updated spice_to_nexus.py

scripts/test_data_conversion.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+# -*- coding: utf-8 -*-
 from tavi.data.spice_to_nexus import convert_spice_to_nexus
 from tavi.data.tavi import TAVI
 

src/tavi/data/tavi.py

@@ -31,14 +31,15 @@ def __init__(self):
     def new_tavi_file(self, file_path):
         """Create a new tavi file"""
         self.file_path = file_path
-        h5py.get_config().track_order = True
-        with h5py.File(file_path, "w") as root:
-            root.create_group("data")
-            root.create_group("processed_data")
-            root.create_group(
-                "fits",
-            )
-            root.create_group("plots")
+
+        try:
+            with h5py.File(file_path, "w", track_order=True) as root:
+                root.create_group("data", track_order=True)
+                root.create_group("processed_data", track_order=True)
+                root.create_group("fits", track_order=True)
+                root.create_group("plots", track_order=True)
+        except OSError:
+            print(f"Cannot create tavi file at {file_path}")
 
     def load_nexus_data_from_disk(self, path_to_hdf5):
         """Load hdf5 data from path_to_hdf5.

tests/test_tavi_data.py

@@ -0,0 +1,57 @@
+# -*- coding: utf-8 -*
+import h5py
+import numpy as np
+
+from tavi.data.spice_to_nexus import _format_spice_header, _read_spice, _read_spice_ub, convert_spice_to_nexus
+from tavi.data.tavi import TAVI
+
+
+def test_read_spice():
+    spice_file = "./test_data/exp424/Datafiles/CG4C_exp0424_scan0001.dat"
+    spice_data, col_headers, headers, unused = _read_spice(spice_file)
+    assert spice_data.shape == (2, 55)
+    assert headers["scan_title"] == ""
+    assert len(unused) == 0
+
+    # unfinished scan
+    spice_file = "./test_data/exp416/Datafiles/CG4C_exp0416_scan0050.dat"
+    spice_data, col_headers, headers, unused = _read_spice(spice_file)
+    assert spice_data.shape == (16, 56)
+
+
+def test_read_spice_ub():
+    spice_ub_file = "./test_data/exp424/UBConf/UB02Jul2024_14108PM.ini"
+    ubconf = _read_spice_ub(spice_ub_file)
+    assert np.allclose(ubconf["Energy"], 4.8)
+    assert len(ubconf) == 13
+
+
+def test_format_spice_header():
+    spice_file = "./test_data/exp424/Datafiles/CG4C_exp0424_scan0001.dat"
+    _, _, headers, _ = _read_spice(spice_file)
+    formatted_headers = _format_spice_header(headers)
+    assert "COM" in formatted_headers.keys()
+    assert isinstance(formatted_headers["scan"], int)
+
+
+def test_spice_to_nexus_conversion():
+    exp_nums = [416, 424, 710, 815, 932, 1031]
+
+    for exp_num in exp_nums:
+        spice_folder = f"./test_data/exp{exp_num}/"
+        nexus_file_name = f"./test_data/nexus_exp{exp_num}.h5"
+        convert_spice_to_nexus(spice_folder, nexus_file_name)
+
+
+def test_new_tavi_file():
+    tavi = TAVI()
+    tavi_file_name = "./test_data/tavi_test.h5"
+    tavi.new_tavi_file(tavi_file_name)
+
+    with h5py.File(tavi_file_name, "r") as f:
+        keys = [key for key in f["/"].keys()]
+    # check if groups preserves the order
+    assert keys[0] == "data"
+    assert keys[1] == "processed_data"
+    assert keys[2] == "fits"
+    assert keys[3] == "plots"