Fixed recursive imports from PycroDataset

pycroscopy/io/hdf_utils.py

@@ -6,13 +6,11 @@ Created on Tue Nov  3 21:14:25 2015
 """
 
 from __future__ import division, print_function, absolute_import, unicode_literals
-import os
 import sys
 import h5py
 from warnings import warn
 import numpy as np
 from .microdata import MicroDataset
-from .pycro_data import PycroDataset
 
 __all__ = ['get_attr', 'getDataSet', 'getH5DsetRefs', 'getH5RegRefIndices', 'get_dimensionality', 'get_sort_order',
            'getAuxData', 'get_attributes', 'getH5GroupRefs', 'checkIfMain', 'checkAndLinkAncillary',
@@ -60,6 +58,8 @@ def get_all_main(parent, verbose=False):
         The datasets found in the file that meet the 'Main Data' criteria.
 
     """
+    from .pycro_data import PycroDataset
+
     main_list = list()
 
     def __check(name, obj):
@@ -98,12 +98,19 @@ def getDataSet(h5_parent, data_name):
     -------
     list of h5py.Reference of the dataset.
     """
+    from .pycro_data import PycroDataset
+
     if isinstance(h5_parent, h5py.File) or isinstance(h5_parent, h5py.Group):
         data_list = []
 
         def findData(name, obj):
             if name.endswith(data_name) and isinstance(obj, h5py.Dataset):
-                data_list.append(PycroDataset(obj))
+                try:
+                    data_list.append(PycroDataset(obj))
+                except TypeError:
+                    data_list.append(obj)
+                except:
+                    raise
 
         h5_parent.visititems(findData)
         return data_list
@@ -136,7 +143,7 @@ def getAuxData(parent_data, auxDataName=None):
         for auxName in auxDataName:
             ref = parent_data.attrs[auxName]
             if isinstance(ref, h5py.Reference) and isinstance(file_ref[ref], h5py.Dataset):
-                data_list.append(PycroDataset(file_ref[ref]))
+                data_list.append(file_ref[ref])
     except KeyError:
         warn('%s is not an attribute of %s'
              % (str(auxName), parent_data.name))
@@ -228,6 +235,8 @@ def getH5DsetRefs(ds_names, h5_refs):
     aux_dset : List of HDF5 dataset references
         Corresponding references
     """
+    from .pycro_data import PycroDataset
+
     aux_dset = []
     for ds_name in ds_names:
         for dset in h5_refs:
@@ -265,6 +274,8 @@ def findDataset(h5_group, ds_name):
     """
     Uses visit() to find all datasets with the desired name
     """
+    from .pycro_data import PycroDataset
+
     # print 'Finding all instances of', ds_name
     ds = []
 
@@ -963,6 +974,8 @@ def create_empty_dataset(source_dset, dtype, dset_name, new_attrs=dict(), skip_r
     h5_new_dset : h5py.Dataset object
         Newly created dataset
     """
+    from .pycro_data import PycroDataset
+
     h5_group = source_dset.parent
     try:
         # Check if the dataset already exists
@@ -1629,6 +1642,8 @@ def get_source_dataset(h5_group):
     h5_source : h5py.Dataset
 
     """
+    from .pycro_data import PycroDataset
+
     h5_parent_group = h5_group.parent
     h5_source = h5_parent_group[h5_group.name.split('/')[-1].split('-')[0]]
     return PycroDataset(h5_source)

pycroscopy/io/pycro_data.py

@@ -10,7 +10,7 @@ import h5py
 import six
 from warnings import warn
 import numpy as np
-from .hdf_utils import checkIfMain, getAuxData, get_attr, get_data_descriptor, get_formatted_labels, \
+from .hdf_utils import checkIfMain, get_attr, get_data_descriptor, get_formatted_labels, \
     get_dimensionality, get_sort_order, get_unit_values, reshape_to_Ndims
 
 
@@ -73,10 +73,14 @@ class PycroDataset(h5py.Dataset):
 
         # User accessible properties
         # The required Position and Spectroscopic datasets
-        self.h5_spec_vals = getAuxData(h5_ref, 'Spectroscopic_Values')[-1]
-        self.h5_spec_inds = getAuxData(h5_ref, 'Spectroscopic_Indices')[-1]
-        self.h5_pos_vals = getAuxData(h5_ref, 'Position_Values')[-1]
-        self.h5_pos_inds = getAuxData(h5_ref, 'Position_Indices')[-1]
+        # self.h5_spec_vals = getAuxData(h5_ref, 'Spectroscopic_Values')[-1]
+        # self.h5_spec_inds = getAuxData(h5_ref, 'Spectroscopic_Indices')[-1]
+        # self.h5_pos_vals = getAuxData(h5_ref, 'Position_Values')[-1]
+        # self.h5_pos_inds = getAuxData(h5_ref, 'Position_Indices')[-1]
+        self.h5_spec_vals = self.file[self.attrs['Spectroscopic_Indices']]
+        self.h5_spec_inds = self.file[self.attrs['Spectroscopic_Indices']]
+        self.h5_pos_vals = self.file[self.attrs['Position_Values']]
+        self.h5_pos_inds = self.file[self.attrs['Position_Indices']]
 
         # The dimension labels
         self.__pos_dim_labels = get_attr(self.h5_pos_inds, 'labels')
@@ -152,18 +156,18 @@ class PycroDataset(h5py.Dataset):
         if self.__sort_dims:
             self.pos_dim_labels = self.__pos_dim_labels[self.__pos_sort_order].tolist()
             self.spec_dim_labels = self.__spec_dim_labels[self.__spec_sort_order].tolist()
-            self.pos_dim_sizes = self.__pos_dim_sizes[self.__pos_sort_order].tolist()
-            self.spec_dim_sizes = self.__spec_dim_sizes[self.__spec_sort_order].tolist()
+            self.pos_dim_sizes = self.__pos_dim_sizes[self.__pos_sort_order]
+            self.spec_dim_sizes = self.__spec_dim_sizes[self.__spec_sort_order]
             self.n_dim_labels = self.__n_dim_labs[self.__n_dim_sort_order].tolist()
-            self.n_dim_sizes = self.__n_dim_sizes[self.__n_dim_sort_order].tolist()
+            self.n_dim_sizes = self.__n_dim_sizes[self.__n_dim_sort_order]
 
         else:
             self.pos_dim_labels = self.__pos_dim_labels.tolist()
             self.spec_dim_labels = self.__spec_dim_labels.tolist()
-            self.pos_dim_sizes = self.__pos_dim_sizes.tolist()
-            self.spec_dim_sizes = self.__spec_dim_sizes.tolist()
+            self.pos_dim_sizes = self.__pos_dim_sizes
+            self.spec_dim_sizes = self.__spec_dim_sizes
             self.n_dim_labels = self.__n_dim_labs.tolist()
-            self.n_dim_sizes = self.__n_dim_sizes.tolist()
+            self.n_dim_sizes = self.__n_dim_sizes
 
     def get_pos_values(self, dim_name):
         """