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towards new pix2pos calibration part 1

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zamofing_t
2022-07-19 10:13:35 +02:00
parent 1696328a53
commit 7209243f2f
2 changed files with 193 additions and 60 deletions
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155
geometry.py
View File

@@ -7,6 +7,10 @@
# *-----------------------------------------------------------------------*
'''
coordinate systems, optical center, xray axis, pixel sizes etc.
ppm= pixel per mm
update_pix2pos
'''
import logging
import numpy as np
@@ -27,41 +31,84 @@ class geometry:
# this coordinate represents also the origin of other coordinates
pass
def zoom2pixsz(self,zoom):
# this returns the pixel size at a given zoom level
def interp_zoom(self,zoom):
# this calculates the interpoated pix2pos coordinate transformation matrix
# the returned value is a 2x2 matrix:
# [pxx pxy]
# [pyx pyy] which is interpolated out of a lookup table
#
# [pxx pxy] [nx]
# [pyx pyy]*[ny] results in a vector in meter of a vector [nx,ny] pixels in x and y direction
pass
# [a b] [mx] [px]
# [ ]*[ ]=[ ]
# [c d] [my] [py]
def set_zoom2pixsz(self,meas):
K,AA=self._lut_pix2pos
pix2pos=self._pix2pos=np.asmatrix(np.ndarray((2,2),np.float))
pix2pos[0,0]=np.interp(zoom,K,AA[:,0,0])
pix2pos[0,1]=np.interp(zoom,K,AA[:,0,1])
pix2pos[1,0]=np.interp(zoom,K,AA[:,1,0])
pix2pos[1,1]=np.interp(zoom,K,AA[:,1,1])
_log.debug('interpolation array:{}'.format(tuple(pix2pos.ravel())))
def update_pix2pos(self,meas):
#calculates _lut_z2p out of measurements
# the _lut_z2p is dictionaty a lookuptable
# zoom {1,200,400,600,800,1000}
#[pxx pxy]
#[pyx pyy]
self._lut_z2p=_lut_z2p={
'zoom': np.array((1,200,400,600,800,1000),dtype=np.float32),
'pixsz': np.array(
#((pxx,pxy),(pyx,pyy)), # zoom n
((( 1,0),(0, 1)), # zoom 1
(( 2,0),(0, 2)), # zoom 200
(( 4,0),(0, 4)), # zoom 400
(( 6,0),(0, 6)), # zoom 600
(( 8,0),(0, 8)), # zoom 800
((10,0),(0,10))), # zoom 1000
dtype=np.float32)}
#
# [a b] [mx] [px]
# [ ]*[ ]=[ ]
# [c d] [my] [py]
#
# [a*mx1 b*my1] [px1]
# [ ... ... ] [...]
# [a*mxn b*myn] =[pxn]
# [c*mx1 d*my1] [py1]
# [ ... ... ] [...]
# [c*mxn d*myn] [pyn]
#
# [mx1 my1 0 0 ] [a] [px1]
# [... .. 0 0 ] [b] [...]
# [mxn myn 0 0 ]*[c]=[pxn]
# [ 0 0 mx1 my1] [d] [py1]
# [ 0 0 ... .. ] [...]
# [ 0 0 mxn myn] [pyn]
#
# A *aa = y
n=len(meas)
zoom =np.ndarray(shape=n,dtype=np.float32)
pixsz=np.ndarray(shape=(n,2,2),dtype=np.float32)
# https://de.wikipedia.org/wiki/Methode_der_kleinsten_Quadrate
for i,(k,v) in enumerate(meas):
pass
self._lut_z2p={ 'zoom': zoom, 'pixsz': pixsz}
# r= A*aa-y
# mit aa=(A.T*A)^-1*A.T*y
# A=np.zeros((d.shape[0]*2,d.shape[1]))
# A[:d.shape[1]-1,:2]=A[d.shape[1]-1:,2:]=d[:,:2]
#
# y=d[:,2:].T.ravel()
# y=np.asmatrix(y).T
#
# A=np.asmatrix(A)
# aa=(A.T*A).I*A.T*y
# a,b,c,d=aa
# a,b,c,d=np.asarray(aa).ravel()
#
# aa=aa.reshape(2,-1)
AA=np.ndarray((len(meas),2,2),np.float)
K=np.array(tuple(meas.keys()),np.float)
self._lut_pix2pos=(K,AA)
for i,(k,v) in enumerate(meas.items()):
m=np.array(v) # measurements
d=m[1:]-m[0] # distances
A=np.zeros((d.shape[0]*2,d.shape[1]),np.float)
A[:d.shape[1]-1,:2]=A[d.shape[1]-1:,2:]=d[:,:2]
y=d[:,2:].T.ravel()
y=np.asmatrix(y).T
A=np.asmatrix(A)
aa=(A.T*A).I*A.T*y
AA[i]=aa.reshape(2,-1)
#bx_coefs = np.polyfit(nbx[0], nbx[1], 3)
#np.poly1d(bx_coefs)
_log.debug('least square data:\nK:{}\nAA:{}'.format(K,AA))
def autofocus(self):
# cam camera object
@@ -75,12 +122,16 @@ class geometry:
def pix2pos(self,p,zoom=None):
# returns the position m(x,y) in meter relative to the optical center at a given zoom level of the pixel p(x,y)
# if zoom=None, the last zoom value is used
pass
if zoom is not None:
self.interp_zoom(zoom)
return np.asarray(self._pix2pos*np.mat(p).T).ravel()
def pos2pix(self,p,zoom=None):
# returns the pixel p(x,y) of the position m(x,y) in meter relative to the optical center at a given zoom level
# if zoom=None, the last zoom value is used
pass
if zoom is not None:
self.interp_zoom(zoom)
return np.asarray(self._pix2pos.I*np.mat(p).T).ravel()
def optctr2xray(self):
# returns the vector m(x,y) of the optical center to the xray
@@ -130,16 +181,48 @@ if __name__ == "__main__":
1000:{'x': (+0.1 , ( 121, 632),(1044, 592)),
'y': (+0.08 , ( 593, 883),( 570, 145))},
}
measure={
1: [(-3.0 , -7.6 , 116.99110193046, 632.5463827525),
(-2.0 , -7.6 , 934.07501517856, 600.7926167715),
(-2.0 , -7.1 , 916.54131238102, 191.0366615002),
(-3.0 , -7.1 , 103.74668003329, 226.2150231456)],
200: [(-3.1 , -7.3 , 113.66321353086, 824.9041423107),
(-2.3 , -7.3 , 1065.97386092697, 792.2851118419),
(-2.3 , -6.7 , 1033.68452410347, 74.0336610693),
(-3.1 , -6.7 , 84.62681572700, 116.6832971512)],
400: [(-3.4 , -6.7 , 155.00053674203, 601.3838942136),
(-3.0 , -6.7 , 957.95919656052, 573.0827012272),
(-3.2 , -6.5 , 541.08684037200, 187.9171307943),
(-3.2 , -6.8 , 564.32152887203, 789.1146957326)],
600: [(-3.3 , -6.8 , 328.27244399903, 509.5061192017),
(-3.1 , -6.8 , 992.78996735279, 488.0323963092),
(-3.2 , -6.9 , 672.03111567934, 832.4122409755),
(-3.2 , -6.7 , 645.70960116180, 164.2534779331)],
800: [(-3.2 , -6.7 , 639.52253576449, 53.4455632943),
(-3.2 , -6.85, 671.47023245203, 882.6335091391),
(-3.3 , -6.75, 105.12470026379, 361.3051859197),
(-3.1 , -6.75, 1195.96864609255, 313.1068618673)],
1000:[(-3.25, -6.75, 195.05641095116, 353.3492286375),
(-3.15, -6.75, 1117.27204644084, 314.9636405871),
(-3.2 , -6.8 , 675.10991143017, 790.3040145281),
(-3.2 , -6.72, 638.98580653116, 59.3803912957)]}
import numpy as np
np.set_printoptions(suppress=True)
np.set_printoptions(linewidth=196)
obj=geometry()
obj.calc_zoom2pixsz(measure)
obj.update_pix2pos(measure)
obj.interp_zoom(1)
obj.interp_zoom(200)
obj.interp_zoom(100)
print(np.asarray(obj._pix2pos*np.mat((1,0)).T).ravel())
print(obj._pix2pos*np.mat((0,1)).T)
print(obj._pix2pos*np.mat((2,.1)).T)

98
swissmx.py
View File

@@ -97,7 +97,7 @@ from PyQt5.QtWidgets import (
QSplashScreen, QTextBrowser, QToolBox, QVBoxLayout, QWidget,)
from PyQt5.uic import loadUiType
from CustomROI import BeamMark
import CustomROI as CstROI
#from CustomROI import BeamMark, Grid, CrystalCircle #ZAC: orig. code
#from GenericDialog import GenericDialog #ZAC: orig. code
#from dialogs.PreferencesDialog import PreferencesDialog #ZAC: orig. code
@@ -119,7 +119,7 @@ from app_config import settings, appsconf, option, toggle_option, simulated
import epics
from epics.ca import pend_event
import camera,backlight,zoom,illumination
import camera,backlight,zoom,illumination,geometry
#_URL = "http://PC12288:8080"
@@ -388,7 +388,7 @@ class Main(QMainWindow, Ui_MainWindow):
def add_beam_marker(self):
w, h = settings.value(BEAM_SIZE)
self._beammark = BeamMark([100, 100], (int(w), int(h)), parent=self)
self._beammark = CstROI.BeamMark([100, 100], (int(w), int(h)), parent=self)
self.vb.addItem(self._beammark)
def camera_pause_toggle(self):
@@ -416,7 +416,7 @@ class Main(QMainWindow, Ui_MainWindow):
else:
sz=self.update_size()
pic=kwargs['value'].reshape(sz[::-1])
_log.debug('new_frame_pv_cb count {}'.format(kwargs['count']))
#_log.debug('new_frame_pv_cb count {}'.format(kwargs['count']))
if pic.dtype==np.int16:
pic.dtype=np.uint16
camera.epics_cam.set_fiducial(pic, 255)
@@ -798,7 +798,8 @@ class Main(QMainWindow, Ui_MainWindow):
grp.layout().addWidget(self._ppm_feature_size_spinbox, 0, 1)
self._ppm_calibration = but = QPushButton("Start calibration")
but.setCheckable(True)
but.clicked.connect(lambda x: self.update_ppm_fitters())
#but.clicked.connect(lambda x: self.update_ppm_fitters())
but.clicked.connect(self.update_ppm_fitters)
grp.layout().addWidget(but, 1, 0, 1, 2)
help = QTextBrowser()
grp.layout().addWidget(help, 2, 0, 5, 2)
@@ -806,9 +807,11 @@ class Main(QMainWindow, Ui_MainWindow):
"""<body>
<h1>Pixel/MM Setup</h1>
<ol>
<li>choose: <b>feature size</b></li>
<li>press: <b>Start calibration</b></li>
<li>for each zoom level, CTRL-Click (left mouse button) <b>2</b> locations which are <b>feature-size</b> apart</li>
<li>for each zoom level:
<li>choose a good fiducial mark
<li>move the stage x/y at min. 3 different locations
<li>CTRL-Click (left mouse button) on the fiducial mark
<li>un-click: <b>Start calibration</b></li>
</ol>
</body>
@@ -960,7 +963,18 @@ class Main(QMainWindow, Ui_MainWindow):
self.beamx_fitter = np.poly1d(bx_coefs)
self.beamy_fitter = np.poly1d(by_coefs)
def update_ppm_fitters(self, calib=None):
def update_ppm_fitters(self, calib):
app=QApplication.instance()
if calib:
_log.info("received new pix2pos calibration")
app._ppmRaw=dict()
else:
app._geometry.update_pix2pos(app._ppmRaw)
del app._ppmRaw
return
if calib is not None:
_log.info("received new calibration for PPM")
self._zoom_to_ppm = calib
@@ -1010,17 +1024,17 @@ class Main(QMainWindow, Ui_MainWindow):
self.pixelsPerMillimeter.emit(ppm)
self.update_beam_marker(value)
def getZoom(self):
return qoptic_zoom.get_position()
# def getZoom(self):
# return qoptic_zoom.get_position()
def getPpm(self):
ppm_fitter = None
try:
ppm_fitter = self.ppm_fitter(self.getZoom())
except Exception as e:
_log.error("garbage in getPpm()")
traceback.print_exc()
return ppm_fitter
# def getPpm(self):
# ppm_fitter = None
# try:
# ppm_fitter = self.ppm_fitter(self.getZoom())
# except Exception as e:
# _log.error("garbage in getPpm()")
# traceback.print_exc()
# return ppm_fitter
def append_to_beam_markers(self, x, y, zoom):
self._beam_markers[zoom] = (x, y)
@@ -1073,7 +1087,7 @@ class Main(QMainWindow, Ui_MainWindow):
try:
ppm = self.ppm_fitter(z)
except:
ppm = 1
ppm = 1E3
x, y = xy.x(), xy.y()
try:
bx, by = self.get_beam_mark_on_camera_xy()
@@ -1103,15 +1117,48 @@ class Main(QMainWindow, Ui_MainWindow):
)
)
def mouse_click_event(self, event):
def mouse_click_event_ppm(self, event):
app=QApplication.instance()
fx_motor, fy_motor, bx_motor, bz_motor, omega_motor = self.get_gonio_tweakers()
zoom = app._zoom.get()
fast_x=self.tweakers["fast_x"];fast_y=self.tweakers["fast_y"]
try:
raw=app._ppmRaw[zoom]
except (AttributeError,KeyError) as e:
if type(e) is AttributeError:
_log.info("")
msg="SwissMX *POST-SAMPLE-TUBE* configuration is incomplete!!!"
QMessageBox.warning(self, "pix2pos calibration", "Press 'Start calibration' button first")
return
app._ppmRaw=dict()
raw=app._ppmRaw[zoom]=list()
#event.screenPos() #position in pixel on the screen
#event.pos() #position in pixel on the widget
#event.scenePos() # position in user coordinates of the widget
#img.mapFromScene(scenePos) #pixel position of the image at scenePos user coordinates
#mousePos=event.pos() #position in pixel on the widget
#scenePos=event.scenePos()
#imgPos = self.img.mapFromScene(scenePos)
#_log.debug('mouse_pos:{} scene_pos:{} imgPos:{}'.format(tuple(mousePos),tuple(scenePos),(imgPos.x(),imgPos.y())))
#_log.debug('fast stage:{} {}'.format(fast_x.get_position(),fast_y.get_position()))
imgPos = self.img.mapFromScene(event.scenePos())
fx=fast_x.get_position();fy=fast_y.get_position()
x=imgPos.x();y=imgPos.y()
_log.debug('append calib: zoom:{} stage_x_y:{}/{} cam_pix_x_y:{}/{}'.format(zoom,fx,fy,x,y))
raw.append((fx,fy,x,y))
def mouse_click_event(self, event):
_log.debug("{}".format(event))
_log.debug(" pos {}".format(event.pos()))
_log.debug("screen pos {}".format(event.screenPos()))
_log.debug("scene pos {}".format(event.scenePos()))
task = self.active_task()
if task==TASK_SETUP_PPM_CALIBRATION:
self.mouse_click_event_ppm(event)
return
app=QApplication.instance()
fx_motor, fy_motor, bx_motor, bz_motor, omega_motor = self.get_gonio_tweakers()
if event.button() == Qt.RightButton:
print_transform(self.vb.childTransform())
@@ -1124,7 +1171,7 @@ class Main(QMainWindow, Ui_MainWindow):
try:
ppm = self.ppm_fitter(zoom_level)
except:
ppm = 1 # 0: do not move if we don't know ppm
ppm = 1E3
dblclick = event.double()
shft = Qt.ShiftModifier & event.modifiers()
ctrl = Qt.ControlModifier & event.modifiers()
@@ -1925,7 +1972,7 @@ class Main(QMainWindow, Ui_MainWindow):
ystep = self._sb_grid_y_step.value()
xoffset = self._sb_grid_x_offset.value()
yoffset = self._sb_grid_y_offset.value()
grid = Grid( x_step=xstep, y_step=ystep, x_offset=xoffset, y_offset=yoffset, gonio_xy=(gx, gy), grid_index=grid_index, parent=self,)
grid = CstROI.Grid( x_step=xstep, y_step=ystep, x_offset=xoffset, y_offset=yoffset, gonio_xy=(gx, gy), grid_index=grid_index, parent=self,)
self._grids.append(grid)
grid.calculate_gonio_xy()
grid.sigRemoveRequested.connect(lambda g=grid: self.remove_grid(g))
@@ -2754,7 +2801,7 @@ class Main(QMainWindow, Ui_MainWindow):
if not (add_xtals and draw_xtals):
continue
_log.debug(f"adding {'fiducial' if is_fiducial else 'xtal'} mark #{n}: {is_fiducial} {gx:.3f}, {gy:.3f}, {cx:.1f}, {cy:.1f}")
m = CrystalCircle(
m = CstROI.CrystalCircle(
gonio_xy=(gx, gy),
parent=self,
model_row_index=n,
@@ -3277,6 +3324,9 @@ def main():
else:
app._camera = camera.epics_cam()
#app._camera.run() is called in center_piece_update
app._geometry=geometry.geometry()
app_icon = QtGui.QIcon()
app_icon.addFile("artwork/logo/16x16.png", QtCore.QSize(16, 16))