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add workbench autofocus.py

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zamofing_t
2022-09-15 07:44:02 +02:00
parent 14260851cf
commit e4b3ad0b5f
6 changed files with 257 additions and 55 deletions
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43
deltatau.py
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@@ -1,43 +0,0 @@
import sys,os,socket
sys.path.insert(0, os.path.expanduser('..'))
hostname=socket.gethostname()
if hostname=='ganymede':
sys.path.insert(0, os.path.expanduser('~/Documents/prj/SwissFEL/PBTools/'))
else:
#sys.path.insert(0, os.path.expanduser('/tmp/zamofing_t/PBTools/'))
sys.path.insert(0, os.path.expanduser('/sf/cristallina/applications/mx/zamofing_t/PBTools/'))
import logging
_log=logging.getLogger(__name__)
from PyQt5.QtWidgets import (QApplication,)
from app_config import AppCfg #settings, option, toggle_option
from pbtools.misc.pp_comm import PPComm
from pbtools.misc.gather import Gather
import shapepath
class Deltatau:
def __init__(self):
app=QApplication.instance()
cfg=app._cfg
host=cfg.value(AppCfg.DT_HOST)
hpp=host.split(':')
param={'host':hpp[0]}
if len(hpp)>1:
param['port']=int(hpp[1])
if len(hpp)>2:
param['fast_gather_port']=int(hpp[2])
_log.info(' -> ssh-tunneling PPComm({host}:{port} {host}:{fast_gather_port})'.format(**param))
try:
self._comm=comm=PPComm(**param,timeout=2.0)
self._gather=gather=Gather(comm)
except (socket.timeout,socket.gaierror) as e:
_log.critical(f'can not connect to deltatau:"{host}" -> {e}')
self._comm=comm=None
self._gather=gather=None
#return
self._shapepath=sp=shapepath.ShapePath(comm, gather, verbose=0xff, sync_mode=1, sync_flag=3)

50
geometry.py
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@@ -247,13 +247,56 @@ class geometry:
_log.debug('least square data:\nK:{}\nAA:{}'.format(K, AA))
def autofocus(self):
@staticmethod
def autofocus(cam,mot,rng=(-1,1),n=30):
# cam camera object
# mot motor object
# 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)
import PIL.Image
from scipy import ndimage
v=np.ndarray(shape=(len(cam),2))
if type(cam) == list:
for i, fn in enumerate(cam):
img=PIL.Image.open(fn)
img=np.asarray(img)
s=ndimage.sobel(img)
v[i,0]=s.sum()
v[i,1]=s.std()
#fft=np.log(np.abs(np.fft.fft2(img)))
#fft=np.fft.fftshift(fft)
#s=np.array(fft.shape,dtype=np.uint16)/2
#fft[300:700,400:800]=0
#v[i,1]=fft.sum()
#if i&0x3==0:
# plt.figure()
# plt.imshow(fft)
fig, ax=plt.subplots()
mx=v.max(0)
mn=v.min(0)
v=(v-mn)/(mx-mn)
#ax.plot(v[:,0])
ax.plot(v)
plt.show()
pass
else:
p0=mot.get_rbv()
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()}')
pass
def pix2pos(self, p, zoom=None):
@@ -558,6 +601,11 @@ if __name__=="__main__":
[2.84446241, 3.54734879, 3.1415]])
plane=geometry.least_square_plane(pts)
if args.mode&0x08:
import glob
imgLst=sorted(glob.glob("scratch/image*.png"))
geometry.autofocus(imgLst,None)
# pix2pos="[[1.0, 200.0, 400.0, 600.0, 800.0], [[[0.001182928623952055, -2.6941995127711305e-05], [-4.043716694634124e-05, -0.0011894314084263825]], [[0.0007955995220142541, -3.175003727901119e-05], [-2.0896601103372113e-05, -0.0008100805094631365]], [[0.00048302539335378367, -1.1661121407652543e-05], [-2.0673746995751222e-05, -0.0004950857899461772]], [[0.00028775903460576395, -1.3762555219494508e-05], [-9.319936861519268e-06, -0.0002889214488565999]], [[0.0001788819256630411, -6.470841493681516e-06], [-2.0336605088889967e-06, -0.0001831131753499113]]]]"

89
psi_device.py Normal file
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@@ -0,0 +1,89 @@
import sys,os,socket
sys.path.insert(0, os.path.expanduser('..'))
hostname=socket.gethostname()
if hostname=='ganymede':
sys.path.insert(0, os.path.expanduser('~/Documents/prj/SwissFEL/PBTools/'))
else:
sys.path.insert(0, os.path.expanduser('/sf/cristallina/applications/mx/zamofing_t/PBTools/'))
sys.path.insert(0, os.path.expanduser("/photonics/home/gac-cristall/Documents/swissmx_cristallina/slic/"))
from slic.core.acquisition import SFAcquisition
import logging
_log=logging.getLogger(__name__)
from PyQt5.QtWidgets import (QApplication,)
from app_config import AppCfg #settings, option, toggle_option
from pbtools.misc.pp_comm import PPComm
from pbtools.misc.gather import Gather
import shapepath
try:
from slic.core.acquisition import SFAcquisition
except ImportError as e:
_log.warning(e)
class Deltatau:
def __init__(self):
app=QApplication.instance()
cfg=app._cfg
host=cfg.value(AppCfg.DT_HOST)
hpp=host.split(':')
param={'host':hpp[0]}
if len(hpp)>1:
param['port']=int(hpp[1])
if len(hpp)>2:
param['fast_gather_port']=int(hpp[2])
_log.info(' -> ssh-tunneling PPComm({host}:{port} {host}:{fast_gather_port})'.format(**param))
try:
self._comm=comm=PPComm(**param,timeout=2.0)
self._gather=gather=Gather(comm)
except (socket.timeout,socket.gaierror) as e:
_log.critical(f'can not connect to deltatau:"{host}" -> {e}')
self._comm=comm=None
self._gather=gather=None
#return
self._shapepath=sp=shapepath.ShapePath(comm, gather, verbose=0xff, sync_mode=1, sync_flag=3)
class Jungfrau:
def __init__(self):
#python /sf/jungfrau/applications/daq_client/daq_client.py -h
#python /sf/jungfrau/applications/daq_client/daq_client.py -p p19739 -t no_beam_test
# -c/sf/cristallina/config/channel_lists/channel_list_bs-e/sf/cristallina/config/channel_lists/channel_list_ca
# -f/sf/cristallina/config/jungfrau/jf_1d5M.json
# --start_pulseid 15382163895 --stop_pulseid 15382163905
#rsync -vai gac-cristall@saresc-cons-03:/sf/jungfrau/applications/daq_client/daq_client.py .
# setup slic parameters
detectors = [ { "name" : "JF17T16V01",
"adc_to_energy" : True,
"compression" : True,
"factor" : 11.33,
"geometry" : True,
"double_pixel_action" : "mask",
"remove_raw_files" : False
} ] #["JF17T16V01"]
bs_channels = [ # have timing signitures
"SARES30-LSCP1-CRISTA1:CH0:1",
# "SARES30-CAMS156-SMX-OAV:FPICTURE"
]
epics_channels = [ # no time signitures
]
try:
self._daq=SFAcquisition(
"cristallina", "p20516",
default_detectors=detectors, default_channels=bs_channels, default_pvs=epics_channels,
rate_multiplicator=1, append_user_tag_to_data_dir=True
)
except NameError as e:
_log.warning(f'Jungfrau not connected: {e}')
self._daq=None
def acquire(self,run_name, n_pulses, wait=False):
if self._daq is not None:
self._daq.acquire( run_name, n_pulses=n_pulses, wait=False)

28
swissmx.py
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@@ -100,8 +100,7 @@ import epics
from epics.ca import pend_event
import camera,backlight,zoom,illumination,geometry
ts.log('Import part 7/8:')
import deltatau
import detector
import psi_device
ts.log('Import part 8/8:')
def tdstamp():
@@ -362,7 +361,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
grp.setTransform(tr) # assign transform
#--- image ---
self._goImg=img=pg.ImageItem()
self._goImg=img=pg.ImageItem() #border=pg.mkPen('r',width=2))
grp.addItem(img)
#--- opctical center ----
@@ -1080,7 +1079,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
#create trace
self.add_camera_trace()
self.add_camera_trace(pFix)
_log.debug(f'dist to beam ({pFix[0]:>0.6g} {pFix[1]:>0.6g}mm)')
fx_motor=self.tweakers["fast_x"]
@@ -1301,7 +1300,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
grp.setTransform(tr)
grpTrc.setTransform(tr)
def add_camera_trace(self):
def add_camera_trace(self,delta_mm):
# add up to tracelen image when moveing motors to new positions
try:
tracelen=self._goTrace._tracelen
@@ -1316,7 +1315,8 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
trImg=self._goImgGrp.transform()
trTrk=self._goTracked.transform()
tr=trImg*trTrk.inverted()[0] # TODO: check if oder correct !!!
img=pg.ImageItem(self._goImg.image)
cm=pg.ColorMap((0,255),((0,0,64),(255,255,128)))#,opacity=.5)
img=pg.ImageItem(self._goImg.image,lut=cm.getLookupTable(0,255))
img.setTransform(tr)
self._goTrace.addItem(img) # automatically added to self.vb
@@ -1598,13 +1598,18 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
plt.stem(x, y)
plt.show(block=False)
step=1
step=2
if step==0:
vb=self.vb
vb.autoRange(items=(self._goImg,))
elif step==1:
testMatplotlib()
if step==3:
elif step==2:
app=QApplication.instance()
cfg=app._cfg
geo=app._geometry
geo.autofocus(app._camera, self.tweakers['base_z'])
elif step==3:
grp=pg.ItemGroup()
vb.addItem(grp)
obj=UsrGO.Marker((100, 100), (100, 100), mode=1)
@@ -2019,11 +2024,11 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
try:
dt=app._deltatau
except AttributeError:
app._deltatau=dt=deltatau.Deltatau()
app._deltatau=dt=psi_device.Deltatau()
try:
jf=app._jungfrau
except AttributeError:
app._jungfrau=jf=detector.Jungfrau()
app._jungfrau=jf=psi_device.Jungfrau()
sp=dt._shapepath
sp.verbose=dt_misc['verbose']
@@ -2042,7 +2047,8 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
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) ater given time
sp.trigger(0.5) # send a start trigger (if needed) after given time
jf.acquire('filename.tmp',sp.points.shape[0])
if not dt._comm is None:
while True:
p=sp.progress()

8
workbench/Readme.md Normal file
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@@ -0,0 +1,8 @@
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.

94
workbench/autofocus.py Normal file
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@@ -0,0 +1,94 @@
# -*- coding: utf-8 -*-
"""
Demonstrate a simple data-slicing task: given 3D data (displayed at top), select
a 2D plane and interpolate data along that plane to generate a slice image
(displayed at bottom).
"""
## Add path to library (just for examples; you do not need this)
import numpy as np
from pyqtgraph.Qt import QtCore, QtGui
import pyqtgraph as pg
app=QtGui.QApplication([])
## Create window with two ImageView widgets
win=QtGui.QMainWindow()
win.resize(800, 800)
win.setWindowTitle('pyqtgraph example: DataSlicing')
cw=QtGui.QWidget()
win.setCentralWidget(cw)
l=QtGui.QGridLayout()
cw.setLayout(l)
imv1=pg.ImageView()
imv2=pg.ImageView()
l.addWidget(imv1, 0, 0)
l.addWidget(imv2, 1, 0)
sld=QtGui.QSlider(QtCore.Qt.Horizontal)
sld.setMinimum(10)
sld.setMaximum(30)
sld.setValue(20)
sld.setTickPosition(QtGui.QSlider.TicksBelow)
sld.setTickInterval(5)
l.addWidget(sld, 2, 0)
win.show()
roi=pg.LineSegmentROI([[10, 64], [120, 64]], pen='r')
imv1.addItem(roi)
x1=np.linspace(-30, 10, 128)[:, np.newaxis, np.newaxis]
x2=np.linspace(-20, 20, 128)[:, np.newaxis, np.newaxis]
y=np.linspace(-30, 10, 128)[np.newaxis, :, np.newaxis]
z=np.linspace(-20, 20, 128)[np.newaxis, np.newaxis, :]
d1=np.sqrt(x1**2+y**2+z**2)
d2=2*np.sqrt(x1[::-1]**2+y**2+z**2)
d3=4*np.sqrt(x2**2+y[:, ::-1]**2+z**2)
data=(np.sin(d1)/d1**2)+(np.sin(d2)/d2**2)+(np.sin(d3)/d3**2)
import PIL.Image
from scipy import ndimage
import glob
imgLst=sorted(glob.glob("image*.png"))
v=np.ndarray(shape=(len(imgLst), 2))
#for i, fn in enumerate(imgLst):
# img=PIL.Image.open(fn)
# img=np.asarray(img)
# s=ndimage.sobel(img)
# v[i, 0]=s.sum()
# v[i, 1]=s.std()
#fig, ax=plt.subplots()
#mx=v.max(0)
#mn=v.min(0)
#v=(v-mn)/(mx-mn)
# ax.plot(v[:,0])
#ax.plot(v)
#plt.show()
# pass
def update():
global data, imv1, imv2, imgLst
d2=roi.getArrayRegion(data, imv1.imageItem, axes=(1, 2))
imv2.setImage(d2)
roi.sigRegionChanged.connect(update)
## Display the data
imv1.setImage(data)
imv1.setHistogramRange(-0.01, 0.01)
imv1.setLevels(-0.003, 0.003)
update()
## Start Qt event loop unless running in interactive mode.
if __name__=='__main__':
import sys
if (sys.flags.interactive!=1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()