pyadps 0.1.0__py3-none-any.whl → 0.1.0b0__py3-none-any.whl

pyadps/utils/script.py

@@ -1,205 +1,155 @@
-import os
+import sys
+
 import matplotlib.pyplot as plt
 import numpy as np
 import pyadps.utils.readrdi as rd
-from pyadps.utils.plotgen import CutBins
+from pyadps.utils.cutbin import CutBins
+from pyadps.utils.plotgen import plotmask, plotvar
 from pyadps.utils.profile_test import side_lobe_beam_angle, trim_ends
-from pyadps.utils.profile_test import regrid2d, regrid3d
-from pyadps.utils.signal_quality import (
-    default_mask,
-    ev_check,
-    false_target,
-    pg_check,
-    correlation_check,
-    echo_check,
-    qc_prompt,
-)
-from pyadps.utils.velocity_test import (
-    despike,
-    flatline,
-    velocity_modifier,
-    wmm2020api,
-    velocity_cutoff,
-)
-
-import pyadps.utils.writenc as wr
+from pyadps.utils.regrid import regrid2d, regrid3d
+from pyadps.utils.signal_quality import (default_mask, ev_check, false_target,
+                                         pg_check, qc_check, qc_prompt)
+from pyadps.utils.velocity_test import (despike, flatline,
+                                        magnetic_declination, velocity_cutoff)
 
 plt.style.use("seaborn-v0_8-darkgrid")
 
 
-def main():
-    # Get the config file
-    try:
-        filepath = input("Enter file name: ")
-        if os.path.exists(filepath):
-            run_script(filepath)
-        else:
-            print("File not found!")
-    except Exception as e:
-        import traceback
-
-        print("Error: Unable to process the data.")
-        traceback.print_exc()
-
-
-# filename = "./metadata/demo.000"
-
-
-def run_script(filename):
-    ds = rd.ReadFile(filename)
-    fl = ds.fixedleader
-    vl = ds.variableleader
-    vel = ds.velocity.data
-    echo = ds.echo.data
-    cor = ds.correlation.data
-    pgood = ds.percentgood.data
-    time = ds.time
-    beamdir = ds.fixedleader.system_configuration()["Beam Direction"]
-
-    # Data pressure = vl.vleader["Pressure"]
-    # beam_angle = int(fl.system_configuration()["Beam Angle"])
-    # blank_size = fl.field()["Blank Transmit"]
-    cell_size = fl.field()["Depth Cell Len"] / 100
-    cells = fl.field()["Cells"]
-    bin1dist = fl.field()["Bin 1 Dist"] / 100
-
-    mean_depth = np.mean(ds.variableleader.depth_of_transducer.data) / 10
-    mean_depth = np.trunc(mean_depth)
-    if beamdir.lower() == "up":
-        sgn = -1
-    else:
-        sgn = 1
-
-    first_depth = mean_depth + sgn * bin1dist
-    last_depth = first_depth + sgn * cells * cell_size
-    z = np.arange(first_depth, last_depth, sgn * cell_size)
-
-    # Original mask created from velocity
-    mask = default_mask(ds)
-    orig_mask = np.copy(mask)
-
-    # Default threshold
-    ct = fl.field()["Correlation Thresh"]
-    et = 0
-    pgt = fl.field()["Percent Good Min"]
-    evt = fl.field()["Error Velocity Thresh"]
-    ft = fl.field()["False Target Thresh"]
-
-    # Get the threshold values
-    ct = qc_prompt(ds, "Correlation Thresh")
-    evt = qc_prompt(ds, "Error Velocity Thresh")
-    pgt = qc_prompt(ds, "Percent Good Min")
-    et = qc_prompt(ds, "Echo Intensity Thresh", echo)
-    ft = qc_prompt(ds, "False Target Thresh")
-
-    # Apply threshold
-    # values, counts = np.unique(mask, return_counts=True)
-    # print(values, counts, np.round(counts * 100 / np.sum(counts)))
-    print("Applying Thresholds")
-    mask = pg_check(ds, mask, pgt)
-    mask = correlation_check(ds, mask, ct)
-    mask = echo_check(ds, mask, et)
-    mask = ev_check(ds, mask, evt)
-    mask = false_target(ds, mask, ft, threebeam=True)
-
-    ########## PROFILE TEST #########
-
-    affirm = input("Would you like to trim the ends? [y/n]: ")
-    if affirm.lower() == "y":
-        mask = trim_ends(ds, mask)
-
-    affirm = input("Would you remove the surface backscatter bins? [y/n]: ")
-    if affirm.lower() == "y":
-        mask = side_lobe_beam_angle(ds, mask)
-
-    affirm = input("Would you like to manually select and mask data? [y/n]: ")
-    if affirm.lower() == "y":
-        manual = CutBins(echo[0, :, :], mask)
-        plt.show()
-        mask = manual.mask()
-
-    affirm = input("Regrid the data based on pressure sensor? [y/n]:")
-    if affirm.lower() == "y":
-        z, vel = regrid3d(ds, vel, -32768)
-        z, echo_reg = regrid3d(ds, echo, -32768)
-        z, correlation_reg = regrid3d(ds, cor, -32768)
-        z, percentgood_reg = regrid3d(ds, pgood, -32768)
-        z, mask = regrid2d(ds, mask, -32768)
-
-    ########## VELOCITY TEST ##########
-    affirm = input("Apply correction for magnetic declination? [y/n]:")
-    if affirm.lower() == "y":
-        lat = input("Enter Latitude: ")
-        lat = float(lat)
-
-        lon = input("Enter Longitude: ")
-        lon = float(lon)
-
-        depth = input("Enter Depth (m): ")
-        depth = float(depth)
-
-        year = input("Year: ")
-        year = int(year)
-
-        mag = wmm2020api(lat, lon, year)
-        vel = velocity_modifier(vel, mag)
-
-    affirm = input("Apply velocity thresholds [y/n]: ")
-    if affirm.lower() == "y":
-        maxuvel = input("Enter maximum zonal velocity: ")
-        maxuvel = float(maxuvel)
-
-        maxvvel = input("Enter maximum meridional velocity: ")
-        maxvvel = float(maxvvel)
-
-        maxwvel = input("Enter maximum vertical velocity: ")
-        maxwvel = float(maxwvel)
-        mask = velocity_cutoff(vel[0, :, :], mask, cutoff=maxuvel)
-        mask = velocity_cutoff(vel[1, :, :], mask, cutoff=maxvvel)
-        mask = velocity_cutoff(vel[2, :, :], mask, cutoff=maxwvel)
-
-    affirm = input("Despike the data? [y/n]: ")
-    if affirm.lower() == "y":
-        despike_kernal = input("Enter despike kernal size:")
-        despike_kernal = int(despike_kernal)
-
-        despike_cutoff = input("Enter despike cutoff (mm/s): ")
-        despike_cutoff = float(despike_cutoff)
-
-        mask = despike(
-            vel[0, :, :], mask, kernal_size=despike_kernal, cutoff=despike_cutoff
-        )
-        mask = despike(
-            vel[1, :, :], mask, kernal_size=despike_kernal, cutoff=despike_cutoff
-        )
-
-    affirm = input("Remove flatlines? [y/n]: ")
-    if affirm.lower() == "y":
-        flatline_kernal = input("Enter despike kernal size:")
-        flatline_kernal = int(flatline_kernal)
-        flatline_cutoff = input("Enter Flatline deviation: [y/n]")
-        flatlineL_cutoff = int(flatline_cutoff)
-        mask = flatline(
-            vel[0, :, :], mask, kernal_size=flatline_kernal, cutoff=flatline_cutoff
-        )
-        mask = flatline(
-            vel[1, :, :], mask, kernal_size=flatline_kernal, cutoff=flatline_cutoff
-        )
-        mask = flatline(
-            vel[2, :, :], mask, kernal_size=flatline_kernal, cutoff=flatline_cutoff
-        )
-    apply_mask = input("Apply mask? [y/n]: ")
-    if apply_mask.lower() == "y":
-        for i in range(4):
-            vel[i, :, :] = np.where(mask == 0, vel[i, :, :], -32768)
-
-    outfilepath = input("Enter output file name (*nc): ")
-    if os.path.exists(outfilepath):
-        if os.path.isfile(outfilepath):
-            print(f"The file already exists: {outfilepath}")
-    else:
-        wr.finalnc(outfilepath, z, mask, time, vel)
-
-
-if __name__ == "__main__":
-    main()
+# Read data
+filename = "/home/amol/Desktop/BGS11000.000"
+ds = rd.ReadFile(filename)
+fl = ds.fixedleader
+vl = ds.variableleader
+vel = ds.velocity.data
+echo = ds.echo.data
+cor = ds.correlation.data
+pgood = ds.percentgood.data
+
+# Data pressure = vl.vleader["Pressure"]
+beam_angle = int(fl.system_configuration()["Beam Angle"])
+cell_size = fl.field()["Depth Cell Len"]
+blank_size = fl.field()["Blank Transmit"]
+cells = fl.field()["Cells"]
+
+# sys.exit()
+
+# Original mask created from velocity
+mask = default_mask(fl, vel)
+orig_mask = np.copy(mask)
+
+# Default threshold
+ct = fl.field()["Correlation Thresh"]
+et = 0
+pgt = fl.field()["Percent Good Min"]
+evt = fl.field()["Error Velocity Thresh"]
+ft = fl.field()["False Target Thresh"]
+
+print(ct, et, pgt, evt, ft)
+
+# Get the threshold values
+ct = qc_prompt(fl, "Correlation Thresh")
+evt = qc_prompt(fl, "Error Velocity Thresh")
+pgt = qc_prompt(fl, "Percent Good Min")
+et = qc_prompt(fl, "Echo Intensity Thresh", echo)
+ft = qc_prompt(fl, "False Target Thresh")
+
+# Apply threshold
+values, counts = np.unique(mask, return_counts=True)
+print(values, counts, np.round(counts * 100 / np.sum(counts)))
+mask = pg_check(pgood, mask, pgt)
+mask = qc_check(cor, mask, ct)
+mask = qc_check(echo, mask, et)
+mask = ev_check(vel[3, :, :], mask, evt)
+mask = false_target(echo, mask, ft, threebeam=True)
+
+
+########## PROFILE TEST #########
+
+affirm = input("Would you like to trim the ends? [y/n]: ")
+if affirm.lower() == "y":
+    mask = trim_ends(vl, mask)
+
+affirm = input("Would you remove the surface backscatter bins? [y/n]: ")
+if affirm.lower() == "y":
+    mask = side_lobe_beam_angle(fl, vl, mask)
+
+affirm = input("Would you like to manually select and mask data?")
+if affirm.lower() == "y":
+    manual = CutBins(echo[0, :, :], mask)
+    plt.show()
+    mask = manual.mask()
+
+affirm = input("Regrid the data based on pressure sensor? [y/n]:")
+if affirm.lower() == "y":
+    z, vel = regrid3d(fl, vl, vel, -32768)
+    z, echo_reg = regrid3d(fl, vl, echo, -32768)
+    z, correlation_reg = regrid3d(fl, vl, cor, -32768)
+    z, percentgood_reg = regrid3d(fl, vl, pgood, -32768)
+    z, mask = regrid2d(fl, vl, mask, -32768)
+
+# affirm = input("Display original and revised mask files? [y/n]:")
+# if affirm.lower() == "y":
+#     plotmask(orig_mask, mask)
+
+
+########## VELOCITY TEST ##########
+affirm = input("Apply correction for magnetic declination? [y/n]:")
+if affirm.lower() == "y":
+    lat = input("Enter Latitude: ")
+    lat = float(lat)
+
+    lon = input("Enter Longitude: ")
+    lon = float(lon)
+
+    depth = input("Enter Depth (m): ")
+    depth = float(depth)
+
+    year = input("Year: ")
+    year = int(year)
+
+    velocity = magnetic_declination(vel, lat, lon, depth, year)
+
+affirm = input("Apply velocity thresholds [y/n]: ")
+if affirm.lower() == "y":
+    maxuvel = input("Enter maximum zonal velocity: ")
+    maxuvel = float(maxuvel)
+
+    maxvvel = input("Enter maximum meridional velocity: ")
+    maxvvel = float(maxvvel)
+
+    maxwvel = input("Enter maximum vertical velocity: ")
+    maxwvel = float(maxwvel)
+    mask = velocity_cutoff(vel[0, :, :], mask, cutoff=maxuvel)
+    mask = velocity_cutoff(vel[1, :, :], mask, cutoff=maxvvel)
+    mask = velocity_cutoff(vel[2, :, :], mask, cutoff=maxwvel)
+
+affirm = input("Despike the data? [y/n]: ")
+if affirm.lower() == "y":
+    despike_kernal = input("Enter despike kernal size:")
+    despike_kernal = int(despike_kernal)
+
+    despike_cutoff = input("Enter despike cutoff (mm/s): ")
+    despike_cutoff = float(despike_cutoff)
+
+    mask = despike(
+        vel[0, :, :], mask, kernal_size=despike_kernal, cutoff=despike_cutoff
+    )
+    mask = despike(
+        vel[1, :, :], mask, kernal_size=despike_kernal, cutoff=despike_cutoff
+    )
+
+affirm = input("Remove flatlines? [y/n]: ")
+if affirm.lower() == "y":
+    flatline_kernal = input("Enter despike kernal size:")
+    flatline_kernal = int(flatline_kernal)
+    flatline_cutoff = input("Enter Flatline deviation: [y/n]")
+    flatlineL_cutoff = int(flatline_cutoff)
+    mask = flatline(
+        velocity[0, :, :], mask, kernal_size=flatline_kernal, cutoff=flatline_cutoff
+    )
+    mask = flatline(
+        velocity[1, :, :], mask, kernal_size=flatline_kernal, cutoff=flatline_cutoff
+    )
+    mask = flatline(
+        velocity[2, :, :], mask, kernal_size=flatline_kernal, cutoff=flatline_cutoff
+    )