Merge pull request nexpy#264 from rayosborn:skip-self-copy-uncopied-data

Skip self-copy when reading uncopied lazy-loaded field

Author: rayosborn

src/nexusformat/nexus/tree.py

@@ -3286,7 +3286,16 @@ def _get_uncopied_data(self, idx=None):
                 return f.readvalue(_path, idx=idx)
             else:
                 if self.nxfilemode == 'rw':
-                    f.copy(_path, self.nxpath)
+                    # Skip the copy if the field already lives at the
+                    # destination path. This happens when a file-backed
+                    # field is deep-copied into a new container that
+                    # ends up at the same on-disk location (e.g. the
+                    # PlotDialog wraps a field in an in-memory NXdata
+                    # whose nxpath collides with the source). HDF5
+                    # otherwise raises 'destination object already
+                    # exists' here.
+                    if _path != self.nxpath:
+                        f.copy(_path, self.nxpath)
                 else:
                     self._create_memfile()
                     f.copy(_path, self._memfile, name='data')

tests/test_files.py

@@ -1,8 +1,9 @@
 import os
 
+import numpy as np
 import pytest
-from nexusformat.nexus.tree import (NXdata, NXentry, NXFile, NXroot, nxload,
-                                    nxopen)
+from nexusformat.nexus.tree import (NXdata, NXentry, NXfield, NXFile, NXroot,
+                                    nxload, nxopen)
 
 
 def test_file_creation(tmpdir):
@@ -80,3 +81,29 @@ def test_file_context_manager(tmpdir, field1, field2):
     assert "entry/data/f2" in w2
     assert "signal" in w2["entry/data"].attrs
     assert "axes" in w2["entry/data"].attrs
+
+
+def test_read_lazy_field_on_copy(tmpdir):
+
+    filename = os.path.join(tmpdir, "file.nxs")
+    shape = (2000, 2000)
+    root = NXroot(NXentry(NXdata(
+        NXfield(np.zeros(shape, dtype=np.int64), name="signal"),
+        name="data")))
+    root["entry/data/signal_mask"] = NXfield(np.zeros(shape, dtype=bool))
+    root["entry/data/signal"].attrs["mask"] = "signal_mask"
+    root.save(filename, mode="w")
+    del root
+
+    root = nxload(filename, "rw")
+    src = root["entry/data"]
+    wrapper = NXdata(src["signal_mask"], name=src.nxname)
+    wrapper.nxgroup = src.nxgroup
+    field = wrapper.nxsignal
+    assert field._uncopied_data is not None
+    assert field._uncopied_data[1] == field.nxpath
+
+    arr = field[()]
+    assert arr.shape == shape
+    assert arr.dtype == bool
+    assert field._uncopied_data is None