fix loop fit

BGlib/be/analysis/be_loop_fitter.py

@@ -351,7 +351,7 @@ def _read_data_chunk(self):
                         0]
             else:
                 this_forc_spec_inds = np.ones(
-                    shape=self.h5_main.h5_spec_inds.shape[1], dtype=np.bool)
+                    shape=self.h5_main.h5_spec_inds.shape[1], dtype=bool)
 
             if self._num_forcs:
                 this_forc_dc_vec = get_unit_values(
@@ -495,7 +495,7 @@ def _read_guess_chunk(self):
                 np.where(self._h5_guess.h5_spec_inds[forc_pos] == forc_ind)[0]
             else:
                 this_forc_spec_inds = np.ones(
-                    shape=self._h5_guess.h5_spec_inds.shape[1], dtype=np.bool)
+                    shape=self._h5_guess.h5_spec_inds.shape[1], dtype=bool)
 
             this_forc_2d = self._guess[:, this_forc_spec_inds]
             if self.verbose and self.mpi_rank == 0:

tests/be/test_be_module.py

@@ -0,0 +1,30 @@
+import unittest
+import sys
+import os
+sys.path.append("../BGlib/")
+import BGlib.be as belib
+import pyUSID as usid
+import h5py
+
+class TestLoadDataset(unittest.TestCase):
+
+    def test_bepfm_dataset(self):
+        #this file is actually a corrupted BEPFM file for which the translator has an auto fix
+        #So we need to download the original file, see if the following works, then delete
+        #TODO: Host hte original file somewhere, use wget
+
+        input_file_path = r'/Users/rvv/Downloads/PTO_a32/BEPFM_1um_afterBEPS_0039.h5'
+        (data_dir, filename) = os.path.split(input_file_path)
+        # No translation here
+        h5_path = input_file_path
+        force = False # Set this to true to force patching of the datafile.
+        tl = belib.translators.LabViewH5Patcher()
+        tl.translate(h5_path, force_patch=force)
+        h5_file = h5py.File(h5_path, 'r+')
+        h5_main = usid.hdf_utils.find_dataset(h5_file, 'Raw_Data')[0]
+        #Let's see if we get the right type of file back...
+        assert type(h5_main) == usid.io.usi_data.USIDataset
+
+    def test_values_as_length(self):
+        print("OK")
+