add a concatenate util class

nxtomomill/nexus/__init__.py

@@ -3,3 +3,4 @@ from .nxobject import NXobject  # noqa F401
 from .nxsample import NXsample  # noqa F401
 from .nxsource import NXsource  # noqa F401
 from .nxtomo import NXtomo  # noqa F401
+from .utils import concatenate  # noqa F401

nxtomomill/nexus/nxdetector.py

@@ -30,7 +30,6 @@ __date__ = "03/02/2022"
 
 
 from functools import partial
-from multiprocessing.sharedctypes import Value
 from operator import is_not
 from silx.utils.proxy import docstring
 from silx.io.url import DataUrl

nxtomomill/nexus/nxtomo.py

@@ -372,7 +372,6 @@ class NXtomo(NXobject):
         nx_tomo.start_time = min(start_times)
         nx_tomo.end_time = max(end_times)
 
-        sample = NXsample.concatenate(tuple([nx_obj.sample for nx_obj in nx_objects]))
         nx_tomo.sample = NXsample.concatenate(
             tuple([nx_obj.sample for nx_obj in nx_objects])
         )

nxtomomill/nexus/test/test_nxtomo.py

@@ -32,7 +32,8 @@ import os
 from tempfile import TemporaryDirectory
 from nxtomomill.nexus.nxdetector import FieldOfView
 import pytest
-from nxtomomill.nexus.nxtomo import NXtomo
+from nxtomomill.nexus import NXtomo
+from nxtomomill.nexus import concatenate
 from datetime import datetime
 from tomoscan.esrf import HDF5TomoScan
 from tomoscan.validator import ReconstructionValidator
@@ -287,7 +288,7 @@ def test_nx_tomo(nexus_path_version):
             )
 
         # test concatenation
-        nx_tomo_concat = NXtomo.concatenate([loaded_nx_tomo, None, loaded_nx_tomo])
+        nx_tomo_concat = concatenate([loaded_nx_tomo, None, loaded_nx_tomo])
         concat_file = os.path.join(folder, "concatenated_nexus_file.hdf5")
 
         nx_tomo_concat.save(
@@ -318,3 +319,6 @@ def test_nx_tomo(nexus_path_version):
                 ]
             ),
         )
+
+        with pytest.raises(TypeError):
+            concatenate([1, 2])

nxtomomill/nexus/utils.py

@@ -35,6 +35,8 @@ import numpy
 import h5py
 from silx.io.utils import h5py_read_dataset
 
+from nxtomomill.nexus.nxobject import NXobject
+
 
 def cast_and_check_array_1D(array, array_name):
     if not isinstance(array, (type(None), numpy.ndarray, Iterable)):
@@ -132,3 +134,12 @@ def get_data(file_path, data_path):
             return h5py_read_dataset(h5f[data_path])
         else:
             return None
+
+
+def concatenate(nx_objects, **kwargs):
+    if len(nx_objects) == 0:
+        return None
+    else:
+        if not isinstance(nx_objects[0], NXobject):
+            raise TypeError("nx_objects are expected to be instances of NXobject")
+        return type(nx_objects[0]).concatenate(nx_objects=nx_objects, **kwargs)