pyadps 0.2.0b0__py3-none-any.whl → 0.3.0__py3-none-any.whl

pyadps/pages/05_Profile_Test.py

@@ -1,575 +0,0 @@
-import numpy as np
-# import pandas as pd
-# import plotly.express as px
-import plotly.graph_objects as go
-import streamlit as st
-from plotly.subplots import make_subplots
-from plotly_resampler import FigureResampler
-from utils.profile_test import side_lobe_beam_angle, manual_cut_bins
-from utils.regrid import regrid2d, regrid3d
-from utils.signal_quality import default_mask
-
-if "flead" not in st.session_state:
-    st.write(":red[Please Select Data!]")
-    st.stop()
-
-# `maskp` holds the temporary changes in the page
-# `profile_mask`
-if "maskp" not in st.session_state:
-    if "qc_mask" not in st.session_state:
-        st.session_state.maskp = np.copy(st.session_state.orig_mask)
-    else:
-        st.session_state.maskp = np.copy(st.session_state.qc_mask)
-
-
-if st.session_state.isQCMask:
-    st.write(":grey[Working on a saved mask file ...]")
-    if st.session_state.isProfileMask:
-        st.write(
-            ":orange[Warning: Profile test already completed. Reset to change settings.]"
-        )
-        reset_selectbox = st.selectbox(
-            "Choose reset option",
-            ("QC Test", "Default"),
-            index=None,
-            placeholder="Reset mask to ...",
-        )
-        if reset_selectbox == "Default":
-            st.write("Default mask file selected")
-            st.session_state.maskp = st.session_state.orig_mask
-        elif reset_selectbox == "QC Test":
-            st.write("QC Test mask file selected")
-            st.session_state.maskp = st.session_state.qc_mask
-        else:
-            st.session_state.maskp = st.session_state.profile_mask
-    else:
-        st.session_state.maskp = st.session_state.qc_mask
-else:
-    st.write(":orange[Creating a new mask file ...]")
-
-mask = st.session_state.maskp
-
-# Load data
-flobj = st.session_state.flead
-vlobj = st.session_state.vlead
-velocity = st.session_state.velocity
-echo = st.session_state.echo
-correlation = st.session_state.correlation
-pgood = st.session_state.pgood
-fdata = flobj.fleader
-vdata = vlobj.vleader
-
-
-ensembles = st.session_state.head.ensembles
-cells = flobj.field()["Cells"]
-x = np.arange(0, ensembles, 1)
-y = np.arange(0, cells, 1)
-
-# Regrided data
-if "velocity_regrid" not in st.session_state:
-    st.session_state.echo_regrid = np.copy(echo)
-    st.session_state.velocity_regrid = np.copy(velocity)
-    st.session_state.correlation_regrid = np.copy(correlation)
-    st.session_state.pgood_regrid = np.copy(pgood)
-    st.session_state.mask_regrid = np.copy(mask)
-
-
-# @st.cache_data
-def fillplot_plotly(
-    data, title="data", maskdata=None, missing=-32768, colorscale="balance"
-):
-    fig = FigureResampler(go.Figure())
-    data = np.int32(data)
-    data1 = np.where(data == missing, np.nan, data)
-    fig.add_trace(
-        go.Heatmap(
-            z=data1,
-            x=x,
-            y=y,
-            colorscale=colorscale,
-            hoverongaps=False,
-        )
-    )
-    if mask is not None:
-        fig.add_trace(
-            go.Heatmap(
-                z=maskdata,
-                x=x,
-                y=y,
-                colorscale="gray",
-                hoverongaps=False,
-                showscale=False,
-                opacity=0.7,
-            )
-        )
-    fig.update_layout(
-        xaxis=dict(showline=True, mirror=True),
-        yaxis=dict(showline=True, mirror=True),
-        title_text=title,
-    )
-    fig.update_xaxes(title="Ensembles")
-    fig.update_yaxes(title="Depth Cells")
-    st.plotly_chart(fig)
-
-
-def fillselect_plotly(data, title="data", colorscale="balance"):
-    fig = FigureResampler(go.Figure())
-    data = np.int32(data)
-    data1 = np.where(data == -32768, None, data)
-    fig.add_trace(
-        go.Heatmap(
-            z=data1,
-            x=x,
-            y=y,
-            colorscale=colorscale,
-            hoverongaps=False,
-        )
-    )
-    # fig.add_trace(
-    #     go.Scatter(x=X, y=Y, marker=dict(color="black", size=16), mode="lines+markers")
-    # )
-    fig.update_layout(
-        xaxis=dict(showline=True, mirror=True),
-        yaxis=dict(showline=True, mirror=True),
-        title_text=title,
-    )
-    fig.update_xaxes(title="Ensembles")
-    fig.update_yaxes(title="Depth Cells")
-    fig.update_layout(clickmode="event+select")
-    event = st.plotly_chart(fig, key="1", on_select="rerun", selection_mode="box")
-
-    return event
-
-
-@st.cache_data
-def trim_ends(start_ens=0, end_ens=0, ens_range=20):
-    depth = vdata["Depth of Transducer"] / 10
-    fig = make_subplots(
-        rows=1,
-        cols=2,
-        subplot_titles=[
-            "Deployment Ensemble",
-            "Recovery Ensemble",
-        ],
-    )
-    fig.add_trace(
-        go.Scatter(
-            x=x[0:ens_range],
-            y=depth[0:ens_range],
-            name="Deployment",
-            mode="markers",
-            marker=dict(color="#1f77b4"),
-        ),
-        row=1,
-        col=1,
-    )
-
-    fig.add_trace(
-        go.Scatter(
-            x=x[-1 * ens_range :],
-            y=depth[-1 * ens_range :],
-            name="Recovery",
-            mode="markers",
-            marker=dict(color="#17becf"),
-        ),
-        row=1,
-        col=2,
-    )
-
-    if start_ens > x[0]:
-        fig.add_trace(
-            go.Scatter(
-                x=x[0:start_ens],
-                y=depth[0:start_ens],
-                name="Selected Points (D)",
-                mode="markers",
-                marker=dict(color="red"),
-            ),
-            row=1,
-            col=1,
-        )
-
-    if end_ens < x[-1] + 1:
-        fig.add_trace(
-            go.Scatter(
-                x=x[end_ens : x[-1] + 1],
-                y=depth[end_ens : x[-1] + 1],
-                name="Selected Points (R)",
-                mode="markers",
-                marker=dict(color="orange"),
-            ),
-            row=1,
-            col=2,
-        )
-
-    fig.update_layout(height=600, width=800, title_text="Transducer depth")
-    fig.update_xaxes(title="Ensembles")
-    fig.update_yaxes(title="Depth (m)")
-    st.plotly_chart(fig)
-
-
-st.header("Profile Test")
-
-############## TRIM ENDS #################
-st.header("Trim Ends", divider="blue")
-n = 20
-m = 20
-if "update_mask" not in st.session_state:
-    st.session_state.update_mask = False
-    st.session_state.endpoints = None
-    st.session_state.isTrimEnds = False
-if "update_mask_cutbin" not in st.session_state:
-    st.session_state.update_mask_cutbin = False
-    st.session_state.isCutBins = False
-
-ens_range = st.number_input("Change range", x[0], x[-1], 20)
-start_ens = st.slider("Deployment Ensembles", 0, ens_range, 0)
-end_ens = st.slider("Recovery Ensembles", x[-1] - ens_range, x[-1] + 1, x[-1] + 1)
-
-n = int(ens_range)
-
-if start_ens or end_ens:
-    trim_ends(start_ens=start_ens, end_ens=end_ens, ens_range=n)
-    # st.session_state.update_mask = False
-
-update_mask = st.button("Update mask data")
-if update_mask:
-    if start_ens > 0:
-        mask[:, :start_ens] = 1
-
-    if end_ens < x[-1]:
-        mask[:, end_ens:] = 1
-
-    st.session_state.ens_range = ens_range
-    st.session_state.start_ens = start_ens
-    st.session_state.end_ens = end_ens
-    st.session_state.maskp = mask
-    st.write(":green[mask data updated]")
-    st.session_state.endpoints = np.array(
-        [st.session_state.start_ens, st.session_state.end_ens]
-    )
-    st.write(st.session_state.endpoints)
-    st.session_state.update_mask = True
-    st.session_state.isTrimEnds = True
-
-if not st.session_state.update_mask:
-    st.write(":red[mask data not updated]")
-
-
-############  CUT BINS (SIDE LOBE) ############################
-st.header("Cut Bins: Side Lobe Contamination", divider="blue")
-st.write(
-    """
-The side lobe echos from hard surface such as sea surface or bottom of the ocean can contaminate
-data closer to this region. The data closer to the surface or bottom can be removed using 
-the relation between beam angle and the thickness of the contaminated layer.
-"""
-)
-
-# Reset mask
-mask = st.session_state.maskp
-beam = st.radio("Select beam", (1, 2, 3, 4), horizontal=True)
-beam = beam - 1
-st.session_state.beam = beam
-fillplot_plotly(echo[beam, :, :], title="Echo Intensity")
-
-orientation = st.session_state.beam_direction
-st.write(f"The orientation is `{orientation}`.")
-water_column_depth = 0
-with st.form(key="cutbin_form"):
-    extra_cells = st.number_input("Additional Cells to Delete", 0, 10, 0)
-    if orientation.lower() == 'down':
-        water_column_depth = st.number_input("Enter water column depth (m): ", 0, 15000, 0) 
-
-    cut_bins_mask = st.form_submit_button(label="Cut bins")
-
-    if cut_bins_mask:
-        st.session_state.extra_cells = extra_cells
-        mask = side_lobe_beam_angle(flobj, vlobj, mask, 
-                                    orientation=orientation,
-                                    water_column_depth=water_column_depth,
-                                    extra_cells=extra_cells)
-        fillplot_plotly(
-            echo[beam, :, :],
-            title="Echo Intensity (Masked)",
-            maskdata=mask,
-        )
-        fillplot_plotly(mask, colorscale="greys", title="Mask Data")
-
-update_mask_cutbin = st.button("Update mask file after cutbin")
-if update_mask_cutbin:
-    st.session_state.maskp = mask
-    st.write(":green[mask file updated]")
-    st.session_state.update_mask_cutbin = True
-    st.session_state.isCutBins = True
-
-if not st.session_state.update_mask_cutbin:
-    st.write(":red[mask file not updated]")
-
-
-########### CUT BINS: Manual #################
-st.header("Cut Bins: Manual", divider="blue")
-# Reset mask
-# Selection of variable (Velocity, Echo Intensity, etc.)
-variable = st.selectbox(
-    "Select Variable to Display",
-    ("Velocity", "Echo Intensity", "Correlation", "Percentage Good")
-)
-
-# Map variable selection to corresponding data
-data_dict = {
-    "Velocity": velocity,
-    "Echo Intensity": echo,
-    "Correlation": correlation,
-    "Percentage Good": pgood,
-}
-
-# User selects beam (1-4)
-beam = st.radio("Select beam", (1, 2, 3, 4), horizontal=True,  key="beam_selection")
-beam_index = beam - 1
-
-# Display the selected variable and beam
-selected_data = data_dict[variable][beam_index, :, :]
-fillplot_plotly(selected_data, title=f"{variable}")
-
-
-st.subheader("Mask Selected Regions")
-with st.form(key="manual_cutbin_form"):
-    st.write("Select the specific range of cells and ensembles to delete")
-
-    # Input for selecting minimum and maximum cells
-    min_cell = st.number_input("Min Cell", 0, int(flobj.field()["Cells"]), 0)
-    max_cell = st.number_input("Max Cell", 0, int(flobj.field()["Cells"]), 10)
-
-    # Input for selecting minimum and maximum ensembles
-    min_ensemble = st.number_input("Min Ensemble", 0, int(flobj.ensembles), 0)
-    max_ensemble = st.number_input("Max Ensemble", 0, int(flobj.ensembles), int(flobj.ensembles))
-
-    # Submit button to apply the mask
-    cut_bins_mask_manual = st.form_submit_button(label="Apply Manual Cut Bins")
-
-    if cut_bins_mask_manual:
-        mask = manual_cut_bins(mask, min_cell, max_cell, min_ensemble, max_ensemble)
-        st.session_state.maskp = mask
-        fillplot_plotly(
-            echo[beam, :, :],
-            title="Echo Intensity (Masked Manually)",
-            maskdata=mask,
-        )
-        fillplot_plotly(mask, colorscale="greys", title="Mask Data")
-
-# Adding the new feature: Delete Single Cell or Ensemble
-st.subheader("Delete Specific Cell or Ensemble")
-
-# Step 1: User chooses between deleting a cell or an ensemble
-delete_option = st.radio("Select option to delete", ("Cell", "Ensemble"), horizontal=True)
-
-# Step 2: Display options based on user's choice
-if delete_option == "Cell":
-    # Option to delete a specific cell across all ensembles
-    with st.form(key="delete_cell_form"):
-        st.write("Select a specific cell to delete across all ensembles")
-        
-        # Input for selecting a single cell
-        cell = st.number_input("Cell", 0, int(flobj.field()["Cells"]), 0, key="single_cell")
-        
-        # Submit button to apply the mask for cell deletion
-        delete_cell = st.form_submit_button(label="Delete Cell")
-
-        if delete_cell:
-            mask[cell, :] = 1  # Mask the entire row for the selected cell
-            st.session_state.maskp = mask
-            fillplot_plotly(
-                echo[beam, :, :],
-                title=f"Echo Intensity (Cell {cell} Deleted Across Ensembles)",
-                maskdata=mask,
-            )
-            fillplot_plotly(mask, colorscale="greys", title="Mask Data")
-
-elif delete_option == "Ensemble":
-    # Option to delete a specific ensemble across all cells
-    with st.form(key="delete_ensemble_form"):
-        st.write("Select a specific ensemble to delete across all cells")
-        
-        # Input for selecting a specific ensemble
-        ensemble = st.number_input("Ensemble", 0, int(flobj.ensembles), 0, key="single_ensemble")
-        
-        # Submit button to apply the mask for ensemble deletion
-        delete_ensemble = st.form_submit_button(label="Delete Ensemble")
-
-        if delete_ensemble:
-            mask[:, ensemble-1] = 1  # Mask the entire column for the selected ensemble
-            st.session_state.maskp = mask
-            fillplot_plotly(
-                echo[beam, :, :],
-                title=f"Echo Intensity (Ensemble {ensemble} Deleted Across Cells)",
-                maskdata=mask,
-            )
-            fillplot_plotly(mask, colorscale="greys", title="Mask Data")
-
-           
-# Layout with two columns
-col1, col2 = st.columns([2, 1])
-
-with col1:
-            
-    # Button to save mask data after manual cut bins, with unique key
-    update_mask_cutbin = st.button("Update mask file after cutbin Manual", key="update_cutbin_button")
-    if update_mask_cutbin:
-        st.session_state.maskp = mask
-        st.write(":green[mask file updated]")
-        st.session_state.update_mask_cutbin = True
-        st.session_state.isCutBins = True
-
-    if not st.session_state.update_mask_cutbin:
-        st.write(":red[mask file not updated]")
-
-with col2:
-    # Button to reset the mask data, with unique key
-    reset_mask_button = st.button("Reset mask data", key="reset_mask_button")
-    if reset_mask_button:
-        st.session_state.maskp = np.copy(st.session_state.orig_mask)
-        st.write(":green[Mask data is reset to default]")
-        st.session_state.isQCMask = False
-        st.session_state.isProfileMask = False
-        st.session_state.isGrid = False
-        st.session_state.isGridSave = False
-        st.session_state.isVelocityMask = False
-
-############ REGRID ###########################################
-st.header("Regrid Depth Cells", divider="blue")
-
-st.write(
-    """
-When the ADCP buoy has vertical oscillations (greater than depth cell size), 
-the depth bins has to be regridded based on the pressure sensor data. The data
-can be regrided either till the surface or till the last bin. 
-If the `Cell` option is selected, ensure that the end data are trimmed.
-Manual option permits choosing the end cell depth.
-"""
-)
-
-if st.session_state.beam_direction.lower() == "up":
-    end_bin_option = st.radio(
-        "Select the depth of last bin for regridding", ("Cell", "Surface", "Manual"), horizontal=True
-    )
-else:
-    end_bin_option = st.radio(
-        "Select the depth of last bin for regridding", ("Cell", "Manual"), horizontal=True
-    )
-
-st.session_state.end_bin_option = end_bin_option 
-st.write(f"You have selected: `{end_bin_option}`")
-
-if end_bin_option == "Manual":
-    mean_depth = np.mean(st.session_state.vlead.vleader["Depth of Transducer"]) / 10
-    mean_depth = round(mean_depth, 2)
-
-    st.write(f"The transducer depth is {mean_depth} m. The value should not exceed the transducer depth")
-    if st.session_state.beam_direction.lower() == "up":
-        boundary = st.number_input("Enter the depth (m):", max_value=int(mean_depth), min_value=0)
-    else:
-        boundary = st.number_input("Enter the depth (m):", min_value=int(mean_depth))
-else:
-    boundary = 0
-
-interpolate = st.radio("Choose interpolation method:", ("nearest", "linear", "cubic"))
-
-regrid_button = st.button(label="Regrid Data")
-
-if regrid_button:
-    st.write(st.session_state.endpoints)
-    z, st.session_state.velocity_regrid = regrid3d(
-        flobj, vlobj, velocity, -32768, 
-        trimends=st.session_state.endpoints, 
-        end_bin_option=st.session_state.end_bin_option, 
-        orientation=st.session_state.beam_direction,
-        method=interpolate,
-        boundary_limit=boundary
-    )
-    st.write(":grey[Regrided velocity ...]")
-    z, st.session_state.echo_regrid = regrid3d(
-        flobj, vlobj, echo, -32768, 
-        trimends=st.session_state.endpoints, 
-        end_bin_option=st.session_state.end_bin_option, 
-        orientation=st.session_state.beam_direction,
-        method=interpolate,
-        boundary_limit=boundary
-    )
-    st.write(":grey[Regrided echo intensity ...]")
-    z, st.session_state.correlation_regrid = regrid3d(
-        flobj, vlobj, correlation, -32768,
-        trimends=st.session_state.endpoints, 
-        end_bin_option=st.session_state.end_bin_option, 
-        orientation=st.session_state.beam_direction,
-        method=interpolate,
-        boundary_limit=boundary
-    )
-    st.write(":grey[Regrided correlation...]")
-    z, st.session_state.pgood_regrid = regrid3d(
-        flobj, vlobj, pgood, -32768,
-        trimends=st.session_state.endpoints, 
-        end_bin_option=st.session_state.end_bin_option, 
-        orientation=st.session_state.beam_direction,
-        method=interpolate,
-        boundary_limit=boundary
-    )
-    st.write(":grey[Regrided percent good...]")
-    z, st.session_state.mask_regrid = regrid2d(
-        flobj, vlobj, mask, 1,
-        trimends=st.session_state.endpoints, 
-        end_bin_option=st.session_state.end_bin_option, 
-        orientation=st.session_state.beam_direction,
-        method="nearest",
-        boundary_limit=boundary
-    )
-
-    st.session_state.depth = z
-
-    st.write(":grey[Regrided mask...]")
-    st.write(":green[All data regrided!]")
-
-    st.write("No. of grid depth bins before regridding: ", np.shape(velocity)[1])
-    st.write(
-        "No. of grid depth bins after regridding: ",
-        np.shape(st.session_state.velocity_regrid)[1],
-    )
-    fillplot_plotly(
-        st.session_state.velocity_regrid[0, :, :], title="Regridded Velocity File"
-    )
-    fillplot_plotly(velocity[0, :, :], title="Original File")
-    fillplot_plotly(
-        st.session_state.mask_regrid, colorscale="greys", title="Regridded Mask File"
-    )
-
-    st.session_state.isGrid = True
-    st.session_state.isGridSave = False
-
-
-########### Save and Reset Mask ##############
-st.header("Save & Reset Mask Data", divider="blue")
-
-col1, col2 = st.columns([1, 1])
-with col1:
-    save_mask_button = st.button(label="Save Mask Data")
-    if save_mask_button:
-        if st.session_state.isGrid:
-            st.session_state.profile_mask = st.session_state.mask_regrid
-            st.session_state.isGridSave = True
-        else:
-            st.session_state.profile_mask = st.session_state.maskp
-        st.session_state.isProfileMask = True
-        st.session_state.isVelocityMask = False
-        st.write(":green[Mask data saved]")
-    else:
-        st.write(":red[Mask data not saved]")
-with col2:
-    reset_mask_button = st.button("Reset mask data")
-    if reset_mask_button:
-        st.session_state.maskp = np.copy(st.session_state.orig_mask)
-        st.write(":green[Mask data is reset to default]")
-        st.session_state.isQCMask = False
-        st.session_state.isProfileMask = False
-        st.session_state.isGrid = False
-        st.session_state.isGridSave = False
-        st.session_state.isVelocityMask = False