Consolidate hkl and ub

pyzebra/app/panel_ccl_integrate.py

@@ -88,7 +88,7 @@ def create():
 
     def _init_datatable():
         scan_list = [s["idx"] for s in det_data["scan"]]
-        hkl = [f'{s["h_index"]} {s["k_index"]} {s["l_index"]}' for s in det_data["scan"]]
+        hkl = [f'{s["h"]} {s["k"]} {s["l"]}' for s in det_data["scan"]]
         scan_table_source.data.update(
             scan=scan_list,
             hkl=hkl,

pyzebra/app/panel_hdf_viewer.py

@@ -618,7 +618,7 @@ def calculate_hkl(det_data, index):
     gammad = det_data["gamma"][index]
     om = det_data["omega"][index]
     nud = det_data["nu"]
-    ub = det_data["UB"]
+    ub = det_data["ub"]
     geometry = det_data["zebra_mode"]
 
     if geometry == "bi":

pyzebra/ccl_io.py

@@ -1,5 +1,4 @@
 import os
-import re
 from collections import defaultdict
 
 import numpy as np
@@ -58,12 +57,7 @@ META_VARS_FLOAT = (
 
 META_UB_MATRIX = ("ub1j", "ub2j", "ub3j")
 
-CCL_FIRST_LINE = (
+CCL_FIRST_LINE = (("idx", int), ("h", float), ("k", float), ("l", float))
-    ("idx", int),
-    ("h_index", float),
-    ("k_index", float),
-    ("l_index", float),
-)
 
 CCL_ANGLES = {
     "bi": (("twotheta", float), ("omega", float), ("chi", float), ("phi", float)),
@@ -111,14 +105,20 @@ def parse_1D(fileobj, data_type):
             variable, value = line.split("=")
             variable = variable.strip()
             value = value.strip()
-            if variable in META_VARS_FLOAT:
+
+            if variable in META_VARS_STR:
+                metadata[variable] = value
+
+            elif variable in META_VARS_FLOAT:
                 if variable == "2-theta":  # fix that angle name not to be an expression
                     variable = "twotheta"
                 metadata[variable] = float(value)
-            elif variable in META_VARS_STR:
+
-                metadata[variable] = value
             elif variable in META_UB_MATRIX:
-                metadata[variable] = re.findall(r"[-+]?\d*\.\d+|\d+", value)
+                if "ub" not in metadata:
+                    metadata["ub"] = np.zeros((3, 3))
+                row = int(variable[-2]) - 1
+                metadata["ub"][row, :] = list(map(float, value.split()))
 
         if "#data" in line:
             # this is the end of metadata and the start of data section
@@ -172,10 +172,9 @@ def parse_1D(fileobj, data_type):
                 s[name].append(float(val))
 
         try:
-            s["h_index"] = float(metadata["title"].split()[-3])
+            s["h"], s["k"], s["l"] = map(float, metadata["title"].split()[-3:])
-            s["k_index"] = float(metadata["title"].split()[-2])
-            s["l_index"] = float(metadata["title"].split()[-1])
         except (ValueError, IndexError):
+            s["h"] = s["k"] = s["l"] = float("nan")
             print("seems hkl is not in title")
 
         s["om"] = np.array(s["om"])
@@ -201,10 +200,8 @@ def parse_1D(fileobj, data_type):
         print("Unknown file extention")
 
     for s in scan:
-        if s["h_index"].is_integer() and s["k_index"].is_integer() and s["l_index"].is_integer():
+        if s["h"].is_integer() and s["k"].is_integer() and s["l"].is_integer():
-            s["h_index"] = int(s["h_index"])
+            s["h"], s["k"], s["l"] = map(int, (s["h"], s["k"], s["l"]))
-            s["k_index"] = int(s["k_index"])
-            s["l_index"] = int(s["l_index"])
             s["indices"] = "hkl"
         else:
             s["indices"] = "real"
@@ -229,7 +226,7 @@ def export_1D(data, path, area_method=AREA_METHODS[0], lorentz=False, hkl_precis
 
         idx_str = f"{scan['idx']:6}"
 
-        h, k, l = scan["h_index"], scan["k_index"], scan["l_index"]
+        h, k, l = scan["h"], scan["k"], scan["l"]
         if scan["indices"] == "hkl":
             hkl_str = f"{h:6}{k:6}{l:6}"
         else:  # scan["indices"] == "real"

pyzebra/h5.py

@@ -69,7 +69,7 @@ def read_detector_data(filepath):
         det_data["wave"] = h5f["/entry1/ZEBRA/monochromator/wavelength"][:]
         det_data["chi"] = h5f["/entry1/sample/chi"][:]  # ch
         det_data["phi"] = h5f["/entry1/sample/phi"][:]  # ph
-        det_data["UB"] = h5f["/entry1/sample/UB"][:].reshape(3, 3)
+        det_data["ub"] = h5f["/entry1/sample/UB"][:].reshape(3, 3)
 
         for var in ("omega", "gamma", "nu", "chi", "phi"):
             if abs(det_data[var][0] - det_data[var][-1]) > 0.1:

pyzebra/merge_function.py

@@ -77,20 +77,7 @@ def merge(scan1, scan2):
 
 
 def check_UB(dict1, dict2, precision=0.01):
-    truth_list = list()
+    return np.max(np.abs(dict1["meta"]["ub"] - dict2["meta"]["ub"])) < precision
-    for i in ["ub1j", "ub2j", "ub3j"]:
-        for j in range(3):
-            if abs(abs(float(dict1["meta"][i][j])) - abs(float(dict2["meta"][i][j]))) < precision:
-
-                truth_list.append(True)
-            else:
-                truth_list.append(False)
-
-    # print(truth_list)
-    if all(truth_list):
-        return True
-    else:
-        return False
 
 
 def check_zebramode(dict1, dict2):

pyzebra/param_study_moduls.py

@@ -416,9 +416,9 @@ def variables(dictionary):
         "Monitor1",
         "Monitor2",
         "Monitor3",
-        "h_index",
+        "h",
-        "l_index",
+        "k",
-        "k_index",
+        "l",
         "n_points",
         "monitor",
         "Time",