Merge branch 'master' into driver-n5245a

microsoft · Jul 20, 2018 · 3d76208 · 3d76208
2 parents 1da1635 + bcedfbc
commit 3d76208
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Showing 42 changed files with 4,958 additions and 657 deletions.
diff --git a/docs/examples/driver_examples/QCodes_example_with_SR86x_with_buffered_readout.ipynb b/docs/examples/driver_examples/QCodes_example_with_SR86x_with_buffered_readout.ipynb
diff --git a/qcodes/data/hdf5_format.py b/qcodes/data/hdf5_format.py
@@ -14,15 +14,15 @@ class HDF5Format(Formatter):
     HDF5 formatter for saving qcodes datasets.
 
     Capable of storing (write) and recovering (read) qcodes datasets.
-           
+
     """
 
     _format_tag = 'hdf5'
 
     def close_file(self, data_set):
         """
         Closes the hdf5 file open in the dataset.
-        
+
         Args:
             data_set (DataSet): DataSet object
         """
@@ -99,6 +99,9 @@ def read(self, data_set, location=None):
             #     set_arrays = ()
             vals = dat_arr.value[:, 0]
             if 'shape' in dat_arr.attrs.keys():
+                # extend with NaN if needed
+                esize = np.prod(dat_arr.attrs['shape'])
+                vals = np.append(vals, [np.nan] * (esize - vals.size))
                 vals = vals.reshape(dat_arr.attrs['shape'])
             if array_id not in data_set.arrays.keys():  # create new array
                 d_array = DataArray(
@@ -207,7 +210,12 @@ def write(self, data_set, io_manager=None, location=None,
             datasetshape = dset.shape
             old_dlen = datasetshape[0]
             x = data_set.arrays[array_id]
-            new_dlen = len(x[~np.isnan(x)])
+            try:
+                # get latest NaN element
+                new_dlen = (~np.isnan(x)).flatten().nonzero()[0][-1] + 1
+            except IndexError:
+                new_dlen = old_dlen
+
             new_datasetshape = (new_dlen,
                                 datasetshape[1])
             dset.resize(new_datasetshape)