File fix_tests_h5py-3.0.patch of Package python-pyUSID

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File fix_tests_h5py-3.0.patch of Package python-pyUSID (Revision 592f6dbdeb0203ebed6d960cc1359358)

Currently displaying revision 592f6dbdeb0203ebed6d960cc1359358 , Show latest

--- a/pyUSID/io/io_utils.py	2020-08-18 08:51:13.000000000 +0700
+++ b/pyUSID/io/io_utils.py	2020-11-05 13:34:24.000000000 +0700
@@ -56,7 +56,8 @@
          'sidpy.io.interface_utils.file_dialog. This copy in pyUSID will'
          'be removed in future release. Please update your import statements',
          FutureWarning)
-    return iut.file_dialog(file_filter=file_filter, caption=caption)
+    #return iut.file_dialog(file_filter=file_filter, caption=caption)
+    return iut.openfile_dialog(file_types=file_filter, caption=caption)
 
 
 def get_time_stamp():
diff -ruN a/pyUSID/io/reg_ref.py b/pyUSID/io/reg_ref.py
--- a/pyUSID/io/reg_ref.py	2020-08-18 08:51:13.000000000 +0700
+++ b/pyUSID/io/reg_ref.py	2020-11-05 13:34:24.000000000 +0700
@@ -7,539 +7,14 @@
 
 from __future__ import division, print_function, absolute_import, unicode_literals
 import sys
-from collections import Iterable
-from warnings import warn
 import h5py
-import numpy as np
+from sidpy.hdf.reg_ref import *
 
 from .hdf_utils import check_if_main
-from .write_utils import clean_string_att
 
 if sys.version_info.major == 3:
     unicode = str
 
-__all__ = ['get_region', 'clean_reg_ref', 'attempt_reg_ref_build', 'copy_reg_ref_reduced_dim',
-           'create_region_reference', 'get_indices_for_region_ref', 'simple_region_ref_copy', 'write_region_references']
-
-
-def get_region(h5_dset, reg_ref_name):
-    """
-    Gets the region in a dataset specified by a region reference
-
-    Parameters
-    ----------
-    h5_dset : h5py.Dataset
-        Dataset containing the region reference
-    reg_ref_name : str / unicode
-        Name of the region reference
-
-    Returns
-    -------
-    value : np.ndarray
-        Data specified by the region reference. Note that a squeeze is applied by default.
-    """
-    warn('pyUSID.io.reg.ref.get_region will be moved to pyNSID in the next '
-         'pyUSID version.', FutureWarning)
-    if not isinstance(reg_ref_name, (str, unicode)):
-        raise TypeError('reg_ref_name should be a string')
-    if not isinstance(h5_dset, h5py.Dataset):
-        raise TypeError('h5_dset should be of type h5py.Dataset')
-    # this may raise KeyErrors. Let it
-    reg_ref = h5_dset.attrs[reg_ref_name]
-    return np.squeeze(h5_dset[reg_ref])
-
-
-def clean_reg_ref(h5_dset, reg_ref_tuple, verbose=False):
-    """
-    Makes sure that the provided instructions for a region reference are indeed valid
-    This method has become necessary since h5py allows the writing of region references larger than the maxshape
-
-    Parameters
-    ----------
-    h5_dset : h5.Dataset instance
-        Dataset to which region references will be added as attributes
-    reg_ref_tuple : list / tuple
-        The slicing information formatted using tuples of slice objects.
-    verbose : Boolean (Optional. Default = False)
-        Whether or not to print status messages
-
-    Returns
-    -------
-    new_reg_refs : tuple
-        Instructions for the corrected region reference
-    """
-    warn('pyUSID.io.reg.ref.clean_reg_ref will be moved to pyNSID in the next '
-         'pyUSID version.', FutureWarning)
-    if not isinstance(reg_ref_tuple, (tuple, dict, slice)):
-        raise TypeError('slices should be a tuple, list, or slice but is instead of type '
-                        '{}'.format(type(reg_ref_tuple)))
-    if not isinstance(h5_dset, h5py.Dataset):
-        raise TypeError('h5_dset should be a h5py.Dataset object but is instead of type '
-                        '{}'.format(type(h5_dset)))
-
-    if isinstance(reg_ref_tuple, slice):
-        # 1D dataset
-        reg_ref_tuple = [reg_ref_tuple]
-
-    if len(reg_ref_tuple) != len(h5_dset.shape):
-        raise ValueError('Region reference tuple did not have the same dimensions as the h5 dataset')
-
-    if verbose:
-        print('Comparing {} with h5 dataset maxshape of {}'.format(reg_ref_tuple, h5_dset.maxshape))
-
-    new_reg_refs = list()
-
-    for reg_ref_slice, max_size in zip(reg_ref_tuple, h5_dset.maxshape):
-        if not isinstance(reg_ref_slice, slice):
-            raise TypeError('slices should be a tuple or a list but is instead of type '
-                            '{}'.format(type(reg_ref_slice)))
-
-        # For now we will simply make sure that the end of the slice is <= maxshape
-        if max_size is not None and reg_ref_slice.stop is not None:
-            reg_ref_slice = slice(reg_ref_slice.start, min(reg_ref_slice.stop, max_size), reg_ref_slice.step)
-
-        new_reg_refs.append(reg_ref_slice)
-
-    if verbose:
-        print('Region reference tuple now: {}'.format(new_reg_refs))
-
-    return tuple(new_reg_refs)
-
-
-def attempt_reg_ref_build(h5_dset, dim_names, verbose=False):
-    """
-
-    Parameters
-    ----------
-    h5_dset : h5.Dataset instance
-        Dataset to which region references need to be added as attributes
-    dim_names : list or tuple
-        List of the names of the region references (typically names of dimensions)
-    verbose : bool, optional. Default=False
-        Whether or not to print debugging statements
-
-    Returns
-    -------
-    labels_dict : dict
-        The slicing information must be formatted using tuples of slice objects.
-        For example {'region_1':(slice(None, None), slice (0,1))}
-    """
-    warn('pyUSID.io.reg.ref.attempt_reg_ref_build will be moved to pyNSID in the next '
-         'pyUSID version.', FutureWarning)
-    if not isinstance(h5_dset, h5py.Dataset):
-        raise TypeError('h5_dset should be a h5py.Dataset object but is instead of type '
-                        '{}.'.format(type(h5_dset)))
-    if not isinstance(dim_names, (list, tuple)):
-        raise TypeError('slices should be a list or tuple but is instead of type '
-                        '{}'.format(type(dim_names)))
-
-    if len(h5_dset.shape) != 2:
-        return dict()
-
-    if not np.all([isinstance(obj, (str, unicode)) for obj in dim_names]):
-        raise TypeError('Unable to automatically generate region references for dataset: {} since one or more names'
-                        ' of the region references was not a string'.format(h5_dset.name))
-
-    labels_dict = dict()
-    if len(dim_names) == h5_dset.shape[0]:
-        if verbose:
-            print('Most likely a spectroscopic indices / values dataset')
-        for dim_index, curr_name in enumerate(dim_names):
-            labels_dict[curr_name] = (slice(dim_index, dim_index + 1), slice(None))
-    elif len(dim_names) == h5_dset.shape[1]:
-        if verbose:
-            print('Most likely a position indices / values dataset')
-        for dim_index, curr_name in enumerate(dim_names):
-            labels_dict[curr_name] = (slice(None), slice(dim_index, dim_index + 1))
-
-    if len(labels_dict) > 0:
-        warn('Attempted to automatically build region reference dictionary for dataset: {}.\n'
-             'Please specify region references as a tuple of slice objects for each attribute'.format(h5_dset.name))
-    else:
-        if verbose:
-            print('Could not build region references since dataset had shape:{} and number of region references is '
-                  '{}'.format(h5_dset.shape, len(dim_names)))
-    return labels_dict
-
-
-def get_indices_for_region_ref(h5_main, ref, return_method='slices'):
-    """
-    Given an hdf5 region reference and the dataset it refers to,
-    return an array of indices within that dataset that
-    correspond to the reference.
-
-    Parameters
-    ----------
-    h5_main : HDF5 Dataset
-        dataset that the reference can be returned from
-    ref : HDF5 Region Reference
-        Region reference object
-    return_method : {'slices', 'corners', 'points'}
-        slices : the reference is return as pairs of slices
-
-        corners : the reference is returned as pairs of corners representing
-        the starting and ending indices of each block
-
-        points : the reference is returns as a list of tuples of points
-
-    Returns
-    -------
-    ref_inds : Numpy Array
-        array of indices in the source dataset that ref accesses
-
-    """
-    warn('pyUSID.io.reg.ref.get_indices_for_region_ref will be moved to pyNSID in the next '
-         'pyUSID version.', FutureWarning)
-    if not isinstance(h5_main, h5py.Dataset):
-        raise TypeError('h5_main should be a h5py.Dataset object')
-    if not isinstance(ref, h5py.RegionReference):
-        raise TypeError('ref should be a h5py.RegionReference object')
-    if return_method is not None:
-        if not isinstance(return_method, (str, unicode)):
-            raise TypeError('return_method should be a string')
-
-    if return_method == 'points':
-        def __corners_to_point_array(start, stop):
-            """
-            Convert a pair of tuples representing two opposite corners of an HDF5 region reference
-            into a list of arrays for each dimension.
-
-            Parameters
-            ----------
-            start : Tuple
-                the starting indices of the region
-            stop : Tuple
-                the final indices of the region
-
-            Returns
-            -------
-            inds : Tuple of arrays
-                the list of points in each dimension
-
-            """
-            ranges = []
-            for i in range(len(start)):
-                if start[i] == stop[i]:
-                    ranges.append([stop[i]])
-                else:
-                    ranges.append(np.arange(start[i], stop[i] + 1, dtype=np.uint))
-            grid = np.meshgrid(*ranges, indexing='ij')
-
-            ref_inds = np.asarray(zip(*(x.flat for x in grid)))
-
-            return ref_inds
-
-        return_func = __corners_to_point_array
-    elif return_method == 'corners':
-        def __corners_to_corners(start, stop):
-            return start, stop
-
-        return_func = __corners_to_corners
-    elif return_method == 'slices':
-        def __corners_to_slices(start, stop):
-            """
-            Convert a pair of tuples representing two opposite corners of an HDF5 region reference
-            into a pair of slices.
-
-            Parameters
-            ----------
-            start : Tuple
-                the starting indices of the region
-            stop : Tuple
-                the final indices of the region
-
-            Returns
-            -------
-            slices : list
-                pair of slices representing the region
-
-            """
-            slices = []
-            for idim in range(len(start)):
-                slices.append(slice(start[idim], stop[idim]))
-
-            return slices
-
-        return_func = __corners_to_slices
-
-    region = h5py.h5r.get_region(ref, h5_main.id)
-    reg_type = region.get_select_type()
-    if reg_type == 2:
-        """
-        Reference is hyperslabs
-        """
-        ref_inds = []
-        for start, end in region.get_select_hyper_blocklist():
-            ref_inds.append(return_func(start, end))
-        ref_inds = np.array(ref_inds).reshape(-1, len(start))
-
-    elif reg_type == 3:
-        """
-        Reference is single block
-        """
-        start, end = region.get_select_bounds()
-
-        ref_inds = return_func(start, end)
-    else:
-        warn('No method currently exists for converting this type of reference.')
-        ref_inds = np.empty(0)
-
-    return ref_inds
-
-
-def copy_reg_ref_reduced_dim(h5_source, h5_target, h5_source_inds, h5_target_inds, key):
-    """
-    Copies a region reference from one dataset to another taking into account that a dimension
-    has been lost from source to target
-
-    Parameters
-    ----------
-    h5_source : HDF5 Dataset
-            source dataset for region reference copy
-    h5_target : HDF5 Dataset
-            target dataset for region reference copy
-    h5_source_inds : HDF5 Dataset
-            indices of each dimension of the h5_source dataset
-    h5_target_inds : HDF5 Dataset
-            indices of each dimension of the h5_target dataset
-    key : String
-            Name of attribute in h5_source that contains
-            the Region Reference to copy
-
-    Returns
-    -------
-    ref_inds : Nx2x2 array of unsigned integers
-            Array containing pairs of points that define
-            the corners of each hyperslab in the region
-            reference
-
-    """
-    warn('pyUSID.io.reg.ref.copy_reg_ref_reduced_dim will be moved to pyNSID in the next '
-         'pyUSID version.', FutureWarning)
-    for param, param_name in zip([h5_source, h5_target, h5_source_inds, h5_target_inds],
-                                 ['h5_source', 'h5_target', 'h5_source_inds', 'h5_target_inds']):
-        if not isinstance(param, h5py.Dataset):
-            raise TypeError(param_name + ' should be a h5py.Dataset object')
-    if not isinstance(key, (str, unicode)):
-        raise TypeError('key should be a string')
-    key = key.strip()
-
-    '''
-    Determine which dimension is missing from the target
-    '''
-    lost_dim = []
-    for dim in h5_source_inds.attrs['labels']:
-        if dim not in h5_target_inds.attrs['labels']:
-            lost_dim.append(np.where(h5_source_inds.attrs['labels'] == dim)[0])
-    ref = h5_source.attrs[key]
-    ref_inds = get_indices_for_region_ref(h5_source, ref, return_method='corners')
-    '''
-    Convert to proper spectroscopic dimensions
-    First is special case for a region reference that spans the entire dataset
-    '''
-    if len(ref_inds.shape) == 2 and all(ref_inds[0] == [0, 0]) and all(ref_inds[1] + 1 == h5_source.shape):
-        ref_inds[1, 1] = h5_target.shape[1] - 1
-        ref_inds = np.expand_dims(ref_inds, 0)
-    else:
-        '''
-    More common case of reference made of hyperslabs
-        '''
-        spec_ind_zeroes = np.where(h5_source_inds[lost_dim] == 0)[1]
-
-        ref_inds = ref_inds.reshape([-1, 2, 2])
-
-        for start, stop in ref_inds[:-1]:
-            start[1] = np.where(start[1] == spec_ind_zeroes)[0]
-            stop[1] = np.where(stop[1] == spec_ind_zeroes - 1)[0] - 1
-
-        ref_inds[-1, 0, 1] = np.where(ref_inds[-1, 0, 1] == spec_ind_zeroes)[0]
-        stop = np.where(ref_inds[-1, 1, 1] == spec_ind_zeroes - 1)[0]
-        if stop.size == 0:
-            stop = len(spec_ind_zeroes)
-        ref_inds[-1, 1, 1] = stop - 1
-    '''
-    Create the new reference from the indices
-    '''
-    h5_target.attrs[key] = create_region_reference(h5_target, ref_inds)
-
-    return ref_inds
-
-
-def create_region_reference(h5_main, ref_inds):
-    """
-    Create a region reference in the destination dataset using an iterable of pairs of indices
-    representing the start and end points of a hyperslab block
-
-    Parameters
-    ----------
-    h5_main : HDF5 dataset
-        dataset the region will be created in
-    ref_inds : Iterable
-        index pairs, [start indices, final indices] for each block in the
-        hyperslab
-
-    Returns
-    -------
-    new_ref : HDF5 Region reference
-        reference in `h5_main` for the blocks of points defined by `ref_inds`
-
-    """
-    warn('pyUSID.io.reg.ref.create_region_reference will be moved to pyNSID '
-         'in the next pyUSID version.', FutureWarning)
-    if not isinstance(h5_main, h5py.Dataset):
-        raise TypeError('h5_main should be a h5py.Dataset object')
-    if not isinstance(ref_inds, Iterable):
-        raise TypeError('ref_inds should be a list or tuple')
-
-    h5_space = h5_main.id.get_space()
-    h5_space.select_none()
-
-    for start, stop in ref_inds:
-        block = stop - start + 1
-        h5_space.select_hyperslab(tuple(start), (1, 1), block=tuple(block), op=1)
-
-    if not h5_space.select_valid():
-        warn('Could not create new region reference.')
-        return None
-    new_ref = h5py.h5r.create(h5_main.id, b'.', h5py.h5r.DATASET_REGION, space=h5_space)
-
-    return new_ref
-
-
-def simple_region_ref_copy(h5_source, h5_target, key):
-    """
-    Copies a region reference from one dataset to another
-    without alteration
-
-    Parameters
-    ----------
-    h5_source : HDF5 Dataset
-            source dataset for region reference copy
-    h5_target : HDF5 Dataset
-            target dataset for region reference copy
-    key : String
-            Name of attribute in h5_source that contains
-            the Region Reference to copy
-
-    Returns
-    -------
-    ref_inds : Nx2x2 array of unsigned integers
-            Array containing pairs of points that define
-            the corners of each hyperslab in the region
-            reference
-
-    """
-    warn('pyUSID.io.reg.ref.simple_region_ref_copy will be moved to pyNSID '
-         'in the next pyUSID version.', FutureWarning)
-    for param, param_name in zip([h5_source, h5_target], ['h5_source', 'h5_target']):
-        if not isinstance(param, h5py.Dataset):
-            raise TypeError(param_name + ' should be a h5py.Dataset object')
-    if not isinstance(key, (str, unicode)):
-        raise TypeError('key should be a string')
-
-    ref = h5_source.attrs[key]
-    ref_inds = get_indices_for_region_ref(h5_source, ref, return_method='corners')
-    ref_inds = ref_inds.reshape([-1, 2, 2])
-    ref_inds[:, 1, 1] = h5_target.shape[1] - 1
-    target_ref = create_region_reference(h5_target, ref_inds)
-    h5_target.attrs[key] = target_ref
-    return ref_inds
-
-
-def copy_all_region_refs(h5_source, h5_target):
-    """
-    Copies only region references from the source dataset to the target dataset
-
-    Parameters
-    ----------
-    h5_source : h5py.Dataset
-        Dataset from which to copy region references
-    h5_target : h5py.Dataset
-        Dataset to which to copy region references to
-
-    """
-    warn('pyUSID.io.reg.ref.copy_all_region_refs will be moved to pyNSID '
-         'in the next pyUSID version.', FutureWarning)
-    if not isinstance(h5_source, h5py.Dataset):
-        raise TypeError("'h5_source' should be a h5py.Dataset object")
-    if not isinstance(h5_target, h5py.Dataset):
-        raise TypeError("'h5_target' should be a h5py.Dataset object")
-    for key in h5_source.attrs.keys():
-        if not isinstance(h5_source.attrs[key], h5py.RegionReference):
-            continue
-        simple_region_ref_copy(h5_source, h5_target, key)
-
-
-def write_region_references(h5_dset, reg_ref_dict, add_labels_attr=True, verbose=False):
-    """
-    Creates attributes of a h5py.Dataset that refer to regions in the dataset
-
-    Parameters
-    ----------
-    h5_dset : h5.Dataset instance
-        Dataset to which region references will be added as attributes
-    reg_ref_dict : dict
-        The slicing information must be formatted using tuples of slice objects.
-        For example {'region_1':(slice(None, None), slice (0,1))}
-    add_labels_attr : bool, optional, default = True
-        Whether or not to write an attribute named 'labels' with the
-    verbose : Boolean (Optional. Default = False)
-        Whether or not to print status messages
-    """
-    warn('pyUSID.io.reg.ref.write_region_references will be moved to pyNSID '
-         'in the next pyUSID version.', FutureWarning)
-    if not isinstance(reg_ref_dict, dict):
-        raise TypeError('slices should be a dictionary but is instead of type '
-                        '{}'.format(type(reg_ref_dict)))
-    if not isinstance(h5_dset, h5py.Dataset):
-        raise TypeError('h5_dset should be a h5py.Dataset object but is instead of type '
-                        '{}'.format(type(h5_dset)))
-
-    if verbose:
-        print('Starting to write Region References to Dataset', h5_dset.name, 'of shape:', h5_dset.shape)
-    for reg_ref_name, reg_ref_tuple in reg_ref_dict.items():
-        if verbose:
-            print('About to write region reference:', reg_ref_name, ':', reg_ref_tuple)
-
-        reg_ref_tuple = clean_reg_ref(h5_dset, reg_ref_tuple, verbose=verbose)
-
-        h5_dset.attrs[reg_ref_name] = h5_dset.regionref[reg_ref_tuple]
-
-        if verbose:
-            print('Wrote Region Reference:%s' % reg_ref_name)
-
-    '''
-    Next, write these label names as an attribute called labels
-    Now make an attribute called 'labels' that is a list of strings 
-    First ascertain the dimension of the slicing:
-    '''
-    if add_labels_attr:
-        found_dim = False
-        dimen_index = None
-
-        for key, val in reg_ref_dict.items():
-            if not isinstance(val, (list, tuple)):
-                reg_ref_dict[key] = [val]
-
-        for dimen_index, slice_obj in enumerate(list(reg_ref_dict.values())[0]):
-            # We make the assumption that checking the start is sufficient
-            if slice_obj.start is not None:
-                found_dim = True
-                break
-        if found_dim:
-            headers = [None] * len(reg_ref_dict)  # The list that will hold all the names
-            for col_name in reg_ref_dict.keys():
-                headers[reg_ref_dict[col_name][dimen_index].start] = col_name
-            if verbose:
-                print('Writing header attributes: {}'.format('labels'))
-            # Now write the list of col / row names as an attribute:
-            h5_dset.attrs['labels'] = clean_string_att(headers)
-        else:
-            warn('Unable to write region references for %s' % (h5_dset.name.split('/')[-1]))
-
-        if verbose:
-            print('Wrote Region References of Dataset %s' % (h5_dset.name.split('/')[-1]))
-
 
 def copy_region_refs(h5_source, h5_target):
     """
@@ -557,8 +32,6 @@
     '''
     Check both h5_source and h5_target to ensure that are Main
     '''
-    warn('pyUSID.io.reg.ref.copy_region_refs will be moved to pyNSID '
-         'in the next pyUSID version.', FutureWarning)
     are_main = all([check_if_main(h5_source), check_if_main(h5_target)])
     if not all([isinstance(h5_source, h5py.Dataset), isinstance(h5_target, h5py.Dataset)]):
         raise TypeError('Inputs to copy_region_refs must be HDF5 Datasets')
diff -ruN a/pyUSID/io/usi_data.py b/pyUSID/io/usi_data.py
+++ b/pyUSID/io/usi_data.py	2020-11-05 13:34:24.000000000 +0700
@@ -20,14 +20,13 @@
 from sidpy.base.string_utils import validate_single_string_arg, \
     validate_list_of_strings
 from sidpy.base.num_utils import contains_integers, get_exponent
-from sidpy.hdf.hdf_utils import get_attr, lazy_load_array
+from sidpy.hdf.hdf_utils import get_attr, lazy_load_array, copy_attributes
 from sidpy.hdf.dtype_utils import flatten_to_real, is_complex_dtype
 from sidpy.viz.jupyter_utils import simple_ndim_visualizer
 from sidpy.viz.plot_utils import plot_map, get_plot_grid_size
 
 from .hdf_utils import check_if_main, create_results_group, write_reduced_anc_dsets, link_as_main, \
-    get_dimensionality, get_sort_order, get_unit_values, reshape_to_n_dims, write_main_dataset, reshape_from_n_dims, \
-    copy_attributes
+    get_dimensionality, get_sort_order, get_unit_values, reshape_to_n_dims, write_main_dataset, reshape_from_n_dims
 from .write_utils import Dimension
 
 if sys.version_info.major == 3:
@@ -489,8 +488,8 @@
         if verbose:
             print('data_slice of shape: {} after squeezing'.format(data_slice.shape))
 
-        pos_inds = self.h5_pos_inds[pos_slice, :]
-        spec_inds = self.h5_spec_inds[:, spec_slice].reshape([self.h5_spec_inds.shape[0], -1])
+        pos_inds = self.h5_pos_inds[pos_slice.ravel(), :]
+        spec_inds = self.h5_spec_inds[:, spec_slice.ravel()].reshape([self.h5_spec_inds.shape[0], -1])
         if verbose:
             print('Sliced position indices:')
             print(pos_inds)
@@ -1255,7 +1254,7 @@
 
         """
         Create the spectral and position labels for the dataset in string form then
-        create the position value array in string form, right-strip the last comma from the 
+        create the position value array in string form, right-strip the last comma from the
         string to deliver the correct number of values, append all of the labels and values together,
         save the data and header to a temporary csv output
         """
--- a/pyUSID/io/write_utils.py	2020-08-18 08:51:13.000000000 +0700
+++ b/pyUSID/io/write_utils.py	2020-11-05 13:34:24.000000000 +0700
@@ -13,10 +13,10 @@
 from enum import Enum
 import numpy as np
 from sidpy.base.num_utils import contains_integers
-from sidpy.base.string_utils import validate_list_of_strings, \
-    validate_single_string_arg
+from sidpy.base.string_utils import validate_list_of_strings
 from sidpy.base import num_utils as nut
 from sidpy.base import string_utils as sut
+from sidpy.sid import Dimension as SIDimension
 
 __all__ = ['clean_string_att', 'get_aux_dset_slicing', 'make_indices_matrix', 'INDICES_DTYPE', 'VALUES_DTYPE', 'get_slope',
            'Dimension', 'build_ind_val_matrices', 'calc_chunks', 'create_spec_inds_from_vals', 'validate_dimensions', 'DimType',
@@ -53,12 +53,13 @@
         return self.value == other.value
 
 
-class Dimension(object):
+class Dimension(SIDimension):
     """
     ..autoclass::Dimension
     """
 
-    def __init__(self, name, units, values, mode=DimType.DEFAULT):
+    def __new__(cls, name, units, values, quantity='generic',
+                dimension_type='unknown', mode=DimType.DEFAULT):
         """
         Simple object that describes a dimension in a dataset by its name, units, and values
 
@@ -78,45 +79,68 @@
             DimType.INCOMPLETE - Data not present for all combinations of values in this dimension and all other
                 dimensions. Examples include spiral scans, sparse sampling, aborted measurements
             DimType.DEPENDENT - Values in this dimension were varied as a function of another (independent) dimension.
+        quantity : str or unicode
+            Physical quantity such as Length
+        dimension_type : str or sidpy.DimensionTypes
+            Type of dimension. such as spectral, spatial, etc.
         """
-        name = validate_single_string_arg(name, 'name')
-
-        if not isinstance(units, (str, unicode)):
-            raise TypeError('units should be a string')
-        units = units.strip()
-
         if isinstance(values, int):
             if values < 1:
-                raise ValueError('values should at least be specified as a positive integer')
-            values = np.arange(values)
-        if not isinstance(values, (np.ndarray, list, tuple)):
-            raise TypeError('values should be array-like')
-
-        if not isinstance(mode, DimType):
-            raise TypeError('mode must be of type pyUSID.DimType. Provided object was of type: {}'.format(type(mode)))
-
-        self.name = name
-        self.units = units
-        self.values = values
+                raise ValueError('values must be a whole number. {} provided'
+                                 ''.format(values))
+        self = SIDimension.__new__(cls, values, name=name, quantity=quantity,
+                                   units=units, dimension_type=dimension_type)
         self.mode = mode
+        return self
+
+    @property
+    def mode(self):
+        return self._mode
+
+    @mode.setter
+    def mode(self, value):
+        if not isinstance(value, DimType):
+            raise TypeError('mode must be of type pyUSID.DimType. Provided '
+                            'object was of type: {}'.format(type(value)))
+        self._mode = value
+
+    @property
+    def units(self):
+        return self._units
+
+    # pyUSID allows empty values for units unlike sid.Dimension
+    @units.setter
+    def units(self, value):
+        if not isinstance(value, (str, unicode)):
+            raise TypeError('units should be a string')
+        self._units = value.strip()
 
     def __repr__(self):
-        return '{} ({}) mode:{} : {}'.format(self.name, self.units, self.mode, self.values)
+        return '{}: {} ({}) mode:{} : {}' \
+               ''.format(self.name, self.quantity, self.units, self.mode,
+                         self.values)
+
+    def __str__(self):
+        return '{}: {} ({}) mode:{} : {}' \
+               ''.format(self.name, self.quantity, self.units, self.mode,
+                         self.values)
 
     def __eq__(self, other):
-        if isinstance(other, Dimension):
-            if self.name != other.name:
-                return False
-            if self.units != other.units:
-                return False
-            if self.mode != other.mode:
-                return False
-            if len(self.values) != len(other.values):
-                return False
-            if not np.allclose(self.values, other.values):
-                return False
-
-        return True
+        # Since __eq__ has not been implemented in sidpy.Dimension:
+        if not isinstance(other, Dimension):
+            raise TypeError('Cannot compare against object type: {}'
+                            ''.format(type(other)))
+        if self._name != other._name:
+            return False
+        if self._quantity != other._quantity:
+            return False
+        if self.mode != other._mode:
+            return False
+        if self._units != other._units:
+            return False
+        if len(self) != len(other):
+            return False
+        return np.allclose(self, other)
 
 
 def validate_dimensions(dimensions, dim_type='Position'):
@@ -191,7 +215,7 @@
 
     Parameters
     ------------
-    num_steps : List / numpy array
+    num_steps : List / numpy array / int
         Number of steps in each spatial or spectral dimension
         Note that the axes must be ordered from fastest varying to slowest varying
     is_position : bool, optional, default = True
@@ -203,10 +227,19 @@
     indices_matrix : 2D unsigned int numpy array
         arranged as [steps, spatial dimension]
     """
+    if isinstance(num_steps, int):
+        num_steps = [num_steps]
     if not isinstance(num_steps, (tuple, list, np.ndarray)):
         raise TypeError('num_steps should be a list / tuple / numpy array')
-    if not contains_integers(num_steps, min_val=1 + int(len(num_steps) > 0)):
-        raise ValueError('num_steps should contain integers greater than equal to 1 (empty dimension) or 2')
+    if isinstance(num_steps, np.ndarray) and num_steps.ndim < 1:
+        num_steps = np.expand_dims(num_steps, 0)
+    if len(num_steps) == 0:
+        raise ValueError('num_steps should not be an empty array or list')
+    if len(num_steps) == 1 and num_steps[0] == 1:
+        num_steps = [1]
+    elif not contains_integers(num_steps, min_val=1 + int(len(num_steps) > 0)):
+        raise ValueError('num_steps should contain integers greater than equal'
+                         ' to 1 (empty dimension) or 2')
 
     num_steps = np.array(num_steps)
     spat_dims = max(1, len(np.where(num_steps > 1)[0]))
+++ b/setup.py	2020-11-05 13:34:24.000000000 +0700
@@ -12,21 +12,14 @@
 
 # TODO: Move requirements to requirements.txt
 requirements = ['numpy>=1.10',
-                'toolz', # dask installation failing without this
-                'cytoolz', # dask installation failing without this
+                'toolz',  # dask installation failing without this
+                'cytoolz',  # dask installation failing without this
                 'dask>=0.10',
                 'h5py>=2.6.0',
-                'pillow',
-                'matplotlib>=2.0.0',
-
+                'pillow',  # Remove once ImageReader is in ScopeReaders
                 'psutil',
                 'six',
-                'joblib>=0.11.0',
-
-                'ipywidgets>=5.2.2',
-                'ipython>=5.1.0,<6;python_version<"3.3"',  # IPython 6.0+ does not support Python 2.6, 2.7, 3.0, 3.1, or 3.2
-                'ipython>=6.0;python_version>="3.3"',  # Beginning with IPython 6.0, Python 3.3 and above is required.
-                'sidpy>=0.0.1'
+                'sidpy>=0.0.2'
                 ]
 
 setup(
@@ -42,9 +35,7 @@
         'Natural Language :: English',
         'Operating System :: OS Independent',
         'Programming Language :: Cython',
-        'Programming Language :: Python :: 2.7',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.4',
         'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
@@ -69,7 +60,6 @@
     # https://setuptools.readthedocs.io/en/latest/setuptools.html#declaring-dependencies
     extras_require={
         'MPI':  ["mpi4py"],
-        'File_Widgets': ['pyqt5'],
     },
     # If there are data files included in your packages that need to be
     # installed, specify them here.  If using Python 2.6 or less, then these
--- a/tests/io/hdf_utils/test_simple.py	2020-08-18 08:51:13.000000000 +0700
+++ b/tests/io/hdf_utils/test_simple.py	2020-11-05 13:34:24.000000000 +0700
@@ -542,25 +542,6 @@
         os.remove(duplicate_path)
 
 
-class TestFindDataset(TestSimple):
-
-    def test_legal(self):
-        with h5py.File(data_utils.std_beps_path, mode='r') as h5_f:
-            h5_group = h5_f['/Raw_Measurement/']
-            with self.assertRaises(TypeError):
-                ret_val = hdf_utils.find_dataset(h5_group, np.arange(4))
-
-    def test_invalid_type_dset(self):
-        with self.assertRaises(TypeError):
-            _ = hdf_utils.find_dataset(4.324, 'Spectroscopic_Indices')
-
-    def test_illegal(self):
-        with h5py.File(data_utils.std_beps_path, mode='r') as h5_f:
-            h5_group = h5_f['/Raw_Measurement/']
-            ret_val = hdf_utils.find_dataset(h5_group, 'Does_Not_Exist')
-            self.assertEqual(len(ret_val), 0)
-
-
 class TestFindResultsGroup(TestSimple):
 
     def test_legal(self):
@@ -1100,60 +1081,6 @@
         self.helper_test(False)
 
 
-class TestCopyAttributes(unittest.TestCase):
-
-    def test_not_h5_dset(self):
-        temp_path = 'copy_attributes.h5'
-        with h5py.File(temp_path, mode='w') as h5_f:
-            h5_grp = h5_f.create_group('Blah')
-            with self.assertRaises(TypeError):
-                hdf_utils.copy_attributes(h5_grp, np.arange(4))
-
-            with self.assertRaises(TypeError):
-                hdf_utils.copy_attributes(np.arange(4), h5_grp)
-        os.remove(temp_path)
-
-    def test_file_dset(self):
-        file_path = 'test.h5'
-        easy_attrs = {'1_string': 'Current', '1_number': 35.23}
-        also_easy_attr = {'N_numbers': [1, -53.6, 0.000463]}
-        hard_attrs = {'N_strings': np.array(['a', 'bc', 'def'], dtype='S')}
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_f.attrs.update(easy_attrs)
-            h5_f.attrs.update(also_easy_attr)
-            h5_f.attrs.update(hard_attrs)
-            h5_dset = h5_f.create_dataset('Main_01', data=[1, 2, 3])
-            hdf_utils.copy_attributes(h5_f, h5_dset)
-            for key, val in easy_attrs.items():
-                self.assertEqual(val, h5_dset.attrs[key])
-            for key, val in also_easy_attr.items():
-                self.assertTrue(np.all([x == y for x, y in zip(val, h5_dset.attrs[key])]))
-            for key, val in hard_attrs.items():
-                self.assertTrue(np.all([x == y for x, y in zip(val, h5_dset.attrs[key])]))
-        os.remove(file_path)
-
-    def test_group_dset(self):
-        file_path = 'test.h5'
-        easy_attrs = {'1_string': 'Current', '1_number': 35.23}
-        also_easy_attr = {'N_numbers': [1, -53.6, 0.000463]}
-        hard_attrs = {'N_strings': np.array(['a', 'bc', 'def'], dtype='S')}
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_group = h5_f.create_group('Group')
-            h5_group.attrs.update(easy_attrs)
-            h5_group.attrs.update(also_easy_attr)
-            h5_group.attrs.update(hard_attrs)
-            h5_dset = h5_f.create_dataset('Main_01', data=[1, 2, 3])
-            hdf_utils.copy_attributes(h5_group, h5_dset)
-            for key, val in easy_attrs.items():
-                self.assertEqual(val, h5_dset.attrs[key])
-            for key, val in also_easy_attr.items():
-                self.assertTrue(np.all([x == y for x, y in zip(val, h5_dset.attrs[key])]))
-            for key, val in hard_attrs.items():
-                self.assertTrue(np.all([x == y for x, y in zip(val, h5_dset.attrs[key])]))
-        os.remove(file_path)
-
 class TestCopyMainAttributes(unittest.TestCase):
 
     def test_valid(self):
@@ -1630,278 +1557,6 @@
             func([1, 2, 5], Dimension('a', 'b', 5))
 
 
-class TestCopyLinkedObjects(TestSimple):
-
-    def validate_copied_dataset(self, h5_f_new, h5_dest, dset_new_name,
-                                dset_data, dset_attrs):
-        self.assertTrue(dset_new_name in h5_f_new.keys())
-        h5_anc_dest = h5_f_new[dset_new_name]
-        self.assertIsInstance(h5_anc_dest, h5py.Dataset)
-        self.assertTrue(np.allclose(dset_data, h5_anc_dest[()]))
-        self.assertEqual(len(dset_attrs),
-                         len(h5_anc_dest.attrs.keys()))
-        for key, val in dset_attrs.items():
-            self.assertEqual(val, h5_anc_dest.attrs[key])
-        self.assertTrue(dset_new_name in h5_dest.attrs.keys())
-        self.assertEqual(h5_f_new[h5_dest.attrs[dset_new_name]],
-                         h5_anc_dest)
-
-    def base_two_dsets_simple_attrs(self, exist_dset_same_data=False,
-                                    exist_dset_diff_data_shape=False,
-                                    exist_dset_diff_data=False,
-                                    exist_grp_inst_dset=False):
-        file_path = 'test.h5'
-        new_path = 'new.h5'
-        data_utils.delete_existing_file(file_path)
-        data_utils.delete_existing_file(new_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_source = h5_f.create_dataset('Main', data=[1, 2, 3])
-            simple_attrs = {'quantity': 'blah', 'units': 'nA'}
-            h5_source.attrs.update(simple_attrs)
-
-            h5_anc_1 = h5_f.create_dataset('Anc_1', data=[4, 5, 6])
-            anc_1_attrs = {'a': 1, 'b': 3}
-            h5_anc_1.attrs.update(anc_1_attrs)
-
-            h5_anc_2 = h5_f.create_dataset('Anc_2', data=[7, 8, 9])
-            anc_2_attrs = {'p': 78, 'j': 8}
-            h5_anc_2.attrs.update(anc_2_attrs)
-
-            h5_source.attrs['Pos_Inds'] = h5_anc_1.ref
-            h5_source.attrs['Pos_Vals'] = h5_anc_2.ref
-
-            with h5py.File(new_path, mode='w') as h5_f_new:
-                h5_dest = h5_f_new.create_dataset('Duplicate', data=[1, 2, 3])
-
-                if exist_dset_same_data:
-                    _ = h5_f_new.create_dataset('Pos_Vals', data=[7, 8, 9])
-                elif exist_dset_diff_data:
-                    _ = h5_f_new.create_dataset('Pos_Vals', data=[8, 1, 3])
-                elif exist_dset_diff_data_shape:
-                    _ = h5_f_new.create_dataset('Pos_Vals',
-                                                data=np.random.rand(5, 3))
-                elif exist_grp_inst_dset:
-                    _ = h5_f_new.create_group('Pos_Vals')
-
-                if sys.version_info.major == 3 and exist_dset_same_data:
-                    with self.assertWarns(UserWarning):
-                        hdf_utils.copy_linked_objects(h5_source, h5_dest,
-                                                      verbose=False)
-                elif exist_dset_diff_data or exist_dset_diff_data_shape:
-                    with self.assertRaises(ValueError):
-                        hdf_utils.copy_linked_objects(h5_source, h5_dest,
-                                                      verbose=False)
-                elif exist_grp_inst_dset:
-                    with self.assertRaises(TypeError):
-                        hdf_utils.copy_linked_objects(h5_source, h5_dest,
-                                                      verbose=False)
-                else:
-                    hdf_utils.copy_linked_objects(h5_source, h5_dest,
-                                                  verbose=False)
-
-                if not exist_dset_diff_data_shape and not exist_dset_diff_data\
-                        and not exist_grp_inst_dset:
-                    self.assertEqual(len(h5_f_new.keys()), 3)
-
-                    self.validate_copied_dataset(h5_f_new, h5_dest, 'Pos_Inds',
-                                                 h5_anc_1[()], anc_1_attrs)
-
-                    self.validate_copied_dataset(h5_f_new, h5_dest, 'Pos_Vals',
-                                                 h5_anc_2[()], anc_2_attrs)
-
-        os.remove(file_path)
-        os.remove(new_path)
-
-    def test_two_dsets_simple_attrs_empty_dest(self):
-        self.base_two_dsets_simple_attrs(exist_dset_same_data=False,
-                                         exist_dset_diff_data_shape=False,
-                                         exist_dset_diff_data=False,
-                                         exist_grp_inst_dset=False)
-
-    def test_existing_anc_dset_same_data_no_attrs(self):
-        self.base_two_dsets_simple_attrs(exist_dset_same_data=True,
-                                         exist_dset_diff_data_shape=False,
-                                         exist_dset_diff_data=False,
-                                         exist_grp_inst_dset=False)
-
-    def test_existing_anc_dset_diff_data(self):
-        self.base_two_dsets_simple_attrs(exist_dset_same_data=False,
-                                         exist_dset_diff_data_shape=False,
-                                         exist_dset_diff_data=True,
-                                         exist_grp_inst_dset=False)
-
-    def test_existing_anc_dset_diff_data_shape(self):
-        self.base_two_dsets_simple_attrs(exist_dset_same_data=False,
-                                         exist_dset_diff_data_shape=True,
-                                         exist_dset_diff_data=False,
-                                         exist_grp_inst_dset=False)
-
-    def test_existing_group_instead_of_det(self):
-        self.base_two_dsets_simple_attrs(exist_dset_same_data=False,
-                                         exist_dset_diff_data_shape=False,
-                                         exist_dset_diff_data=False,
-                                         exist_grp_inst_dset=True)
-
-    def test_target_group(self):
-        file_path = 'test.h5'
-        new_path = 'new.h5'
-        data_utils.delete_existing_file(file_path)
-        data_utils.delete_existing_file(new_path)
-        
-        with h5py.File(file_path, mode='w') as h5_f:
-            
-            h5_source = h5_f.create_dataset('Main', data=[1, 2, 3])
-            simple_attrs = {'quantity': 'blah', 'units': 'nA'}
-            h5_source.attrs.update(simple_attrs)
-
-            h5_anc_1 = h5_f.create_dataset('Anc_1', data=[4, 5, 6])
-            anc_1_attrs = {'a': 1, 'b': 3}
-            h5_anc_1.attrs.update(anc_1_attrs)
-
-            h5_anc_2 = h5_f.create_dataset('Anc_2', data=[7, 8, 9])
-            anc_2_attrs = {'p': 78, 'j': 8}
-            h5_anc_2.attrs.update(anc_2_attrs)
-
-            h5_source.attrs['Pos_Inds'] = h5_anc_1.ref
-            h5_source.attrs['Pos_Vals'] = h5_anc_2.ref
-            
-            with h5py.File(new_path, mode='w') as h5_f_new:
-                h5_dest_gp = h5_f_new.create_group('Target')
-                
-                hdf_utils.copy_linked_objects(h5_source, h5_dest_gp, verbose=False)
-          
-                self.assertTrue('Pos_Inds' in h5_dest_gp)
-                self.assertTrue('Pos_Vals' in h5_dest_gp)
-                
-                self.assertFalse('Pos_Inds' in h5_dest_gp.parent)
-                self.assertFalse('Pos_Vals' in h5_dest_gp.parent)
-          
-        os.remove(file_path)
-        os.remove(new_path)
-
-class TestCopyDataset(TestSimple):
-
-    def validate_copied_dataset(self, h5_f_new, dset_new_name,
-                                dset_data, dset_attrs):
-        self.assertTrue(dset_new_name in h5_f_new.keys())
-        h5_anc_dest = h5_f_new[dset_new_name]
-        self.assertIsInstance(h5_anc_dest, h5py.Dataset)
-        self.assertTrue(np.allclose(dset_data, h5_anc_dest[()]))
-        self.assertEqual(len(dset_attrs),
-                         len(h5_anc_dest.attrs.keys()))
-        for key, val in dset_attrs.items():
-            self.assertEqual(val, h5_anc_dest.attrs[key])
-
-    def base_test(self, exist_dset_same_data=False, use_alias=False,
-                  exist_dset_diff_data_shape=False, exist_dset_diff_data=False,
-                  exist_grp_inst_dset=False):
-        file_path = 'test.h5'
-        new_path = 'new.h5'
-        data_utils.delete_existing_file(file_path)
-        data_utils.delete_existing_file(new_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_source = h5_f.create_dataset('Original', data=[1, 2, 3])
-            simple_attrs = {'quantity': 'blah', 'units': 'nA'}
-            h5_source.attrs.update(simple_attrs)
-
-            with h5py.File(new_path, mode='w') as h5_f_new:
-
-                if use_alias:
-                    alias = 'Duplicate'
-                else:
-                    alias = 'Original'
-
-                if exist_dset_same_data:
-                    _ = h5_f_new.create_dataset(alias, data=[1, 2, 3])
-                elif exist_dset_diff_data:
-                    _ = h5_f_new.create_dataset(alias, data=[8, 1, 3])
-                elif exist_dset_diff_data_shape:
-                    _ = h5_f_new.create_dataset(alias,
-                                                data=np.random.rand(5, 3))
-                elif exist_grp_inst_dset:
-                    _ = h5_f_new.create_group(alias)
-
-                if use_alias:
-                    al_arg = alias
-                else:
-                    al_arg = None
-
-                func = hdf_utils.copy_dataset
-                args = [h5_source, h5_f_new]
-                kwargs = {'alias': al_arg, 'verbose': False}
-
-                if exist_dset_diff_data or exist_dset_diff_data_shape:
-                    with self.assertRaises(ValueError):
-                        _ = func(*args, **kwargs)
-                elif exist_grp_inst_dset:
-                    with self.assertRaises(TypeError):
-                        _ = func(*args, **kwargs)
-                else:
-                    _ = func(*args, **kwargs)
-
-                if not exist_dset_diff_data_shape and not exist_dset_diff_data\
-                        and not exist_grp_inst_dset:
-                    self.assertEqual(len(h5_f_new.keys()), 1)
-                    self.validate_copied_dataset(h5_f_new, alias,
-                                                 h5_source[()], simple_attrs)
-
-        os.remove(file_path)
-        os.remove(new_path)
-
-    def test_exact_copy(self):
-        self.base_test(exist_dset_same_data=False, use_alias=False,
-                       exist_dset_diff_data_shape=False,
-                       exist_dset_diff_data=False, exist_grp_inst_dset=False)
-
-    def test_copy_w_alias(self):
-        self.base_test(exist_dset_same_data=False, use_alias=True,
-                       exist_dset_diff_data_shape=False,
-                       exist_dset_diff_data=False, exist_grp_inst_dset=False)
-
-    def test_existing_group_same_name(self):
-        self.base_test(exist_dset_same_data=False, use_alias=False,
-                       exist_dset_diff_data_shape=False,
-                       exist_dset_diff_data=False, exist_grp_inst_dset=True)
-
-    def test_existing_dset_same_name_data(self):
-        self.base_test(exist_dset_same_data=True, use_alias=False,
-                       exist_dset_diff_data_shape=False,
-                       exist_dset_diff_data=False, exist_grp_inst_dset=False)
-
-    def test_existing_dset_same_name_diff_data_shape(self):
-        self.base_test(exist_dset_same_data=False, use_alias=False,
-                       exist_dset_diff_data_shape=True,
-                       exist_dset_diff_data=False, exist_grp_inst_dset=False)
-
-    def test_existing_dset_same_name_diff_data(self):
-        self.base_test(exist_dset_same_data=False, use_alias=False,
-                       exist_dset_diff_data_shape=False,
-                       exist_dset_diff_data=True, exist_grp_inst_dset=False)
-
-"""
-    def test_linking_main_plus_other_dsets(self):
-        file_path = 'check_and_link_ancillary.h5'
-        data_utils.delete_existing_file(file_path)
-        shutil.copy(data_utils.std_beps_path, file_path)
-        with h5py.File(file_path, mode='r+') as h5_f:
-            h5_grp = h5_f['Raw_Measurement']
-            h5_dset_source = h5_grp['Ancillary']
-            h5_main = h5_grp['source_main']
-            att_names = ['Spectroscopic_Values', 'Position_Indices', 'X', 'Y']
-            expected = [h5_grp[name] for name in att_names]
-            hdf_utils.check_and_link_ancillary(h5_dset_source, att_names,
-                                               h5_main=h5_main,
-                                               anc_refs=expected[2:])
-            for key, val in h5_dset_source.attrs.items():
-                print(key, val)
-            self.assertEqual(len(h5_dset_source.attrs.keys()), len(att_names))
-            self.assertEqual(set(att_names), set(h5_dset_source.attrs.keys()))
-            for name, exp_val in zip(att_names, expected):
-                actual = h5_dset_source.attrs[name]
-                self.assertIsInstance(actual, h5py.Reference)
-                self.assertEqual(h5_f[actual], exp_val)
-        os.remove(file_path)
-"""
 class TestValidateAncDsetAttrs(TestSimple):
 
     def test_blah(self):
diff -ruN a/tests/io/test_reg_ref.py b/tests/io/test_reg_ref.py
--- a/tests/io/test_reg_ref.py	2020-08-18 08:51:13.000000000 +0700
+++ b/tests/io/test_reg_ref.py	2020-11-05 13:34:24.000000000 +0700
@@ -24,326 +24,16 @@
 
 class TestRegRef(unittest.TestCase):
 
-    @staticmethod
-    def __delete_existing_file(file_path):
-        if os.path.exists(file_path):
-            os.remove(file_path)
-
-    @staticmethod
-    def __write_safe_attrs(h5_object, attrs):
-        for key, val in attrs.items():
-            h5_object.attrs[key] = val
-
-    @staticmethod
-    def __write_string_list_as_attr(h5_object, attrs):
-        for key, val in attrs.items():
-            h5_object.attrs[key] = np.array(val, dtype='S')
-
-    @staticmethod
-    def __write_aux_reg_ref(h5_dset, labels, is_spec=True):
-        for index, reg_ref_name in enumerate(labels):
-            if is_spec:
-                reg_ref_tuple = (slice(index, index + 1), slice(None))
-            else:
-                reg_ref_tuple = (slice(None), slice(index, index + 1))
-            h5_dset.attrs[reg_ref_name] = h5_dset.regionref[reg_ref_tuple]
-
-    @staticmethod
-    def __write_main_reg_refs(h5_dset, attrs):
-        for reg_ref_name, reg_ref_tuple in attrs.items():
-            h5_dset.attrs[reg_ref_name] = h5_dset.regionref[reg_ref_tuple]
-        TestRegRef.__write_string_list_as_attr(h5_dset, {'labels': list(attrs.keys())})
-
     def setUp(self):
         data_utils.make_beps_file()
 
     def tearDown(self):
         data_utils.delete_existing_file(data_utils.std_beps_path)
-        
-    def test_get_indices_for_region_ref_corners(self):
-        with h5py.File(data_utils.std_beps_path, mode='r') as h5_f:
-            h5_main = h5_f['/Raw_Measurement/source_main']
-            ref_in = get_attr(h5_main, 'even_rows')
-            ret_val = reg_ref.get_indices_for_region_ref(h5_main, ref_in, 'corners')
-            expected_pos = np.repeat(np.arange(h5_main.shape[0])[::2], 2)
-            expected_spec = np.tile(np.array([0, h5_main.shape[1] - 1]), expected_pos.size // 2)
-            expected_corners = np.vstack((expected_pos, expected_spec)).T
-            self.assertTrue(np.allclose(ret_val, expected_corners))
-
-    def test_get_indices_for_region_ref_slices(self):
-        with h5py.File(data_utils.std_beps_path, mode='r') as h5_f:
-            h5_main = h5_f['/Raw_Measurement/source_main']
-            ref_in = get_attr(h5_main, 'even_rows')
-            ret_val = reg_ref.get_indices_for_region_ref(h5_main, ref_in, 'slices')
-            spec_slice = slice(0, h5_main.shape[1] - 1, None)
-            expected_slices = np.array([[slice(x, x, None), spec_slice] for x in np.arange(h5_main.shape[0])[::2]])
-            self.assertTrue(np.all(ret_val == expected_slices))
 
     def test_copy_reg_ref_reduced_dim(self):
         # TODO: Fill this test in at earliest convenience. Overriden temporarily
         assert True
 
-    def test_write_reg_ref_main_one_dim(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        data = np.random.rand(7)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Main', data=data)
-            reg_refs = {'even_rows': (slice(0, None, 2)),
-                        'odd_rows': (slice(1, None, 2))}
-            reg_ref.write_region_references(h5_dset, reg_refs, add_labels_attr=True)
-            self.assertEqual(len(h5_dset.attrs), 1 + len(reg_refs))
-            actual = get_attr(h5_dset, 'labels')
-            self.assertTrue(np.all([x == y for x, y in zip(actual, ['even_rows', 'odd_rows'])]))
-
-            expected_data = [data[0:None:2], data[1:None:2]]
-            written_data = [h5_dset[h5_dset.attrs['even_rows']], h5_dset[h5_dset.attrs['odd_rows']]]
-
-            for exp, act in zip(expected_data, written_data):
-                self.assertTrue(np.allclose(exp, act))
-
-        os.remove(file_path)
-
-    def test_write_reg_ref_main_1st_dim(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        data = np.random.rand(5, 7)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Main', data=data)
-            reg_refs = {'even_rows': (slice(0, None, 2), slice(None)),
-                        'odd_rows': (slice(1, None, 2), slice(None))}
-            reg_ref.write_region_references(h5_dset, reg_refs, add_labels_attr=True)
-            self.assertEqual(len(h5_dset.attrs), 1 + len(reg_refs))
-            actual = get_attr(h5_dset, 'labels')
-            self.assertTrue(np.all([x == y for x, y in zip(actual, ['even_rows', 'odd_rows'])]))
-
-            expected_data = [data[0:None:2], data[1:None:2]]
-            written_data = [h5_dset[h5_dset.attrs['even_rows']], h5_dset[h5_dset.attrs['odd_rows']]]
-
-            for exp, act in zip(expected_data, written_data):
-                self.assertTrue(np.allclose(exp, act))
-
-        os.remove(file_path)
-
-    def test_write_reg_ref_main_2nd_dim(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        data = np.random.rand(5, 7)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Main', data=data)
-            reg_refs = {'even_rows': (slice(None), slice(0, None, 2)),
-                        'odd_rows': (slice(None), slice(1, None, 2))}
-            reg_ref.write_region_references(h5_dset, reg_refs, add_labels_attr=False)
-            self.assertEqual(len(h5_dset.attrs), len(reg_refs))
-            self.assertTrue('labels' not in h5_dset.attrs.keys())
-
-            expected_data = [data[:, 0:None:2], data[:, 1:None:2]]
-            written_data = [h5_dset[h5_dset.attrs['even_rows']], h5_dset[h5_dset.attrs['odd_rows']]]
-
-            for exp, act in zip(expected_data, written_data):
-                self.assertTrue(np.allclose(exp, act))
-
-        os.remove(file_path)
-
-    def test_simple_region_ref_copy(self):
-        # based on test_hdf_writer.test_write_legal_reg_ref_multi_dim_data()
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            data = np.random.rand(5, 7)
-            h5_orig_dset = h5_f.create_dataset('test', data=data)
-            self.assertIsInstance(h5_orig_dset, h5py.Dataset)
-
-            attrs = {'labels': {'even_rows': (slice(0, None, 2), slice(None)),
-                                'odd_rows': (slice(1, None, 2), slice(None))}}
-
-            data_utils.write_main_reg_refs(h5_orig_dset, attrs['labels'])
-            h5_f.flush()
-
-            # two atts point to region references. one for labels
-            self.assertEqual(len(h5_orig_dset.attrs), 1 + len(attrs['labels']))
-
-            # check if the labels attribute was written:
-
-            self.assertTrue(np.all([x in list(attrs['labels'].keys()) for x in get_attr(h5_orig_dset,
-                                                                                                  'labels')]))
-
-            expected_data = [data[:None:2], data[1:None:2]]
-            written_data = [h5_orig_dset[h5_orig_dset.attrs['even_rows']], h5_orig_dset[h5_orig_dset.attrs['odd_rows']]]
-
-            for exp, act in zip(expected_data, written_data):
-                self.assertTrue(np.allclose(exp, act))
-
-            # Now write a new dataset without the region reference:
-            h5_new_dset = h5_f.create_dataset('other', data=data)
-            self.assertIsInstance(h5_orig_dset, h5py.Dataset)
-            h5_f.flush()
-
-            for key in attrs['labels'].keys():
-                reg_ref.simple_region_ref_copy(h5_orig_dset, h5_new_dset, key)
-
-            # now check to make sure that this dataset also has the same region references:
-            written_data = [h5_new_dset[h5_new_dset.attrs['even_rows']], h5_new_dset[h5_new_dset.attrs['odd_rows']]]
-
-            for exp, act in zip(expected_data, written_data):
-                self.assertTrue(np.allclose(exp, act))
-
-        os.remove(file_path)
-
-    def test_create_region_ref(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        data = np.random.rand(5, 7)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Source', data=data)
-            pos_inds = np.arange(0, h5_dset.shape[0], 2)
-            ref_inds = [((pos_start, 0), (pos_start, h5_dset.shape[1]-1)) for pos_start in pos_inds]
-            ref_inds = np.array(ref_inds)
-            this_reg_ref = reg_ref.create_region_reference(h5_dset, ref_inds)
-            ref_slices = list()
-            for start, stop in ref_inds:
-                ref_slices.append([slice(start[0], stop[0]+1), slice(start[1], None)])
-
-            h5_reg = h5_dset[this_reg_ref]
-
-            h5_slice = np.vstack([h5_dset[pos_slice, spec_slice] for (pos_slice, spec_slice) in ref_slices])
-
-            self.assertTrue(np.allclose(h5_reg, h5_slice))
-
-        os.remove(file_path)
-
-    def test_get_region_illegal_01(self):
-        with h5py.File(data_utils.std_beps_path, mode='r') as h5_f:
-            with self.assertRaises(KeyError):
-                reg_ref.get_region(h5_f['/Raw_Measurement/source_main'], 'non_existent')
-
-    def test_get_region_legal_01(self):
-        with h5py.File(data_utils.std_beps_path, mode='r') as h5_f:
-            h5_source = h5_f['/Raw_Measurement/source_main']
-            returned = reg_ref.get_region(h5_source, 'even_rows')
-            self.assertTrue(np.all(returned == h5_source[range(0, h5_source.shape[0], 2)]))
-            
-    def test_clean_reg_refs_1d(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Test', data=np.random.rand(7))
-            ref_in = (slice(0, None, 2))
-            cleaned = reg_ref.clean_reg_ref(h5_dset, ref_in)
-            self.assertEqual(ref_in, cleaned[0])
-        os.remove(file_path)
-
-    def test_clean_reg_refs_2d(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Test', data=np.random.rand(7, 5))
-            ref_in = (slice(0, None, 2), slice(None))
-            cleaned = reg_ref.clean_reg_ref(h5_dset, ref_in)
-            self.assertTrue(np.all([x == y for x, y in zip(ref_in, cleaned)]))
-        os.remove(file_path)
-
-    def test_clean_reg_refs_illegal_too_many_slices(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Test', data=np.random.rand(7, 5))
-            ref_in = (slice(0, None, 2), slice(None), slice(1, None, 2))
-            with self.assertRaises(ValueError):
-                _ = reg_ref.clean_reg_ref(h5_dset, ref_in)
-
-        os.remove(file_path)
-
-    def test_clean_reg_refs_illegal_too_few_slices(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Test', data=np.random.rand(7, 5))
-            ref_in = (slice(0, None, 2))
-            with self.assertRaises(ValueError):
-                _ = reg_ref.clean_reg_ref(h5_dset, ref_in)
-
-        os.remove(file_path)
-
-    def test_clean_reg_refs_out_of_bounds(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Test', data=np.random.rand(7, 5))
-            ref_in = (slice(0, 13, 2), slice(None))
-            expected = (slice(0, 7, 2), slice(None))
-            cleaned = reg_ref.clean_reg_ref(h5_dset, ref_in, verbose=False)
-            self.assertTrue(np.all([x == y for x, y in zip(expected, cleaned)]))
-        os.remove(file_path)
-
-    def test_attempt_reg_ref_build_spec(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Indices', data=np.random.rand(2, 5))
-            dim_names = ['Bias', 'Cycle']
-            expected = {'Bias': (slice(0, 1), slice(None)),
-                        'Cycle': (slice(1, 2), slice(None))}
-            if sys.version_info.major == 3:
-                with self.assertWarns(UserWarning):
-                    cleaned = reg_ref.attempt_reg_ref_build(h5_dset, dim_names)
-            else:
-                cleaned = reg_ref.attempt_reg_ref_build(h5_dset, dim_names)
-            for key, value in expected.items():
-                self.assertEqual(value, cleaned[key])
-        os.remove(file_path)
-
-    def test_attempt_reg_ref_build_pos(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Indices', data=np.random.rand(5, 2))
-            dim_names = ['Bias', 'Cycle']
-            expected = {'Bias': (slice(None), slice(0, 1)),
-                        'Cycle': (slice(None), slice(1, 2))}
-            if sys.version_info.major == 3:
-                with self.assertWarns(UserWarning):
-                    cleaned = reg_ref.attempt_reg_ref_build(h5_dset, dim_names)
-            else:
-                cleaned = reg_ref.attempt_reg_ref_build(h5_dset, dim_names)
-            for key, value in expected.items():
-                self.assertEqual(value, cleaned[key])
-        os.remove(file_path)
-
-    def test_attempt_reg_ref_build_pos_too_many_dims(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Indices', data=np.random.rand(5, 2))
-            dim_names = ['Bias', 'Cycle', 'Blah']
-            ret_val = reg_ref.attempt_reg_ref_build(h5_dset, dim_names)
-            self.assertEqual(ret_val, dict())
-        os.remove(file_path)
-
-    def test_attempt_reg_ref_build_pos_too_few_dims(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset = h5_f.create_dataset('Indices', data=np.random.rand(5, 2))
-            dim_names = ['Bias']
-            ret_val = reg_ref.attempt_reg_ref_build(h5_dset, dim_names)
-            self.assertEqual(ret_val, dict())
-        os.remove(file_path)
-
-    def test_copy_region_refs(self):
-        file_path = 'test.h5'
-        data_utils.delete_existing_file(file_path)
-        data = np.random.rand(11, 7)
-        with h5py.File(file_path, mode='w') as h5_f:
-            h5_dset_source = h5_f.create_dataset('Source', data=data)
-            h5_dset_dest = h5_f.create_dataset('Target', data=data)
-            source_ref = h5_dset_source.regionref[0:-1:2]
-            h5_dset_source.attrs['regref'] = source_ref
-
-            reg_ref.copy_region_refs(h5_dset_source, h5_dset_dest)
-
-            self.assertTrue(
-                np.allclose(h5_dset_source[h5_dset_source.attrs['regref']],
-                            h5_dset_dest[h5_dset_dest.attrs['regref']]))
 
-        os.remove(file_path)
+if __name__ == '__main__':
+    unittest.main()
diff -ruN a/tests/io/test_usi_dataset.py b/tests/io/test_usi_dataset.py
--- a/tests/io/test_usi_dataset.py	2020-08-18 08:51:13.000000000 +0700
+++ b/tests/io/test_usi_dataset.py	2020-11-05 13:34:24.000000000 +0700
@@ -339,7 +339,8 @@
             usi_main = USIDataset(h5_f['/Raw_Measurement/source_main'])
             actual, success = usi_main.slice(slice_dict,
                                              ndim_form=result_as_nd,
-                                             lazy=lazy_result)
+                                             lazy=lazy_result,
+                                             verbose=verbose)
             if verbose:
                 print('Status: {}, actual.shape: {}, actual.dtype: {}, '
                       'type(actual): {}'.format(success, actual.shape,
--- a/tests/io/test_write_utils.py	2020-08-18 08:51:13.000000000 +0700
+++ b/tests/io/test_write_utils.py	2020-11-05 13:34:24.000000000 +0700
@@ -22,14 +22,29 @@
         with self.assertRaises(ValueError):
             _ = write_utils.make_indices_matrix([1, 2, 3])
 
+    def test_just_size_of_one_dim(self):
+        expected = np.expand_dims(np.arange(4), axis=0)
+        ret_val = write_utils.make_indices_matrix(4, is_position=False)
+        self.assertTrue(np.allclose(expected, ret_val))
+
+    def test_empty_list(self):
+        with self.assertRaises(ValueError):
+            _ = write_utils.make_indices_matrix([])
+
+    def test_single_value_dimension_int_input(self):
+        expected = np.expand_dims(np.arange(1), axis=0)
+        ret_val = write_utils.make_indices_matrix(1, is_position=False)
+        self.assertTrue(np.allclose(expected, ret_val))
+
+    def test_single_value_dimension_list_input(self):
+        expected = np.expand_dims(np.arange(1), axis=0)
+        ret_val = write_utils.make_indices_matrix([1], is_position=False)
+        self.assertTrue(np.allclose(expected, ret_val))
+
     def test_non_int_dim_sizes(self):
         with self.assertRaises(ValueError):
             _ = write_utils.make_indices_matrix([1.233, 2.4, 3])
 
-    def test_not_list(self):
-        with self.assertRaises(TypeError):
-            _ = write_utils.make_indices_matrix(1)
-
     def test_weird_inputs(self):
         with self.assertRaises(ValueError):
             _ = write_utils.make_indices_matrix([2, 'hello', 3])
@@ -111,12 +126,14 @@
 
     def test_repr(self):
         name = 'Bias'
+        quantity = 'generic'
         units = 'V'
-        values = np.arange(5)
+        values = np.arange(5, dtype=np.float)
 
         descriptor = write_utils.Dimension(name, units, len(values))
+        print(type(descriptor))
         actual = '{}'.format(descriptor)
-        expected = '{} ({}) mode:{} : {}'.format(name, units, descriptor.mode, values)
+        expected = '{}: {} ({}) mode:{} : {}'.format(name, quantity, units, descriptor.mode, values)
         self.assertEqual(actual, expected)
 
     def test_equality(self):
@@ -130,23 +147,28 @@
     def test_inequality(self):
         name = 'Bias'
         units = 'V'
+        values = [0, 1, 2, 3]
 
-        self.assertNotEqual(write_utils.Dimension(name, units, [0, 1, 2, 3]),
-                            write_utils.Dimension(name, units, [0, 1, 2, 4]))
-
-        self.assertNotEqual(write_utils.Dimension('fdfd', units, [0, 1, 2, 3]),
-                            write_utils.Dimension(name, units, [0, 1, 2, 3]))
-
-        self.assertNotEqual(write_utils.Dimension(name, 'fdfd', [0, 1, 2, 3]),
-                            write_utils.Dimension(name, units, [0, 1, 2, 3]))
-
-        self.assertNotEqual(write_utils.Dimension(name, units, [0, 1, 2, 3],
-                                                  mode=write_utils.DimType.DEPENDENT),
-                            write_utils.Dimension(name, units, [0, 1, 2, 3],
-                                                  mode=write_utils.DimType.INCOMPLETE))
-
-        self.assertNotEqual(write_utils.Dimension(name, units, [0, 1, 2]),
-                            write_utils.Dimension(name, units, [0, 1, 2, 3]))
+        left = write_utils.Dimension(name, units, values)
+        right = write_utils.Dimension(name, units, [0, 1, 2, 4])
+        self.assertFalse(left == right)
+
+        left = write_utils.Dimension(name, units, [0, 1, 2])
+        right = write_utils.Dimension(name, units, values)
+        self.assertFalse(left == right)
+
+        left = write_utils.Dimension('name', units, values)
+        right = write_utils.Dimension(name, units, values)
+        self.assertFalse(left == right)
+
+        left = write_utils.Dimension(name, 'units', values)
+        right = write_utils.Dimension(name, units, values)
+        self.assertFalse(left == right)
+
+        left = write_utils.Dimension(name, units, values,
+                                     mode=write_utils.DimType.DEPENDENT)
+        right = write_utils.Dimension(name, units, values)
+        self.assertFalse(left == right)
 
     def test_invalid_mode(self):
         with self.assertRaises(TypeError):

--- a/.travis.yml	2020-08-18 08:51:13.000000000 +0700
+++ b/.travis.yml	2020-11-05 13:34:24.000000000 +0700
@@ -1,11 +1,9 @@
 language: python
 python:
   - '3.7'
-  - '2.7'
   - '3.8'
   - '3.6'
   - '3.5'
-  - '3.4'
 before_install:
   - sudo apt-get update -qq
   - pip  install coveralls

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File fix_tests_h5py-3.0.patch of Package python-pyUSID (Revision 592f6dbdeb0203ebed6d960cc1359358)

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