pyadps 0.2.1b0__py3-none-any.whl → 0.3.0b0__py3-none-any.whl

pyadps/pages/04_QC_Test.py

@@ -1,334 +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 streamlit.runtime.state import session_state
-from utils.signal_quality import ev_check, false_target, pg_check, qc_check
-
-if "flead" not in st.session_state:
-    st.write(":red[Please Select Data!]")
-    st.stop()
-
-# `mask` holds the temporary changes in the page
-# `qcmask` holds the final changes in the page
-if "mask" not in st.session_state:
-    st.session_state.mask = np.copy(st.session_state.orig_mask)
-
-if not st.session_state.isQCMask:
-    st.write(":grey[Creating a new mask file ...]")
-    st.session_state.qc_mask = np.copy(st.session_state.orig_mask)
-    st.session_state.isSubmit = False
-else:
-    st.write(":grey[Working on a saved mask file ...]")
-    st.write(":orange[WARNING! QC test already completed. Reset to change settings.]")
-    reset_button1 = st.button("Reset Mask Data")
-    if reset_button1:
-        st.session_state.mask = np.copy(st.session_state.orig_mask)
-        st.session_state.qc_mask = np.copy(st.session_state.orig_mask)
-        st.write(":green[Mask data is reset to default]")
-
-if "isThresh" not in st.session_state:
-    st.session_state.isThresh = False
-
-# 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
-ensembles = st.session_state.head.ensembles
-cells = flobj.field()["Cells"]
-fdata = flobj.fleader
-vdata = vlobj.vleader
-x = np.arange(0, ensembles, 1)
-y = np.arange(0, cells, 1)
-
-
-@st.cache_data
-def fillplot_plotly(data, colorscale="balance"):
-    fig = FigureResampler(go.Figure())
-    data1 = np.where(data == -32768, np.nan, data)
-    fig.add_trace(
-        go.Heatmap(z=data1[:, 0:-1], x=x, y=y, colorscale=colorscale, hoverongaps=False)
-    )
-    st.plotly_chart(fig)
-
-
-@st.cache_data
-def plot_noise(dep=0, rec=-1):
-    n = dep
-    m = rec
-    colorleft = [
-        "rgb(240, 255, 255)",
-        "rgb(115, 147, 179)",
-        "rgb(100, 149, 237)",
-        "rgb(15, 82, 186)",
-    ]
-    colorright = [
-        "rgb(250, 200, 152)",
-        "rgb(255, 165, 0)",
-        "rgb(255, 95, 31)",
-        "rgb(139, 64, 0)",
-    ]
-    fig = make_subplots(
-        rows=1,
-        cols=2,
-        subplot_titles=[
-            f"Deployment Ensemble ({x[n]+1})",
-            f"Recovery Ensemble ({x[m]+1})",
-        ],
-    )
-    for i in range(4):
-        fig.add_trace(
-            go.Scatter(
-                x=echo[i, :, n],
-                y=y,
-                name=f"Beam (D) {i+1}",
-                line=dict(color=colorleft[i]),
-            ),
-            row=1,
-            col=1,
-        )
-    for i in range(4):
-        fig.add_trace(
-            go.Scatter(
-                x=echo[i, :, m],
-                y=y,
-                name=f"Beam (R)  {i+1}",
-                line=dict(color=colorright[i]),
-            ),
-            row=1,
-            col=2,
-        )
-
-    fig.update_layout(height=600, width=800, title_text="Echo Intensity")
-    fig.update_xaxes(title="Echo (count)")
-    fig.update_yaxes(title="Cells")
-    st.plotly_chart(fig)
-    
-#########  NOISE FLOOR IDENTIFICATION ##############
-dn = rn = 1
-st.header("Noise Floor Identification", divider="blue")
-st.write(
-    """
-    If the ADCP has collected data from the air either 
-    before deployment or after recovery, this data can 
-    be used to estimate the echo intensity threshold. 
-    The plots below show the echo intensity from the first 
-    and last ensembles. The noise level is typically around 
-    30-40 counts throughout the entire profile.
-"""
-)
-dn = st.number_input("Deployment Ensemble", x[0] + 1, x[-1] + 1, x[0] + 1)
-# r = st.number_input("Recovery Ensemble", -1 * (x[-1] + 1), -1 * (x[0] + 1), -1)
-rn = st.number_input("Recovery Ensemble", x[0] + 1, x[-1] + 1, x[-1] + 1)
-dn = dn - 1
-rn = rn - 1
-
-plot_noise(dep=dn, rec=rn)
-
-
-################## QC Test ###################
-
-st.header("Quality Control Tests", divider="blue")
-st.write("")
-
-left, right = st.columns([1, 1])
-with left:
-    st.write(""" Teledyne RDI recommends these quality control tests, 
-                 some of which can be configured before deployment. 
-                 The pre-deployment values configured for the ADCP are listed 
-                 in the table below. The noise-floor identification graph above 
-                 can assist in determining the echo intensity threshold. 
-                 For more information about these tests, 
-                 refer to *Acoustic Doppler Current Profiler Principles of 
-                 Operation: A Practical Primer* by Teledyne RDI.""")
-    fdata = st.session_state.flead.field()
-    st.divider()
-    st.write(":blue-background[Additional Information:]")
-    st.write(f"Number of Pings per Ensemble: `{fdata["Pings"]}`")
-    st.write(f"Number of Beams: `{fdata["Beams"]}`")
-    st.divider()
-    st.write(":red-background[Thresholds used during deployment:]")
-    thresh = pd.DataFrame(
-        [
-            ["Correlation", fdata["Correlation Thresh"]],
-            ["Error Velocity", fdata["Error Velocity Thresh"]],
-            ["Echo Intensity", 0],
-            ["False Target", fdata["False Target Thresh"]],
-            ["Percentage Good", fdata["Percent Good Min"]],
-        ],
-        columns=["Threshold", "Values"],
-    )
-
-    st.write(thresh)
-
-with right:
-    with st.form(key="my_form"):
-        st.write("Would you like to apply new threshold?")
-
-        ct = st.number_input(
-            "Select Correlation Threshold",
-            0,
-            255,
-            fdata["Correlation Thresh"],
-        )
-
-        evt = st.number_input(
-            "Select Error Velocity Threshold",
-            0,
-            9999,
-            fdata["Error Velocity Thresh"],
-        )
-
-        et = st.number_input(
-            "Select Echo Intensity Threshold",
-            0,
-            255,
-            0,
-        )
-
-        ft = st.number_input(
-            "Select False Target Threshold",
-            0,
-            255,
-            fdata["False Target Thresh"],
-        )
-
-        option = st.selectbox(
-            "Would you like to use a three-beam solution?", (True, False)
-        )
-
-        pgt = st.number_input(
-            "Select Percent Good Threshold",
-            0,
-            100,
-            fdata["Percent Good Min"],
-        )
-        submit_button = st.form_submit_button(label="Submit")
-
-
-mask = st.session_state.mask
-with left:
-    if submit_button:
-        st.session_state.newthresh = pd.DataFrame(
-            [
-                ["Correlation", str(ct)],
-                ["Error Velocity", str(evt)],
-                ["Echo Intensity", str(et)],
-                ["False Target", str(ft)],
-                ["Three Beam", str(option)],
-                ["Percentage Good", str(pgt)],
-            ],
-            columns=["Threshold", "Values"],
-        )
-        st.session_state.isThresh = True
-        # st.write(st.session_state.newthresh)
-
-        mask = pg_check(pgood, mask, pgt, threebeam=option)
-        mask = qc_check(correlation, mask, ct)
-        mask = qc_check(echo, mask, et)
-        mask = ev_check(velocity[3, :, :], mask, evt)
-        mask = false_target(echo, mask, ft, threebeam=True)
-        st.session_state.mask = mask
-
-    if st.session_state.isThresh:
-        st.write(":green-background[Current Thresholds]")
-        st.write(st.session_state.newthresh)
-
-
-
-st.header("Mask File", divider="blue")
-st.write(
-"""
-Displayed the mask file. 
-Ensure to save any necessary changes or apply additional thresholds if needed.
-"""
-)
-
-
-if st.button("Display mask file"):
-    st.subheader("Default Mask File")
-    st.write(
-    """
-ADCP assigns missing values based on thresholds set before deployment.
-These values cannot be recovered and the default 
-"""
-)
-    fillplot_plotly(st.session_state.orig_mask, colorscale="greys")
-
-
-    st.subheader("Update Mask File")
-    st.write(
-    """
-Update, display and save the updated mask file after applying threshold.
-If thresholds are not saved, default mask file is used. 
-"""
-)
-# values, counts = np.unique(mask, return_counts=True)
-    fillplot_plotly(st.session_state.mask, colorscale="greys")
-
-############## SENSOR HEALTH ######################
-st.header("Sensor Health", divider="blue")
-st.write("The following details can be used to determine whether the additional sensors are functioning properly.")
-# ################## Pressure Sensor Check ###################
-# st.subheader("Pressure Sensor Check", divider="orange")
-#
-# st.subheader("Temperature Sensor Check", divider="orange")
-#
-# st.subheader("Tilt Sensor Check", divider="orange")
-################## Fix Orientation ###################
-st.subheader("Fix Orientation", divider="orange")
-
-
-if st.session_state.beam_direction == 'Up':
-    beamalt = 'Down' 
-else:
-    beamalt = 'Up'
-st.write(f"The current orientation of ADCP is `{st.session_state.beam_direction}`. Use the below option to correct the orientation.")
-
-beamdir_select = st.radio(f'Change orientation to {beamalt}', ['No', 'Yes'])
-if beamdir_select == 'Yes':
-    st.session_state.beam_direction = beamalt
-    st.write(f"The orientation changed to `{st.session_state.beam_direction}`")
-
-
-
-
-################## Save Button #############
-st.header("Save Data", divider="blue")
-col1, col2 = st.columns([1, 1])
-with col1:
-    save_mask_button = st.button(label="Save Mask Data")
-
-    if save_mask_button:
-        # st.session_state.mask = mask
-        st.session_state.qc_mask = np.copy(st.session_state.mask)
-        st.session_state.isQCMask = True
-        st.session_state.isProfileMask = False
-        st.session_state.isGridSave = False
-        st.session_state.isVelocityMask = False
-        st.write(":green[Mask file 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.mask = np.copy(st.session_state.orig_mask)
-        st.session_state.isQCMask = False
-        st.session_state.isGrid = False
-        st.session_state.isProfileMask = False
-        st.session_state.isVelocityMask = False
-        st.write(":green[Mask data is reset to default]")
-
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