My goal is to plot a profile of a 2D FITS file that I already asked the user for with a try/except. I want to slice a part of this FITS file and then plot this part. I will just put my whole code here. I don't think there is anything wrong with the try/except part but the slicing and plotting have some erros.
My main problem is that the programme is giving me the following error ValueError: x and y can be no greater than 2-D, but have shapes (1L,) and (1L, 28L, 28L)
import os
files = [f for f in os.listdir('.') if os.path.isfile(f)]
for f in files:
if f.endswith(".fits"):
print(f)
which gives me the two FITS files i have in my folder
from astropy.io import fits
valid = False
while not valid:
filename = input("Name of 2D FITS file:")
hdulist = fits.open(filename)
hdr= hdulist[0].header
try:
naxis = hdr['NAXIS']
valid = (naxis == 2)
if not valid:
print("Data structure is not two dimensional")
except Exception as e:
print(e)
valid = False
print("Valid input:", valid)
hdulist = fits.open(filename)
hdr= hdulist[0].header
Here ends my try/except and starts the messy part where i try to slice the FITS file over an angle
from matplotlib.pyplot import figure, show
from astropy.io import fits
data=hdulist[0].data
B=input("Enter the y value of the pixel defined as your starting value of the slice B=")
C=input("Enter the y value of the pixel defined as your stopping value of the slice C=")
D=input("Enter the x value of the pixel defined as your starting value of the slice D=")
E=input("Enter the x value of the pixel defined as your stopping value of the slice E=")
A = data[B:C,D:E]
astd = A.std()
print(astd)
fig = figure()
frame = fig.add_subplot(1,1,1)
mappable = frame.imshow(A, interpolation='none', origin="lower", cmap='jet', vmin=1500, vmax=8000)
cbar = fig.colorbar(mappable, ax=frame, fraction=0.046, pad=0.04)
show()
#the figure below always adjusts the axis such that the starting value is in the
#lower left corner and the stopping value in the upper right corner
import math
R= math.degrees(math.atan((C-B)/(E-D)))
L= ((E-D)**2+(C-B)**2)**(0.5)
print("The line from the starting to the stopping point has a length of:", L)
print("The line from the starting to the stopping point has an angle in degrees of:", R)
F=int(L)
print(F)
This gives me a slice, now i want to put this in a profile and plot the whole thing.
# construct interpolation function
import numpy
import scipy
from scipy import interpolate
x = numpy.arange(data.shape[1])
y = numpy.arange(data.shape[0])
f = scipy.interpolate.interp2d(x, y, data)
# extract values on line from D, B to E, C (degrees are not even necessary)
num_points = F
xvalues = numpy.linspace(D, E, num_points)
yvalues = numpy.linspace(B, C, num_points)
zvalues = f(xvalues, yvalues)
print(zvalues)
import numpy as np
from numpy import random
from matplotlib.pyplot import figure, show
from scipy import stats
from numpy import pi
profile=np.array([zvalues])
This is where i start to design the plot i used a previous design where velocity was used therefore the name "vels"
#Plot of profile
vels = np.linspace(0, 100, len(profile))
gam = profile.sum()
XY = (vels*profile).sum()
X0 = XY/gam
var = (1/gam)*(profile*(vels-X0)**2).sum()
sigma = var**0.5
skew = (1/gam)*(profile*(vels-X0)**3).sum()/sigma**3
kurt = (1/gam)*(profile*(vels-X0)**4).sum()/sigma**4
print("Mean:", X0)
print("Standard deviation:", sigma)
print("Skewness:", skew)
print("Fisher Kurtosis:", kurt-3)
a=profile.max
N=1000
def f(x,mu,sigma,a):
return a*(np.exp)((-(x-mu)**2)/(2*sigma**2))
fig = figure()
frame = fig.add_subplot(1,1,1)
frame.plot(vels, profile,)
frame.plot(vels,f(vels,X0, sigma,profile.max()), color="pink")
frame.set_xlabel('x-axis')
frame.set_ylabel('y-axis')
frame.grid(True)
show()
This is what the programme returns once I try to execute it.
('Mean:', 0.0)
('Standard deviation:', 0.0)
('Skewness:', nan)
('Fisher Kurtosis:', nan)
C:\Users\Thomas\Anaconda2\lib\site-packages\ipykernel\__main__.py:10: RuntimeWarning: invalid value encountered in double_scalars
C:\Users\Thomas\Anaconda2\lib\site-packages\ipykernel\__main__.py:11: RuntimeWarning: invalid value encountered in double_scalars
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-13-80786b6f31c3> in <module>()
24 fig = figure()
25 frame = fig.add_subplot(1,1,1)
---> 26 frame.plot(vels, profile,)
27 frame.plot(vels,f(vels,X0, sigma,profile.max()), color="pink")
28 frame.set_xlabel('x-axis')
C:\Users\Thomas\Anaconda2\lib\site-packages\matplotlib\__init__.pyc in inner(ax, *args, **kwargs)
1889 warnings.warn(msg % (label_namer, func.__name__),
1890 RuntimeWarning, stacklevel=2)
-> 1891 return func(ax, *args, **kwargs)
1892 pre_doc = inner.__doc__
1893 if pre_doc is None:
C:\Users\Thomas\Anaconda2\lib\site-packages\matplotlib\axes\_axes.pyc in plot(self, *args, **kwargs)
1404 kwargs = cbook.normalize_kwargs(kwargs, _alias_map)
1405
-> 1406 for line in self._get_lines(*args, **kwargs):
1407 self.add_line(line)
1408 lines.append(line)
C:\Users\Thomas\Anaconda2\lib\site-packages\matplotlib\axes\_base.pyc in _grab_next_args(self, *args, **kwargs)
405 return
406 if len(remaining) <= 3:
--> 407 for seg in self._plot_args(remaining, kwargs):
408 yield seg
409 return
C:\Users\Thomas\Anaconda2\lib\site-packages\matplotlib\axes\_base.pyc in _plot_args(self, tup, kwargs)
383 x, y = index_of(tup[-1])
384
--> 385 x, y = self._xy_from_xy(x, y)
386
387 if self.command == 'plot':
C:\Users\Thomas\Anaconda2\lib\site-packages\matplotlib\axes\_base.pyc in _xy_from_xy(self, x, y)
245 if x.ndim > 2 or y.ndim > 2:
246 raise ValueError("x and y can be no greater than 2-D, but have "
--> 247 "shapes {} and {}".format(x.shape, y.shape))
248
249 if x.ndim == 1:
ValueError: x and y can be no greater than 2-D, but have shapes (1L,) and (1L, 28L, 28L)
