use h5py_read_dataset where needed

xsocs/io/XsocsH5.py

@@ -39,6 +39,11 @@ import numpy as _np
 from .XsocsH5Base import XsocsH5Base
 from ._utils import str_to_h5_utf8, find_NX_class
 
+try:  # silx >= 0.14
+    from silx.io.utils import h5py_read_dataset
+except ImportError:  # Fall back for silx < 0.14
+    from ..util.silx_io_utils import h5py_read_dataset
+
 
 class InvalidEntryError(Exception):
     pass
@@ -80,7 +85,7 @@ class XsocsH5(XsocsH5Base):
     def title(self, entry):
         with self._get_file() as h5_file:
             path = entry + '/title'
-            return h5_file[path][()]
+            return h5py_read_dataset(h5_file[path], decode_ascii=True)
 
     @_process_entry
     def entry_filename(self, entry):

xsocs/process/merge/KmapMerger.py

@@ -47,6 +47,11 @@ import fabio
 from ...io import XsocsH5
 from ... import config
 
+try:  # silx >= 0.14
+    from silx.io.utils import h5py_read_dataset
+except ImportError:  # Fall back for silx < 0.14
+    from ...util.silx_io_utils import h5py_read_dataset
+
 
 _logger = logging.getLogger(__name__)
 
@@ -397,7 +402,7 @@ class KmapMerger(object):
             except KeyError:
                 raise ValueError('Scan ID {0} not found.'.format(scan_id))
 
-            command = scan['title'][()]
+            command = h5py_read_dataset(scan['title'], decode_ascii=True)
 
         try:
             return parse_scan_command(command)
@@ -426,7 +431,8 @@ class KmapMerger(object):
             calibration = {}
 
             # Parse spec header to find calibration
-            header = scan['instrument/specfile/scan_header'][()]
+            header = h5py_read_dataset(
+                scan['instrument/specfile/scan_header'], decode_ascii=True)
             for line in header:
                 if line.startswith('#UDETCALIB ') or line.startswith('#UMONO '):
                     params = line.split(' ')[1].strip().split(',')
@@ -746,7 +752,8 @@ def _add_edf_data(scan_id,
 
             entry_h5f.copy_group(spec_h5_fn, scan_id, entry)
             with h5py.File(spec_h5_fn, mode='r') as spec_h5:
-                command = spec_h5[scan_id]['title'][()]
+                command = h5py_read_dataset(
+                    spec_h5[scan_id]['title'], decode_ascii=True)
                 command_params = parse_scan_command(command)
 
             entry_h5f.set_scan_params(entry, **command_params)

xsocs/process/merge/KmapSpecParser.py

@@ -39,6 +39,10 @@ from threading import Thread
 
 import h5py
 from silx.io import convert
+try:  # silx >= 0.14
+    from silx.io.utils import h5py_read_dataset
+except ImportError:  # Fall back for silx < 0.14
+    from ...util.silx_io_utils import h5py_read_dataset
 
 
 # regular expression matching the imageFile comment line
@@ -246,7 +250,8 @@ def _spec_get_img_filenames(spec_h5_filename):
         regx = re.compile(_IMAGEFILE_LINE_PATTERN)
 
         for k_scan, v_scan in h5_f.items():
-            header = v_scan['instrument/specfile/scan_header'][()]
+            header = h5py_read_dataset(
+                v_scan['instrument/specfile/scan_header'], decode_ascii=True)
             imgfile_match = [m for line in header
                              if line.startswith('#C imageFile')
                              for m in [regx.match(line.strip())] if m]