.color_bar(cmin,cmax,ncol=240,zlabel=clab,font=font,fontsize=fontsize,color=color,ymin=ystart,ymax=ystart+totalheight,xmin0=xpos[1]+0.02,xmax0=xpos[1]+0.04)