def internal_nan_mask(a, x=None, y=None):
"""return a mask with True on internal nans."""
if x is None:
x = np.arange(np.shape(a)[1])
if y is None:
y = np.arange(np.shape(a)[0])
sx = [np.min(x), np.max(x)]
sy = [np.min(y), np.max(y)]
# b is 1 where a is nan, 0 othewise
#used to detect when a region is made of nans
aisnan = np.where(np.isnan(a), True, False)
#plt.figure(); plot_data(b,x,y)
#plt.title('b')
# s is different integer for each contiguous region, can be
s = label(aisnan)[0]
#plt.figure()
#plot_data(s)
#m_int mask of internal nan regions of a
m_int = np.zeros(a.shape).astype(bool)
for i in range(np.max(s) + 1):
c = s == i
if aisnan[c].all():
#plt.figure()
#plot_data(c,x,y)
#for each one find hull and check if it touches borders
p = matrix_to_points2(c, x, y)
p = p[p[:, 2] != 0, :] #keep only points of current region
ssx = span(p[:, 0]) #ranges of points in region
ssy = span(p[:, 1])
#print(i,sx,sy,ssx,ssy)
if (ssx[0] > sx[0] and ssx[1] < sx[1] and ssy[0] > sy[0]
and ssy[1] < sy[1]):
#print(i,'internal')
import pdb
#pdb.set_trace()
m_int = np.logical_or(m_int, c != 0)
#print(len(np.where(m_int!=0)[0]))
#plt.figure()
#plot_points(p,scatter=1)
#p=p[~np.isnan(p[:,2]),:]
#h=points_find_hull(p)
#plot_poly(h,'bo')
'''
if not(((h[0,:] <= min(x)).any() or
(h[0,:] >= max(x)).any() or
(h[1,:] <= min(y)).any() or
(h[1,:] >= max(y))).any()):
print(i,'internal')
m_int=np.logical_or(m_int,c==1)
'''
return m_int
def fitsAFM_reader(fitsfile, sizeum=None):
"""return x,y (vectors) and data (matrix) from fits file. AFM file"""
a = fits.open(fitsfile)
header = a[0].header
data = a[0].data
a.close()
#z in m
from pySurf.points import level_points
data = level_points(data)
assert data.shape[0] == data.shape[
1] #if not, it's first time it happens, check axis.
x = np.linspace(1, sizeum[0], data.shape[0]) / 1000. #convert in mm
y = np.linspace(1, sizeum[1], data.shape[1]) / 1000.
data = data * 1e6 #convert from m to um
return matrix_to_points2(data, x, y)
def topoints(self):
return matrix_to_points2(self.data, self.x, self.y)
def topoints(self):
"""convenience function to get points using matrix_to_points2."""
return matrix_to_points2(self.data, self.x, self.y)