Update comm_export.py

reworked function to export data. Added lorenntz to decide if Lorentz correction should be done and also export_fit to decide whether fitter or itegrated area is to be exported (added also to fit2.py)

pyzebra/comm_export.py

@@ -1,121 +1,65 @@
-
+import numpy as np
-def fill_string(string, total_lenght):
-    """fills string to tatal_length with whitespaces
-    :arg string - string to fill
-    :arg total_lenght - length of the final string
-    :return string of the lenght of total_lenght
-    """
-    white_spaces = " " * total_lenght
-    return_string = white_spaces[: -len(str(string))] + str(string)
-    return return_string
 
 
-def export_comm(data, path):
+def correction(value, lorentz=True, zebra_mode="--", ang1=0, ang2=0):
+    if lorentz is False:
+        return value
+    else:
+        if zebra_mode == "bi":
+            corr_value = np.abs(value * np.sin(ang1))
+            return corr_value
+        elif zebra_mode == "nb":
+            corr_value = np.abs(value * np.sin(ang1) * np.cos(ang2))
+            return corr_value
+
+
+def export_comm(data, path, lorentz=False):
     """exports data in the *.comm format
+    :param lorentz: perform Lorentz correction
     :param path: path to file + name
     :arg data - data to export, is dict after peak fitting
+
     """
 
+    align = ">"
     if data["meta"]["indices"] == "hkl":
         extension = ".comm"
-        with open(str(path + extension), "w") as out_file:
+        padding = [6, 4, 10, 8]
-            for keys in data["Measurements"]:
-                try:
-                    meas_number_str = fill_string(keys[1:], 6)
-                    h_str = fill_string(int(data["Measurements"][str(keys)]["h_index"]), 4)
-                    k_str = fill_string(int(data["Measurements"][str(keys)]["k_index"]), 4)
-                    l_str = fill_string(int(data["Measurements"][str(keys)]["l_index"]), 4)
-                    int_str = fill_string(
-                        "{:10.2f}".format(data["Measurements"][str(keys)]["fit"]["g_amp"][0]), 10
-                    )
-                    sigma_str = fill_string(
-                        "{:10.2f}".format(data["Measurements"][str(keys)]["fit"]["g_width"][0]), 10
-                    )
-                    if data["meta"]["zebra_mode"] == 'bi':
-                        twotheta_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["twotheta_angle"]), 8
-                        )
-                        omega_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["omega_angle"]), 8
-                         )
-                        chi_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["chi_angle"]), 8
-                        )
-                        phi_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["phi_angle"]), 8
-                        )
-                    elif data["meta"]["zebra_mode"] == 'nb':
-                        twotheta_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["gamma_angle"]), 8
-                        )
-                        omega_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["omega_angle"]), 8
-                         )
-                        chi_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["nu_angle"]), 8
-                        )
-                        phi_str = fill_string(
-                             "{:8.2f}".format(data["Measurements"][str(keys)]["unkwn_angle"]), 8
-                        )
-
-                    line = (
-                        meas_number_str
-                        + h_str
-                        + l_str
-                        + k_str
-                        + int_str
-                        + sigma_str
-                        + twotheta_str
-                        + omega_str
-                        + chi_str
-                        + phi_str
-                        + "\n"
-                    )
-                    out_file.write(line)
-                except KeyError:
-                    print("Measurement skipped - no fit value for:", keys)
-
     elif data["meta"]["indices"] == "real":
         extension = ".incomm"
+        padding = [4, 6, 10, 8]
+
     with open(str(path + extension), "w") as out_file:
         for keys in data["Measurements"]:
+            print(keys)
             try:
-                    meas_number_str = fill_string(keys[1:], 4)
+                meas_number_str = f"{keys[1:]:{align}{padding[0]}}"
-                    h_str = fill_string(int(data["Measurements"][str(keys)]["h_index"]), 6)
+                h_str = f'{int(data["Measurements"][str(keys)]["h_index"]):{padding[1]}}'
-                    k_str = fill_string(int(data["Measurements"][str(keys)]["k_index"]), 6)
+                k_str = f'{int(data["Measurements"][str(keys)]["k_index"]):{padding[1]}}'
-                    l_str = fill_string(int(data["Measurements"][str(keys)]["l_index"]), 6)
+                l_str = f'{int(data["Measurements"][str(keys)]["l_index"]):{padding[1]}}'
-                    int_str = fill_string(
+                if data["Measurements"][str(keys)]["fit"]["export_fit"] is True:
-                        "{:10.2f}".format(data["Measurements"][str(keys)]["fit"]["g_amp"][0]), 10
+                    area = float(data["Measurements"][str(keys)]["fit"]["g_amp"][0]) + float(
+                        data["Measurements"][str(keys)]["fit"]["l_amp"][0]
                     )
-                    sigma_str = fill_string(
+                else:
-                        "{:10.2f}".format(data["Measurements"][str(keys)]["fit"]["g_width"][0]), 10
+                    area = float(data["Measurements"][str(keys)]["fit"]["int_area"]) - float(
-                    )
+                        data["Measurements"][str(keys)]["fit"]["int_background"][0]
-                    if data["meta"]["zebra_mode"] == 'bi':
-                        twotheta_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["twotheta_angle"]), 8
-                        )
-                        omega_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["omega_angle"]), 8
-                        )
-                        chi_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["chi_angle"]), 8
-                        )
-                        phi_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["phi_angle"]), 8
-                        )
-                    elif data["meta"]["zebra_mode"] == 'nb':
-                        twotheta_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["gamma_angle"]), 8
-                        )
-                        omega_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["omega_angle"]), 8
-                        )
-                        chi_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["nu_angle"]), 8
-                        )
-                        phi_str = fill_string(
-                            "{:8.2f}".format(data["Measurements"][str(keys)]["unkwn_angle"]), 8
                     )
+
+                if data["meta"]["zebra_mode"] == "bi":
+                    int_str = f'{"{:8.2f}".format(correction(area, lorentz, data["meta"]["zebra_mode"], data["Measurements"][str(keys)]["twotheta_angle"])):{align}{padding[2]}}'                    
+                    angle_str1 = f'{data["Measurements"][str(keys)]["twotheta_angle"]:{padding[3]}}'
+                    angle_str2 = f'{data["Measurements"][str(keys)]["omega_angle"]:{padding[3]}}'
+                    angle_str3 = f'{data["Measurements"][str(keys)]["chi_angle"]:{padding[3]}}'
+                    angle_str4 = f'{data["Measurements"][str(keys)]["phi_angle"]:{padding[3]}}'
+                elif data["meta"]["zebra_mode"] == "nb":
+                    int_str = f'{"{:8.2f}".format(correction(area, lorentz, data["meta"]["zebra_mode"], data["Measurements"][str(keys)]["gamma_angle"],data["Measurements"][str(keys)]["nu_angle"])):{align}{padding[2]}}'
+                    angle_str1 = f'{data["Measurements"][str(keys)]["gamma_angle"]:{padding[3]}}'
+                    angle_str2 = f'{data["Measurements"][str(keys)]["omega_angle"]:{padding[3]}}'
+                    angle_str3 = f'{data["Measurements"][str(keys)]["nu_angle"]:{padding[3]}}'
+                    angle_str4 = f'{data["Measurements"][str(keys)]["unkwn_angle"]:{padding[3]}}'
+
+                sigma_str = f'{"{:8.2f}".format(float(data["Measurements"][str(keys)]["fit"]["g_width"][0])):{align}{padding[2]}}'
                 line = (
                     meas_number_str
                     + h_str
@@ -123,12 +67,14 @@ def export_comm(data, path):
                     + k_str
                     + int_str
                     + sigma_str
-                        + twotheta_str
+                    + angle_str1
-                        + omega_str
+                    + angle_str2
-                        + chi_str
+                    + angle_str3
-                        + phi_str
+                    + angle_str4
                     + "\n"
                 )
                 out_file.write(line)
+
             except KeyError:
                 print("Measurement skipped - no fit value for:", keys)
+