def get_streak_mask(img, pix_pts, **kwargs):
#streak = Streak(gaussian_filter(img,sig_G),
assert (has_astride)
streak = Streak(img, output_path='.', **kwargs)
streak.detect()
edges = streak.streaks
if not edges:
return np.ones(img.shape, bool)
verts = [np.vstack((edge['x'], edge['y'])).T for edge in edges]
paths = [plt.mpl.path.Path(v) for v in verts]
contains = np.vstack([p.contains_points(pix_pts) for p in paths])
mask = np.any(contains, 0).reshape(img_sh)
return np.logical_not(mask)
def _set_streak_mask( self, **kwargs):
streak = Streak(self.img,
output_path='.',
**kwargs)
streak.detect()
edges = streak.streaks
if not edges:
print("no edges!")
self.mask =np.ones(self.img.shape, bool )
verts = [ np.vstack(( edge['x'], edge['y'])).T
for edge in edges]
paths = [ plt.mpl.path.Path(v)
for v in verts ]
contains = np.vstack( [ p.contains_points(self.pix_pts)
for p in paths ])
mask = np.any( contains,0).reshape( self.img.shape)
self.mask = np.logical_not(mask)
def plot_streak(img, ax, sig_G_lst=[0], **kwargs):
assert (has_astride)
m = np.median(img[img > 0])
s = np.std(img[img > 0])
ax.imshow(img, vmax=m + 4 * s, vmin=m - s, cmap='viridis')
for sig_G in sig_G_lst:
streak = Streak(gaussian_filter(img, sig_G), output_path='.', **kwargs)
streak.detect()
edges = streak.streaks
if not edges:
return 0
verts = [np.vstack((edge['x'], edge['y'])).T for edge in edges]
paths = [plt.mpl.path.Path(v) for v in verts]
for p in paths:
patch = plt.mpl.patches.PathPatch(p,
facecolor='none',
lw=2,
edgecolor='Deeppink')
ax.add_patch(patch)
def find_streaks():
plt.style.use(astropy_mpl_style)
for filename in glob.glob("*.fits"):
fits.info(filename)
# Read a fits image and create a Streak instance.
streak = Streak(filename)
# Detect streaks.
streak.detect()
# Write outputs and plot figures.
streak.write_outputs()
streak.plot_figures()
def _set_streak_mask(self, sig_G=None, **kwargs):
assert (has_astride)
if sig_G is not None:
streak = Streak(gauss_filt(self.img, sig_G),
output_path='.',
**kwargs)
streak.detect()
else:
streak = Streak(self.img, output_path='.', **kwargs)
streak.detect()
self.streak = streak
edges = streak.streaks
if not edges:
self.has_streak = False
self.mask = np.ones(self.img.shape, bool)
self.circulaity = []
self.streak_centers = []
self.roundness = []
self.areas = []
return
verts = [np.vstack((edge['x'], edge['y'])).T for edge in edges]
paths = [plt.mpl.path.Path(v) for v in verts]
self.streak_centers = [ [edge['y_center'], \
edge['x_center']] for edge in edges ]
self.circularity = [edge['shape_factor'] for edge in edges]
self.roundness = [edge['radius_deviation'] for edge in edges]
self.areas = [edge['area'] for edge in edges]
contains = np.vstack([p.contains_points(self.pix_pts) for p in paths])
self.streak_masks = [c.reshape(self.img.shape) for c in contains]
mask = np.any(contains, 0).reshape(self.img.shape)
self.mask = np.logical_not(mask)
self.has_streak = True
def find_edges(img, sig_G=0, **kwargs):
streak = Streak(gaussian_filter(img,sig_G), **kwargs)
streak.detect()
return streak.streaks
nrows=6
ncols=7
fig,axs = plt.subplots(nrows=nrows, ncols=ncols)
k = 0
for row in xrange(nrows):
for col in xrange( ncols):
img = subs[k]
ax = axs[row,col]
ax.clear()
ax.set_title(str(k))
ax.imshow(img, aspect='auto')
# raw version
streak = Streak(gaussian_filter(img,0), output_path='.',
min_points=0,
shape_cut=1,
area_cut=10,
radius_dev_cut=0.,
connectivity_angle=10.)
streak.detect()
edges = streak.streaks
if edges:
verts = [ np.vstack(( edge['x'], edge['y'])).T
for edge in edges]
paths = [ plt.mpl.path.Path(v)
for v in verts ]
for p in paths:
patch = plt.mpl.patches.PathPatch(p, facecolor='none', lw=2, edgecolor='Deeppink')
ax.add_patch(patch)
# smoothed version
streak = Streak(gaussian_filter(img,1.4), output_path='.',
def do_one(ff, output_path, shape, area, contour, rad, angle, remove_bkg,
bkg_box_size, min_points, max_area):
"""
process a directory one fits-file (ff)
"""
try:
# Read a fits image and create a Streak instance.
streak = Streak(ff, output_path=output_path)
# Detect streaks.
# Set the parameters
streak.shape_cut = shape
streak.area_cut = area
streak.contour_threshold = contour
streak.remove_bkg = remove_bkg
streak.radius_dev_cut = rad
streak.connectivity_angle = angle
streak.remove_bkg = remove_bkg
streak.bkg_box_size = bkg_box_size
streak.min_points = min_points
streak.detect()
# filter out the detections that are too big
for edge in streak.streaks:
if edge['area'] > max_area:
streak.streaks.remove(edge)
n = len(streak.streaks)
except:
n = -1
if n > 0:
# Write outputs and plot figures.
streak.write_outputs()
streak.plot_figures()
if n == 0:
sys.stdout.write('.')
elif n < 0:
sys.stdout.write('X')
elif n < 10:
sys.stdout.write('%d' % n)
else:
sys.stdout.write('*')
sys.stdout.flush()
return n
def do_one(ff, output_path=None, shape=None, area=None, contour=None):
"""
process a directory one fits-file (ff)
"""
# Read a fits image and create a Streak instance.
streak = Streak(ff, output_path=output_path)
# Detect streaks.
# streak.shape_cut = .14
# streak.area_cut = 120
# streak.contour_threshold = 12
#Customization of values
streak.shape_cut = shape
streak.area_cut = area
streak.contour_threshold = contour
streak.detect()
# Write outputs and plot figures.
streak.write_outputs()
streak.plot_figures()
streakfile = output_path + "/streaks.txt"
fp = open(streakfile)
lines = fp.readlines()
fp.close()
#print("streaks found %d" % (len(lines)-1))
#print("%d " % (len(lines)-1))
n = len(lines) - 1
if n == 0:
sys.stdout.write('.')
elif n < 10:
sys.stdout.write('%d' % n)
else:
sys.stdout.write('*')
sys.stdout.flush()
#Delete/move files
#if n == 0:
# shutil.rmtree(output_path)
return int(n)
#def do_one(ff,output_path=None,shape=None,area=None,contour=None): BACKUP
"""
process a directory one fits-file (ff)
"""
# Read a fits image and create a Streak instance.
streak = Streak(ff, output_path=output_path)
# Detect streaks.
# streak.shape_cut = .14
# streak.area_cut = 120
# streak.contour_threshold = 12
#Customization of values
streak.shape_cut = shape
streak.area_cut = area
streak.contour_threshold = contour
streak.detect()
# Write outputs and plot figures.
streak.write_outputs()
streak.plot_figures()
streakfile = output_path + "/streaks.txt"
fp = open(streakfile)
lines = fp.readlines()
fp.close()
#print("streaks found %d" % (len(lines)-1))
#print("%d " % (len(lines)-1))
n = len(lines) - 1
if n == 0:
sys.stdout.write('.')
elif n < 10:
sys.stdout.write('%d' % n)
else:
sys.stdout.write('*')
sys.stdout.flush()
#Delete/move files
if n == 0:
shutil.rmtree(output_path)
return int(n)