Lazy save improvement

doc/user_guide/io.rst

@@ -405,21 +405,31 @@ Extra saving arguments
 - ``compression``: One of ``None``, ``'gzip'``, ``'szip'``, ``'lzf'`` (default is ``'gzip'``).
   ``'szip'`` may be unavailable as it depends on the HDF5 installation including it.
 
-.. note::
-
-    HyperSpy uses h5py for reading and writing HDF5 files and, therefore, it
-    supports all `compression filters supported by h5py <https://docs.h5py.org/en/stable/high/dataset.html#dataset-compression>`_.
-    The default is ``'gzip'``. It is possible to enable other compression filters
-    such as ``blosc`` by installing e.g. `hdf5plugin <https://github.com/silx-kit/hdf5plugin>`_.
-    However, be aware that loading those files will require installing the package
-    providing the compression filter. If not available an error will be raised.
-
-    Compression can significantly increase the saving speed. If file size is not
-    an issue, it can be disabled by setting ``compression=None``. Notice that only
-    ``compression=None`` and ``compression='gzip'`` are available in all platforms,
-    see the `h5py documentation <https://docs.h5py.org/en/stable/faq.html#what-compression-processing-filters-are-supported>`_
-    for more details. Therefore, if you choose any other compression filter for
-    saving a file, be aware that it may not be possible to load it in some platforms.
+    .. note::
+
+        HyperSpy uses h5py for reading and writing HDF5 files and, therefore, it
+        supports all `compression filters supported by h5py <https://docs.h5py.org/en/stable/high/dataset.html#dataset-compression>`_.
+        The default is ``'gzip'``. It is possible to enable other compression filters
+        such as ``blosc`` by installing e.g. `hdf5plugin <https://github.com/silx-kit/hdf5plugin>`_.
+        However, be aware that loading those files will require installing the package
+        providing the compression filter. If not available an error will be raised.
+
+        Compression can significantly increase the saving speed. If file size is not
+        an issue, it can be disabled by setting ``compression=None``. Notice that only
+        ``compression=None`` and ``compression='gzip'`` are available in all platforms,
+        see the `h5py documentation <https://docs.h5py.org/en/stable/faq.html#what-compression-processing-filters-are-supported>`_
+        for more details. Therefore, if you choose any other compression filter for
+        saving a file, be aware that it may not be possible to load it in some platforms.
+
+- ``chunks``: tuple of interger or None. Define the chunking used for saving
+  the dataset. If None, calculates chunks for the signal, with preferably at
+  least one chunk per signal space.
+- ``close_file``: if ``False``, doesn't close the file after writing. The file
+  should not be closed if the data need to be accessed lazily after saving.
+  Default is ``True``.
+- ``write_dataset``: if ``False``, doesn't write the dataset when writing the file.
+  This can be useful to overwrite signal attributes only (for example ``axes_manager``)
+  without having to write the whole dataset, which can take time. Default is ``True``.
 
 
 .. _zspy-format:
@@ -666,7 +676,7 @@ Extra saving arguments
   scalebar. Useful to set formattiong, location, etc. of the scalebar. See the
   `matplotlib-scalebar <https://pypi.org/project/matplotlib-scalebar/>`_
   documentation for more information.
-- ``output_size`` : (int, tuple of length 2 or None, optional): the output size 
+- ``output_size`` : (int, tuple of length 2 or None, optional): the output size
   of the image in pixels:
 
   * if ``int``, defines the width of the image, the height is
@@ -1827,7 +1837,7 @@ Extra loading arguments
   acquired last frame, which typically occurs when the acquisition was
   interrupted. When loading incomplete data (``only_valid_data=False``),
   the missing data are filled with zeros. If ``sum_frames=True``, this argument
-  will be ignored to enforce consistent sum over the mapped area. 
+  will be ignored to enforce consistent sum over the mapped area.
   (default True).
 
 

hyperspy/_signals/lazy.py

@@ -167,13 +167,21 @@ def rechunk(self,
                                                                   **kwargs)
                                                 )
 
-
     def close_file(self):
         """Closes the associated data file if any.
 
         Currently it only supports closing the file associated with a dask
         array created from an h5py DataSet (default HyperSpy hdf5 reader).
 
+        """
+        try:
+            self._get_file_handle().close()
+        except AttributeError:
+            _logger.warning("Failed to close lazy Signal file")
+
+    def _get_file_handle(self, warn=True):
+        """Return file handle when possible; currently only hdf5 file are
+        supported.
         """
         arrkey = None
         for key in self.data.dask.keys():
@@ -182,9 +190,12 @@ def close_file(self):
                 break
         if arrkey:
             try:
-                self.data.dask[arrkey].file.close()
-            except AttributeError:
-                _logger.exception("Failed to close lazy Signal file")
+                return self.data.dask[arrkey].file
+            except (AttributeError, ValueError):
+                if warn:
+                    _logger.warning("Failed to retrieve file handle, either "
+                                    "the file is already closed or it is not "
+                                    "a hdf5 file.")
 
     def _get_dask_chunks(self, axis=None, dtype=None):
         """Returns dask chunks.

hyperspy/axes.py

@@ -289,9 +289,10 @@ def __init__(self,
 
         self.events = Events()
         if '_type' in kwargs:
-            if kwargs.get('_type') != self.__class__.__name__:
-                raise ValueError('The passed `_type` of axis is inconsistent '
-                                'with the given attributes')
+            _type = kwargs.get('_type')
+            if _type != self.__class__.__name__:
+                raise ValueError(f'The passed `_type` ({_type}) of axis is '
+                                 'inconsistent with the given attributes.')
         _name = self.__class__.__name__
         self.events.index_changed = Event("""
             Event that triggers when the index of the `{}` changes

hyperspy/io.py

@@ -26,7 +26,7 @@
 from natsort import natsorted
 from inspect import isgenerator
 from pathlib import Path
-from collections import MutableMapping
+from collections.abc import MutableMapping
 
 from hyperspy.drawing.marker import markers_metadata_dict_to_markers
 from hyperspy.exceptions import VisibleDeprecationWarning
@@ -277,6 +277,17 @@ def load(filenames=None,
         acquisition stopped before the end: if True, load only the acquired
         data. If False, fill empty data with zeros. Default is False and this
         default value will change to True in version 2.0.
+    chunks : tuple of integer or None
+        Only for hspy files. Define the chunking used for saving the dataset.
+        If None, calculates chunks for the signal, with preferably at least
+        one chunk per signal space.
+    close_file : bool, optional
+        Only for hspy files. Close the file after writing, default is True.
+    write_dataset : bool, optional
+        Only for hspy files. If True, write the dataset, otherwise, don't
+        write it. Useful to save attributes without having to write the whole
+        dataset. Default is True.
+
 
     Returns
     -------
@@ -516,6 +527,11 @@ def load_with_reader(
             signal.tmp_parameters.folder = folder
             signal.tmp_parameters.filename = filename
             signal.tmp_parameters.extension = extension.replace('.', '')
+            # original_filename and original_file are used to keep track of
+            # where is the file which has been open lazily
+            signal.tmp_parameters.original_folder = folder
+            signal.tmp_parameters.original_filename = filename
+            signal.tmp_parameters.original_extension = extension.replace('.', '')
             # test if binned attribute is still in metadata
             if signal.metadata.has_item('Signal.binned'):
                 for axis in signal.axes_manager.signal_axes: