Merge pull request #3539 from tifuchs/fio_support

LGTM

CI fails due to another issue with `pywin32` with `pyside2`.

doc/source/modules/io/fioh5.rst

@@ -0,0 +1,35 @@
+
+.. currentmodule:: silx.io
+
+:mod:`fioh5`: h5py-like API to FIO file
+----------------------------------------
+
+.. automodule:: silx.io.fioh5
+
+
+Classes
++++++++
+
+- :class:`FioH5`
+- :class:`FioFile`
+
+.. autoclass:: FioH5
+    :members:
+    :show-inheritance:
+    :undoc-members:
+    :inherited-members: name, basename, attrs, h5py_class, parent,
+        get, keys, values, items,
+    :special-members: __getitem__, __len__, __contains__, __enter__, __exit__, __iter__
+    :exclude-members: add_node
+
+.. autoclass:: FioFile
+
+.. autoclass:: silx.io.commonh5.Group
+    :show-inheritance:
+    :undoc-members:
+    :members: name, basename, file, attrs, h5py_class, parent,
+        get, keys, values, items, visit, visititems
+    :special-members: __getitem__, __len__, __contains__, __iter__
+    :exclude-members: add_node
+
+.. autofunction:: is_fiofile

doc/source/modules/io/index.rst

@@ -16,6 +16,7 @@
    specfile.rst
    specfilewrapper.rst
    spech5.rst
+   fioh5.rst
    url.rst
    utils.rst
    h5py_utils.rst

src/silx/app/convert.py

@@ -38,6 +38,7 @@
 
 import silx.io
 from silx.io.specfile import is_specfile
+from silx.io.fioh5 import is_fiofile
 from silx.io import fabioh5
 
 _logger = logging.getLogger(__name__)
@@ -167,6 +168,26 @@ def contains_specfile(filenames):
     return False
 
 
+def contains_fiofile(filenames):
+    """Return True if any file in a list are FIO files.
+    :param List[str] filenames: list of filenames
+    """
+    for fname in filenames:
+        if is_fiofile(fname):
+            return True
+    return False
+
+
+def are_all_fiofile(filenames):
+    """Return True if all files in a list are FIO files.
+    :param List[str] filenames: list of filenames
+    """
+    for fname in filenames:
+        if not is_fiofile(fname):
+            return False
+    return True
+
+
 def main(argv):
     """
     Main function to launch the converter as an application
@@ -178,11 +199,12 @@ def main(argv):
     parser.add_argument(
         'input_files',
         nargs="*",
-        help='Input files (EDF, TIFF, SPEC...). When specifying multiple '
-             'files, you cannot specify both fabio images and SPEC files. '
-             'Multiple SPEC files will simply be concatenated, with one '
-             'entry per scan. Multiple image files will be merged into '
-             'a single entry with a stack of images.')
+        help='Input files (EDF, TIFF, FIO, SPEC...). When specifying '
+             'multiple files, you cannot specify both fabio images '
+             'and SPEC (or FIO) files. Multiple SPEC or FIO files will '
+             'simply be concatenated, with one entry per scan. '
+             'Multiple image files will be merged into a single '
+             'entry with a stack of images.')
     # input_files and --filepattern are mutually exclusive
     parser.add_argument(
         '--file-pattern',
@@ -459,6 +481,7 @@ def check_gzip_compression_opts(value):
 
     if (len(options.input_files) > 1 and
             not contains_specfile(options.input_files) and
+            not contains_fiofile(options.input_files) and
             not options.add_root_group) or options.file_pattern is not None:
         # File series -> stack of images
         input_group = fabioh5.File(file_series=options.input_files)
@@ -474,6 +497,7 @@ def check_gzip_compression_opts(value):
 
     elif len(options.input_files) == 1 or \
             are_all_specfile(options.input_files) or\
+            are_all_fiofile(options.input_files) or\
             options.add_root_group:
         # single file, or spec files
         h5paths_and_groups = []

src/silx/io/convert.py

@@ -25,7 +25,7 @@
 by *silx* into HDF5 file. Currently, SPEC file and fabio images are the
 supported formats.
 
-Read the documentation of :mod:`silx.io.spech5` and :mod:`silx.io.fabioh5` for
+Read the documentation of :mod:`silx.io.spech5`, :mod:`silx.io.fioh5` and :mod:`silx.io.fabioh5` for
 information on the structure of the output HDF5 files.
 
 Text strings are written to the HDF5 datasets as variable-length utf-8.