def drift_to_beam(cam,
xmotor,
zmotor,
pixelsize,
tolerance=5,
max_iterations=100):
"""
Moves the camera *cam* with motors *xmotor* and *zmotor* until the
center of mass is nearer than *tolerance*-pixels to the center of the
frame or *max_iterations* is reached.
To convert pixelcoordinates to realworld-coordinates of the motors the
*pixelsize* (scalar or 2-element array-like, e.g. [4*q.um, 5*q.um]) is
needed.
"""
def take_frame():
cam.trigger()
return gaussian_filter(cam.grab().astype(np.float32), 40.0)
units = (u for u in pixelsize.units if pixelsize.units[u] > 0.0)
units = q.parse_expression(' * '.join(units))
ps = np.tile(pixelsize.magnitude, 2)[:2] * units
img = take_frame()
frm_center = (np.array(img.shape) - 1) / 2
d = center_of_mass(img - img.min()) - frm_center
iter_ = 0
while ((d**2).sum() > tolerance**2) and (iter_ < max_iterations):
fut_0 = zmotor.move(d[0] * ps[0])
fut_1 = xmotor.move(d[1] * ps[1])
wait([fut_0, fut_1])
img = take_frame()
if img.sum() == 0:
LOG.debug("drift_to_beam: Frame is empty (sum == 0). " +
"Can't follow center of mass.")
raise ProcessException("There is nothing to see! "
"Can't follow the center of mass.")
d = center_of_mass(img - img.min()) - frm_center
iter_ += 1
if iter_ < max_iterations:
return True
else:
return False
def drift_to_beam(cam, xmotor, zmotor, pixelsize, tolerance=5,
max_iterations=100):
"""
drift_to_beam(cam, xmotor, zmotor, pixelsize, tolerance=5, max_iterations=100)
Moves the camera *cam* with motors *xmotor* and *zmotor* until the
center of mass is nearer than *tolerance*-pixels to the center of the
frame or *max_iterations* is reached.
To convert pixelcoordinates to realworld-coordinates of the motors the
*pixelsize* (scalar or 2-element array-like, e.g. [4*q.um, 5*q.um]) is
needed.
"""
def take_frame():
cam.trigger()
return gaussian_filter(cam.grab().astype(np.float32), 40.0)
units = (u for u in pixelsize.units if pixelsize.units[u] > 0.0)
units = q.parse_expression(' * '.join(units))
ps = np.tile(pixelsize.magnitude, 2)[:2] * units
img = take_frame()
frm_center = (np.array(img.shape)-1)/2
d = center_of_mass(img-img.min()) - frm_center
iter_ = 0
while ((d**2).sum() > tolerance**2) and (iter_ < max_iterations):
fut_0 = zmotor.move(d[0]*ps[0])
fut_1 = xmotor.move(d[1]*ps[1])
wait([fut_0, fut_1])
img = take_frame()
if img.sum() == 0:
LOG.debug("drift_to_beam: Frame is empty (sum == 0). " +
"Can't follow center of mass.")
raise ProcessException("There is nothing to see! "
"Can't follow the center of mass.")
d = center_of_mass(img-img.min()) - frm_center
iter_ += 1
if iter_ < max_iterations:
return True
else:
return False
def find_beam(cam, xmotor, zmotor, pixelsize, xborder, zborder,
xstep=None, zstep=None, thres=1000):
"""
find_beam(cam, xmotor, zmotor, pixelsize, xborder, zborder, xstep=None, zstep=None, thres=1000)
Scans the area defined by xborder and zborder for the beam until
beam_visible returns True.
Startpoint is the current motor-position if this position is inside the
defined area else it start from the center of that area.
It searches in a spiral around the startpoint.
*cam* is the camera-device, *xmotor* the motor-device horizontally aligned
to the image and *zmotor* the motor-device vertically aligned to the image.
*pixelsize* determines the realworld size of an image pixels (scalar or
2-element array-like, e.g. [4*q.um, 5*q.um]). *xborder* and *zborder*
define the search area. Each constructed with a start- and an end-value
(e.g. [-1.2*q.mm, 5.5*q.mm]).
Optional arguments *xstep* and *zstep* define the length of one movement
in the specific direction. Defaults are calculated from cam_img.shape and
*pixelsize*.
Optional argument *thres* will be past to beam_visible().
"""
def beam_visible(img, thres):
"""
Simple grayvalue-threshold that defines the beam to be visible in *img*.
"""
return (img >= thres).any()
def check(rel_move):
"""Move to new position and check if the beam is visible."""
fut_0 = zmotor.move(rel_move[0]*q.um)
fut_1 = xmotor.move(rel_move[1]*q.um)
wait([fut_0, fut_1])
cam.trigger()
img = gaussian_filter(cam.grab().astype(np.float32), 40.0)
img_shape[0] = img.shape
bv = beam_visible(img, thres)
return bv
def spiral_scan():
"""
Generator for returning rel. movement to the next position of the
scanpath.
"""
def trydir(dr):
"""
Check if position in direction *dr* is unchecked or outside the
search-area.
Result: 2 - ok; 1 - outside; 0 - inside but already used
"""
tmp = sp_pos + dir2rpos[dr]
inside = (tmp >= 0).all() and (tmp < sp_shape).all()
unused = (not scanned_points[tmp[0], tmp[1]]) if inside else False
return 1 if not inside else 2 if unused else 0
def next_move(pos, dr, rel_move=True):
"""
Moves relativ in the direction *dr* (or to position *dr* if
rel_move==False) and marks new position as scanned.
Clips movement at border of the scanarea if needed.
"""
old = np.array(pos).copy()
if rel_move:
pos += dir2rpos[dr]
else:
pos[0], pos[1] = dr[0], dr[1]
scanned_points[pos[0], pos[1]] = True
if (old == 0).any() or (old == sp_shape-1).any() or \
(pos == 0).any() or (pos == sp_shape-1).any():
new_pos = np.array([zpos, xpos]) + step * (pos-[nz0, nx0])
clip = np.append((new_pos < [zborder[0], xborder[0]]),
(new_pos > [zborder[1], xborder[1]]))
new_pos[0] = zborder[1] if clip[2] else \
zborder[0] if clip[0] else new_pos[0]
new_pos[1] = xborder[1] if clip[3] else \
xborder[0] if clip[1] else new_pos[1]
old_pos = np.array([zmotor.position.to(q.um.units).magnitude,
xmotor.position.to(q.um.units).magnitude])
return new_pos - old_pos
else:
if rel_move:
return step * dir2rpos[dr]
else:
return step * (pos - old)
def decide_dir():
"""
Picks a direction to go and updates direction of search-rotation.
"""
dr = np.array(map(trydir, range(4))) == 2
r = np.arange(4)[dr][0]
w0 = sp_pos-[nz0, nx0]
w1 = w0 + dir2rpos[r]
w = np.arctan2(w1[0], w1[1]) - np.arctan2(w0[0], w0[1])
search_rot[0] = int((w % (2*np.pi)) < np.pi)
return r
xpos = xmotor.position.to(q.um.units).magnitude
zpos = zmotor.position.to(q.um.units).magnitude
search_rot = [0]
rdir2try = [[1, 0, 3], [3, 0, 1]]
dir2rpos = [[1, 0], [0, 1], [-1, 0], [0, -1]]
step = img_shape[0] * \
np.array([x.to(q.um.units).magnitude for x in ps])
step[0] = step[0] if zstep is None else zstep.to(q.um.units).magnitude
step[1] = step[1] if xstep is None else xstep.to(q.um.units).magnitude
nz0 = int((zpos-zborder[0])/step[0]) + \
((zpos-zborder[0]) % step[0] > step[0]/2.)
nz1 = int((zborder[1]-zpos)/step[0]) + \
((zborder[1]-zpos) % step[0] > step[0]/2.)
nx0 = int((xpos-xborder[0])/step[1]) + \
((xpos-xborder[0]) % step[1] > step[1]/2.)
nx1 = int((xborder[1]-xpos)/step[1]) + \
((xborder[1]-xpos) % step[1] > step[1]/2.)
sp_shape = np.array([nz0+nz1+1, nx0+nx1+1])
scanned_points = np.zeros(sp_shape, np.bool_)
sp_pos = np.array([nz0, nx0])
scanned_points[sp_pos[0], sp_pos[1]] = True
while not scanned_points.all():
skip = False
try:
sdir = decide_dir()
yield next_move(sp_pos, sdir)
except IndexError:
skip = True
while (not scanned_points.all()) and (not skip):
sr = search_rot[0]
for rd in rdir2try[sr]:
rd = (sdir + rd) % 4
c = trydir(rd)
if c == 2:
break
elif c == 1:
search_rot[0] = (search_rot[0]+1) % 2
if c == 2:
sdir = rd
yield next_move(sp_pos, sdir)
continue
break
if not scanned_points.all():
ind = np.indices(sp_shape)
mask = np.logical_not(scanned_points)
ind = np.array([ind[0][mask], ind[1][mask]])
dist = ((ind-np.array([nz0, nx0]).reshape(2, 1))**2).sum(0)
sort_pos = ind[:, np.argsort(dist)]
n_pos = sort_pos[:, 0]
r = next_move(sp_pos, n_pos, False)
yield r
units = (u for u in pixelsize.units if pixelsize.units[u] > 0.0)
units = q.parse_expression(' * '.join(units))
ps = np.tile(pixelsize.magnitude, 2)[:2] * units
xborder = np.array([xborder[0].to(q.um.units).magnitude,
xborder[1].to(q.um.units).magnitude])
zborder = np.array([zborder[0].to(q.um.units).magnitude,
zborder[1].to(q.um.units).magnitude])
# startpoint
img_shape = [0]
xpos = xmotor.position.to(q.um.units).magnitude
zpos = zmotor.position.to(q.um.units).magnitude
outside = (xpos < xborder[0]) or (xpos > xborder[1]) or \
(zpos < zborder[0]) or (zpos > zborder[1])
rmov = (zborder.mean() - zpos, xborder.mean() - xpos) if outside \
else (0*zpos, 0*xpos)
if check(rmov):
return True
# scan
for rmov in spiral_scan():
if check(rmov):
return True
return False
def find_beam(cam,
xmotor,
zmotor,
pixelsize,
xborder,
zborder,
xstep=None,
zstep=None,
thres=1000):
"""
Scans the area defined by xborder and zborder for the beam until
beam_visible returns True.
Startpoint is the current motor-position if this position is inside the
defined area else it start from the center of that area.
It searches in a spiral around the startpoint.
*cam* is the camera-device, *xmotor* the motor-device horizontally aligned
to the image and *zmotor* the motor-device vertically aligned to the image.
*pixelsize* determines the realworld size of an image pixels (scalar or
2-element array-like, e.g. [4*q.um, 5*q.um]). *xborder* and *zborder*
define the search area. Each constructed with a start- and an end-value
(e.g. [-1.2*q.mm, 5.5*q.mm]).
Optional arguments *xstep* and *zstep* define the length of one movement
in the specific direction. Defaults are calculated from cam_img.shape and
*pixelsize*.
Optional argument *thres* will be past to beam_visible().
"""
def beam_visible(img, thres):
"""
Simple grayvalue-threshold that defines the beam to be visible in *img*.
"""
return (img >= thres).any()
def check(rel_move):
"""Move to new position and check if the beam is visible."""
fut_0 = zmotor.move(rel_move[0] * q.um)
fut_1 = xmotor.move(rel_move[1] * q.um)
wait([fut_0, fut_1])
cam.trigger()
img = gaussian_filter(cam.grab().astype(np.float32), 40.0)
img_shape[0] = img.shape
bv = beam_visible(img, thres)
return bv
def spiral_scan():
"""
Generator for returning rel. movement to the next position of the
scanpath.
"""
def trydir(dr):
"""
Check if position in direction *dr* is unchecked or outside the
search-area.
Result: 2 - ok; 1 - outside; 0 - inside but already used
"""
tmp = sp_pos + dir2rpos[dr]
inside = (tmp >= 0).all() and (tmp < sp_shape).all()
unused = (not scanned_points[tmp[0], tmp[1]]) if inside else False
return 1 if not inside else 2 if unused else 0
def next_move(pos, dr, rel_move=True):
"""
Moves relativ in the direction *dr* (or to position *dr* if
rel_move==False) and marks new position as scanned.
Clips movement at border of the scanarea if needed.
"""
old = np.array(pos).copy()
if rel_move:
pos += dir2rpos[dr]
else:
pos[0], pos[1] = dr[0], dr[1]
scanned_points[pos[0], pos[1]] = True
if (old == 0).any() or (old == sp_shape-1).any() or \
(pos == 0).any() or (pos == sp_shape-1).any():
new_pos = np.array([zpos, xpos]) + step * (pos - [nz0, nx0])
clip = np.append((new_pos < [zborder[0], xborder[0]]),
(new_pos > [zborder[1], xborder[1]]))
new_pos[0] = zborder[1] if clip[2] else \
zborder[0] if clip[0] else new_pos[0]
new_pos[1] = xborder[1] if clip[3] else \
xborder[0] if clip[1] else new_pos[1]
old_pos = np.array([
zmotor.position.to(q.um.units).magnitude,
xmotor.position.to(q.um.units).magnitude
])
return new_pos - old_pos
else:
if rel_move:
return step * dir2rpos[dr]
else:
return step * (pos - old)
def decide_dir():
"""
Picks a direction to go and updates direction of search-rotation.
"""
dr = np.array(map(trydir, range(4))) == 2
r = np.arange(4)[dr][0]
w0 = sp_pos - [nz0, nx0]
w1 = w0 + dir2rpos[r]
w = np.arctan2(w1[0], w1[1]) - np.arctan2(w0[0], w0[1])
search_rot[0] = int((w % (2 * np.pi)) < np.pi)
return r
xpos = xmotor.position.to(q.um.units).magnitude
zpos = zmotor.position.to(q.um.units).magnitude
search_rot = [0]
rdir2try = [[1, 0, 3], [3, 0, 1]]
dir2rpos = [[1, 0], [0, 1], [-1, 0], [0, -1]]
step = img_shape[0] * \
np.array([x.to(q.um.units).magnitude for x in ps])
step[0] = step[0] if zstep is None else zstep.to(q.um.units).magnitude
step[1] = step[1] if xstep is None else xstep.to(q.um.units).magnitude
nz0 = int((zpos-zborder[0])/step[0]) + \
((zpos-zborder[0]) % step[0] > step[0]/2.)
nz1 = int((zborder[1]-zpos)/step[0]) + \
((zborder[1]-zpos) % step[0] > step[0]/2.)
nx0 = int((xpos-xborder[0])/step[1]) + \
((xpos-xborder[0]) % step[1] > step[1]/2.)
nx1 = int((xborder[1]-xpos)/step[1]) + \
((xborder[1]-xpos) % step[1] > step[1]/2.)
sp_shape = np.array([nz0 + nz1 + 1, nx0 + nx1 + 1])
scanned_points = np.zeros(sp_shape, np.bool_)
sp_pos = np.array([nz0, nx0])
scanned_points[sp_pos[0], sp_pos[1]] = True
while not scanned_points.all():
skip = False
try:
sdir = decide_dir()
yield next_move(sp_pos, sdir)
except IndexError:
skip = True
while (not scanned_points.all()) and (not skip):
sr = search_rot[0]
for rd in rdir2try[sr]:
rd = (sdir + rd) % 4
c = trydir(rd)
if c == 2:
break
elif c == 1:
search_rot[0] = (search_rot[0] + 1) % 2
if c == 2:
sdir = rd
yield next_move(sp_pos, sdir)
continue
break
if not scanned_points.all():
ind = np.indices(sp_shape)
mask = np.logical_not(scanned_points)
ind = np.array([ind[0][mask], ind[1][mask]])
dist = ((ind - np.array([nz0, nx0]).reshape(2, 1))**2).sum(0)
sort_pos = ind[:, np.argsort(dist)]
n_pos = sort_pos[:, 0]
r = next_move(sp_pos, n_pos, False)
yield r
units = (u for u in pixelsize.units if pixelsize.units[u] > 0.0)
units = q.parse_expression(' * '.join(units))
ps = np.tile(pixelsize.magnitude, 2)[:2] * units
xborder = np.array([
xborder[0].to(q.um.units).magnitude,
xborder[1].to(q.um.units).magnitude
])
zborder = np.array([
zborder[0].to(q.um.units).magnitude,
zborder[1].to(q.um.units).magnitude
])
# startpoint
img_shape = [0]
xpos = xmotor.position.to(q.um.units).magnitude
zpos = zmotor.position.to(q.um.units).magnitude
outside = (xpos < xborder[0]) or (xpos > xborder[1]) or \
(zpos < zborder[0]) or (zpos > zborder[1])
rmov = (zborder.mean() - zpos, xborder.mean() - xpos) if outside \
else (0*zpos, 0*xpos)
if check(rmov):
return True
# scan
for rmov in spiral_scan():
if check(rmov):
return True
return False
