pyadps 0.1.1__py3-none-any.whl → 0.2.0b0__py3-none-any.whl

pyadps/utils/cutbin.py

@@ -0,0 +1,413 @@
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+from matplotlib.widgets import Button, RadioButtons, RectangleSelector, Slider
+
+from pyadps.utils import readrdi as rd
+
+
+class CutBins:
+    def __init__(
+        self, data, mask, newmask=False, t1=0, t2=200, tinc=500, z1=0, z2=-1, zinc=0
+    ):
+        # DATA SETUP
+        self.orig_data = data
+        self.orig_shape = np.shape(self.orig_data)
+        self.fill = 999
+        self.maskarray = mask
+        if not newmask:
+            self.orig_data[self.maskarray == 1] = self.fill
+
+        self.t1, self.t2, self.tinc = t1, t2, tinc
+        self.z1, self.z2, self.zinc = z1, z2, zinc
+        if z2 == -1:
+            self.z2 = self.orig_shape[0]
+
+        self.data = self.orig_data[self.z1 : self.z2, self.t1 : self.t2]
+        self.orig_subset = self.orig_data[self.z1 : self.z2, self.t1 : self.t2]
+        self.datacopy = np.copy(self.orig_data)
+        self.datamin = np.min(self.orig_data)
+        self.datamax = np.max(self.orig_data)
+        self.shape = np.shape(self.data)
+
+        # PLOT SETUP
+        self.t = np.arange(self.t1, self.t2)
+        self.z = np.arange(self.z1, self.z2)
+        self.tickinterval = int((self.t2 - self.t1) / 5)
+        self.xticks = np.arange(self.t1, self.t2, self.tickinterval)
+        self.X, self.Y = np.meshgrid(self.t, self.z)
+        self.fig, self.axs = plt.subplot_mosaic(
+            [["a", "b"], ["c", "b"]],
+            figsize=(12, 10),
+            width_ratios=[2, 1],
+            height_ratios=[1.75, 1],
+        )
+        self.fig.set_facecolor("darkgrey")
+        plt.subplots_adjust(top=0.82, right=0.95)
+
+        # ADDING WIDGET AXES
+        self.ax_clear_button = self.fig.add_axes(rect=(0.125, 0.90, 0.08, 0.025))
+        self.ax_delete_button = self.fig.add_axes(rect=(0.225, 0.90, 0.08, 0.025))
+        self.ax_refill_button = self.fig.add_axes(rect=(0.325, 0.90, 0.08, 0.025))
+        self.ax_next_button = self.fig.add_axes(rect=(0.630, 0.65, 0.02, 0.050))
+        self.ax_previous_button = self.fig.add_axes(rect=(0.075, 0.65, 0.02, 0.050))
+        self.ax_radio_button = self.fig.add_axes(rect=(0.725, 0.87, 0.10, 0.10))
+        self.ax_exit_button = self.fig.add_axes(rect=(0.825, 0.025, 0.08, 0.035))
+        self.ax_hslider = self.fig.add_axes(rect=(0.125, 0.85, 0.50, 0.03))
+        self.ax_vslider = self.fig.add_axes(rect=(0.04, 0.25, 0.03, 0.50))
+
+        self.ax_delete_button.set_visible(False)
+        self.ax_refill_button.set_visible(False)
+
+        # --- Slider settings ---
+        # Initial slider settings
+        self.hevent = 0
+        self.vevent = 0
+
+        # Slider options
+        self.hslider = Slider(
+            ax=self.ax_hslider,
+            label="Ensemble",
+            valmin=self.t1,
+            valmax=self.t2,
+            valinit=self.hevent,
+            valfmt="%i",
+            valstep=1,
+        )
+
+        self.vslider = Slider(
+            ax=self.ax_vslider,
+            label="Bins",
+            valmin=self.z1,
+            valmax=self.z2,
+            valinit=self.vevent,
+            valfmt="%i",
+            valstep=1,
+            orientation="vertical",
+        )
+
+        # Button Labels
+        self.clear_button = Button(self.ax_clear_button, "Clear")
+        self.delete_button = Button(self.ax_delete_button, "Delete")
+        self.refill_button = Button(self.ax_refill_button, "Refill")
+        self.previous_button = Button(self.ax_previous_button, "<")
+        self.next_button = Button(self.ax_next_button, ">")
+        self.exit_button = Button(self.ax_exit_button, "Save & Exit")
+        # self.cell_button = Button(self.ax_cell_button, "Cell")
+        # self.ensemble_button = Button(self.ax_ensemble_button, "Ensemble")
+        self.radio_button = RadioButtons(
+            self.ax_radio_button, ("Bin", "Ensemble", "Cell", "Region")
+        )
+
+        # --------------PLOTS---------------------
+
+        # Settings colorbar extreme to black
+        cmap = mpl.cm.turbo.with_extremes(over="k")
+        # FILL PLOT
+        self.mesh = self.axs["a"].pcolormesh(
+            self.X, self.Y, self.data, cmap=cmap, picker=True, vmin=0, vmax=255
+        )
+        plt.colorbar(self.mesh, orientation="horizontal")
+        self.axs["a"].set_xlim([self.t1, self.t2])
+        self.axs["a"].set_ylim([self.z1, self.z2])
+        # Draw vertical and horizontal lines
+        (self.vline,) = self.axs["a"].plot(
+            [self.t1, self.t1], [self.z1, self.z2], color="r", linewidth=2.5
+        )
+        (self.hline,) = self.axs["a"].plot(
+            [self.t1, self.t2], [self.z1, self.z1], color="r", linewidth=2.5
+        )
+
+        # PROFILE
+        (self.profile,) = self.axs["b"].plot(
+            self.data[self.z1 : self.z2, self.t1 + self.hevent], range(self.z1, self.z2)
+        )
+
+        self.axs["b"].set_xlim([self.datamin, self.datamax])
+        self.profile_text = self.axs["b"].text(
+            0.95,
+            0.95,
+            f"Ensemble No.: {self.t1 + self.hevent}",
+            verticalalignment="bottom",
+            horizontalalignment="right",
+            transform=self.axs["b"].transAxes,
+            color="k",
+            fontsize=12,
+        )
+
+        # TIME SERIES
+        (self.tseries,) = self.axs["c"].plot(
+            range(self.t1, self.t2), self.data[self.z1 + self.vevent, self.t1 : self.t2]
+        )
+        self.axs["c"].set_ylim([self.datamin, self.datamax])
+        self.tseries_text = self.axs["c"].text(
+            0.90,
+            0.90,
+            f"Bin No.: {self.z1 + self.vevent}",
+            verticalalignment="bottom",
+            horizontalalignment="right",
+            transform=self.axs["c"].transAxes,
+            color="k",
+            fontsize=12,
+        )
+        # --------------END PLOTS---------------------
+
+        # EVENTS
+        self.onclick = self.onclick_bin
+        self.hslider.on_changed(self.hupdate)
+        self.vslider.on_changed(self.vupdate)
+        self.clear_button.on_clicked(self.clear)
+        self.radio_button.on_clicked(self.radio)
+        self.cid = self.fig.canvas.mpl_connect("pick_event", self.onclick)
+
+        self.delete_button.on_clicked(self.boxdelete)
+        self.refill_button.on_clicked(self.boxrefill)
+        self.next_button.on_clicked(self.next)
+        self.previous_button.on_clicked(self.previous)
+        self.exit_button.on_clicked(self.exit)
+
+    def next(self, event):
+        if self.t2 <= self.orig_shape[1]:
+            # Next works till the last subset. The if statement checks for last subset.
+            self.t1 = self.t1 + self.tinc
+            self.t2 = self.t2 + self.tinc
+            if self.t2 > (self.orig_shape[1]):
+                # If in last subset create a dummy data set with missing value.
+                self.data = self.datacopy[
+                    self.z1 : self.z2, self.t1 : self.orig_shape[1]
+                ]
+                self.orig_subset = self.orig_data[
+                    self.z1 : self.z2, self.t1 : self.orig_shape[1]
+                ]
+                self.missing = (
+                    np.ones((self.z2 - self.z1, self.t2 - self.orig_shape[1]))
+                    * self.fill
+                )
+                # self.data consist of data along with flagged value
+                self.data = np.append(self.data, self.missing, axis=1)
+                # self.orig_subset contains only the subset of the original data
+                # Useful for plotting time series and profiles
+                self.orig_subset = np.append(self.orig_subset, self.missing, axis=1)
+            else:
+                self.data = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+                self.orig_subset = self.orig_data[self.z1 : self.z2, self.t1 : self.t2]
+
+            self.mesh.set_array(self.data)
+            self.tick = np.arange(self.t1, self.t2, self.tickinterval)
+            self.axs["a"].set_xticks(self.xticks, self.tick)
+
+            self.profile.set_xdata(self.orig_subset[:, self.hevent])
+            self.profile_text.set_text(f"Ensemble No.: {self.t1 + self.hevent}")
+            self.vline.set_xdata([self.hevent, self.hevent])
+
+            self.tseries.set_ydata(self.orig_subset[self.vevent, :])
+            self.tseries_text.set_text(f"Bin No.: {self.z1 + self.vevent}")
+            self.hline.set_ydata([self.vevent, self.vevent])
+
+            self.fig.canvas.draw()
+
+    def previous(self, event):
+        if self.t1 >= self.tinc:
+            self.t1 = self.t1 - self.tinc
+            self.t2 = self.t2 - self.tinc
+            self.tick = np.arange(self.t1, self.t2, self.tickinterval)
+            self.data = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+            self.axs["a"].set_xticks(self.xticks, self.tick)
+            self.mesh.set_array(self.data)
+
+            # Reset sliders
+            self.profile.set_xdata(self.orig_data[self.z1 : self.z2, self.hevent])
+            self.profile_text.set_text(f"Ensemble No.: {self.hevent}")
+            self.vline.set_xdata([self.hevent, self.hevent])
+
+            self.tseries.set_ydata(self.orig_data[self.vevent, self.t1 : self.t2])
+            self.tseries_text.set_text(f"Bin No.: {self.z1 + self.vevent}")
+            self.hline.set_ydata([self.vevent, self.vevent])
+
+            self.fig.canvas.draw()
+
+    def radio(self, event):
+        self.fig.canvas.mpl_disconnect(self.cid)
+        if event == "Bin":
+            self.cid = self.fig.canvas.mpl_connect("pick_event", self.onclick_bin)
+        elif event == "Ensemble":
+            self.cid = self.fig.canvas.mpl_connect("pick_event", self.onclick_ens)
+        elif event == "Cell":
+            self.cid = self.fig.canvas.mpl_connect("pick_event", self.onclick_cell)
+        else:
+            self.rid = RectangleSelector(
+                self.axs["a"],
+                self.onclick_box,
+                useblit=True,
+                minspanx=2,
+                minspany=2,
+                interactive=True,
+            )
+
+    def clear(self, event):
+        if event.button == 1:
+            self.datacopy = np.copy(self.orig_data)
+            if self.t2 >= (self.orig_shape[1]):
+                test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+                test = np.append(test, self.missing, axis=1)
+            else:
+                test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+
+            # self.mesh.set_array(self.datacopy[self.z1 : self.z2, self.t1 : self.t2])
+            self.mesh.set_array(test)
+            self.fig.canvas.draw()
+
+    def hupdate(self, event):
+        self.hevent = event
+        self.profile.set_xdata(self.orig_subset[:, self.hevent])
+        self.profile_text.set_text(f"Ensemble No.: {self.t1 + self.hevent}")
+        self.vline.set_xdata([self.hevent, self.hevent])
+
+    def vupdate(self, event):
+        self.vevent = event
+        self.tseries.set_ydata(self.orig_subset[self.vevent, :])
+        self.tseries_text.set_text(f"Bin No.: {self.z1 + self.vevent}")
+        self.hline.set_ydata([self.vevent, self.vevent])
+
+    def onclick_bin(self, event):
+        ind = event.ind
+        x = ind // (self.t[-1] + 1)
+        # y = ind % (self.t[-1] + 1)
+        xx = self.z1 + x
+        # yy = self.t1 + y
+        if np.all(self.datacopy[xx, :] == self.fill):
+            self.datacopy[xx, :] = np.copy(self.orig_data[xx, :])
+
+        else:
+            self.datacopy[xx, :] = self.fill
+
+        if self.t2 >= (self.orig_shape[1]):
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+            test = np.append(test, self.missing, axis=1)
+        else:
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+
+        # self.mesh.set_array(self.datacopy[self.z1 : self.z2, self.t1 : self.t2])
+        self.mesh.set_array(test)
+        self.hline.set_ydata([x, x])
+        self.vslider.set_val(x[0])
+        self.fig.canvas.draw()
+
+    def onclick_ens(self, event):
+        ind = event.ind
+        if np.size(ind) != 1:
+            return
+        # x = ind // (self.t[-1] + 1)
+        y = ind % (self.t[-1] + 1)
+        yy = self.t1 + y
+
+        if yy < self.orig_shape[1]:
+            if np.all(self.datacopy[:, yy] == self.fill):
+                self.datacopy[:, yy] = np.copy(self.orig_data[:, yy])
+            else:
+                self.datacopy[:, yy] = self.fill
+
+        if self.t2 >= (self.orig_shape[1]):
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+            test = np.append(test, self.missing, axis=1)
+        else:
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+        # self.mesh.set_array(self.datacopy[self.z1 : self.z2, self.t1 : self.t2])
+        self.mesh.set_array(test)
+        self.hline.set_xdata([y, y])
+        self.hslider.set_val(y[0])
+        self.fig.canvas.draw()
+
+    def onclick_cell(self, event):
+        ind = event.ind
+        if np.size(ind) != 1:
+            return
+        x = ind // (self.t[-1] + 1)
+        y = ind % (self.t[-1] + 1)
+        xx = self.z1 + x
+        yy = self.t1 + y
+
+        if yy < self.orig_shape[1]:
+            if self.datacopy[xx, yy] == self.fill:
+                self.datacopy[xx, yy] = np.copy(self.orig_data[x, y])
+            else:
+                self.datacopy[xx, yy] = self.fill
+
+        if self.t2 > (self.orig_shape[1]):
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+            test = np.append(test, self.missing, axis=1)
+        else:
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+
+        # self.mesh.set_array(self.datacopy[self.z1 : self.z2, self.t1 : self.t2])
+        self.mesh.set_array(test)
+        self.vline.set_xdata([y, y])
+        self.hline.set_ydata([x, x])
+        self.hslider.set_val(y[0])
+        self.vslider.set_val(x[0])
+        self.fig.canvas.draw()
+
+    def onclick_box(self, eclick, erelease):
+        self.ax_delete_button.set_visible(True)
+        self.ax_refill_button.set_visible(True)
+        plt.gcf().canvas.draw()
+        self.x11, self.y11 = int(eclick.xdata), int(eclick.ydata)
+        self.x22, self.y22 = int(erelease.xdata) + 1, int(erelease.ydata) + 1
+
+        print(
+            f"({self.x11:3.2f}, {self.y11:3.2f}) --> ({self.x22:3.2f}, {self.y22:3.2f})"
+        )
+        print(f" The buttons you used were: {eclick.button} {erelease.button}")
+
+    def boxdelete(self, event):
+        z1 = self.z1 + self.y11 + 1
+        z2 = self.z1 + self.y22
+        t1 = self.t1 + self.x11 + 1
+        t2 = self.t1 + self.x22
+        self.datacopy[z1:z2, t1:t2] = self.fill
+
+        if self.t2 > (self.orig_shape[1]):
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+            test = np.append(test, self.missing, axis=1)
+        else:
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+
+        # self.mesh.set_array(self.datacopy[self.z1 : self.z2, self.t1 : self.t2])
+        self.mesh.set_array(test)
+        self.fig.canvas.draw()
+
+    def boxrefill(self, event):
+        z1 = self.z1 + self.y11 + 1
+        z2 = self.z1 + self.y22
+        t1 = self.t1 + self.x11 + 1
+        t2 = self.t1 + self.x22
+        self.datacopy[z1:z2, t1:t2] = self.orig_data[z1:z2, t1:t2]
+
+        if self.t2 > (self.orig_shape[1]):
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+            test = np.append(test, self.missing, axis=1)
+        else:
+            test = self.datacopy[self.z1 : self.z2, self.t1 : self.t2]
+        # self.mesh.set_array(self.datacopy[self.z1 : self.z2, self.t1 : self.t2])
+        self.mesh.set_array(test)
+        self.fig.canvas.draw()
+
+    def exit(self, event):
+        plt.close()
+
+    def mask(self):
+        self.maskarray[self.datacopy == self.fill] = 1
+        return self.maskarray
+
+
+# filename = "BGS11000.000"
+# ds = rd.echo(filename, run="fortran")
+# echo = ds[0, :, :]
+# shape = echo.shape
+# mask = np.zeros(shape)
+
+# manual = CutBins(echo, mask)
+# plt.show()
+# mask = manual.mask()
+# plt.pcolormesh(mask)
+# plt.show()

pyadps/utils/metadata/config.ini

@@ -4,9 +4,8 @@ input_file_path = /home/user/data/
 input_file_name = adcp_raw.000
 
 # Output file settings. Do not enter file extension.
-output_file_path = /home/nio/Videos/output/
+output_file_path = /home/user/output/
 output_file_name_raw = adcp_raw.nc
-output_file_name_vlead = adcp_vlead.nc
 output_file_name_processed = adcp_proc.nc
 
 # Choose between 'netcdf' or 'csv' for the raw output format
@@ -17,18 +16,11 @@ output_format_processed = csv
 
 [DownloadOptions]
 # Options to download raw and/or processed output files
-axis_option = ensemble
 download_raw = True
-download_vlead = True
 download_processed = True
 apply_mask = True
 download_mask = True
 
-[SensorTest]
-sensor_test = True
-transducer_depth = 200
-
-
 [QCTest]
 # Enable or Disable QC Test (True/False)
 qc_test = True
@@ -38,8 +30,6 @@ echo_intensity = 40
 false_target = 50
 three_beam = True
 percentage_good = 50
-orientation = up
-
 
 [ProfileTest]
 # Enable or Disable Profile Test (True/False)
@@ -49,22 +39,17 @@ trim_ends_start_index = 2
 trim_ends_end_index = 17086
 cut_bins = True
 cut_bins_add_cells = 2
-manual_cutbins = True
-manual_cut_bins = [2,10,0,8000] [40,42,0,8000] [12,14,0,8000]
 regrid = True
-regrid_option = Cell
-regrid_interpolation = nearest
-transducer_depth = 200
-water_column_depth = 200
+regrid_option = Bin
 
 [VelocityTest]
 # Enable or Disable Velocity Test (True/False)
 velocity_test = True
 magnetic_declination = True
 latitude = 0.0
-longitude = 83.0
+longitude = 0.1
 depth = 0
-year = 2025
+year = 2024
 cutoff = True
 max_zonal_velocity = 250
 max_meridional_velocity = 250
@@ -94,6 +79,3 @@ file_created_by = xxxx
 contact = abcd
 comments = No comments
 
-
-
-