mxcubecore 1.403.0__py3-none-any.whl → 1.405.0__py3-none-any.whl

mxcubecore/HardwareObjects/LNLS/read_transmission_mnc.py

@@ -1,149 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""Transmission control for MANACA.
-Attenuator: ABS-300-12-C-DN-DN40 Flanges.
-Foils: #1, 8 um Al;
-       #2, 10 um Al;
-       #3, 20 um Al;
-       #4, 80 um Al;
-       #5, 160 um Al;
-       #6, 320 um Al;
-       #7, 800 um Al;
-       #8, 1500 um Al;
-       #9, 8 um Ti;
-       #10, 10 um Cu
-       #11, 5 um Au;
-       #12, 25 um Zr.
- Here we use the Beer-Lambert law to calculate the transmission/attenuation: I = I0 * e^-(MU * d)
- were I is the transmitted (final) beam intensity, I0 is the incident (initial) beam intensity,
- MU is the linear attenuation coefficient (cm^-1) and d is the thickness of the foil (cm).
-"""
-
-import argparse
-import math
-
-from epics import PV
-
-
-def read_input():
-    # Read inputs from terminal
-    ap = argparse.ArgumentParser()
-    ap.add_argument(
-        "-e",
-        "--energy",
-        required=True,
-        type=float,
-        help="Energy of the x-ray beam [keV]",
-    )
-    args = vars(ap.parse_args())
-    return args
-
-
-def read_transmission(energy):
-    # Expressions (interpolation) for calculations of MU (linear attenuation coefficient [cm^-1]) for each material in function of the beam energy.
-    # The data used to obtain the expressions (curve fitting) are from  "https://physics.nist.gov/PhysRefData/FFast/html/form.html"
-    # This attenuation coefficients can be verified and optimised after experimental validation at the beamline.
-    MU_Al = (
-        (78657.01011 * math.exp(-energy / 0.65969))
-        + (6406.36151 * math.exp(-energy / 1.63268))
-        + (492.29999 * math.exp(-energy / 4.42554))
-        + (3.2588)
-    )
-    MU_Ti = (
-        (28062.17632 * math.exp(-energy / 1.88062))
-        + (6354120 * math.exp(-energy / 0.49973))
-        + (2257.91488 * math.exp(-energy / 5.28296))
-        + (17.4342)
-    )
-    MU_Cu = (
-        (1147850000 * math.exp(-energy / 0.56933))
-        + (2582.7593 * math.exp(-energy / 8.40671))
-        + (30628.08291 * math.exp(-energy / 2.98937))
-        + (22.4187)
-    )
-    MU_Au = (42783.04258 * math.exp(-energy / 5.39244)) + (399.59714)
-    MU_Zr = (11143.28458 * math.exp(-energy / 5.87029)) + (102.27474)
-    MU_EMPTY = 0.0
-
-    foils_pv = {
-        "F1_Al": (8, MU_Al, PV("MNC:B:RIO01:9425A:bi11"), PV("MNC:B:RIO01:9425A:bi12")),
-        "F2_Al": (
-            10,
-            MU_Al,
-            PV("MNC:B:RIO01:9425A:bi10"),
-            PV("MNC:B:RIO01:9425A:bi13"),
-        ),
-        "F3_Al": (20, MU_Al, PV("MNC:B:RIO01:9425A:bi9"), PV("MNC:B:RIO01:9425A:bi14")),
-        "F4_Al": (80, MU_Al, PV("MNC:B:RIO01:9425A:bi8"), PV("MNC:B:RIO01:9425A:bi15")),
-        "F5_Al": (
-            160,
-            MU_Al,
-            PV("MNC:B:RIO01:9425A:bi7"),
-            PV("MNC:B:RIO01:9425A:bi16"),
-        ),
-        "F6_Al": (
-            320,
-            MU_Al,
-            PV("MNC:B:RIO01:9425A:bi6"),
-            PV("MNC:B:RIO01:9425A:bi17"),
-        ),
-        "F7_Al": (
-            800,
-            MU_Al,
-            PV("MNC:B:RIO01:9425A:bi5"),
-            PV("MNC:B:RIO01:9425A:bi18"),
-        ),
-        "F8_Al": (
-            1500,
-            MU_Al,
-            PV("MNC:B:RIO01:9425A:bi4"),
-            PV("MNC:B:RIO01:9425A:bi19"),
-        ),
-        "F9_Ti": (8, MU_Ti, PV("MNC:B:RIO01:9425A:bi3"), PV("MNC:B:RIO01:9425A:bi20")),
-        "F10_Cu": (
-            10,
-            MU_Cu,
-            PV("MNC:B:RIO01:9425A:bi2"),
-            PV("MNC:B:RIO01:9425A:bi21"),
-        ),
-        "F11_Au": (5, MU_Au, PV("MNC:B:RIO01:9425A:bi1"), PV("MNC:B:RIO01:9425A:bi22")),
-        "F12_Zr": (
-            25,
-            MU_Zr,
-            PV("MNC:B:RIO01:9425A:bi0"),
-            PV("MNC:B:RIO01:9425A:bi23"),
-        ),
-    }
-
-    # check what foils are in the the beam and calculate MU*x and then calculate transmission
-
-    # the commented lines below works for the attenuator expected logic (0 for foil out and 1 for foil in).
-    # as the current logic is inverted (1 is foil out and 0 is foil in) use the uncommented lines.
-    foils_in = []
-    for foil in foils_pv.keys():
-        # if foils_pv[foil][2].get() == 1 and foils_pv[foil][3].get() == 0:
-        if foils_pv[foil][2].get() == 0 and foils_pv[foil][3].get() == 1:
-            atten_mu_x = float(foils_pv[foil][0] * 1.0e-4) * foils_pv[foil][1]
-            foils_in.append(atten_mu_x)
-            status = 0
-        # elif foils_pv[foil][2].get() == 0 and foils_pv[foil][3].get() == 1:
-        elif foils_pv[foil][2].get() == 1 and foils_pv[foil][3].get() == 0:
-            status = 0
-        else:
-            status = 1
-
-    MU_x = sum(foils_in)
-    transmission = 1.0 * (math.exp(-MU_x))
-
-    return transmission, status
-
-
-def main():
-    energy = read_input()["energy"]
-    T = read_transmission(energy)
-    transmission = round(T[0] * 100, 2)
-    foil_status = T[1]
-
-
-if __name__ == "__main__":
-    main()

mxcubecore/HardwareObjects/LNLS/set_transmission_mnc.py

@@ -1,306 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-"""Transmission control for MANACA.
-Attenuator: ABS-300-12-C-DN-DN40 Flanges.
-Foils: #1, 8 um Al;
-       #2, 10 um Al;
-       #3, 20 um Al;
-       #4, 80 um Al;
-       #5, 160 um Al;
-       #6, 320 um Al;
-       #7, 800 um Al;
-       #8, 1500 um Al;
-       #9, 8 um Ti;
-       #10, 10 um Cu
-       #11, 5 um Au;
-       #12, 25 um Zr.
- Here we use the Beer-Lambert law to calculate the transmission/attenuation: I = I0 * e^-(MU * d)
- were I is the transmitted (final) beam intensity, I0 is the incident (initial) beam intensity,
- MU is the linear attenuation coefficient (cm^-1) and d is the thickness of the foil (cm).
-"""
-
-import argparse
-import itertools
-import math
-import time
-
-from epics import PV
-
-
-def read_input():
-    # Read inputs from terminal
-    ap = argparse.ArgumentParser()
-    ap.add_argument(
-        "-e",
-        "--energy",
-        required=True,
-        type=float,
-        help="Energy of the x-ray beam [keV]",
-    )
-    ap.add_argument(
-        "-t",
-        "--transmission",
-        required=True,
-        type=float,
-        help="Transmission to be set, [%]",
-    )
-    args = vars(ap.parse_args())
-    return args
-
-
-def get_transmission(energy, transmission):
-    transmission = transmission / 100
-    # Expressions (interpolation) for calculations of MU (linear attenuation coefficient [cm^-1]) for each material in function of the beam energy.
-    # The data used to obtain the expressions (curve fitting) are from  "https://physics.nist.gov/PhysRefData/FFast/html/form.html"
-    # This attenuation coefficients can be verified and optimised after experimental validation at the beamline.
-    MU_Al = (
-        (78657.01011 * math.exp(-energy / 0.65969))
-        + (6406.36151 * math.exp(-energy / 1.63268))
-        + (492.29999 * math.exp(-energy / 4.42554))
-        + (3.2588)
-    )
-    MU_Ti = (
-        (28062.17632 * math.exp(-energy / 1.88062))
-        + (6354120 * math.exp(-energy / 0.49973))
-        + (2257.91488 * math.exp(-energy / 5.28296))
-        + (17.4342)
-    )
-    MU_Cu = (
-        (1147850000 * math.exp(-energy / 0.56933))
-        + (2582.7593 * math.exp(-energy / 8.40671))
-        + (30628.08291 * math.exp(-energy / 2.98937))
-        + (22.4187)
-    )
-    MU_Au = (42783.04258 * math.exp(-energy / 5.39244)) + (399.59714)
-    MU_Zr = (11143.28458 * math.exp(-energy / 5.87029)) + (102.27474)
-    MU_EMPTY = 0.0
-    # Foils in ABS-attenuator. The dictionary gives the foil position and material in the key (e.g. 'F1_Al', position 1 occupied by an aluminium foil),
-    # and the thickness [um] in the value. The list gives the positions and materials, similar to the dictionary, and it is used in the combination.
-    foils_dict = {
-        "F0_EMPTY": 0,
-        "F1_Al": 8,
-        "F2_Al": 10,
-        "F3_Al": 20,
-        "F4_Al": 80,
-        "F5_Al": 160,
-        "F6_Al": 320,
-        "F7_Al": 800,
-        "F8_Al": 1500,
-        "F9_Ti": 8,
-        "F10_Cu": 10,
-        "F11_Au": 5,
-        "F12_Zr": 25,
-    }
-
-    attenuator_position = [
-        "F0_EMPTY",
-        "F1_Al",
-        "F2_Al",
-        "F3_Al",
-        "F4_Al",
-        "F5_Al",
-        "F6_Al",
-        "F7_Al",
-        "F8_Al",
-        "F9_Ti",
-        "F10_Cu",
-        "F11_Au",
-        "F12_Zr",
-    ]
-    # conditions to use only the continuous part of the absorption spectra and not the edge region. It can be optimised after experimental validation.
-    if energy < 6.5:
-        attenuator_position = attenuator_position[0:9]
-    elif 6.5 <= energy < 9.5:
-        attenuator_position = attenuator_position[0:10]
-    elif 9.5 <= energy < 15.0:
-        attenuator_position = attenuator_position[0:11]
-    elif 15.0 <= energy < 18.5:
-        attenuator_position = attenuator_position[0:12]
-    elif energy >= 18.5:
-        attenuator_position = attenuator_position[0:13]
-
-    foils_comb = []
-    atten_coef_sum = []
-
-    # calculate the all possible unique combinations
-    for i in range(1, len(attenuator_position) + 1):
-        product = itertools.combinations(attenuator_position, i)
-        for item in product:
-            foils_comb.append(list(item))
-    # calculate the product of MU (cm^-1) * thickness (cm) for each material (MU * d)
-    # and sum the products to obtain the total (final) attenuation for each possible combination.
-    # and put the results (total attenuation) in a list.
-    comb_sum = []
-    for item in foils_comb:
-        comb_tmp = []
-        for sub_item in item:
-            if "_Al" in sub_item:
-                atten_mu_x = float(foils_dict[sub_item] * 1.0e-4) * MU_Al
-                comb_tmp.append(atten_mu_x)
-            elif "_Ti" in sub_item:
-                atten_mu_x = float(foils_dict[sub_item] * 1.0e-4) * MU_Ti
-                comb_tmp.append(atten_mu_x)
-            elif "_Cu" in sub_item:
-                atten_mu_x = float(foils_dict[sub_item] * 1.0e-4) * MU_Cu
-                comb_tmp.append(atten_mu_x)
-            elif "_Au" in sub_item:
-                atten_mu_x = float(foils_dict[sub_item] * 1.0e-4) * MU_Au
-                comb_tmp.append(atten_mu_x)
-            elif "_Zr" in sub_item:
-                atten_mu_x = float(foils_dict[sub_item] * 1.0e-4) * MU_Zr
-                comb_tmp.append(atten_mu_x)
-            elif "_EMPTY" in sub_item:
-                atten_mu_x = float(foils_dict[sub_item] * 1.0e-4) * MU_EMPTY
-                comb_tmp.append(atten_mu_x)
-
-        comb_sum.append(sum(comb_tmp))
-
-    # create a dictionary to correlate the combinations of foils (value) with the total attenuation (key)
-    FOILS = dict(zip(comb_sum, foils_comb))
-    # calculate the transmission for each combination using the product calculated before (the keys of FOILS)
-    FOILS_T = {1.0 * (math.exp(-k)): v for k, v in FOILS.items()}
-    # find the closest transmission that is possible to obtain with the foils on ABS-300.
-    closest_transmission = min(
-        FOILS_T.keys(), key=lambda k: abs(float(k) - transmission)
-    )
-    # get the foil combination for the closest transmission found
-    filter_combination = FOILS_T[closest_transmission]
-
-    return transmission, closest_transmission, filter_combination
-
-
-def set_foils(filter_combination):
-    # declare a list with available foils and a dictionary with epics PV class (FOIL ACT, FOIL IN, FOIL OUT) for each foil
-    attenuator_position = [
-        "F1_Al",
-        "F2_Al",
-        "F3_Al",
-        "F4_Al",
-        "F5_Al",
-        "F6_Al",
-        "F7_Al",
-        "F8_Al",
-        "F9_Ti",
-        "F10_Cu",
-        "F11_Au",
-        "F12_Zr",
-    ]
-
-    foils_pv = {
-        "F1_Al": (
-            PV("MNC:B:RIO01:9474C:bo0"),
-            PV("MNC:B:RIO01:9425A:bi11"),
-            PV("MNC:B:RIO01:9425A:bi12"),
-        ),
-        "F2_Al": (
-            PV("MNC:B:RIO01:9474C:bo1"),
-            PV("MNC:B:RIO01:9425A:bi10"),
-            PV("MNC:B:RIO01:9425A:bi13"),
-        ),
-        "F3_Al": (
-            PV("MNC:B:RIO01:9474C:bo2"),
-            PV("MNC:B:RIO01:9425A:bi9"),
-            PV("MNC:B:RIO01:9425A:bi14"),
-        ),
-        "F4_Al": (
-            PV("MNC:B:RIO01:9474C:bo3"),
-            PV("MNC:B:RIO01:9425A:bi8"),
-            PV("MNC:B:RIO01:9425A:bi15"),
-        ),
-        "F5_Al": (
-            PV("MNC:B:RIO01:9474C:bo4"),
-            PV("MNC:B:RIO01:9425A:bi7"),
-            PV("MNC:B:RIO01:9425A:bi16"),
-        ),
-        "F6_Al": (
-            PV("MNC:B:RIO01:9474C:bo5"),
-            PV("MNC:B:RIO01:9425A:bi6"),
-            PV("MNC:B:RIO01:9425A:bi17"),
-        ),
-        "F7_Al": (
-            PV("MNC:B:RIO01:9474C:bo6"),
-            PV("MNC:B:RIO01:9425A:bi5"),
-            PV("MNC:B:RIO01:9425A:bi18"),
-        ),
-        "F8_Al": (
-            PV("MNC:B:RIO01:9474C:bo7"),
-            PV("MNC:B:RIO01:9425A:bi4"),
-            PV("MNC:B:RIO01:9425A:bi19"),
-        ),
-        "F9_Ti": (
-            PV("MNC:B:RIO01:9474D:bo0"),
-            PV("MNC:B:RIO01:9425A:bi3"),
-            PV("MNC:B:RIO01:9425A:bi20"),
-        ),
-        "F10_Cu": (
-            PV("MNC:B:RIO01:9474D:bo1"),
-            PV("MNC:B:RIO01:9425A:bi2"),
-            PV("MNC:B:RIO01:9425A:bi21"),
-        ),
-        "F11_Au": (
-            PV("MNC:B:RIO01:9474D:bo2"),
-            PV("MNC:B:RIO01:9425A:bi1"),
-            PV("MNC:B:RIO01:9425A:bi22"),
-        ),
-        "F12_Zr": (
-            PV("MNC:B:RIO01:9474D:bo3"),
-            PV("MNC:B:RIO01:9425A:bi0"),
-            PV("MNC:B:RIO01:9425A:bi23"),
-        ),
-    }
-
-    # setup the foils: check foil status, put the foils in the 'filter_combination' and remove the others
-
-    wt = 0.1
-
-    # the commented lines below works for the attenuator expected logic (0 for foil out and 1 for foil in).
-    # as the current logic is inverted (1 is foil out and 0 is foil in) use the uncommented lines.
-
-    for foil in attenuator_position:
-        if foil in filter_combination:
-            # if foils_pv[foil][1].get() == 0 and foils_pv[foil][2].get() == 1:
-            if foils_pv[foil][1].get() == 1 and foils_pv[foil][2].get() == 0:
-                # foils_pv[foil][0].put(1)
-                foils_pv[foil][0].put(0)
-                status = 0
-                time.sleep(wt)
-            # elif foils_pv[foil][1].get() == 1 and foils_pv[foil][2].get() == 0:
-            elif foils_pv[foil][1].get() == 0 and foils_pv[foil][2].get() == 1:
-                status = 0
-            elif foils_pv[foil][1].get() == foils_pv[foil][2].get():
-                status = 1
-                break
-        else:
-            # if foils_pv[foil][1].get() == 0 and foils_pv[foil][2].get() == 1:
-            if foils_pv[foil][1].get() == 1 and foils_pv[foil][2].get() == 0:
-                status = 0
-            # elif foils_pv[foil][1].get() == 1 and foils_pv[foil][2].get() == 0:
-            elif foils_pv[foil][1].get() == 0 and foils_pv[foil][2].get() == 1:
-                # foils_pv[foil][0].put(0)
-                foils_pv[foil][0].put(1)
-                status = 0
-                time.sleep(wt)
-            elif foils_pv[foil][1].get() == foils_pv[foil][2].get():
-                status = 1
-                break
-
-    return status
-
-
-def main():
-    energy = read_input()["energy"]
-    transmission = read_input()["transmission"]
-    transmission_setup = get_transmission(energy, transmission)
-    # transmission required by the user
-    user_transmission = transmission_setup[0] * 100
-    # real transmission got with calculated foil combination
-    actual_transmission = round(transmission_setup[1] * 100, 2)
-    # calculated foil combination to get the required transmission
-    filter_combination = transmission_setup[2]
-    # put the foils and check if the they were correctly positioned (status:0 = ok; 1 = fail)
-    foil_status = set_foils(filter_combination)
-
-
-if __name__ == "__main__":
-    main()