code style

xsocs/io/XsocsH5.py

@@ -46,9 +46,9 @@ class InvalidEntryError(Exception):
 ScanPositions = namedtuple('ScanPositions',
                            ['motor_0', 'pos_0', 'motor_1', 'pos_1', 'shape'])
 
-MOTORCOLS = {"pix":"adcY",
-             "piy":"adcX",
-             "piz":"adcZ"}
+MOTORCOLS = {"pix": "adcY",
+             "piy": "adcX",
+             "piz": "adcZ"}
 
 
 def _process_entry(method):
@@ -61,7 +61,6 @@ def _process_entry(method):
     return _method
 
 
-
 class XsocsH5(XsocsH5Base):
 
     TOP_ENTRY = 'global'
@@ -93,9 +92,8 @@ class XsocsH5(XsocsH5Base):
             # when there is no attribute NX_class (should return the default
             # None)
             self.__entries = sorted([key for key in h5_file
-                if ('NX_class' in h5_file[key].attrs and
-                    h5_file[key].attrs[
-                        'NX_class'].decode() == 'NXentry')])
+                                     if ('NX_class' in h5_file[key].attrs and
+                                         h5_file[key].attrs['NX_class'].decode() == 'NXentry')])
 
     def entries(self):
         if self.__entries is None:
@@ -152,7 +150,6 @@ class XsocsH5(XsocsH5Base):
         """
         return self.__detector_params(entry, 'image_roi_offset')
 
-
     @_process_entry
     def n_images(self, entry):
         # TODO : make sure that data.ndims = 3
@@ -176,8 +173,9 @@ class XsocsH5(XsocsH5Base):
 
     @_process_entry
     def image_cumul(self, entry, dtype=None):
-        """
-        Returns the summed intensity for each image.
+        """Returns the summed intensity for each image.
+
+        :param str entry:
         :param dtype: dtype passed to the numpy.sum function.
             Default is numpy.double.
         :type dtype: numpy.dtype
@@ -226,12 +224,12 @@ class XsocsH5(XsocsH5Base):
 
     @_process_entry
     def is_regular_grid(self, entry):
-        # TODO
-        """
-        For now grids are always regular
-        :param entry:
-        :return:
+        """For now grids are always regular
+
+        :param str entry:
+        :rtype: bool
         """
+        # TODO
         return True
 
     @_process_entry
@@ -331,8 +329,8 @@ class XsocsH5(XsocsH5Base):
 
 class XsocsH5Writer(XsocsH5):
 
-    def __init__(self, h5_f, mode='a', **kwargs):
-        super(XsocsH5Writer, self).__init__(h5_f, mode=mode, **kwargs)
+    def __init__(self, h5_f, mode='a'):
+        super(XsocsH5Writer, self).__init__(h5_f, mode=mode)
 
     def __set_detector_params(self, entry, params):
         with self._get_file() as h5_file:
@@ -399,7 +397,7 @@ class XsocsH5Writer(XsocsH5):
             grp.attrs['interpretation'] = _np.string_('image')
 
             # setting the nexus classes
-            #entry_grp.attrs['NX_class'] = _np.string_('NXentry')
+            # entry_grp.attrs['NX_class'] = _np.string_('NXentry')
 
             grp = entry_grp.require_group('instrument')
             grp.attrs['NX_class'] = _np.string_('NXinstrument')

xsocs/io/XsocsH5Base.py

@@ -37,6 +37,22 @@ import h5py as _h5py
 import numpy as _np
 
 
+# We have to work around a limitation of the h5py.Group.copy method
+# that fails when a group already exists in the destination file.
+def _copy_obj(name, obj, src_grp=None, dest_grp=None):
+    if isinstance(obj, _h5py.Group):
+        dest_grp.require_group(name)
+    else:
+        src_grp.copy(name,
+                     dest_grp,
+                     name=name,
+                     shallow=False,
+                     expand_soft=True,
+                     expand_external=True,
+                     expand_refs=True,
+                     without_attrs=False)
+
+
 class XsocsH5Base(object):
     # TODO : mechanism to test file type (isValid whatever)
 
@@ -153,11 +169,10 @@ class XsocsH5Base(object):
             dset[()] = value
 
     def _set_array_data(self, path, value):
-        """
-        Sets the given numpy array at the given path in this HDF5 file.
+        """Sets the given numpy array at the given path in this HDF5 file.
+
         :param path:
         :param value:
-        :return:
         """
         with self._get_file() as h5_f:
             dset = h5_f.require_dataset(path,
@@ -169,6 +184,7 @@ class XsocsH5Base(object):
         """
         Creates a dataset as the given path. All extra arguments are passed
         to h5py.DataSet.create_dataset.
+
         :param path:
         :param args:
         :param kwargs:
@@ -187,8 +203,8 @@ class XsocsH5Base(object):
 
     @contextmanager
     def item_context(self, item_path, **kwargs):
-        """
-        Context manager for the image dataset.
+        """Context manager for the image dataset.
+
         WARNING: only to be used as a context manager!
         WARNING: the data set must exist. see also QSpaceH5Writer.init_cube
         """
@@ -202,26 +218,11 @@ class XsocsH5Base(object):
             del item
 
     def copy_group(self, src_h5f, src_path, dest_path):
-        """
-        Recursively copies an object from one HDF5 file to another.
+        """Recursively copies an object from one HDF5 file to another.
+
         Warning : it fails if it finds a conflict with an already existing
         dataset.
         """
-        # We have to work around a limitation of the h5py.Group.copy method
-        # that fails when a group already exists in the destination file.
-        def _copy_obj(name, obj, src_grp=None, dest_grp=None):
-            if isinstance(obj, _h5py.Group):
-                dest_grp.require_group(name)
-            else:
-                src_grp.copy(name,
-                             dest_grp,
-                             name=name,
-                             shallow=False,
-                             expand_soft=True,
-                             expand_external=True,
-                             expand_refs=True,
-                             without_attrs=False)
-
         with _h5py.File(src_h5f, 'r') as src_h5:
             with self._get_file() as h5_file:
                 src_grp = src_h5[src_path]