saving document, plane and fiducal fitter

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')
+      _log.warning(f'{AppCfg.GEO_PIX2POS} not defined. use default')
-      import numpy as np
       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):

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)
 

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((
+    # A=np.array((
-      (0,0,1,0,0,0),
+    #  (0,0,1,0,0,0),
-      (0,0,0,0,0,1),
+    #  (0,0,0,0,0,1),
-      (0,1,1,0,0,0),
+    #  (0,1,1,0,0,0),
-      (0,0,0,0,1,1),
+    #  (0,0,0,0,1,1),
-      (1,0,1,0,0,0),
+    #  (1,0,1,0,0,0),
-      (0,0,0,1,0,1),
+    #  (0,0,0,1,0,1),
-      (1,1,1,0,0,0),
+    #  (1,1,1,0,0,0),
-      (0,0,0,1,1,1)), np.float)
+    #  (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()
+    if sort:
-    y=y[s,:]
+      # p01 ----------- p11
-    s=y[:2,0].argsort()
+      #  |               |
-    y[:2,:]=y[:2,:][s,:]
+      #  |               |
-    s=y[2:,0].argsort()
+      # p00-------------p10
-    y[2:,:]=y[2:,:][s,:]
+      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(self,points):
-  def least_square_plane(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:

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
 
 

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_sz=cfg.value(AppCfg.GEO_BEAM_SZ)
-      bm_pos=np.array(tuple(map(float, cfg.value(AppCfg.GEO_BEAM_POS))))/1000
+      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
+    #self._is_aborted = False
-    method = self._tabs_daq_methods.currentWidget().accessibleName()
+    #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,
+          tr.setMatrix(1,                 trf[1,0]/trf[0,0], 0,
-                       0, 100, 0,
+                       trf[0,1]/trf[1,1], 1,                 0,
-                       0,   0, 1)
+                       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 ****************