pyadps 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

pyadps/utils/signal_quality.py

@@ -54,7 +54,7 @@ def qc_check(var, mask, cutoff=0):
     return mask
 
 
-def correlation_check(ds, mask, cutoff=64):
+def correlation_check(ds, mask, cutoff,threebeam,beam_ignore=None):
     """
     Perform an correlation check on the provided variable and update the 
     mask to mark valid and invalid values based on a cutoff threshold.
@@ -93,10 +93,15 @@ def correlation_check(ds, mask, cutoff=64):
     >>> outmask = correlation_check(ds, mask, cutoff=9999)
     """
     correlation = ds.correlation.data
+    if threebeam ==True:
+        if beam_ignore == None:
+            correlation = correlation
+        else:
+            correlation = np.delete(correlation,beam_ignore,axis=0) 
     mask = qc_check(correlation, mask, cutoff=cutoff)
     return mask
 
-def echo_check(ds, mask, cutoff=40):
+def echo_check(ds, mask, cutoff, threebeam, beam_ignore=None):
     """
     Perform an echo intensity check on the provided variable and update the 
     mask to mark valid and invalid values based on a cutoff threshold.
@@ -137,6 +142,11 @@ def echo_check(ds, mask, cutoff=40):
     """
 
     echo = ds.echo.data
+    if threebeam ==True:
+        if beam_ignore == None:
+           echo  = echo
+        else:
+            echo = np.delete(echo,beam_ignore,axis=0)
     mask = qc_check(echo, mask, cutoff=cutoff)
     return mask
 
@@ -246,7 +256,7 @@ def pg_check(ds, mask, cutoff=0, threebeam=True):
     return mask
 
 
-def false_target(ds, mask, cutoff=255, threebeam=True):
+def false_target(ds, mask, cutoff=255, threebeam=True, beam_ignore=None):
     """
     Apply a false target detection algorithm based on echo intensity values. 
     This function identifies invalid or false targets in the data and updates 
@@ -292,12 +302,14 @@ def false_target(ds, mask, cutoff=255, threebeam=True):
     """
 
     echo = ds.echo.data
+    if beam_ignore != None:
+        echo = np.delete(echo,beam_ignore, axis=0)
 
     shape = np.shape(echo)
     for i in range(shape[1]):
         for j in range(shape[2]):
             x = np.sort(echo[:, i, j])
-            if threebeam:
+            if threebeam and beam_ignore is None:
                 if x[-1] - x[1] > cutoff:
                     mask[i, j] = 1
             else:

pyadps/utils/writenc.py

@@ -70,8 +70,8 @@ def flead_ncatt(fl_obj, ncfile_id, ens=0):
 def rawnc(
     infile,
     outfile,
-    time,
-    axis_option=None,
+    axis_option="time",
+    fixensemble=True,
     attributes=None,
     t0="hours since 2000-01-01",
 ):
@@ -91,7 +91,12 @@ def rawnc(
 
     outnc = nc4.Dataset(outfile, "w", format="NETCDF4")
 
-    flead = rd.FixedLeader(infile)
+    ds = rd.ReadFile(infile)
+    if fixensemble and not ds.isFixedEnsemble:
+        ds.fixensemble()
+
+    head = ds.fileheader
+    flead = ds.fixedleader
     cell_list = flead.fleader["Cells"]
     beam_list = flead.fleader["Beams"]
 
@@ -102,8 +107,11 @@ def rawnc(
         primary_axis = "ensemble"
         ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
         ensemble.axis = "T"
+        # Add ensemble
+        total_ensembles = ds.ensembles
+        ensemble = np.arange(1, total_ensembles + 1, 1)
     elif axis_option == "time":
-        tsize = len(time)
+        tsize = ds.ensembles
         outnc.createDimension("time", tsize)
         primary_axis = "time"
         time_var = outnc.createVariable("time", "i4", ("time",))
@@ -112,6 +120,7 @@ def rawnc(
         time_var.long_name = "time"
 
         # Convert time_data to numerical format
+        time = ds.time
         nctime = pd2nctime(time, t0)
         time_var[:] = nctime
 
@@ -134,7 +143,7 @@ def rawnc(
     cell[:] = np.arange(1, max(cell_list) + 1, 1)
     beam[:] = np.arange(1, max(beam_list) + 1, 1)
 
-    varlist = rd.FileHeader(infile).data_types(1)
+    varlist = head.data_types(1)
     varlist.remove("Fixed Leader")
     varlist.remove("Variable Leader")
 
@@ -145,10 +154,8 @@ def rawnc(
             varid[i] = outnc.createVariable(
                 item, "i2", (primary_axis, "cell", "beam"), fill_value=-32768
             )
-            # varid[i].missing_value = -32768
-            vel = getattr(rd, item)
-            var = vel(infile).data
-            # var = rd.variables(infile, item)
+            vel = getattr(ds, item.lower())
+            var = vel.data
 
         else:
             # Unsigned integers might be assigned for future netcdf versions
@@ -156,14 +163,10 @@ def rawnc(
             varid[i] = outnc.createVariable(
                 format_item, "i2", (primary_axis, "cell", "beam")
             )
-            datatype = getattr(rd, format_item)
-            var = np.array(datatype(infile).data, dtype="int16")
-            # var = np.array(rd.variables(infile, item), dtype="int16")
+            datatype = getattr(ds, format_item.lower())
+            var = np.array(datatype.data, dtype="int16")
 
         vshape = var.T.shape
-        if i == 0:
-            if primary_axis == "ensemble":
-                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
 
         varid[i][0 : vshape[0], 0 : vshape[1], 0 : vshape[2]] = var.T
 
@@ -179,11 +182,12 @@ def rawnc(
 
     outnc.close()
 
+
 def flead_nc(
     infile,
     outfile,
-    time,
-    axis_option=None,
+    axis_option="time",
+    fixensemble=True,
     attributes=None,
     t0="hours since 2000-01-01",
 ):
@@ -196,6 +200,11 @@ def flead_nc(
     """
     outnc = nc4.Dataset(outfile, "w", format="NETCDF4")
 
+    # Read Binary File
+    ds = rd.ReadFile(infile)
+    if fixensemble:
+        ds.fixensemble()
+    flead = ds.fixedleader
     # Dimensions
     # Define the primary axis based on axis_option
     if axis_option == "ensemble":
@@ -203,8 +212,12 @@ def flead_nc(
         primary_axis = "ensemble"
         ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
         ensemble.axis = "T"
+        # Add ensemble
+        total_ensembles = ds.ensembles
+        ensemble = np.arange(1, total_ensembles + 1, 1)
+
     elif axis_option == "time":
-        tsize = len(time)
+        tsize = ds.ensembles
         outnc.createDimension("time", tsize)
         primary_axis = "time"
         time_var = outnc.createVariable("time", "i4", ("time",))
@@ -213,6 +226,7 @@ def flead_nc(
         time_var.long_name = "time"
 
         # Convert time_data to numerical format
+        time = ds.time
         nctime = pd2nctime(time, t0)
         time_var[:] = nctime
 
@@ -220,8 +234,6 @@ def flead_nc(
         raise ValueError(f"Invalid axis_option: {axis_option}.")
 
     # Variables
-
-    flead = rd.FixedLeader(infile)
     fdict = flead.fleader
     varid = [0] * len(fdict)
 
@@ -234,9 +246,6 @@ def flead_nc(
         )
         var = values
         vshape = var.shape
-        if i == 0:
-            if primary_axis == "ensemble":
-                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
 
         varid[i][0 : vshape[0]] = var
         i += 1
@@ -248,11 +257,12 @@ def flead_nc(
 
     outnc.close()
 
+
 def vlead_nc(
     infile,
     outfile,
-    time,
-    axis_option=None,
+    axis_option="time",
+    fixensemble=True,
     attributes=None,
     t0="hours since 2000-01-01",
 ):
@@ -263,8 +273,14 @@ def vlead_nc(
         infile (string): Input file path including filename
         outfile (string): Output file path including filename
     """
+    # Create output NetCDF File
     outnc = nc4.Dataset(outfile, "w", format="NETCDF4")
 
+    # Read Binary File
+    ds = rd.ReadFile(infile)
+    if fixensemble:
+        ds.fixensemble()
+    vlead = ds.variableleader
     # Dimensions
     # Define the primary axis based on axis_option
     if axis_option == "ensemble":
@@ -272,8 +288,11 @@ def vlead_nc(
         primary_axis = "ensemble"
         ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
         ensemble.axis = "T"
+        # Add ensemble
+        total_ensembles = ds.ensembles
+        ensemble = np.arange(1, total_ensembles + 1, 1)
     elif axis_option == "time":
-        tsize = len(time)
+        tsize = ds.ensembles
         outnc.createDimension("time", tsize)
         primary_axis = "time"
         time_var = outnc.createVariable("time", "i4", ("time",))
@@ -282,15 +301,14 @@ def vlead_nc(
         time_var.long_name = "time"
 
         # Convert time_data to numerical format
+        time = ds.time
         nctime = pd2nctime(time, t0)
         time_var[:] = nctime
 
     else:
         raise ValueError(f"Invalid axis_option: {axis_option}.")
 
-    # Variables
-
-    vlead = rd.VariableLeader(infile)
+    # Read Data
     vdict = vlead.vleader
     varid = [0] * len(vdict)
 
@@ -302,12 +320,10 @@ def vlead_nc(
             format_item, "i4", primary_axis, fill_value=-32768
         )
         var = values
-        vshape = var.shape
-        if i == 0:
-            if primary_axis == "ensemble":
-                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+        # vshape = var.shape
 
-        varid[i][0 : vshape[0]] = var
+        varid[i][0 : ds.ensembles] = var
+        # varid[i][0 : vshape[0]] = var
         i += 1
 
     # Add global attributes if provided
@@ -319,7 +335,16 @@ def vlead_nc(
 
 
 def finalnc(
-    outfile, depth, final_mask, final_echo, final_corr , final_pgood, time, data, t0="hours since 2000-01-01", attributes=None
+    outfile,
+    depth,
+    final_mask,
+    final_echo,
+    final_corr,
+    final_pgood,
+    time,
+    data,
+    t0="hours since 2000-01-01",
+    attributes=None,
 ):
     """
     Function to create the processed NetCDF file.
@@ -345,9 +370,9 @@ def finalnc(
         depth = depth[::-1]
         data = data[:, ::-1, :]
         final_mask = final_mask[::-1, :]
-        final_echo = final_echo[:,::-1, :]
-        final_corr = final_corr[:,::-1, :]
-        final_pgood = final_pgood[:,::-1, :]
+        final_echo = final_echo[:, ::-1, :]
+        final_corr = final_corr[:, ::-1, :]
+        final_pgood = final_pgood[:, ::-1, :]
 
     ncfile = nc4.Dataset(outfile, mode="w", format="NETCDF4")
     # Check if depth is scalar or array
@@ -390,41 +415,65 @@ def finalnc(
     mvel = ncfile.createVariable("mask", np.float32, ("time", "depth"), fill_value=fill)
     mvel.long_name = "Velocity Mask (1: bad value, 0: good value)"
 
-    echo1 = ncfile.createVariable("echo1", np.float32, ("time", "depth"), fill_value=-32768)
+    echo1 = ncfile.createVariable(
+        "echo1", np.float32, ("time", "depth"), fill_value=-32768
+    )
     echo1.long_name = "Echo intensity Beam 1"
 
-    echo2 = ncfile.createVariable("echo2", np.float32, ("time", "depth"), fill_value=-32768)
+    echo2 = ncfile.createVariable(
+        "echo2", np.float32, ("time", "depth"), fill_value=-32768
+    )
     echo2.long_name = "Echo intensity Beam 2"
 
-    echo3 = ncfile.createVariable("echo3", np.float32, ("time", "depth"), fill_value=-32768)
+    echo3 = ncfile.createVariable(
+        "echo3", np.float32, ("time", "depth"), fill_value=-32768
+    )
     echo3.long_name = "Echo intensity Beam 3"
 
-    echo4 = ncfile.createVariable("echo4", np.float32, ("time", "depth"), fill_value=-32768)
+    echo4 = ncfile.createVariable(
+        "echo4", np.float32, ("time", "depth"), fill_value=-32768
+    )
     echo4.long_name = "Echo intensity Beam 4"
 
-    corr1 = ncfile.createVariable("corr1", np.float32, ("time", "depth"), fill_value=-32768)
+    corr1 = ncfile.createVariable(
+        "corr1", np.float32, ("time", "depth"), fill_value=-32768
+    )
     corr1.long_name = "Beam 1 correlation"
 
-    corr2 = ncfile.createVariable("corr2", np.float32, ("time", "depth"), fill_value=-32768)
+    corr2 = ncfile.createVariable(
+        "corr2", np.float32, ("time", "depth"), fill_value=-32768
+    )
     corr2.long_name = "Beam 2 correlation"
 
-    corr3 = ncfile.createVariable("corr3", np.float32, ("time", "depth"), fill_value=-32768)
+    corr3 = ncfile.createVariable(
+        "corr3", np.float32, ("time", "depth"), fill_value=-32768
+    )
     corr3.long_name = "Beam 3 correlation"
 
-    corr4 = ncfile.createVariable("corr4", np.float32, ("time", "depth"), fill_value=-32768)
-    corr4.long_name = "Beam 4 correlation"  
+    corr4 = ncfile.createVariable(
+        "corr4", np.float32, ("time", "depth"), fill_value=-32768
+    )
+    corr4.long_name = "Beam 4 correlation"
 
-    pgd1 = ncfile.createVariable("pgd1", np.float32, ("time", "depth"), fill_value=-32768)
+    pgd1 = ncfile.createVariable(
+        "pgd1", np.float32, ("time", "depth"), fill_value=-32768
+    )
     pgd1.long_name = "Percent Good Beam 1"
 
-    pgd2 = ncfile.createVariable("pgd2", np.float32, ("time", "depth"), fill_value=-32768)
+    pgd2 = ncfile.createVariable(
+        "pgd2", np.float32, ("time", "depth"), fill_value=-32768
+    )
     pgd2.long_name = "Percent Good Beam 2"
 
-    pgd3 = ncfile.createVariable("pgd3", np.float32, ("time", "depth"), fill_value=-32768)
+    pgd3 = ncfile.createVariable(
+        "pgd3", np.float32, ("time", "depth"), fill_value=-32768
+    )
     pgd3.long_name = "Percent Good Beam 3"
 
-    pgd4 = ncfile.createVariable("pgd4", np.float32, ("time", "depth"), fill_value=-32768)
-    pgd4.long_name = "Percent Good Beam 4"   
+    pgd4 = ncfile.createVariable(
+        "pgd4", np.float32, ("time", "depth"), fill_value=-32768
+    )
+    pgd4.long_name = "Percent Good Beam 4"
 
     nctime = pd2nctime(time, t0)
     # write data

{pyadps-0.1.1.dist-info → pyadps-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pyadps
-Version: 0.1.1
+Version: 0.1.3
 Summary: A Python package for ADCP data processing
 Home-page: https://pyadps.readthedocs.io/en/latest/index.html
 License: MIT

pyadps-0.1.3.dist-info/RECORD

@@ -0,0 +1,33 @@
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+pyadps/utils/profile_test.py,sha256=gnbS6ZsqKvv2tcHTj-Fi_VNOszbxDcPxl77_n4dLzSo,29237
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+pyadps/utils/velocity_test.py,sha256=O8dgjv_5pxhJq6QuWHxysMjNzxSnob_2KPLInmO1kHI,6112
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+pyadps-0.1.3.dist-info/entry_points.txt,sha256=-oZhbbJq8Q29uNVh5SmzOLp9OeFM9VUzHVxovfI4LXA,126
+pyadps-0.1.3.dist-info/RECORD,,

pyadps-0.1.1.dist-info/RECORD

@@ -1,47 +0,0 @@
-pyadps/Home_Page.py,sha256=j_-3fsp1hkhpNEl5jE-CEQvClDGpMi1H3ZQPXfuKWBg,1782
-pyadps/__init__.py,sha256=bNCm6_WIhiwvaUeOZhRkyLZyzzUKfSH80Fslg0JPJyk,232
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-pyadps/pages/04_Sensor_Health.py,sha256=2Qnwl7D46H-f8LmXLVZj5X36h8MjRwmVRK6Bs_wuB_k,33905
-pyadps/pages/05_QC_Test.py,sha256=8wt7h-RHLOf3GZ8-B_kXA0IqzHTBwW_H7YQFEk5EM6E,15904
-pyadps/pages/06_Profile_Test.py,sha256=zH2TdpEzRFUiXSDQGfdeSsGYAihdCRuj4YgsedB61E0,34776
-pyadps/pages/07_Velocity_Test.py,sha256=K4vEiLPMXrU4JMLj-mIA1G4H5ORozMbHMiMov3ZZXP0,23008
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