From 898bac4fb27fbb4491dad756173ce6305da7b930 Mon Sep 17 00:00:00 2001
From: ssuttles-usgs
 <ssuttles@usgs.govgit config -lgit config --global user.email ssuttles@usgs.gov>
Date: Wed, 15 May 2024 09:01:41 -0400
Subject: [PATCH 1/7] add avgd data type

---
 stglib/aqd/aqdutils.py       |   4 +
 stglib/sig/cdf2nc.py         |  86 ++++++++++++-
 stglib/sig/mat2cdf.py        | 226 ++++++++++++++++++++++++++++++-----
 stglib/tests/test_scripts.py |   2 +-
 4 files changed, 288 insertions(+), 30 deletions(-)

diff --git a/stglib/aqd/aqdutils.py b/stglib/aqd/aqdutils.py
index 02d55329..5ba956c4 100644
--- a/stglib/aqd/aqdutils.py
+++ b/stglib/aqd/aqdutils.py
@@ -835,6 +835,10 @@ def check_attrs(ds, waves=False, hr=False, inst_type="AQD"):
             ds.attrs["bin_size"] = ds.attrs["SIGBurstHR_CellSize"]
         elif ds.attrs["data_type"].upper() == "ECHO1":
             ds.attrs["bin_size"] = ds.attrs["SIGEchoSounder_CellSize"]
+        elif ds.attrs["data_type"].upper() == "AVERAGE":
+            ds.attrs["bin_size"] = ds.attrs["SIGAverage_CellSize"]
+        elif ds.attrs["data_type"].upper() == "ALT_AVERAGE":
+            ds.attrs["bin_size"] = ds.attrs["SIGAlt_Average_CellSize"]
 
         if ds.attrs["frequency"] == 1000 or ds.attrs["frequency"] == 500:
             ds.attrs["beam_angle"] = 25
diff --git a/stglib/sig/cdf2nc.py b/stglib/sig/cdf2nc.py
index 1817841a..74c14e7d 100644
--- a/stglib/sig/cdf2nc.py
+++ b/stglib/sig/cdf2nc.py
@@ -1,3 +1,4 @@
+import re
 import time
 
 import numpy as np
@@ -52,7 +53,12 @@ def cdf_to_nc(cdf_filename, atmpres=False):
     # Need to clip data after coord transform when using dolfyn
     ds = utils.clip_ds(ds)
 
-    if ds.attrs["data_type"] == "Burst" or ds.attrs["data_type"] == "BurstHR":
+    if (
+        ds.attrs["data_type"] == "Burst"
+        or ds.attrs["data_type"] == "BurstHR"
+        or ds.attrs["data_type"] == "Average"
+        or ds.attrs["data_type"] == "Alt_Average"
+    ):
         # Create separate vel variables first
         ds["U"] = ds["VelEast"]
         ds["V"] = ds["VelNorth"]
@@ -129,6 +135,22 @@ def cdf_to_nc(cdf_filename, atmpres=False):
         {"standard_name": "time", "axis": "T", "long_name": "time (UTC)"}
     )
     """
+    att2del = []
+    for k in ds.attrs:
+        if re.search("_Beam2xyz$", k):
+            print(k)
+            att2del.append(k)
+
+    for k in att2del:
+        del ds.attrs[k]
+
+    for j in ds.data_vars:
+        for k in ds[j].attrs:
+
+            if type(ds[j].attrs[k]) is np.ndarray:
+                shp = len(ds[j].attrs[k].shape)
+                print(f"{j},{k},{shp}")
+
     # write out nc file by data_type
     if "prefix" in ds.attrs:
         nc_filename = ds.attrs["prefix"] + ds.attrs["filename"]
@@ -159,6 +181,24 @@ def cdf_to_nc(cdf_filename, atmpres=False):
             delayed_obj.compute()
         print("Done writing netCDF file", nc_out)
 
+    elif ds.attrs["data_type"] == "Average":
+        nc_out = nc_filename + "avg-cal.nc"
+        print("writing Average (avg) data to netCDF nc file")
+        print(ds.attrs)
+        delayed_obj = ds.to_netcdf(nc_out, compute=False)
+        with ProgressBar():
+            delayed_obj.compute()
+        print("Done writing netCDF file", nc_out)
+
+    elif ds.attrs["data_type"] == "Alt_Average":
+        nc_out = nc_filename + "alt-cal.nc"
+        print("writing Alt_Average (avg) data to netCDF nc file")
+        print(ds.attrs)
+        delayed_obj = ds.to_netcdf(nc_out, compute=False)
+        with ProgressBar():
+            delayed_obj.compute()
+        print("Done writing netCDF file", nc_out)
+
     utils.check_compliance(nc_out, conventions=ds.attrs["Conventions"])
 
     end_time = time.time()
@@ -286,6 +326,10 @@ def ds_rename_sig(ds, waves=False):
         "AmpBeam5": "amp_b5",
         "CorBeam5": "corr_b5",
         "Echo": "echo_amp",
+        "Headingstd": "Hdg_std",
+        "Pitchstd": "Ptch_std",
+        "Rollstd": "Roll_std",
+        "Pressurestd": "Pres_std",
     }
 
     for v in varnames:
@@ -695,6 +739,46 @@ def ds_add_attrs_sig(ds):
             }
         )
 
+    if "Hdg_std" in ds:
+        ds["Hdg_std"].attrs.update(
+            {
+                "units": "degrees",
+                "long_name": "Instrument heading standard deviation",
+                "standard_name": "platform_orientation",
+                "cell_methods": "time: standard_deviation",
+            }
+        )
+
+    if "Ptch_std" in ds:
+        ds["Ptch_std"].attrs.update(
+            {
+                "units": "degrees",
+                "long_name": "Instrument pitch standard deviation",
+                "standard_name": "platform_pitch",
+                "cell_methods": "time: standard_deviation",
+            }
+        )
+
+    if "Roll_std" in ds:
+        ds["Roll_std"].attrs.update(
+            {
+                "units": "degrees",
+                "long_name": "Instrument roll standard deviation",
+                "standard_name": "platform_roll",
+                "cell_methods": "time: standard_deviation",
+            }
+        )
+
+    if "Pres_std" in ds:
+        ds["Pres_std"].attrs.update(
+            {
+                "units": "dbar",
+                "long_name": "Uncorrected pressure standard deviation",
+                "standard_name": "sea_water_pressure",
+                "cell_methods": "time: standard_deviation",
+            }
+        )
+
     return ds
 
 
diff --git a/stglib/sig/mat2cdf.py b/stglib/sig/mat2cdf.py
index 3be0fa6f..57cac9a4 100644
--- a/stglib/sig/mat2cdf.py
+++ b/stglib/sig/mat2cdf.py
@@ -52,6 +52,23 @@ def load_mat_file(filnam):
             * np.arange(mat["Config"]["EchoSounder_NCells"])
         )
 
+    if mat["Config"]["Plan_AverageEnabled"] == "True":
+        bindistAVG = (
+            mat["Config"]["Average_BlankingDistance"]
+            + mat["Config"]["Average_CellSize"] / 2
+            + mat["Config"]["Average_CellSize"]
+            * np.arange(mat["Config"]["Average_NCells"])
+        )
+
+    if "Alt_Plan_AveargedEnabled" in mat["Config"]:
+        if mat["Config"]["Alt_Plan_AverageEnabled"] == "True":
+            bindistAltAVG = (
+                mat["Config"]["Alt_Average_BlankingDistance"]
+                + mat["Config"]["Alt_Average_CellSize"] / 2
+                + mat["Config"]["Alt_Average_CellSize"]
+                * np.arange(mat["Config"]["Alt_Average_NCells"])
+            )
+
     ds_dict = {}  # initialize dictionary for xarray datasets
     if (
         mat["Config"]["Plan_BurstEnabled"] == "True"
@@ -59,22 +76,26 @@ def load_mat_file(filnam):
         and mat["Config"]["Burst_Altimeter"] == "True"
     ):
         # BurstRawAltimeter
-        dsbra = xr.Dataset()
-        dsbra["time"] = xr.DataArray(
-            [matlab2datetime(x) for x in mat["Data"]["BurstRawAltimeter_Time"]],
-            dims="time",
-        )
-        dsbra["time"] = pd.DatetimeIndex(dsbra["time"])
-        dsbra["time"] = pd.DatetimeIndex(dsbra["time"])
-        dsbra.attrs["data_type"] = "BurstRawAltimeter"
-        ds_dict["dsbra"] = dsbra
+        if "BurstRawAltimeter_Time" in mat["Data"]:
+            dsbra = xr.Dataset()
+            dsbra["time"] = xr.DataArray(
+                [matlab2datetime(x) for x in mat["Data"]["BurstRawAltimeter_Time"]],
+                dims="time",
+            )
+            dsbra["time"] = pd.DatetimeIndex(dsbra["time"])
+            dsbra["time"] = pd.DatetimeIndex(dsbra["time"])
+            dsbra.attrs["data_type"] = "BurstRawAltimeter"
+            ds_dict["dsbra"] = dsbra
 
     if (
         mat["Config"]["Plan_BurstEnabled"] == "True"
         and mat["Config"]["Burst_NBeams"] == 5
     ):
         # IBurst
-        if mat["Config"]["Burst_HighResolution5"] == "True":
+        if (
+            mat["Config"]["Burst_HighResolution5"] == "True"
+            and "IBurstHR_Time" in mat["Data"]
+        ):
             dsi = xr.Dataset()
             dsi["time"] = pd.DatetimeIndex(
                 xr.DataArray(
@@ -87,7 +108,7 @@ def load_mat_file(filnam):
             dsi.attrs["data_type"] = "IBurstHR"
             ds_dict["dsi"] = dsi
 
-        else:
+        elif "IBurst_Time" in mat["Data"]:
             dsi = xr.Dataset()
             dsi["time"] = pd.DatetimeIndex(
                 xr.DataArray(
@@ -102,7 +123,10 @@ def load_mat_file(filnam):
 
     if mat["Config"]["Plan_BurstEnabled"] == "True":
         # Burst
-        if mat["Config"]["Burst_HighResolution"] == "True":
+        if (
+            mat["Config"]["Burst_HighResolution"] == "True"
+            and "BurstHR_Time" in mat["Data"]
+        ):
             dsb = xr.Dataset()
             dsb["time"] = pd.DatetimeIndex(
                 xr.DataArray(
@@ -115,7 +139,7 @@ def load_mat_file(filnam):
             dsb.attrs["data_type"] = "BurstHR"
             ds_dict["dsb"] = dsb
 
-        else:
+        elif "Burst_Time" in mat["Data"]:
             dsb = xr.Dataset()
             dsb["time"] = pd.DatetimeIndex(
                 xr.DataArray(
@@ -133,18 +157,54 @@ def load_mat_file(filnam):
         and mat["Config"]["Burst_EchoSounder"] == "True"
     ):
         # echo1 data - only handling echo1 data to start
-        freq1 = mat["Config"]["EchoSounder_Frequency1"]
-        dse1 = xr.Dataset()
-        dse1["time"] = pd.DatetimeIndex(
-            xr.DataArray(
-                [matlab2datetime(x) for x in mat["Data"][f"Echo1Bin1_{freq1}kHz_Time"]],
-                dims="time",
+        if "EchoSounder_Frequency1" in mat["Config"]:
+            freq1 = mat["Config"]["EchoSounder_Frequency1"]
+            if f"Echo1Bin1_{freq1}kHz_Time" in mat["Data"]:
+                dse1 = xr.Dataset()
+                dse1["time"] = pd.DatetimeIndex(
+                    xr.DataArray(
+                        [
+                            matlab2datetime(x)
+                            for x in mat["Data"][f"Echo1Bin1_{freq1}kHz_Time"]
+                        ],
+                        dims="time",
+                    )
+                )
+                dse1["time"] = pd.DatetimeIndex(dse1["time"])
+                dse1["bindist"] = xr.DataArray(bindistECHO, dims="bindist")
+                dse1.attrs["data_type"] = "Echo1"
+                ds_dict["dse1"] = dse1
+
+    if mat["Config"]["Plan_AverageEnabled"] == "True":
+        if "Average_Time" in mat["Data"]:
+            # Average
+            dsa = xr.Dataset()
+            dsa["time"] = pd.DatetimeIndex(
+                xr.DataArray(
+                    [matlab2datetime(x) for x in mat["Data"]["Average_Time"]],
+                    dims="time",
+                )
             )
-        )
-        dse1["time"] = pd.DatetimeIndex(dse1["time"])
-        dse1["bindist"] = xr.DataArray(bindistECHO, dims="bindist")
-        dse1.attrs["data_type"] = "Echo1"
-        ds_dict["dse1"] = dse1
+            dsa["time"] = pd.DatetimeIndex(dsa["time"])
+            dsa["bindist"] = xr.DataArray(bindistAVG, dims="bindist")
+            dsa.attrs["data_type"] = "Average"
+            ds_dict["dsa"] = dsa
+
+    if "Alt_Plan_AveargedEnabled" in mat["Config"]:
+        if mat["Config"]["Alt_Plan_AverageEnabled"] == "True":
+            if "Alt_Average_Time" in mat["Data"]:
+                # Alt Average
+                dsalt = xr.Dataset()
+                dsalt["time"] = pd.DatetimeIndex(
+                    xr.DataArray(
+                        [matlab2datetime(x) for x in mat["Data"]["Alt_Average_Time"]],
+                        dims="time",
+                    )
+                )
+                dsalt["time"] = pd.DatetimeIndex(dsalt["time"])
+                dsalt["bindist"] = xr.DataArray(bindistAltAVG, dims="bindist")
+                dsalt.attrs["data_type"] = "Alt_Average"
+                ds_dict["dsalt"] = dsalt
 
     for k in mat["Data"]:
         if "BurstRawAltimeter" in k:
@@ -253,6 +313,66 @@ def load_mat_file(filnam):
 
                 else:
                     print("still need to process", k, mat["Data"][k].shape)
+
+        elif re.match("^Average_", k):
+            if "_Time" not in k:
+                if mat["Data"][k].ndim == 1:
+                    dsa[k.split("_")[1]] = xr.DataArray(mat["Data"][k], dims="time")
+                elif mat["Data"][k].ndim == 2:
+                    if "AHRSRotationMatrix" in k:
+                        coords = {"dimRM": np.arange(9)}
+                        dsa["AHRSRotationMatrix"] = xr.DataArray(
+                            mat["Data"][k], dims=["time", "dimRM"]
+                        )
+                    if "Magnetometer" in k:
+                        coords = {"dimM": np.arange(3)}
+                        dsa["Magnetometer"] = xr.DataArray(
+                            mat["Data"][k], dims=["time", "dimM"]
+                        )
+                    if "Accelerometer" in k:
+                        coords = {"dimA": np.arange(3)}
+                        dsa["Accelerometer"] = xr.DataArray(
+                            mat["Data"][k], dims=["time", "dimA"]
+                        )
+                    # only checks to see if cells match on first sample
+                    elif dsa.attrs["data_type"] == "Average":
+                        if mat["Data"][k].shape[1] == mat["Data"]["Average_NCells"][0]:
+                            dsa[k.split("_")[1]] = xr.DataArray(
+                                mat["Data"][k], dims=["time", "bindist"]
+                            )
+
+                    else:
+                        print("still need to process", k, mat["Data"][k].shape)
+
+        elif re.match("^Alt_Average_", k):
+            if "_Time" not in k:
+                if mat["Data"][k].ndim == 1:
+                    dsalt[k.split("_")[2]] = xr.DataArray(mat["Data"][k], dims="time")
+                elif mat["Data"][k].ndim == 2:
+                    if "AHRSRotationMatrix" in k:
+                        coords = {"dimRM": np.arange(9)}
+                        dsalt["AHRSRotationMatrix"] = xr.DataArray(
+                            mat["Data"][k], dims=["time", "dimRM"]
+                        )
+                    if "Magnetometer" in k:
+                        coords = {"dimM": np.arange(3)}
+                        dsalt["Magnetometer"] = xr.DataArray(
+                            mat["Data"][k], dims=["time", "dimM"]
+                        )
+                    if "Accelerometer" in k:
+                        coords = {"dimA": np.arange(3)}
+                        dsalt["Accelerometer"] = xr.DataArray(
+                            mat["Data"][k], dims=["time", "dimA"]
+                        )
+                    # only checks to see if cells match on first sample
+                    elif dsalt.attrs["data_type"] == "Alt_Average":
+                        if mat["Data"][k].shape[1] == mat["Data"]["Average_NCells"][0]:
+                            dsalt[k.split("_")[2]] = xr.DataArray(
+                                mat["Data"][k], dims=["time", "bindist"]
+                            )
+
+                    else:
+                        print("still need to process", k, mat["Data"][k].shape)
         else:
             print("missing variable:", k)
 
@@ -271,7 +391,7 @@ def load_mat_file(filnam):
 
 def read_config_mat(mat, ds):
     for k in mat["Config"]:
-        if k == "Burst_Beam2xyz":
+        if re.search("_Beam2xyz$", k):
             ds.attrs[f"SIG{k}"] = str(mat["Config"][k])
         else:
             ds.attrs[f"SIG{k}"] = mat["Config"][k]
@@ -295,8 +415,8 @@ def add_units(mat, ds):
 
 def add_transmatrix(mat, ds):
     for k in mat["Config"]:
-        if "Beam2xyz" in k:
-            var = k.split("_")[1]
+        if f"{ds.attrs['data_type']}_Beam2xyz" in k:
+            var = k.split("_")[-1]
             ds[var] = xr.DataArray(mat["Config"][k])
 
 
@@ -347,7 +467,11 @@ def loadpar(f):
             print(f"Finished writing data to {cdf_filename}")
 
     matfiles = glob.glob(f"{basefile}_*.mat")
-    Parallel(n_jobs=-1, verbose=10)(delayed(loadpar)(f) for f in matfiles)
+    print(matfiles)
+    if len(matfiles) > 1:
+        Parallel(n_jobs=-1, verbose=10)(delayed(loadpar)(f) for f in matfiles)
+    else:
+        loadpar(matfiles[0])
 
     dsd = load_mat_file(matfiles[0])  # get minimal dsd file for below
     cdffiles = glob.glob(f"{prefix}{outdir}*-raw.cdf")
@@ -453,6 +577,52 @@ def loadpar(f):
                 f"Failed to read or write netCDF file(s) for data_type {dse1.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
             )
 
+    if "dsa" in dsd:
+        dsa = dsd["dsa"]
+        fin = outdir + f"*-{dsa.attrs['data_type']}-*.cdf"
+        try:
+            ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
+            ds = aqdutils.check_attrs(ds, inst_type="SIG")
+            if "Beam2xyz" in ds:
+                if "time" in ds["Beam2xyz"].dims:
+                    ds["Beam2xyz"] = ds["Beam2xyz"].isel(time=0, drop=True)
+            # write out all into single -raw.cdf files per data_type
+            cdf_filename = prefix + ds.attrs["filename"] + "_avgd-raw.cdf"
+            print("writing Average to netcdf")
+            delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
+            with ProgressBar():
+                delayed_obj.compute()
+
+            print(f"Finished writing data to {cdf_filename}")
+
+        except ValueError as ve:
+            print(
+                f"Failed to read or write netCDF file(s) for data_type {dsa.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
+            )
+
+    if "dsalt" in dsd:
+        dsalt = dsd["dsalt"]
+        fin = outdir + f"*-{dsalt.attrs['data_type']}-*.cdf"
+        try:
+            ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
+            ds = aqdutils.check_attrs(ds, inst_type="SIG")
+            if "Beam2xyz" in ds:
+                if "time" in ds["Beam2xyz"].dims:
+                    ds["Beam2xyz"] = ds["Beam2xyz"].isel(time=0, drop=True)
+            # write out all into single -raw.cdf files per data_type
+            cdf_filename = prefix + ds.attrs["filename"] + "_altavgd-raw.cdf"
+            print("writing Average to netcdf")
+            delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
+            with ProgressBar():
+                delayed_obj.compute()
+
+            print(f"Finished writing data to {cdf_filename}")
+
+        except ValueError as ve:
+            print(
+                f"Failed to read or write netCDF file(s) for data_type {dsalt.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
+            )
+
     toc = time.time()
     etime = round(toc - tic, 0)
     print(f"elapsed time = {etime}")
diff --git a/stglib/tests/test_scripts.py b/stglib/tests/test_scripts.py
index 5c4bc254..087a2219 100644
--- a/stglib/tests/test_scripts.py
+++ b/stglib/tests/test_scripts.py
@@ -363,7 +363,7 @@ def sig_nc(nc_file):
     assert "Done writing netCDF file" in result.stdout.decode("utf8")
 
 
-@pytest.mark.skip(reason="works locally but not on github built-in checks")
+# @pytest.mark.skip(reason="works locally but not on github built-in checks")
 def test_sig():
     sig_mat("glob_att1126_sig1.txt", "sig1126_config.yaml")
     print(os.listdir())

From 7c6cfba3eb9d4d73d7f71b1d01cc8f6189c730e4 Mon Sep 17 00:00:00 2001
From: ssuttles-usgs
 <ssuttles@usgs.govgit config -lgit config --global user.email ssuttles@usgs.gov>
Date: Wed, 15 May 2024 10:19:45 -0400
Subject: [PATCH 2/7] check tests

---
 stglib/tests/test_scripts.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/stglib/tests/test_scripts.py b/stglib/tests/test_scripts.py
index 087a2219..759e5efc 100644
--- a/stglib/tests/test_scripts.py
+++ b/stglib/tests/test_scripts.py
@@ -363,7 +363,9 @@ def sig_nc(nc_file):
     assert "Done writing netCDF file" in result.stdout.decode("utf8")
 
 
-# @pytest.mark.skip(reason="works locally but not on github built-in checks")
+pytest.mark.skip(reason="works locally but not on github built-in checks")
+
+
 def test_sig():
     sig_mat("glob_att1126_sig1.txt", "sig1126_config.yaml")
     print(os.listdir())

From 30ecb688848ddd4631f1528a46037d473cb6edfb Mon Sep 17 00:00:00 2001
From: ssuttles-usgs
 <ssuttles@usgs.govgit config -lgit config --global user.email ssuttles@usgs.gov>
Date: Thu, 16 May 2024 19:03:57 -0400
Subject: [PATCH 3/7] add tmat + fixes

---
 stglib/core/utils.py         |   2 +-
 stglib/sig/cdf2nc.py         | 119 +++++++++++++++++++++++++++--------
 stglib/sig/mat2cdf.py        |   7 ++-
 stglib/tests/test_scripts.py |   4 +-
 4 files changed, 98 insertions(+), 34 deletions(-)

diff --git a/stglib/core/utils.py b/stglib/core/utils.py
index 83e59f41..8d53095e 100644
--- a/stglib/core/utils.py
+++ b/stglib/core/utils.py
@@ -179,7 +179,7 @@ def add_min_max(ds, exclude_vars=None):
 
     exclude = list(ds.dims)
     [exclude.append(k) for k in ds.variables if "time" in k]
-    exclude.extend(["TIM", "TransMatrix", "orientmat"])
+    exclude.extend(["TIM", "TransMatrix", "orientmat", "beam2xyz"])
     if exclude_vars:
         exclude.extend(exclude_vars)
 
diff --git a/stglib/sig/cdf2nc.py b/stglib/sig/cdf2nc.py
index 74c14e7d..b41f1ea1 100644
--- a/stglib/sig/cdf2nc.py
+++ b/stglib/sig/cdf2nc.py
@@ -89,6 +89,8 @@ def cdf_to_nc(cdf_filename, atmpres=False):
 
     ds = aqdutils.make_bin_depth(ds)
 
+    ds = ds_make_tmat(ds)
+
     ds = ds_make_magaccel_vars(ds)
 
     ds = ds_make_ahrs_vars(ds)
@@ -107,11 +109,6 @@ def cdf_to_nc(cdf_filename, atmpres=False):
     ds = aqdutils.ds_add_attrs(ds, inst_type="SIG")  # for common adcp vars
     ds = ds_add_attrs_sig(ds)  # for signature vars
 
-    # Add min/max values
-    # if ds.attrs["data_type"] not in ["Echo1"]:
-    print("add max/min variable attributes")
-    ds = utils.add_min_max(ds)
-
     # Add DELTA_T for EPIC compliance
     # ds = utils.add_delta_t(ds)
 
@@ -123,33 +120,18 @@ def cdf_to_nc(cdf_filename, atmpres=False):
 
     ds = utils.add_standard_names(ds)  # add common standard names
 
-    # ds = drop_unused_dims(ds)
+    ds = drop_unused_dims(ds)
 
-    # ds = fix_encoding(ds)
+    ds = fix_encoding(ds)
 
     ds = utils.ds_add_lat_lon(ds)
 
     ds = utils.ds_coord_no_fillvalue(ds)
-    """
-    ds["time"].attrs.update(
-        {"standard_name": "time", "axis": "T", "long_name": "time (UTC)"}
-    )
-    """
-    att2del = []
-    for k in ds.attrs:
-        if re.search("_Beam2xyz$", k):
-            print(k)
-            att2del.append(k)
 
-    for k in att2del:
-        del ds.attrs[k]
+    ds = drop_attrs(ds)
 
-    for j in ds.data_vars:
-        for k in ds[j].attrs:
-
-            if type(ds[j].attrs[k]) is np.ndarray:
-                shp = len(ds[j].attrs[k].shape)
-                print(f"{j},{k},{shp}")
+    # Add min/max values
+    ds = utils.add_min_max(ds)
 
     # write out nc file by data_type
     if "prefix" in ds.attrs:
@@ -173,7 +155,7 @@ def cdf_to_nc(cdf_filename, atmpres=False):
             delayed_obj.compute()
         print("Done writing netCDF file", nc_out)
 
-    elif ds.attrs["data_type"] == "Echo1":
+    elif ds.attrs["data_type"] == "EchoSounder":
         nc_out = nc_filename + "e1-cal.nc"
         print("writing Echo1 (echo1) data to netCDF nc file")
         delayed_obj = ds.to_netcdf(nc_out, compute=False)
@@ -224,6 +206,50 @@ def drop_unused_dims(ds):
     return ds
 
 
+def drop_attrs(ds):
+    """Drop some global attrs"""
+    att2del = []
+    for k in ds.attrs:
+        if re.search("_Beam2xyz$", k):
+            att2del.append(k)
+
+    for k in att2del:
+        del ds.attrs[k]
+
+    # Get rid of some of the instrument header attributes for other data_types
+    dtlist = [
+        "Burst",
+        "BurstHR",
+        "IBurst",
+        "IBurstHR",
+        "EchoSounder",
+        "Average",
+        "Alt_Average",
+        "Alt_Burst",
+    ]
+    if ds.attrs["data_type"] in dtlist:
+        dtlist.remove(ds.attrs["data_type"])
+
+    rm = []  # initialize list of attrs to be removed
+    for k in dtlist:
+        for j in ds.attrs:
+            if re.match(f"^SIG{k}_", j):
+                rm.append(j)
+    for k in rm:
+        del ds.attrs[k]
+
+    """
+    for j in ds.data_vars:
+        for k in ds[j].attrs:
+
+            if type(ds[j].attrs[k]) is np.ndarray:
+                shp = len(ds[j].attrs[k].shape)
+                print(f"{j},{k},{shp}")
+    """
+
+    return ds
+
+
 def ds_drop(ds):
     """
     Drop old DataArrays from Dataset that won't make it into the final .nc file
@@ -254,7 +280,7 @@ def ds_drop(ds):
         "VelY",
         "VelZ1",
         "VelZ2",
-        "Beam2xyz",
+        # "Beam2xyz",
         "AHRSRotationMatrix",
         "AHRSGyroX",
         "AHRSGyroY",
@@ -330,6 +356,7 @@ def ds_rename_sig(ds, waves=False):
         "Pitchstd": "Ptch_std",
         "Rollstd": "Roll_std",
         "Pressurestd": "Pres_std",
+        # "Beam2xyz": "TransMatrix",
     }
 
     for v in varnames:
@@ -739,6 +766,14 @@ def ds_add_attrs_sig(ds):
             }
         )
 
+    if "TransMatrix" in ds:
+        ds["TransMatrix"].attrs.update(
+            {
+                "units": "1",
+                "long_name": "Instrument Transformation Matrix",
+            }
+        )
+
     if "Hdg_std" in ds:
         ds["Hdg_std"].attrs.update(
             {
@@ -848,3 +883,33 @@ def ds_make_ahrs_vars(ds):
         )
 
     return ds
+
+
+def ds_make_tmat(ds):
+    """
+    add instrument Transformation Matrix to xarray Dataset
+    """
+    # rename to TransMatrix
+    varnames = {"Beam2xyz": "TransMatrix"}
+    for v in varnames:
+        if v in ds:
+            ds = ds.rename({v: varnames[v]})
+
+    # swap dims in Tmat
+    if "TransMatrix" in ds.data_vars:
+        n = ds["TransMatrix"].shape[0]
+        if n == 4:
+            if "inst4" not in ds.dims:
+                ds["inst4"] = xr.DataArray(["X", "Y", "Z1", "Z2"], dims="inst4")
+
+            if "beam" not in ds.dims:
+                ds["beam"] = xr.DataArray(
+                    range(1, ds["NBeams"][0].values + 1), dims="beam"
+                )
+
+            v = "TransMatrix"
+            tdims = ds[v].dims
+            ds[v] = ds[v].swap_dims({tdims[0]: "inst4"})
+            ds[v] = ds[v].swap_dims({tdims[1]: "beam"})
+
+    return ds
diff --git a/stglib/sig/mat2cdf.py b/stglib/sig/mat2cdf.py
index 57cac9a4..1a313654 100644
--- a/stglib/sig/mat2cdf.py
+++ b/stglib/sig/mat2cdf.py
@@ -60,7 +60,7 @@ def load_mat_file(filnam):
             * np.arange(mat["Config"]["Average_NCells"])
         )
 
-    if "Alt_Plan_AveargedEnabled" in mat["Config"]:
+    if "Alt_Plan_AverageEnabled" in mat["Config"]:
         if mat["Config"]["Alt_Plan_AverageEnabled"] == "True":
             bindistAltAVG = (
                 mat["Config"]["Alt_Average_BlankingDistance"]
@@ -172,7 +172,7 @@ def load_mat_file(filnam):
                 )
                 dse1["time"] = pd.DatetimeIndex(dse1["time"])
                 dse1["bindist"] = xr.DataArray(bindistECHO, dims="bindist")
-                dse1.attrs["data_type"] = "Echo1"
+                dse1.attrs["data_type"] = "EchoSounder"
                 ds_dict["dse1"] = dse1
 
     if mat["Config"]["Plan_AverageEnabled"] == "True":
@@ -190,7 +190,7 @@ def load_mat_file(filnam):
             dsa.attrs["data_type"] = "Average"
             ds_dict["dsa"] = dsa
 
-    if "Alt_Plan_AveargedEnabled" in mat["Config"]:
+    if "Alt_Plan_AverageEnabled" in mat["Config"]:
         if mat["Config"]["Alt_Plan_AverageEnabled"] == "True":
             if "Alt_Average_Time" in mat["Data"]:
                 # Alt Average
@@ -580,6 +580,7 @@ def loadpar(f):
     if "dsa" in dsd:
         dsa = dsd["dsa"]
         fin = outdir + f"*-{dsa.attrs['data_type']}-*.cdf"
+        print(fin)
         try:
             ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
             ds = aqdutils.check_attrs(ds, inst_type="SIG")
diff --git a/stglib/tests/test_scripts.py b/stglib/tests/test_scripts.py
index 759e5efc..087a2219 100644
--- a/stglib/tests/test_scripts.py
+++ b/stglib/tests/test_scripts.py
@@ -363,9 +363,7 @@ def sig_nc(nc_file):
     assert "Done writing netCDF file" in result.stdout.decode("utf8")
 
 
-pytest.mark.skip(reason="works locally but not on github built-in checks")
-
-
+# @pytest.mark.skip(reason="works locally but not on github built-in checks")
 def test_sig():
     sig_mat("glob_att1126_sig1.txt", "sig1126_config.yaml")
     print(os.listdir())

From 6c8bd76f89731bddcf206819d4b8d71bf1bab8d6 Mon Sep 17 00:00:00 2001
From: ssuttles-usgs
 <ssuttles@usgs.govgit config -lgit config --global user.email ssuttles@usgs.gov>
Date: Tue, 21 May 2024 13:34:58 -0400
Subject: [PATCH 4/7] add tests, clean-up code

---
 .gitattributes                                |   2 +
 stglib/sig/cdf2nc.py                          |  69 ++--
 stglib/sig/mat2cdf.py                         | 147 ++------
 stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt | 319 ++++++++++++++++++
 stglib/tests/data/gatts_MIA23SH2_cf_rev.txt   |  22 ++
 .../data/mat3/MIA23Sig1000_0001_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0002_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0003_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0004_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0005_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0006_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0007_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0008_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0009_avgd.mat      |   3 +
 .../data/mat3/MIA23Sig1000_0010_avgd.mat      |   3 +
 stglib/tests/data/sig_avg_config.yaml         |  17 +
 stglib/tests/test_scripts.py                  |   6 +-
 17 files changed, 458 insertions(+), 154 deletions(-)
 create mode 100644 stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt
 create mode 100644 stglib/tests/data/gatts_MIA23SH2_cf_rev.txt
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0001_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0002_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0003_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0004_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0005_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0006_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0007_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0008_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0009_avgd.mat
 create mode 100644 stglib/tests/data/mat3/MIA23Sig1000_0010_avgd.mat
 create mode 100644 stglib/tests/data/sig_avg_config.yaml

diff --git a/.gitattributes b/.gitattributes
index 07b88009..dd01487a 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -4,3 +4,5 @@ stglib/_version.py export-subst
 stglib/tests/data/055109_20220808_1605.zip filter=lfs diff=lfs merge=lfs -text
 stglib/tests/data/055109_20220808_1605_config.yaml filter=lfs diff=lfs merge=lfs -text
 stglib/tests/data/gatts_055109_20220808_1605.txt filter=lfs diff=lfs merge=lfs -text
+stglib/tests/data/*.cdf filter=lfs diff=lfs merge=lfs -text
+stglib/tests/data/mat3/* filter=lfs diff=lfs merge=lfs -text
diff --git a/stglib/sig/cdf2nc.py b/stglib/sig/cdf2nc.py
index b41f1ea1..bdfe4610 100644
--- a/stglib/sig/cdf2nc.py
+++ b/stglib/sig/cdf2nc.py
@@ -46,7 +46,6 @@ def cdf_to_nc(cdf_filename, atmpres=False):
     # print(ds)
 
     # create Z depending on orientation
-    # ds, T, T_orig = aqdutils.set_orientation(ds, ds["Burst_Beam2xyz"].values)
     ds = utils.create_z(ds)
 
     # Clip data to in/out water times or via good_ens
@@ -109,6 +108,8 @@ def cdf_to_nc(cdf_filename, atmpres=False):
     ds = aqdutils.ds_add_attrs(ds, inst_type="SIG")  # for common adcp vars
     ds = ds_add_attrs_sig(ds)  # for signature vars
 
+    ds = fix_encoding(ds)
+
     # Add DELTA_T for EPIC compliance
     # ds = utils.add_delta_t(ds)
 
@@ -122,8 +123,6 @@ def cdf_to_nc(cdf_filename, atmpres=False):
 
     ds = drop_unused_dims(ds)
 
-    ds = fix_encoding(ds)
-
     ds = utils.ds_add_lat_lon(ds)
 
     ds = utils.ds_coord_no_fillvalue(ds)
@@ -166,7 +165,6 @@ def cdf_to_nc(cdf_filename, atmpres=False):
     elif ds.attrs["data_type"] == "Average":
         nc_out = nc_filename + "avg-cal.nc"
         print("writing Average (avg) data to netCDF nc file")
-        print(ds.attrs)
         delayed_obj = ds.to_netcdf(nc_out, compute=False)
         with ProgressBar():
             delayed_obj.compute()
@@ -175,7 +173,6 @@ def cdf_to_nc(cdf_filename, atmpres=False):
     elif ds.attrs["data_type"] == "Alt_Average":
         nc_out = nc_filename + "alt-cal.nc"
         print("writing Alt_Average (avg) data to netCDF nc file")
-        print(ds.attrs)
         delayed_obj = ds.to_netcdf(nc_out, compute=False)
         with ProgressBar():
             delayed_obj.compute()
@@ -238,15 +235,6 @@ def drop_attrs(ds):
     for k in rm:
         del ds.attrs[k]
 
-    """
-    for j in ds.data_vars:
-        for k in ds[j].attrs:
-
-            if type(ds[j].attrs[k]) is np.ndarray:
-                shp = len(ds[j].attrs[k].shape)
-                print(f"{j},{k},{shp}")
-    """
-
     return ds
 
 
@@ -280,7 +268,6 @@ def ds_drop(ds):
         "VelY",
         "VelZ1",
         "VelZ2",
-        # "Beam2xyz",
         "AHRSRotationMatrix",
         "AHRSGyroX",
         "AHRSGyroY",
@@ -356,7 +343,6 @@ def ds_rename_sig(ds, waves=False):
         "Pitchstd": "Ptch_std",
         "Rollstd": "Roll_std",
         "Pressurestd": "Pres_std",
-        # "Beam2xyz": "TransMatrix",
     }
 
     for v in varnames:
@@ -384,19 +370,26 @@ def ds_rename_sig(ds, waves=False):
 
 def fix_encoding(ds):
     """ensure we don't set dtypes uint for CF compliance"""
-    if "sample" not in ds.dims:
+    if "units" in ds["time"].encoding:
+        ds["time"].encoding.pop("units")
+
+    tstep = ds["time"][1] - ds["time"][0]
+    # if "sample" not in ds.dims:
+    if tstep < np.timedelta64(1, "m"):
         print(
-            "make time encoding to dtype double because no sample dimension, round to milliseconds first"
+            f"make time encoding to dtype double because tstep {tstep} seconds is < 1 minute, round to milliseconds first"
         )
         ds["time"] = ds["time"].dt.round("ms")  # round time to milliseconds first
+        print("make time encoding to dtype double because time step < 1 minute")
         ds["time"].encoding["dtype"] = "double"
-        """if ds[var].max() > 2**31 - 1 or ds[var].min() < -(2**31):
-                print(
-                    f"warning {var} may be too big to fit in int32: min {ds[var].min().values}, max {ds[var].max().values} so make double"
-                )
-               ds[var].encoding["dtype"] = "double"
-               """
+
     else:
+        print(
+            f"make time encoding int because tstep {tstep} seconds is >= 1 minute, round time to seconds first"
+        )
+        ds["time"] = ds["time"].dt.round(
+            "s"
+        )  # round time to seconds if time interval >= 1 minute
         ds["time"].encoding["dtype"] = "i4"
 
     if "beam" in ds.dims:
@@ -417,27 +410,39 @@ def ds_add_attrs_sig(ds):
     """
     add attributes to xarray Dataset
     """
-    """
-    ds["time"].attrs.update(
-        {"standard_name": "time", "axis": "T", "long_name": "time (UTC)"}
-    )
-    """
+
     if "earth" in ds:
         ds["earth"].attrs.update(
             {
-                "units": "1",
+                # "units": "1",
                 "long_name": "Earth Reference Frame",
             }
         )
 
+    if "earth4" in ds:
+        ds["earth4"].attrs.update(
+            {
+                # "units": "1",
+                "long_name": "Earth Reference Frame for 4 beam ADCP",
+            }
+        )
+
     if "inst" in ds:
         ds["inst"].attrs.update(
             {
-                "units": "1",
+                # "units": "1",
                 "long_name": "Instrumnet Reference Frame",
             }
         )
 
+    if "inst4" in ds:
+        ds["inst4"].attrs.update(
+            {
+                # "units": "1",
+                "long_name": "Instrumnet Reference Frame for 4 beam ADCP",
+            }
+        )
+
     if "beam" in ds:
         ds["beam"].attrs.update(
             {
@@ -769,7 +774,7 @@ def ds_add_attrs_sig(ds):
     if "TransMatrix" in ds:
         ds["TransMatrix"].attrs.update(
             {
-                "units": "1",
+                # "units": "1",
                 "long_name": "Instrument Transformation Matrix",
             }
         )
diff --git a/stglib/sig/mat2cdf.py b/stglib/sig/mat2cdf.py
index 1a313654..6a1854ee 100644
--- a/stglib/sig/mat2cdf.py
+++ b/stglib/sig/mat2cdf.py
@@ -467,7 +467,7 @@ def loadpar(f):
             print(f"Finished writing data to {cdf_filename}")
 
     matfiles = glob.glob(f"{basefile}_*.mat")
-    print(matfiles)
+    # print(matfiles)
     if len(matfiles) > 1:
         Parallel(n_jobs=-1, verbose=10)(delayed(loadpar)(f) for f in matfiles)
     else:
@@ -488,9 +488,10 @@ def loadpar(f):
         chunksizes = {"time": 200000, "bindist": 48}
         print(f"Using default chunksizes = {chunksizes}")
 
-    if "dsb" in dsd:
-        dsb = dsd["dsb"]
-        fin = outdir + f"*-{dsb.attrs['data_type']}-*.cdf"
+    for k in dsd:
+        # dsb = dsd["dsb"]
+        fin = outdir + f"*-{dsd[k].attrs['data_type']}-*.cdf"
+        print(k)
         try:
             ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
             ds = aqdutils.check_attrs(ds, inst_type="SIG")
@@ -498,8 +499,27 @@ def loadpar(f):
                 if "time" in ds["Beam2xyz"].dims:
                     ds["Beam2xyz"] = ds["Beam2xyz"].isel(time=0, drop=True)
             # write out all into single -raw.cdf files per data_type
-            cdf_filename = prefix + ds.attrs["filename"] + "_burst-raw.cdf"
-            print("writing Burst to netcdf")
+            if (
+                ds.attrs["data_type"].lower() == "burst"
+                or ds.attrs["data_type"].lower() == "bursthr"
+            ):
+                ftype = "burst"
+            elif (
+                ds.attrs["data_type"].lower() == "iburst"
+                or ds.attrs["data_type"].lower() == "ibursthr"
+            ):
+                ftype = "iburst"
+            elif ds.attrs["data_type"].lower() == "echosounder":
+                ftype = "echo1"
+            elif ds.attrs["data_type"].lower() == "burstrawaltimeter":
+                ftype = "burstrawalt"
+            elif ds.attrs["data_type"].lower() == "average":
+                ftype = "avgd"
+            elif ds.attrs["data_type"].lower() == "alt_average":
+                ftype = "altavgd"
+
+            cdf_filename = prefix + ds.attrs["filename"] + f"_{ftype}-raw.cdf"
+            print(f"writing {ftype} to netcdf")
             delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
             with ProgressBar():
                 delayed_obj.compute()
@@ -508,120 +528,7 @@ def loadpar(f):
 
         except ValueError as ve:
             print(
-                f"Failed to read or write netCDF file(s) for data_type {dsb.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
-            )
-
-    if "dsi" in dsd:
-        dsi = dsd["dsi"]
-        fin = outdir + f"*-{dsi.attrs['data_type']}-*.cdf"
-        try:
-            ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
-            ds = aqdutils.check_attrs(ds, inst_type="SIG")
-            if "Beam2xyz" in ds:
-                if "time" in ds["Beam2xyz"].dims:
-                    ds["Beam2xyz"] = ds["Beam2xyz"].isel(time=0, drop=True)
-            # write out all into single -raw.cdf files per data_type
-            cdf_filename = prefix + ds.attrs["filename"] + "_iburst-raw.cdf"
-            print("writing IBurst to netcdf")
-            delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
-            with ProgressBar():
-                delayed_obj.compute()
-
-            print(f"Finished writing data to {cdf_filename}")
-
-        except ValueError as ve:
-            print(
-                f"Failed to read or write netCDF file(s) for data_type {dsi.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
-            )
-
-    if "dsbra" in dsd:
-        dsbra = dsd["dsbra"]
-        fin = outdir + f"*-{dsbra.attrs['data_type']}-*.cdf"
-        try:
-            ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
-            ds = aqdutils.check_attrs(ds, inst_type="SIG")
-            # write out all into single -raw.cdf files per data_type
-            cdf_filename = prefix + ds.attrs["filename"] + "_burstrawalt-raw.cdf"
-            print("writing BurstRawAltimeter to netcdf")
-            delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
-            with ProgressBar():
-                delayed_obj.compute()
-
-            print(f"Finished writing data to {cdf_filename}")
-
-        except ValueError as ve:
-            print(
-                f"Failed to read or write netCDF file(s) for data_type {dsbra.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
-            )
-
-    if "dse1" in dsd:
-        dse1 = dsd["dse1"]
-        try:
-            fin = outdir + f"*-{dse1.attrs['data_type']}-*.cdf"
-            ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
-            ds = aqdutils.check_attrs(ds, inst_type="SIG")
-            if "Beam2xyz" in ds:
-                if "time" in ds["Beam2xyz"].dims:
-                    ds["Beam2xyz"] = ds["Beam2xyz"].isel(time=0, drop=True)
-            # write out all into single -raw.cdf files per data_type
-            cdf_filename = prefix + ds.attrs["filename"] + "_echo1-raw.cdf"
-            print("writing Echo1 to netcdf")
-            delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
-            with ProgressBar():
-                delayed_obj.compute()
-
-            print(f"Finished writing data to {cdf_filename}")
-
-        except ValueError as ve:
-            print(
-                f"Failed to read or write netCDF file(s) for data_type {dse1.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
-            )
-
-    if "dsa" in dsd:
-        dsa = dsd["dsa"]
-        fin = outdir + f"*-{dsa.attrs['data_type']}-*.cdf"
-        print(fin)
-        try:
-            ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
-            ds = aqdutils.check_attrs(ds, inst_type="SIG")
-            if "Beam2xyz" in ds:
-                if "time" in ds["Beam2xyz"].dims:
-                    ds["Beam2xyz"] = ds["Beam2xyz"].isel(time=0, drop=True)
-            # write out all into single -raw.cdf files per data_type
-            cdf_filename = prefix + ds.attrs["filename"] + "_avgd-raw.cdf"
-            print("writing Average to netcdf")
-            delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
-            with ProgressBar():
-                delayed_obj.compute()
-
-            print(f"Finished writing data to {cdf_filename}")
-
-        except ValueError as ve:
-            print(
-                f"Failed to read or write netCDF file(s) for data_type {dsa.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
-            )
-
-    if "dsalt" in dsd:
-        dsalt = dsd["dsalt"]
-        fin = outdir + f"*-{dsalt.attrs['data_type']}-*.cdf"
-        try:
-            ds = xr.open_mfdataset(fin, parallel=True, chunks=chunksizes)
-            ds = aqdutils.check_attrs(ds, inst_type="SIG")
-            if "Beam2xyz" in ds:
-                if "time" in ds["Beam2xyz"].dims:
-                    ds["Beam2xyz"] = ds["Beam2xyz"].isel(time=0, drop=True)
-            # write out all into single -raw.cdf files per data_type
-            cdf_filename = prefix + ds.attrs["filename"] + "_altavgd-raw.cdf"
-            print("writing Average to netcdf")
-            delayed_obj = ds.to_netcdf(cdf_filename, compute=False)
-            with ProgressBar():
-                delayed_obj.compute()
-
-            print(f"Finished writing data to {cdf_filename}")
-
-        except ValueError as ve:
-            print(
-                f"Failed to read or write netCDF file(s) for data_type {dsalt.attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
+                f"Failed to read or write netCDF file(s) for data_type {dsd[k].attrs['data_type']} to make composite -raw.cdf file, due to Value Error: '{ve}'"
             )
 
     toc = time.time()
diff --git a/stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt b/stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt
new file mode 100644
index 00000000..73989c7a
--- /dev/null
+++ b/stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt
@@ -0,0 +1,319 @@
+netcdf MIAsigavg-cal {
+dimensions:
+        time = 14921 ;
+        inst4 = 4 ;
+        beam = 4 ;
+        z = 15 ;
+        inst = 3 ;
+        latitude = 1 ;
+        longitude = 1 ;
+variables:
+        int time(time) ;
+                time:standard_name = "time" ;
+                time:axis = "T" ;
+                time:long_name = "time (UTC)" ;
+                time:units = "seconds since 2023-06-23 16:00:00" ;
+                time:calendar = "proleptic_gregorian" ;
+        int status(time) ;
+                status:long_name = "Status Code" ;
+                status:units = "1" ;
+                status:minimum = 944504834U ;
+                status:maximum = 944505858U ;
+        int error(time) ;
+                error:long_name = "Error Code" ;
+                error:units = "1" ;
+                error:minimum = 0U ;
+                error:maximum = 0U ;
+        int sample(time) ;
+                sample:long_name = "sample number" ;
+                sample:units = "1" ;
+                sample:minimum = 1U ;
+                sample:maximum = 120U ;
+        float ambig_vel(time) ;
+                ambig_vel:_FillValue = NaNf ;
+                ambig_vel:units = "m s-1" ;
+                ambig_vel:long_name = "Ambiguity velocity" ;
+                ambig_vel:minimum = 10.725f ;
+                ambig_vel:maximum = 10.77105f ;
+        float Bat_106(time) ;
+                Bat_106:_FillValue = NaNf ;
+                Bat_106:long_name = "Battery voltage" ;
+                Bat_106:units = "V" ;
+                Bat_106:epic_code = 106 ;
+                Bat_106:minimum = 18.3f ;
+                Bat_106:maximum = 18.7f ;
+        float Hdg_1215(time) ;
+                Hdg_1215:_FillValue = NaNf ;
+                Hdg_1215:units = "degrees" ;
+                Hdg_1215:long_name = "Instrument Heading" ;
+                Hdg_1215:epic_code = 1215 ;
+                Hdg_1215:note = "Heading is degrees true. Converted from magnetic with magnetic variation of -7.250000." ;
+                Hdg_1215:standard_name = "platform_orientation" ;
+                Hdg_1215:minimum = 0.6727271f ;
+                Hdg_1215:maximum = 1.6725f ;
+        float Ptch_1216(time) ;
+                Ptch_1216:_FillValue = NaNf ;
+                Ptch_1216:long_name = "Instrument Pitch" ;
+                Ptch_1216:units = "degrees" ;
+                Ptch_1216:epic_code = 1216 ;
+                Ptch_1216:standard_name = "platform_pitch" ;
+                Ptch_1216:minimum = 3.86575f ;
+                Ptch_1216:maximum = 3.983917f ;
+        float Roll_1217(time) ;
+                Roll_1217:_FillValue = NaNf ;
+                Roll_1217:long_name = "Instrument Roll" ;
+                Roll_1217:units = "degrees" ;
+                Roll_1217:epic_code = 1217 ;
+                Roll_1217:standard_name = "platform_roll" ;
+                Roll_1217:minimum = 0.11f ;
+                Roll_1217:maximum = 0.2039166f ;
+        float Tx_1211(time) ;
+                Tx_1211:_FillValue = NaNf ;
+                Tx_1211:long_name = "Instrument Internal Temperature" ;
+                Tx_1211:units = "degree_C" ;
+                Tx_1211:epic_code = 1211 ;
+                Tx_1211:minimum = 29.3915f ;
+                Tx_1211:maximum = 32.70192f ;
+        float SV_80(time) ;
+                SV_80:_FillValue = NaNf ;
+                SV_80:units = "m s-1" ;
+                SV_80:epic_code = 80 ;
+                SV_80:long_name = "Speed of Sound" ;
+                SV_80:standard_name = "speed_of_sound_in_sea_water" ;
+                SV_80:minimum = 1544.4f ;
+                SV_80:maximum = 1551.037f ;
+        float P_1(time) ;
+                P_1:_FillValue = NaNf ;
+                P_1:long_name = "Uncorrected pressure" ;
+                P_1:units = "dbar" ;
+                P_1:epic_code = 1 ;
+                P_1:standard_name = "sea_water_pressure" ;
+                P_1:minimum = 2.794817f ;
+                P_1:maximum = 3.990317f ;
+        float xmit_energy(time) ;
+                xmit_energy:_FillValue = NaNf ;
+                xmit_energy:long_name = "Transmit Energy" ;
+                xmit_energy:units = "dB" ;
+                xmit_energy:minimum = 94.f ;
+                xmit_energy:maximum = 106.f ;
+        int corr_nominal(time) ;
+                corr_nominal:long_name = "Nominal Correlation" ;
+                corr_nominal:units = "percent" ;
+                corr_nominal:minimum = 60UB ;
+                corr_nominal:maximum = 60UB ;
+        float TransMatrix(inst4, beam) ;
+                TransMatrix:units = "1" ;
+                TransMatrix:long_name = "Instrument Transformation Matrix" ;
+        double z(z) ;
+                z:long_name = "height relative to sea bed" ;
+                z:positive = "up" ;
+                z:axis = "Z" ;
+                z:units = "m" ;
+                z:standard_name = "height" ;
+        float u_1205(time, z) ;
+                u_1205:_FillValue = NaNf ;
+                u_1205:long_name = "Eastward Velocity" ;
+                u_1205:epic_code = 1205 ;
+                u_1205:units = "m s-1" ;
+                u_1205:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
+                u_1205:standard_name = "eastward_sea_water_velocity" ;
+                u_1205:minimum = -0.3043381f ;
+                u_1205:maximum = 0.4729342f ;
+        float v_1206(time, z) ;
+                v_1206:_FillValue = NaNf ;
+                v_1206:long_name = "Northward Velocity" ;
+                v_1206:epic_code = 1206 ;
+                v_1206:units = "m s-1" ;
+                v_1206:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
+                v_1206:standard_name = "northward_sea_water_velocity" ;
+                v_1206:minimum = -0.5342383f ;
+                v_1206:maximum = 0.5213875f ;
+        float w_1204(time, z) ;
+                w_1204:_FillValue = NaNf ;
+                w_1204:long_name = "Vertical Velocity" ;
+                w_1204:epic_code = 1204 ;
+                w_1204:units = "m s-1" ;
+                w_1204:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
+                w_1204:standard_name = "upward_sea_water_velocity" ;
+                w_1204:minimum = -0.238696f ;
+                w_1204:maximum = 0.4404314f ;
+        float w2_1204(time, z) ;
+                w2_1204:_FillValue = NaNf ;
+                w2_1204:long_name = "Vertical Velocity (2nd)" ;
+                w2_1204:units = "m s-1" ;
+                w2_1204:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
+                w2_1204:minimum = -0.2421437f ;
+                w2_1204:maximum = 0.4456696f ;
+        int beam(beam) ;
+                beam:units = "1" ;
+                beam:long_name = "Beam Reference Frame" ;
+        float vel(beam, time, z) ;
+                vel:_FillValue = NaNf ;
+                vel:units = "m s-1" ;
+                vel:standard_name = "radial_sea_water_velocity_away_from_instrument" ;
+                vel:long_name = "Beam Velocity" ;
+                vel:minimum = -0.3223417f, -0.2583833f, -0.414f, -0.4104f ;
+                vel:maximum = 0.4921f, 0.3793f, 0.4010909f, 0.4465818f ;
+        float corr(beam, time, z) ;
+                corr:_FillValue = NaNf ;
+                corr:units = "percent" ;
+                corr:standard_name = "beam_consistency_indicator_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water" ;
+                corr:long_name = "Acoustic Signal Correlation" ;
+                corr:minimum = 18UB, 22UB, 27UB, 22UB ;
+                corr:maximum = 100UB, 100UB, 100UB, 100UB ;
+        float amp(beam, time, z) ;
+                amp:_FillValue = NaNf ;
+                amp:units = "dB" ;
+                amp:standard_name = "signal_intensity_from_multibeam_acoustic_doppler_velocity_sensor_in_sea_water" ;
+                amp:long_name = "Acoustic Signal Amplitude" ;
+                amp:minimum = 44.5f, 46.5f, 41.f, 46.f ;
+                amp:maximum = 85.5f, 85.5f, 85.5f, 85.5f ;
+        float bin_depth(time, z) ;
+                bin_depth:_FillValue = NaNf ;
+                bin_depth:units = "m" ;
+                bin_depth:long_name = "bin depth" ;
+                bin_depth:note = "Actual depth time series of velocity bins. Calculated as pressure (P_1) - bindist." ;
+                bin_depth:minimum = -0.205183312296867 ;
+                bin_depth:maximum = 3.79031686484814 ;
+        string inst4(inst4) ;
+                inst4:units = "1" ;
+                inst4:long_name = "Instrumnet Reference Frame for 4 beam ADCP" ;
+        string inst(inst) ;
+                inst:units = "1" ;
+                inst:long_name = "Instrumnet Reference Frame" ;
+        float mag(inst, time) ;
+                mag:_FillValue = NaNf ;
+                mag:units = "uT" ;
+                mag:long_name = "Magnetometer Data" ;
+                mag:minimum = 28.60167f, 4.251818f, -43.2275f ;
+                mag:maximum = 28.88334f, 4.851666f, -42.97417f ;
+        float accel(inst, time) ;
+                accel:_FillValue = NaNf ;
+                accel:units = "m s-2" ;
+                accel:long_name = "Vector Acceleration of Instrument" ;
+                accel:minimum = 0.6620033f, 0.01975891f, 9.775846f ;
+                accel:maximum = 0.6824808f, 0.03638933f, 9.784853f ;
+        double latitude(latitude) ;
+                latitude:units = "degree_north" ;
+                latitude:axis = "Y" ;
+                latitude:long_name = "Latitude" ;
+                latitude:standard_name = "latitude" ;
+                latitude:epic_code = 500 ;
+        double longitude(longitude) ;
+                longitude:units = "degree_east" ;
+                longitude:axis = "X" ;
+                longitude:long_name = "Longitude" ;
+                longitude:standard_name = "longitude" ;
+                longitude:epic_code = 502 ;
+
+// global attributes:
+                :data_type = "Average" ;
+                :SIGSerialNo = 101042 ;
+                :SIGInstrumentName = "Signature1000" ;
+                :SIGAnalogBoardRev = "F-1" ;
+                :SIGDigitalBoardRev = "I-3" ;
+                :SIGSensorBoardRev = "I-0" ;
+                :SIGInterfaceBoardRev = "H-2" ;
+                :SIGFPGAVersion = 185 ;
+                :SIGFWVersion = 2214 ;
+                :SIGComType = "RS232" ;
+                :SIGBaudrate = 9600. ;
+                :SIGLedEnabled = "ON24H" ;
+                :SIGOrientation = "AUTOZUPDOWN" ;
+                :SIGHeadFrequency = 1000. ;
+                :SIGHasAccelerometer = "True" ;
+                :SIGHasMagnetometer = "True" ;
+                :SIGHasPressure = "True" ;
+                :SIGHasTemperature = "True" ;
+                :SIGHasCompass = "True" ;
+                :SIGHx = 25. ;
+                :SIGHy = 15. ;
+                :SIGHz = 0. ;
+                :SIGPressureOffset = 10. ;
+                :SIGDeclination = 0. ;
+                :SIGPlan_BurstEnabled = "True" ;
+                :SIGPlan_AverageEnabled = "True" ;
+                :SIGPlan_Salinity = 35. ;
+                :SIGPlan_Filename = "MIA23Sig1000.ad2cp" ;
+                :SIGPlan_MaxVerticalVelocity = 10 ;
+                :SIGPlan_ProfileInterval = 120 ;
+                :SIGPlan_AverageDepthInterval = 0 ;
+                :SIGPlan_BurstInterval = 3600 ;
+                :SIGPlan_BurstDepthInterval = 0 ;
+                :SIGPlan_SoundVelocity = 0. ;
+                :SIGPlan_SerialOutputEnabled = "False" ;
+                :SIGAlt_Plan_BurstEnabled = "True" ;
+                :SIGAlt_Plan_AverageEnabled = "True" ;
+                :SIGAlt_Plan_Salinity = 35. ;
+                :SIGAlt_Plan_Filename = "MIA23Sig1000.ad2cp" ;
+                :SIGAlt_Plan_MaxVerticalVelocity = 10 ;
+                :SIGAlt_Plan_ProfileInterval = 120 ;
+                :SIGAlt_Plan_AverageDepthInterval = 0 ;
+                :SIGAlt_Plan_BurstInterval = 3600 ;
+                :SIGAlt_Plan_BurstDepthInterval = 0 ;
+                :SIGAlt_Plan_SoundVelocity = 0. ;
+                :SIGAlt_Plan_SerialOutputEnabled = "False" ;
+                :SIGAverage_Altimeter = "False" ;
+                :SIGAverage_IceTrack = "False" ;
+                :SIGAverage_AverageInterval = 120 ;
+                :SIGAverage_BlankingDistance = 0.100000001490116 ;
+                :SIGAverage_CellSize = 0.200000002980232 ;
+                :SIGAverage_NBeams = 4 ;
+                :SIGAverage_NCells = 32 ;
+                :SIGAverage_ChannelBeamSel = 0 ;
+                :SIGAverage_CoordSystem = "BEAM" ;
+                :SIGAverage_DataFormat = 3 ;
+                :SIGAverage_NPings = 480 ;
+                :SIGAverage_Bandwidth = "BROAD" ;
+                :SIGAverage_PowerLevel = 0. ;
+                :SIGAverage_VelocityPrecision = 0. ;
+                :SIGAverage_VelocityRange = 5. ;
+                :SIGAverage_BottomTrack = "False" ;
+                :MOORING = "MIA23SH2" ;
+                :PROGRAM = "Coastal and Marine Hazards and Resources Program" ;
+                :PROJECT = "Coral Reefs" ;
+                :EXPERIMENT = "Miami X-Reefs" ;
+                :Region = "Florida" ;
+                :CruiseID = "2023-623-FA" ;
+                :SciPi = "Curt Storlazzi, Olivia Cheriton, Kurt Rosenberger" ;
+                :Year = 2023. ;
+                :Site = "SH2" ;
+                :platform_type = "Artificial Reef Box" ;
+                :latitude = 25.866503 ;
+                :longitude = -80.116706 ;
+                :LatLonDatum = "WGS84" ;
+                :WATER_DEPTH = 5. ;
+                :Deployment_date = "2023-06-23 15:30" ;
+                :Recovery_date = "2024-01-17 10:00" ;
+                :OFAFunding = "" ;
+                :CollaboratingAgency = "University of Miami" ;
+                :DESCRIPTION = "Seahive structure" ;
+                :WATER_DEPTH_SOURCE = "pressure data" ;
+                :magnetic_variation = -7.25 ;
+                :Conventions = "CF-1.8" ;
+                :basefile = "mat3/MIA23Sig1000" ;
+                :outdir = "mat3/" ;
+                :filename = "MIAsig" ;
+                :ClockError = 0 ;
+                :orientation = "UP" ;
+                :head_rotation = "horizontal" ;
+                :initial_instrument_height = 1. ;
+                :initial_instrument_height_note = "From seabed" ;
+                :zeroed_pressure = "Yes" ;
+                :cutoff_ampl = 0 ;
+                :trim_method = "water level sl" ;
+                :trim_surf_bins = 3 ;
+                :history = "2024-05-21T16:26:54.999377+00:00: Processed using mat2cdf.py with stglib 0.15.0+31.g30ecb68.dirty, xarray 2024.2.0, NumPy 1.26.4, netCDF4 1.6.5, Python 3.11.8.\n2024-05-21T16:27:17.727304+00:00: Data clipped using Deployment_date of 2023-06-23 15:30 and Recovery_date of 2024-01-17 10:00.\n2024-05-21T16:27:17.738401+00:00: Rotating heading and horizontal velocities by -7.25 degrees.\n2024-05-21T16:27:17.761806+00:00: Trimmed velocity data using NON-atmospherically corrected pressure (water level) and sidelobes 
+(with 3 additional surface bins removed).\n2024-05-21T16:27:18.023571+00:00: Processed to CF-1.8 using runsigcdf2nc.py.\n" ;
+                :nominal_sensor_depth_note = "WATER_DEPTH - initial_instrument_height" ;
+                :nominal_sensor_depth = 4. ;
+                :transducer_offset_from_bottom = 1. ;
+                :serial_number = 101042 ;
+                :frequency = 1000. ;
+                :instrument_type = "Signature1000" ;
+                :bin_size = 0.200000002980232 ;
+                :beam_angle = 25 ;
+                :nominal_instrument_depth = 4. ;
+                :start_time = "2023-06-23T16:00:00.000000000" ;
+                :stop_time = "2023-08-04T02:08:00.000000000" ;
+}
\ No newline at end of file
diff --git a/stglib/tests/data/gatts_MIA23SH2_cf_rev.txt b/stglib/tests/data/gatts_MIA23SH2_cf_rev.txt
new file mode 100644
index 00000000..58750e4d
--- /dev/null
+++ b/stglib/tests/data/gatts_MIA23SH2_cf_rev.txt
@@ -0,0 +1,22 @@
+MOORING; MIA23SH2
+PROGRAM; Coastal and Marine Hazards and Resources Program
+PROJECT; Coral Reefs
+EXPERIMENT; Miami X-Reefs
+Region; Florida
+CruiseID; 2023-623-FA
+SciPi; Curt Storlazzi, Olivia Cheriton, Kurt Rosenberger
+Year; 2023
+Site; SH2
+platform_type; Artificial Reef Box
+latitude; 25.866503
+longitude; -80.116706
+LatLonDatum; WGS84
+WATER_DEPTH; 5
+Deployment_date; 2023-06-23 15:30
+Recovery_date; 2024-01-17 10:00
+OFAFunding;	
+CollaboratingAgency; University of Miami
+DESCRIPTION; Seahive structure
+WATER_DEPTH_SOURCE; pressure data
+magnetic_variation; -7.25
+Conventions; CF-1.8
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0001_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0001_avgd.mat
new file mode 100644
index 00000000..874a5a99
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0001_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:de6330ee07c2a5c9205807e78a60e16299bbbbc33daa29f7e50531765a04712b
+size 8028264
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0002_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0002_avgd.mat
new file mode 100644
index 00000000..4d35ad62
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0002_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bd3101c8cc862e691cfff949daad0872cf6cb025e662fec18e0efb4b5cd9df83
+size 8076984
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0003_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0003_avgd.mat
new file mode 100644
index 00000000..a3ff1b93
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0003_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6f897836370464d1e2a1e8b42a71df2efbd84da45087c70b94fa2acbee0f91f3
+size 8056432
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0004_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0004_avgd.mat
new file mode 100644
index 00000000..d1c8644d
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0004_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9b0813860f425c58df6921e8d16435008aa6e757a22b2cc7f3bd2d60e7e053df
+size 8048648
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0005_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0005_avgd.mat
new file mode 100644
index 00000000..8bb6e83a
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0005_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:dc3834b613d47bb330a9fbfd6a3ab249998c626cf7dd3624d7f588601873eef2
+size 8076984
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0006_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0006_avgd.mat
new file mode 100644
index 00000000..b131568e
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0006_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0cd5e77f66bc8be87d84da2d7d058c6c6deb843d8d6281eafb51f06bf9ec407d
+size 8051296
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0007_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0007_avgd.mat
new file mode 100644
index 00000000..b51913b5
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0007_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:eb412d050e951070e11305a19b83ef3fe51f2f627432b1746f4513c46d76d99f
+size 8053944
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0008_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0008_avgd.mat
new file mode 100644
index 00000000..18fe89ad
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0008_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:de51c763d5055cdca830cf75d72f9954c86c8e95b9a8e44ee992f240a80edafa
+size 8076984
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0009_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0009_avgd.mat
new file mode 100644
index 00000000..405501e6
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0009_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:55742a7d938f4335c7eb59e9b256ab02798d1efedb670be4e20a785dbfa57401
+size 8046160
diff --git a/stglib/tests/data/mat3/MIA23Sig1000_0010_avgd.mat b/stglib/tests/data/mat3/MIA23Sig1000_0010_avgd.mat
new file mode 100644
index 00000000..5bf02a39
--- /dev/null
+++ b/stglib/tests/data/mat3/MIA23Sig1000_0010_avgd.mat
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:359f3f2eaf13fb2a0bde4224f8bbecfaffdfcefe5d893b0eef09399fbf1c0803
+size 8058920
diff --git a/stglib/tests/data/sig_avg_config.yaml b/stglib/tests/data/sig_avg_config.yaml
new file mode 100644
index 00000000..c3e99c41
--- /dev/null
+++ b/stglib/tests/data/sig_avg_config.yaml
@@ -0,0 +1,17 @@
+basefile: 'mat3/MIA23Sig1000'
+outdir: 'mat3/'
+filename: 'MIAsig'
+#basefile: 'mat/MIA23Sig1000'
+#outdir: 'cdf2/' #directory to write out raw cdf files
+#filename: 'MIAsig2'   # name of output file, -raw.cdf or .nc will be appended to this
+#LatLonDatum: 'NAD83'
+ClockError: 0 #sec 
+#ClockDrift: 15 #sec < 60 s no need to apply correction
+orientation: 'UP'          # use this to identify orientation of profiler
+head_rotation: 'horizontal' #will probably be 'horizontal'
+initial_instrument_height: 1.  # meters
+initial_instrument_height_note: 'From seabed'
+zeroed_pressure: 'Yes' # was pressure zeroed before deployment
+cutoff_ampl: 0   # set to 0, otherwise it automatically specifies cutoff based on amplitude which is a weird thing to do
+trim_method: 'water level sl'  # Water Level SL trims bin if any part of bin or side lobe is out of water - works best when pressure is corrected for atmospheric
+trim_surf_bins: 3 #trim add'l surface bins
\ No newline at end of file
diff --git a/stglib/tests/test_scripts.py b/stglib/tests/test_scripts.py
index 087a2219..b92afdd3 100644
--- a/stglib/tests/test_scripts.py
+++ b/stglib/tests/test_scripts.py
@@ -363,14 +363,16 @@ def sig_nc(nc_file):
     assert "Done writing netCDF file" in result.stdout.decode("utf8")
 
 
-# @pytest.mark.skip(reason="works locally but not on github built-in checks")
+@pytest.mark.skip(reason="works locally but not on github built-in checks")
 def test_sig():
     sig_mat("glob_att1126_sig1.txt", "sig1126_config.yaml")
-    print(os.listdir())
     sig_nc("11261sig_burst-raw.cdf")
     sig_mat("glob_att1126_sig2.txt", "sig11262_config.yaml")
     sig_nc("11262sig_burst-raw.cdf")
     sig_nc("11262sig_echo1-raw.cdf")
+    sig_mat("gatts_MIA23SH2_cf_rev.txt", "sig_avg_config.yaml")
+    sig_nc("MIAsig_avgd-raw.cdf")
+    sig_nc("MIAsig_altavgd-raw.cdf")
 
 
 def hobo_raw(glob_att, config_yaml):

From 61ec48584c96f6ee2f4c0c22d27a7602db72deb0 Mon Sep 17 00:00:00 2001
From: ssuttles-usgs
 <ssuttles@usgs.govgit config -lgit config --global user.email ssuttles@usgs.gov>
Date: Wed, 22 May 2024 11:23:39 -0400
Subject: [PATCH 5/7] final clean-up and checks for PR

---
 stglib/core/utils.py                          |   2 +-
 stglib/sig/cdf2nc.py                          |  29 +-
 stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt | 319 ------------------
 3 files changed, 15 insertions(+), 335 deletions(-)
 delete mode 100644 stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt

diff --git a/stglib/core/utils.py b/stglib/core/utils.py
index 8d53095e..83e59f41 100644
--- a/stglib/core/utils.py
+++ b/stglib/core/utils.py
@@ -179,7 +179,7 @@ def add_min_max(ds, exclude_vars=None):
 
     exclude = list(ds.dims)
     [exclude.append(k) for k in ds.variables if "time" in k]
-    exclude.extend(["TIM", "TransMatrix", "orientmat", "beam2xyz"])
+    exclude.extend(["TIM", "TransMatrix", "orientmat"])
     if exclude_vars:
         exclude.extend(exclude_vars)
 
diff --git a/stglib/sig/cdf2nc.py b/stglib/sig/cdf2nc.py
index bdfe4610..6a1a4471 100644
--- a/stglib/sig/cdf2nc.py
+++ b/stglib/sig/cdf2nc.py
@@ -75,7 +75,7 @@ def cdf_to_nc(cdf_filename, atmpres=False):
                 dim="beam",
             )
         if "CorBeam1" in ds:
-            ds["corr"] = xr.concat(
+            ds["cor"] = xr.concat(
                 [ds[f"CorBeam{i}"] for i in range(1, ds["NBeams"][0].values + 1)],
                 dim="beam",
             )
@@ -334,10 +334,10 @@ def ds_rename_sig(ds, waves=False):
         "AltimeterQualityAST": "ast_quality",
         "AltimeterTimeOffsetAST": "ast_offset_time",
         "AltimeterPressure": "ast_pressure",
-        "NominalCorrelation": "corr_nominal",
+        "NominalCorrelation": "cor_nominal",
         "VelBeam5": "vel_b5",
         "AmpBeam5": "amp_b5",
-        "CorBeam5": "corr_b5",
+        "CorBeam5": "cor_b5",
         "Echo": "echo_amp",
         "Headingstd": "Hdg_std",
         "Pitchstd": "Ptch_std",
@@ -373,14 +373,13 @@ def fix_encoding(ds):
     if "units" in ds["time"].encoding:
         ds["time"].encoding.pop("units")
 
-    tstep = ds["time"][1] - ds["time"][0]
+    tstep = ds["time"][1] - ds["time"][0]  # use time step to select time encoding
     # if "sample" not in ds.dims:
     if tstep < np.timedelta64(1, "m"):
         print(
             f"make time encoding to dtype double because tstep {tstep} seconds is < 1 minute, round to milliseconds first"
         )
         ds["time"] = ds["time"].dt.round("ms")  # round time to milliseconds first
-        print("make time encoding to dtype double because time step < 1 minute")
         ds["time"].encoding["dtype"] = "double"
 
     else:
@@ -398,7 +397,7 @@ def fix_encoding(ds):
     for var in ds.data_vars:
         if ds[var].dtype == "uint32" or ds[var].dtype == "uint8":
             ds[var].encoding["dtype"] = "int32"
-        if var in ["corr", "corr_b5"]:
+        if var in ["cor", "cor_b5"]:
             ds[var].encoding["dtype"] = "float32"
         if ds[var].dtype == "float64":
             ds[var].encoding["dtype"] = "float32"
@@ -431,7 +430,7 @@ def ds_add_attrs_sig(ds):
         ds["inst"].attrs.update(
             {
                 # "units": "1",
-                "long_name": "Instrumnet Reference Frame",
+                "long_name": "Instrument Reference Frame",
             }
         )
 
@@ -439,7 +438,7 @@ def ds_add_attrs_sig(ds):
         ds["inst4"].attrs.update(
             {
                 # "units": "1",
-                "long_name": "Instrumnet Reference Frame for 4 beam ADCP",
+                "long_name": "Instrument Reference Frame for 4 beam ADCP",
             }
         )
 
@@ -560,8 +559,8 @@ def ds_add_attrs_sig(ds):
             }
         )
 
-    if "corr" in ds:
-        ds["corr"].attrs.update(
+    if "cor" in ds:
+        ds["cor"].attrs.update(
             {
                 "units": "percent",
                 "standard_name": "beam_consistency_indicator_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water",
@@ -569,8 +568,8 @@ def ds_add_attrs_sig(ds):
             }
         )
 
-    if "corr_b5" in ds:
-        ds["corr_b5"].attrs.update(
+    if "cor_b5" in ds:
+        ds["cor_b5"].attrs.update(
             {
                 "units": "percent",
                 "standard_name": "beam_consistency_indicator_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water",
@@ -578,8 +577,8 @@ def ds_add_attrs_sig(ds):
             }
         )
 
-    if "corr_nominal" in ds:
-        ds["corr_nominal"].attrs.update(
+    if "cor_nominal" in ds:
+        ds["cor_nominal"].attrs.update(
             {
                 "units": "percent",
                 "long_name": "Nominal Correlation",
@@ -625,7 +624,7 @@ def ds_add_attrs_sig(ds):
         ds["brangeAST"].attrs.update(
             {
                 "units": "m",
-                # "standard_name": "altimeter_range",
+                "standard_name": "altimeter_range",
                 "long_name": "Acoustic Surface Tracking (AST) Range",
             }
         )
diff --git a/stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt b/stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt
deleted file mode 100644
index 73989c7a..00000000
--- a/stglib/tests/data/MIAsigavg-cal.nc_ncdump.txt
+++ /dev/null
@@ -1,319 +0,0 @@
-netcdf MIAsigavg-cal {
-dimensions:
-        time = 14921 ;
-        inst4 = 4 ;
-        beam = 4 ;
-        z = 15 ;
-        inst = 3 ;
-        latitude = 1 ;
-        longitude = 1 ;
-variables:
-        int time(time) ;
-                time:standard_name = "time" ;
-                time:axis = "T" ;
-                time:long_name = "time (UTC)" ;
-                time:units = "seconds since 2023-06-23 16:00:00" ;
-                time:calendar = "proleptic_gregorian" ;
-        int status(time) ;
-                status:long_name = "Status Code" ;
-                status:units = "1" ;
-                status:minimum = 944504834U ;
-                status:maximum = 944505858U ;
-        int error(time) ;
-                error:long_name = "Error Code" ;
-                error:units = "1" ;
-                error:minimum = 0U ;
-                error:maximum = 0U ;
-        int sample(time) ;
-                sample:long_name = "sample number" ;
-                sample:units = "1" ;
-                sample:minimum = 1U ;
-                sample:maximum = 120U ;
-        float ambig_vel(time) ;
-                ambig_vel:_FillValue = NaNf ;
-                ambig_vel:units = "m s-1" ;
-                ambig_vel:long_name = "Ambiguity velocity" ;
-                ambig_vel:minimum = 10.725f ;
-                ambig_vel:maximum = 10.77105f ;
-        float Bat_106(time) ;
-                Bat_106:_FillValue = NaNf ;
-                Bat_106:long_name = "Battery voltage" ;
-                Bat_106:units = "V" ;
-                Bat_106:epic_code = 106 ;
-                Bat_106:minimum = 18.3f ;
-                Bat_106:maximum = 18.7f ;
-        float Hdg_1215(time) ;
-                Hdg_1215:_FillValue = NaNf ;
-                Hdg_1215:units = "degrees" ;
-                Hdg_1215:long_name = "Instrument Heading" ;
-                Hdg_1215:epic_code = 1215 ;
-                Hdg_1215:note = "Heading is degrees true. Converted from magnetic with magnetic variation of -7.250000." ;
-                Hdg_1215:standard_name = "platform_orientation" ;
-                Hdg_1215:minimum = 0.6727271f ;
-                Hdg_1215:maximum = 1.6725f ;
-        float Ptch_1216(time) ;
-                Ptch_1216:_FillValue = NaNf ;
-                Ptch_1216:long_name = "Instrument Pitch" ;
-                Ptch_1216:units = "degrees" ;
-                Ptch_1216:epic_code = 1216 ;
-                Ptch_1216:standard_name = "platform_pitch" ;
-                Ptch_1216:minimum = 3.86575f ;
-                Ptch_1216:maximum = 3.983917f ;
-        float Roll_1217(time) ;
-                Roll_1217:_FillValue = NaNf ;
-                Roll_1217:long_name = "Instrument Roll" ;
-                Roll_1217:units = "degrees" ;
-                Roll_1217:epic_code = 1217 ;
-                Roll_1217:standard_name = "platform_roll" ;
-                Roll_1217:minimum = 0.11f ;
-                Roll_1217:maximum = 0.2039166f ;
-        float Tx_1211(time) ;
-                Tx_1211:_FillValue = NaNf ;
-                Tx_1211:long_name = "Instrument Internal Temperature" ;
-                Tx_1211:units = "degree_C" ;
-                Tx_1211:epic_code = 1211 ;
-                Tx_1211:minimum = 29.3915f ;
-                Tx_1211:maximum = 32.70192f ;
-        float SV_80(time) ;
-                SV_80:_FillValue = NaNf ;
-                SV_80:units = "m s-1" ;
-                SV_80:epic_code = 80 ;
-                SV_80:long_name = "Speed of Sound" ;
-                SV_80:standard_name = "speed_of_sound_in_sea_water" ;
-                SV_80:minimum = 1544.4f ;
-                SV_80:maximum = 1551.037f ;
-        float P_1(time) ;
-                P_1:_FillValue = NaNf ;
-                P_1:long_name = "Uncorrected pressure" ;
-                P_1:units = "dbar" ;
-                P_1:epic_code = 1 ;
-                P_1:standard_name = "sea_water_pressure" ;
-                P_1:minimum = 2.794817f ;
-                P_1:maximum = 3.990317f ;
-        float xmit_energy(time) ;
-                xmit_energy:_FillValue = NaNf ;
-                xmit_energy:long_name = "Transmit Energy" ;
-                xmit_energy:units = "dB" ;
-                xmit_energy:minimum = 94.f ;
-                xmit_energy:maximum = 106.f ;
-        int corr_nominal(time) ;
-                corr_nominal:long_name = "Nominal Correlation" ;
-                corr_nominal:units = "percent" ;
-                corr_nominal:minimum = 60UB ;
-                corr_nominal:maximum = 60UB ;
-        float TransMatrix(inst4, beam) ;
-                TransMatrix:units = "1" ;
-                TransMatrix:long_name = "Instrument Transformation Matrix" ;
-        double z(z) ;
-                z:long_name = "height relative to sea bed" ;
-                z:positive = "up" ;
-                z:axis = "Z" ;
-                z:units = "m" ;
-                z:standard_name = "height" ;
-        float u_1205(time, z) ;
-                u_1205:_FillValue = NaNf ;
-                u_1205:long_name = "Eastward Velocity" ;
-                u_1205:epic_code = 1205 ;
-                u_1205:units = "m s-1" ;
-                u_1205:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
-                u_1205:standard_name = "eastward_sea_water_velocity" ;
-                u_1205:minimum = -0.3043381f ;
-                u_1205:maximum = 0.4729342f ;
-        float v_1206(time, z) ;
-                v_1206:_FillValue = NaNf ;
-                v_1206:long_name = "Northward Velocity" ;
-                v_1206:epic_code = 1206 ;
-                v_1206:units = "m s-1" ;
-                v_1206:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
-                v_1206:standard_name = "northward_sea_water_velocity" ;
-                v_1206:minimum = -0.5342383f ;
-                v_1206:maximum = 0.5213875f ;
-        float w_1204(time, z) ;
-                w_1204:_FillValue = NaNf ;
-                w_1204:long_name = "Vertical Velocity" ;
-                w_1204:epic_code = 1204 ;
-                w_1204:units = "m s-1" ;
-                w_1204:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
-                w_1204:standard_name = "upward_sea_water_velocity" ;
-                w_1204:minimum = -0.238696f ;
-                w_1204:maximum = 0.4404314f ;
-        float w2_1204(time, z) ;
-                w2_1204:_FillValue = NaNf ;
-                w2_1204:long_name = "Vertical Velocity (2nd)" ;
-                w2_1204:units = "m s-1" ;
-                w2_1204:note = "Velocity bins trimmed if out of water or if side lobes intersect sea surface (with 3 additional surface bins removed)." ;
-                w2_1204:minimum = -0.2421437f ;
-                w2_1204:maximum = 0.4456696f ;
-        int beam(beam) ;
-                beam:units = "1" ;
-                beam:long_name = "Beam Reference Frame" ;
-        float vel(beam, time, z) ;
-                vel:_FillValue = NaNf ;
-                vel:units = "m s-1" ;
-                vel:standard_name = "radial_sea_water_velocity_away_from_instrument" ;
-                vel:long_name = "Beam Velocity" ;
-                vel:minimum = -0.3223417f, -0.2583833f, -0.414f, -0.4104f ;
-                vel:maximum = 0.4921f, 0.3793f, 0.4010909f, 0.4465818f ;
-        float corr(beam, time, z) ;
-                corr:_FillValue = NaNf ;
-                corr:units = "percent" ;
-                corr:standard_name = "beam_consistency_indicator_from_multibeam_acoustic_doppler_velocity_profiler_in_sea_water" ;
-                corr:long_name = "Acoustic Signal Correlation" ;
-                corr:minimum = 18UB, 22UB, 27UB, 22UB ;
-                corr:maximum = 100UB, 100UB, 100UB, 100UB ;
-        float amp(beam, time, z) ;
-                amp:_FillValue = NaNf ;
-                amp:units = "dB" ;
-                amp:standard_name = "signal_intensity_from_multibeam_acoustic_doppler_velocity_sensor_in_sea_water" ;
-                amp:long_name = "Acoustic Signal Amplitude" ;
-                amp:minimum = 44.5f, 46.5f, 41.f, 46.f ;
-                amp:maximum = 85.5f, 85.5f, 85.5f, 85.5f ;
-        float bin_depth(time, z) ;
-                bin_depth:_FillValue = NaNf ;
-                bin_depth:units = "m" ;
-                bin_depth:long_name = "bin depth" ;
-                bin_depth:note = "Actual depth time series of velocity bins. Calculated as pressure (P_1) - bindist." ;
-                bin_depth:minimum = -0.205183312296867 ;
-                bin_depth:maximum = 3.79031686484814 ;
-        string inst4(inst4) ;
-                inst4:units = "1" ;
-                inst4:long_name = "Instrumnet Reference Frame for 4 beam ADCP" ;
-        string inst(inst) ;
-                inst:units = "1" ;
-                inst:long_name = "Instrumnet Reference Frame" ;
-        float mag(inst, time) ;
-                mag:_FillValue = NaNf ;
-                mag:units = "uT" ;
-                mag:long_name = "Magnetometer Data" ;
-                mag:minimum = 28.60167f, 4.251818f, -43.2275f ;
-                mag:maximum = 28.88334f, 4.851666f, -42.97417f ;
-        float accel(inst, time) ;
-                accel:_FillValue = NaNf ;
-                accel:units = "m s-2" ;
-                accel:long_name = "Vector Acceleration of Instrument" ;
-                accel:minimum = 0.6620033f, 0.01975891f, 9.775846f ;
-                accel:maximum = 0.6824808f, 0.03638933f, 9.784853f ;
-        double latitude(latitude) ;
-                latitude:units = "degree_north" ;
-                latitude:axis = "Y" ;
-                latitude:long_name = "Latitude" ;
-                latitude:standard_name = "latitude" ;
-                latitude:epic_code = 500 ;
-        double longitude(longitude) ;
-                longitude:units = "degree_east" ;
-                longitude:axis = "X" ;
-                longitude:long_name = "Longitude" ;
-                longitude:standard_name = "longitude" ;
-                longitude:epic_code = 502 ;
-
-// global attributes:
-                :data_type = "Average" ;
-                :SIGSerialNo = 101042 ;
-                :SIGInstrumentName = "Signature1000" ;
-                :SIGAnalogBoardRev = "F-1" ;
-                :SIGDigitalBoardRev = "I-3" ;
-                :SIGSensorBoardRev = "I-0" ;
-                :SIGInterfaceBoardRev = "H-2" ;
-                :SIGFPGAVersion = 185 ;
-                :SIGFWVersion = 2214 ;
-                :SIGComType = "RS232" ;
-                :SIGBaudrate = 9600. ;
-                :SIGLedEnabled = "ON24H" ;
-                :SIGOrientation = "AUTOZUPDOWN" ;
-                :SIGHeadFrequency = 1000. ;
-                :SIGHasAccelerometer = "True" ;
-                :SIGHasMagnetometer = "True" ;
-                :SIGHasPressure = "True" ;
-                :SIGHasTemperature = "True" ;
-                :SIGHasCompass = "True" ;
-                :SIGHx = 25. ;
-                :SIGHy = 15. ;
-                :SIGHz = 0. ;
-                :SIGPressureOffset = 10. ;
-                :SIGDeclination = 0. ;
-                :SIGPlan_BurstEnabled = "True" ;
-                :SIGPlan_AverageEnabled = "True" ;
-                :SIGPlan_Salinity = 35. ;
-                :SIGPlan_Filename = "MIA23Sig1000.ad2cp" ;
-                :SIGPlan_MaxVerticalVelocity = 10 ;
-                :SIGPlan_ProfileInterval = 120 ;
-                :SIGPlan_AverageDepthInterval = 0 ;
-                :SIGPlan_BurstInterval = 3600 ;
-                :SIGPlan_BurstDepthInterval = 0 ;
-                :SIGPlan_SoundVelocity = 0. ;
-                :SIGPlan_SerialOutputEnabled = "False" ;
-                :SIGAlt_Plan_BurstEnabled = "True" ;
-                :SIGAlt_Plan_AverageEnabled = "True" ;
-                :SIGAlt_Plan_Salinity = 35. ;
-                :SIGAlt_Plan_Filename = "MIA23Sig1000.ad2cp" ;
-                :SIGAlt_Plan_MaxVerticalVelocity = 10 ;
-                :SIGAlt_Plan_ProfileInterval = 120 ;
-                :SIGAlt_Plan_AverageDepthInterval = 0 ;
-                :SIGAlt_Plan_BurstInterval = 3600 ;
-                :SIGAlt_Plan_BurstDepthInterval = 0 ;
-                :SIGAlt_Plan_SoundVelocity = 0. ;
-                :SIGAlt_Plan_SerialOutputEnabled = "False" ;
-                :SIGAverage_Altimeter = "False" ;
-                :SIGAverage_IceTrack = "False" ;
-                :SIGAverage_AverageInterval = 120 ;
-                :SIGAverage_BlankingDistance = 0.100000001490116 ;
-                :SIGAverage_CellSize = 0.200000002980232 ;
-                :SIGAverage_NBeams = 4 ;
-                :SIGAverage_NCells = 32 ;
-                :SIGAverage_ChannelBeamSel = 0 ;
-                :SIGAverage_CoordSystem = "BEAM" ;
-                :SIGAverage_DataFormat = 3 ;
-                :SIGAverage_NPings = 480 ;
-                :SIGAverage_Bandwidth = "BROAD" ;
-                :SIGAverage_PowerLevel = 0. ;
-                :SIGAverage_VelocityPrecision = 0. ;
-                :SIGAverage_VelocityRange = 5. ;
-                :SIGAverage_BottomTrack = "False" ;
-                :MOORING = "MIA23SH2" ;
-                :PROGRAM = "Coastal and Marine Hazards and Resources Program" ;
-                :PROJECT = "Coral Reefs" ;
-                :EXPERIMENT = "Miami X-Reefs" ;
-                :Region = "Florida" ;
-                :CruiseID = "2023-623-FA" ;
-                :SciPi = "Curt Storlazzi, Olivia Cheriton, Kurt Rosenberger" ;
-                :Year = 2023. ;
-                :Site = "SH2" ;
-                :platform_type = "Artificial Reef Box" ;
-                :latitude = 25.866503 ;
-                :longitude = -80.116706 ;
-                :LatLonDatum = "WGS84" ;
-                :WATER_DEPTH = 5. ;
-                :Deployment_date = "2023-06-23 15:30" ;
-                :Recovery_date = "2024-01-17 10:00" ;
-                :OFAFunding = "" ;
-                :CollaboratingAgency = "University of Miami" ;
-                :DESCRIPTION = "Seahive structure" ;
-                :WATER_DEPTH_SOURCE = "pressure data" ;
-                :magnetic_variation = -7.25 ;
-                :Conventions = "CF-1.8" ;
-                :basefile = "mat3/MIA23Sig1000" ;
-                :outdir = "mat3/" ;
-                :filename = "MIAsig" ;
-                :ClockError = 0 ;
-                :orientation = "UP" ;
-                :head_rotation = "horizontal" ;
-                :initial_instrument_height = 1. ;
-                :initial_instrument_height_note = "From seabed" ;
-                :zeroed_pressure = "Yes" ;
-                :cutoff_ampl = 0 ;
-                :trim_method = "water level sl" ;
-                :trim_surf_bins = 3 ;
-                :history = "2024-05-21T16:26:54.999377+00:00: Processed using mat2cdf.py with stglib 0.15.0+31.g30ecb68.dirty, xarray 2024.2.0, NumPy 1.26.4, netCDF4 1.6.5, Python 3.11.8.\n2024-05-21T16:27:17.727304+00:00: Data clipped using Deployment_date of 2023-06-23 15:30 and Recovery_date of 2024-01-17 10:00.\n2024-05-21T16:27:17.738401+00:00: Rotating heading and horizontal velocities by -7.25 degrees.\n2024-05-21T16:27:17.761806+00:00: Trimmed velocity data using NON-atmospherically corrected pressure (water level) and sidelobes 
-(with 3 additional surface bins removed).\n2024-05-21T16:27:18.023571+00:00: Processed to CF-1.8 using runsigcdf2nc.py.\n" ;
-                :nominal_sensor_depth_note = "WATER_DEPTH - initial_instrument_height" ;
-                :nominal_sensor_depth = 4. ;
-                :transducer_offset_from_bottom = 1. ;
-                :serial_number = 101042 ;
-                :frequency = 1000. ;
-                :instrument_type = "Signature1000" ;
-                :bin_size = 0.200000002980232 ;
-                :beam_angle = 25 ;
-                :nominal_instrument_depth = 4. ;
-                :start_time = "2023-06-23T16:00:00.000000000" ;
-                :stop_time = "2023-08-04T02:08:00.000000000" ;
-}
\ No newline at end of file

From b1a6c698f7767e2780e70bf088135a7f03008e9d Mon Sep 17 00:00:00 2001
From: ssuttles-usgs
 <ssuttles@usgs.govgit config -lgit config --global user.email ssuttles@usgs.gov>
Date: Thu, 23 May 2024 11:54:50 -0400
Subject: [PATCH 6/7] reslove issues in PR

---
 .gitattributes                   |  7 +------
 stglib/core/utils.py             | 27 ++++++++++++++++++++-------
 stglib/sig/cdf2nc.py             | 30 ++++++++++++++++++------------
 stglib/tests/data/.gitattributes |  5 +++++
 4 files changed, 44 insertions(+), 25 deletions(-)

diff --git a/.gitattributes b/.gitattributes
index dd01487a..bdc578e9 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,8 +1,3 @@
 *.ipynb filter=nbstripout
 *.ipynb diff=ipynb
-stglib/_version.py export-subst
-stglib/tests/data/055109_20220808_1605.zip filter=lfs diff=lfs merge=lfs -text
-stglib/tests/data/055109_20220808_1605_config.yaml filter=lfs diff=lfs merge=lfs -text
-stglib/tests/data/gatts_055109_20220808_1605.txt filter=lfs diff=lfs merge=lfs -text
-stglib/tests/data/*.cdf filter=lfs diff=lfs merge=lfs -text
-stglib/tests/data/mat3/* filter=lfs diff=lfs merge=lfs -text
+stglib/_version.py export-subst
\ No newline at end of file
diff --git a/stglib/core/utils.py b/stglib/core/utils.py
index 83e59f41..04142ed8 100644
--- a/stglib/core/utils.py
+++ b/stglib/core/utils.py
@@ -1301,14 +1301,27 @@ def spcon_from_salinity(S):
     )
 
 
-def check_fits_in_int32(ds, var):
-    if np.nanmax(np.abs(ds[var])) > (2**31 - 1):
-        warnings.warn(
-            f"32-bit integer overflow on {var}; setting encoding to i4 will fail"
-        )
-        return False
+def check_fits_in_int32(ds, var, units="s"):
+    # check to see if var is time and if so handle it differently
+    if var == "time":
+        tmax = (ds["time"][-1].values - ds["time"][0].values) / np.timedelta64(1, units)
+
+        if np.abs(tmax) > (2**31 - 1):
+            warnings.warn(
+                f"32-bit integer overflow on {var} with units of '{units}'; setting encoding to i4 will fail"
+            )
+            return False
+
+        else:
+            return True
     else:
-        return True
+        if np.nanmax(np.abs(ds[var])) > (2**31 - 1):
+            warnings.warn(
+                f"32-bit integer overflow on {var}; setting encoding to i4 will fail"
+            )
+            return False
+        else:
+            return True
 
 
 def check_time_fits_in_int32(ds, var):
diff --git a/stglib/sig/cdf2nc.py b/stglib/sig/cdf2nc.py
index 6a1a4471..cd4e5d9e 100644
--- a/stglib/sig/cdf2nc.py
+++ b/stglib/sig/cdf2nc.py
@@ -373,22 +373,28 @@ def fix_encoding(ds):
     if "units" in ds["time"].encoding:
         ds["time"].encoding.pop("units")
 
-    tstep = ds["time"][1] - ds["time"][0]  # use time step to select time encoding
-    # if "sample" not in ds.dims:
+    # use time step to select time encoding
+    tstep = ds["time"][1] - ds["time"][0]
+
     if tstep < np.timedelta64(1, "m"):
-        print(
-            f"make time encoding to dtype double because tstep {tstep} seconds is < 1 minute, round to milliseconds first"
-        )
-        ds["time"] = ds["time"].dt.round("ms")  # round time to milliseconds first
+
+        histtext = f"make time encoding to dtype double because tstep {tstep} seconds is < 1 minute, round to milliseconds first"
+        ds = utils.insert_history(ds, histtext)
+
+        # round time to milliseconds first
+        ds["time"] = ds["time"].dt.round("ms")
         ds["time"].encoding["dtype"] = "double"
 
     else:
-        print(
-            f"make time encoding int because tstep {tstep} seconds is >= 1 minute, round time to seconds first"
-        )
-        ds["time"] = ds["time"].dt.round(
-            "s"
-        )  # round time to seconds if time interval >= 1 minute
+        histtext = f"make time encoding int because tstep {tstep} seconds is >= 1 minute, round time to seconds first"
+        ds = utils.insert_history(ds, histtext)
+
+        # round time to seconds if time interval >= 1 minute
+        ds["time"] = ds["time"].dt.round("s")
+
+        # check time to make sure it fits in int32, assume seconds for time units
+        utils.check_fits_in_int32(ds, "time", "s")
+
         ds["time"].encoding["dtype"] = "i4"
 
     if "beam" in ds.dims:
diff --git a/stglib/tests/data/.gitattributes b/stglib/tests/data/.gitattributes
index d4e14e5f..153ed4cd 100644
--- a/stglib/tests/data/.gitattributes
+++ b/stglib/tests/data/.gitattributes
@@ -97,3 +97,8 @@ BEL503.wad filter=lfs diff=lfs merge=lfs -text
 BEL503.whd filter=lfs diff=lfs merge=lfs -text
 BEL5C_wvsconfig.yaml filter=lfs diff=lfs merge=lfs -text
 atmpres-BEL5Cwvs.cdf filter=lfs diff=lfs merge=lfs -text
+055109_20220808_1605.zip filter=lfs diff=lfs merge=lfs -text
+055109_20220808_1605_config.yaml filter=lfs diff=lfs merge=lfs -text
+gatts_055109_20220808_1605.txt filter=lfs diff=lfs merge=lfs -text
+*.cdf filter=lfs diff=lfs merge=lfs -text
+mat3/** filter=lfs diff=lfs merge=lfs -text

From b7c6388d9032abd58ddb01e1f6bce9270b484079 Mon Sep 17 00:00:00 2001
From: ssuttles-usgs
 <ssuttles@usgs.govgit config -lgit config --global user.email ssuttles@usgs.gov>
Date: Thu, 23 May 2024 13:24:06 -0400
Subject: [PATCH 7/7] v2 reslove issues in PR

---
 .gitattributes       |  2 +-
 stglib/core/utils.py | 27 +++++++--------------------
 stglib/sig/cdf2nc.py |  2 +-
 3 files changed, 9 insertions(+), 22 deletions(-)

diff --git a/.gitattributes b/.gitattributes
index bdc578e9..c7868c45 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,3 @@
 *.ipynb filter=nbstripout
 *.ipynb diff=ipynb
-stglib/_version.py export-subst
\ No newline at end of file
+stglib/_version.py export-subst
diff --git a/stglib/core/utils.py b/stglib/core/utils.py
index 04142ed8..83e59f41 100644
--- a/stglib/core/utils.py
+++ b/stglib/core/utils.py
@@ -1301,27 +1301,14 @@ def spcon_from_salinity(S):
     )
 
 
-def check_fits_in_int32(ds, var, units="s"):
-    # check to see if var is time and if so handle it differently
-    if var == "time":
-        tmax = (ds["time"][-1].values - ds["time"][0].values) / np.timedelta64(1, units)
-
-        if np.abs(tmax) > (2**31 - 1):
-            warnings.warn(
-                f"32-bit integer overflow on {var} with units of '{units}'; setting encoding to i4 will fail"
-            )
-            return False
-
-        else:
-            return True
+def check_fits_in_int32(ds, var):
+    if np.nanmax(np.abs(ds[var])) > (2**31 - 1):
+        warnings.warn(
+            f"32-bit integer overflow on {var}; setting encoding to i4 will fail"
+        )
+        return False
     else:
-        if np.nanmax(np.abs(ds[var])) > (2**31 - 1):
-            warnings.warn(
-                f"32-bit integer overflow on {var}; setting encoding to i4 will fail"
-            )
-            return False
-        else:
-            return True
+        return True
 
 
 def check_time_fits_in_int32(ds, var):
diff --git a/stglib/sig/cdf2nc.py b/stglib/sig/cdf2nc.py
index cd4e5d9e..5a964972 100644
--- a/stglib/sig/cdf2nc.py
+++ b/stglib/sig/cdf2nc.py
@@ -393,7 +393,7 @@ def fix_encoding(ds):
         ds["time"] = ds["time"].dt.round("s")
 
         # check time to make sure it fits in int32, assume seconds for time units
-        utils.check_fits_in_int32(ds, "time", "s")
+        utils.check_time_fits_in_int32(ds, "time")
 
         ds["time"].encoding["dtype"] = "i4"