enhance calibration + minor fixes

Readme.md

@@ -83,10 +83,10 @@ DST=/sf/cristallina/applications/mx/zamofing_t/
 # /sf/cristallina/applications/mx
 
 ssh saresc-cons-02 mkdir /tmp/zamofing_t/
-rsync -vai ~/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX saresc-cons-03:$DST
+rsync -vai --delete ~/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX saresc-cons-03:$DST
-rsync -vai ~/Documents/prj/SwissFEL/PBTools saresc-cons-03:$DST
+rsync -vai --delete ~/Documents/prj/SwissFEL/PBTools saresc-cons-03:$DST
 
-cd /tmp/zamofing_t/ESB_MX/python/SwissMX/
+cd /sf/cristallina/applications/mx/zamofing_t/ESB_MX/python/SwissMX/
 /opt/gfa/python-3.7/latest/bin/python swissmx.py 
 
 /opt/gfa/python-3.8/latest/bin/pip install qtawesome --user

app_config.py

@@ -187,11 +187,11 @@ class AppCfg(QSettings):
         if key==AppCfg.DT_MISC:
           val={'show_plots': True, 'vel_scl': 1.0, 'pt2pt_time': 10.0,'sync_mode':1,'sync_flag':3,'verbose':0xff}
         elif key==AppCfg.GBL_MISC:
-          val={'img_trace':4}
+          val={'img_trace_len':4}
         else:
           val={}
     elif key in (AppCfg.GEO_BEAM_SZ,AppCfg.GEO_BEAM_POS,):
-      val=np.array(tuple(map(float, val)))/1000
+      val=np.array(tuple(map(float, val)))
     elif key in (AppCfg.GEO_OPT_CTR):
       val=np.array(tuple(map(float, val)))
     return val
@@ -227,7 +227,7 @@ class WndParameter(QMainWindow):
     #GEO_CAM_PARAM
     gbl_misc        = cfg.value(AppCfg.GBL_MISC)
     gbl_dev_prefix = cfg.value(AppCfg.GBL_DEV_PREFIX)
-    geo_beam_sz    = cfg.value(AppCfg.GEO_BEAM_SZ)*1000
+    geo_beam_sz    = cfg.value(AppCfg.GEO_BEAM_SZ)
     dft_pos_pst    = cfg.value(AppCfg.DFT_POS_PST)
     dft_pos_col    = cfg.value(AppCfg.DFT_POS_COL)
     dft_pos_bklgt  = cfg.value(AppCfg.DFT_POS_BKLGT)
@@ -276,7 +276,7 @@ verbose bits:
           {'name':'smaract motors', 'value':gbl_dev_prefix[1], 'type':'str'},
         ]},
         {'name':AppCfg.GBL_MISC, 'title':'miscellaneous', 'type':'group', 'children':[
-          {'name':'img_trace', 'value':gbl_misc['img_trace'], 'type':'int', 'tip':tip_sync_flag},
+          {'name':'img_trace_len', 'value':gbl_misc['img_trace_len'], 'type':'int', 'tip':tip_sync_flag},
           #{'name':'verbose', 'value':gbl_misc['verbose'], 'type':'int', 'tip':tip_verbose},
         ]},
       #  {'name':AppCfg.GEO_CAM_TRF, 'value':cfg.value(AppCfg.GEO_CAM_TRF), 'type':'str'},
@@ -394,7 +394,10 @@ verbose bits:
         except AttributeError as e:
           _log.warning('can not set beam size to application window')
         else:
+          v=v/1000 # convert from um to mm
+          bm.blockSignals(True) # avoid to call cb_marker_moved
           bm.setSize(v)
+          bm.blockSignals(False)
       elif par_nm==AppCfg.GEO_CAM_PARAM:
         d=dict(map(lambda x:(x.name(),x.value()), parent.children()))
         try:
@@ -441,6 +444,18 @@ verbose bits:
       elif par_nm in (AppCfg.GBL_MISC,AppCfg.DT_MISC):
         d=dict(map(lambda x:(x.name(),x.value()), parent.children()))
         cfg.setValue(par_nm, d)
+        if par_nm in (AppCfg.GBL_MISC):
+          try:
+            grp=self.parent()._goTrace
+            vb=self.parent().vb
+          except AttributeError as e:
+            _log.warning('can not access the application window')
+          else:
+            grp._tracelen=tl=d['img_trace_len']
+            cld=grp.childItems()
+            while len(cld)>tl:
+              vb.removeItem(cld[0])
+              cld=grp.childItems()
       else:
         _log.warning(f'can\'t save parameter:{childName} change:{change} data:{str(data)}')
         raise

epics_widgets/SmaractMotorTweak.py

@@ -130,6 +130,14 @@ class SmaractMotorTweak(QWidget, Ui_MotorTweak):
     def get_rbv(self):
         return self._pv_readback.get(use_monitor=False)
 
+    def get_val(self):
+        # return self._motor.get('VAL')
+        try:
+            v=self._val
+        except AttributeError:
+            self._val=v=self._pv_drive.get()
+        return v
+
     def is_homed(self):
         pend_event()
         return 1 == self._pv_is_homed.get(use_monitor=False)

swissmx.py

@@ -403,8 +403,8 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
     self.vb.addItem(grp)
 
     #--- beam marker ---
-    size_eu=cfg.value(AppCfg.GEO_BEAM_SZ)
+    size_eu=cfg.value(AppCfg.GEO_BEAM_SZ)/1000 # convert from um to mm
-    pos_eu=cfg.value(AppCfg.GEO_BEAM_POS)
+    pos_eu=cfg.value(AppCfg.GEO_BEAM_POS)/1000 # convert from um to mm
     self._goBeamMarker=obj=UsrGO.Marker(pos_eu-size_eu/2,size_eu,mode=0)
     obj.sigRegionChangeFinished.connect(self.cb_marker_moved)
     #bm.setTransform(tr)  # assign transform
@@ -639,7 +639,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
         param=cam.get_param()
 
         paramSv=cfg.value(AppCfg.GEO_CAM_PARAM)
-        if paramSv is None:
+        if not paramSv:
           cfg.setValue(AppCfg.GEO_CAM_PARAM, param)
         else:
           for k,v in param.items():
@@ -747,15 +747,17 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
     if obj==self._goOptCtr:
       oc_pos=obj.pos()
       oc_sz=obj.size()
-      geo._opt_ctr=opt_ctr=np.array(-oc_pos-oc_sz/2)
+      geo._opt_ctr=opt_ctr=np.array(oc_pos+oc_sz/2)
-      _log.debug(f'{obj}->{opt_ctr} !!! NOT SAVED IN CONFIG !!!')
+      if (QMessageBox.question(self, "save config", f"save optical center position {opt_ctr} permanently?",
-      #cfg.setValue(AppCfg.GEO_OPT_CTR,bm_pos)
+                               QMessageBox.Yes|QMessageBox.No, QMessageBox.No, )==QMessageBox.Yes):
+        cfg.setValue(AppCfg.GEO_OPT_CTR,opt_ctr)
     elif obj==self._goBeamMarker:
       bm_pos=obj.pos()
       bm_sz=obj.size()
-      obj._pos_eu=bm_pos=-geo.pix2pos(bm_pos+opt_ctr+bm_sz/2)
+      pos=np.array(bm_pos+bm_sz/2)*1000 # convert from mm to um
-      _log.debug(f'{obj}->{bm_pos} !!! NOT SAVED IN CONFIG !!!')
+      if (QMessageBox.question(self, "save config", f"save beam marker position {pos} permanently?",
-      #cfg.setValue(AppCfg.GEO_BEAM_POS,bm_pos)
+                               QMessageBox.Yes|QMessageBox.No, QMessageBox.No, )==QMessageBox.Yes):
+        cfg.setValue(AppCfg.GEO_BEAM_POS,pos)
       self.track_objects()
 
   def cb_zoom_changed(self, value):
@@ -1022,6 +1024,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
       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))
+      self._wd_calib_tree.setData(app._raw_pix2pos)
     elif self._btn_opt_ctr.isChecked():
       try:
         raw=app._raw_opt_ctr[zoom]
@@ -1031,9 +1034,11 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
       x=imgPos.x();y=imgPos.y()
       _log.debug('append calib: zoom:{} cam_pix_x_y:{}/{}'.format(zoom, x, y))
       raw.append(( x, y))
+      self._wd_calib_tree.setData(app._raw_opt_ctr)
     else:
      QMessageBox.warning(self, "calibration", "no calibration started yet.\nPress 'pix2pos' or 'opt_ctr' button first")
 
+
   def cb_mouse_click(self, event):
     #_log.debug("{}".format(event))
     #_log.debug("screen pos {}".format(event.screenPos()))  #pixel position on the whole screen
@@ -1298,17 +1303,39 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
 
   def add_camera_trace(self):
     # add up to tracelen image when moveing motors to new positions
-    tracelen=4
+    try:
-    img=pg.ImageItem(self._goImg.image)
+      tracelen=self._goTrace._tracelen
+    except AttributeError:
+      app=QApplication.instance()
+      cfg=app._cfg
+      tracelen=self._goTrace._tracelen=cfg.value(AppCfg.GBL_MISC)['img_trace_len']
+    if tracelen==0:
+      return
+
+
     trImg=self._goImgGrp.transform()
     trTrk=self._goTracked.transform()
-
     tr=trImg*trTrk.inverted()[0]  # TODO: check if oder correct !!!
+    img=pg.ImageItem(self._goImg.image)
     img.setTransform(tr)
-    self._goTrace.addItem(img)
+    self._goTrace.addItem(img) # automatically added to self.vb
-    cld=self._goTrace.childItems()
+
-    if len(cld) > tracelen:
+
-      self.vb.removeItem(cld[0])
+    cldLst=self._goTrace.childItems()
+    if len(cldLst)>tracelen: #check if one image needs to be removed
+      r1=self.vb.itemBoundingRect(img)
+      for c in cldLst[:-1]:
+        #check overlap with newest image, and remove previous if it is more than 30%
+        r2=self.vb.itemBoundingRect(c)
+        r3=r1.intersected(r2)
+        s3=r3.size()
+        s1=r1.size()
+        if s3.width()/s1.width()>0.3 and s3.height()/s1.height()>0.3:
+          self.vb.removeItem(c)
+          return
+      self.vb.removeItem(cldLst[0]) #if no one was removes, remove oldest
+
+
 
   def cb_modify_app_param(self):
     wnd=WndParameter(self)
@@ -1601,6 +1628,8 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
     pass
 
   def prepare_wd_tabs_left(self):
+
+
     tabs = self._wd_tabs_left
     tabs.currentChanged.connect(self.cb_switch_task)
 
@@ -1617,17 +1646,60 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
 
     setup_tab.layout().addWidget(tbox)
 
-    # Jungfrau parameters
+    # -------- DAQ Methods Tabs --------
+    self.build_tab_module_fix_target()
+    self._OLD_build_daq_methods_grid_tab()
+    self._OLD_build_daq_methods_prelocated_tab() #ZAC: orig. code
+    self._OLD_create_helical_widgets() #ZAC: orig. code
+    self._OLD_build_daq_methods_embl_tab()
+    #self._OLD_build_sample_selection_tab()
+
+    # -------- group geometry calibration --------
     block = QWidget()
+    block.setAccessibleName(TASK_SETUP_GEOMETRY_CALIB)
+    block.setContentsMargins(0, 0, 0, 0)
+    block.setLayout(QVBoxLayout())
+    grp = QWidget()
+    block.layout().addWidget(grp)
+    block.layout().addStretch()
+    grp.setLayout(QGridLayout())
+    tbox.addItem(block, "geometry calibration")
+    #grp.layout().addWidget(QLabel("feature size (µM)"), 0, 0)
+    #self._ppm_feature_size_spinbox = QDoubleSpinBox()
+    #self._ppm_feature_size_spinbox.setRange(5, 10000)
+    #self._ppm_feature_size_spinbox.setValue(50)
+    #self._ppm_feature_size_spinbox.setDecimals(0)
+    #self._ppm_feature_size_spinbox.setSuffix(" µM")
+    #grp.layout().addWidget(self._ppm_feature_size_spinbox, 0, 1)
+    self._btn_pix2pos = but = QPushButton("Pixel to position calibration")
+    but.setCheckable(True)
+    but.clicked.connect(self.cb_update_pix2pos)
+    grp.layout().addWidget(but, 0, 0)
+    self._btn_opt_ctr = but = QPushButton("Optical center calibration")
+    but.setCheckable(True)
+    but.clicked.connect(self.cb_update_opt_ctr)
+    grp.layout().addWidget(but, 1, 0)
+
+    self._wd_calib_tree=tree=pg.DataTreeWidget(data=None)
+    grp.layout().addWidget(tree, 2, 0)
+
+    tbox.currentChanged.connect(self.cb_switch_task)
+
+    # final stretch
+    # setup_tab.layout().addStretch()
+    exp_tab.layout().addStretch()
+
+    # Jungfrau parameters
+    block=QWidget()
     block.setAccessibleName(TASK_JUNGFRAU_SETTINGS)
     block.setContentsMargins(0, 0, 0, 0)
     block.setLayout(QVBoxLayout())
-    #self.jungfrau = jungfrau_widget.JungfrauWidget() #ZAC: orig. code
+    # self.jungfrau = jungfrau_widget.JungfrauWidget() #ZAC: orig. code
-    #block.layout().addWidget(self.jungfrau) #ZAC: orig. code
+    # block.layout().addWidget(self.jungfrau) #ZAC: orig. code
     block.layout().addStretch()
     tbox.addItem(block, "Jungfrau Parameters")
 
-  #   # group beam box
+    #   # -------- group beam box --------
     #   block = QWidget()
     #   block.setAccessibleName(TASK_SETUP_BEAM_CENTER)
     #   block.setContentsMargins(0, 0, 0, 0)
@@ -1668,7 +1740,7 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
     # """
     #   )
 
-  #   # group regions
+    #   # -------- group regions --------
     #   block = QWidget()
     #   block.setAccessibleName(TASK_SETUP_ROI)
     #   block.setContentsMargins(0, 0, 0, 0)
@@ -1685,7 +1757,7 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
     #   but.clicked.connect(self.roi_add_line)
     #   grp.layout().addWidget(but, 0, 1)
     #
-  #   # group camera settings
+    #   # -------- group camera settings --------
     #   block = QWidget()
     #   block.setAccessibleName(TASK_SETUP_CAMERA)
     #   block.setContentsMargins(0, 0, 0, 0)
@@ -1728,77 +1800,6 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
     #
     #   grp.layout().addWidget(self._label_transforms, row, 0, 1, 2)
 
-    # group geometry calibration
-    block = QWidget()
-    block.setAccessibleName(TASK_SETUP_GEOMETRY_CALIB)
-    block.setContentsMargins(0, 0, 0, 0)
-    block.setLayout(QVBoxLayout())
-    grp = QWidget()
-    block.layout().addWidget(grp)
-    block.layout().addStretch()
-    grp.setLayout(QGridLayout())
-    tbox.addItem(block, "geometry calibration")
-    #grp.layout().addWidget(QLabel("feature size (µM)"), 0, 0)
-    #self._ppm_feature_size_spinbox = QDoubleSpinBox()
-    #self._ppm_feature_size_spinbox.setRange(5, 10000)
-    #self._ppm_feature_size_spinbox.setValue(50)
-    #self._ppm_feature_size_spinbox.setDecimals(0)
-    #self._ppm_feature_size_spinbox.setSuffix(" µM")
-    #grp.layout().addWidget(self._ppm_feature_size_spinbox, 0, 1)
-    self._btn_pix2pos = but = QPushButton("pix2pos")
-    but.setCheckable(True)
-    but.clicked.connect(self.cb_update_pix2pos)
-    grp.layout().addWidget(but, 0, 0)
-    self._btn_opt_ctr = but = QPushButton("opt_ctr")
-    but.setCheckable(True)
-    but.clicked.connect(self.cb_update_opt_ctr)
-    grp.layout().addWidget(but, 1, 0)
-
-    help = QTextBrowser()
-    grp.layout().addWidget(help, 2, 0)
-    help.setHtml(
-      """<body>
-  <h2>Pixel to position calibration</h2>
-  <ol>
-  <li>press: <b>pix2pos</b></li>
-  <li>for each zoom level:
-  <li>choose a good fiducial mark
-  <li>move the stage x/y at min. 3 different locations
-  <li>Click (left mouse button) on the fiducial mark 
-  <li>un-click: <b>pix2pos</b></li>
-  </ol>
-  <h2>optical center calibration</h2>
-  <ol>
-  <li>press: <b>opt_ctr</b></li>
-  <li>choose at least 3 fiducial mark visible at various zoom levels
-  <li>for at least two zoom level:
-  <li>Click (left mouse button) on the fiducial marks 
-  <li>un-click: <b>opt_ctr</b></li>
-  </ol>
-  </body>
-  """
-    )
-
-    # grp = PpmToolBox(viewbox=self.vb, camera=sample_camera, signals=self)
-    # grp.setAccessibleName(TASK_SETUP_PPM_CALIBRATION_TBOX)
-    # grp.pixelPerMillimeterCalibrationChanged.connect(self.update_ppm_fitters)
-    # tbox.addItem(grp, "PPM ToolBox")
-    # self._ppm_toolbox = grp
-
-    tbox.currentChanged.connect(self.cb_switch_task)
-
-    # final stretch
-    # setup_tab.layout().addStretch()
-    exp_tab.layout().addStretch()
-
-    # DAQ Methods Tabs
-    self.build_tab_module_fix_target()
-    self._OLD_build_daq_methods_grid_tab()
-    self._OLD_build_daq_methods_prelocated_tab() #ZAC: orig. code
-    self._OLD_create_helical_widgets() #ZAC: orig. code
-    self._OLD_build_daq_methods_embl_tab()
-    #self._OLD_build_sample_selection_tab()
-
   def build_tab_module_fix_target(self):
     #tab = self._tab_daq_method_prelocated
     try:
@@ -1856,6 +1857,13 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
     app=QApplication.instance()
     if calib:
       _log.info("received new pix2pos calibration")
+      QMessageBox.information(self,'Pixel to position calibration','''\  
+- for each zoom level:
+  - choose a good fiducial mark
+  - move the stage x/y at min. 3 different locations
+  - click (left mouse button) on that fiducial mark 
+- un-click button "Pixel to position calibration"
+''')
       app._raw_pix2pos=dict()
     else:
       s=str(app._raw_pix2pos).replace('),','),\n    ').replace('],','],\n')
@@ -1870,21 +1878,38 @@ Author Thierry Zamofing (thierry.zamofing@psi.ch)
   def cb_update_opt_ctr(self, calib):
     app=QApplication.instance()
     if calib:
-      _log.info("received new pix2pos calibration")
+      _log.info("received new opt_ctr calibration")
+      QMessageBox.information(self,'Optical center calibration','''\
+- choose the biggest zoom level to start
+- choose at least 3 fiducial marks
+- for at least two zoom level:
+  - Click (left mouse button) on the fiducial marks (always in the same order)
+- un-click button "Optical center calibration"
+''')
+
       app._raw_opt_ctr=dict()
     else:
-      s=str(app._raw_opt_ctr).replace('),','),\n    ').replace('],','],\n')
-      print(s)
-      res=QMessageBox.question(self, "calibration", f"use calibration\n{s} ? ")
-      if res==QMessageBox.Yes:
       geo=app._geometry
-        geo.update_optical_center(app._raw_opt_ctr)
+      ocOld=geo._opt_ctr
-        app._cfg.setValue(AppCfg.GEO_OPT_CTR, geo._opt_ctr)
+      try:
-        go=self._goOptCtr
+        geo.update_optical_center(app._raw_opt_ctr,True)
-        oc_sz=go.size()
+      except BaseException as e:
-        go.setPos(-geo._opt_ctr-oc_sz/2)
+        _log.warning(e)
+        QMessageBox.warning(self, "calibration", f"rejected\n{e}")
         del app._raw_opt_ctr
         return
+      del app._raw_opt_ctr
+      go=self._goOptCtr
+      oc_sz=go.size()
+      go.blockSignals(True)  # avoid to call cb_marker_moved
+      go.setPos(geo._opt_ctr-oc_sz/2)
+      res=QMessageBox.question(self, "calibration", f"keep new optical center\n{geo._opt_ctr} ? ")
+      if res==QMessageBox.Yes:
+        app._cfg.setValue(AppCfg.GEO_OPT_CTR, geo._opt_ctr)
+      else:
+        geo._opt_ctr=ocOld
+        go.setPos(geo._opt_ctr-oc_sz/2)
+      go.blockSignals(False)  # allow to call cb_marker_moved
 
   def module_fix_target_add_obj(self,*args,**kwargs):
     mft=self._moduleFixTarget