beamline staff changes as of 261020

pxii_bec/bec_widgets/profiles/DailySetup.ini

@@ -0,0 +1,605 @@
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+
+[profile]
+created_at=2026-10-10T16:30:18Z
+quick_select=true
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truncated
+screenshot_at=2026-10-10T20:20:15Z

pxii_bec/bec_widgets/profiles/daily_setup.ini

@@ -0,0 +1,457 @@
+[BECDockArea]
+acceptDrops=false
+accessibleDescription=
+accessibleIdentifier=
+accessibleName=
+autoFillBackground=false
+baseSize=@Size(0 0)
+contextMenuPolicy=@Variant(\0\0\0\x7f\0\0\0\x16Qt::ContextMenuPolicy\0\0\0\0\x1)
+cursor=@Variant(\0\0\0J\0\0)
+enabled=true
+focusPolicy=@Variant(\0\0\0\x7f\0\0\0\x10Qt::FocusPolicy\0\0\0\0\0)
+geometry=@Rect(0 23 1670 1505)
+inputMethodHints=@Variant(\0\0\0\x7f\0\0\0\x14Qt::InputMethodHint\0\0\0\0\0)
+layoutDirection=@Variant(\0\0\0\x7f\0\0\0\x14Qt::LayoutDirection\0\0\0\0\0)
+maximumSize=@Size(16777215 16777215)
+minimumSize=@Size(0 0)
+mode=creator
+mouseTracking=false
+sizeIncrement=@Size(0 0)
+sizePolicy=@Variant(\0\0\0K\0\0\0U)
+statusTip=
+tabletTracking=false
+toolTip=
+toolTipDuration=-1
+whatsThis=
+windowFilePath=
+windowModality=@Variant(\0\0\0\x7f\0\0\0\x13Qt::WindowModality\0\0\0\0\0)
+windowModified=false
+windowOpacity=1
+windowTitle=BEC - TestLayout4
+workspace_is_locked=false
+
+[BECDockArea.ads%3A%3ACDockManager.ads%3A%3ACDockSplitter.ads%3A%3ACDockSplitter.ads%3A%3ACDockAreaWidget.Info.dockWidgetScrollArea.qt_scrollarea_viewport.Info]
+acceptDrops=false
+accessibleDescription=
+accessibleIdentifier=
+accessibleName=
+autoFillBackground=true
+baseSize=@Size(0 0)
+contextMenuPolicy=@Variant(\0\0\0\x7f\0\0\0\x16Qt::ContextMenuPolicy\0\0\0\0\x1)
+cursor=@Variant(\0\0\0J\0\0)
+enabled=true
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pxii_bec/daily_setup_files/.~lock.daily_beamline_health.csv#

@@ -0,0 +1 @@
+,e18747,x10sa-cons-02.psi.ch,28.09.2026 21:41,file:///home/e18747/.config/libreoffice/4;

pxii_bec/daily_setup_files/daily_beamline_health.csv

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+2026-10-08T12:23:01,20000,-0.118,1.18e+12,981,951,-0.84128,1.91026,-0.84177,1.90955,-0.6,-0.1,37.40,-1.39,-1.55193,-0.84179,2.98751,1.41052,1.90955,2.99617
+2026-10-08T12:36:12,12398,-0.122,7.54e+12,1014,1011,-0.84177,1.90955,-0.84063,1.91046,-0.0,0.3,27.70,-2.63,-1.55164,-0.84064,2.98980,1.41097,1.91046,2.99798
+2026-10-08T14:05:15,12400,-0.125,7.53e+12,1010,997,-0.84063,1.91038,-0.83988,1.91091,-0.6,-0.2,22.53,-2.62,-1.55143,-0.83988,2.99126,1.41118,1.91089,2.99881
+2026-10-09T08:39:08,12400,-0.123,7.52e+12,1021,1015,-0.83960,1.91196,-0.83836,1.91302,-0.7,-0.0,25.21,-2.48,-1.55103,-0.83836,2.99472,1.41226,1.91302,3.00306
+2026-10-09T09:09:02,12400,-0.123,7.84e+12,975,956,-0.83837,1.91304,-0.83871,1.91193,-0.4,-0.1,26.17,-2.47,-1.55112,-0.83871,2.99398,1.41169,1.91192,3.00089
+2026-10-11T13:43:17,12400,-0.003,9.40e+12,1046,974,-0.84349,1.90884,-0.84328,1.91123,-0.5,0.3,-11.57,0.25,-1.55229,-0.84327,2.98450,1.41135,1.91124,2.99953
+2026-10-11T13:44:35,12400,-0.003,8.89e+12,959,963,-0.84328,1.91121,-0.84349,1.90923,-1.0,-0.5,4.12,-0.10,-1.55233,-0.84350,2.98406,1.41036,1.90923,2.99553
+2026-10-11T13:46:10,15000,0.000,3.88e+12,997,974,-0.84348,1.90922,-0.84349,1.90922,-0.5,-0.7,7.75,-0.22,-1.55235,-0.84348,2.98409,1.41036,1.90924,2.99551
+2026-10-11T13:57:05,15000,-0.000,3.88e+12,999,972,-0.84348,1.90924,-0.84346,1.90924,-0.8,-0.5,7.18,-0.03,-1.55236,-0.84348,2.98415,1.41037,1.90926,2.99557
+2026-10-11T14:06:33,15000,0.000,3.89e+12,1000,972,-0.84349,1.90922,-0.84349,1.90923,-0.9,-0.5,5.01,-0.04,-1.55235,-0.84347,2.98411,1.41035,1.90923,2.99548
+2026-10-11T14:14:45,12400,-0.002,8.88e+12,997,971,-0.84349,1.90924,-0.84350,1.90923,-0.8,-0.3,4.65,-0.12,-1.55235,-0.84350,2.98404,1.41035,1.90923,2.99552
+2026-10-11T14:30:55,12400,-0.002,8.87e+12,998,974,-0.84348,1.90922,-0.84349,1.90924,-1.0,-0.9,4.66,-0.26,-1.55235,-0.84350,2.98410,1.41035,1.90922,2.99549
+2026-10-11T14:46:28,12400,-0.002,8.73e+12,988,976,-0.84348,1.90922,-0.84349,1.90925,0.7,-1.1,9.50,-0.33,-1.55234,-0.84349,2.98406,1.41034,1.90921,2.99547
+2026-10-11T14:51:26,12400,-0.002,8.75e+12,995,975,-0.84349,1.90923,-0.84348,1.90921,-0.5,-0.9,7.19,-0.16,-1.55234,-0.84347,2.98412,1.41038,1.90924,2.99546
+2026-10-11T15:00:54,12400,-0.002,8.77e+12,995,977,-0.84350,1.90924,-0.84325,1.90923,-0.5,0.3,6.43,0.09,-1.55229,-0.84326,2.98451,1.41035,1.90923,2.99550
+2026-10-11T15:14:21,12400,-0.002,8.83e+12,993,971,-0.84326,1.90925,-0.84327,1.90924,-0.0,-0.2,6.62,-0.12,-1.55229,-0.84326,2.98454,1.41036,1.90923,2.99549
+2026-10-11T15:17:41,12400,-0.002,8.86e+12,995,968,-0.84327,1.90923,-0.84326,1.90921,-0.2,0.2,6.43,0.13,-1.55230,-0.84328,2.98450,1.41035,1.90922,2.99549
+2026-10-12T09:45:04,12400,0.000,8.91e+12,983,951,-0.84303,1.90992,-0.84353,1.90914,-0.7,-0.3,4.88,0.31,-1.55229,-0.84354,2.98386,1.41029,1.90909,2.99524
+2026-10-14T08:55:40,12400,0.000,8.77e+12,1033,1005,-0.84345,1.90907,-0.84247,1.91088,-0.5,0.3,10.83,0.85,-1.55198,-0.84249,2.98585,1.41119,1.91089,2.99878
+2026-10-15T09:34:37,12400,-0.000,8.83e+12,959,923,-0.84246,1.91085,-0.84368,1.90935,0.7,-0.0,8.69,0.17,-1.55226,-0.84369,2.98353,1.41042,1.90936,2.99573
+2026-10-16T08:40:24,12400,-0.000,8.80e+12,1004,979,-0.84368,1.90932,-0.84343,1.90991,0.2,0.1,13.56,0.51,-1.55222,-0.84343,2.98403,1.41066,1.90985,2.99675
+2026-10-16T15:14:36,12400,-0.000,8.78e+12,982,956,-0.84344,1.90983,-0.84379,1.90948,0.6,-0.1,12.88,0.34,-1.55234,-0.84380,2.98332,1.41047,1.90947,2.99601
+2026-10-17T12:28:51,12400,-0.038,9.12e+12,1017,1181,-0.84379,1.90942,-0.83817,1.91044,-0.2,-0.6,6.60,-5.16,-1.55092,-0.83817,2.99459,1.41097,1.91047,2.99800
+2026-10-17T21:52:03,12400,-0.042,9.16e+12,993,968,-0.83965,1.91067,-0.83966,1.91068,-0.2,0.1,6.30,-3.83,-1.55129,-0.83964,2.99155,1.41106,1.91066,2.99839
+2026-10-19T09:06:34,12400,-0.044,9.12e+12,987,952,-0.83966,1.91067,-0.84014,1.91068,0.8,-0.2,5.30,-4.09,-1.55137,-0.84013,2.99058,1.41107,1.91067,2.99843

pxii_bec/daily_setup_files/weekly_beamline_health.csv

@@ -10,3 +10,12 @@
 "2026-09-30T11:45:21",12400,5.307,-0.0417,0.14,0.874,0.102,0.152,0.224,-0.639,0.014,-0.0129,0.0118,-0.0001,-0.0399,-0.0652,6.1,-1.63
 2026-09-30T12:07:53,12400,5.307,-0.042,0.14,0.874,0.101,0.152,0.219,-0.639,0.0145,-0.0108,0.0138,0.000447,-0.0467,-0.066,7.24,-1.65
 2026-09-30T12:15:59,12400,5.307,-0.0418,0.14,0.874,0.101,0.152,0.221,-0.639,0.0144,-0.0105,0.012,-0.00118,-0.0414,-0.0618,6.36,-1.54
+2026-10-07T09:34:08,12400,5.307,-0.1193,0.130,0.881,0.088,0.163,0.184,-0.589,0.0961,0.0611,-0.0289,-0.1239,-0.1618,-0.0831,26.4,-2.1
+2026-10-11T14:05:28,12400,5.310,-0.0036,0.130,0.873,0.092,0.156,0.180,-0.637,0.0954,0.0073,-0.0118,0.0191,-0.0440,-0.0014,3.8,-0.1,0.25
+2026-10-11T14:14:13,12400,5.310,-0.0033,,,0.093,0.156,0.182,-0.636,0.0977,0.0072,-0.0168,0.0181,-0.0418,-0.0021,3.5,-0.1,0.25
+2026-10-11T14:23:25,12400,5.310,-0.0019,,,0.093,0.156,0.181,-0.637,0.1022,0.0046,-0.0068,0.0224,-0.0518,-0.0005,5.1,-0.1,0.25
+2026-10-11T14:30:23,12400,5.310,-0.0013,,,0.093,0.156,0.185,-0.635,0.0970,0.0061,-0.0078,0.0209,-0.0287,-0.0040,1.3,-0.2,0.25
+2026-10-11T14:45:55,12400,5.310,-0.0021,,,,,,,,,,,,,,,0.25
+2026-10-11T15:00:21,12400,5.310,-0.0023,0.130,0.873,0.093,0.174,0.177,-0.636,0.1009,0.0066,-0.0069,0.0183,-0.0608,-0.0088,6.6,-0.3,0.25
+2026-10-14T08:55:03,12400,5.310,0.0001,0.130,0.873,0.085,0.157,0.172,-0.638,0.1177,0.0063,-0.0048,0.0302,-0.0618,-0.0162,6.8,-0.5,0.25
+2026-10-17T12:28:09,12400,5.309,-0.0382,0.125,0.881,0.077,0.167,0.171,-0.529,0.1176,0.0800,-0.0212,-0.2063,-0.0501,-0.4810,4.8,-7.0,0.25

pxii_bec/daily_setup_files/weekly_beamline_health2.csv

@@ -0,0 +1,10 @@
+timestamp,energy_eV,id_gap_mm,pitch_offset_mrad,fe_x,fe_y,bsf_x,bsf_y,ss_x,ss_y,lu_Xnorm,lu_Ynorm,ss_Xnorm,ss_Ynorm,bcu_Xnorm,bcu_Ynorm,bcu_beam_x,bcu_beam_y
+2026-09-24T21:42:20,12400.0338140146,5.307,-0.042640079687493,0.140288499999999,0.872397500000001,0.097923887634334,0.153298136901654,0.21542,-0.64411,,,,,,,,
+2026-09-28T19:57:16,12399.9628462791,5.307,-0.044554079687435,0.140375499999999,0.872320000000001,0.105040205383357,0.148134944152631,0.22142,-0.6395,,,,,,,,
+2026-09-28T20:08:25,12399.9609373482,5.307,-0.044496079687582,0.1403535,0.872312500000001,0.104503286743221,0.148356196594037,0.22431,-0.64021,-0.001605502500174,-0.011175883290173,-0.01409593110007,,0.11351579437023,-0.118069917719052,,
+2026-09-30T08:58:15,12399.7329928229,5.307,-0.044525079687622,0.139911,0.88608,0.10406555023199,0.17099928588847,0.19652,-0.2202,0.081590727629084,0.411812820368516,0.033582789254866,,-0.112479632399972,-0.816516017074602,,
+2026-09-30T09:08:53,12399.747477715,5.307,-0.042524079687558,0.139926999999998,0.864803500000001,0.103701246643123,0.143616435241498,0.24392,-1.0175,-0.063997780917417,-0.289248157407647,-0.079407668513141,,0.034774101807238,0.983399612330604,,
+2026-09-30T10:49:14,12400.0475135773,5.30728340148926,-0.042002079687512,0.139973999999999,0.8737165,0.103015554809627,0.152205226135052,0.2194,-0.6346,0.012092898871937,-0.017654174479793,0.01164915499848,,-0.038458560216091,-0.056822442194876,,
+2026-09-30T11:04:59,12400.034824637,5.30728340148926,-0.041712079687562,0.140038499999999,0.873851000000002,0.102714193725642,0.152251956176556,0.22052,-0.64071,0.01188100007843,-0.012323516377797,0.013475582102897,-0.002578973845116,-0.042749327098526,-0.061238705041222,,
+2026-09-30T11:39:23,12400,5.307,-0.042,0.140108499999998,0.873990000000001,0.102007521057185,0.152334925842084,0.22002,-0.64121,0.0135,-0.0108,0.0095,0.000379,-0.0371,-0.0659,5.64,-1.65
+2026-09-30T11:45:21,12400,5.307,-0.0417,0.14,0.874,0.102,0.152,0.224,-0.639,0.014,-0.0129,0.0118,-0.0001,-0.0399,-0.0652,6.1,-1.63

pxii_bec/device_configs/pxii-devices.yaml

@@ -65,15 +65,15 @@ aerotech:
       mount: 0
       work: 0
     x:
-      in: 0.05999397
+      in: 0.05999735
       out: -10
       safe: -50
     y:
       mount: -0.0
-      work: -0.02799609
+      work: -0.03099898
     z:
       mount: 0
-      work: -0.0090036
+      work: -0.0090031
 bcu_bpm1:
   description: BCU BPM Channel 1
   deviceClass: ophyd.EpicsSignalRO
@@ -302,7 +302,7 @@ bs_x:
   onFailure: buffer
   readoutPriority: baseline
   userParameter:
-    in: 0.2038985
+    in: 0.44000227
 bs_y:
   description: Beamstop Y
   deviceClass: ophyd_devices.EpicsMotor
@@ -314,7 +314,7 @@ bs_y:
   onFailure: buffer
   readoutPriority: baseline
   userParameter:
-    in: 0.9064885
+    in: -3.3000017
 bs_z:
   description: Beamstop Z
   deviceClass: ophyd_devices.EpicsMotor
@@ -560,6 +560,8 @@ dcm_pitch:
   enabled: true
   onFailure: buffer
   readoutPriority: baseline
+  userParameter:
+    offset: 0
 dcm_x:
   description: DCM Lateral
   deviceClass: ophyd_devices.EpicsMotorEC
@@ -1310,6 +1312,17 @@ samcam_sigma:
   onFailure: buffer
   readOnly: true
   readoutPriority: monitored
+samcam_thresh:
+  description: Sample Camera Threshold
+  deviceClass: ophyd.EpicsSignal
+  deviceConfig:
+    auto_monitor: true
+    read_pv: X10SA-ES-MS:Stats5:CentroidThreshold
+  deviceTags:
+  - scam
+  enabled: true
+  onFailure: buffer
+  readoutPriority: baseline
 samcam_x:
   description: Sample Camera X
   deviceClass: ophyd.EpicsSignalRO
@@ -1758,7 +1771,6 @@ transm:
   deviceClass: ophyd_devices.EpicsSignal
   deviceConfig:
     read_pv: X10SA-ES-SSFI:TRANSM-SET
-    write_pv: X10SA-ES-SSFI:TRANSM-SET
   deviceTags:
   - transm
   enabled: true

pxii_bec/macros/EvalFlux.py

@@ -2,68 +2,71 @@ def evalflux():
 
     from APscripts import read_data_csv, fitpoly
 
-    data=read_data_csv('FLUX_x10sa_20260709_174259.txt')
-
-    einv=data[:, 0]
-    fcalfinv = data[:, 6] # if energy top down
+    data = read_data_csv("FLUX_x10sa_20260709_174259.txt")
 
+    einv = data[:, 0]
+    fcalfinv = data[:, 6]  # if energy top down
 
     e = einv[::-1]
     flcf = fcalfinv[::-1]
 
     # omit the last values (>= 27 keV)
 
-    len(e) # = 25
+    len(e)  # = 25
     e = e[0:21]
-    flcf =flcf[0:21]/1.e9 ## divide by 1e9 for better readability
+    flcf = flcf[0:21] / 1.0e9  ## divide by 1e9 for better readability
 
     fitpoly(e, flcf, 3)
 
     # Polynomial coefficients of the fit fct:  3 [-0.00026213  0.01171065 -0.05379571  0.04478851]
 
 
-def csplinex(x,y,en):
+def csplinex(x, y, en):
     from scipy.interpolate import CubicSpline
 
     # Create spline
     cs = CubicSpline(x, y)
-    y_cs = cs(en) 
+    y_cs = cs(en)
     return y_cs
 
-    
+
 def flux_bcu():
-    e = get_current_energy()/1000.
-    bcusum = read_av(dev.bcu_bpmsum,10)
-    flux = fl_bcubpm(e,bcusum)
-    return f"{flux:.2e}"  
-    
+    e = get_current_energy() / 1000.0
+    bcusum = read_av(dev.bcu_bpmsum, 10)
+    flux = fl_bcubpm(e, bcusum)
+    return f"{flux:.2e}"
+
+
 def flux_i1():
-    e = get_current_energy()/1000
-    i1 = read_av(dev.i1,10)
+    e = get_current_energy() / 1000
+    i1 = read_av(dev.i1, 10)
     flux = fl_i1(e, i1)
-    return f"{flux:.2e}"  
-    
-def fl_bcubpm(e,bcusum):
-    import numpy as np    
-    fact = 1.e9 
-    coeff = [-0.00026213,  0.01171065, -0.05379571,  0.04478851]
-    if e > 24 :
-        coeff = [4.83704287e-05, -3.17174523e-03,  7.33131161e-02, -5.91926617e-01, 1.66572494e+00]
+    return f"{flux:.2e}"
+
+
+def fl_bcubpm(e, bcusum):
+    import numpy as np
+
+    fact = 1.0e9
+    coeff = [-0.00026213, 0.01171065, -0.05379571, 0.04478851]
+    if e > 24:
+        coeff = [4.83704287e-05, -3.17174523e-03, 7.33131161e-02, -5.91926617e-01, 1.66572494e00]
     polynomial = np.poly1d(coeff)
     fl = polynomial(e) * bcusum * fact
-    #print(f'flux from {bcusum} with en {e} is {fl:.2e} ph/s')
-    
-    return fl 
-    
-def fl_i1(e,i1):
+    # print(f'flux from {bcusum} with en {e} is {fl:.2e} ph/s')
+
+    return fl
+
+
+def fl_i1(e, i1):
     import pandas as pd
 
     file = "luts/I1flcalf.csv"
-    df = pd.read_csv(file)  
+    df = pd.read_csv(file)
     a = df["En"]
     b = df["Fl/I1"]
-    
-    fl_i1 =  csplinex(a,b,e) *i1 
-    print(f'flux from {i1} with en {e} is {fl_i1:.2} ph/s ')
+
+    fl_i1 = csplinex(a, b, e) * i1
+    print(f"flux from {i1} with en {e} is {fl_i1:.2} ph/s ")
 
     return fl_i1

pxii_bec/macros/KB_Class.py

@@ -13,10 +13,12 @@ class KBMirror:
             self.P2 = 0.583490
             self.P3 = -0.372950
             self.L1 = -0.955798
-            self.curv_approx_fact =  0.9550 # 0.9550 # origin: 1.0121 
-            self.s1 = 24.15   
+            self.curv_approx_fact = 0.9550  # 0.9550 # origin: 1.0121
+            self.s1 = 24.15
             self.s2 = 1.45
-            self.asym0 = 0.114 ## origin: 0.0.08  + 0.034  # user asymm, eg 0.4750, will be added ( - sign) 
+            self.asym0 = (
+                0.114  ## origin: 0.0.08  + 0.034  # user asymm, eg 0.4750, will be added ( - sign)
+            )
 
         elif self.mirror_type == "PXII_HFM":
             self.C0 = 0.060453
@@ -24,10 +26,12 @@ class KBMirror:
             self.P2 = 0.586057
             self.P3 = -0.088093
             self.L1 = -0.999445
-            self.curv_approx_fact = 0.8810   # origin: # 0.995 
-            self.s1 = 24.90   
+            self.curv_approx_fact = 0.8810  # origin: # 0.995
+            self.s1 = 24.90
             self.s2 = 0.7
-            self.asym0 = 0.06455    ## origin: -0.0107 + 0.07525          # added user asymm 2.75 (-sign)  
+            self.asym0 = (
+                0.06455  ## origin: -0.0107 + 0.07525          # added user asymm 2.75 (-sign)
+            )
 
         else:
             raise ValueError(f"Unknown mirror type: {self.mirror_type}")
@@ -59,7 +63,7 @@ class KBMirror:
         return s2, R
 
     def get_benders(self, th=3.0, defocus_mm=0.0, user_asymmetry=0.0):
-        asym = self.asym0 - user_asymmetry #### sign is important! 
+        asym = self.asym0 - user_asymmetry  #### sign is important!
         s2_target = self.s2 + defocus_mm / 1000
         curv = self.ellipse_to_curvature(s2_target, th)
         BU, BD = self.curvature_to_bend(curv, asym)
@@ -69,16 +73,12 @@ class KBMirror:
         curv, asym = self.bend_to_curvature(BU, BD)
         s2_rb, R0 = self.curvature_to_ellipse(curv, th)
         defocus_mm = (s2_rb - self.s2) * 1000
-        bend_rad_m = 1/curv *1000
+        bend_rad_m = 1 / curv * 1000
         return {
             "curvature": curv,
-            "bend_rad_m":  bend_rad_m,
-            "bend_rad0_m":  R0,
+            "bend_rad_m": bend_rad_m,
+            "bend_rad0_m": R0,
             "asymmetry": asym,
             "s2": s2_rb,
-            "defocus_mm": defocus_mm
+            "defocus_mm": defocus_mm,
         }
-
-
-
-    

pxii_bec/macros/Undu_Helpers.py

@@ -45,8 +45,40 @@ def exponential_func2(x, a, b, c, d):
 
 ##################################
 
-
+# #####  Sept 2026 Data ######################################
 def return_harmon():
+    # from 3rd to 19th Energy range from 6 keV to 30 keV
+    # harmonics, Sept 2026
+    import numpy as np
+
+    nharm = 19
+    h = [np.array([]) for _ in range(nharm + 1)]
+    h[0] = np.array([0])
+    h[1] = np.array([0])
+    h[2] = np.array([0])
+    h[3] = np.array([0.095, -0.276, 4.154])  # 3rd harmon
+    h[4] = np.array([0.00692593, -0.131504, 1.45763, -0.864603])
+    h[5] = np.array([0.00269444 , - 0.0616905 , 0.967925,  - 0.295405])
+    h[6] = np.array([ 0.00248148 , - 0.0767908 , 1.2178 , - 1.91516  ])
+    h[7] = np.array([0.00110017 , - 0.0369968 , 0.77334 ,- 0.688198  ])
+    h[8] = np.array([0.000643939 , - 0.0226645 , 0.570453 , - 0.0479048  ])
+    h[9] = np.array([0.00021633 , -0.00619517  , 0.315392 , 0.971667  ])
+    h[10] = np.array([ 0.000708236 , - 0.0357576 , 0.851686 - 2.48765  ])
+    h[11] = np.array([ 0.000589549 , -0.0328631 , 0.837705 , - 2.90326 ])
+    h[12] = np.array([ 0.00218182 , 0.1212 , 1.74739 ])
+    h[13] = np.array([ 0.197702, 0.757869 ])
+    h[14] = np.array([ 0.183733, 0.762778 ])
+    h[15] = np.array([ 0.170381, 0.783155 ])
+    h[16] = np.array([ 0.157321,  0.850464 ])
+    h[17] = np.array([0.1466, 0.8906  ])
+    h[18] = np.array([0.1362, 0.9538  ])
+    h[19] = np.array([0.128, 0.985 ])
+
+
+    return h
+
+# #####  July 2025 Data ######################################
+def return_harmon_old():
     # from 3rd to 21th Energy range from 6 keV to 30 keV
     # harmonics, July 2025
     import numpy as np
@@ -97,7 +129,7 @@ def plot_harmon(e_start, e_end, h_no, pr_out=False):
     plt.show()
 
 
-def setu19(en, *harm_no, detune=0, simul = 0):
+def setu19(en, *harm_no, detune=0, simul = 0, iexp = 0):
     """
     set the U19 to the gaps defined in Jul2025, or the "theoretical" ones for higher
     harmonics
@@ -106,32 +138,43 @@ def setu19(en, *harm_no, detune=0, simul = 0):
     en in keV, possibly select a special harmonics, or detune [0/1] to a value
     with a nicer beam shape but less flux
     """
-    g0 = dev.id_gap.readback.get()
-
-    fitpar_u19 = np.array([2.17078531, 0.519452, -0.00720255])  # measured from U19
+    if not simul:
+        g0 = dev.id_gap.readback.get()
 
+    #fitpar_u19 = np.array([2.17078531, 0.519452, -0.00720255])  # measured from U19
+    fitpar_u19 = np.array([ 2.22322523,  0.50396248, -0.00783873]) # measured from U19, Sept2026
+    
     h_all = return_harmon()
     # dep on energy -> select harmonics
     if harm_no:
         harm = int(harm_no[0])
+
         print("Selected harmonics is:", harm)
 
     else:
         print("Using the default optimised harmonics")
         if en <= 7:
             harm = 3  #   h = h[3]
-        elif 7 < en <= 10:
+        elif 7 < en <= 10.5:
             harm = 5
-        elif 10 < en <= 13:
+        elif 10.5 < en < 13:
             harm = 7
-        elif 13 < en <= 16:
+        elif 13 <= en <= 16.5:
             harm = 9
-        elif 16 < en <= 19:
+        elif 16.5 < en <= 19.5:
             harm = 11
-        elif 19 < en <= 22: ## 22 
+        elif 19.5 < en <= 22.5: 
             harm = 13
+        elif 22.5 < en <= 25.5: ## 22 
+            harm = 15
+        elif 25.5 < en <= 28.5: ## 22 
+            harm = 17
+        elif 28.5 < en <= 30: ## 22 
+            harm = 19
+            
+            
 
-    if (en <= 22 and harm <=13):
+    if (en <= 30 and harm <=19):
         h = h_all[harm]
         print(f"harmonics is {harm}.")
 
@@ -146,25 +189,17 @@ def setu19(en, *harm_no, detune=0, simul = 0):
     # 29: 15, 17, 19
     # 30: 19
     ##
-    if (en > 22 and harm_no):
-        harm = int(harm_no[0])
-        print("Selected harmonics is:", harm)
-        n= harm
+    if (iexp and harm_no):
+        harm_selected = int(harm_no[0])
+        print("Selected harmonics is:", harm_selected)
+        n= harm_selected
         enorm = en / n
         g = exponential_func0(enorm, fitpar_u19[0], fitpar_u19[1], fitpar_u19[2])
-    else:    
-        if 22 < en <= 25:
-            n = 15
-            enorm = en / n
-            g = exponential_func0(enorm, fitpar_u19[0], fitpar_u19[1], fitpar_u19[2])
-        elif 25 < en <= 29:
-            n = 17
-            enorm = en / n
-            g = exponential_func0(enorm, fitpar_u19[0], fitpar_u19[1], fitpar_u19[2])
-        elif 29 < en:
-            n = 19
-            enorm = en / n
-            g = exponential_func0(enorm, fitpar_u19[0], fitpar_u19[1], fitpar_u19[2])
+    elif (iexp):    
+        n = harm  # default for that energy range, as set before 
+        enorm = en / n
+        print('exp fct fit used')
+        g = exponential_func0(enorm, fitpar_u19[0], fitpar_u19[1], fitpar_u19[2])
 
         
     if not simul:
@@ -180,7 +215,7 @@ def setu19(en, *harm_no, detune=0, simul = 0):
     # print("move disabled!!")
         scans.umv(dev.id_gap, g, relative=False)
 
-    return g
+    return round(g,4) 
 
 
 ##################################
@@ -201,7 +236,8 @@ def harmon_walk(estart=7.5, end_en=13):
 
 ##################################
 def gap_harm(e=12.4):
-    fitpar_u19 = np.array([2.17078531, 0.519452, -0.00720255])
+    # old values fitpar_u19 = np.array([2.17078531, 0.519452, -0.00720255])
+    fitpar_u19 = np.array([2.22322523,  0.50396248, -0.00783873]) 
     fitpar_u17 = np.array([2.17078572, 0.46477267, -0.005766])
     e = float(input("Please enter an energy between 6 and 30: "))
 
@@ -396,7 +432,7 @@ def gscan(deltag = 0.05,centre=0, gomax=0, detune=0,sett=1, silent=0, iplot=1, i
     indmax = np.argmax(bpm_data)
     gmax = gap_data[indmax]
 
-    gcen, xm = fit_plot(gap_data, bpm_data, model="voigt", silent=silent, iplot=iplot)
+    gcen, xm = fit_plot(gap_data, bpm_data, tmodel="voigt", silent=silent, iplot=iplot)
 
     if gomax:
         gm = xm
@@ -419,3 +455,30 @@ def gscan(deltag = 0.05,centre=0, gomax=0, detune=0,sett=1, silent=0, iplot=1, i
             print("Fit too far off, try using option gomax=1")
 
     return gm, xm 
+
+##################################
+
+def bfield_x10sa(gap):
+    if gap < 4.5 or gap > 20:
+        print("no valid gap!") 
+        return
+
+    ### values for the U19
+    l_u = 19
+    a = 3.22482942
+    b = -0.30100054
+    c = 0.00808649
+    
+    b0 = exponential_func0(gap, a,b,c )
+    b0= round(b0,4)
+    # K  =  e/mc * l_u/2pi * B
+    k = round(0.0934 *l_u * b0,2)
+    
+    print(f'### X10SA and U19 ###  ')   
+    print(f'for a gap of {gap} mm : ')   
+    print(f'B0 = {b0}')
+    print(f'K = {k}')
+    
+    return b0, k
+
+##################################

pxii_bec/macros/analyse_luts.py

@@ -12,7 +12,7 @@ from pxii_bec.scripts import beamline_context as bl
 def get_data(filename):
     """Open the raw DCM calibration data file."""
 
-    filename = bl.env.lut_dir / f"{filename}.csv"
+    filename = bl.env.lut_dir / f"{filename}"
 
     return pd.read_csv(filename)
 
@@ -168,8 +168,69 @@ def lut_plot(
 
     return fit
 
+def pitch_analysis(filename, save=False):
+    """Compare DCM pitch calibration against energy and Bragg angle."""
 
-def pitch_analysis(filename, fit_order=3, save=False):
+    df = get_data(filename)
+
+    fits = {}
+
+    for xname, fit_order in [("energy", 4), ("bragg", 2)]:
+
+        x = df[xname].to_numpy()
+        pitch = df["pitch"].to_numpy()
+
+        fit = lut_plot(
+            df[[xname, "pitch"]].to_numpy(),
+            xname="Energy" if xname == "energy" else "Bragg angle",
+            yname="pitch",
+            title=f"DCM_Pitch_Calibration_{xname}",
+            fit_order=fit_order,
+            save=save,
+        )
+
+        # Calculate residuals
+        fitted_pitch = np.polyval(fit, x)
+        residuals = pitch - fitted_pitch
+
+        rms = np.sqrt(np.mean(residuals**2))
+        max_residual = np.max(np.abs(residuals))
+
+        print(f"\n{xname.capitalize()} fit (order {fit_order})")
+        print(f"RMS residual: {rms:.6g}")
+        print(f"Max residual: {max_residual:.6g}")
+
+        for xi, residual in zip(x, residuals):
+            print(f"  {xi:10.3f}: {residual:+.6g}")
+
+        fits[xname] = {
+            "fit": fit,
+            "residuals": residuals,
+            "rms": rms,
+            "max_residual": max_residual,
+        }
+
+    return fits
+
+def pitch_analysis_bragg(filename, fit_order=2, save=False):
+    """Fit and plot the DCM pitch calibration."""
+
+    df = get_data(filename)
+
+    pitch = df[["bragg", "pitch"]]
+
+    fit = lut_plot(
+        pitch.to_numpy(),
+        xname="Bragg angle",
+        yname="pitch",
+        title="DCM_Pitch_Calibration",
+        fit_order=fit_order,
+        save=save,
+    )
+
+    return fit
+
+def pitch_analysis_energy(filename, fit_order=3, save=False):
     """Fit and plot the DCM pitch calibration."""
 
     df = get_data(filename)
@@ -328,8 +389,8 @@ def ge_edge_analysis(filename, save=False):
     # ----------------------------------------------------------
 
     if save:
-        signal_file = bl.env.lut_dir / f"{filename}_signal.png"
-        derivative_file = bl.env.lut_dir / f"{filename}_derivative.png"
+        signal_file = bl.env.daily_setup_dir / "Ge_edge_signal.png"
+        derivative_file = bl.env.daily_setup_dir / "Ge_edge_derivative.png"
 
         fig1.savefig(signal_file, bbox_inches="tight", dpi=150)
         fig2.savefig(derivative_file, bbox_inches="tight", dpi=150)
@@ -347,25 +408,77 @@ def ge_edge_analysis(filename, save=False):
         "expected_edge": expected_edge,
         "measured_edge": measured_edge,
         "energy_offset": energy_offset,
-        "derivative": derivative,
+        "signal_png": signal_file,
+        "derivative_png": derivative_file,
     }
 
-def perp_analysis():
+def perp_analysis(filename):
     """Select the DCM perpendicular translation calibration data."""
 
-    df = get_data()
+    df = get_data(filename)
+    sel = df[['energy','dcm_perp', 'xi_cam_x']]
+    savefile = bl.env.lut_dir / "perp_actual_calc.csv"
+    with open(savefile, 'w', encoding='utf-8') as f:
+        f.write("energy,calc_perp,actual_perp\n")
 
-    conv_factor = 12365.75 / (2 * 3.13481)
+    energies = [8000, 10000, 12400, 15000, 18000, 20000, 22000, 25000]
+    for energy in energies:
 
-    df["costheta"] = np.cos(conv_factor / df["energy"])
+        data = sel[sel['energy']== energy]
+        print(data)
 
-    perp = df[["costheta", "bsccam_x"]]
+        target = 149.4 # value of xi_cam_x at 12.4 keV
 
-    return (
-        perp.to_numpy(),
-        "costheta",
-        "bsccam_x",
-    )
+        x = data["dcm_perp"].to_numpy()
+        y = data["xi_cam_x"].to_numpy()
+
+        # Linear fit: gap = slope * energy + intercept
+        slope, intercept = np.polyfit(x, y, 1)
+
+        # perp_value = intercept/-slope
+        perp_value = (target - intercept)/slope
+        calc_per = calc_perp_position(energy)
+
+
+        with open(savefile, 'a', encoding='utf-8') as f:
+            f.write(f"{energy},{calc_per:.4f},{perp_value:.4f}\n")
+
+        # print(
+        #     f"Energy = {energy} eV, "
+        #     f"Calculated perp = {calc_per:.4f}, "
+        #     f"Actual perp = {perp_value:.4f}"
+        #     )
+
+
+        # fig, ax = plt.subplots(figsize = (5,7))
+        # ax.scatter(x,y)
+        # ax.set_title(f"{energy}")
+    
+        # # Generate fitted line only over the measured range
+        # x_fit = np.linspace(x.min(), x.max(), 100)
+        # y_fit = slope * x_fit + intercept
+
+        # # # Plot fit first and get its automatically assigned colour
+        # line, = ax.plot(
+        #     x_fit,
+        #     y_fit,
+        #     label=energy,
+        # )
+        # plt.show()
+
+    # return results
+
+    # conv_factor = 12365.75 / (2 * 3.13481)
+
+    # df["costheta"] = np.cos(conv_factor / df["energy"])
+
+    # perp = df[["costheta", "bsccam_x"]]
+
+    # return (
+    #     perp.to_numpy(),
+    #     "costheta",
+    #     "bsccam_x",
+    # )
 
 
 def roll_analysis():
@@ -528,4 +641,5 @@ def gap_analysis(save=False):
 
     print("}")
 
-    return results
+    return results
+

pxii_bec/macros/beamline_planner.py

@@ -2,6 +2,7 @@
 
 from collections import defaultdict, deque
 from enum import Enum
+
 # from pxii_bec.scripts import beamline_context as bl
 
 # from enums import BeamlineState, TemperatureMode
@@ -74,7 +75,6 @@ class StateChangePlanner:
             state_name = BeamlineState(state_name)
         target = self._merged_state(state_name, modifier)
 
-
         plan = self._plan(target)
 
         print("PLAN:")
@@ -102,7 +102,7 @@ class StateChangePlanner:
     def available_states(self):
         """Return a list of available states"""
         return list(self.states.keys())
-    
+
     def state_devices(self):
         """Return the set of devices that participate in
         beamline state definitions"""
@@ -111,14 +111,13 @@ class StateChangePlanner:
 
         for state in self.states.values():
             devices.update(state.keys())
-        
+
         return sorted(devices)
 
     def get_positions(self):
         """Return current positions of devices that are used
         in state transitions"""
-        return {name: self.devices[name].pos
-                for name in self.state_devices()}
+        return {name: self.devices[name].pos for name in self.state_devices()}
 
     def print_positions(self):
         """Return current state of all devices"""
@@ -131,7 +130,7 @@ class StateChangePlanner:
         """Return a dict of {device: (before, after)} pairs for devices that changed state"""
         after = self.get_positions()
         return {k: (before[k], after[k]) for k in before if before[k] != after[k]}
-    
+
     def __get_closest_states(self):
         """
         Return states ordered by number of mismatches.
@@ -148,21 +147,9 @@ class StateChangePlanner:
             for dev, expected in config.items():
 
                 if not self.devices[dev].is_at(expected):
-                    mismatches.append(
-                        (
-                            dev,
-                            self.devices[dev].pos,
-                            expected,
-                        )
-                    )
+                    mismatches.append((dev, self.devices[dev].pos, expected))
 
-            results.append(
-                (
-                    state.name,
-                    len(mismatches),
-                    mismatches,
-                )
-            )
+            results.append((state.name, len(mismatches), mismatches))
 
         return sorted(results, key=lambda x: x[1])
 
@@ -173,10 +160,7 @@ class StateChangePlanner:
             print(f"\n{state}: {count} mismatch(es)")
 
             for dev, actual, expected in mismatches:
-                print(
-                    f"  {dev:15s} "
-                    f"{actual:10s} -> {expected}"
-                )  
+                print(f"  {dev:15s} " f"{actual:10s} -> {expected}")
 
     def current_state(self):
         """Return all current matching BeamlineState and TemperatureMode combinations,

pxii_bec/macros/beampos_with_en.py

@@ -1,19 +1,19 @@
 def beampos_with_en(planner):
-    deltat = 2 
-    record_beampos_until("23:00",planner,interval_minutes=deltat)
+    deltat = 2
+    record_beampos_until("23:00", planner, interval_minutes=deltat)
     bl_energy(6000)
-    record_beampos_until("00:00",planner,interval_minutes=deltat)
-    bl_energy(8000)    
-    record_beampos_until("01:00",planner,interval_minutes=deltat)
-    bl_energy(10000)    
-    record_beampos_until("02:00",planner,interval_minutes=deltat)
+    record_beampos_until("00:00", planner, interval_minutes=deltat)
+    bl_energy(8000)
+    record_beampos_until("01:00", planner, interval_minutes=deltat)
+    bl_energy(10000)
+    record_beampos_until("02:00", planner, interval_minutes=deltat)
     bl_energy(12000)
-    record_beampos_until("03:00",planner,interval_minutes=deltat)
+    record_beampos_until("03:00", planner, interval_minutes=deltat)
     bl_energy(12400)
-    record_beampos_until("04:00",planner,interval_minutes=deltat)
+    record_beampos_until("04:00", planner, interval_minutes=deltat)
     bl_energy(14000)
-    record_beampos_until("05:00",planner,interval_minutes=deltat)
+    record_beampos_until("05:00", planner, interval_minutes=deltat)
     bl_energy(16000)
-    record_beampos_until("06:00",planner,interval_minutes=deltat)
+    record_beampos_until("06:00", planner, interval_minutes=deltat)
     bl_energy(18000)
-    record_beampos_until("07:00",planner,interval_minutes=deltat)
+    record_beampos_until("07:00", planner, interval_minutes=deltat)

pxii_bec/macros/build_devices.py

@@ -63,14 +63,7 @@ def build_devices(yaml_file):
     return state_devices
 
 
-def update_position(
-    device,
-    position,
-    value,
-    axis=None,
-    force=False,
-    max_delta=0.5,
-):
+def update_position(device, position, value, axis=None, force=False, max_delta=0.5):
     """
     Update a single saved position in memory.
 
@@ -189,13 +182,7 @@ def update_positions(updates):
     return save_and_reload()
 
 
-def save_current_position(
-    device,
-    position,
-    axis=None,
-    force=False,
-    max_delta=0.5,
-):
+def save_current_position(device, position, axis=None, force=False, max_delta=0.5):
     """
     Save the current motor position as a named position.
     """

pxii_bec/macros/calculator.py

@@ -2,6 +2,7 @@
 
 from dataclasses import dataclass
 import numpy as np
+
 # from pxii_parameters import (EnergyDefaults, CamConversion)
 
 
@@ -60,9 +61,7 @@ def convert_to_degrees(angle_mrad: float) -> float:
     return np.rad2deg(angle_mrad / 1000)
 
 
-def create_conversion_result(
-    energy_ev: float, wavelength: float, bragg_angle_mrad: float
-) -> dict:
+def create_conversion_result(energy_ev: float, wavelength: float, bragg_angle_mrad: float) -> dict:
     """
     Creates a dictionary containing converted values of energy and angles.
 
@@ -226,9 +225,7 @@ def validate_energy(energy_ev):
     return energy_ev
 
 
-def convert_from_bragg(
-    bragg_angle_mrad: float, temp=120, print_result: bool = False
-) -> dict:
+def convert_from_bragg(bragg_angle_mrad: float, temp=120, print_result: bool = False) -> dict:
     """
     Convert the Bragg angle to wavelength and energy, returning the result as a dictionary.
 
@@ -274,9 +271,7 @@ def convert_from_energy(energy_ev: float, temp=120, print_result: bool = False)
     """
     energy_ev = validate_energy(energy_ev)
     wavelength = calculate_wavelength_from_energy(energy_ev)
-    bragg_angle_mrad = float(
-        calculate_bragg_angle_from_wavelength(wavelength, temp=temp)
-    )
+    bragg_angle_mrad = float(calculate_bragg_angle_from_wavelength(wavelength, temp=temp))
     result = create_conversion_result(energy_ev, wavelength, bragg_angle_mrad)
     if print_result:
         print_conversion_result(result)
@@ -284,9 +279,7 @@ def convert_from_energy(energy_ev: float, temp=120, print_result: bool = False)
 
 
 def convert_from_wavelength(
-    wavelength: float,
-    temp: float = 120,
-    print_result: bool = False,
+    wavelength: float, temp: float = 120, print_result: bool = False
 ) -> dict:
     """
     Convert a given wavelength value into corresponding energy, Bragg angle, and
@@ -312,19 +305,14 @@ def convert_from_wavelength(
             outside of the permitted range, returns None.
     """
     energy_ev = calculate_energy_from_wavelength(wavelength)
-    bragg_angle_mrad = float(
-        calculate_bragg_angle_from_wavelength(wavelength, temp=temp)
-    )
+    bragg_angle_mrad = float(calculate_bragg_angle_from_wavelength(wavelength, temp=temp))
     result = create_conversion_result(energy_ev, wavelength, bragg_angle_mrad)
     if print_result:
         print_conversion_result(result)
     return result
 
 
-def calc_perp_position(
-    energy_ev: float,
-    print_result: bool = False,
-) -> float:
+def calc_perp_position(energy_ev: float, beam_offset = None, print_result: bool = False) -> float:
     """
     Calculate the perpendicular motor position based on provided energy in electron-volts (eV).
 
@@ -344,8 +332,12 @@ def calc_perp_position(
         None
     """
     result = convert_from_energy(energy_ev, print_result=False)
+
+    if beam_offset is None:
+        beam_offset = EnergyDefaults.beam_offset
+
     bragg_angle_rad = result["bragg_angle_mrad"] / 1000
-    perp_offset = float(EnergyDefaults.beam_offset / (2 * np.cos(bragg_angle_rad))) - 3
+    perp_offset = float(beam_offset / (2 * np.cos(bragg_angle_rad))) - 3
     if print_result:
         print(f"Perp = {perp_offset: .4f}")
     return perp_offset
@@ -355,7 +347,7 @@ def calc_scam_microns(pixels, zoom=1000):
     """Convert pixels to microns for the sample camera"""
     return float(pixels / (CamConversion.a * np.exp(CamConversion.b * zoom)))
 
+
 def calc_sscam_microns(pixels):
     """Convert pixels to microns for the ss camera"""
-    return pixels*20
-
+    return pixels * 20

pxii_bec/macros/calibrate_bpm.py

@@ -8,35 +8,172 @@ import numpy as np
 import pandas as pd
 import matplotlib.pyplot as plt
 
+from pxii_bec.scripts import beamline_context as bl
+from pxii_bec.macros.beamline_planner import BeamlineState
 
-# def compute_norm(n_readings=5):
-#     """Average normalized BPM X/Y from repeated sets of four channels."""
 
-#     xn_values = []
-#     yn_values = []
+def compute_norm_ss(n_readings=5):
+    """Average normalized BPM X/Y from repeated sets of four channels."""
 
-#     for _ in range(n_readings):
-#         bpm1 = dev.bcu_bpm1.read()["bcu_bpm1"]["value"]
-#         bpm2 = dev.bcu_bpm2.read()["bcu_bpm2"]["value"]
-#         bpm3 = dev.bcu_bpm3.read()["bcu_bpm3"]["value"]
-#         bpm4 = dev.bcu_bpm4.read()["bcu_bpm4"]["value"]
+    xn_values = []
+    yn_values = []
+    for _ in range(n_readings):
+        bpm1 = dev.ss_bpm1.read()["ss_bpm1"]["value"]
+        bpm2 = dev.ss_bpm2.read()["ss_bpm2"]["value"]
+        bpm3 = dev.ss_bpm3.read()["ss_bpm3"]["value"]
+        bpm4 = dev.ss_bpm4.read()["ss_bpm4"]["value"]
 
-#         total = bpm1 + bpm2 + bpm3 + bpm4
+        total = bpm1 + bpm2 + bpm3 + bpm4
 
-#         if total == 0:
-#             continue
+        if total == 0:
+            continue
 
-#         xn = ((bpm1 + bpm2) - (bpm3 + bpm4)) / total
-#         yn = ((bpm1 + bpm3) - (bpm2 + bpm4)) / total
+        xn = ((bpm1 + bpm2) - (bpm3 + bpm4)) / total
+        yn = ((bpm1 + bpm3) - (bpm2 + bpm4)) / total
 
-#         xn_values.append(xn)
-#         yn_values.append(yn)
+        xn_values.append(xn)
+        yn_values.append(yn)
 
-#         time.sleep(0.1)
+        time.sleep(0.1)
 
-#     return float(np.mean(xn_values)), float(np.mean(yn_values))
+    return {
+        "ss_Xnorm": float(np.mean(xn_values)), 
+        "ss_Ynorm": float(np.mean(yn_values)),
+    }
 
 
+def compute_norm_lu(n_readings=5):
+    """Average normalized BPM X/Y from repeated sets of four channels."""
+
+    xn_values = []
+    yn_values = []
+
+    for _ in range(n_readings):
+        bpm1 = dev.lu_bpm1.read()["lu_bpm1"]["value"]
+        bpm2 = dev.lu_bpm2.read()["lu_bpm2"]["value"]
+        bpm3 = dev.lu_bpm3.read()["lu_bpm3"]["value"]
+        bpm4 = dev.lu_bpm4.read()["lu_bpm4"]["value"]
+
+        total = bpm1 + bpm2 + bpm3 + bpm4
+
+        if total == 0:
+            continue
+
+        xn = ((bpm1 + bpm2) - (bpm3 + bpm4)) / total
+        yn = ((bpm1 + bpm3) - (bpm2 + bpm4)) / total
+
+        xn_values.append(xn)
+        yn_values.append(yn)
+
+        time.sleep(0.1)
+
+    return {
+        "lu_Xnorm": float(np.mean(xn_values)), 
+        "lu_Ynorm": float(np.mean(yn_values)),
+    }
+
+
+
+def run_calibration_ss():
+    """Scan bpm in x and y and record normalised x and y positions"""
+    centred_x = 2.8625
+    centred_y = -1.3874
+    now = datetime.now()
+    fnow = filenow()
+    print(f"moving bpm to {centred_x}, {centred_y}")
+    umv(dev.ss_bpm_y, centred_y)
+    umv(dev.ss_bpm_x, centred_x)
+
+    # # # Calibrate in X
+    # umv(dev.bsf_sl_xsize, 0.3)
+    # umv(dev.bsf_sl_xsize, 0.4)
+    # filename = bl.env.lut_dir / "bpm_calib" / f"ss_bpm_x_{fnow}.csv"
+    # xn_data = []
+    # x_positions = np.linspace(centred_x - 0.3, centred_x + 0.3, 51)
+    # with open(filename, "w", encoding="utf-8") as f:
+    #     f.write(f"Xpos,Xnorm,BPM1,BPM2,BPM3,BPM4\n")
+    # for x in x_positions:
+    #     umv(dev.ss_bpm_x, x)
+    #     print(f"Moving BPM X to {x} mm")
+    #     time.sleep(0.2)
+    #     xn, yn = compute_norm_ss()
+    #     xn_data.append(xn)
+    #     with open(filename, "a", encoding="utf-8") as f:
+    #         f.write(f"{x},{xn}\n")
+
+    # # Calibrate in Y
+    umv(dev.ss_bpm_x, centred_x)
+    umv(dev.bsf_sl_xsize, 0.3)
+    umv(dev.bsf_sl_ysize, 0.4)
+    filename = bl.env.lut_dir / "bpm_calib" / f"ss_bpm_y_{fnow}.csv"
+    y_positions = np.linspace(centred_y - 0.04, centred_y + 0.04, 41)
+    yn_data = []
+    with open(filename, "w", encoding="utf-8") as f:
+        f.write(f"Ypos,Ynorm,BPM1,BPM2,BPM3,BPM4\n")
+    for y in y_positions:
+        umv(dev.ss_bpm_y, y)
+        print(f"Moving BPM Y to {y} mm")
+        time.sleep(0.2)
+        xn, yn = compute_norm_ss()
+        yn_data.append(yn)
+        with open(filename, "a", encoding="utf-8") as f:
+            f.write(f"{y},{yn}\n")
+
+    umv(dev.ss_bpm_x, centred_x)
+    umv(dev.ss_bpm_y, centred_y)
+    umv(dev.bsf_sl_ysize, 3.0)
+    umv(dev.bsf_sl_xsize, 3.0)
+
+def run_calibration_lu():
+    """Scan bpm in x and y and record normalised x and y positions"""
+    centred_x = 2.1816
+    centred_y = 3.0175
+    now = datetime.now()
+    fnow = filenow()
+    print(f"moving bpm to {centred_x}, {centred_y}")
+    umv(dev.lu_bpm_y, centred_y)
+    umv(dev.lu_bpm_x, centred_x)
+
+    # # Calibrate in X
+    # umv(dev.bsf_sl_xsize, 0.3)
+    # umv(dev.bsf_sl_xsize, 0.4)
+    # filename = bl.env.lut_dir / "bpm_calib" / f"lu_bpm_x_{fnow}.csv"
+    # xn_data = []
+    # x_positions = np.linspace(centred_x - 0.3, centred_x + 0.3, 51)
+    # with open(filename, "w", encoding="utf-8") as f:
+    #     f.write(f"Xpos,Xnorm\n")
+    # for x in x_positions:
+    #     umv(dev.lu_bpm_x, x)
+    #     print(f"Moving BPM X to {x} mm")
+    #     time.sleep(0.2)
+    #     xn, yn = compute_norm_lu()
+    #     xn_data.append(xn)
+    #     with open(filename, "a", encoding="utf-8") as f:
+    #         f.write(f"{x},{xn}\n")
+
+    # # Calibrate in Y
+    umv(dev.lu_bpm_x, centred_x)
+    umv(dev.bsf_sl_xsize, 0.3)
+    umv(dev.bsf_sl_ysize, 0.4)
+    filename = bl.env.lut_dir / "bpm_calib" / f"lu_bpm_y_{fnow}.csv"
+    y_positions = np.linspace(centred_y - 0.04, centred_y + 0.04, 41)
+    yn_data = []
+    with open(filename, "w", encoding="utf-8") as f:
+        f.write(f"Ypos,Ynorm,BPM1,BPM2,BPM3,BPM4\n")
+    for y in y_positions:
+        umv(dev.lu_bpm_y, y)
+        print(f"Moving BPM Y to {y} mm")
+        time.sleep(0.2)
+        xn, yn = compute_norm_lu()
+        yn_data.append(yn)
+        with open(filename, "a", encoding="utf-8") as f:
+            f.write(f"{y},{yn}\n")
+
+    umv(dev.lu_bpm_x, centred_x)
+    umv(dev.lu_bpm_y, centred_y)
+    umv(dev.bsf_sl_ysize, 3.0)
+    umv(dev.bsf_sl_xsize, 3.0)
+
 def run_calibration(env):
     """Scan bpm in x and y and record normalised x and y positions"""
     centred_x = 0.444
@@ -86,27 +223,20 @@ def run_calibration(env):
     umv(dev.bcu_bpm_y, centred_y)
     umv(dev.ss_sl_ysize, 3.0)
 
-def read_bpm_calibration_data(
-    env,
-    x_y,
-    rundate,
-    bpm_name="bcu_bpm",
-):
+
+def read_bpm_calibration_data(env, x_y, rundate, bpm_name="bcu_bpm"):
     """Read BPM calibration data from CSV."""
 
     filename = env.lut_dir / f"bpm_calib/{bpm_name}_{x_y}_{rundate}.csv"
 
-    data = np.loadtxt(
-        filename,
-        delimiter=",",
-        skiprows=1,
-    )
+    data = np.loadtxt(filename, delimiter=",", skiprows=1)
 
     position = data[:, 0]
     bpm_norm = data[:, 1]
 
     return position, bpm_norm
 
+
 # def fit_bpm_linear(env, filename, x_y, plot=True):
 #     """
 #     Fit the linear region of a BPM calibration scan.
@@ -200,31 +330,17 @@ def read_bpm_calibration_data(
 #         plt.tight_layout()
 #         plt.show()
 
-#     return result   
-
-
+#     return result
 
 
 def polynomial_calibration(
-    env,
-    x_y,
-    rundate,
-    bpm_name="bcu_bpm",
-    degree=5,
-    signal_limit=0.9,
-    plot=True,
+    env, x_y, rundate, bpm_name="bcu_bpm", degree=5, signal_limit=0.9, plot=True
 ):
 
     # BPM centre during calibration run
-    bpm_centre = {"x": 0.441,"y": -1.5405,}
+    bpm_centre = {"x": 0.441, "y": -1.5405}
 
-
-    xdata, ydata = read_bpm_calibration_data(
-        env,
-        x_y,
-        rundate=rundate,
-        bpm_name=bpm_name,
-    )
+    xdata, ydata = read_bpm_calibration_data(env, x_y, rundate=rundate, bpm_name=bpm_name)
 
     # Keep useful BPM range
     mask = np.abs(ydata) < signal_limit
@@ -262,26 +378,13 @@ def polynomial_calibration(
     print(f"    crosshair_bpm_position = None")
 
     if plot:
-        signal_fit = np.linspace(
-            signal.min(),
-            signal.max(),
-            500,
-        )
+        signal_fit = np.linspace(signal.min(), signal.max(), 500)
 
         position_fit = np.polyval(coeffs, signal_fit)
 
         plt.figure(figsize=(7, 5))
-        plt.scatter(
-            ydata,
-            xdata,
-            alpha=0.4,
-            label="Calibration data",
-        )
-        plt.plot(
-            signal_fit,
-            position_fit,
-            label=f"{degree}th-order polynomial",
-        )
+        plt.scatter(ydata, xdata, alpha=0.4, label="Calibration data")
+        plt.plot(signal_fit, position_fit, label=f"{degree}th-order polynomial")
 
         plt.xlabel(f"BPM {x_y} normalized signal")
         plt.ylabel(f"BPM {x_y} position (mm)")
@@ -292,5 +395,3 @@ def polynomial_calibration(
         plt.show()
 
     return coeffs
-
-

pxii_bec/macros/check.py

@@ -5,7 +5,6 @@ from datetime import datetime
 
 from bec_lib.device import Signal, Positioner
 
-
 # -------------------------------------------------------------------
 # Status Enum
 # -------------------------------------------------------------------

pxii_bec/macros/chmirrh.py

@@ -1,136 +1,134 @@
-import numpy as np 
-import math, time 
+import numpy as np
+import math, time
 import matplotlib.pyplot as plt
 import scipy
+
 ########################################################
-### scan FE slits and check BPMs before and after mirror 
+### scan FE slits and check BPMs before and after mirror
 ########################################################
 
-def gaussfit(x,y,p):
-# define a gaussian fitting function where
-# p[0] = amplitude
-# p[1] = mean
-# p[2] = sigma
-# p[3] = const offset 
-    
-    fitfct = lambda p, x0: p[0]*np.exp(-(x0-p[1])**2/(2.0*p[2]**2))+p[3]
-    #fitfct = lambda p, x0: p[0]*np.exp(-(x0-p[1])**2/(2.0*p[2]**2))
-    errfct = lambda p, x0,y0: fitfct(p,x0)-y0  
+
+def gaussfit(x, y, p):
+    # define a gaussian fitting function where
+    # p[0] = amplitude
+    # p[1] = mean
+    # p[2] = sigma
+    # p[3] = const offset
+
+    fitfct = lambda p, x0: p[0] * np.exp(-((x0 - p[1]) ** 2) / (2.0 * p[2] ** 2)) + p[3]
+    # fitfct = lambda p, x0: p[0]*np.exp(-(x0-p[1])**2/(2.0*p[2]**2))
+    errfct = lambda p, x0, y0: fitfct(p, x0) - y0
 
     # guess fit parameters
-    ind0 = np.where(y==max(y))[0] 
-    p0=np.c_[max(y), x[ind0], np.std(y), np.mean(y[0:5])]
-    #p0=scipy.c_[max(y), np.where(y==max(y))[0], np.std(y)]
-                  # array generation [[]], and taking only one dimens
+    ind0 = np.where(y == max(y))[0]
+    p0 = np.c_[max(y), x[ind0], np.std(y), np.mean(y[0:5])]
+    # p0=scipy.c_[max(y), np.where(y==max(y))[0], np.std(y)]
+    # array generation [[]], and taking only one dimens
     # fit a gaussian to the correlation function
 
-    #print('p0 = ' , p0)
-    p1, success = scipy.optimize.leastsq(errfct, p0.copy()[0],
-                                     args=(x,y))
+    # print('p0 = ' , p0)
+    p1, success = scipy.optimize.leastsq(errfct, p0.copy()[0], args=(x, y))
 
-    #plt.figure()
-    bestfit=fitfct(p1,x)
-    #print('************************', x,y)
-    plt.plot(x,y,'r*')    
-    plt.plot(x,bestfit,'r-')
+    # plt.figure()
+    bestfit = fitfct(p1, x)
+    # print('************************', x,y)
+    plt.plot(x, y, "r*")
+    plt.plot(x, bestfit, "r-")
 
     # different fit fct
-    #popt, pcov = curve_fit(fitfct, x, y)
-    #newfit=fitfct(popt,x)
-    #plt.plot(x,newfit,'g+')
+    # popt, pcov = curve_fit(fitfct, x, y)
+    # newfit=fitfct(popt,x)
+    # plt.plot(x,newfit,'g+')
 
-    
     plt.show()
 
     return bestfit, p1
 
-def scan_fe_sl(dir = "y"):
-    if dir in ["y","v"]:
-        sdir ="vertical"
+
+def scan_fe_sl(dir="y"):
+    if dir in ["y", "v"]:
+        sdir = "vertical"
         fe_size0 = dev.fe_sl_ysize.user_readback.get()
-        print('Closing vertical FE slits to 0.1')  
+        print("Closing vertical FE slits to 0.1")
         umv(dev.fe_sl_ysize, 0.1)
-        s = scans.line_scan(dev.fe_sl_ycen,-1,1, exp_time=02., steps=21, relative=True)
+        s = scans.line_scan(dev.fe_sl_ycen, -1, 1, exp_time=02.0, steps=21, relative=True)
         time.sleep(0.1)
         umv(dev.fe_sl_ysize, fe_size0)
-        print(f'Opening {sdir} FE slits to {fe_size0}')
-    if dir in ["x","h"]:
-        sdir ="horizontal"
+        print(f"Opening {sdir} FE slits to {fe_size0}")
+    if dir in ["x", "h"]:
+        sdir = "horizontal"
         fe_size0 = dev.fe_sl_xsize.user_readback.get()
-        print('Closing horizontal FE slits to 0.1')  
+        print("Closing horizontal FE slits to 0.1")
         umv(dev.fe_sl_xsize, 0.1)
-        s = scans.line_scan(dev.fe_sl_xcen,-1,1, exp_time=02., steps=21, relative=True)
+        s = scans.line_scan(dev.fe_sl_xcen, -1, 1, exp_time=02.0, steps=21, relative=True)
         time.sleep(0.1)
         umv(dev.fe_sl_xsize, fe_size0)
-        print(f'Opening {sdir} FE slits to {fe_size0}')
+        print(f"Opening {sdir} FE slits to {fe_size0}")
     else:
-        print('no valid direction, doing nothing') 
-    
-def mirrh(dir='y'):
-    
-    #dat_ss = read_data_csv("/home/anuschka/SS_pitch2p94.csv")
-    #dat_bcu = read_data_csv("/home/anuschka/BCU_pitch2p94.csv")
+        print("no valid direction, doing nothing")
+
+
+def mirrh(dir="y"):
+
+    # dat_ss = read_data_csv("/home/anuschka/SS_pitch2p94.csv")
+    # dat_bcu = read_data_csv("/home/anuschka/BCU_pitch2p94.csv")
 
     scan_fe_sl(dir=dir)
     ind = -1
-    if dir in ["x","h"]:
-        slitmot = 'fe_sl_xcen'
-    if dir in ["y","v"]:
-        slitmot = 'fe_sl_ycen'        
-    
-    dat_ss = save_data(ind, slitmot, 'ss_bpmsum', isave = 0)
-    dat_bcu = save_data(ind, slitmot, 'bcu_bpmsum', isave = 0)
-    
+    if dir in ["x", "h"]:
+        slitmot = "fe_sl_xcen"
+    if dir in ["y", "v"]:
+        slitmot = "fe_sl_ycen"
 
-    data_xs = dat_ss[0]      # csv would be: dat_ss[:, 0]
+    dat_ss = save_data(ind, slitmot, "ss_bpmsum", isave=0)
+    dat_bcu = save_data(ind, slitmot, "bcu_bpmsum", isave=0)
+
+    data_xs = dat_ss[0]  # csv would be: dat_ss[:, 0]
     data_ys = dat_ss[1]
-    
+
     data_xb = dat_bcu[0]
     data_yb = dat_bcu[1]
 
-    #plt.figure()
+    # plt.figure()
 
-    #plt.plot(data_xs, data_ys, "*")
-    #plt.plot(data_xb, data_yb, "+")
+    # plt.plot(data_xs, data_ys, "*")
+    # plt.plot(data_xb, data_yb, "+")
 
-    data_ys_norm = data_ys/max(data_ys) # looks better than data_ys/sum(data_ys)
-    data_yb_norm = data_yb/max(data_yb)
+    data_ys_norm = data_ys / max(data_ys)  # looks better than data_ys/sum(data_ys)
+    data_yb_norm = data_yb / max(data_yb)
 
     plt.figure()
 
     plt.plot(data_xs, data_ys_norm, "*")
     plt.plot(data_xb, data_yb_norm, "+")
 
-
-    y= data_ys_norm
-    xm = np.where(y==max(y))[0]
+    y = data_ys_norm
+    xm = np.where(y == max(y))[0]
     xmi = data_xs[xm]
-    #print('xm, xmi', xm, xmi) 
+    # print('xm, xmi', xm, xmi)
 
-    pf1 = [1, xmi , np.std(data_ys_norm), np.mean(y[0:5])]     # bg = 0 
-    fit_s, ps = gaussfit(data_xs,data_ys_norm, pf1) 
+    pf1 = [1, xmi, np.std(data_ys_norm), np.mean(y[0:5])]  # bg = 0
+    fit_s, ps = gaussfit(data_xs, data_ys_norm, pf1)
 
-    y= data_yb_norm
-    xm = np.where(y==max(y))[0]
+    y = data_yb_norm
+    xm = np.where(y == max(y))[0]
     xmi = data_xb[xm]
-    #print('xm, xmi', xm, xmi) 
+    # print('xm, xmi', xm, xmi)
 
     pf2 = [1, xmi, np.std(data_yb_norm), np.mean(y[0:5])]  # bg = -11
-    fit_b, pb = gaussfit(data_xb,data_yb_norm, pf2) 
-
+    fit_b, pb = gaussfit(data_xb, data_yb_norm, pf2)
 
     plt.figure()
 
-    plt.plot(data_xs, fit_s-ps[3], "*")
-    plt.plot(data_xs, fit_s-ps[3])
-    plt.plot(data_xb, fit_b-pb[3], "+")
-    plt.plot(data_xb, fit_b-pb[3])
+    plt.plot(data_xs, fit_s - ps[3], "*")
+    plt.plot(data_xs, fit_s - ps[3])
+    plt.plot(data_xb, fit_b - pb[3], "+")
+    plt.plot(data_xb, fit_b - pb[3])
 
-    print('Fit Params of First BPM, SS, ps', ps)
-    print('Fit Params of Second BPM, BCU, pb', pb)
+    print("Fit Params of First BPM, SS, ps", ps)
+    print("Fit Params of Second BPM, BCU, pb", pb)
     print()
-    if abs(ps[1]-pb[1]) > 0.05:
-        print('***** WARNING ******, mirror height not ok')
-    if abs(ps[2]-pb[2]) > 0.05:
-        print('***** WARNING ******, mirror not catching full beam')
-    
+    if abs(ps[1] - pb[1]) > 0.05:
+        print("***** WARNING ******, mirror height not ok")
+    if abs(ps[2] - pb[2]) > 0.05:
+        print("***** WARNING ******, mirror not catching full beam")

pxii_bec/macros/create_daily_setup_gui.py

@@ -0,0 +1,29 @@
+def create_daily_setup():
+    dock = bec.gui.new("DailySetup")
+    # plot1 = dock.new(widget="Waveform", object_name= "Plot_1")
+    # plot2 = dock.new(widget="Waveform", object_name= "Plot_2", relative_to="Plot_1", where="bottom")
+    # plot3 = dock.new(widget="Waveform", object_name= "Plot_3", relative_to = "Plot_2", where="bottom")
+    # plot4 = dock.new(widget="Waveform", object_name= "Plot_4", relative_to="Plot_1", where="right")
+    # plot5 = dock.new(widget="Waveform", object_name= "Plot_5", relative_to="Plot_2", where="right")
+    # plot6 = dock.new(widget="Waveform", object_name= "Plot_6", relative_to="Plot_3", where="right")
+    # log = dock.new(widget="TextBox", object_name= "Info", relative_to="Plot_1",where="left")
+    # progress = dock.new(widget="TextBox", object_name= "Progress", relative_to="Info", where="left")
+    progress = dock.new(widget="TextBox", object_name= "Progress")
+    log = dock.new(widget="TextBox", object_name= "Info", relative_to="Progress", where ="right")
+    plot1 = dock.new(widget="Waveform", object_name= "Plot_1", relative_to="Info", where ="right")
+    plot2 = dock.new(widget="Waveform", object_name= "Plot_2", relative_to="Plot_1", where="right")
+    plot3 = dock.new(widget="Waveform", object_name= "Plot_3", relative_to = "Plot_1", where="bottom")
+    plot4 = dock.new(widget="Waveform", object_name= "Plot_4", relative_to="Plot_2", where="bottom")
+    plot5 = dock.new(widget="Waveform", object_name= "Plot_5", relative_to = "Plot_3", where="bottom")
+    plot6 = dock.new(widget="Waveform", object_name= "Plot_6", relative_to="Plot_4", where="bottom")
+    dock.set_layout_ratios(
+    horizontal=[1,2,1.2,1.2],
+    vertical=[1,1,1],
+    )
+
+    progress.set_plain_text("")
+    log.set_plain_text("")
+
+    dock.save_profile()
+
+

pxii_bec/macros/devices_manager.py

@@ -1,9 +1,9 @@
 """
 This module manages the initialization of devices."""
 
-#from guards import attach_guards
-#from policies import attach_policies
-#from build_devices import build_devices
+# from guards import attach_guards
+# from policies import attach_policies
+# from build_devices import build_devices
 
 
 class DeviceManager:

pxii_bec/macros/enScan.py

@@ -11,7 +11,7 @@ def en_plothist(hindex: int, signal_name: str, isave=1):
     s=scans.line_scan(dev.dcm_bragg, 178.5, 179.5, steps=240, relative=False
     data_x, data_y = en_plothist(-1,"bcu_bpmsum")
 
-    scanned with 
+    scanned with
     scans.line_scan(dev.aerotech.y,-0.05,0.05, steps=101, settling_time=0.5, relative=True)
     """
 
@@ -21,54 +21,56 @@ def en_plothist(hindex: int, signal_name: str, isave=1):
 
     if hindex < 0:
         h = bec.history[hindex]
-        print('by scan number')
+        print("by scan number")
     else:
         h = bec.history.get_by_scan_number(hindex)
-        print('by scan number')
+        print("by scan number")
 
     md = h.metadata["bec"]
-    sno = md['dataset_number']
+    sno = md["dataset_number"]
     print(f"number of scan = {sno}")
-    scanvar = list(md["args"].keys())[0]  # string, returns the variable of the last performed scan
+    #scanvar = list(md["args"].keys())[0]  # string, returns the variable of the last performed scan
     # data = h.devices[device_name][signal].read()["value"]
     # data_x = h.devices.dcm_pitch.dcm_pitch.read()["value"]
     # data_y = h.devices.lu_bpmsum.lu_bpmsum.read()["value"]
     # data_x = h.devices[device_name][device_name].read()["value"]
 
-    # that works ... 
-    #print(list(md['args'].keys()))
-    val = list(md['args'].keys())
-    #val[0] = 'aerotech.x'
-    devicenam =  val[0]
-    print('device = ', devicenam)
+    # that works ...
+    # print(list(md['args'].keys()))
+    ## val = list(md["args"].keys())   no longer !!!!! to be checked !!! 
+    # val[0] = 'aerotech.x'
+    ##devicenam = val[0]
+    ##print("device = ", devicenam)
+    devicenam = md["scan_report_devices"][0].decode()
+
+    
     data_xd = md["positions"]  # last scan knows which device ... however, double array
     data_x = data_xd.flatten()
     print("dx = ", data_x)
-    #data_y = h.devices[signal_name][signal_name].read()["value"]
+    # data_y = h.devices[signal_name][signal_name].read()["value"]
     data_y1 = h.devices["bcu_bpmsum"]["bcu_bpmsum"].read()["value"]
     data_y2 = h.devices["ss_bpmsum"]["ss_bpmsum"].read()["value"]
-    
-    #print("dy = ", data_y)
 
-    data_y = data_y1/data_y2
-    rev = 0 
-    #if val[0][9] == 'x':
+    # print("dy = ", data_y)
+
+    data_y = data_y1 / data_y2
+    rev = 0
+    # if val[0][9] == 'x':
     #     rev = 1
-    smoothplotgrad(data_x, data_y, reverse = rev)
-   # g, xm = justfit(data_x, data_y, model=model, ibg=ibg)
+    smoothplotgrad(data_x, data_y, reverse=rev)
+    # g, xm = justfit(data_x, data_y, model=model, ibg=ibg)
 
-#    plt.ion()
-#    plt.figure()
-#    plt.plot(data_x, data_y, "*")
-#    plt.plot(data_x, g.best_fit)
-#    plt.xlabel(scanvar)
-#    plt.ylabel(signal_name)
-#    plt.show()
+    #    plt.ion()
+    #    plt.figure()
+    #    plt.plot(data_x, data_y, "*")
+    #    plt.plot(data_x, g.best_fit)
+    #    plt.xlabel(scanvar)
+    #    plt.ylabel(signal_name)
+    #    plt.show()
 
-#    gcen = g.pars["center"].value
+    #    gcen = g.pars["center"].value
 
-
-    if isave: 
+    if isave:
         ans = "n"
         ans = input("Store data in csv file? y/n ")
         if ans == "y":
@@ -79,5 +81,4 @@ def en_plothist(hindex: int, signal_name: str, isave=1):
             with open(filename, "w") as f:
                 np.savetxt(f, combined, delimiter=",", fmt="%.9e")
 
-
     return data_x, data_y

pxii_bec/macros/findattr.py

@@ -3,8 +3,9 @@
 
 # if you know the attribute you are searching for:
 
+
 def check_attr(obj, attr):
-# att as string 
+    # att as string
 
     attr = getattr(obj, attr)
 
@@ -13,7 +14,9 @@ def check_attr(obj, attr):
         print("values:", attr.values())
         print("items:", attr.items())
 
-# Automatically Detect All Dictionary Attributes:   
+
+# Automatically Detect All Dictionary Attributes:
+
 
 def list_dict_attr_single(obj):
     for attr_name, value in vars(obj).items():
@@ -22,8 +25,9 @@ def list_dict_attr_single(obj):
             print("  Keys:", list(value.keys()))
             print("  Items:")
             for key, val in value.items():
-                print(f"     {key} -> {val}") 
-            
+                print(f"     {key} -> {val}")
+
+
 # Also Handle Nested Dictionaries:
 
 
@@ -34,16 +38,11 @@ def list_dict_attr(obj):
             print(" " * indent + str(key) + ":", end=" ")
             if isinstance(value, dict):
                 print()
-                print_dict(value, indent+1)
+                print_dict(value, indent + 1)
             else:
-                print(value) 
-    
+                print(value)
+
     for attr_name, value in vars(obj).items():
         if isinstance(value, dict):
             print(f"\nDictionary attribute: {attr_name}")
             print_dict(value)
-            
-
-
-
-

pxii_bec/macros/flux_di.py

@@ -1,131 +1,132 @@
 #!/usr/bin/env python
-# ### PYTHON pro to determine the flux from the current 
-# ### on a Si diode 
-# ### A Pauluhn, Dec 2012 
-# ### from IDL pro flux_diode.pro (2010) 
+# ### PYTHON pro to determine the flux from the current
+# ### on a Si diode
+# ### A Pauluhn, Dec 2012
+# ### from IDL pro flux_diode.pro (2010)
 
 
 ## NOTE: for TRANSFER DIODE:
-## switch off ANY ambient light 
-## note that: 10 um Si, and 0 um Al  for transfer diode Hamamatsu 
+## switch off ANY ambient light
+## note that: 10 um Si, and 0 um Al  for transfer diode Hamamatsu
 
-# ### import the standard 
-import os, sys, string, time 
+# ### import the standard
+import os, sys, string, time
 import re
 import numpy as np
 import math
 
 
-
-
 def fluxcalc(curr, en, t_air, t_si, t_al):
 
-    #------ parameters:
-    rsi = 2.33      # g/cm^3 density of Si
-    ral = 2.699     # g/cm^3 density of Al 
-    rair = 1.205e-3  # g/cm^3 density of air 
+    # ------ parameters:
+    rsi = 2.33  # g/cm^3 density of Si
+    ral = 2.699  # g/cm^3 density of Al
+    rair = 1.205e-3  # g/cm^3 density of air
 
-    eps_si = 3.62 # eV , energy req for charge separation in Si (el/hole pair) 
-    e = 1.602e-19 # As , elem charge 
+    eps_si = 3.62  # eV , energy req for charge separation in Si (el/hole pair)
+    e = 1.602e-19  # As , elem charge
 
     t_si = 0.0012  # thickness of diode in cm (==12 micrometres) ; [*10000]
-    t_al = 0.002   # thickness of diode in cm (==20 micrometres) 
+    t_al = 0.002  # thickness of diode in cm (==20 micrometres)
 
-    #--------- calc----------------------------------------------------
-    #energy deposit in Silicon
-    #ratio of photoelectric cross section to density for Silicon
-    #alog10(A_Si)= 4.158 - 2.238*alog10(Ep) - 0.477*alog10(Ep)^2 + 0.0789*alog10(Ep)^3 
+    # --------- calc----------------------------------------------------
+    # energy deposit in Silicon
+    # ratio of photoelectric cross section to density for Silicon
+    # alog10(A_Si)= 4.158 - 2.238*alog10(Ep) - 0.477*alog10(Ep)^2 + 0.0789*alog10(Ep)^3
 
-    ps = np.poly1d([0.0789, - 0.477, - 2.238, 4.158])
-    #print ps
-    # ps.c 
-    # print ps(2.3) 
+    ps = np.poly1d([0.0789, -0.477, -2.238, 4.158])
+    # print ps
+    # ps.c
+    # print ps(2.3)
 
-    leval = math.log10(en) 
-    hlp_si = ps(leval) 
-    a_si = np.pow(10, hlp_si) 
-    #efact = np.exp(-A_Si*rsi*t_Si) 
-    #sifact =1 - efact
-    sifact = - np.expm1(-a_si*rsi*t_si) 
-    #print 'sifact = ', sifact
+    leval = math.log10(en)
+    hlp_si = ps(leval)
+    a_si = np.pow(10, hlp_si)
+    # efact = np.exp(-A_Si*rsi*t_Si)
+    # sifact =1 - efact
+    sifact = -np.expm1(-a_si * rsi * t_si)
+    # print 'sifact = ', sifact
 
-    fl = 1000.*curr * eps_si/1.602/en/sifact *1.e13 # curr expected in A
-    #print 'fl = ', fl 
+    fl = 1000.0 * curr * eps_si / 1.602 / en / sifact * 1.0e13  # curr expected in A
+    # print 'fl = ', fl
+
+    # Aluminium attenuation
+    # ratio of photoelectric cross section to density for Aluminium
+    pa = np.poly1d([0.0638, -0.413, -2.349, 4.106])
 
-    #Aluminium attenuation
-    #ratio of photoelectric cross section to density for Aluminium
-    pa = np.poly1d([ 0.0638, - 0.413, - 2.349, 4.106])
-    
     hlp_al = pa(leval)
-    a_al = pow(10, hlp_al) 
+    a_al = pow(10, hlp_al)
 
     # attenuation due to aluminium
-    alfact = np.exp(-a_al*ral*t_al)
-    #print 'alfact = ', alfact
+    alfact = np.exp(-a_al * ral * t_al)
+    # print 'alfact = ', alfact
     # Air attenuation
     # ratio of photoelectric cross section to density for air
 
-    pair = np.poly1d([0.928, - 2.348, - 1.026, 3.153])
+    pair = np.poly1d([0.928, -2.348, -1.026, 3.153])
     hlp_air = pair(leval)
-    a_air = np.pow(10, hlp_air) 
+    a_air = np.pow(10, hlp_air)
 
-    #print('hlp_air, a_air, rair, t_air = ', hlp_air, a_air, rair , t_air)
+    # print('hlp_air, a_air, rair, t_air = ', hlp_air, a_air, rair , t_air)
 
-    # attenuation due to air 
-    airfact = np.exp(-a_air*rair*t_air/10.)
-    #airfact = 1.
+    # attenuation due to air
+    airfact = np.exp(-a_air * rair * t_air / 10.0)
+    # airfact = 1.
 
-    
-    #print 'airfact = ', airfact
-    #print ' t_air = ', t_air 
+    # print 'airfact = ', airfact
+    # print ' t_air = ', t_air
 
-    # total flux from photocurrent 
-    fl = fl/alfact/airfact
-    #print 'fl = ', fl 
+    # total flux from photocurrent
+    fl = fl / alfact / airfact
+    # print 'fl = ', fl
+
+    return fl
 
-    return fl 
 
 #
 # Main
 #
 
-def flux_x10sa(curr, en, silent = 0):
+
+def flux_x10sa(curr, en, silent=0):
     # curr = input('Please enter the current [in A] ')
     curr = float(curr)
     if not silent:
-        print('Current =  ', curr)
+        print("Current =  ", curr)
     # en = input('Please enter the energy [in keV] ')
     en = float(en)
     if not silent:
-        print('Energy =  ', en)
+        print("Energy =  ", en)
     ## d_det = input('Please enter the detector distance [in mm] ')
     d_det = dev.det_z.user_readback.get()
-    d_off = 15 ## at X10SA   ### input('Please enter the OFFSET of the diode to det surface [in mm] ') 
-    
-    t_air = float(d_det) +  float(d_off)
+    d_off = (
+        15  ## at X10SA   ### input('Please enter the OFFSET of the diode to det surface [in mm] ')
+    )
 
-    t_si = 12 # um ## at X10SA    
+    t_air = float(d_det) + float(d_off)
+
+    t_si = 12  # um ## at X10SA
     #  t_si = input('Please enter the Si thickness of diode [in um] ') #  if not silent:
-    t_si = float(t_si) / 10000. # to cm 
+    t_si = float(t_si) / 10000.0  # to cm
 
-    t_al = 20 # um ## at X10SA
-    #  t_al = input('Please enter the Al thickness of diode [in um] ') 
-    t_al = float(t_al) / 10000. # to cm
+    t_al = 20  # um ## at X10SA
+    #  t_al = input('Please enter the Al thickness of diode [in um] ')
+    t_al = float(t_al) / 10000.0  # to cm
 
     if not silent:
-        print('Air path length (CARE ! add det distance and offset of diode) =  ', t_air) # include additional diode distance
+        print(
+            "Air path length (CARE ! add det distance and offset of diode) =  ", t_air
+        )  # include additional diode distance
 
-
-    fl = fluxcalc(curr, en, t_air,t_si, t_al)
+    fl = fluxcalc(curr, en, t_air, t_si, t_al)
     if not silent:
-        print( " Diode Current = %.6f  A " % curr)
-        print( " Energy = %.4f  keV "  % en )
+        print(" Diode Current = %.6f  A " % curr)
+        print(" Energy = %.4f  keV " % en)
 
-        #print( " Thickness of active Si layer = %.4f\t  cm " % t_si) #*10000. 
-        #print( " Thickness of Al layer in front of diode = %.4f\t  cm "  % t_al) #*10000. 
-        print( " Length of path of air in front of diode = %.4f\t  mm " % t_air) #*10000.
+        # print( " Thickness of active Si layer = %.4f\t  cm " % t_si) #*10000.
+        # print( " Thickness of Al layer in front of diode = %.4f\t  cm "  % t_al) #*10000.
+        print(" Length of path of air in front of diode = %.4f\t  mm " % t_air)  # *10000.
 
-        print (" Flux = %6.2e\t ph/s "  % fl)
+        print(" Flux = %6.2e\t ph/s " % fl)
 
     return fl
-

pxii_bec/macros/flux_macros.py

@@ -256,7 +256,7 @@ def bpm2flux(energy=None, bpmsum=None, transm=None):
 
     """
     calibration_min_energy = 6500
-    calibration_max_energy = 21000
+    # calibration_max_energy = 21000
 
     if energy is None:
         energy = get_current_energy()
@@ -266,14 +266,14 @@ def bpm2flux(energy=None, bpmsum=None, transm=None):
         # bpmsum =  read_av(dev.bcu_bpmsum,10) # do not add to traffic jam
 
     if transm is None:
-        transm = dev.transm.read()["transm"]["value"]
+        transm = dev.transm.read(cached=True)["transm"]["value"]
 
-    if not calibration_min_energy <= energy <= calibration_max_energy:
-        raise ValueError(
-            f"Energy {energy:.0f} eV is outside the calibrated range "
-            f"{calibration_min_energy:.0f}–"
-            f"{calibration_max_energy:.0f} eV"
-        )
+    # if not calibration_min_energy <= energy <= calibration_max_energy:
+    #     raise ValueError(
+    #         f"Energy {energy:.0f} eV is outside the calibrated range "
+    #         f"{calibration_min_energy:.0f}–"
+    #         f"{calibration_max_energy:.0f} eV"
+    #     )
 
     # coeffs = [
     #    1.06436277e5,
@@ -296,3 +296,17 @@ def bpm2flux(energy=None, bpmsum=None, transm=None):
         )
 
     return float(flux), float(full_flux)
+
+def transmission_for_flux(target_flux):
+    """
+    Calculate the transmission required to give target_flux
+    at the current energy.
+
+    Transmission is returned as a fraction from 0 to 1.
+    """
+
+    _, full_flux = bpm2flux()
+
+    transmission = target_flux / full_flux
+
+    return float(np.clip(transmission, 0.0, 1.0))

pxii_bec/macros/knifehist.py

@@ -10,7 +10,7 @@ def knife_plothist(hindex: int, signal_name: str, isave=1):
     Example:
     data_x, data_y = knife_plothist(-1,"xidode")
 
-    scanned with 
+    scanned with
     scans.line_scan(dev.aerotech.y,-0.05,0.05, steps=101, settling_time=0.5, relative=True)
     """
 
@@ -20,13 +20,13 @@ def knife_plothist(hindex: int, signal_name: str, isave=1):
 
     if hindex < 0:
         h = bec.history[hindex]
-        print('by scan number')
+        print("by scan number")
     else:
         h = bec.history.get_by_scan_number(hindex)
-        print('by scan number')
+        print("by scan number")
 
     md = h.metadata["bec"]
-    sno = md['dataset_number']
+    sno = md["dataset_number"]
     print(f"number of scan = {sno}")
     scanvar = list(md["args"].keys())[0]  # string, returns the variable of the last performed scan
     # data = h.devices[device_name][signal].read()["value"]
@@ -34,37 +34,36 @@ def knife_plothist(hindex: int, signal_name: str, isave=1):
     # data_y = h.devices.lu_bpmsum.lu_bpmsum.read()["value"]
     # data_x = h.devices[device_name][device_name].read()["value"]
 
-    # that works ... 
-    #print(list(md['args'].keys()))
-    val = list(md['args'].keys())
-    #val[0] = 'aerotech.x'
-    devicenam =  val[0]
-    print('device = ', devicenam)
+    # that works ...
+    # print(list(md['args'].keys()))
+    val = list(md["args"].keys())
+    # val[0] = 'aerotech.x'
+    devicenam = val[0]
+    print("device = ", devicenam)
     data_xd = md["positions"]  # last scan knows which device ... however, double array
     data_x = data_xd.flatten()
     print("dx = ", data_x)
-    #data_y = h.devices[signal_name][signal_name].read()["value"]
-    data_y = h.devices["xidiode"]["xidiode"].read()["value"]    
+    # data_y = h.devices[signal_name][signal_name].read()["value"]
+    data_y = h.devices["xidiode"]["xidiode"].read()["value"]
     print("dy = ", data_y)
 
-    rev = 0 
-    if val[0][9] == 'x':
+    rev = 0
+    if val[0][9] == "x":
         rev = 1
-    smoothplotgrad(data_x, data_y, reverse = rev)
-   # g, xm = justfit(data_x, data_y, model=model, ibg=ibg)
+    smoothplotgrad(data_x, data_y, reverse=rev)
+    # g, xm = justfit(data_x, data_y, model=model, ibg=ibg)
 
-#    plt.ion()
-#    plt.figure()
-#    plt.plot(data_x, data_y, "*")
-#    plt.plot(data_x, g.best_fit)
-#    plt.xlabel(scanvar)
-#    plt.ylabel(signal_name)
-#    plt.show()
+    #    plt.ion()
+    #    plt.figure()
+    #    plt.plot(data_x, data_y, "*")
+    #    plt.plot(data_x, g.best_fit)
+    #    plt.xlabel(scanvar)
+    #    plt.ylabel(signal_name)
+    #    plt.show()
 
-#    gcen = g.pars["center"].value
+    #    gcen = g.pars["center"].value
 
-
-    if isave: 
+    if isave:
         ans = "n"
         ans = input("Store data in csv file? y/n ")
         if ans == "y":
@@ -75,5 +74,4 @@ def knife_plothist(hindex: int, signal_name: str, isave=1):
             with open(filename, "w") as f:
                 np.savetxt(f, combined, delimiter=",", fmt="%.9e")
 
-
     return data_x, data_y

pxii_bec/macros/luts/.~lock.dcm_calibration_4thOct.csv#

@@ -0,0 +1 @@
+,mcauley_k,x10sa-vcons-01.psi.ch,08.10.2026 15:28,file:///home/mcauley_k/.config/libreoffice/4;

pxii_bec/macros/luts/.~lock.temp.csv#

@@ -0,0 +1 @@
+,mcauley_k,x10sa-vcons-01.psi.ch,08.10.2026 13:22,file:///home/mcauley_k/.config/libreoffice/4;

pxii_bec/macros/luts/20260930_ge_edge.csv

@@ -0,0 +1,62 @@
+Energy,Bragg,bcu_bpmsum
+10953.10,181.54,470.19
+10957.97,181.46,438.23
+10962.84,181.38,400.62
+10967.71,181.30,356.31
+10972.59,181.22,306.11
+10977.48,181.13,260.07
+10982.37,181.05,220.42
+10987.26,180.97,183.83
+10992.16,180.89,149.68
+10997.06,180.81,118.61
+11001.97,180.73,92.83
+11006.88,180.64,71.99
+11011.79,180.56,55.37
+11016.71,180.48,42.38
+11021.64,180.40,32.61
+11026.57,180.32,25.78
+11031.50,180.24,20.77
+11036.44,180.16,17.35
+11041.38,180.07,14.84
+11046.33,179.99,12.82
+11051.28,179.91,11.37
+11056.23,179.83,10.35
+11061.19,179.75,9.51
+11066.16,179.67,8.88
+11071.13,179.59,8.40
+11076.10,179.50,7.76
+11081.08,179.42,7.14
+11086.06,179.34,6.48
+11091.05,179.26,5.77
+11096.04,179.18,4.60
+11101.04,179.10,2.02
+11106.04,179.01,-0.36
+11111.05,178.93,-0.44
+11116.06,178.85,-0.49
+11121.07,178.77,-0.56
+11126.09,178.69,-0.61
+11131.12,178.61,-0.59
+11136.15,178.53,-0.78
+11141.18,178.44,-0.69
+11146.22,178.36,-0.77
+11151.26,178.28,-0.95
+11156.31,178.20,-0.89
+11161.36,178.12,-0.93
+11166.42,178.04,-0.83
+11171.48,177.95,-0.80
+11176.54,177.87,-0.86
+11181.62,177.79,-0.84
+11186.69,177.71,-0.84
+11191.77,177.63,-0.81
+11196.86,177.55,-0.87
+11201.95,177.47,-0.81
+11207.04,177.38,-0.87
+11212.14,177.30,-0.85
+11217.24,177.22,-0.87
+11222.35,177.14,-0.89
+11227.46,177.06,-0.89
+11232.58,176.98,-0.98
+11237.70,176.89,-1.00
+11242.83,176.81,-0.91
+11247.96,176.73,-0.94
+11253.10,176.65,-0.93

pxii_bec/macros/luts/20260930_ge_edge_coarse.csv

@@ -0,0 +1,42 @@
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pxii_bec/macros/luts/20260930_ge_edge_fine.csv

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pxii_bec/macros/luts/20261007_ge_edge_coarse.csv

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pxii_bec/macros/luts/20261007_ge_edge_fine.csv

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pxii_bec/macros/luts/20261011_ge_edge_medium.csv

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pxii_bec/macros/luts/20261014_ge_edge_medium.csv

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pxii_bec/macros/luts/20261017_ge_edge_medium.csv

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pxii_bec/macros/luts/bs_checks_20260914.csv

@@ -0,0 +1,14 @@
+Energy,I2_in,I2_out
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pxii_bec/macros/luts/daily_beamline_health.csv

@@ -0,0 +1,2 @@
+timestamp,energy_eV,flux_ph_s,beam_start_x_px,beam_start_y_px,vfm_ydr_start_mm,hfm_xd_start_mm,vfm_ydr_final_mm,hfm_xd_final_mm,beam_final_x_um,beam_final_y_um,vfm_y_mm,vfm_ydr_mm,vfm_pitch_mrad,hfm_x_mm,hfm_xd_mm,hfm_pitch_mrad
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pxii_bec/macros/luts/dcm_calibration_20260923.csv

@@ -0,0 +1,14 @@
+energy,scan,reason
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pxii_bec/macros/luts/dcm_calibration_20261004.csv

@@ -0,0 +1,15 @@
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pxii_bec/macros/luts/dcm_calibration_20261004.csv_2

@@ -0,0 +1,15 @@
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pxii_bec/macros/luts/dcm_calibration_20261004_first_half.csv

@@ -0,0 +1,14 @@
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pxii_bec/macros/luts/dcm_calibration_4thOct.csv

@@ -0,0 +1,28 @@
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pxii_bec/macros/luts/dcm_calibration_fail_20261004.csv

@@ -0,0 +1 @@
+energy,scan,reason

pxii_bec/macros/luts/gap_scint_20261005-1702.csv

@@ -0,0 +1 @@
+energy,lu_bpmsum,lu_Xnorm,lu_Ynorm,samcam_x,samcam_y

pxii_bec/macros/luts/gap_scint_20261005-1703.csv

@@ -0,0 +1 @@
+energy,lu_bpmsum,lu_Xnorm,lu_Ynorm,samcam_x,samcam_y

pxii_bec/macros/luts/gap_scint_20261005-1707.csv

@@ -0,0 +1 @@
+energy,lu_bpmsum,lu_Xnorm,lu_Ynorm,samcam_x,samcam_y

pxii_bec/macros/luts/gap_scint_20261005-1709.csv

@@ -0,0 +1 @@
+energy,gap,lu_bpmsum,lu_Xnorm,lu_Ynorm,samcam_x,samcam_y

pxii_bec/macros/luts/gap_scint_20261005-1710.csv

@@ -0,0 +1 @@
+energy,gap,lu_bpmsum,lu_Xnorm,lu_Ynorm,samcam_x,samcam_y

pxii_bec/macros/luts/gap_scint_20261005-1713.csv

@@ -0,0 +1 @@
+energy,gap,lu_bpmsum,lu_Xnorm,lu_Ynorm,samcam_x,samcam_y

pxii_bec/macros/luts/gap_scint_20261005-1716.csv

@@ -0,0 +1,21 @@
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pxii_bec/macros/luts/gap_xi_20261005-1702.csv

@@ -0,0 +1 @@
+energy,lu_bpmsum,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y

pxii_bec/macros/luts/gap_xi_20261005-1703.csv

@@ -0,0 +1 @@
+energy,lu_bpmsum,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y

pxii_bec/macros/luts/gap_xi_20261005-1707.csv

@@ -0,0 +1,21 @@
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pxii_bec/macros/luts/gap_xi_20261005-1709.csv

@@ -0,0 +1 @@
+energy,gap,lu_bpmsum,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y

pxii_bec/macros/luts/gap_xi_20261005-1710.csv

@@ -0,0 +1 @@
+energy,gap,lu_bpmsum,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y

pxii_bec/macros/luts/gap_xi_20261005-1713.csv

@@ -0,0 +1,21 @@
+energy,gap,lu_bpmsum,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y
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pxii_bec/macros/luts/gap_xi_20261005-1716.csv

@@ -0,0 +1 @@
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pxii_bec/macros/luts/perp.csv

@@ -0,0 +1,49 @@
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pxii_bec/macros/luts/perp_1.csv

@@ -0,0 +1,50 @@
+energy,dcm_pitch,dcm_perp,lu_bpmsum,lu_Xnorm,lu_Ynorm,bcu_bpmsum,bcu_x,bcu_y,samcam_x,samcam_y
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+

pxii_bec/macros/luts/perp_actual_calc.csv

@@ -0,0 +1,9 @@
+energy,calc_perp,actual_perp
+8000,0.0961,0.1716
+10000,0.0604,0.1549
+12400,0.0389,0.1239
+15000,0.0264,0.1273
+18000,0.0183,0.1242
+20000,0.0148,0.1322
+22000,0.0122,0.1089
+25000,0.0094,0.1293

pxii_bec/macros/luts/perp_xi_20261005-1539.csv

@@ -0,0 +1,7 @@
+energy,dcm_pitch,dcm_perp,lu_bpms,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y
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+12400,-5.54117,0.03912,1656.2,0.043,0.021,149.4,207.9

pxii_bec/macros/luts/perp_xi_20261005-1541.csv

@@ -0,0 +1,37 @@
+energy,dcm_pitch,dcm_perp,lu_bpms,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y
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+20000,-5.52897,0.01418,149.5,0.122,0.041,150.2,208.0

pxii_bec/macros/luts/perp_xi_20261005-1607.csv

@@ -0,0 +1,7 @@
+energy,dcm_pitch,dcm_perp,lu_bpms,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y
+22000,-5.52975,-0.03800,95.9,0.445,0.057,155.6,208.2
+22000,-5.52920,-0.01307,95.4,0.305,0.054,153.2,208.1
+22000,-5.52841,0.01204,94.1,0.155,0.059,150.5,207.8
+22000,-5.52737,0.03716,91.9,-0.005,0.057,147.8,208.0
+22000,-5.52685,0.06211,90.4,-0.163,0.055,145.3,208.3
+22000,-5.52868,0.01139,93.3,0.156,0.058,150.5,207.9

pxii_bec/macros/luts/perp_xi_20261005-1615.csv

@@ -0,0 +1,7 @@
+energy,dcm_pitch,dcm_perp,lu_bpms,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y
+25000,-5.52920,-0.09079,52.0,0.654,0.081,164.6,209.6
+25000,-5.52891,-0.06548,50.5,0.556,0.083,161.6,209.5
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+25000,-5.51861,-0.04039,29.1,0.349,0.120,149.6,208.4

pxii_bec/macros/luts/perp_xi_20261005-1620.csv

@@ -0,0 +1,6 @@
+energy,dcm_pitch,dcm_perp,lu_bpms,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y
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+25000,-5.52557,0.05990,47.5,-0.060,0.079,145.4,208.1

pxii_bec/macros/luts/perp_xi_20261005-1631.csv

@@ -0,0 +1,7 @@
+energy,dcm_pitch,dcm_perp,lu_bpms,lu_Xnorm,lu_Ynorm,xi_cam_x,xi_cam_y
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+25000,-5.52786,-0.01596,49.2,0.338,0.087,155.0,209.1
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+25000,-5.52743,0.00884,47.8,0.203,0.094,152.1,209.0

pxii_bec/macros/luts/pitch_comparison.csv

@@ -0,0 +1,14 @@
+energy,23rd Sep,6th Sep,offset
+6000,-5.561,-5.5182,-0.0428
+8000,-5.5432,-5.5032,-0.04
+10000,-5.5349,-5.4956,-0.039300000000001
+12000,-5.5297,-5.4906,-0.0391
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+16000,-5.5244,-5.4856,-0.0388
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+26000,-5.5183,-5.4791,-0.0392
+28000,-5.5179,-5.4791,-0.0388
+30000,-5.518,,

pxii_bec/macros/luts/roll_20260923_6000.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+3.000000,532.1747746692758
+3.375000,646.8383766556484
+3.750000,758.2370844371503
+4.125000,870.6457787689487
+4.500000,980.6793737229799
+4.875000,1080.7759963202259
+5.250000,1182.3265384715614
+5.625000,1290.697731056017
+6.000000,1376.2798011728055

pxii_bec/macros/luts/roll_20260924_25000.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+1.000000,692.942650491312
+1.875000,755.6432908308136
+2.750000,819.8962183038443
+3.625000,883.0441749851776
+4.500000,944.625963858652
+5.375000,1004.513235574581
+6.250000,1061.1821742077382
+7.125000,1116.371127886505
+8.000000,1169.189245633994

pxii_bec/macros/luts/roll_20260924_6000.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+3.000000,532.1747746692758
+3.375000,646.8383766556484
+3.750000,758.2370844371503
+4.125000,870.6457787689487
+4.500000,980.6793737229799
+4.875000,1080.7759963202259
+5.250000,1182.3265384715614
+5.625000,1290.697731056017
+6.000000,1376.2798011728055

pxii_bec/macros/luts/roll_20260930_25000.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+1.000000,620.3258474297603
+1.875000,727.3412656967532
+2.750000,831.2895400246484
+3.625000,936.7106895320477
+4.500000,1039.8208898439514
+5.375000,1139.02499725308
+6.250000,1232.640351083367
+7.125000,1322.7239076386252
+8.000000,1408.4337046604637

pxii_bec/macros/luts/roll_20260930_6000.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+3.000000,367.5626514183679
+3.250000,490.76539071940647
+3.500000,614.0409323259951
+3.750000,734.2089839347528
+4.000000,854.3453573633882
+4.250000,969.9637066596362
+4.500000,1084.8613752711697
+4.750000,1195.432631465686
+5.000000,1299.759493848411

pxii_bec/macros/luts/roll_20261008_25000.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+1.000000,645.3410172392396
+1.875000,716.7857063422749
+2.750000,798.4006801804591
+3.625000,879.2062486869808
+4.500000,948.0120679453303
+5.375000,1010.590100145263
+6.250000,1067.4532506840437
+7.125000,1123.6687191435465
+8.000000,1176.749800578109

pxii_bec/macros/luts/roll_20261008_6000.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+2.000000,329.981417633099
+2.250000,405.3057428861756
+2.500000,483.27540977301703
+2.750000,554.0746091974096
+3.000000,630.9466804651072
+3.250000,706.8771151250418
+3.500000,782.8947653437505
+3.750000,857.5768007188707
+4.000000,931.2567888482613

pxii_bec/macros/luts/roll_20261009_6000.csv

@@ -0,0 +1 @@
+Roll,Y pos

pxii_bec/macros/luts/temp.csv

@@ -0,0 +1,10 @@
+Roll,Y pos
+2.000000,329.981417633099
+2.250000,405.3057428861756
+2.500000,483.27540977301703
+2.750000,554.0746091974096
+3.000000,630.9466804651072
+3.250000,706.8771151250418
+3.500000,782.8947653437505
+3.750000,857.5768007188707
+4.000000,931.2567888482613

pxii_bec/macros/mxcomm_analysis.py

@@ -101,11 +101,38 @@ def fit(data, fit_params):
         params["base_intercept"].set(value=y_min)
         params["base_slope"].set(value=0)
 
+    # # Add peak-specific parameters
+    # params.update(peak_model.guess(processed_data["y_to_fit"], x=processed_data["x_data"]))
+
+    # # Perform the fitting
+    # lmfit_result = full_model.fit(processed_data["y_to_fit"], params, x=processed_data["x_data"])
+
     # Add peak-specific parameters
-    params.update(peak_model.guess(processed_data["y_to_fit"], x=processed_data["x_data"]))
+    x_data = np.asarray(processed_data["x_data"])
+
+    params.update(
+        peak_model.guess(
+            processed_data["y_to_fit"],
+            x=x_data,
+        )
+    )
+
+    # Constrain peak width to something physically resolvable by the scan
+    step = np.median(np.diff(np.sort(x_data)))
+    scan_range = np.ptp(x_data)
+
+    if "peak_sigma" in params:
+        params["peak_sigma"].set(
+            min=0.5 * step,
+            max=0.5 * scan_range,
+    )
 
     # Perform the fitting
-    lmfit_result = full_model.fit(processed_data["y_to_fit"], params, x=processed_data["x_data"])
+    lmfit_result = full_model.fit(
+        processed_data["y_to_fit"],
+        params,
+        x=x_data,
+    )   
 
     # Find the X that gives the max Y
     max_index = np.argmax(processed_data["y_to_fit"])
@@ -125,6 +152,7 @@ def fit(data, fit_params):
 
     centre_stderr = lmfit_result.params["peak_center"].stderr
     height_stderr = lmfit_result.params["peak_height"].stderr
+        
 
     snr = height / noise if noise > 0 else np.inf
 
@@ -166,8 +194,8 @@ def check_peak_fit(x_data, result, min_fwhm_steps=3):
     centre = result["centre"]
     fwhm = result["fwhm"]
 
-    step_size = np.mean(np.diff(x_data))
-    fwhm_steps = result["fwhm"] / abs(step_size)
+
+    fwhm_steps = fwhm / step
 
     problems = []
 
@@ -189,8 +217,19 @@ def check_peak_fit(x_data, result, min_fwhm_steps=3):
 
     if centre_stderr is None:
         problems.append("centre uncertainty could not be estimated")
-    elif centre_stderr > 0.2 * fwhm:
-        problems.append(f"centre uncertainty is large " f"({centre_stderr:.3g})")
+    elif centre_stderr > 0.5 * step:
+        problems.append(
+            f"centre uncertainty is large "
+            f"({centre_stderr:.3g}, "
+            f"{centre_stderr / step:.2f} scan steps)"
+        )
+
+    print("FIT DEBUG")
+    print(f"centre       : {centre}")
+    print(f"fwhm         : {fwhm}")
+    print(f"step         : {step}")
+    print(f"fwhm/step    : {fwhm / step}")
+    print(f"centre error : {result.get('centre_stderr')}")
 
     return {"success": not problems, "problems": problems}
 

pxii_bec/macros/mxcomm_utils.py

@@ -4,104 +4,16 @@ import epics
 import time
 import numpy as np
 import matplotlib.pyplot as plt
-from pxii_bec.scripts import beamline_context as bl
 
 # =============================================================================
 # Camera utilities
 # =============================================================================
 
-def read_scintXY(zoom=800, image=False):
-    """Get the X and Y beam positions from the sample camera at
-    a sepcified zoom. Default zoom is 800"""
-
-     # Target position on sample camera
-    x_target = BeamMove.scint_target_x
-    y_target = BeamMove.scint_target_y 
-
-    results = {}
-
-    # Ensure shutter and detector cover are closed before changing states
-    dev.bcu_shutter.put(0)
-    if bl.d["det_cov"].pos != "close":
-        bl.d["det_cov"].move("close")
-    try:
-        # set transmission to 10%
-        current_transm = get_value(dev.transm)
-        if abs(current_transm - 0.1) > 0.01:
-            dev.transm.put(0.1)
-        # set camera zoom
-        if get_value(dev.scam_zoom) != zoom:
-            umv(dev.scam_zoom, zoom)
-        # move to beam visualisation
-
-        if not bl.planner.is_state(BeamlineState.BEAM_VISUALISATION):
-            bl.planner.move_to(BeamlineState.BEAM_VISUALISATION)
-        # open shutter
-        dev.bcu_shutter.put(1)
-
-        # set autoexposure and check there is a reading in the image
-        time.sleep(0.5)
-        auto_exposure(cam="samcam", max_iter=25)
-        time.sleep(0.2)
-
-        max_signal = get_value(dev.samcam_max)
-        results["max_signal"] = max_signal
-
-        if max_signal < BeamMove.min_scint_signal:
-            return {
-                "ok": False,
-                "message": (
-                    f"No beam detected on the scintillator "
-                    f"(max signal = {max_signal:.0f})"
-                ),
-                "max_signal": max_signal,
-            }
 
 
-        x_px = dev.samcam_x.read()["samcam_x"]["value"]
-        y_px = dev.samcam_y.read()["samcam_y"]["value"]
-        results["X_pixels"] = x_px
-        results["Y_pixels"] = y_px
-
-        results["ok"] = True
-        results["message"] = (
-            f"Beam detected at X={x_px:.1f}, Y ={y_px:.1f} px"
-        )
-      
-        # Calculate difference from target position
-        diff_x = x_target - x_px
-        diff_y = y_target - y_px
-        results["X_diff_px"] = diff_x
-        results["Y diff_px"] = diff_y
-
-        # Convert to pixels
-        diff_x_mic = calc_scam_microns(diff_x, zoom)
-        diff_y_mic = calc_scam_microns(diff_y, zoom)
-        results["X_diff_microns"] = diff_x_mic
-        results["Y_diff_microns"] = diff_y_mic
-
-        # Measure beamsize
-        x_fwhm, y_fwhm = measure_beamsize()
-        results["X_FWHM"] = x_fwhm
-        results["Y_FWHM"] = y_fwhm
-
-        print(f"Beam position: X = {results['X_pixels']:.1f} px, "
-              f"Y = {results['Y_pixels']:.1f} px\n"
-              f"Distance from crosshair: X = {results['X_diff_microns']:.1f} microns, "
-              f"Y = {results['Y_diff_microns']:.1f} microns\n",
-              f"X size (fwhm) = {results["X_FWHM"]:.1f} microns, "
-              f"Y size (fwhm) = {results["Y_FWHM"]:.1f} microns")
-
-        if image:
-            imagedata = get_cam_image(Cameras.sample)
-            results["image"] = imagedata
 
 
-        return results
     
-    finally:
-        # print("done")
-        dev.bcu_shutter.put(0)
 
 
 def get_cam_image(prefix):
@@ -291,3 +203,5 @@ def create_empty_daily_report(filename):
 
     return filename
 
+
+

pxii_bec/macros/position_device.py

@@ -5,6 +5,7 @@ from typing import Callable, List, Dict, Optional, Union
 from bec_lib.logger import bec_logger
 from bec_lib.device import Device
 
+
 def motor_resolver(bec_name):
     """Used to handle aerotech and smargon motors"""
 
@@ -24,6 +25,7 @@ def motor_resolver(bec_name):
 
     raise ValueError(f"Cannot resolve motor for '{bec_name}'")
 
+
 @dataclass
 class PositionDevice:
     """Generic device that moves between named or numeric positions"""
@@ -53,14 +55,20 @@ class PositionDevice:
         if isinstance(target, str):
             name = target.lower()
             try:
-                bec_logger.logger.info(f"attempting to find position {name} from bec device {self.bec_name} userParameter.")
+                bec_logger.logger.info(
+                    f"attempting to find position {name} from bec device {self.bec_name} userParameter."
+                )
                 bec_device: Device = dev[self.bec_name]
                 position = bec_device.user_parameter[target]
 
-                bec_logger.logger.info(f"obtained position {position} - compare to cached value {self.positions.get(target)}")
+                bec_logger.logger.info(
+                    f"obtained position {position} - compare to cached value {self.positions.get(target)}"
+                )
                 return position
             except Exception as e:
-                bec_logger.logger.debug(f"Failed to fetch user parameter for device {self.bec_name} and target {target} from bec, falling back to cached position {e}")
+                bec_logger.logger.debug(
+                    f"Failed to fetch user parameter for device {self.bec_name} and target {target} from bec, falling back to cached position {e}"
+                )
 
                 if name not in self.positions:
                     raise ValueError(f"Unknown position '{target}'")
@@ -100,7 +108,6 @@ class PositionDevice:
 
         return scans.mv(self.mot_device, pos, relative=False)
 
-
     # def set_position(self, target: Union[str, float]):
     #     """Only to be used for testing purposes, bypasses guards"""
     #     pos = self._resolve_target(target)
@@ -129,5 +136,3 @@ class PositionDevice:
 
         pos = self._resolve_target(target)
         return abs(self.actual - pos) <= self.tol
-
- 

pxii_bec/macros/pxii_energy.py

@@ -88,42 +88,126 @@ def mono_pitch_scan(plot=True, window_name="Fitting", plot_widget=None):
     # Set fine pitch to middle of its' travel range
     scans.umv(EnergyDefaults.mono_fpitch, pos["dcm_fine_pitch"], relative=False)
     # Move DCM pitch to starting value
-    scans.umv(EnergyDefaults.mono_pitch, pos["dcm_pitch"]-0.04, relative=False)
+    pitch_offset = dev.dcm_pitch.user_parameter["offset"]
+    scans.umv(EnergyDefaults.mono_pitch, pos["dcm_pitch"]+pitch_offset, relative=False)
 
     # Go to peak using default parameters from EnergyDefaults
-    if plot:
-        print("Scanning monochromator pitch and moving to peak, with plotting.")
+    result = go_to_peak(
+        EnergyDefaults.mono_pitch,
+        EnergyDefaults.signals["sig1"],
+        -EnergyDefaults.pitch_scan["halfwidth"],
+        EnergyDefaults.pitch_scan["halfwidth"],
+        steps=EnergyDefaults.pitch_scan["steps"],
+        relative=True,
+        settle=0.01,
+        plot=plot,
+        confirm=False,
+        min_fwhm_steps=1.1,
+        window_name=window_name if plot else None,
+        plot_widget=plot_widget if plot else None,
+    )
+
+    extended_scan = False
+
+    if not result["success"]:
+        extended_scan = True
+
+        extended_range = 2 * EnergyDefaults.pitch_scan["halfwidth"]
+        extended_steps = 2 * EnergyDefaults.pitch_scan["steps"]
+
+        print("Scanning monochromator pitch over a broader range.")
+
         result = go_to_peak(
             EnergyDefaults.mono_pitch,
             EnergyDefaults.signals["sig1"],
-            -EnergyDefaults.pitch_scan["halfwidth"],
-            EnergyDefaults.pitch_scan["halfwidth"],
-            steps=EnergyDefaults.pitch_scan["steps"],
+            -extended_range,
+            extended_range,
+            steps=extended_steps,
             relative=True,
             settle=0.01,
-            plot=True,
+            plot=plot,
             confirm=False,
             min_fwhm_steps=1.1,
-            window_name=window_name,
-            plot_widget=plot_widget,
-        )
-    else:
-        print("Scanning monochromator pitch and moving to peak, without plotting.")
-        result = go_to_peak(
-            EnergyDefaults.mono_pitch,
-            EnergyDefaults.signals["sig1"],
-            -EnergyDefaults.pitch_scan["halfwidth"],
-            EnergyDefaults.pitch_scan["halfwidth"],
-            steps=EnergyDefaults.pitch_scan["steps"],
-            relative=True,
-            settle=0.01,
-            plot=False,
-            min_fwhm_steps=1.5,
-            confirm=False,
+            window_name=window_name if plot else None,
+            plot_widget=plot_widget if plot else None,
         )
 
+    result["extended_scan"] = extended_scan
     return result
 
+    # if plot:
+    #     print("Scanning monochromator pitch and moving to peak, with plotting.")
+    #     result = go_to_peak(
+    #         EnergyDefaults.mono_pitch,
+    #         EnergyDefaults.signals["sig1"],
+    #         -EnergyDefaults.pitch_scan["halfwidth"],
+    #         EnergyDefaults.pitch_scan["halfwidth"],
+    #         steps=EnergyDefaults.pitch_scan["steps"],
+    #         relative=True,
+    #         settle=0.01,
+    #         plot=True,
+    #         confirm=False,
+    #         min_fwhm_steps=1.1,
+    #         window_name=window_name,
+    #         plot_widget=plot_widget,
+    #     )
+    #     result["extended_scan"] = False
+
+    #     if not result["success"]:
+    #         extended_range = 2 * EnergyDefaults.pitch_scan["halfwidth"]
+    #         extended_steps = 2 * EnergyDefaults.pitch_scan["steps"]
+    #         print("Scanning monochromator pitch over a broader range.")
+    #         result = go_to_peak(
+    #             EnergyDefaults.mono_pitch,
+    #             EnergyDefaults.signals["sig1"],
+    #             -extended_range,
+    #             extended_range,
+    #             steps=extended_steps,
+    #             relative=True,
+    #             settle=0.01,
+    #             plot=True,
+    #             confirm=False,
+    #             min_fwhm_steps=1.1,
+    #             window_name=window_name,
+    #             plot_widget=plot_widget,
+    #         )
+    #         result["extended_scan"] = True
+
+    # else:
+    #     print("Scanning monochromator pitch and moving to peak, without plotting.")
+    #     result = go_to_peak(
+    #         EnergyDefaults.mono_pitch,
+    #         EnergyDefaults.signals["sig1"],
+    #         -EnergyDefaults.pitch_scan["halfwidth"],
+    #         EnergyDefaults.pitch_scan["halfwidth"],
+    #         steps=EnergyDefaults.pitch_scan["steps"],
+    #         relative=True,
+    #         settle=0.01,
+    #         plot=False,
+    #         min_fwhm_steps=1.1,
+    #         confirm=False,
+    #     )
+    #     result["extended_scan"] = False
+
+    #     if not result["success"]:
+    #         extended_range = 2 * EnergyDefaults.pitch_scan["halfwidth"]
+    #         extended_steps = 2 * EnergyDefaults.pitch_scan["steps"]
+    #         print("Scanning monochromator pitch over a broader range.")
+    #         result2 = go_to_peak(
+    #             EnergyDefaults.mono_pitch,
+    #             EnergyDefaults.signals["sig1"],
+    #             -extended_range,
+    #             extended_range,
+    #             steps=extended_steps,
+    #             relative=True,
+    #             settle=0.01,
+    #             plot=True,
+    #             confirm=False,
+    #             min_fwhm_steps=1.1,
+    #         ) 
+    #         result["extended_scan"] = True       
+    # return result
+
 
 # Specific functions - need to be edited for each beamline
 
@@ -172,12 +256,13 @@ def get_dcm_motors_positions(energy_ev):
     """
     # dcm_motor_values = get_value_from_lut(energy_ev)
     dcm_motor_values = {}
-    pitch = float(np.poly1d(Calibration.pitch_calib)(energy_ev))
+    # pitch = float(np.poly1d(Calibration.pitch_calib)(energy_ev))
     # pitch = -5.5
     fpitch = 5.0
     roll = EnergyDefaults.mono_roll_value
     perp = calc_perp_position(energy_ev, print_result=False)
     bragg_angle = convert_from_energy(energy_ev, print_result=False)["bragg_angle_mrad"]
+    pitch = float(np.poly1d(Calibration.pitch_calib)(bragg_angle))
     dcm_motor_values.update(
         {
             "bragg_angle": bragg_angle,
@@ -309,24 +394,36 @@ def bl_energy(
 #     return gap
 
 
+# def calc_gap(energy_ev, print_result=True):
+#     """Calculate the undulator gap for the given energy."""
+
+#     harmonic_values = Gap.get_harmonic_values(energy_ev)
+
+#     if harmonic_values is None:
+#         return None
+
+#     gap = np.poly1d(harmonic_values)(energy_ev)
+#     gap *= Gap.correction_factor
+
+#     if print_result:
+#         harmonic = Gap.get_harmonic_by_energy(energy_ev)
+#         print(f"Calculated gap is {gap:.3f} mm " f"using {harmonic}")
+
+#     return gap
+
 def calc_gap(energy_ev, print_result=True):
     """Calculate the undulator gap for the given energy."""
 
-    harmonic_values = Gap.get_harmonic_values(energy_ev)
-
-    if harmonic_values is None:
-        return None
-
-    gap = np.poly1d(harmonic_values)(energy_ev)
-    gap *= Gap.correction_factor
+    harmonic, gap = Gap.calculate_gap(energy_ev)
 
     if print_result:
-        harmonic = Gap.get_harmonic_by_energy(energy_ev)
-        print(f"Calculated gap is {gap:.3f} mm " f"using {harmonic}")
+        print(
+            f"Calculated gap is {gap:.4f} mm "
+            f"using H{harmonic}"
+        )
 
     return gap
 
-
 def set_gap(energy_ev, print_result=False):
     """Set the undulator gap."""
 

pxii_bec/macros/pxii_energy.py.bak

@@ -0,0 +1,347 @@
+"""Script to change energy at PXII by setting gap, DCM motors and mirror stripe
+
+Moving DCM motors - implemented for Bragg, pitch and perp
+Gap - optional, can be switched off using move_gap=False
+Mirrors - change of mirror stripe is not yet implemented
+Plotting optional
+
+"""
+
+import numpy as np
+
+# from pxii_gap import set_gap
+# from mx_methods import go_to_peak
+# from pxii_parameters import EnergyDefaults, Calibration
+
+# from calculator import (
+#     calc_perp_position,
+#     validate_energy,
+#     convert_from_bragg,
+#     convert_from_energy,
+# )
+
+
+def get_current_energy():
+    """
+    Returns the energy in eV from the current bragg angle.
+    """
+    current_bragg_angle = dev.dcm_bragg.user_readback.get(cached=True)
+    current_energy = convert_from_bragg(current_bragg_angle, print_result=False)["energy_ev"]
+    return current_energy
+
+
+# Functions below are common to all beamlines
+def calculate_energy_difference(current_energy, target_energy):
+    """
+    Calculate the absolute difference in energy between the current energy level
+    and the target energy level.
+    """
+    return abs(target_energy - current_energy)
+
+
+def get_mirror_stripe(energy_ev):
+    """
+    Determines the mirror stripe material based on the energy level provided
+     and the specified thresholds for silicon, rhodium, and platinum.
+
+    Args:
+        energy_ev (float): Energy level in electron volts, used to determine
+            the corresponding material type.
+
+    Returns:
+        str: A string indicating the material type corresponding to the provided
+            energy level. Possible values are "silicon", "rhodium", or "platinum".
+    """
+    if energy_ev <= EnergyDefaults.stripe_thresholds["silicon"]:
+        return "silicon"
+    if (
+        EnergyDefaults.stripe_thresholds["silicon"]
+        < energy_ev
+        <= EnergyDefaults.stripe_thresholds["rhodium"]
+    ):
+        return "rhodium"
+    return "platinum"
+
+
+def set_mirror_stripe(energy_ev):
+    """
+    Selects and sets the appropriate mirror stripe based on the given energy value
+    in electron volts (eV).
+
+    Args:
+        energy_ev (float): The energy value in electron volts
+
+    Returns:
+        None
+    """
+    selected_stripe = get_mirror_stripe(energy_ev)
+    print(f"Selected mirror stripe: {selected_stripe}")
+
+
+def mono_pitch_scan(plot=True, window_name="Fitting", plot_widget=None):
+    """Scan the monochromator pitch and move to the peak."""
+    # Move to the calculated pitch value for the current energy
+    print("Starting Mono Pitch Scan.")
+    energy = get_current_energy()
+    pos = get_dcm_motors_positions(energy)
+    print(f"Setting DCM Pitch to default value of {pos['dcm_pitch']}")
+    # Set fine pitch to middle of its' travel range
+    scans.umv(EnergyDefaults.mono_fpitch, pos["dcm_fine_pitch"], relative=False)
+    # Move DCM pitch to starting value
+    scans.umv(EnergyDefaults.mono_pitch, pos["dcm_pitch"]-0.12, relative=False)
+
+    # Go to peak using default parameters from EnergyDefaults
+    if plot:
+        print("Scanning monochromator pitch and moving to peak, with plotting.")
+        result = go_to_peak(
+            EnergyDefaults.mono_pitch,
+            EnergyDefaults.signals["sig1"],
+            -EnergyDefaults.pitch_scan["halfwidth"],
+            EnergyDefaults.pitch_scan["halfwidth"],
+            steps=EnergyDefaults.pitch_scan["steps"],
+            relative=True,
+            settle=0.01,
+            plot=True,
+            confirm=False,
+            min_fwhm_steps=1.1,
+            window_name=window_name,
+            plot_widget=plot_widget,
+        )
+    else:
+        print("Scanning monochromator pitch and moving to peak, without plotting.")
+        result = go_to_peak(
+            EnergyDefaults.mono_pitch,
+            EnergyDefaults.signals["sig1"],
+            -EnergyDefaults.pitch_scan["halfwidth"],
+            EnergyDefaults.pitch_scan["halfwidth"],
+            steps=EnergyDefaults.pitch_scan["steps"],
+            relative=True,
+            settle=0.01,
+            plot=False,
+            min_fwhm_steps=1.5,
+            confirm=False,
+        )
+
+    return result
+
+
+# Specific functions - need to be edited for each beamline
+
+
+def move_gap_if_needed(energy_ev, move_gap=True):
+    """
+    Move the gap position based on energy if the move_gap flag is set.
+
+    Args:
+        energy_ev (float): The energy value in electron volts (eV) used for gap movement.
+        move_gap (bool): A flag indicating whether the gap position should be moved or not.
+
+    Returns:
+        None
+    """
+    if move_gap:
+        set_gap(energy_ev)
+    else:
+        print("Not moving gap.")
+
+
+# def get_roll(energy_ev):
+#     """Calculates the roll based on calibration data."""
+#     calib = Calibration()
+#     roll = np.poly1d(calib.roll)(energy_ev)
+#     if roll < 0:
+#         return 0
+#     if roll >= 9.95:
+#         return 9.95
+#     return float(roll)
+
+
+def get_dcm_motors_positions(energy_ev):
+    """
+    Pitch and roll are calculated based on fits of the measured calibration values.
+    Perp and Bragg are calculated based on the energy value via calculator.py.
+
+    Arguments:
+        energy_ev (float): The energy value in electron volts for which the
+                           DCM motor positions are to be calculated.
+
+    Returns:
+        dict: A dictionary containing the calculated DCM motor positions
+              including values retrieved from the lookup table, Bragg angle
+              in milliradians, and perpendicular position.
+    """
+    # dcm_motor_values = get_value_from_lut(energy_ev)
+    dcm_motor_values = {}
+    pitch = float(np.poly1d(Calibration.pitch_calib)(energy_ev))
+    # pitch = -5.5
+    fpitch = 5.0
+    roll = EnergyDefaults.mono_roll_value
+    perp = calc_perp_position(energy_ev, print_result=False)
+    bragg_angle = convert_from_energy(energy_ev, print_result=False)["bragg_angle_mrad"]
+    dcm_motor_values.update(
+        {
+            "bragg_angle": bragg_angle,
+            "perp": perp,
+            "dcm_pitch": pitch,
+            "dcm_roll": roll,
+            "dcm_fine_pitch": fpitch,
+        }
+    )
+    return dcm_motor_values
+
+
+def move_dcm_motors(energy_ev):
+    """
+    Move the DCM bragg, pitch and perp motors to the required positions
+    for the given energy in eV.
+
+    """
+    dcm_pos = get_dcm_motors_positions(energy_ev)
+    print(
+        f"Moving DCM bragg: {dcm_pos['bragg_angle']: .5g} mrad, "
+        f"DCM perp: {dcm_pos['perp']: .3g} mm, "
+        # f"DCM pitch fixed at -5.304 mrad, "
+        f"DCM pitch: {dcm_pos['dcm_pitch']: .5g} mrad, "
+        f"DCM Roll: {dcm_pos['dcm_roll']:.5g} V"
+    )
+    # umv(EnergyDefaults.energy, dcm_pos["bragg_angle"])
+    # umv(EnergyDefaults.mono_perp, dcm_pos["perp"])
+    # umv(EnergyDefaults.mono_pitch, dcm_pos["dcm_pitch"])
+    # umv(EnergyDefaults.mono_roll, dcm_pos["dcm_roll"])
+    # print("\n***DCM Roll movement is currently disabled ***\n")
+    scans.umv(EnergyDefaults.mono_fpitch, dcm_pos["dcm_fine_pitch"], relative=False)
+    scans.umv(
+        EnergyDefaults.energy,
+        dcm_pos["bragg_angle"],
+        EnergyDefaults.mono_perp,
+        dcm_pos["perp"],
+        EnergyDefaults.mono_pitch,
+        dcm_pos["dcm_pitch"],
+        EnergyDefaults.mono_roll,
+        dcm_pos["dcm_roll"],
+        relative=False,
+    )
+
+
+def bl_energy(
+    energy_ev, move_gap=True, mono_scan=True, plot=True, window_name="Fitting", plot_widget=None
+):
+    """
+    Adjusts the beamline's energy to the specified energy in electron volts (eV).
+    The function validates the target energy, checks the current energy, and makes
+    adjustments only if the energy difference is significant enough. It performs
+    necessary operations including moving the gap, changing DCM motors, updating
+    the mirror stripe, and scanning to find the optimal DCM pitch.
+
+    Args:
+        energy_ev: Target energy in electron volts to which the beamline should be adjusted.
+        move_gap: Boolean flag indicating whether to adjust the gap before setting energy.
+        plot: Boolean flag indicating whether to plot the DCM pitch scan for finding the peak.
+
+    Returns:
+        None
+    """
+    energy_ev = validate_energy(energy_ev)  # Ensure energy is valid.
+
+    # Check current energy to avoid unnecessary adjustments.
+
+    current_energy = get_current_energy()
+    energy_diff = calculate_energy_difference(current_energy, energy_ev)
+
+    if energy_diff <= EnergyDefaults.min_energy_change:
+        print(f"Energy change of {energy_diff:.2f} eV is too small, not changing energy.")
+        return
+
+    transmission = get_value(dev.transm)
+
+    # Step 1: Move the gap if needed.
+    move_gap_if_needed(energy_ev, move_gap)
+
+    # Step 2: Move and set the DCM motors.
+    move_dcm_motors(energy_ev)
+
+    # Step 3: Reset the transmission after the energy change
+    print(f"Setting transmission to {transmission}")
+    dev.transm.put(transmission)
+
+    # Step 4: Update the mirror stripe.
+    set_mirror_stripe(energy_ev)
+
+    # Step 5: Perform DCM pitch scan and move to peak.
+    if mono_scan:
+        if plot:
+            result = mono_pitch_scan(plot=True, window_name=window_name, plot_widget=plot_widget)
+            return result
+        else:
+            mono_pitch_scan(plot=False)
+
+
+# def new_calc_gap(energy_ev):
+#     """
+#     Calculates the gap based on the given energy
+#     """
+#     gapval = Gap()
+#     harmonic_values = gapval.get_harmonic_values(energy_ev)
+#     if harmonic_values is not None:
+#         fit = np.poly1d(harmonic_values)(energy_ev)
+#         gap_value = fit * 0.9994
+#         return gap_value
+#     return None
+
+# def set_gap(energy_ev, print_result=True):
+#     """
+#     set the gap
+#     """
+#     gap = new_calc_gap(energy_ev)
+#     # else:
+#     #     gap = calc_gap(energy_kev)
+#     if gap is not None and Harmonics.min_gap_value <= gap <= 20:
+#         umv(dev.id_gap, gap)
+#         if print_result:
+#             print(f"Setting gap to {gap:.3f} mm")
+#     else:
+#         umv(dev.id_gap, Harmonics.min_gap_value)
+#         # msg = (
+#         #     f"Position {gap: .3f} mm is outside the allowed scan range of "
+#         #     f"4.5 to 20 mm. Not changing the gap."
+#         # )
+#         # raise ValueError(msg)
+#     return gap
+
+
+def calc_gap(energy_ev, print_result=True):
+    """Calculate the undulator gap for the given energy."""
+
+    harmonic_values = Gap.get_harmonic_values(energy_ev)
+
+    if harmonic_values is None:
+        return None
+
+    gap = np.poly1d(harmonic_values)(energy_ev)
+    gap *= Gap.correction_factor
+
+    if print_result:
+        harmonic = Gap.get_harmonic_by_energy(energy_ev)
+        print(f"Calculated gap is {gap:.3f} mm " f"using {harmonic}")
+
+    return gap
+
+
+def set_gap(energy_ev, print_result=False):
+    """Set the undulator gap."""
+
+    gap = calc_gap(energy_ev)
+
+    if gap is not None and Gap.minimum_gap <= gap <= 20:
+        umv(dev.id_gap, gap)
+
+        if print_result:
+            harmonic = Gap.get_harmonic_by_energy(energy_ev)
+            print(f"Setting gap to {gap:.3f} mm " f"using {harmonic}")
+
+    else:
+        raise ValueError(
+            f"Cannot calculate a valid gap for {energy_ev:.0f} eV. " f"Calculated gap: {gap}"
+        )
+
+    return gap

pxii_bec/macros/pxii_parameters.py

@@ -20,8 +20,7 @@ class EnergyDefaults:
     mono_fpitch = dev.dcm_fpitch
     mono_perp = dev.dcm_perp
     mono_roll = dev.dcm_froll
-    mono_roll_value = 4.36 
-    LUT_table = "luts/energy_lut.csv"
+    mono_roll_value = 3.88 
     stripe_thresholds = {"silicon": 9000, "rhodium": 20000, "platinum": 40000}
     pitch_scan = {"halfwidth": 0.075, "steps": 20}
 
@@ -30,127 +29,105 @@ class EnergyDefaults:
 class Calibration:
     """Calibration parameters for PXII optics"""
 
-    pitch_calib = [-7.60082220e-19, 6.09893342e-14, -1.81702221e-09, 2.45457520e-05, -5.61275367e00]
+    # pitch_calib = [-7.60082220e-19, 6.09893342e-14, -1.81702221e-09, 2.45457520e-05, -5.61275367e00]
+
+    pitch_calib = [-1.84031410e-07,-6.76777668e-05, -5.59684124]
 
     # roll = np.array([2.28291039e-03, -2.41928101e01])
 
 
 @dataclass(frozen=True)
 class Gap:
-    """Fit parameters to calculate undulator gap from energy."""
+    """PXII U19 undulator gap calibration.
+
+    Harmonic fits are from Anuschka's September 2026 calibration.
+    For a requested energy, use the highest odd harmonic whose
+    calculated gap remains >= minimum_gap.
+    """
 
     minimum_gap = 4.5
+    selection_min_gap = 4.505
     maximum_gap = 20.0
-    correction_factor = 0.9994
 
+    # Anuschka's September 2026 harmonic fits.
+    # Energy input is in keV, gap output is in mm.
     harmonics = {
-        "H3": np.array([9.37600000e-04, 2.98800000e-01]),
-        "H5": np.array([5.10102857e-04, 7.99666667e-01]),
-        "H7": np.array([3.58874286e-04, 8.60410476e-01]),
-        "H9": np.array([2.74520000e-04, 9.25540000e-01]),
-        "H11": np.array([2.24457143e-04, 9.25714286e-01]),
-        "H13": np.array([1.88834286e-04, 9.47505714e-01]),
-        "H15": np.array([1.63434286e-04, 9.52602857e-01]),
-        "H17": np.array([1.43320000e-04, 9.77500000e-01]),
-        "H19": np.array([1.27940000e-04, 9.85770000e-01]),
+        3: np.array([0.095, -0.276, 4.154]),
+        5: np.array([0.00269444, -0.0616905, 0.967925, -0.295405]),
+        7: np.array([0.00110017, -0.0369968, 0.77334, -0.688198]),
+        9: np.array([0.00021633, -0.00619517, 0.315392, 0.971667]),
+        11: np.array([0.000589549, -0.0328631, 0.837705, -2.90326]),
+        13: np.array([0.197702, 0.757869]),
+        15: np.array([0.170381, 0.783155]),
+        17: np.array([0.1466, 0.8906]),
+        19: np.array([0.128, 0.985]),
     }
 
     @classmethod
-    def minimum_energy(cls, harmonic):
-        """
-        Return the lowest energy that can be reached with this harmonic
-        without the corrected gap going below the minimum gap.
-        """
-        slope, intercept = cls.harmonics[harmonic]
-
-        # calc_gap() applies the correction factor afterwards,
-        # so account for it here as well.
-        raw_minimum_gap = cls.minimum_gap / cls.correction_factor
-
-        return (raw_minimum_gap - intercept) / slope
+    def calculate_gap_for_harmonic(cls, energy_ev, harmonic):
+        """Calculate gap for a specified harmonic."""
+        energy_kev = energy_ev / 1000.0
+        return np.polyval(cls.harmonics[harmonic], energy_kev)
 
     @classmethod
     def get_harmonic_by_energy(cls, energy_ev):
         """
-        Return the appropriate harmonic for the requested energy.
+        Select the highest odd harmonic that gives a valid gap.
 
-        Switch to the next harmonic as soon as it can produce the
-        requested energy without requiring a gap below minimum_gap.
+        This selects the harmonic whose gap is closest to the
+        minimum allowed gap of 4.5 mm, while maintaining a small
+        safety margin of 0.005 mm.
         """
-        selected = None
+
+        valid = []
 
         for harmonic in cls.harmonics:
-            if energy_ev >= cls.minimum_energy(harmonic):
-                selected = harmonic
-            else:
-                break
+            gap = cls.calculate_gap_for_harmonic(
+                energy_ev,
+                harmonic,
+            )
 
-        return selected
+            if cls.selection_min_gap <= gap <= cls.maximum_gap:
+                valid.append((harmonic, gap))
 
-    @classmethod
-    def get_harmonic_values(cls, energy_ev):
-        """
-        Return the fit coefficients for the appropriate harmonic.
-        """
-        harmonic = cls.get_harmonic_by_energy(energy_ev)
-
-        if harmonic is None:
+        if not valid:
             return None
 
-        return cls.harmonics[harmonic]
+        # Closest valid gap to the minimum gap
+        harmonic, gap = min(
+            valid,
+            key=lambda x: x[1] - cls.selection_min_gap,
+        )
 
+        return harmonic
+    
     @classmethod
     def calculate_gap(cls, energy_ev):
-        """
-        Calculate the corrected undulator gap for the requested energy.
+        """Return selected harmonic and calculated gap."""
 
-        Returns
-        -------
-        tuple
-            (harmonic, gap)
-        """
         harmonic = cls.get_harmonic_by_energy(energy_ev)
 
         if harmonic is None:
-            raise ValueError(f"{energy_ev:.0f} eV is below the minimum calibrated energy.")
+            raise ValueError(
+                f"No valid harmonic found for {energy_ev:.0f} eV."
+            )
 
-        slope, intercept = cls.harmonics[harmonic]
-
-        gap = slope * energy_ev + intercept
-        gap *= cls.correction_factor
+        gap = cls.calculate_gap_for_harmonic(
+            energy_ev,
+            harmonic,
+        )
 
+        # Final check against actual motor limits
         if not cls.minimum_gap <= gap <= cls.maximum_gap:
             raise ValueError(
                 f"Calculated gap {gap:.3f} mm for {energy_ev:.0f} eV "
-                f"using {harmonic} is outside the allowed range "
+                f"using H{harmonic} is outside the allowed range "
                 f"{cls.minimum_gap:.1f}-{cls.maximum_gap:.1f} mm."
             )
 
         return harmonic, gap
 
 
-@dataclass(frozen=True)
-class Harmonics:
-    """Anuschka's harmonics data for PXII U19 Undulator"""
-
-    min_gap_value = 4.5
-    map = {
-        3: np.array([1.07141725, -0.52834258]),
-        4: np.array([0.007111, -0.13678409, 1.52295567, -1.06882785]),
-        5: np.array([0.00315051, -0.0766359, 1.13107469, -0.86442062]),
-        6: np.array([0.00162862, -0.04452336, 0.82948259, -0.37329674]),
-        7: np.array([0.00080764, -0.02418882, 0.59212947, 0.15702886]),
-        8: np.array([1.16699242e-03, -4.68207543e-02, 9.43972396e-01, -1.94201019e00]),
-        9: np.array([0.00048419, -0.02010648, 0.55514114, -0.38180067]),
-        10: np.array([2.11583333e-04, -8.03503571e-03, 3.43141595e-01, 6.02318000e-01]),
-        11: np.array([0.00334392, -0.18405336, 3.58338994, -19.3640241]),
-        12: np.array([3.20520798e-05, 2.39253145e-03, 8.09198503e-02, 2.22897377e00]),
-        13: np.array([0.00278744, 0.07979874, 2.05143916]),
-    }
-    energy_ranges = {3: (0, 7), 5: (7, 10), 7: (10, 13), 9: (13, 16), 11: (16, 19), 13: (19, 22)}
-    high_energy = [(15, (23, 25)), (17, (25, 29)), (19, (29, float("inf")))]
-
-
 @dataclass(frozen=True)
 class CamConversion:
     """Convert pixels to microns for sample camera"""
@@ -165,8 +142,8 @@ class BCU_BPM_X_Calibration:
     signal_limit = 0.90
     # centred_position = 0.441
     centred_position = -0.009  # where the bpm was during calibration
-    crosshair_signal = -0.00339158
-    crosshair_bpm_position = 0.0532
+    crosshair_signal = -0.0209
+    crosshair_bpm_position = 0.0738
 
 
 # @dataclass(frozen=True)
@@ -174,8 +151,8 @@ class BCU_BPM_Y_Calibration:
     coeffs = (-0.14645507, 0.010016, 0.08258468, -0.00547233, -0.02715706, -1.54419084)
     signal_limit = 0.95
     centred_position = -1.540 # where the bpm was during calibration
-    crosshair_signal = -0.00392027
-    crosshair_bpm_position = -1.548
+    crosshair_signal = 0.00156
+    crosshair_bpm_position = -1.5459
 
 
 # @dataclass(frozen=True)

pxii_bec/macros/pxii_setup.py

@@ -0,0 +1,353 @@
+"""PXII-specific operational helpers used by routine daily/weekly setup.
+
+BEC loads macro files into a shared namespace, so these functions deliberately use
+the standard BEC globals (dev, umv, get_value, etc.) rather than importing other
+macro files.  Nothing in this module should be promoted to mxcomm_* unless it is
+truly beamline-independent.
+"""
+
+import time
+from dataclasses import dataclass
+from datetime import datetime
+
+import numpy as np
+from pxii_bec.scripts import beamline_context as bl
+from pxii_bec.macros.beamline_planner import BeamlineState
+
+
+# =============================================================================
+# Energy
+# =============================================================================
+
+def daily_energy(energy, scan_mono=True, plot_widget=None):
+    """Set PXII energy/gap and optionally optimise DCM pitch."""
+
+    current_energy = get_current_energy()
+    mono_result = {"extended_scan": False}
+
+    if abs(energy - current_energy) > 1:
+        bl_energy(energy, window_name="DailySetup", plot_widget=plot_widget)
+        # bl_energy performs the normal energy move.  Keep mono_result benign
+        # here so the result handling below is defined for both code paths.
+    else:
+        gap_actual = dev.id_gap.position
+        gap_req = calc_gap(energy)
+
+        if abs(gap_actual - gap_req) > 0.05:
+            if dev.id_gap.moving():
+                return {
+                    "ok": False,
+                    "message": "Undulator gap is moving",
+                    "energy": current_energy,
+                }
+            umv(dev.id_gap, gap_req)
+
+        if scan_mono:
+            mono_result = mono_pitch_scan(
+                window_name="DailySetup", plot_widget=plot_widget
+            )
+
+    new_energy = get_current_energy()
+    calib_pitch = get_dcm_motors_positions(energy)["dcm_pitch"]
+    pitch_offset = get_value(dev.dcm_pitch) - calib_pitch
+
+    if not mono_result.get("extended_scan", False):
+        return {
+            "ok": True,
+            "message": (
+                f"Beamline energy set to {new_energy:.0f} eV, "
+                f"pitch offset = {pitch_offset:.3f} mrad"
+            ),
+            "energy": new_energy,
+            "pitch_offset": pitch_offset,
+        }
+
+    return {
+        "ok": True,
+        "warning": True,
+        "message": (
+            "Warning - DCM pitch is not within expected tolerance. "
+            "The DCM may need to be re-calibrated. "
+            f"Pitch offset = {pitch_offset:.3f} mrad"
+        ),
+        "energy": new_energy,
+        "pitch_offset": pitch_offset,
+    }
+
+
+# =============================================================================
+# Sample-camera scintillator measurements
+# =============================================================================
+
+def predict_scint_transmission(target_flux=None):
+    """Predict PXII transmission required for a scintillator measurement."""
+    if target_flux is None:
+        target_flux = BeamMove.scint_target_flux
+    _, full_flux = bpm2flux()
+    if not np.isfinite(full_flux) or full_flux <= 0:
+        raise ValueError(
+            "Cannot predict scintillator transmission: "
+            f"invalid full flux ({full_flux:.3g} ph/s)"
+        )
+    return float(np.clip(target_flux / full_flux, 0.001, 1.0))
+
+
+def auto_exposure(cam="samcam", target=200, tol=5, gain=0.9,
+                  min_exp=0.00001, max_exp=0.2, max_iter=10):
+    """Adjust PXII camera exposure to reach the requested maximum signal."""
+    if cam == "samcam":
+        exposure = dev.samcam_exp.read()["samcam_exp"]["value"]
+    else:
+        exposure = dev.ss_xicam_exp.read()["ss_xicam_exp"]["value"]
+
+    print(f"Starting exposure = {exposure:.4f} s")
+    for _ in range(max_iter):
+        time.sleep(0.1)
+        if cam == "samcam":
+            maxval = dev.samcam_max.read()["samcam_max"]["value"]
+        else:
+            maxval = dev.ss_xicam_max.read()["ss_xicam_max"]["value"]
+        if maxval is None:
+            print("No reading — check camera.")
+            break
+        error = target - maxval
+        if abs(error) <= tol:
+            break
+        new_exp = exposure * (1 + gain * error / target)
+        new_exp = max(min_exp, min(max_exp, new_exp))
+        if cam == "samcam":
+            dev.samcam_exp.put(new_exp)
+        else:
+            dev.ss_xicam_exp.put(new_exp)
+        exposure = new_exp
+    print(f"New exposure time is {exposure:.3g}")
+    return exposure
+
+
+def prepare_scint_measurement(autoexp=True, zoom=1000):
+    """Put PXII into the standard state for a scintillator measurement."""
+    transmission = predict_scint_transmission()
+    print(f"Predicted scintillator transmission: {transmission:.2%}")
+    dev.transm.put(transmission)
+    time.sleep(3)
+    if get_value(dev.scam_zoom) != zoom:
+        umv(dev.scam_zoom, zoom)
+    if not bl.planner.is_state(BeamlineState.BEAM_VISUALISATION):
+        bl.planner.move_to(BeamlineState.BEAM_VISUALISATION)
+    dev.bcu_shutter.put(1)
+    time.sleep(0.5)
+    if autoexp:
+        auto_exposure(cam="samcam", max_iter=25)
+    return zoom
+
+
+def measure_beamsize(cam="samcam"):
+    """Return PXII sample-camera beam FWHM in microns."""
+    a = dev.samcam_xsig.read()["samcam_xsig"]["value"]
+    b = dev.samcam_ysig.read()["samcam_ysig"]["value"]
+    zoom = dev.scam_zoom.read()["scam_zoom"]["value"]
+    sx = calc_scam_microns(a, zoom=zoom) * 2.35
+    sy = calc_scam_microns(b, zoom=zoom) * 2.35
+    print(f"FWHM in um : {(sx, sy)}")
+    return sx, sy
+
+
+def read_scintXY(image=False, measure_size=True):
+    """Read PXII beam position from the sample-camera scintillator image."""
+    x_target = BeamMove.scint_target_x
+    y_target = BeamMove.scint_target_y
+    zoom = get_value(dev.scam_zoom)
+    max_signal = get_value(dev.samcam_max)
+    thresh = get_value(dev.samcam_thresh)
+    if max_signal < thresh:
+        return {
+            "ok": False,
+            "message": (
+                "Insufficient signal for centroid calculation "
+                f"(max signal = {max_signal:.0f}, threshold = {thresh:.0f})"
+            ),
+            "max_signal": max_signal,
+        }
+    x_px = dev.samcam_x.read()["samcam_x"]["value"]
+    y_px = dev.samcam_y.read()["samcam_y"]["value"]
+    diff_x = x_target - x_px
+    diff_y = y_target - y_px
+    results = {
+        "ok": True,
+        "message": f"Beam detected at X={x_px:.1f}, Y={y_px:.1f} px",
+        "max_signal": max_signal,
+        "X_pixels": x_px,
+        "Y_pixels": y_px,
+        "X_diff_px": diff_x,
+        "Y_diff_px": diff_y,
+        "X_diff_microns": calc_scam_microns(diff_x, zoom),
+        "Y_diff_microns": calc_scam_microns(diff_y, zoom),
+    }
+    if measure_size:
+        results["X_FWHM"], results["Y_FWHM"] = measure_beamsize()
+    print(
+        f"Beam position: X = {x_px:.1f} px, Y = {y_px:.1f} px\n"
+        f"Distance from crosshair: X = {results['X_diff_microns']:.1f} microns, "
+        f"Y = {results['Y_diff_microns']:.1f} microns\n"
+    )
+    if image:
+        results["image"] = get_cam_image(Cameras.sample)
+    return results
+
+
+def finish_scint_measurement():
+    dev.bcu_shutter.put(0)
+
+
+# =============================================================================
+# Slit centring used by weekly checks
+# =============================================================================
+
+@dataclass
+class SlitAxis:
+    name: str
+    centre_motor: object
+    size_motor: object
+    scan_range: float = 2.0
+
+@dataclass
+class Slit:
+    name: str
+    x: SlitAxis
+    y: SlitAxis
+
+def centre_axis(axis, detector, slit_size=0.5, final_size=3.0, window_name=None, plot_widget=None):
+    print(f"\nAligning {axis.name}")
+    umv(axis.size_motor, slit_size)
+    start = axis.centre_motor.position
+    try:
+        go_to_peak(axis.centre_motor, detector, start-axis.scan_range,
+                   start+axis.scan_range, 50, confirm=False, window_name=window_name,
+                   plot_widget=plot_widget)
+        centre = get_value(axis.centre_motor)
+        print(f"{axis.name}: centre = {centre:.4f}")
+        return centre
+    finally:
+        umv(axis.size_motor, final_size)
+
+def centre_slit(slit, detector, slit_size=0.5, final_size=3.0, window_name=None, x_plot_widget=None, y_plot_widget=None):
+    print(f"\n=== Aligning {slit.name} ===")
+    x = centre_axis(slit.x, detector, slit_size, final_size,window_name=window_name,plot_widget=x_plot_widget)
+    y = centre_axis(slit.y, detector, slit_size, final_size, window_name=window_name,plot_widget=y_plot_widget)
+    print(f"=== Finished {slit.name} ===")
+    return {"x": x, "y": y}
+
+def define_slits():
+    def axis(prefix, direction):
+        return SlitAxis(
+            name=f"{prefix}_sl_{direction}",
+            centre_motor=getattr(dev, f"{prefix}_sl_{direction}cen"),
+            size_motor=getattr(dev, f"{prefix}_sl_{direction}size"),
+        )
+    return [Slit(name, axis(name, "x"), axis(name, "y"))
+            for name in ("bsf", "ss", "bcu")]
+
+def centre_one(name, detector, window_name=None, x_plot_widget=None, y_plot_widget=None):
+    for slit in define_slits():
+        if slit.name == name:
+            return centre_slit(slit, detector,window_name=window_name,x_plot_widget=x_plot_widget,y_plot_widget=y_plot_widget)
+    raise ValueError(f"Unknown PXII slit set: {name}")
+
+
+# =============================================================================
+# Ge energy calibration diagnostic
+# =============================================================================
+
+def scan_ge(edge=11103.1, mode="coarse"):
+    """Scan the PXII Ge K edge and return the generated CSV filename."""
+    if mode == "coarse":
+        scan_range, scanpoints = 100, 41
+    if mode == "medium":
+        scan_range, scanpoints = 40, 41
+    elif mode == "fine":
+        scan_range, scanpoints = 15, 61
+    else:
+        raise ValueError(f"Unknown scan mode '{mode}'. Use 'coarse', 'medium' or 'fine'.")
+
+    start_eV, end_eV = edge-scan_range, edge+scan_range
+    start_bragg = convert_from_energy(start_eV)["bragg_angle_mrad"]
+    end_bragg = convert_from_energy(end_eV)["bragg_angle_mrad"]
+    bragg_points = np.linspace(start_bragg, end_bragg, scanpoints)
+    filename = bl.env.lut_dir / f"{datetime.now():%Y%m%d}_ge_edge_{mode}.csv"
+
+    with open(filename, "w") as f:
+        f.write("Energy,Bragg,ss_bpmsum,bcu_bpmsum,transmission\n")
+
+    print(f"\nGe edge {mode} scan: {start_eV:.1f}-{end_eV:.1f} eV")
+    bl_energy(start_eV)
+    dev.transm.put(1)
+    time.sleep(2)
+    umv(dev.ss_f4_x, 6.0)
+    time.sleep(3)
+
+    try:
+        for bragg in bragg_points:
+            scans.umv(dev.dcm_bragg, bragg, relative=False)
+            energy = convert_from_bragg(bragg)["energy_ev"]
+            ss = get_value(dev.ss_bpmsum)
+            vals = []
+            for _ in range(5):
+                vals.append(dev.bcu_bpmsum.read()["bcu_bpmsum"]["value"])
+                time.sleep(0.1)
+            inten = float(np.mean(vals))
+            transmission = inten / ss
+            with open(filename, "a") as f:
+                f.write(f"{energy:.2f},{bragg:.2f},{ss:.2f},{inten:.2f},{transmission:.6f}\n")
+    finally:
+        bl_energy(12400)
+        dev.transm.put(0.1)
+        time.sleep(2)
+
+    print(f"Scan complete. Results written to {filename}")
+    return filename
+
+def prepare_ss_xi_measurement(autoexp=True):
+    """Prepare for taking a reading of the beam from the SS Xray eye"""
+    
+    # move to x-ray eye into the beam
+    umv(dev.ss_xi_x, 7.0)
+
+    # set autoexposure and check there is a reading in the image
+    if autoexp:
+        auto_exposure(cam="ss_xicam", max_iter=25)
+
+def finish_ss_xi_measurement():
+    '''Move the SS xray eye out of the beam'''
+    umv(dev.ss_xi_x, -7)
+
+def read_ss_xicamXY():
+    """Read the beam position at the SS xray eye camera"""
+    results = {}
+    max_signal = get_value(dev.ss_xicam_max)
+    results["max_signal"] = max_signal
+    # thresh = get_value(dev.samcam_thresh)   
+    thresh = 150
+    if max_signal < thresh:
+        return {
+            "ok": False,
+            "message": (
+                f"Insufficient signal for centroid calculation "
+                f"(max signal = {max_signal:.0f}, threshold = {thresh:.0f})"
+            ),
+            "max_signal": max_signal,
+        }
+
+
+    x_px = dev.ss_xicam_x.read()["ss_xicam_x"]["value"]
+    y_px = dev.ss_xicam_y.read()["ss_xicam_y"]["value"]
+    results["X_pixels"] = x_px
+    results["Y_pixels"] = y_px
+
+    results["ok"] = True
+    results["message"] = (
+        f"Beam detected at X={x_px:.1f}, Y ={y_px:.1f} px"
+    )
+    print(f"Beam position: X = {results['X_pixels']:.1f} px, "
+            f"Y = {results['Y_pixels']:.1f} px\n")
+
+    return results

pxii_bec/macros/temp.py

@@ -0,0 +1,30 @@
+import time
+import subprocess
+import shlex
+import csv
+import base64
+import numpy as np
+from datetime import datetime
+from contextlib import contextmanager
+from dataclasses import dataclass
+from pxii_bec.scripts import beamline_context as bl
+from pxii_bec.macros.beamline_planner import BeamlineState
+import matplotlib.pyplot as plt
+from matplotlib.patches import Ellipse
+
+def test_daily_html_report():
+    filename = bl.env.daily_setup_dir / "daily_beam.png"
+    image_src = image_to_data_uri(filename)
+
+    html = f"""
+<h1>Testing html</h1>
+<img src = '{image_src}' width='450'>
+<table>
+<tr><th>Pre- checks</th><th>OK</th>
+<tr><th>Set energy</th><th>OK</th>
+<th>Measure flux</th><th>OK</th>
+</table>
+"""
+
+    plot1, plot2, plot3, plot4, info, progress, report = select_daily_setup_gui()
+    info.set_html_text(f"{html}")