def make_array(cube, dim, cut=50, t=0, s=0, w=0, nw=nw, nt=nt, ns=4):
'''
Make a 3d cube in a chosen direction. x,y,[t,s or w]
INPUT:
cube : filename, has to be .icube or .fcube
dim : chosen cube direction. t,s or w. Input as string.
cut : trims pixels off of the images edge to remove edge detector effects. Default = 50 px
t : chosen timestep default = 0
s : chosen stokes paramater default = 0
w : chosen wavelength step default = 0
nw : number of wavelength steps. Should be defined outside function or as global.
nt : number of scans. Should be defined outside function or as global.
ns : number of stokes parameters. Default = 4.
OUTPUT:
numpy cube with a shape of 'len(dim), nx,ny'
AUTHOR: A.G.M. Pietrow (2018)
EXAMPLE:
cube = 'cube.icube'
nw = 20
nt = 4
cube_w = make_array(cube, 'w') # returns a wavelength cut cube @ s=0 and t=0.
cube_w = make_array(cube, 'w', s=1, t=3) # returns a wavelength cut cube @ s=1 and t=3.
cube_t = make_array(cube, 't', s=2, w=10) # returns a timeseries in line core @ s=2
'''
if dim == 't':
#t = var
var_counter = nt
elif dim == 's':
#s = var
var_counter = ns
elif dim == 'w':
#w = var
var_counter = nw
else:
raise ValueError("Dim must be \'t\',\'s\' or \'w\'.")
cube_array = []
for i in range(var_counter):
idx = t*nw*ns + s*nw + w
im = sl.get(cube,idx)[cut:-cut, cut:-cut]
cube_array = np.append(cube_array, im)
nx, ny = im.shape
if dim == 't':
t = t + 1
elif dim == 's':
s = s + 1
elif dim == 'w':
w = w + 1
return cube_array.reshape(var_counter, nx,ny)
def updatefig(t=t, s=s, w=w, *args):
global var, meanim, stdim
var += 1
if var == var_counter:
var = 0
if dim == 't':
t = var
elif dim == 's':
s = var
elif dim == 'w':
w = var
else:
raise ValueError("Dim must be t,s or w.")
idx = t * nw * ns + s * nw + w
im = sl.get(cube, idx)[cut:-cut, cut:-cut]
meanim = np.mean(im)
stdim = np.std(im)
if mn == sd and mn == 0:
a = plt.imshow(im,
vmax=meanim + 2 * stdim,
vmin=meanim - 2 * stdim,
cmap='gray',
animated=True)
else:
a = plt.imshow(im,
vmax=mn + 2 * sd,
vmin=mn - 2 * sd,
cmap='gray',
animated=True)
print(a, t, s, w, meanim, stdim)
return a,
def animatecrisp(cube,
dim,
nw,
nt,
cut=50,
t=0,
s=0,
w=0,
ns=4,
interval=75,
cmap='gray'):
'''
crispex cubes are formated as an entire scan for one time and stokes.
function is WIP
'''
fig = plt.figure()
#plot once to establish window
idx = t * nw * ns + s * nw + w
im = sl.get(cube, idx)[cut:-cut, cut:-cut]
global meanim, stdim #make global to use inside loop
meanim = np.mean(im)
stdim = np.std(im)
a = plt.imshow(im,
vmax=meanim + 2 * stdim,
vmin=meanim - 2 * stdim,
cmap=cmap,
animated=True)
#Check which variable we are looping over
global var #make global to inside loop
var = 0
var_counter = 0
if dim == 't':
var_counter = nt
elif dim == 's':
var_counter = ns
elif dim == 'w':
var_counter = nw
else:
raise ValueError("Dim must be t,s or w.")
def updatefig(t=t, s=s, w=w, *args):
global var, meanim, stdim
var += 1
if var == var_counter:
var = 0
if dim == 't':
t = var
elif dim == 's':
s = var
elif dim == 'w':
w = var
else:
raise ValueError("Dim must be t,s or w.")
idx = t * nw * ns + s * nw + w
im = sl.get(cube, idx)[cut:-cut, cut:-cut]
meanim = np.mean(im)
stdim = np.std(im)
if mn == sd and mn == 0:
a = plt.imshow(im,
vmax=meanim + 2 * stdim,
vmin=meanim - 2 * stdim,
cmap='gray',
animated=True)
else:
a = plt.imshow(im,
vmax=mn + 2 * sd,
vmin=mn - 2 * sd,
cmap='gray',
animated=True)
print(a, t, s, w, meanim, stdim)
return a,
ani = animation.FuncAnimation(fig,
updatefig,
fargs=(t, s, w),
interval=interval,
blit=True)
plt.colorbar()
plt.show()
