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various fixes

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This commit is contained in:
zamofing_t
2022-09-16 12:25:36 +02:00
parent 6a7b5ab91e
commit ba4f5feecb
7 changed files with 141 additions and 87 deletions
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14
app_config.py
View File

@@ -263,10 +263,10 @@ verbose bits:
0x01 basic info
0x02 plot sorting steps
0x04 list program
0x04 upload progress
0x08 plot gather path
0x10 plot pvt trajectory (before motion)
0x20 print sync details
0x08 upload progress
0x10 plot gather path
0x20 plot pvt trajectory (before motion)
0x40 print sync details
'''
params=[
@@ -330,9 +330,9 @@ verbose bits:
{'name':'Delta Tau Parameters', 'type':'group','expanded':False, 'children':[
{'name':AppCfg.DT_HOST ,'title':'host name (host[:port:port_gather])','value':dt_host ,'type':'str'} ,
{'name':AppCfg.DT_MISC, 'title':'miscellaneous', 'type':'group', 'children':[
{'name':'show plots after collection', 'value':dt_misc['show_plots'], 'type':'bool','tip':"This is a checkbox"},
{'name':'velocity_scale', 'value':dt_misc['vel_scl'], 'type':'float', 'limits':(0, 1), 'step':0.1, 'tip':"This is a checkbox"},
{'name':'pt2pt_time', 'value':dt_misc['pt2pt_time'],'type':'float', 'step':0.1,'tip':"This is a checkbox"},
{'name':'show_plots', 'value':dt_misc['show_plots'], 'type':'bool', 'title':'show plots after collection'},
{'name':'vel_scl', 'value':dt_misc['vel_scl'], 'type':'float', 'limits':(0, 1), 'step':0.1, 'title':'velocity_scale', 'tip':"scale between smooth(1.0) and stop and go(0.0)"},
{'name':'pt2pt_time', 'value':dt_misc['pt2pt_time'], 'type':'float', 'step':0.1,'tip':"time in ms from point to point"},
{'name':'sync_mode', 'value':dt_misc['sync_mode'], 'type':'int', 'tip':tip_sync_mode},
{'name':'sync_flag', 'value':dt_misc['sync_flag'], 'type':'int', 'tip':tip_sync_flag},
{'name':'verbose', 'value':dt_misc['verbose'], 'type':'int', 'tip':tip_verbose},

27
camera.py
View File

@@ -109,34 +109,27 @@ class epics_cam(object):
def get_image(self):
_log.warning('this can be very slow. Use callbacks if possible.')
try:
pv_pic=self.getPv('FPICTURE')
except AttributeError:
imgSeq=self._sim['imgSeq']
except AttributeError: pass
else:
imgSeq=self._sim['imgSeq']
idx=self._sim['imgIdx']
self._sim['imgIdx']=(idx + 1) % imgSeq.shape[0]
#_log.debug('simulated idx:{}'.format(idx))
self.pic=pic=imgSeq[idx]
self._pic=pic=imgSeq[idx]
return pic
try:
pic=self._pic
return pic
except AttributeError as e:
pass
pv_pic=self.getPv('FPICTURE')
sz=self._sz
pic = pv_pic.get(count=sz[0]*sz[1], as_numpy=True).reshape(sz[::-1])
epics_cam.set_fiducial(pic,255)
except AttributeError as e:
_log.warning("failed to fetch image")
else:
if pic.dtype==np.int16:
pic.dtype=np.uint16
try:
trf=self._transformation
except AttributeError as e:
pass
else:
if trf[1,0]==0:
pic=pic[::trf[0,0],::trf[1,1]]
else:
pic=pic[::trf[0,1],::trf[1,0]].T
self.pic=pic
self._pic=pic
return pic
def stop(self,v=CameraStatus.IDLE):

19
geometry.py
View File

@@ -256,13 +256,13 @@ class geometry:
_log.debug('least square data:\nK:{}\nAA:{}'.format(K, AA))
@staticmethod
def autofocus(cam,mot,rng=(-1,1),n=30,saveImg=False):
def autofocus(cam,mot,rng=(-1,1),n=30,progressDlg=None,saveImg=False):
# cam camera object
# mot motor 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
# roi region of interrest to calculate sharpness
# mode mode to calculate sharpness (sum/max-min/hist? of edge detection in roi)
# progressDlg a pg.ProgressDialog to allow to abort the function call
if mot is not None:
p0=mot.get_rbv()
else:
@@ -295,13 +295,19 @@ class geometry:
img=np.asarray(img)
else:
mot.move_abs(p, wait=True)
img=cam._pic # get_image()
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()
@@ -333,8 +339,7 @@ class geometry:
img=PIL.Image.open(cam)
img=np.asarray(img)
else:
img=cam._pic # get_image()
img16=np.array(img, np.int16)
img=cam.get_image() # get latest image
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

10
psi_device.py
View File

@@ -15,7 +15,7 @@ _log=logging.getLogger(__name__)
from PyQt5.QtWidgets import (QApplication,)
from app_config import AppCfg #settings, option, toggle_option
import epics
from pbtools.misc.pp_comm import PPComm
from pbtools.misc.gather import Gather
import shapepath
@@ -25,6 +25,7 @@ try:
except ImportError as e:
_log.warning(e)
class Deltatau:
def __init__(self):
app=QApplication.instance()
@@ -83,7 +84,14 @@ class Jungfrau:
except NameError as e:
_log.warning(f'Jungfrau not connected: {e}')
self._daq=None
self._pv_pulse_id=epics.PV('SAR-EXPMX-EVR0:RX-PULSEID')
def acquire(self,run_name, n_pulses, wait=False):
if self._daq is not None:
self._pulse_id_start=self._pv_pulse_id.value
self._daq.acquire( run_name, n_pulses=n_pulses, wait=False)
def gather_upload(self):
self._pulse_id_end=self._pv_pulse_id.value

36
swissmx.py
View File

@@ -30,6 +30,7 @@ logging.getLogger('matplotlib').setLevel(logging.INFO)
logging.getLogger('PIL').setLevel(logging.INFO)
logging.getLogger('illumination').setLevel(logging.INFO)
logging.getLogger('zoom').setLevel(logging.INFO)
logging.getLogger('pbtools.misc.pp_comm').setLevel(logging.INFO)
_log = logging.getLogger("swissmx")
#_log.setLevel(logging.INFO)
@@ -47,6 +48,8 @@ import sys, os, time
import json, re
import random, signal, subprocess
import matplotlib as mpl
import matplotlib.pyplot as plt
mpl.use('Qt5Agg') # needed to avoid blocking of ui !
TASK_JUNGFRAU_SETTINGS = "jungfrau_settings"
@@ -1595,7 +1598,10 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
app=QApplication.instance()
geo=app._geometry
#geo.autofocus(app._camera, self.tweakers['base_z'],rng=(-1, 1), n=30,saveImg=True)
geo.autofocus(app._camera, self.tweakers['base_z'],rng=(-1, 1), n=10)
n=10
rng=(-1, 1)
with pg.ProgressDialog('Progress', 0, n) as dlg:
geo.autofocus(app._camera, self.tweakers['base_z'],rng, n,dlg)
def cb_find_fiducial(self):
app=QApplication.instance()
@@ -2059,8 +2065,17 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
sp.verbose=dt_misc['verbose']
sp.points=kwargs['points']
sp.meta['pt2pt_time']=dt_misc['pt2pt_time']
with pg.ProgressDialog('Progress', 0, 100) as dlg:
dlg.setWindowModality(Qt.WindowModal)
#dlg.setRange(0, 0)
#dlg.setCancelButtonText("Abort Acquisition")
#dlg.canceled.connect(self.complete_daq)
#dlg.setAutoClose(True)
#dlg.show()
dlg.setLabelText("Setup Gather/Sync");dlg+=5
sp.setup_gather()
sp.setup_sync(verbose=sp.verbose&0x20, timeOfs=0.05)
sp.setup_sync(verbose=sp.verbose&0x40, timeOfs=0.05)
try:
p=geo._fitPlane
sp.setup_coord_trf(cz=f'{p[0]:+.18g}X{p[1]:+.18g}Y{p[2]:+.18g}') # reset to shape path system
@@ -2068,21 +2083,32 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
_log.warning('no plane fitting done. z does not move')
sp.setup_coord_trf() # reset to shape path system
# sp.meta['pt2pt_time']=10 #put between setup_sync and setup_motion to have more motion points than FEL syncs
dlg.setLabelText("Download motion program");dlg+=5
sp.setup_motion(fnPrg=fn+'.prg', mode=3, scale=1., dwell=10)
dlg.setLabelText("Homing and get ready");dlg+=35
sp.homing() # homing if needed
sp.run() # start motion program
sp.wait_armed() # wait until motors are at first position
sp.trigger(0.5) # send a start trigger (if needed) after given time
#PV with the current pulse
# [sf-lc7a ~]$ caget
jf.acquire('filename.tmp',sp.points.shape[0])
if not dt._comm is None:
dlg.setLabelText("run motion/acquisition")
dlg.setMaximum(sp.points.shape[0])
while True:
p=sp.progress()
if p<0: break
_log.info(f'progress {p}/{sp.points.shape[0]}')
if p<0 or dlg.wasCanceled():
break
#_log.info(f'progress {p}/{sp.points.shape[0]}')
dlg.setValue(p)
time.sleep(.1)
if not dlg.wasCanceled():
jf.gather_upload()
dlg.setLabelText("upload gather data")
sp.gather_upload(fnRec=fn+'.npz')
if dt_misc['show_plots']:
dp=deltatau.shapepath.DebugPlot(sp)
dp=psi_device.shapepath.DebugPlot(sp)
dp.plot_gather(mode=11)
plt.show(block=False)
#plt.show(block=True)

6
workbench/autofocus.py
View File

@@ -107,9 +107,9 @@ class autofocus(QtGui.QMainWindow):
# fft[300:700,400:800]=0
# v[i,1]=fft.sum()
self._imv1.setImage(sb,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
#self._imv2.setImage(sb,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
self._imv2.setImage(sbLut,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
self._imv1.setImage(img,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
self._imv2.setImage(sb,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
#self._imv2.setImage(sbLut,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
mtr=self._metrics
mtr[i, 0]=img.std()

54
workbench/fiducialDetection.py
View File

@@ -69,13 +69,26 @@ class fiducial(QtGui.QMainWindow):
self._imgLst=imgLst=sorted(glob.glob("../scratch/fiducial/*.png"))
self._metrics=mtr=np.ndarray(shape=(len(imgLst), 5))
mtr[:]=0
self._sld=sld=QtGui.QSlider(QtCore.Qt.Horizontal)
sld.setMinimum(0)
sld.setMaximum(len(imgLst)-1)
sld.setValue(0)
sld.setTickPosition(QtGui.QSlider.TicksBelow)
sld.setTickInterval(1)
sld.valueChanged.connect(self.cb_sld_change)
self._sldImgIdx=sld1=QtGui.QSlider(QtCore.Qt.Horizontal)
sld1.setMinimum(0)
sld1.setMaximum(len(imgLst)-1)
sld1.setValue(0)
sld1.setTickPosition(QtGui.QSlider.TicksBelow)
sld1.setTickInterval(1)
sld1.valueChanged.connect(self.cb_sld_change)
self._sldTplSz=sld2=QtGui.QSlider(QtCore.Qt.Horizontal)
sld2.setMinimum(0)
sld2.setMaximum(300)
sld2.setValue(90)
sld2.valueChanged.connect(self.cb_sld_change)
self._sldTplBrd=sld3=QtGui.QSlider(QtCore.Qt.Horizontal)
sld3.setMinimum(3)
sld3.setMaximum(50)
sld3.setValue(20)
sld3.valueChanged.connect(self.cb_sld_change)
self._imv1=imv1=pg.ImageView()
self._imv2=imv2=pg.ImageView()
@@ -91,10 +104,12 @@ class fiducial(QtGui.QMainWindow):
pw.resize(100,100)
pw.setMaximumSize(2000,200)
l.addWidget(sld, 0, 0)
l.addWidget(imv1, 1, 0)
l.addWidget(imv2, 2, 0)
l.addWidget(pw, 3, 0)
l.addWidget(sld1, 0, 0)
l.addWidget(sld2, 1, 0)
l.addWidget(sld3, 2, 0)
l.addWidget(imv1, 3, 0)
l.addWidget(imv2, 4, 0)
l.addWidget(pw, 5, 0)
## Display the data
self.cb_sld_change(0,True)
@@ -108,7 +123,7 @@ class fiducial(QtGui.QMainWindow):
self._imv2.setLevels(0, 1)
def cb_sld_change(self,val,auto=False):
i=self._sld.value()
i=self._sldImgIdx.value()
_log.debug(f'{i}')
fn= self._imgLst[i]
img=PIL.Image.open(fn)
@@ -134,15 +149,17 @@ class fiducial(QtGui.QMainWindow):
#fid=np.ones((250,250),dtype=np.uint8)*255
#fid[20:230,20:230]=0
sz=(90, 90); brd=(20, 20) # zoom 001
#sz=(130, 130); brd=(20, 20) # zoom 200
#sz=(210, 210); brd=(20, 20) # zoom 400
#sz=( 84, 84); brd=( 7, 7) # zoom 001
#sz=(128, 128); brd=( 9, 9) # zoom 200
#sz=(200, 200); brd=(13, 13) # zoom 400
v=self._sldTplSz.value(); sz=(v,v)
v=self._sldTplBrd.value(); brd=(v,v)
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
mask=np.ones((sz[1]+2*brd[1],sz[0]+2*brd[0]),dtype=np.uint8)*255
mask[2*brd[1]:sz[1],2*brd[0]:sz[0]]=0
#https://docs.opencv.org/4.5.2/d4/dc6/tutorial_py_template_matching.html
#res = cv.matchTemplate(img,fid,cv.TM_CCORR_NORMED )
res = cv.matchTemplate(img,fid,cv.TM_CCORR_NORMED,mask=mask)
@@ -177,6 +194,11 @@ class fiducial(QtGui.QMainWindow):
self._imv1.setImage(img,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
self._imv2.setImage(res,autoRange=auto,autoLevels=auto,autoHistogramRange=auto)
pos=mtr.mean(0)[::-1]+(fw2,fh2)
print(fid)
print(mask)
print(corr)
print(mtr)
print(f'TplSz:{sz} TplBrd:{brd}')
_log.debug(f'position: {pos} correlation:{corr.mean()}')