diff --git a/app_config.py b/app_config.py
index f053a1d..88d93f4 100644
--- a/app_config.py
+++ b/app_config.py
@@ -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):
diff --git a/camera.py b/camera.py
index f7385ff..57d203c 100755
--- a/camera.py
+++ b/camera.py
@@ -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)
diff --git a/geometry.py b/geometry.py
index 3720043..b507da3 100755
--- a/geometry.py
+++ b/geometry.py
@@ -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:
diff --git a/pyqtUsrObj.py b/pyqtUsrObj.py
index 99917da..a51ad9c 100644
--- a/pyqtUsrObj.py
+++ b/pyqtUsrObj.py
@@ -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
diff --git a/swissmx.py b/swissmx.py
index a907f8c..2cd6473 100755
--- a/swissmx.py
+++ b/swissmx.py
@@ -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()", "Grid()"])
@@ -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 ****************