def medianstack(filelist, ext=0, **options):
"""
Compute the median for a list of images.
Usefull to elliminate cosmic rays from dark images
Syntax:
medianstack(filelist)
return an image which is the median stack form the files in the current directory
example:
med = medianstack([dk1, dk2, dk3], 0)
compute median for images dk1, dk2 and dk3 using extension 0
TODO:
Check if filelist is a list of images o list of strings and then perform
the computation accordingly
"""
#check if filelist is a list, if not raise error
try:
if (isinstance(filelist, list) and len(filelist) > 1):
pass
else:
raise Exception
except:
print("Not a list or len < 2")
return None
#check if elements in filelist is Image or string
if all([isinstance(i, Image) for i in filelist]):
imagesdata = [i.get_data() for i in filelist]
im = filelist[0].copy()
im.filename = 'medianstack'
im.data = np.median(imagesdata, axis=0)
return im
if all([isinstance(i, str) for i in filelist]):
#copy first image on list to get same dim
imagesdata = [Image(i, ext).get_data() for i in filelist]
im = Image(filelist[0], ext)
im.filename = 'medianstack'
im.data = np.median(imagesdata, axis=0)
return im
elif all([isinstance(i, Path) for i in filelist]):
#copy first image on list to get same dim
imagesdata = [Image(i, ext).get_data() for i in filelist]
im = Image(filelist[0], ext)
im.filename = 'medianstack'
im.data = np.median(imagesdata, axis=0)
return im
return None
def stdstack(filelist, ext=0, **options):
"""
Compute the standard deviation in z direction for a list of images.
Syntax:
stdstack(filelist)
return an image which is the std pixel by pixel for the files in the list
example:
stdmap = stdstack([dk1, dk2, dk3,..,dkn], 0)
compute median for images dk1, dk2, dk3 to dkn using extension 0
"""
#check if filelist is a list, if not raise error
try:
if (isinstance(filelist, list) and len(filelist) > 1):
pass
else:
raise Exception
except:
print("Not a list or len < 2")
return None
#check if elements in filelist are Images or string
if all([isinstance(i, Image) for i in filelist]):
imagesdata = [i.get_data() for i in filelist]
im = filelist[0].copy()
im.filename = 'stdstack'
im.data = np.std(imagesdata, axis=0)
return im
#check if filelist are files names
if all([isinstance(i, str) for i in filelist]):
#copy first image on list to get same dim
imagesdata = [Image(i, ext).get_data() for i in filelist]
im = Image(filelist[0], ext)
im.filename = 'stdstack'
im.data = np.std(imagesdata, axis=0)
return im
elif all([isinstance(i, Path) for i in filelist]):
#copy first image on list to get same dim
imagesdata = [Image(i, ext).get_data() for i in filelist]
im = Image(filelist[0], ext)
im.filename = 'stdstack'
im.data = np.std(imagesdata, axis=0)
return im
return None
def meanstack(filelist, ext=0, **options):
"""
Compute the mean for a list of images.
Syntax:
medianstack(filelist)
return an image which is the median stack form the files in the current directory
example:
med = meanstack([dk1, dk2, dk3], 0)
compute median for images dk1, dk2 and dk3 using extension 0
TODO:
Check if filelist is a list of images o list of strings and then perform
the computation accordingly
"""
#check if filelist is a list, if not raise error
try:
if (isinstance(filelist,list) and len(filelist)>1):
pass
else:
raise Exception
except:
print("Not a list or len < 2")
return None
#check if elements in filelist is Image or string
allimages = [isinstance(i,Image) for i in filelist]
if all(allimages):
imagesdata = [i.get_data() for i in filelist]
im = filelist[0].copy()
im.filename = 'meanstack'
im.data=np.mean(imagesdata, axis = 0)
return im
#check if filelist are files names
allfiles = [isinstance(i,str) for i in filelist]
if all(allfiles):
#copy first image on list to get same dim
imagesdata = [Image(i,ext).get_data() for i in filelist]
im = Image(filelist[0],ext)
im.filename = 'meanstack'
im.data=np.mean(imagesdata, axis = 0)
return im
return None
def stdstack(filelist, ext=0, **options):
"""
Compute the standard deviation in z direction for a list of images.
Syntax:
stdstack(filelist)
return an image which is the std pixel by pixel for the files in the list
example:
stdmap = stdstack([dk1, dk2, dk3,..,dkn], 0)
compute median for images dk1, dk2, dk3 to dkn using extension 0
"""
#check if filelist is a list, if not raise error
try:
if (isinstance(filelist,list) and len(filelist)>1):
pass
else:
raise Exception
except:
print("Not a list or len < 2")
return None
#check if elements in filelist are Images or string
allimages = [isinstance(i,Image) for i in filelist]
if all(allimages):
imagesdata = [i.get_data() for i in filelist]
im = filelist[0].copy()
im.filename = 'stdstack'
im.data=np.std(imagesdata, axis = 0)
return im
#check if filelist are files names
allfiles = [isinstance(i,str) for i in filelist]
if all(allfiles):
#copy first image on list to get same dim
imagesdata = [Image(i,ext).get_data() for i in filelist]
im = Image(filelist[0],ext)
im.filename = 'stdstack'
im.data=np.std(imagesdata, axis = 0)
return im
return None