friday updates

pxii_bec/device_configs/pxii-beamline-states.yaml

@@ -54,8 +54,6 @@ states:
     diag_y: out
     fl_bright: 'on'
     aerotech_x: in
-    aerotech_y: work
-    aerotech_z: work
     # aerotech_u: mount
     # smargon_x: mount
     # smargon_y: mount

pxii_bec/device_configs/pxii-devices.yaml

@@ -70,7 +70,7 @@ aerotech:
       safe: -50
     y:
       mount: -0.0
-      work: -0.022
+      work: -0.016
     z:
       mount: 0
       work: 0
@@ -303,7 +303,7 @@ bs_y:
   onFailure: buffer
   readoutPriority: baseline
   userParameter:
-    in: -2.654
+    in: -2.454
 bs_z:
   description: Beamstop Z
   deviceClass: ophyd_devices.EpicsMotor
@@ -433,7 +433,7 @@ coll_x:
   onFailure: buffer
   readoutPriority: baseline
   userParameter:
-    in: -2.72
+    in: -2.889
 coll_y:
   description: Collimator Y
   deviceClass: ophyd_devices.EpicsMotor
@@ -445,7 +445,7 @@ coll_y:
   onFailure: buffer
   readoutPriority: baseline
   userParameter:
-    in: 39.188
+    in: 39.139
     intermediate: 32
     out: 20.002
     park: 1
@@ -630,10 +630,10 @@ diag_y:
   onFailure: buffer
   readoutPriority: baseline
   userParameter:
-    i1: 41
+    i1: 40.8
     out: 20.0
     park: 1
-    scint: 36.004
+    scint: 35.74
     tol: 0.3
     type: continuous
 diag_z:

pxii_bec/macros/APscripts.py

@@ -1658,7 +1658,7 @@ def fluxcal(start_en=13, stop_en=14, step =1):
     filename = dirname + f"FLUX_x10sa_{timestamp}.txt"
 
     with open(filename, "w") as f:
-        np.savetxt(f, combined, delimiter=",", fmt="%9f")
+        np.savetxt(f, combined, delimiter=",", fmt=".9f")
 
 
     elapsed_time = time.perf_counter()-tstart

pxii_bec/macros/calibrate_bpm.py

@@ -46,11 +46,6 @@ def read_currents():
     bpm3 = np.mean(vals_bpm3)
     bpm4 = np.mean(vals_bpm4)
    
-    # 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"]
-    # print(f"bpm1 = {bpm1:.3f}, bpm2 = {bpm2:.3f}, bpm3 = {bpm3:.3f}, bpm4 = {bpm4:.3f}")
     return {"bpm1": bpm1, "bpm2": bpm2, "bpm3": bpm3, "bpm4": bpm4}
 
 
@@ -138,21 +133,6 @@ def run_calibration():
     umv(dev.ss_sl_ysize, 3.0)
 
 
-# Read data from BPM calibration files
-# def fit_bpm_data(x_y):
-#     """
-#     Read data from bpm calibration files.
-#     """
-#     filedir = "luts/bpm_calib/"
-#     rundate= "02072130_"
-#     name = f"bcu_bpm_{x_y}.csv"
-#     filename = filedir + rundate + name
-#     data = np.loadtxt(filename, delimiter=",", skiprows=1)
-#     xdata = data[:, 0]
-#     ydata = data[:, 1]
-#     return xdata, ydata
-
-
 
 def fit_bpm_data(x_y, rundate="02072130_", bpm_name="bcu_bpm"):
     CALIB_DIR = "luts/bpm_calib/"
@@ -193,9 +173,9 @@ def linear_calibration(
     x_fit = np.linspace(min(xdata), max(xdata), 100)
     plt.plot(x_fit, m * x_fit + c, "r--", label=f"Fit: Linear")
 
-    plt.xlabel("HFM Lat Position")
-    plt.ylabel("SamCam X")
-    plt.title("Zoom Calibration")
+    plt.xlabel("label")
+    plt.ylabel("label")
+    plt.title("title")
     plt.legend()
     plt.grid(True)
     plt.tight_layout()
@@ -477,8 +457,6 @@ def calibrate_bpm_flux(ave = 5):
         f.write("Energy,Transmission,BPMSum,Flux\n")
     print("Energy,Transmission,BPMSum,Flux\n")
     energies = [12400,7000,8000,9000,10000,11000,13000,14000,15000,16000,18000,20000,25000]
-    # energies = [7000,8000,9000,10000]
-    # transmissions = [1, 0.5, 0.2, 0.1, 0.05, 0.01]
     transmissions = [1, 0.9, 0.8, 0.7, 0.6, 0.5,0.4,0.3,0.2,0.1]
 
     for energy in energies:
@@ -513,7 +491,7 @@ def calibrate_bpm_flux(ave = 5):
     umv(dev.id_gap, 20)
 
 def analyse_bpm_flux_calibration(
-    filename="luts/bpm_calib/bpm_flux_comb.csv",
+    filename="luts/bpm_calib/bpm_flux_20260708b.csv",
     force_zero_intercept=False,
 ):
     data = pd.read_csv(filename)
@@ -576,44 +554,117 @@ def analyse_bpm_flux_calibration(
     print(dict)
     return results
 
-def get_flux_calibration(energy):
-    filename = "luts/bpm_calib/bpm_flux_fits_zero.csv"
-    default_slope = 4.42e8
-    default_intercept = -1.66e11
+def linear_bpm_flux_calib():
+    filename = 'luts/bpm_calib/fits-25.csv'
+    df = pd.read_csv(filename)
+    energies = df["Energy"].to_numpy()
+    intercepts = df["Intercept"].to_numpy()
+    slopes = df["Slope"].to_numpy()
+    # --- Plot ---
+    plt.figure(figsize=(7, 5))
+    plt.scatter(energies, slopes, color="red")
 
-    try:
-        df = pd.read_csv(filename)
-        energies = df["Energy"].to_numpy()
-        intercepts = df["Intercept"].to_numpy()
-        slopes = df["Slope"].to_numpy()
-        slope_interp = CubicSpline(energies, slopes)
-        intercept_interp = CubicSpline(energies, intercepts)
-        slope = slope_interp(energy)
-        intercept = intercept_interp(energy)
-        print(f"Using data from calibration file")
-    except FileNotFoundError:
-        print("Cannot access calibration file, using default parameters")
-        slope = default_slope
-        intercept = default_intercept
+    x_fit = np.linspace(min(energies), max(energies), 100)
+    coeffs = np.polyfit(energies, slopes,1)
+    y_fit = np.poly1d(coeffs)
+    plt.plot(x_fit, y_fit(x_fit)),    
+    plt.xlabel("Energy eV")
+    plt.ylabel("Slope")
+    plt.title(f"Energies vs slopes, coeffs = {coeffs}")
+    # plt.legend()
+    plt.grid(True)
+    plt.tight_layout()
+    plt.savefig(f"luts/bpm_calib/slopes_vs_energy")
+    plt.show()
+    return coeffs
+
+
+# def get_flux_calibration(energy):
+#     # filename = "luts/bpm_calib/bpm_flux_fits.csv"
+#     filename = 'luts/bpm_calib/fits-25.csv'
+#     default_slope = 4.42e8
+#     default_intercept = -1.66e11
+
+#     try:
+#         df = pd.read_csv(filename)
+#         energies = df["Energy"].to_numpy()
+#         intercepts = df["Intercept"].to_numpy()
+#         slopes = df["Slope"].to_numpy()
+#         slope_interp = CubicSpline(energies, slopes)
+#         intercept_interp = CubicSpline(energies, intercepts)
+#         slope = slope_interp(energy)
+#         intercept = intercept_interp(energy)
+#         print(f"Using data from calibration file")
+#          # --- Plot ---
+#         plt.figure(figsize=(7, 5))
+#         plt.scatter(energies, slopes, color="red")
+
+#         x_fit = np.linspace(min(energies), max(energies), 100)
+#         coeffs = np.polyfit(energies, slopes,1)
+#         print("linear co-efficients: ", coeffs)
+#         y_fit = np.poly1d(coeffs)
+#         plt.plot(x_fit, y_fit(x_fit)), 
+#         # "r--", label=f"Fit: Slope = {slope:.5g}, Intercept = {intercept:.5g}")
+      
+#         plt.xlabel("Energy")
+#         plt.ylabel("Slope")
+#         plt.title(f"{energy} eV")
+#         # plt.legend()
+#         plt.grid(True)
+#         plt.tight_layout()
+#         plt.show()
+#     except FileNotFoundError:
+#         print("Cannot access calibration file, using default parameters")
+#         slope = default_slope
+#         intercept = default_intercept
     
-    return slope, intercept
+#     return coeffs
+
+
+def bpm2flux(energy=None, bpmsum=None, transm=None):
+    """
+    Calculate the flux from BCU BPM reading.
+    Option to provide energy, bpmsum reading and transmission. 
+    If these are not given, the current values are used.
+
+    Returns the flux at the sample (after attenuators) and a calculated
+    value of the full flux if attenuation was 0.
+    
+    """
+    calibration_min_energy = 6500
+    calibration_max_energy = 21000
 
-def bpm2flux(energy=None,bpmsum=None):
     if energy is None:
         energy = get_current_energy()
+
     if bpmsum is None:
-        bpmsum = dev.bcu_bpmsum.read()['bcu_bpmsum']['value']
+        bpmsum = dev.bcu_bpmsum.read()["bcu_bpmsum"]["value"]
 
-    print(f"BCU_bpmsum = {bpmsum}")
+    if transm is None:
+        transm = dev.transm.read()['transm']['value']
 
-    slope, intercept = get_flux_calibration(energy)
+    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"
+        )
 
-    calc = slope * bpmsum + intercept
-    flux = f"{calc:.5g}"
-    print(flux)
-    return float(calc)
+    coeffs = [
+        1.06436277e5,
+        -6.38943746e8,
+    ]
 
+    calibration_factor = np.polyval(coeffs, energy)
+    flux = calibration_factor * bpmsum
+    full_flux = flux/transm
+    if transm == 1:
+        print(f"Transmission = {transm*100:.5g} %, Flux = {flux: .3g} ph/s,\n")
+    else:
+        print(f"Transmission = {transm*100: .5g} %, Flux = {flux: .3g} ph/s,\n"
+            f"Flux with 100 % transmission would be {full_flux: .3g} ph/s")
 
+    return float(flux), float(full_flux)
 
 
     

pxii_bec/macros/katscripts.py

@@ -1494,12 +1494,35 @@ import matplotlib.pyplot as plt
 from epics import caget
 
 
-def scan_scin_focus():
+def scan_scin_focus(type = 'fine'):
     z0 = dev.diag_z.position
 
-    z_positions = np.linspace(-9,9,30)
-    contrasts = []
+    if z0-5 <= -10:
+        min = -9.5
+    else:
+        min = z0-5
+    
+    if z0+5 >=10:
+        max = 9.5
+    else:
+        max = z0+5
 
+    if type == 'fine':
+        steps = 100
+    elif type == 'coarse':
+        steps = 30
+    else:
+        steps = 60
+    umv(dev.scam_zoom, 1000)
+    dev.transm.put(0.1)
+
+    auto_exposure("samcam", target=200, max_iter=20)
+    time.sleep(0.2)
+
+    z_positions = np.linspace(min,max,steps)
+
+    
+    contrasts = []
 
 
     for z in z_positions: