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saving document, plane and fiducal fitter

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This commit is contained in:
zamofing_t
2022-08-30 15:46:45 +02:00
parent 011eaa3e31
commit 7deda365c1
5 changed files with 172 additions and 40 deletions
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37
app_config.py
View File

@@ -10,9 +10,25 @@ _log = logging.getLogger(__name__)
from PyQt5.QtCore import QSettings
from PyQt5.QtWidgets import QApplication, QLineEdit
import os, json, yaml
import json
import numpy as np
import GenericDialog
class MyJsonEncoder(json.JSONEncoder):
""" Special json encoder for numpy types """
def default(self, obj):
if isinstance(obj, np.integer):
return int(obj)
elif isinstance(obj, np.floating):
return float(obj)
elif isinstance(obj, np.ndarray):
return obj.tolist()
elif type(obj) not in (dict,list,str,int):
_log.error('dont know how to json')
return repr(obj)
return json.JSONEncoder.default(self, obj)
class AppCfg(QSettings):
GEO_OPT_CTR='geometry/opt_ctr'
@@ -87,8 +103,7 @@ class AppCfg(QSettings):
self.setValue(AppCfg.GEO_BEAM_POS, [23.4, -54.2]) # beam position relativ to optical center in mm
if AppCfg.GEO_PIX2POS not in keys:
_log.warning(f'{AppCfg.GEO_OPT_CTR} not defined. use default')
import numpy as np
_log.warning(f'{AppCfg.GEO_PIX2POS} not defined. use default')
lut_pix2pos=(np.array([1., 200., 400., 600., 800., 1000.]),
np.array([[[ 2.42827273e-03, -9.22117396e-05],
[-1.10489804e-04, -2.42592492e-03]],
@@ -106,7 +121,6 @@ class AppCfg(QSettings):
if AppCfg.GEO_OPT_CTR not in keys:
_log.warning(f'{AppCfg.GEO_OPT_CTR} not defined. use default')
import numpy as np
opt_ctr=np.array([603.28688025, 520.01112846])
self.setValue(AppCfg.GEO_OPT_CTR, opt_ctr)
@@ -129,10 +143,25 @@ class AppCfg(QSettings):
# print(data)
def setValue(self, key: str, val): #overload to debug
# only simple lists, str, int, float can not be serialized nicely
t=type(val)
if key in (AppCfg.GEO_PIX2POS):
val=json.dumps(val, cls=MyJsonEncoder)
elif key in (AppCfg.GEO_OPT_CTR,AppCfg.GEO_BEAM_SZ,AppCfg.GEO_BEAM_POS,):
val=val.tolist()
elif type(val)==tuple:
val=list(val)
return super(AppCfg, self).setValue(key,val)
def value(self,key,*vargs,**kwargs): #overload to debug
val=super(AppCfg, self).value(key,*vargs,**kwargs)
if key in (AppCfg.GEO_PIX2POS):
val=json.loads(val)#, object_hook=MyJsonDecoder)
val=(np.array(val[0]),np.array(val[1]))
elif key in (AppCfg.GEO_BEAM_SZ,AppCfg.GEO_BEAM_POS,):
val=np.array(tuple(map(float, val)))/1000
elif key in (AppCfg.GEO_OPT_CTR):
val=np.array(tuple(map(float, val)))
return val
#@property
#def value(self):

10
camera.py
View File

@@ -258,9 +258,15 @@ class epics_cam(object):
imgSeq=np.ndarray(shape=(len(glb),sz[1],sz[0]),dtype=np.uint8) # shape is (n,h,w)
for i,fn in enumerate(glb):
img=PIL.Image.open(fn)
assert(img.mode=='L') # 8 bit grayscale
#assert(img.mode=='L') # 8 bit grayscale
assert(sz==img.size)
imgSeq[i,:,:]=np.array(img.getdata()).reshape(sz[::-1])
if img.mode in ('L'):
#imgSeq[i, :, :]=np.asarray(img)
imgSeq[i,:,:]=np.array(img.getdata()).reshape(sz[::-1])
elif img.mode=='LA':
imgSeq[i, :, :]=np.asarray(img)[:,:,0]
else:
raise TypeError(f'unsupported image mode format {img.mode}')
pic=imgSeq[i]
epics_cam.set_fiducial(pic, 255)

76
geometry.py
View File

@@ -268,7 +268,7 @@ class geometry:
pass
@staticmethod
def least_square_trf(points):
def least_square_trf(points,fid=None,sort=True):
# inputs are 4 points of a parallelogram
# this function returns the least square transformation
#[ px] [a b c ] [ q ]
@@ -287,35 +287,71 @@ class geometry:
#
# A *aa = y
A=np.array((
(0,0,1,0,0,0),
(0,0,0,0,0,1),
(0,1,1,0,0,0),
(0,0,0,0,1,1),
(1,0,1,0,0,0),
(0,0,0,1,0,1),
(1,1,1,0,0,0),
(0,0,0,1,1,1)), np.float)
# A=np.array((
# (0,0,1,0,0,0),
# (0,0,0,0,0,1),
# (0,1,1,0,0,0),
# (0,0,0,0,1,1),
# (1,0,1,0,0,0),
# (0,0,0,1,0,1),
# (1,1,1,0,0,0),
# (0,0,0,1,1,1)), np.float)
if fid is None:
fid=np.array(((0,0),(0,1),(1,0),(1,1)))
elif type(fid)!=np.ndarray:
fid=np.array(fid)
y=points # sort points p00 p01 p10 p11
s=y[:,1].argsort()
y=y[s,:]
s=y[:2,0].argsort()
y[:2,:]=y[:2,:][s,:]
s=y[2:,0].argsort()
y[2:,:]=y[2:,:][s,:]
if sort:
# p01 ----------- p11
# | |
# | |
# p00-------------p10
def sort(a):
s=a[:,0].argsort()
a=a[s,:]
s=a[:2,1].argsort()
a[:2,:]=a[:2,:][s,:]
s=a[2:,1].argsort()
a[2:,:]=a[2:,:][s,:]
return a
y=sort(y)
fid=sort(fid)
A=np.ndarray((len(fid)*2,6))
i=0
for q,r in fid:
A[i] =(q,r,1,0,0,0)
A[i+1]=(0,0,0,q,r,1)
i+=2
y=np.asmatrix(y.ravel()).T
A=np.asmatrix(A)
aa=(A.T*A).I*A.T*y
aa=aa.reshape((2,3))
return aa
@staticmethod
def least_square_plane(points):
def least_square_plane(self,points):
#inputs are multiple (x,y,z) points
# this function returns the parameters of least square fitted plane x=x,y=y,z=ax+bx+c
pass
# a b c
# [px1 py1 1 ] [a] [pz1]
# [px2 py2 1 ] [b] [pz2]
# [... ... 1 ]*[c]=[...]
# [pxn pyn 1 ] [pzn]
A=np.ndarray((points.shape[0],3))
y=points[:,2]
A[:,2]=1
A[:,0:2]=points[:,:2]
y=np.asmatrix(y.ravel()).T
A=np.asmatrix(A)
aa=(A.T*A).I*A.T*y
aa=aa.A.ravel()
for p in points:
print(f'{p}->{aa[0]*p[0]+aa[1]*p[1]+aa[2]}')
self._fitPlane=aa
if __name__=="__main__":
@@ -473,7 +509,7 @@ if __name__=="__main__":
[40, 35],
[10, 35],
[40, 15]])
pts=-pts
#pts=-pts
for p in pts:

21
pyqtUsrObj.py
View File

@@ -12,6 +12,8 @@ TODO: Dimension of pyqtgraph is in um not pixel (as now)
'''
#import initExample ## Add path to library (just for examples; you do not need this)
import logging
_log=logging.getLogger(__name__)
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
@@ -316,7 +318,8 @@ class Path(pg.ROI):
p.drawLines(lh,lv)
def __repr__(self):
s=f'{self.__class__.__name__}:(pos:{itr2str(self.pos())}, size:{itr2str(self.size())}, cnt:{self._cnt}, ficucialScale:{self._fidScl}}}'
s=f'{self.__class__.__name__}:(pos:{itr2str(self.pos())}, size:{itr2str(self.size())}, numFid:{self._fiducial.shape[0]}, numPts:{self._path.shape[0]}, ficucialScale:{self._fidScl}}}'
return s
def obj2json(self,encoder):
@@ -373,7 +376,15 @@ class FixTargetFrame(pg.ROI):
}
def __init__( self, pos=(0,0), size=(100,100), tpl='test', dscr=None, **kwargs):
trf=kwargs.pop('trf',None)
pg.ROI.__init__(self, pos, size, **kwargs)
if trf is not None:
t=self.transform()
t.setMatrix(trf[0][0], trf[0][1], 0,
trf[1][0], trf[1][1], 0,
0, 0, 1)
self.setTransform(t)
#fiducial type 0: 5 squares with pitch 120 um
if dscr is not None:
self._dscr=dscr
@@ -383,6 +394,9 @@ class FixTargetFrame(pg.ROI):
self.addScaleHandle([1, 1], [0, 0])
self.addScaleHandle([0, 0], [1, 1])
self.addScaleRotateHandle([1, 0], [0, 0])
#self.sigHoverEvent.connect(self.hover)
# def hover(self):
# _log.debug(f'hover {self}')
def paint(self, p, *args):
#pg.ROI.paint(self, p, *args)
@@ -445,6 +459,11 @@ class FixTargetFrame(pg.ROI):
'size':tuple(self.size()),
'dscr': self._dscr
}
trf=self.transform()
if not trf.isIdentity():
obj_info(trf)
trf=((trf.m11(),trf.m12()),(trf.m21(),trf.m22()))
jsn['trf']=trf
return jsn

68
swissmx.py
View File

@@ -64,6 +64,7 @@ TASK_SETUP_CAMERA = "setup_camera"
TASK_SETUP_ROI = "setup_rois"
TASK_SAMPLE_SELECTION = "task_sample_selection"
TASK_SCREENING = "screening"
TASK_FIX_TARGET = "fix_trg"
TASK_GRID = "grid"
TASK_PRELOCATED = "prelocated"
TASK_HELICAL = "helical"
@@ -407,13 +408,14 @@ class SwissMxWnd(QMainWindow, Ui_MainWindow):
self._goGrid=grid=pg.GridItem() # green grid and labels
grid.opts['pen']=QPen(QColor(0, 255, 0))
grid.opts['textPen']=QPen(QColor(0, 255, 0))
#tr.reset()
tr.reset()
#grid.setTransform(tr) # assign transform
vb.addItem(grid)
#--- beam marker ---
bm_sz=np.array((50, 40)) # it is immidiatly repositioned in zoom_changed_cb
self._goBeamMarker=bm=UsrGO.Marker(-opt_ctr-bm_sz/2,bm_sz,mode=0)
bm.setTransform(tr) # assign transform
vb.addItem(bm)
#--- opctical center ----
@@ -717,8 +719,8 @@ class SwissMxWnd(QMainWindow, Ui_MainWindow):
_log.warning(e)
else:
opt_ctr=geo._opt_ctr
bm_sz=np.array(tuple(map(float, cfg.value(AppCfg.GEO_BEAM_SZ))))/1000
bm_pos=np.array(tuple(map(float, cfg.value(AppCfg.GEO_BEAM_POS))))/1000
bm_sz=cfg.value(AppCfg.GEO_BEAM_SZ)
bm_pos=cfg.value(AppCfg.GEO_BEAM_POS)
bm_sz=np.abs(geo.pos2pix(bm_sz))
bm_pos=-opt_ctr-geo.pos2pix(bm_pos)-bm_sz/2
bm=self._goBeamMarker
@@ -936,7 +938,7 @@ class SwissMxWnd(QMainWindow, Ui_MainWindow):
#_log.debug(f"vb pos {self.vb.mapFromScene(p)}") #pixel position on the scene (including black frame)
#for o in self.vb.childGroup.childItems():
# _log.debug(f"{type(o)} pos {o.mapFromScene(p)}") #pixel position on the scene (including black frame)
_log.debug(f"currentItem:{event.currentItem}")
task = self.active_task()
if task==TASK_SETUP_GEOMETRY_CALIB:
self.mouse_click_event_geometry_calib(event)
@@ -1235,11 +1237,40 @@ class SwissMxWnd(QMainWindow, Ui_MainWindow):
def execute_collection(self):
app=QApplication.instance()
geo=app._geometry
#zoom=app._zoom.get_val()
task = self.active_task()
self._is_aborted = False
method = self._tabs_daq_methods.currentWidget().accessibleName()
#self._is_aborted = False
#method = self._tabs_daq_methods.currentWidget().accessibleName()
if task == TASK_GRID:
if task == TASK_FIX_TARGET:
#self.re_connect_collect_button(callback=self.collect_abort_grid, accessibleName="grid_abort", label="Abort Grid Scan",)
#self._inspect = self._grid_inspect_area
#self._inspect.setPlainText("")
fast_x=self.tweakers["fast_x"];
fast_y=self.tweakers["fast_y"]
fx=fast_x.get_val()
fy=fast_y.get_val()
opt_ctr=geo._opt_ctr
for go in self._goTracked['objLst']:
points=go.get_points() #points in coordinate system of ROI
# names consists of abrevations
# part 0: po=position sz=size dt=delta
# part 1: px=pixel eu=engineering units (e.g. mm)
po_px=go.pos()
sz_px=go.size()
tr=go.transform() # TODO: this is not yet used
UsrGO.obj_info(tr)
dt_px=-opt_ctr-po_px
dt_eu=geo.pix2pos(dt_px)+(fx,fy)
for i in range(points.shape[0]):
points[i,:]=dt_eu+geo.pix2pos(points[i,:])#*tr
self.daq_collect_points(points, visualizer_method="grid", visualizer_params=None)
elif task == TASK_GRID:
self.re_connect_collect_button(
callback=self.collect_abort_grid,
accessibleName="grid_abort",
@@ -1541,6 +1572,7 @@ class SwissMxWnd(QMainWindow, Ui_MainWindow):
self._moduleFixTarget =mft = ModuleFixTarget.WndFixTarget(self,data)
tab = self._tabs_daq_methods.insertTab(0,mft,'Fix Target')
mft.setAccessibleName(TASK_FIX_TARGET)
self._tabs_daq_methods.setCurrentWidget(mft) #set this as the active tabs
mft._cbType.addItems(["Fiducial", "FixTarget(12.5x12.5)", "FixTarget(23.0x23.0)", "FixTarget(<param>)", "Grid(<param>)"])
@@ -1677,20 +1709,30 @@ class SwissMxWnd(QMainWindow, Ui_MainWindow):
for go in reversed(objLst):
if type(go)==UsrGO.FixTargetFrame:
if j==4:
trf=geometry.geometry.least_square_trf(ptFitTrf)
#fid=np.array(((0.1, 0.1), (0.1, 1.1), (1.1, 0.1), (1.1, 1.1)))
fid=np.array(go._dscr['fiducial']['pos'])
sz=np.array(go._dscr['size'])
fid=fid/sz
trf=geometry.geometry.least_square_trf(ptFitTrf,fid)
tr=go.transform()
tr.setMatrix(100, 0, 0,
0, 100, 0,
0, 0, 1)
tr.setMatrix(1, trf[1,0]/trf[0,0], 0,
trf[0,1]/trf[1,1], 1, 0,
0, 0, 1)
go.setTransform(tr)
go.setPos(trf[:,2])
go.setSize((1,1))
#go.setSize((1,1))
sz=(trf[0,0],trf[1,1])
go.setSize(sz)
j=0
elif type(go)==UsrGO.Fiducial:
ptFitTrf[j]=go.pos()+go.size()/2
ptFitPlane[i]=go._xyz
i+=1;j+=1
plane=geometry.geometry.least_square_plane(ptFitPlane)
app=QApplication.instance()
geo=app._geometry
if n>=3:
geo.least_square_plane(ptFitPlane)
# **************** OBSOLETE AND/OR OLD STUFF ****************