Skip to content

Commit

Permalink
docstring
Browse files Browse the repository at this point in the history
  • Loading branch information
@julienguy
julienguy committed Nov 13, 2020
1 parent ffd2934 commit 627e3f8
Showing 1 changed file with 99 additions and 16 deletions.
115 changes: 99 additions & 16 deletions bin/desi_focus
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,16 @@ RPIXSCALE=2048.

def fit_centroid_barycenter(stamp):
"""
fit the centroid of a 2D image square stamp of size (2*hw+1,2*hw+1)
Fit the centroid of a 2D image square stamp of size (2*hw+1,2*hw+1)
in a coordinate system centered on the stamp, i.e. the central pixel has coordinates = (0,0)
Args:
stamp: 2D numpy array image centered on a spot
Returns:
xc: float, center of spot x coordinate (axis=1 for numpy 2D arrays)
yc: float, center of spot y coordinate (axis=0 for numpy 2D arrays)
flux: float, counts in stamp
"""

hw=stamp.shape[0]//2
Expand All @@ -43,29 +51,74 @@ def fit_centroid_barycenter(stamp):
xc=np.sum(x1d*np.sum(stamp,axis=0))/norm
yc=np.sum(x1d*np.sum(stamp,axis=1))/norm

# uncertainties, made up for now ...
xe=1.
ye=1.

return xc,yc,xe,ye,norm
return xc,yc,norm


def psf(i0,i1,xc,yc,sigma):
"""
Returns the integral of a Gaussian PSF in a pixel
Args:
i0: pixel index along axis=0 (y)
i1: pixel index along axis=1 (x)
xc: float, center of spot x coordinate (axis=1 for numpy 2D arrays)
yc: float, center of spot y coordinate (axis=0 for numpy 2D arrays)
sigma: float, sigma of Gaussian in units of pixel
Returns:
float, integral of a Gaussian PSF in the pixel
"""
a=1/(np.sqrt(2)*sigma)
return 0.25*(erf(a*(i1+0.5-xc))-erf(a*(i1-0.5-xc)))*(erf(a*(i0+0.5-yc))-erf(a*(i0-0.5-yc)))

def dpsfdxc(i0,i1,xc,yc,sigma):
"""
Returns the derivative of the integral of a Gaussian PSF in a pixel with respect to xc
Args:
i0: pixel index along axis=0 (y)
i1: pixel index along axis=1 (x)
xc: float, center of spot x coordinate (axis=1 for numpy 2D arrays)
yc: float, center of spot y coordinate (axis=0 for numpy 2D arrays)
sigma: float, sigma of Gaussian in units of pixel
Returns:
float, derivative integral of a Gaussian PSF in the pixel with respect to xc
"""
a=1/(np.sqrt(2)*sigma)
return -a*0.25*2/np.sqrt(np.pi)*(np.exp(-(a*(i1+0.5-xc))**2)-np.exp(-(a*(i1-0.5-xc))**2))*(erf(a*(i0+0.5-yc))-erf(a*(i0-0.5-yc)))

def dpsfdyc(i0,i1,xc,yc,sigma):
"""
Returns the derivative of the integral of a Gaussian PSF in a pixel with respect to yc
Args:
i0: pixel index along axis=0 (y)
i1: pixel index along axis=1 (x)
xc: float, center of spot x coordinate (axis=1 for numpy 2D arrays)
yc: float, center of spot y coordinate (axis=0 for numpy 2D arrays)
sigma: float, sigma of Gaussian in units of pixel
Returns:
float, derivative integral of a Gaussian PSF in the pixel with respect to yc
"""
a=1/(np.sqrt(2)*sigma)
return -a*0.25*2/np.sqrt(np.pi)*(erf(a*(i1+0.5-xc))-erf(a*(i1-0.5-xc)))*(np.exp(-(a*(i0+0.5-yc))**2)-np.exp(-(a*(i0-0.5-yc))**2))

def fit_centroid_gaussian(stamp,sigma=1.,noise=10.):
"""
fit the centroid of a 2D image square stamp of size (2*hw+1,2*hw+1)
Fit the centroid of a 2D image square stamp of size (2*hw+1,2*hw+1)
in a coordinate system centered on the stamp, i.e. the central pixel has coordinates = (0,0)
Args:
stamp: 2D numpy array image centered on a spot
sigma: float, sigma value for 2D Gaussian
noise: rms of noise in pixels (same unit as values in stamp)
Returns:
xc: float, center of spot x coordinate (axis=1 for numpy 2D arrays)
yc: float, center of spot y coordinate (axis=0 for numpy 2D arrays)
flux: float, counts in stamp
"""
# iterative gauss-newton fit
n0=stamp.shape[0]
Expand Down Expand Up @@ -102,23 +155,39 @@ def fit_centroid_gaussian(stamp,sigma=1.,noise=10.):
xc -= float(n1//2)
yc -= float(n0//2)

xe = noise * np.sqrt(Ai[1,1])
ye = noise * np.sqrt(Ai[2,2])

return xc,yc,xe,ye,flux
return xc,yc,flux

def fit_centroid(stamp,noise=10.):
"""
fit the centroid of a 2D image square stamp of size (2*hw+1,2*hw+1)
Fit the centroid of a 2D image square stamp of size (2*hw+1,2*hw+1)
in a coordinate system centered on the stamp, i.e. the central pixel has coordinates = (0,0)
Args:
stamp: 2D numpy array image centered on a spot
sigma: float, sigma value for 2D Gaussian
noise: rms of noise in pixels (same unit as values in stamp)
Returns:
xc: float, center of spot x coordinate (axis=1 for numpy 2D arrays)
yc: float, center of spot y coordinate (axis=0 for numpy 2D arrays)
flux: float, counts in stamp
"""

#return fit_centroid_gaussian(stamp,sigma=1.2,noise=noise)
return fit_centroid_barycenter(stamp)

def fit_gaussian_sigma(stamp,sigma=1.0,xc=0.,yc=0.) :
"""
fit gaussian sigma
Fit Gaussian sigma
Args:
stamp: 2D numpy array image centered on a spot
sigma: float, initial sigma value used to initialize the fit
xc: float, center of spot x coordinate (axis=1 for numpy 2D arrays)
yc: float, center of spot y coordinate (axis=0 for numpy 2D arrays)
Returns:
float, best fit sigma value
"""

assert(stamp.shape[0]%2==1) # odd
Expand All @@ -144,6 +213,17 @@ def fit_gaussian_sigma(stamp,sigma=1.0,xc=0.,yc=0.) :


def piston_and_tilt_to_gauge_offsets(camera_spectro,focus_plane_coefficients) :
"""
Computes gauge offsets to apply for a given best focus plane as a function of xccd and yccd
Args:
camera_spectro: str, camera identifier starting with b, r or z for NIR
focus_plane_coefficients: array with 3 values (c0,c1,c2), defining the best focus plane offsets: c0+c1*(xccd/2048-1)+c2*(yccd/2048-1) in microns
Returns:
dictionnary of offsets to apply, in mm, for the "TOP","LEFT" and "RIGHT" gauge
"""


c=camera_spectro[0].upper()
if c=="B" :
Expand Down Expand Up @@ -191,7 +271,10 @@ def piston_and_tilt_to_gauge_offsets(camera_spectro,focus_plane_coefficients) :
return best_focus_gauge_offset

def test_gauge_offsets() :
# copied from DESI-5084 https://desi.lbl.gov/DocDB/cgi-bin/private/RetrieveFile?docid=5084;filename=DESI_doc_5084_Spectrographs_Tests_Summary_Mayall.xlsx;version=1
"""
Test function
"""
# copied from DESI-5084 https://desi.lbl.gov/DocDB/cgi-bin/private/RetrieveFile?docid=5084;filename=DESI_doc_5084_Spectrographs_Tests_Summary_Mayall.xlsx;version=1

# BLUE RED NIR
# piston (mm) tilt/X(deg) tilt/Y(deg) piston (mm) tilt/X(deg) tilt/Y(deg) piston (mm) tilt/X(deg) tilt/Y(deg)
Expand Down Expand Up @@ -257,14 +340,14 @@ def test_gauge_offsets() :

def match_same_system(x1,y1,x2,y2,remove_duplicates=True) :
"""
match two catalogs, assuming the coordinates are in the same coordinate system (no transfo)
Match two catalogs, assuming the coordinates are in the same coordinate system (no transfo)
Args:
x1 : float numpy array of coordinates along first axis of cartesian coordinate system
y1 : float numpy array of coordinates along second axis in same system
x2 : float numpy array of coordinates along first axis in same system
y2 : float numpy array of coordinates along second axis in same system
returns:
Returns:
indices_2 : integer numpy array. if ii is a index array for entries in the first catalog,
indices_2[ii] is the index array of best matching entries in the second catalog.
(one should compare x1[ii] with x2[indices_2[ii]])
Expand Down

0 comments on commit 627e3f8

Please sign in to comment.