pyadps 0.1.0b0__py3-none-any.whl → 0.2.0b0__py3-none-any.whl

pyadps/utils/writenc.py

@@ -68,9 +68,9 @@ def flead_ncatt(fl_obj, ncfile_id, ens=0):
             setattr(ncfile_id, format_key, format(value))
 
 
-def main(infile, outfile, attributes=None):
+def rawnc(infile, outfile, time, axis_option=None, attributes=None, t0="hours since 2000-01-01"):
     """
-    Main function to create netcdf file. Stores 3-D data types like
+    rawnc is a function to create netcdf file. Stores 3-D data types like
     velocity, echo, correlation, and percent good.
 
     Args:
@@ -90,14 +90,33 @@ def main(infile, outfile, attributes=None):
     beam_list = flead.fleader["Beams"]
 
     # Dimensions
-    outnc.createDimension("ensemble", None)
+    # Define the primary axis based on axis_option
+    if axis_option == "ensemble":
+        outnc.createDimension("ensemble", None)
+        primary_axis = "ensemble"
+        ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
+        ensemble.axis = "T"
+    elif axis_option == "time":
+        tsize = len(time)
+        outnc.createDimension("time", tsize)
+        primary_axis = "time"
+        time_var = outnc.createVariable("time", "i4", ("time",))
+        time_var.axis = "T"
+        time_var.units = t0
+        time_var.long_name = "time"
+
+        # Convert time_data to numerical format
+        nctime = pd2nctime(time, t0)
+        time_var[:] = nctime
+
+    else:
+        raise ValueError(f"Invalid axis_option: {axis_option}.")
+
     outnc.createDimension("cell", max(cell_list))
     outnc.createDimension("beam", max(beam_list))
 
     # Variables
     # Dimension Variables
-    ensemble = outnc.createVariable("ensemble", "u4", ("ensemble",))
-    ensemble.axis = "T"
     cell = outnc.createVariable("cell", "i2", ("cell",))
     cell.axis = "Z"
     beam = outnc.createVariable("beam", "i2", ("beam",))
@@ -118,9 +137,9 @@ def main(infile, outfile, attributes=None):
     for i, item in enumerate(varlist):
         if item == "Velocity":
             varid[i] = outnc.createVariable(
-                item, "i2", ("ensemble", "cell", "beam"), fill_value=-32768
+                item, "i2", (primary_axis, "cell", "beam"), fill_value=-32768
             )
-            varid[i].missing_value = -32768
+            # varid[i].missing_value = -32768
             vel = getattr(rd, item)
             var = vel(infile).data
             # var = rd.variables(infile, item)
@@ -129,7 +148,7 @@ def main(infile, outfile, attributes=None):
             # Unsigned integers might be assigned for future netcdf versions
             format_item = item.replace(" ", "")  # For percent good
             varid[i] = outnc.createVariable(
-                format_item, "i2", ("ensemble", "cell", "beam")
+                format_item, "i2", (primary_axis, "cell", "beam")
             )
             datatype = getattr(rd, format_item)
             var = np.array(datatype(infile).data, dtype="int16")
@@ -137,7 +156,13 @@ def main(infile, outfile, attributes=None):
 
         vshape = var.T.shape
         if i == 0:
-            ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+            if primary_axis == "time":
+                time[:] = np.arange(1, vshape[0] + 1, 1)
+            elif primary_axis == "ensemble":
+                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+            else:
+                raise ValueError(f"Invalid axis_option: {axis_option}.")
+
         varid[i][0 : vshape[0], 0 : vshape[1], 0 : vshape[2]] = var.T
         
     # Add global attributes if provided
@@ -152,7 +177,7 @@ def main(infile, outfile, attributes=None):
     outnc.close()
 
 
-def vlead_nc(infile, outfile, attributes=None):
+def vlead_nc(infile, outfile, time, axis_option=None, attributes=None, t0="hours since 2000-01-01"):
     """
     Function to create ncfile containing Variable Leader.
 
@@ -163,12 +188,29 @@ def vlead_nc(infile, outfile, attributes=None):
     outnc = nc4.Dataset(outfile, "w", format="NETCDF4")
 
     # Dimensions
-    outnc.createDimension("ensemble", None)
+    # Define the primary axis based on axis_option
+    if axis_option == "ensemble":
+        outnc.createDimension("ensemble", None)
+        primary_axis = "ensemble"
+        ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
+        ensemble.axis = "T"
+    elif axis_option == "time":
+        tsize = len(time)
+        outnc.createDimension("time", tsize)
+        primary_axis = "time"
+        time_var = outnc.createVariable("time", "i4", ("time",))
+        time_var.axis = "T"
+        time_var.units = t0
+        time_var.long_name = "time"
+
+        # Convert time_data to numerical format
+        nctime = pd2nctime(time, t0)
+        time_var[:] = nctime
+
+    else:
+        raise ValueError(f"Invalid axis_option: {axis_option}.")
 
     # Variables
-    # Dimension Variables
-    ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
-    ensemble.axis = "T"
 
     vlead = rd.VariableLeader(infile)
     vdict = vlead.vleader
@@ -179,12 +221,17 @@ def vlead_nc(infile, outfile, attributes=None):
     for key, values in vdict.items():
         format_item = key.replace(" ", "_")
         varid[i] = outnc.createVariable(
-            format_item, "i4", "ensemble", fill_value=-32768
+            format_item, "i4", primary_axis, fill_value=-32768
         )
         var = values
         vshape = var.shape
         if i == 0:
-            ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+            if primary_axis == "time":
+                time[:] = np.arange(1, vshape[0] + 1, 1)
+            elif primary_axis == "ensemble":
+                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+            else:
+                raise ValueError(f"Invalid axis_option: {axis_option}.")
 
         varid[i][0 : vshape[0]] = var
         i += 1
@@ -208,6 +255,20 @@ def finalnc(outfile, depth, time, data, t0="hours since 2000-01-01", attributes=
         data (numpy array): Velocity (beam, depth, time)
         t0 (string): Time unit and origin
     """
+    fill = -32768
+
+    # Change velocity to cm/s
+    data = data.astype(np.float64)
+    data[data > fill] /= 10 
+
+    # Change depth to positive
+    depth = abs(depth)
+
+    # Reverse the arrays if depth in descending order
+    if np.all(depth[:-1] >= depth[1:]):
+        depth = depth[::-1]
+        data = data[:, ::-1, :]
+
     ncfile = nc4.Dataset(outfile, mode="w", format="NETCDF4")
     # Check if depth is scalar or array
     if np.isscalar(depth):
@@ -221,21 +282,22 @@ def finalnc(outfile, depth, time, data, t0="hours since 2000-01-01", attributes=
     z = ncfile.createVariable("depth", np.float32, ("depth"))
     z.units = "m"
     z.long_name = "depth"
+    z.positive = "down"
 
     t = ncfile.createVariable("time", np.float32, ("time"))
     t.units = t0
     t.long_name = "time"
 
     # Create 2D variables
-    uvel = ncfile.createVariable("u", np.float32, ("time", "depth"), fill_value=-32768)
+    uvel = ncfile.createVariable("u", np.float32, ("time", "depth"), fill_value=fill)
     uvel.units = "cm/s"
     uvel.long_name = "zonal_velocity"
 
-    vvel = ncfile.createVariable("v", np.float32, ("time", "depth"), fill_value=-32768)
+    vvel = ncfile.createVariable("v", np.float32, ("time", "depth"), fill_value=fill)
     vvel.units = "cm/s"
     vvel.long_name = "meridional_velocity"
 
-    wvel = ncfile.createVariable("w", np.float32, ("time", "depth"), fill_value=-32768)
+    wvel = ncfile.createVariable("w", np.float32, ("time", "depth"), fill_value=fill)
     wvel.units = "cm/s"
     wvel.long_name = "vertical_velocity"
 
@@ -247,7 +309,7 @@ def finalnc(outfile, depth, time, data, t0="hours since 2000-01-01", attributes=
 
     nctime = pd2nctime(time, t0)
     # write data
-    z[:] = depth * -1
+    z[:] = depth
     t[:] = nctime
     uvel[:, :] = data[0, :, :].T
     vvel[:, :] = data[1, :, :].T

{pyadps-0.1.0b0.dist-info → pyadps-0.2.0b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyadps
-Version: 0.1.0b0
+Version: 0.2.0b0
 Summary: A Python package for ADCP data processing
 Home-page: https://example.com
 License: MIT
@@ -12,6 +12,7 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Provides-Extra: tests
 Requires-Dist: cmake (>=3.30.2)
 Requires-Dist: matplotlib (>=3.8.4)

pyadps-0.2.0b0.dist-info/RECORD

@@ -0,0 +1,31 @@
+pyadps/Home_Page.py,sha256=gC0eFMtn85U_A4KcVlCEzXkB6a_J0WD3vpK691Kmyw8,1180
+pyadps/__init__.py,sha256=bNCm6_WIhiwvaUeOZhRkyLZyzzUKfSH80Fslg0JPJyk,232
+pyadps/__main__.py,sha256=cIFUayxPnKl00oIR99L6IUEvc8trW7dijtfBQCAen5c,356
+pyadps/pages/01_Read_File.py,sha256=nN05FfZZ1wWOY0T1HRKQ9e2SGoKcc1eQLnTQnmQlfQw,8904
+pyadps/pages/02_View_Raw_Data.py,sha256=-Txl4seQG_c1iAyKRDGONebOARmgEelTgYw19DajToo,3675
+pyadps/pages/03_Download_Raw_File.py,sha256=XBpn4Jt4f9XjZoELS7svJW8S5JBFJnKPUkuIgsHlz_w,8787
+pyadps/pages/04_QC_Test.py,sha256=RR6xos_jgTVrxve8GyrUxvWhEmxpLgbQ-Cx-xAazsls,10335
+pyadps/pages/05_Profile_Test.py,sha256=TBqxJ4TRM7TN5Y7UxXkVtyfS6isD7FWzyS4wuZw79XE,19570
+pyadps/pages/06_Velocity_Test.py,sha256=pBl56ITM-fTM5UnfB_qcYdzWNtmlhD5ZeGUGLwrBKj8,12066
+pyadps/pages/07_Write_File.py,sha256=hzhKxQXwoMa-WC7Co3ufkqPAS_iLkqea6I_OusDQUM4,16115
+pyadps/pages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyadps/utils/__init__.py,sha256=NJQy9tUDnAOvX9-c47LjBJzxYeICC4y-WBv44pOL09k,402
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+pyadps/utils/signal_quality.py,sha256=E1lZWZfdUnbc5c02px5WWU8b12DnkeCo-gRHjIoe18s,4170
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+pyadps-0.2.0b0.dist-info/LICENSE,sha256=sfY_7DzQF5FxnO2T6ek74dfm5uBmwEp1oEg_WlzNsb8,1092
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+pyadps-0.2.0b0.dist-info/entry_points.txt,sha256=qS5lbmTJLC4Ys0nu4-2tJoBpAHxTREta30KFrDyTfsY,90
+pyadps-0.2.0b0.dist-info/RECORD,,

{pyadps-0.1.0b0.dist-info → pyadps-0.2.0b0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 1.9.1
 Root-Is-Purelib: true
 Tag: py3-none-any

{pyadps-0.1.0b0.dist-info → pyadps-0.2.0b0.dist-info}/entry_points.txt

@@ -1,3 +1,4 @@
 [console_scripts]
+run-auto=pyadps.utils.autoprocess:main
 run-pyadps=pyadps.__main__:main
 

pyadps-0.1.0b0.dist-info/RECORD

@@ -1,29 +0,0 @@
-pyadps/Home_Page.py,sha256=gC0eFMtn85U_A4KcVlCEzXkB6a_J0WD3vpK691Kmyw8,1180
-pyadps/__init__.py,sha256=bNCm6_WIhiwvaUeOZhRkyLZyzzUKfSH80Fslg0JPJyk,232
-pyadps/__main__.py,sha256=cIFUayxPnKl00oIR99L6IUEvc8trW7dijtfBQCAen5c,356
-pyadps/pages/01_Read_File.py,sha256=ndBslgOHxbk6U6AMKL2uEnwCFL7rukpx8CqfM-_LXz8,8788
-pyadps/pages/02_View_Raw_Data.py,sha256=-Txl4seQG_c1iAyKRDGONebOARmgEelTgYw19DajToo,3675
-pyadps/pages/03_Download_Raw_File.py,sha256=YdGnlx6ZsJ_vAEK8086sCIHewvi9gg0d2yWl7s7qeNU,8216
-pyadps/pages/04_QC_Test.py,sha256=uawHLN9X7X7ykOZtI_viMMG-OlEEerm2X8uJFyWiRzo,8363
-pyadps/pages/05_Profile_Test.py,sha256=wQ_jXaaaEPCdb4yWzITHuGlkbGdw97ZnlK_4ppF7XS4,12114
-pyadps/pages/06_Velocity_Test.py,sha256=8AtUC3V7BJPuxVe1gMkrdwG0_XZwE0DE4bRCW86Luto,9666
-pyadps/pages/07_Write_File.py,sha256=7SBx4IDV4Oi6CBPvTzV7dJCvjGOimr6FwSEksk_rQBk,13481
-pyadps/pages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-pyadps/utils/metadata/flmeta.json,sha256=diIB9nht_0uw9YJNSFGdZYGzeVbR-07zIZS9Nf4VPSE,14245
-pyadps/utils/metadata/vlmeta.json,sha256=_dkQlGkkUvpAIM7S6kEUenSaiCpOrwXg8n1aU3dDF3s,22535
-pyadps/utils/plotgen.py,sha256=ylYPxBmrtPc_ssgEwyUixc6p3QuNcTs88LgJHWk_Vag,7129
-pyadps/utils/profile_test.py,sha256=1Ot8_1z9VUfX4bmVp-_P_QStrnbkVDwLth2pQQCJTrM,5652
-pyadps/utils/pyreadrdi.py,sha256=MX5xe5qKwFMF1RWeCQ3-vBDxm9nP0UbHsEJzSDewnuY,34807
-pyadps/utils/readrdi.py,sha256=jRtzMsaAd_raDD5fmAjVXK5M18QgukmW7SmmACI98o0,44975
-pyadps/utils/regrid.py,sha256=Oh1s4g83EWOvCfOkFiEpNoEI3ARwMukjlmVCi834KYM,3269
-pyadps/utils/script.py,sha256=yf3AZS3FMS2xk77rwezGA8WefwV03vIRQ6HraoeLuBA,4965
-pyadps/utils/signal_quality.py,sha256=E1lZWZfdUnbc5c02px5WWU8b12DnkeCo-gRHjIoe18s,4170
-pyadps/utils/velocity_test.py,sha256=keNd2DNBF0E0FhkqGHXM-zapA5xCEvvh8eyBd3xacvU,3555
-pyadps/utils/writenc.py,sha256=fJi7KSUS5AqZt-YNVsfM74Q0Dq54FUiPyMkNFRc83MQ,7663
-pyadps-0.1.0b0.dist-info/LICENSE,sha256=sfY_7DzQF5FxnO2T6ek74dfm5uBmwEp1oEg_WlzNsb8,1092
-pyadps-0.1.0b0.dist-info/METADATA,sha256=EYXVTygVzbyau6IJ4ro7iWq0Yv_3YobAO4KPoNeQp4c,4187
-pyadps-0.1.0b0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pyadps-0.1.0b0.dist-info/entry_points.txt,sha256=jFrXjOakSOPFOv2iDeYx_fI9FxdL1wXQ6FghECFpsvg,51
-pyadps-0.1.0b0.dist-info/RECORD,,