try to cleanup stuff(3)

ModuleFixTarget.py

@@ -16,7 +16,7 @@ This contains a Widget to handle FixTargetFrames and fiducials, calculate final
 import logging
 _log=logging.getLogger(__name__)
 
-import json, base64, yaml
+import os, json, base64, yaml
 import numpy as np
 import pyqtUsrObj as UsrGO
 import pyqtgraph as pg
@@ -47,6 +47,22 @@ class MyJsonEncoder(json.JSONEncoder):
         return repr(obj)
     return json.JSONEncoder.default(self, obj)
 
+  def iterencode(self, o, _one_shot=False):
+    list_lvl = 0
+    l=super().iterencode(o, _one_shot=_one_shot)
+    #l=tuple(l);print(''.join(l)) # helpful to debug
+    for s in l:
+      if s.startswith('['):
+        list_lvl += 1
+      if list_lvl > 0:
+        s = s[0]+s[1:].replace('\n', '').strip()
+        s = s.replace('\n', '').rstrip()
+        #self.item_separator):
+        #self.key_separator
+      if s.endswith(']'):
+        list_lvl -= 1
+      yield s
+
 def MyJsonDecoder(dct):
     if isinstance(dct, dict):
       if '__class__' in dct:
@@ -173,28 +189,10 @@ class WndFixTarget(QWidget):
     #bm_pos_eu=self._goBeamMarker._pos_eu
     #bm_size_eu=self._goBeamMarker._size_eu
     try:
-      #parse the parameters: 'key:value [,key:value]'
+      #parse the parameters: as yaml string.
-      # as key value separator : and = are allowed
+      # allows : without space, allows () as []
-      #examples:
+      # no {} to define a dictionary
-      #Fiducial:
+      # e.g. 'a:ggf,b:5,c:[5,6.1],d(8,9,3)'
-      #  no param
-      #FixTarget(12.5x12.5), FixTarget(23.0x23.0), FixTarget(test):
-      #  code_gen:2
-      #  code_gen=3 | tmove=10 | twait=30
-      #Grid():
-      #  size:(30, 20)
-      #  cnt:(30, 22)
-      #  fiducialSize:0.1
-      #SwissMX():
-      #  ofs:(.2, .2)
-      #  width:10
-      #  fidScl:.02
-      #  fiducial:((.1, .1), (.1, 2.7), (10.3, .1), (10.3, 2.7))
-      #SwissFEL():
-      #  ofs:(.2, .2)
-      #  width:10
-      #  fidScl:.02
-      #  fiducial:((.1, .1), (.1, 2.2), (10.3, .1), (10.3, 2.2))
 
       param=param.replace(':', ': ')  # allow gen:4 without space
       param=yaml.safe_load(param)  # "ofs":[10, 5],"width":200,"fidScl":0.5,"fiducial":[[18,7],[25,16],[70, 20]]
@@ -376,7 +374,10 @@ class WndFixTarget(QWidget):
     #df = pd.DataFrame(data)
     #df.to_csv(filename, float_format="%.6f")
     #import numpy as np
-    ext=filename.rsplit('.',1)[1].lower()
+    base,ext=os.path.splitext(filename)
+    if not ext.lower():
+      ext='json'
+      filename=base+'.'+ext
     try:
       wnd=app._mainWnd
     except AttributeError:
@@ -386,7 +387,7 @@ class WndFixTarget(QWidget):
       grp=wnd._goTracked
       data=grp.childItems()
 
-    if ext=='json':
+    if ext.lower()=='json':
       with open(filename, 'w') as f:
         json.dump(data, f,cls=MyJsonEncoder, indent=2)#separators=(',', ':')
     else:

Readme.md

@@ -102,3 +102,114 @@ python swissmx.py --sim 0xc0
 ```
 Document to start SwissMX in cristallina environment (maintained by John):
 https://docs.google.com/document/d/1yEmV_DbRBKQKVCoovjXriNgSjNEBaz50WA0l3yA5jtg/edit#heading=h.z9io692b8tow
+
+## code generation parameters
+```
+copied from: PBSwissMX/python/shapepath.py: ShapePath.setup_motion
+
+    generates program <prgId> and saves to fnPrg
+    the type of generated program is defined by <mode>$
+    -> the list af all points that will be  moved at, is in 'mot_pts'
+
+    (m)= mandatory
+    (o)= optional
+    common kwargs:
+      scale      : (o) scaling velocity (default=1. value=0 would stop at each point
+      cnt        : (o) move path multiple times (default=1)
+      dwell      : (o) dwell time at end (default=100ms)
+
+    mode:0  unused
+    mode:1  pvt motion point list
+            common kwargs plus:
+              points : (m) point list
+              trf    : (o) transformation that will be done on 'points', mot_pts=trf*points
+    mode:2  unused
+    mode:3  pvt motion point list using inverse fft velocity
+            common kwargs plus:
+              points : (m) point list
+              trf    : (o)  transformation that will be done on 'points', mot_pts=trf*points
+              numPad : (o) number of padding points to reduce aliasing (default=16)
+    mode:4  pvt motion short code using grid parameters
+            common kwargs plus:
+              trf : (o) transformation that will be done on 'grid points'
+              grid: (m) grid parameters: {orig:(0,0),pitch(10,10),cnt:(10,10),mode:0}
+    mode:5  pvt motion 'stop and go' short code using grid parameters.
+            Instead of continous motion it moves and waits as given in the parameters
+            common kwargs plus:
+              trf :  (o) transformation that will be done on 'grid points'
+              grid:  (m) grid parameters: {orig:(0,0),pitch(10,10),cnt:(10,10),mode:0}
+              tmove: (m) time to move in ms (move start on FEL-trigger
+              twait: (m) time to wait in ms
+              (tmove+twait will be rounded to a multiple of fel_per)
+    mode:6  pvt motion 'hit and return using grid parameters. continous motion on 2n ells to pump then same 2n wells to probe, then go 2 rows down
+            common kwargs plus:
+              trf   : (o) transformation that will be done on 'grid points'
+              grid  : (m) grid parameters: {orig:(0,0),pitch(10,10),cnt:(10,10),mode:0}
+              ssz   : (m) section size (in wells)
+              smv   : (o) time(in num of shots) to move to next section (horiz/vert)
+                      default is (ssz[0]-1,ssz[1])
+              sdelay: (o) shots count of delay. Default is ssz[0]*ssz[1]
+
+Examples:
+  mode:1
+  mode:3
+  mode:4
+  mode:5,tmove:20,twait:30
+  mode:6,ssz:(4,3)
+```
+## graphical object parameters
+```
+  FixTarget:
+    90*40+480*2=4560
+    60*30+360*2=2520
+    2520-240=2280  
+    4560-240=4320
+    size in mm, dscr.size in user units (um)
+   "size:(6,3.5),
+    dscr: {
+      size:(4560,2520), 
+      fiducial:{type:0,pos:((240,240),(4320,240),(240,2280),(4320,2280))},
+      grid:{pos:(480,360),pitch:(90,60),count:(40,30)}
+    }"
+
+  grid:
+    size, fiducialSize in mm:
+    (60-1)*.120 -> 7.08mm
+    (45-1)*.120 -> 5.28mm
+    fiducialSize -> 0.1mm
+    "size:(7.08,5.28),cnt:(60,45),fiducialSize:.01"
+
+  SwissMX():
+   "ofs:[.2,.2],width:10,fidScl:.02,fiducial:[[.1,.1],[.1,2.7],[10.3,.1],[10.3, 2.7]]"
+  SwissFEL():
+   "ofs:[.2,.2],width:10,fidScl:.02,fiducial:[[.1,.1],[.1,2.2],[10.3,.1],[10.3,2.2]]"
+```
+
+## fully parameter examples:
+```
+  "mode:4,size:(7.08,5.28), cnt:(60,45), fiducialSize:.01"   -> add a grid
+
+  "mode:6,ssz:(4,3), size:(7.08,5.28), cnt:(60,45), fiducialSize:.01"   -> add a grid
+  "mode:6,ssz:(4,3), size:(3,1.5), cnt:(30,15), fiducialSize:.01"   -> add a grid
+
+  "mode:6,ssz:(6,8), 
+  dscr: {
+    size:(4560,2520),
+    fiducial:{type:0,pos:((240,240),(4320,240),(240,2280),(4320,2280))},
+    grid:{pos:(480,360),pitch:(90,60),count:(40,30)}
+  }"  -> add a FixTarget
+
+
+```
+
+
+## testing hit and return:
+```
+-> add a FixTarget
+ "mode:6,ssz:(6,8), 
+  dscr: {
+    size:(4560,2520),
+    fiducial:{type:0,pos:((240,240),(4320,240),(240,2280),(4320,2280))},
+    grid:{pos:(480,360),pitch:(90,60),count:(40,30)}
+  }"  -> add a FixTarget
+```

pyqtUsrObj.py

@@ -251,13 +251,33 @@ class Grid(UsrROI):
 
   def get_scan_param(self):
     'returns scan parameters for scanning with deltatau. the format is as used for shapepath'
-    scan=1 # snake motion Y fast, X slow (default)
     cnt=np.array(self._cnt, np.int32)
-    sz=np.array(self.size())
+    grid={'pos':tuple(self.pos()), 'pitch':tuple(np.array(self.size())/cnt), 'count':self._cnt}
-    pitch=sz/cnt
+    use_trf=self._param.get('use_trf', True)  # do not use coordinate transformation
+    mode=self._param.get('mode',1)
+    num_pts=np.array(self._cnt, np.int32).prod()
+    param={'num_pts':num_pts}
+    param.update(self._param)
+
+    # TODO: simplify !!!
+    t=self.transform() #obj_info(t)
+    p=np.array(self.pos())
+    s=1#self.size()/self._dscr['size']
+    trf=np.array(((t.m11(),t.m12()),(t.m21(),t.m22()),(0,0)))
+    trf[2,:]=p  # shift origin
+    trf[:2,:]=(trf[:2,:].T*s).T # same as np.asmatrix(np.diag(s))*trf[:2,:], trf[:2,:]*=s not working, scale before rot / shear
+
+    pos=np.array((0,0)) #np.array(grid['pos'])  # in um
+    pitch=np.array(grid['pitch'])  # in um
+    trf2=np.asmatrix(np.identity(3))
+    trf2[:, :2]=trf
+    trf2*=np.asmatrix(((1000, 0, 0), (0, 1000, 0), (0, 0, 1)))
+    trf3=np.asmatrix(((pitch[0], 0, 0), (0, pitch[1], 0), (pos[0], pos[1], 1)))
+    trf=(trf3*trf2)[:, :2]
+
+    if mode in (1,3): # needs all points, not grid
+      scan=1 # snake motion Y fast, X slow (default)
       xx, yy=np.meshgrid(range(cnt[0]), range(cnt[1]))
-
-
       if scan==0: # snake motion X fast, Y slow
         for i in range(1,cnt[1],2):
           xx[i]=xx[i][::-1]
@@ -266,10 +286,20 @@ class Grid(UsrROI):
         yy=yy.T
         for i in range(1, cnt[0], 2):
           yy[i]=yy[i][::-1]
-    pts=np.array([xx.reshape(-1), yy.reshape(-1)], dtype=np.float64).transpose()*pitch
+
-    param={'points':pts}
+      pts=np.array([xx.reshape(-1), yy.reshape(-1)], dtype=np.float64).transpose() #*pitch
-    param.update(self._param)
+
-    assert(param.get('code_gen',0)==0) # this provides fully x,y motor coordinates
+      if not use_trf:
+        pts=(np.hstack((pts, np.ones((pts.shape[0], 1))))*trf).A
+      param['trf']=trf
+      param['points']=pts
+    else:
+      if use_trf:
+        param.update({'grid':grid, 'trf':trf})
+      else:
+        g=grid.copy() #has not be tested !
+        g['pos']=tuple((np.array((0,0,1))*trf).A.reshape(-1).tolist())
+        param.update({'grid':p, 'trf':trf})
     return param
 
 
@@ -371,11 +401,9 @@ class Path(UsrROI):
     s=self.size()/self.szOrig
     trf=np.array(((t.m11(),t.m12()),(t.m21(),t.m22()),(0,0)))
     trf[2,:]=p  # shift origin
-    #trf[:2, 0]*=s[0];trf[:2, 1]*=s[1] #scaling (before rotation shear)
+    trf[:2,:]=(trf[:2,:].T*s).T
-    trf[:2,:]=(trf[:2,:].T*s).T # same as np.asmatrix(np.diag(s))*trf[:2,:], trf[:2,:]*=s not working, scale before rot / shear
-
     # trf*'gridpos in um' -> motor pos in mm
-    param={'points':self._path,'trf':trf}
+    param={'num_pts':len(self._path),'trf':trf,'points':self._path}
     param.update(self._param)
     return param
 

swissmx.py

@@ -1527,7 +1527,7 @@ class WndSwissMx(QMainWindow, Ui_MainWindow):
         if type(go)==UsrGO.Fiducial:
           continue
         t=type(go)
-        if t not in(UsrGO.FixTargetFrame,UsrGO.Path):
+        if t not in(UsrGO.FixTargetFrame,UsrGO.Path,UsrGO.Grid):
           _log.warning(f'{t} not supported for FixTargetFrame ->skipped:{go}')
           continue
         try:
@@ -2025,7 +2025,7 @@ object settings:
     ofs:[.2,.2]
     width:10
     fidScl:.02
-    fiducial:[[.1,.1],[[.1,2.2],[10.3,.1],[10.3,2.2]]
+    fiducial:[[.1,.1],[.1,2.2],[10.3,.1],[10.3,2.2]]
 ''')
 
     mft._btnAdd.clicked.connect(self.module_fix_target_add_obj)
@@ -2146,19 +2146,16 @@ object settings:
       go=UsrGO.Fiducial((fx-l/2,fy-l/2), (l, l),bz)
       go.sigRegionChangeFinished.connect(self.cb_fiducial_update_z)
     elif idx==1:
-      v=geo.pos2pix((12.5, 0))
+      #v=geo.pos2pix((12.5, 0));l=np.linalg.norm(v);l=12.5
-      l=np.linalg.norm(v)
+      sz=param.pop('size',(12.5, 12.5))
-      l=12.5
-      #ctr=bm_pos+bm_sz/2
       go=UsrGO.FixTargetFrame((fx-l/2,fy-l/2), (l, l), tpl='12.5x12.5',**param)
     elif idx==2:
-      v=geo.pos2pix((23, 0))
+      #v=geo.pos2pix((23, 0));l=np.linalg.norm(v)#l=23
-      l=np.linalg.norm(v)
+      sz=param.pop('size',(23, 23))
-      l=23
       go=UsrGO.FixTargetFrame((fx-l/2,fy-l/2), (l, l), tpl='23.0x23.0',**param)
     elif idx==3:
-      w,h=(.120*12, .120*8)
+      sz=param.pop('size',(.120*12, .120*8))
-      go=UsrGO.FixTargetFrame((fx-w/2,fy-h/2), (w, h), tpl='test',**param)
+      go=UsrGO.FixTargetFrame((fx-sz[0]/2,fy-sz[1]/2), sz, tpl='test',**param)
     elif idx==4:
       w,h=size=param.pop('size',(30, 20))
       cnt=param.pop('cnt',(30, 22))