updated scan class

Author: bingli621

.DS_Store

@@ -216,24 +216,24 @@ def to_nexus(self, path_to_nexus: str, name="scan") -> None:
         with h5py.File(path_to_nexus, "a") as nexus_file:
             scan_grp = nexus_file.require_group(name + "/")
             NexusEntry._write_recursively(self, scan_grp)
-            # create soft link for data
-            def_y = nexus_file[name]["data"].attrs["signal"]
-            def_x = nexus_file[name]["data"].attrs["axes"]
-            path_y = _find_val_path(def_y, nexus_file)
-            path_x = _find_val_path(def_x, nexus_file)
-
-            if path_y is not None:
-                def_y = "data/" + def_y
-                if isinstance(scan_grp.get(def_y), h5py.Dataset):
-                    del scan_grp[def_y]
-                scan_grp[def_y] = h5py.SoftLink(path_y)
-                scan_grp[def_y + "/"].attrs["target"] = path_y
-            if path_x is not None:
-                def_x = "data/" + def_x
-                if isinstance(scan_grp.get(def_x), h5py.Dataset):
-                    del scan_grp[def_x]
-                scan_grp[def_x] = h5py.SoftLink(path_x)
-                scan_grp[def_x + "/"].attrs["target"] = path_x
+            if "data" in scan_grp:  # create soft link for data
+                def_y = scan_grp["data"].attrs["signal"]
+                def_x = scan_grp["data"].attrs["axes"]
+                path_y = _find_val_path(def_y, nexus_file)
+                path_x = _find_val_path(def_x, nexus_file)
+
+                if path_y is not None:
+                    def_y = "data/" + def_y
+                    if isinstance(scan_grp.get(def_y), h5py.Dataset):
+                        del scan_grp[def_y]
+                    scan_grp[def_y] = h5py.SoftLink(path_y)
+                    scan_grp[def_y + "/"].attrs["target"] = path_y
+                if path_x is not None:
+                    def_x = "data/" + def_x
+                    if isinstance(scan_grp.get(def_x), h5py.Dataset):
+                        del scan_grp[def_x]
+                    scan_grp[def_x] = h5py.SoftLink(path_x)
+                    scan_grp[def_x + "/"].attrs["target"] = path_x
 
             # Create the ATTRIBUTES
             scan_grp.attrs["file_name"] = os.path.abspath(path_to_nexus)

src/tavi/data/nxentry.py

@@ -12,14 +12,14 @@ class ScanInfo:
     """Metadata containing scan information"""
 
     scan_num: Optional[int] = None
+    scan_title: str = ""
+    def_y: str = "detector"
+    def_x: str = "s1"
     start_time: Optional[str] = None
     end_time: Optional[str] = None
-    scan_title: str = ""
-    # preset_type: str = "normal"
+    preset_type: str = "normal"
     preset_channel: str = "time"
     preset_value: float = 1.0
-    def_y: str = "detector"
-    def_x: str = "s1"
 
 
 @dataclass
@@ -29,6 +29,8 @@ class SampleUBInfo:
     sample_name: str = ""
     lattice_constants: tuple = (1.0, 1.0, 1.0, 90.0, 90.0, 90.0)
     ub_matrix: Optional[np.ndarray] = None
+    u: Optional[np.ndarray] = None
+    v: Optional[np.ndarray] = None
     # ub_mode: int = 0  # mode for UB determination in SPICE
     # angle_mode: int = 0  # mode for goni angle calculation in SPICE
     plane_normal: Optional[np.ndarray] = None

src/tavi/data/scan.py

@@ -71,7 +71,7 @@ def read_spice_ubconf(ub_file_name: str) -> dict:
     Returns:
     """
     ubconf: dict[str, Any] = {}
-    with open(ub_file_name, encoding="utf-8") as f:
+    with open(ub_file_name, 'r', encoding="utf-8") as f:
         all_content = f.readlines()
 
     for idx, line in enumerate(all_content):
@@ -129,8 +129,16 @@ def _create_spicelogs(path_to_scan_file: str) -> dict:
 
     scan_path = os.path.abspath(path_to_scan_file)
     (*folder_path, _, _) = scan_path.split("/")
-    ub_file_path = "/".join(folder_path + ["UBConf", metadata["ubconf"]])
-    ub_conf_dict = {"file_path": ub_file_path}
+    ub_file_path = os.path.join('/',*folder_path,"UBConf", metadata["ubconf"])
+    ub_temp_file_path = os.path.join('/',*folder_path,"UBConf", "temp", metadata["ubconf"])
+
+    if os.path.isfile(ub_file_path):
+        ub_conf_dict = {"file_path": ub_file_path}
+    elif os.path.isfile(ub_temp_file_path):
+        ub_conf_dict = {"file_path": ub_temp_file_path}
+    else:
+        ub_conf_dict = {"file_path": ""}
+        print(f"Cannot find UB file {metadata["ubconf"]}")
     ubconf = read_spice_ubconf(ub_file_path)
     for k, v in ubconf.items():
         ub_conf_dict.update({k: v})

src/tavi/data/spice_reader.py

@@ -4,8 +4,8 @@
 
 import h5py
 
+from tavi.data.scan import Scan
 from tavi.data.scan_group import ScanGroup
-from tavi.data.scan_old.scan import Scan
 
 
 class TAVI(object):

src/tavi/data/tavi.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Optional, Union
 
-from tavi.data.scan_old.scan import Scan
+from tavi.data.scan import Scan
 from tavi.instrument.goni import Goniometer
 from tavi.instrument.mono_ana import MonoAna
 from tavi.instrument.tas_cmponents import Collimators, Detector, Distances, Guide, Monitor, Source

src/tavi/instrument/tas_base.py

@@ -1,8 +1,9 @@
+import os
+
 import h5py
 import numpy as np
 import pytest
 
-from tavi.data.nxdict import spice_scan_to_nxdict
 from tavi.data.nxentry import NexusEntry
 
 
@@ -37,19 +38,23 @@ def test_get_dataset(nexus_entries):
 
 
 def test_to_nexus(nexus_entries):
-    path_to_nexus_entry = "./test_data/scan_to_nexus_test.h5"
+    path_to_nexus = "./test_data/scan_to_nexus_test.h5"
     for scan_num, nexus_entry in nexus_entries.items():
-        nexus_entry.to_nexus(path_to_nexus_entry, scan_num)
+        nexus_entry.to_nexus(path_to_nexus, scan_num)
 
-    with h5py.File(path_to_nexus_entry, "r") as nexus_file:
+    with h5py.File(path_to_nexus, "r") as nexus_file:
         assert str(nexus_file["scan0034"]["title"].asstr()[...]) == "scan_title_34"
         assert nexus_file["scan0034"].attrs["NX_class"] == "NXentry"
+    os.remove(path_to_nexus)
 
 
-def test_from_nexus(nexus_entries):
-    path_to_nexus_entry = "./test_data/scan_to_nexus_test.h5"
-    entries = NexusEntry.from_nexus(path_to_nexus_entry)
+def test_from_nexus_get_all(nexus_entries):
+    # generate NeXus file
+    path_to_nexus = "./test_data/scan_to_nexus_test.h5"
+    for scan_num, nexus_entry in nexus_entries.items():
+        nexus_entry.to_nexus(path_to_nexus, scan_num)
 
+    entries = NexusEntry.from_nexus(path_to_nexus)
     scan0034 = entries["scan0034"]
     assert scan0034["definition"] == nexus_entries["scan0034"]["definition"]
     assert np.allclose(
@@ -75,28 +80,38 @@ def test_from_nexus(nexus_entries):
         scan0034.get("instrument/analyser/a2"),
         np.array([242.0, 242.1, 242.2]),
     )
+    assert np.allclose(
+        scan0034.get("data/a1"),
+        np.array([142.0, 142.1, 142.2]),
+    )
 
     scan0035 = entries["scan0035"]
     assert scan0035.get("title") == "scan_title_35"
+    os.remove(path_to_nexus)
 
 
-def test_from_nexus_single_scan():
-    path_to_nexus_entry = "./test_data/scan_to_nexus_test.h5"
-    nexus_entries = NexusEntry.from_nexus(path_to_nexus_entry, scan_num=35)
+def test_from_nexus_get_one(nexus_entries):
+    # generate NeXus
+    path_to_nexus = "./test_data/scan_to_nexus_test.h5"
+    for scan_num, nexus_entry in nexus_entries.items():
+        nexus_entry.to_nexus(path_to_nexus, scan_num)
+
+    nexus_entries = NexusEntry.from_nexus(path_to_nexus, scan_num=35)
     scan0035 = nexus_entries["scan0035"]
     assert scan0035.get("title") == "scan_title_35"
 
 
-def test_from_nexus_IPTS32124_CG4C_exp0424():
+def test_from_nexus_real_data():
     path_to_nexus_entry = "./test_data/IPTS32124_CG4C_exp0424/scan0034.h5"
     nexus_entries = NexusEntry.from_nexus(path_to_nexus_entry)
+
     scan0034 = nexus_entries["scan0034"]
     assert scan0034.get("definition") == "NXtas"
     assert scan0034.get("end_time") == "2024-07-03T02:41:28"
     assert np.allclose(scan0034.get("s1")[0:3], [36.14, 36.5025, 36.855])
 
 
-def test_from_spice_IPTS32124_CG4C_exp0424_single_scan():
+def test_from_spice_get_one():
     path_to_spice_entry = "./test_data/exp424"
     scan0034 = NexusEntry.from_spice(path_to_spice_entry, 34)["scan0034"]
 
@@ -105,7 +120,7 @@ def test_from_spice_IPTS32124_CG4C_exp0424_single_scan():
     assert np.allclose(scan0034.get("s1")[0:3], np.array([36.14, 36.5025, 36.855]))
 
 
-def test_from_spice_IPTS32124_CG4C_exp0424_all_scan():
+def test_from_spice_get_all():
     path_to_spice_entry = "./test_data/exp424"
     scans = NexusEntry.from_spice(path_to_spice_entry)
 
@@ -120,36 +135,35 @@ def test_from_spice_IPTS32124_CG4C_exp0424_all_scan():
 
 
 def test_get_from_daslogs():
-    path_to_nexus_entry = "./test_data/spice_to_nexus_test_scan34.h5"
+    path_to_nexus_entry = "./test_data/IPTS32124_CG4C_exp0424/scan0034.h5"
     scan0034 = NexusEntry.from_nexus(path_to_nexus_entry, 34)["scan0034"]
     assert scan0034.get_metadata_from_daslogs("sense") == "-+-"
     assert np.allclose(scan0034.get_data_from_daslogs("s1")[0:3], np.array([36.14, 36.5025, 36.855]))
 
 
-def test_spice_scan_to_nexus():
+def test_spice_to_nexus_one():
 
-    path_to_spice_entry = "./test_data/exp424"
-    path_to_nexus_entry = "./test_data/spice_to_nxdict_test_scan0034.h5"
-    scan0034 = NexusEntry.from_spice(path_to_spice_entry, 34)
+    path_to_spice_folder = "./test_data/exp424"
+    path_to_nexus = "./test_data/spice_to_nxdict_test_scan0034.h5"
+    scan0034 = NexusEntry.from_spice(path_to_spice_folder, 34)
     for scan_name, scan in scan0034.items():
-        scan.to_nexus(path_to_nexus_entry, name=scan_name)
+        scan.to_nexus(path_to_nexus, name=scan_name)
 
+    with h5py.File(path_to_nexus, "r") as nexus_file:
+        assert len(nexus_file) == 1
+    os.remove(path_to_nexus)
 
-def test_spice_data_to_nexus():
-    path_to_spice_data = "./test_data/exp424"
-    scan_dict = spice_scan_to_nxdict(path_to_spice_data)
 
-    entries = {"scan0034": nxdict}
-    nexus_entries = {}
-    for scan_num, scan_content in entries.items():
-        content_list = []
-        for key, val in scan_content.items():
-            content_list.append((key, val))
-        nexus_entries.update({scan_num: NexusEntry(content_list)})
-    # generate h5 file
-    path_to_nexus_entry = "./test_data/spice_to_nxdict_test_scan0034.h5"
-    for scan_num, nexus_entry in nexus_entries.items():
-        nexus_entry.to_nexus(path_to_nexus_entry, scan_num)
+def test_spice_to_nexus_all():
+    path_to_spice_folder = "./test_data/exp424"
+    path_to_nexus = "./test_data/spice_to_nxdict_test_all.h5"
+    scan_dict = NexusEntry.from_spice(path_to_spice_folder)
+
+    for scan_name, scan in scan_dict.items():
+        scan.to_nexus(path_to_nexus, name=scan_name)
+    with h5py.File(path_to_nexus, "r") as nexus_file:
+        assert len(nexus_file) == 92
+    os.remove(path_to_nexus)
 
 
 @pytest.fixture

test_data/.DS_Store

@@ -55,4 +55,7 @@ def test_create_spicelogs():
 def test_create_spicelogs_single_point():
     path_to_spice_data = "./test_data/exp815/Datafiles/HB1_exp0815_scan0001.dat"
     spicelogs = _create_spicelogs(path_to_spice_data)
-    assert len(spicelogs.keys()) == 1  # metadata only, no data columns
+    # metadata and ubconf only, no data columns
+    assert "metadata" in spicelogs
+    assert "ub_conf" in spicelogs
+    assert len(spicelogs) == 2

test_data/exp424/.DS_Store

@@ -24,6 +24,26 @@ def test_new_tavi_file_at_given_path():
     os.remove(tavi_file_name)
 
 
+def test_new_tavi_file_without_path():
+    tavi = TAVI()
+    tavi.new_file()
+    tavi.save_file()
+
+    with h5py.File(tavi.file_path, "r") as f:
+        keys = [key for key in f["/"].keys()]
+    # check if groups preserves the order
+    assert keys[1] == "processed_data"
+    # delete file
+    os.remove(tavi.file_path)
+
+
+# TODO
+def test_load_spice_data_from_disk():
+    tavi = TAVI()
+    tavi_file_name = "./test_data/tavi_test_exp424.h5"
+    tavi.new_file(tavi_file_name)
+
+
 def test_load_nexus_data_from_disk():
     tavi = TAVI()
     tavi_file_name = "./test_data/tavi_test_exp424.h5"
@@ -55,16 +75,3 @@ def test_open_tavi_file():
 
     assert len(scans := tavi.data["IPTS32124_CG4C_exp0424"]) == 92
     assert scans["scan0001"].scan_info.scan_num == 1
-
-
-def test_new_tavi_file_without_path():
-    tavi = TAVI()
-    tavi.new_file()
-    tavi.save_file()
-
-    with h5py.File(tavi.file_path, "r") as f:
-        keys = [key for key in f["/"].keys()]
-    # check if groups preserves the order
-    assert keys[1] == "processed_data"
-    # delete file
-    os.remove(tavi.file_path)