From 9affa83cea49b52b8e1505d24cb96ab06dff06ad Mon Sep 17 00:00:00 2001
From: jmcvey3 <53623232+jmcvey3@users.noreply.github.com>
Date: Fri, 9 Feb 2024 11:18:21 -0800
Subject: [PATCH] Reinstate some skipped ping logic

---
 dolfyn/io/nortek2_lib.py | 43 ++++++++++++++++++++++------------------
 1 file changed, 24 insertions(+), 19 deletions(-)

diff --git a/dolfyn/io/nortek2_lib.py b/dolfyn/io/nortek2_lib.py
index 5be0ae9d..b0412f5a 100644
--- a/dolfyn/io/nortek2_lib.py
+++ b/dolfyn/io/nortek2_lib.py
@@ -166,31 +166,36 @@ def _check_index(idx, infile, fix_hw_ens=False, dp=False):
     N_id = len(uid)
     FLAG = False
 
-    # Hack for estimating if dual profile exists, won't always work
-    # Should add as reader input
+    # Are there better ways to detect dual profile?
     if (21 in uid) and (22 in uid):
-        warnings.warn("Dual Profile detected...")
+        warnings.warn("Dual Profile detected... Two datasets will be returned.")
         dp = True
 
     # This loop fixes 'skips' inside the file
-    if not dp:
-        for id in uid:
-            # These are the indices for this ID
-            inds = np.nonzero(idx['ID'] == id)[0]
-
-            # These are bad steps in the indices for this ID
-            ibad = np.nonzero(np.diff(inds) > N_id)[0]
-            # Will need to fix for dual profile ADCPs
-            for ib in ibad:
-                FLAG = True
-                # The ping number reported here may not be quite right if
-                # the ensemble count is wrong.
-                warnings.warn("Skipped ping (ID: {}) in file {} at ensemble {}."
-                              .format(id, infile, idx['ens'][inds[ib + 1] - 1]))
-                hwe[inds[(ib + 1):]] += 1
-                ens[inds[(ib + 1):]] += 1
+    for id in uid:
+        # These are the indices for this ID
+        inds = np.nonzero(idx['ID'] == id)[0]
+        # These are bad steps in the indices for this ID
+        ibad = np.nonzero(np.diff(inds) > N_id)[0]
+        # Check if spacing is equal for dual profiling ADCPs
+        if dp:
+            skip_size = np.diff(ibad)
+            avg_skip = np.median(skip_size)
+            # assume last "ibad" element is always good for dp's
+            mask = np.append(skip_size - avg_skip, 0).astype(bool)
+            ibad = ibad[mask]
+        for ib in ibad:
+            FLAG = True
+            # The ping number reported here may not be quite right if
+            # the ensemble count is wrong.
+            warnings.warn("Skipped ping (ID: {}) in file {} at ensemble {}."
+                          .format(id, infile, idx['ens'][inds[ib + 1] - 1]))
+            hwe[inds[(ib + 1):]] += 1
+            ens[inds[(ib + 1):]] += 1
 
+    if not dp:
         # This block fixes skips that originate from before this file.
+        # Check first N id's and correct
         delta = max(hwe[:N_id]) - hwe[:N_id]
         for d, id in zip(delta, idx['ID'][:N_id]):
             if d != 0: