def outChannelMask(im, chAngle=0):
"""Creates a mask that excludes the channel
Parameters
----------
im: 2d array
The image
chAngle: number
The angle of the channel in radians
Returns
-------
mask: 2d array
the mask excluding the channel
Notes
-----
The channel should be clear(ish) on the image.
The angle should be aligned with the channel
"""
im=np.array(im,dtype='float32')
#Remove clear dust
mask=rmbg.backgroundMask(im, nstd=6)
im[~mask]=np.nan
#get edge
scharr=cr.Scharr_edge(im)
#Orientate image along x if not done
if chAngle !=0:
scharr= ir.rotate_scale(scharr, -chAngle,1,np.nan)
#get profile
prof=np.nanmean(scharr,1)
#get threshold
threshold=np.nanmean(prof)+3*np.nanstd(prof)
mprof=prof>threshold
edgeargs=np.flatnonzero(mprof)
if edgeargs.size > 2:
mask=np.zeros(im.shape)
mask[edgeargs[0]-5:edgeargs[-1]+5,:]=2
if chAngle !=0:
mask= ir.rotate_scale(mask, chAngle,1,np.nan)
mask=np.logical_and(mask<1, np.isfinite(im))
else:
mask= None
return mask
def channels_edges(bg, approxwidth, angle=None, std=10, Nwalls=8):
"""
Get the position of the edges
Parameters
----------
bg: 2d array
image containning the 4 channels
approxwidth: integer
the approximate width
angle: float
if given, angle at which the edges are
std: integer
Tolerence on wall position in pixels
Returns
-------
edges: 1d integer array
Position in the rotated image of the edges in pixels
"""
bg = bg / rmbg.polyfit2d(bg)
if angle is not None:
bg = ir.rotate_scale(bg, -angle, 1, borderValue=np.nan)
prof = gfilter(np.nanmean(bg, 0), 3)
edges = np.abs(np.diff(prof))
edges[np.isnan(edges)] = 0
#create approximate walls
x = np.arange(len(edges))
gwalls = np.zeros(len(edges), dtype=float)
for center in (1 + np.arange(Nwalls)) * approxwidth:
gwalls += edges.max() * np.exp(-(x - center)**2 / (2 * std**2))
#Get best fit for approximate walls
c = int(
np.correlate(edges, gwalls, mode='same').argmax() - len(gwalls) / 2)
'''
from matplotlib.pyplot import plot, figure, imshow
figure()
imshow(bg)
figure()
plot(edges)
plot(gwalls)
figure()
plot(np.correlate(edges,gwalls,mode='same'))
#'''
#Roll
gwalls = np.roll(gwalls, c)
if c < 0:
gwalls[c:] = 0
else:
gwalls[:c] = 0
#label wall position
label, n = msr.label(gwalls > .1 * gwalls.max())
#Get the positions
edges = np.squeeze(msr.maximum_position(edges, label, range(1, n + 1)))
assert len(edges) == 8, 'Did not detect 8 edges'
return edges
def remove_bg(im, bg, edgesOut=None):
"""
Flatten and background subtract images
Parameters
----------
im: 2d array
list of images containning the 4 channels
bg: 2d array
Background corresponding to the list
edgesOut: 1d array
output for the edges
Returns
-------
flatIm: 2d array
Flattened image
"""
#Get bg angle (the other images are the same)
infoDict = {}
angle = bg_angle(im, bg, infoDict)
approxwidth = infoDict['BrightInfos']['width']
#Get the mask
maskbg = channels_mask(bg, approxwidth, angle, edgesOut)
#rotate and flatten the bg
bg = ir.rotate_scale(bg, -angle, 1, borderValue=np.nan)
im = ir.rotate_scale(im, -angle, 1, borderValue=np.nan)
maskim = ir.rotate_scale_shift(maskbg,
infoDict['diffAngle'],
infoDict['diffScale'],
infoDict['offset'],
borderValue=np.nan) > .5
maskim = binary_erosion(maskim, iterations=15)
#Get Intensity
ret = rmbg.remove_curve_background(im,
bg,
maskbg=maskbg,
maskim=maskim,
bgCoord=True,
reflatten=True)
return ret
def flat_image(im, pixsize, chanWidth=300e-6):
"""
Flatten the image
Parameters
----------
im: 2d array
image
pixsize: float
pixel size in [m]
chanWidth: float, defaults 300e-6
channel width in [m]
Returns
-------
im: 2d array
The flattened image
"""
im=np.asarray(im,dtype=float)
#remove peaks
im[rmbg.getPeaks(im, maxsize=20*20)]=np.nan
#straighten
angle=dp.image_angle(im-np.nanmedian(im))
im=ir.rotate_scale(im,-angle,1,borderValue=np.nan)
#Get center
prof=np.nanmean(im,0)
flatprof=prof-np.nanmedian(prof)
flatprof[np.isnan(flatprof)]=0
x=np.arange(len(prof))-dp.center(flatprof)
x=x*pixsize
#Create mask
channel=np.abs(x)<chanWidth/2
mask=np.ones(np.shape(im))
mask[:,channel]=0
#Flatten
im=im/rmbg.polyfit2d(im,mask=mask)-1
"""
from matplotlib.pyplot import figure, imshow,plot
figure()
imshow(im)
imshow(mask,alpha=.5,cmap='Reds')
# plot(x,flatprof)
# plot(x,np.correlate(flatprof,flatprof[::-1],mode='same'))
#"""
return im
def flat_image(im, frac=.7, infosOut=None, subtract=False):
"""
Flatten input images
Parameters
----------
im: 2d array
The image
frac: float
fraction of the profile taken by fluorescence from channels
infosOut: dict, defaults None
dictionnary containing the return value of straight_image_infos
subtract: Bool
Should the shape be subtracted instead of divided
Returns
-------
im: 2d array
The flattened image
"""
#Detect Angle
angle = dp.image_angle(im - np.median(im))
im = ir.rotate_scale(im, -angle, 1, borderValue=np.nan)
#Get channels infos
w, a, origin = straight_image_infos(im)
#get mask
mask = np.ones(np.shape(im)[1])
for i in range(4):
amin = origin + 2 * i * w - frac * w
amax = origin + 2 * i * w + frac * w
mask[int(amin):int(amax)] = 0
mask = mask > 0
mask = np.tile(mask[None, :], (np.shape(im)[0], 1))
#Flatten
if not subtract:
im = im / rmbg.polyfit2d(im, mask=mask) - 1
else:
im = im - rmbg.polyfit2d(im, mask=mask)
# import matplotlib.pyplot as plt
# plt.figure()
# plt.imshow(rmbg.polyfit2d(im,mask=mask))
# plt.colorbar()
# plt.figure()
# plt.imshow(im)
# plt.imshow(mask,alpha=.5)
if infosOut is not None:
infosOut['infos'] = (w, a, origin)
return im
def extract_profiles(im, imSlice=None, flatten=False):
'''
Extract profiles from image
Parameters
----------
im: 2d array
The flat image
imSlice: slice
Slice of the image to consider
flatten: Bool, Defaults False
Should the image be flatten
Returns
-------
profiles: 2d array
The four profiles
'''
im = np.asarray(im)
if imSlice is not None:
im = im[imSlice]
infos = {}
if flatten:
im = flat_image(im, infosOut=infos)
angle = dp.image_angle(im)
im = ir.rotate_scale(im, -angle, 1, borderValue=np.nan)
if not flatten:
infos['infos'] = straight_image_infos(im)
"""
profiles0=extract_profiles_flatim(im[:100],infos['infos'])
for p in profiles0:
p/=np.mean(p)
profiles1=extract_profiles_flatim(im[-100:],infos['infos'])
for p in profiles1:
p/=np.mean(p)
from matplotlib.pyplot import plot, figure, imshow
figure()
plot(np.ravel(profiles0))
plot(np.ravel(profiles1))
#"""
profiles = extract_profiles_flatim(im, infos['infos'])
return profiles
def image_infos(im):
"""
Get the image angle, channel width, proteind offset, and origin
Parameters
----------
im: 2d array
The image
Returns
-------
dict: dictionnary
dictionnary containing infos
"""
imflat = im
#Detect Angle
angle = dp.image_angle(imflat)
im = ir.rotate_scale(im, -angle, 1, borderValue=np.nan)
#Get channels infos
w, a, origin = straight_image_infos(im)
retdict = {'angle': angle, 'origin': origin, 'width': w, 'offset': a}
return retdict
def outGaussianBeamMask(data, chAngle=0):
"""
get the outside of the channel from a gaussian fit
Parameters
----------
data: 2d array
The image
chAngle: number
The angle of the channel in radians
Returns
-------
mask: 2d array
the mask excluding the channel
"""
data=np.asarray(data)
#Filter to be used
gfilter=scipy.ndimage.filters.gaussian_filter1d
#get profile
if chAngle!=0:
data=ir.rotate_scale(data, -chAngle,1,np.nan)
profile=np.nanmean(data,1)
#guess position of max
amax= profile.size//2
#get X and Y
X0=np.arange(profile.size)-amax
Y0=profile
#The cutting values are when the profiles goes below zero
rlim=np.flatnonzero(np.logical_and(Y0<0,X0>0))[0]
llim=np.flatnonzero(np.logical_and(Y0<0,X0<0))[-1]
#We can now detect the true center
fil=gfilter(profile,21)
X0=X0-X0[np.nanargmax(fil[llim:rlim])]-llim
#restrict to the correct limits
X=X0[llim:rlim]
Y=Y0[llim:rlim]-np.nanmin(Y0)
#Fit the log, which should be a parabola
c=np.polyfit(X,np.log(Y),2)
#Deduce the variance
var=-1/(2*c[0])
#compute the limits (3std, restricted to half the image)
mean=np.nanargmax(fil[llim:rlim])+llim
dist=int(3*np.sqrt(var))
if dist > profile.size//4:
dist = profile.size//4
llim=mean-dist
if llim < 0:
return None
rlim=mean+dist
if rlim>profile.size:
return None
#get mask
mask=np.ones(data.shape)
if chAngle!=0:
idx=np.indices(mask.shape)
idx[1]-=mask.shape[1]//2
idx[0]-=mask.shape[0]//2
X=np.cos(chAngle)*idx[1]+np.sin(chAngle)*idx[0]
Y=np.cos(chAngle)*idx[0]-np.sin(chAngle)*idx[1]
mask[np.abs(Y-mean+mask.shape[0]//2)<dist]=0
else:
mask[llim:rlim,:]=0
#mask=np.logical_and(mask>.5, np.isfinite(data))
mask=mask>.5
return mask
"""
def extract_profile(flatim, pixsize, chanWidth=300e-6,*,reflatten=True,ignore=10):
"""
Get profile from a flat image
Parameters
----------
flatim: 2d array
flat image
pixsize: float
pixel size in [m]
chanWidth: float, defaults 300e-6
channel width in [m]
reflatten: Bool, defaults True
Should we reflatten the profile?
ignore: int, defaults 10
The number of pixels to ignore if reflattening
Returns
-------
im: 2d array
The flattened image
"""
#Orientate
flatim=ir.rotate_scale(flatim,-dp.image_angle(flatim)
,1, borderValue=np.nan)
#get profile
prof=np.nanmean(flatim,0)
#Center X
X=np.arange(len(prof))*pixsize
center=dp.center(prof)*pixsize
inchannel=np.abs(X-center)<.45*chanWidth
X=X-(dp.center(prof[inchannel])+np.argmax(inchannel))*pixsize
#get what is out
out=np.logical_and(np.abs(X)>.55*chanWidth,np.isfinite(prof))
if reflatten:
#fit ignoring extreme 10 pix
fit=np.polyfit(X[out][ignore:-ignore],prof[out][ignore:-ignore],2)
bgfit=fit[0]*X**2+fit[1]*X+fit[2]
#Flatten the profile
prof=(prof+1)/(bgfit+1)-1
#We restrict the profile to channel width - widthcut
Npix=int(chanWidth//pixsize)+1
Xc=np.arange(Npix)-(Npix-1)/2
Xc*=pixsize
finterp=interpolate.interp1d(X, prof,bounds_error=False,fill_value=0)
"""
from matplotlib.pyplot import figure, imshow,plot
figure()
plot(X,prof)
#"""
return finterp(Xc)
"""