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better but not yet perfect autofocus

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zamofing_t
2022-09-19 17:20:00 +02:00
parent 21afed9739
commit c3542ad38c
7 changed files with 223 additions and 93 deletions
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18
Readme.md
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@@ -320,9 +320,23 @@ X10193.88 Y-8892
-> z has wrong sign !
----------------
avoid constand RBV event:
caput SAR-ESPMX:MOT_FX 0.001
caput SAR-ESPMX:MOT_FY 0.001
---------- TODO ----------
-faster autofocus:
- move at constant speed and acquire as fast as possible instead stop and go motion
- find fiducials:
- fix openCV version problems
- configuration: use the current config as default values
- automation: towards automatic alignement
!!!!!!!!!!! AFTER COLLECTION GRAPHICAL OVERLAY OBJECTS ARE SHIFTED !!!!!!!!!!!
!!!!!!!!!!! IF MOVING ON THE EPICS PANEL, THE OBJECTS GET OUT OF SYNC !!!!!!!!

246
geometry.py
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@@ -255,84 +255,6 @@ class geometry:
_log.debug('least square data:\nK:{}\nAA:{}'.format(K, AA))
@staticmethod
def autofocus(cam,mot,rng=(-1,1),n=30,progressDlg=None,saveImg=False):
# cam camera object
# mot motor object (e.g. SimMotorTweak)
# rng region (min max relative to current position) to seek
# n number of images to take in region
# progressDlg a pg.ProgressDialog to allow to abort the function call
if mot is not None:
p0=mot.get_rbv()
else:
p0=0
if saveImg:
for i,p in enumerate(np.linspace(p0+rng[0],p0+rng[1],n)):
mot.move_abs(p,wait=True)
pic=cam._pic# get_image()
mx=pic.max()
if pic.max()>255:
scl=2**int(round(np.log2(mx)-8))
pic=np.array(pic/scl, dtype=np.uint8)
elif pic.dtype!=np.uint8:
pic=np.array(pic, dtype=np.uint8)
img=PIL.Image.fromarray(pic)
fn=f'/tmp/image{i:03d}.png'
img.save(fn)
_log.debug(f'{fn} {pic.dtype} {pic.min()} {pic.max()}')
mot.move_abs(p0)
return p0
else:
if type(cam) == list:
imgLst=cam
n=len(imgLst)
mtr=np.ndarray(shape=(n,))
posLst=np.linspace(p0+rng[0], p0+rng[1], n)
for i,p in enumerate(posLst):
if type(cam)==list:
img=PIL.Image.open(imgLst[i])
img=np.asarray(img)
else:
mot.move_abs(p, wait=True)
img=cam.get_image() # get latest image
img16=np.array(img, np.int16)
msk=np.array(((1, 0, -1), (2, 0, -2), (1, 0, -1)), np.int16)
sb1=signal.convolve2d(img16, msk, mode='same', boundary='fill', fillvalue=0)
sb2=signal.convolve2d(img16, msk.T, mode='same', boundary='fill', fillvalue=0)
sb=np.abs(sb1)+np.abs(sb2)
mtr[i]=sb.sum()
try:
progressDlg+=1
if progressDlg.wasCanceled():
return
except TypeError as e:
pass
_log.debug(f'{i}/{p:.4g} -> {mtr[i]:.4g}')
mx=mtr.argmax()
_log.debug(f'best focus at idx:{mx}= pos:{posLst[mx]} = metric:{mtr[mx]:.6g}')
if mx>1 and mx+2<=len(posLst):
#fit parabola and interpolate:
# y=ax2+bx+c, at positions x=-1, 0, 1, y'= 2a+b == 0 (top of parabola)
# calc a,b,c:
# y(-1)=a-b+c
# y( 0)= +c
# y( 1)=a+b+c
# c=y(0)
# b=(y(1)-y(-1))/2
# a=(y(1)+y(-1))/2-y(0)
# x=-b/2a=(y(-1)-y(1))/2(y(-1)+y(1)-2y(0))
u,v,w=mtr[mx-1:mx+2]
d=posLst[1]-posLst[0]
p=posLst[mx]+d*.5*(u-w)/(u+w-2*v)
else:
p=posLst[mx]
if mot is not None:
mot.move_abs(p)
return p
pass
@staticmethod
def find_fiducial(cam,sz=(210,210),brd=(20,20)):
if type(cam)==str:
@@ -340,6 +262,8 @@ class geometry:
img=np.asarray(img)
else:
img=cam.get_image() # get latest image
if img.dtype==np.uint16:
img=np.array(img,np.uint8)
fid=np.ones((sz[1]+2*brd[1],sz[0]+2*brd[0]),dtype=np.uint8)*255
fid[brd[1]:sz[1]+brd[1],brd[0]:sz[0]+brd[0]]=0
@@ -481,6 +405,169 @@ class geometry:
self._fitPlane=aa
class autofocus:
def __init__(self,cam,mot=None):
# cam camera object or image list
# mot motor object (e.g. SimMotorTweak) or None
# rng region (min max relative to current position) to seek
self._cam=cam
self._mot=mot
def save_img(self,rng=(-1,1),n=30,progressDlg=None):
mot=self._mot
cam=self._cam
try:
p0=mot.get_rbv()
except AttributeError:
_log.warning('needs a real motor')
return
for i,p in enumerate(np.linspace(p0+rng[0],p0+rng[1],n)):
mot.move_abs(p,wait=True)
try:
pic=cam._pic
except AttributeError:
pic=cam.get_image()
mx=pic.max()
if pic.max()>255:
scl=2**int(round(np.log2(mx)-8))
pic=np.array(pic/scl, dtype=np.uint8)
elif pic.dtype!=np.uint8:
pic=np.array(pic, dtype=np.uint8)
img=PIL.Image.fromarray(pic)
fn=f'/tmp/image{i:03d}.png'
img.save(fn)
_log.debug(f'{fn} {pic.dtype} {pic.min()} {pic.max()}')
mot.move_abs(p0)
def cb_autofocus(self,*args,**kwargs):
cam=self._cam
mot=self._mot
mtr=self._mtr
msk=self._msk
idx=self._idx
p=mot.get_rbv()
img16=np.array(cam._pic, np.int16)
sb1=signal.convolve2d(img16, msk, mode='same', boundary='fill', fillvalue=0)
sb2=signal.convolve2d(img16, msk.T, mode='same', boundary='fill', fillvalue=0)
sb=np.abs(sb1)+np.abs(sb2)
m=sb.sum()
mtr[idx,:]=(p,m)
_log.debug(f'{args} {kwargs} p:{p} mtr={m}')
print(p)
if abs(p-self._pDst)<0.01:
_log.debug(f'DONE->{self._idx}')
del cam.process
print(mtr[:idx,:])
mx=mtr[:,1].argmax()
self._af=self.interpolate(mtr[:idx,0], mtr[:idx,1])
return
self._idx+=1
#if p==mot.move_abs(p0+rng[1], wait=False)
# move to sharp location
# and unregister callback
def run_continous(self,rng=(-1,1),velo=0.5):
#do not stop and go, use ballback for processing
mot=self._mot
cam=self._cam
p0=mot.get_rbv()
v=mot._motor.get('VELO')
p0=mot.get_rbv()
mot._motor.put('VELO',2)
mot.move_abs(p0+rng[0], wait=True)
mot._motor.put('VELO',velo)
n=int((rng[1]-rng[0])/velo)*20 # assume max 20fps
self._mtr=mtr=np.ndarray(shape=(n,2))
self._idx=0
self._pDst=p0+rng[1]
self._msk=np.array(((1, 0, -1), (2, 0, -2), (1, 0, -1)), np.int16)
cam.process=self.cb_autofocus
mot.move_abs(p0+rng[1], wait=False)
import pyqtgraph as pg
import time
with pg.ProgressDialog('Progress', 0, n) as dlg:
while True:
try:
p=self._af
except AttributeError:
time.sleep(.1)
dlg.setValue(self._idx)
continue
break
_log.debug(f' Final AF:{p}')
mot._motor.put('VELO',2)
mot.move_abs(p, wait=False)
@staticmethod
def interpolate(posLst,mtr):
mx=mtr[:].argmax()
_log.debug(f'best focus at idx:{mx}= pos:{posLst[mx]} = metric:{mtr[mx]:.6g}')
if mx>1 and mx+2<=mtr.shape[0]:
#fit parabola and interpolate:
# y=ax2+bx+c, at positions x=-1, 0, 1, y'= 2a+b == 0 (top of parabola)
# calc a,b,c:
# y(-1)=a-b+c
# y( 0)= +c
# y( 1)=a+b+c
# c=y(0)
# b=(y(1)-y(-1))/2
# a=(y(1)+y(-1))/2-y(0)
# x=-b/2a=(y(-1)-y(1))/2(y(-1)+y(1)-2y(0))
u,v,w=mtr[mx-1:mx+2]
d=posLst[1]-posLst[0]
p=posLst[mx]+d*.5*(u-w)/(u+w-2*v)
else:
p=posLst[mx]
return p
def run(self,rng=(-1,1),n=30,progressDlg=None,saveImg=False):
# rng region (min max relative to current position) to seek
# n number of images to take in region
# progressDlg a pg.ProgressDialog to allow to abort the function call
mot=self._mot
cam=self._cam
if mot is not None:
p0=mot.get_rbv()
else:
p0=0
if type(cam) == list:
imgLst=cam
n=len(imgLst)
mtr=np.ndarray(shape=(n,))
posLst=np.linspace(p0+rng[0], p0+rng[1], n)
for i,p in enumerate(posLst):
if type(cam)==list:
img=PIL.Image.open(imgLst[i])
img=np.asarray(img)
else:
mot.move_abs(p, wait=True)
img=cam.get_image() # get latest image
img16=np.array(img, np.int16)
msk=np.array(((1, 0, -1), (2, 0, -2), (1, 0, -1)), np.int16)
sb1=signal.convolve2d(img16, msk, mode='same', boundary='fill', fillvalue=0)
sb2=signal.convolve2d(img16, msk.T, mode='same', boundary='fill', fillvalue=0)
sb=np.abs(sb1)+np.abs(sb2)
mtr[i]=sb.sum()
try:
progressDlg+=1
if progressDlg.wasCanceled():
return
except TypeError as e:
pass
_log.debug(f'{i}/{p:.4g} -> {mtr[i]:.4g}')
p=autofocus.interpolate(posLst,mtr)
if mot is not None:
mot.move_abs(p)
return p
if __name__=="__main__":
import argparse
@@ -676,7 +763,8 @@ if __name__=="__main__":
if args.mode&0x08:
import glob
imgLst=sorted(glob.glob("scratch/autofocus2/image*.png"))
geometry.autofocus(imgLst,None)
af=autofocus(imgLst,None)
af.run()
if args.mode&0x10:
geometry.find_fiducial("scratch/fiducial/image001.png")

35
swissmx.py
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@@ -666,6 +666,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
def cb_new_frame_pv(self, **kwargs):
#thrd=threading.current_thread()
#_log.debug(f'thread:{thrd.getName()}, {thrd.native_id}')
#_log.debug(f"{kwargs['timestamp']}")
app=QApplication.instance()
cam=app._camera
@@ -679,6 +680,11 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
pic.dtype=np.uint16
camera.epics_cam.set_fiducial(pic, 255)
cam._pic=pic
cam._timestamp=kwargs['timestamp']
try:
cam.process()
except AttributeError as e:
pass
# self._goImg.setImage(cam._pic) caused some deadlocks.
# therefore try to update the image with signals instead
self.sigNewCamImg.emit()
@@ -1613,14 +1619,39 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
af_range=misc['af_range']
n=misc['af_steps']
rng=(-af_range/2, af_range/2)
with pg.ProgressDialog('Progress', 0, n) as dlg:
geo.autofocus(app._camera, self.tweakers['base_z'],rng, n,dlg)
#geo.autofocus(app._camera, self.tweakers['base_z'],rng, n,dlg)
af= geometry.autofocus(app._camera, self.tweakers['base_z'])
# af.run(rng, n, dlg)
#with pg.ProgressDialog('Progress', 0, n) as dlg:
af.run_continous(rng=(-.5, .5), velo=0.3)
def cb_find_fiducial(self):
app=QApplication.instance()
geo=app._geometry
#geo.autofocus(app._camera, self.tweakers['base_z'],rng=(-1, 1), n=30,saveImg=True)
pos,corr=geo.find_fiducial(app._camera, sz=(210,210),brd=(20,20))
fx=self.tweakers["fast_x"].get_rbv()
fy=self.tweakers["fast_y"].get_rbv()
bz=self.tweakers["base_z"].get_rbv()
#oc=geo._opt_ctr
#bm_pos=self._goBeamMarker.pos()
#bm_sz=self._goBeamMarker.size()
#pos_eu=geo.pix2pos(pos)
#pImg=pg.Point(self._goImg.mapFromScene(pos))
#pTrk=pg.Point(self._goTracked.mapFromScene(pos))
pos_scn=self._goImg.mapToScene(pg.Point(pos))
pos_eu=self._goTracked.mapFromScene(pos_scn)
l=.120
#go=UsrGO.Fiducial((fx-l/2, fy-l/2), (l, l), bz)
go=UsrGO.Fiducial((pos_eu.x()-l/2, pos_eu.y()-l/2), (l, l), bz)
go.sigRegionChangeFinished.connect(self.cb_fiducial_update_z)
grp=self._goTracked
grp.addItem(go)
self._moduleFixTarget._tree.setData(grp.childItems())
pass
def cb_testcode(self):

4
toolbox/Readme.md Normal file
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@@ -0,0 +1,4 @@
toolbox
--------
this directory contains test applications to analyse data and try basic functionalities.

0
workbench/autofocus.py → toolbox/autofocus.py
View File

5
workbench/fiducialDetection.py → toolbox/fiducialDetection.py
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@@ -34,7 +34,8 @@ def set_fiducial(pic):
pic[0:6, 0:5]=f*pic.max()
def wtestimages():
fn=os.path.expanduser('~/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/SwissMX/scratch/fiducial/image{idx:03d}.png')
#fn=os.path.expanduser('~/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/SwissMX/scratch/fiducial/image{idx:03d}.png')
fn=os.path.expanduser('../scratch/fiducial/image{idx:03d}.png')
img=np.kron(np.array([[1, 0] * 5, [0, 1] * 5] * 6,dtype=np.uint8), np.ones((100, 100),dtype=np.uint8)*255)
set_fiducial(img)
pil_img=PIL.Image.fromarray(img)
@@ -52,7 +53,7 @@ def wtestimages():
img=np.ndarray((1200,1000))
wtestimages()
#wtestimages()
class fiducial(QtGui.QMainWindow):

8
workbench/Readme.md
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@@ -1,8 +0,0 @@
testApps
--------
this directory contains test applications to analyse data and try basig functionalities.
'scratch' contains quick and dirty basic tests
'testApps' contains clean small applications to tests e.g. image analysis stuff.