Beam hardening test corrections and small config.py bug fix

src/tomocupy/config.py

@@ -773,7 +773,7 @@ def update_hdf_process(fname, args=None, sections=None):
                         hdf_file.require_dataset(dataset, shape=(1,), dtype=dt)
                         log.info(name + ': ' + str(value))
                         try:
-                            hdf_file[dataset][0] = np.string_(str(value))
+                            hdf_file[dataset][0] = np.bytes_(str(value))
                         except TypeError:
                             log.error(
                                 "Could not convert value {}".format(value))

src/tomocupy/processing/proc_functions.py

@@ -69,7 +69,6 @@ def darkflat_correction(self, data, dark, flat):
         dark0 = cp.mean(dark0, axis=0)
         res = (data.astype(args.dtype, copy=False)-dark0) / \
             (flat0-dark0+flat0*1e-5)
-
         return res
 
     def minus_log(self, data):

tests/test_full.py

@@ -9,11 +9,15 @@
 
 prefix = 'tomocupy recon --file-name data/test_data.h5 --reconstruction-type full --rotation-axis 782.5 --nsino-per-chunk 4'
 prefix2 = 'tomocupy recon --file-name data/Downsampled_WB.h5 --reconstruction-type full --nsino-per-chunk 4 --rotation-axis 808 --sample-material Pb '
-prefix3 = '--filter-1-auto True --filter-2-auto True --filter-3-auto True --sample-density 11.34 --dezinger 3 '
+prefix3 = '--read-pixel-size --read-scintillator --filter-1-auto True --filter-2-auto True --filter-3-auto True --sample-density 11.34 --dezinger 3 '
 prefix4 = '--filter-1-density 1.85 --filter-2-density 8.9 --filter-3-density 8.9' 
 prefix5 = '--filter-1-density 0.0 --filter-2-density 0.0 --filter-3-density 0.0' 
 cmd_dict = {
     f'{prefix} ': 28.307,
+    f'{prefix2} {prefix3} {prefix5} --beam-hardening-method standard --calculate-source standard': 3251.278,
+    f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard': 3250.038,
+    f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard --calculate-source standard': 3250.038,
+    f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard --calculate-source standard --e-storage-ring 3.0': 1590.9,
     f'{prefix} --reconstruction-algorithm lprec ': 27.992,
     f'{prefix} --reconstruction-algorithm linerec ': 28.341,
     f'{prefix} --dtype float16': 24.186,
@@ -38,9 +42,9 @@
     f'{prefix} --bright-ratio 10': 32.631,
     f'{prefix} --end-column 1535': 28.293,
     f'{prefix} --end-column 1535 --binning 3': 1.82,    
-    f'{prefix2} {prefix3} {prefix5} --beam-hardening-method standard --calculate-source standard': 3255.912,
-    f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard': 3248.832,
-    f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard --calculate-source standard': 3254.634,
+    f'{prefix2} {prefix3} {prefix5} --beam-hardening-method standard --calculate-source standard': 3256.6,
+    f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard': 3250.0,
+    f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard --calculate-source standard': 3255.3,
     f'{prefix2} {prefix3} {prefix4} --beam-hardening-method standard --calculate-source standard --e-storage-ring 3.0 --b-storage-ring 0.3': 822.178,    
 }
 
@@ -87,6 +91,5 @@ def test_full_recon(self):
             self.assertAlmostEqual(ssum, cmd[1], places=0)
 
 
-
 if __name__ == '__main__':
     unittest.main(testLoader=SequentialTestLoader(), failfast=True)