Add test data

jmcvey3 · Mar 7, 2024 · aa2cf0b · aa2cf0b
1 parent c5bc8c5
commit aa2cf0b
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Showing 6 changed files with 22 additions and 13 deletions.
diff --git a/dolfyn/example_data/dual_profile.ad2cp b/dolfyn/example_data/dual_profile.ad2cp
diff --git a/dolfyn/io/base.py b/dolfyn/io/base.py
@@ -131,8 +131,7 @@ def _create_dataset(data):
 
     ds_dict['beam'] = {"dims": ('beam'), "data": beams}
     ds_dict['dir'] = {"dims": ('dir'), "data": beams}
-    data['units'].update({'beam': '1',
-                          'dir': '1'})
+    data['units'].update({'beam': '1', 'dir': '1'})
     data['long_name'].update({'beam': 'Beam Reference Frame',
                               'dir': 'Reference Frame'})
 
@@ -156,14 +155,11 @@ def _create_dataset(data):
                     tg = ''
                 ds_dict['earth'] = {"dims": ('earth'), "data": ['E', 'N', 'U']}
                 ds_dict['inst'] = {"dims": ('inst'), "data": ['X', 'Y', 'Z']}
-                data['units'].update({'earth': '1',
-                                      'inst': '1'})
-                data['long_name'].update({'earth': 'Earth Reference Frame',
-                                          'inst': 'Instrument Reference Frame'})
-
                 ds_dict[key] = {"dims": ('earth', 'inst', 'time' + tg), "data": data['data_vars'][key]}
-                data['units'].update({key: data['units']['orientmat']})
-                data['long_name'].update({key: data['long_name']['orientmat']})
+                data["units"].update({"earth": "1", "inst": "1", key: data["units"]["orientmat"]})
+                data["long_name"].update({"earth": "Earth Reference Frame",
+                                          "inst": "Instrument Reference Frame",
+                                          key: data["long_name"]["orientmat"]})
 
         # quaternion units never change
         elif 'quaternions' in key:

diff --git a/dolfyn/io/nortek2.py b/dolfyn/io/nortek2.py
@@ -472,7 +472,7 @@ def _reorg(dat):
             dnow['usec100'].astype('uint32') * 100)
         tmp = lib._beams_cy_int2dict(
             lib._collapse(dnow['beam_config'], exclude=collapse_exclude,
-                          name='beam_config'), 21)
+                          name='beam_config'), 21)  # always 21 here
         cfg['n_cells' + tag] = tmp['n_cells']
         cfg['coord_sys_axes' + tag] = tmp['cy']
         cfg['n_beams' + tag] = tmp['n_beams']
@@ -587,7 +587,7 @@ def _clean_dp_skips(data):
         skips = np.where(data[id]['ver'] != 0)
         for var in data[id]:
             if var not in ['units', 'long_name', 'standard_name']:
-                data[id][var] = np.squeeze(data[id][var][..., skips])
+                data[id][var] = np.squeeze(data[id][var][..., skips], axis=-2)
 
 
 def _reduce(data):

diff --git a/dolfyn/io/nortek2_lib.py b/dolfyn/io/nortek2_lib.py
@@ -186,7 +186,7 @@ def _check_index(idx, infile, fix_hw_ens=False, dp=False):
                 if c > 1:
                     skip_size[skip_size == n] = 0
             # assume last "ibad" element is always good for dp's
-            mask = np.append(skip_size, 0).astype(bool)
+            mask = np.append(skip_size, 0).astype(bool) if any(skip_size) else []
             ibad = ibad[mask]
         for ib in ibad:
             FLAG = True
@@ -437,7 +437,8 @@ def _beams_cy_int2dict(val, id):
     """
     if id == 28:  # 0x1C (echosounder)
         return dict(n_cells=val)
-
+    elif id in [26, 31]:
+        return dict(n_cells=val & (2**10 - 1), cy="beam", n_beams=1)
     return dict(
         n_cells=val & (2 ** 10 - 1),
         cy=['ENU', 'XYZ', 'beam', None][val >> 10 & 3],

diff --git a/dolfyn/tests/data/dual_profile.nc b/dolfyn/tests/data/dual_profile.nc
diff --git a/dolfyn/tests/test_read_adp.py b/dolfyn/tests/test_read_adp.py
@@ -33,6 +33,7 @@
 dat_sig_skip = load('Sig_SkippedPings01.nc')
 dat_sig_badt = load('Sig1000_BadTime01.nc')
 dat_sig5_leiw = load('Sig500_last_ensemble_is_whole.nc')
+dat_sig_dp2 = load("dual_profile.nc")
 
 
 def test_io_rdi(make_data=False):
@@ -97,6 +98,8 @@ def test_io_nortek2(make_data=False):
     td_sig_ieb = read('VelEchoBT01.ad2cp', nens=nens)
     td_sig_ie = read('Sig500_Echo.ad2cp', nens=nens)
     td_sig_tide = read('Sig1000_tidal.ad2cp', nens=nens)
+    # Only need to test 2nd dataset
+    td_sig_dp1, td_sig_dp2 = read("dual_profile.ad2cp")
 
     with pytest.warns(UserWarning):
         # This issues a warning...
@@ -119,6 +122,7 @@ def test_io_nortek2(make_data=False):
     os.remove(tb.exdt('Sig_SkippedPings01.ad2cp.index'))
     os.remove(tb.exdt('Sig500_last_ensemble_is_whole.ad2cp.index'))
     os.remove(tb.rfnm('Sig1000_BadTime01.ad2cp.index'))
+    os.remove(tb.exdt("dual_profile.ad2cp.index"))
 
     if make_data:
         save(td_sig, 'BenchFile01.nc')
@@ -130,6 +134,7 @@ def test_io_nortek2(make_data=False):
         save(td_sig_skip, 'Sig_SkippedPings01.nc')
         save(td_sig_badt, 'Sig1000_BadTime01.nc')
         save(td_sig5_leiw, 'Sig500_last_ensemble_is_whole.nc')
+        save(td_sig_dp2, "dual_profile.nc")
         return
 
     assert_allclose(td_sig, dat_sig, atol=1e-6)
@@ -141,6 +146,7 @@ def test_io_nortek2(make_data=False):
     assert_allclose(td_sig5_leiw, dat_sig5_leiw, atol=1e-6)
     assert_allclose(td_sig_skip, dat_sig_skip, atol=1e-6)
     assert_allclose(td_sig_badt, dat_sig_badt, atol=1e-6)
+    assert_allclose(td_sig_dp2, dat_sig_dp2, atol=1e-6)
 
 
 def test_nortek2_crop(make_data=False):