pyadps 0.2.1b0__tar.gz → 0.3.0b0__tar.gz

{pyadps-0.2.1b0 → pyadps-0.3.0b0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pyadps
-Version: 0.2.1b0
+Version: 0.3.0b0
 Summary: A Python package for ADCP data processing
 Home-page: https://example.com
 License: MIT
@@ -22,9 +22,9 @@ Requires-Dist: numpy (>=1.26.4)
 Requires-Dist: pandas (>=2.2.2)
 Requires-Dist: plotly (>=5.22.0)
 Requires-Dist: plotly-resampler (>=0.10.0)
+Requires-Dist: pygeomag (>=1.1.0,<2.0.0)
 Requires-Dist: scipy (>=1.14.0)
 Requires-Dist: streamlit (>=1.36.0)
-Requires-Dist: wmm2020 (>=1.1.1)
 Project-URL: Documentation, https://example.com/docs
 Project-URL: Repository, https://github.com/p-amol/pyadps
 Description-Content-Type: text/markdown

{pyadps-0.2.1b0 → pyadps-0.3.0b0}/pyproject.toml

@@ -1,19 +1,19 @@
 [tool.poetry]
 name = "pyadps"
-version = "0.2.1-beta"
+version = "0.3.0-beta"
 description = "A Python package for ADCP data processing"
 authors = ["P. Amol <prakashamol@gmail.com>"]
 readme = "README.md"
 license = "MIT"
-homepage = "https://example.com"  # You can add your homepage URL or GitHub URL here
-repository = "https://github.com/p-amol/pyadps"  # Replace with your repository link
-documentation = "https://example.com/docs"  # Optional documentation link
+homepage = "https://example.com" # You can add your homepage URL or GitHub URL here
+repository = "https://github.com/p-amol/pyadps" # Replace with your repository link
+documentation = "https://example.com/docs" # Optional documentation link
 keywords = ["adcp", "data-processing", "oceanography"]
 include = ["utils/metadata/*.json"]
 classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: MIT License",
-    "Operating System :: OS Independent"
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
 ]
 
 
@@ -23,13 +23,14 @@ streamlit = ">=1.36.0"
 numpy = ">=1.26.4"
 matplotlib = ">=3.8.4"
 scipy = ">=1.14.0"
-wmm2020 = ">=1.1.1"
 cmake = ">=3.30.2"
 pandas = ">=2.2.2"
 netCDF4 = ">=1.7.1"
 plotly = ">=5.22.0"
 plotly-resampler = ">=0.10.0"
 meson = ">=1.4.1"
+pygeomag = "^1.1.0"
+
 
 [tool.poetry.extras]
 tests = ["pytest"]
@@ -41,5 +42,3 @@ run-auto = "pyadps.utils.autoprocess:main"
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
-
-

{pyadps-0.2.1b0 → pyadps-0.3.0b0}/src/pyadps/pages/01_Read_File.py

@@ -1,12 +1,15 @@
 import os
 import tempfile
 
+import numpy as np
 import pandas as pd
 import streamlit as st
 import utils.readrdi as rd
-import utils.writenc as wr
-from streamlit.runtime.state import session_state
 from utils.signal_quality import default_mask
+from utils.readrdi import ReadFile
+
+# To make the page wider if the user presses the reload button.
+st.set_page_config(layout="wide")
 
 """
 Streamlit page to load ADCP binary file and display File Header
@@ -110,7 +113,7 @@ if uploaded_file is not None:
     correlation = ds.correlation.data
     echo = ds.echo.data
     pgood = ds.percentgood.data
-    beamdir = ds.fixedleader.system_configuration()['Beam Direction']
+    beamdir = ds.fixedleader.system_configuration()["Beam Direction"]
 
     st.session_state.fname = uploaded_file.name
     st.session_state.head = ds.fileheader
@@ -121,6 +124,14 @@ if uploaded_file is not None:
     st.session_state.correlation = ds.correlation.data
     st.session_state.pgood = ds.percentgood.data
     st.session_state.beam_direction = beamdir
+    st.session_state.sound_speed = ds.variableleader.speed_of_sound.data
+    st.session_state.depth = ds.variableleader.depth_of_transducer.data
+    st.session_state.temperature = (
+        ds.variableleader.temperature.data * ds.variableleader.temperature.scale
+    )
+    st.session_state.salinity = (
+        ds.variableleader.salinity.data * ds.variableleader.salinity.scale
+    )
 
     # st.session_state.flead = flead
     # st.session_state.vlead = vlead
@@ -134,6 +145,9 @@ if uploaded_file is not None:
 elif "flead" in st.session_state:
     st.write("You selected `%s`" % st.session_state.fname)
 else:
+    # reset the cache and resources if the user press reload button.
+    st.cache_data.clear()
+    st.cache_resource.clear()
     st.stop()
 
 ########## TIME AXIS ##############
@@ -168,10 +182,63 @@ date_df = pd.DataFrame(
 st.session_state.date = pd.to_datetime(date_df)
 st.session_state.date1 = pd.to_datetime(date_df)
 st.session_state.date2 = pd.to_datetime(date_df)
+st.session_state.ensemble_axis = np.arange(0, st.session_state.head.ensembles, 1)
 
 
-
-######### MASK DATA ##############
+# ---------- Initialize all options -------------
+# ------------------
+# Global Tests
+# ------------------
+# Checks if the following tests are carried out
+st.session_state.isSensorTest = False
+st.session_state.isQCTest = False
+st.session_state.isProfileTest = False
+st.session_state.isGrid = False
+st.session_state.isGridSave = False
+st.session_state.isVelocityTest = False
+
+# Check if visiting the page first time
+st.session_state.isFirstSensorVisit = True
+st.session_state.isFirstQCVisit = True
+st.session_state.isFirstProfileVisit = True
+st.session_state.isFirstVelocityVisit = True
+# ------------------
+# Local Tests:
+# ------------------
+st.session_state.isRollCheck = False
+st.session_state.isPitchCheck = False
+
+st.session_state.isQCCheck = False
+st.session_state.isBeamModified = False
+
+st.session_state.isTrimEndsCheck = False
+st.session_state.isCutBinSideLobeCheck = False
+st.session_state.isCutBinManualCheck = False
+st.session_state.isRegridCheck = False
+
+st.session_state.isMagnetCheck = False
+st.session_state.isDespikeCheck = False
+st.session_state.isFlatlineCheck = False
+st.session_state.isCutoffCheck = False
+
+
+# ------------------
+# Data Modifications
+# ------------------
+# SENSOR TEST
+# Velocity Modified Based on Sound
+st.session_state.isVelocityModifiedSound = False
+# Transducer depth modified based on Pressure sensor
+st.session_state.isDepthModified = False
+st.session_state.isTemperatureModified = False
+st.session_state.isSalinityModified = False
+# QC TEST
+st.session_state.isBeamModified = False
+# VELOCITY TEST
+# Velocity Modified based on magnetic declination
+st.session_state.isVelocityModifiedMagnet = False
+
+# MASK DATA
 # The velocity data has missing values due to the cutoff
 # criteria used before deployment. The `default_mask` uses
 # the velocity to create a mask. This mask  file is stored
@@ -180,16 +247,17 @@ st.session_state.date2 = pd.to_datetime(date_df)
 # WARNING: Never Change `st.session_state.orig_mask` in the code!
 #
 if "orig_mask" not in st.session_state:
-    st.session_state.orig_mask = default_mask(
-        st.session_state.flead, st.session_state.velocity
-    )
+    ds = st.session_state.ds
+    st.session_state.orig_mask = default_mask(ds)
 
-# Checks if the following quality checks are carried out
-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
+# ----------------------
+# Page returning options
+# ----------------------
+# This checks if we have returned back to the page after saving the data
+st.session_state.isSensorPageReturn = False
+st.session_state.isQCPageReturn = False
+st.session_state.isProfilePageReturn = False
+st.session_state.isVelocityPageReturn = False
 
 ########## FILE HEADER ###############
 st.header("File Header", divider="blue")
@@ -266,10 +334,18 @@ if flead_check_button:
 
 flead_button = st.button("Fixed Leader")
 if flead_button:
+    # Pandas array should have all elements with same data type.
+    # Except Sl. no., which is np.uint64, rest are np.int64.
+    # Convert all datatype to uint64
+    fl_dict = st.session_state.flead.field().items()
+    new_dict = {}
+    for key, value in fl_dict:
+        new_dict[key] = value.astype(np.uint64)
+
     df = pd.DataFrame(
         {
-            "Fields": st.session_state.flead.field().keys(),
-            "Values": st.session_state.flead.field().values(),
+            "Fields": new_dict.keys(),
+            "Values": new_dict.values(),
         }
     )
     st.dataframe(df, use_container_width=True)
@@ -287,4 +363,3 @@ with right:
     df = df.astype("str")
     st.write((df.style.map(color_bool2)))
     # st.dataframe(df)
-

pyadps-0.3.0b0/src/pyadps/pages/02_View_Raw_Data.py

@@ -0,0 +1,164 @@
+import matplotlib.pyplot as plt
+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_resampler import FigureResampler
+
+if "flead" not in st.session_state:
+    st.write(":red[Please Select Data!]")
+    st.stop()
+
+# Load data
+fdata = st.session_state.flead.fleader
+vdata = st.session_state.vlead.vleader
+velocity = st.session_state.velocity
+echo = st.session_state.echo
+correlation = st.session_state.correlation
+pgood = st.session_state.pgood
+
+x = np.arange(0, st.session_state.head.ensembles, 1)
+y = np.arange(0, fdata["Cells"][0], 1)
+
+X, Y = np.meshgrid(x, y)
+
+
+@st.cache_data
+def fillplot_matplotlib(data):
+    fig, ax = plt.subplots()
+    cs = ax.contourf(X, Y, data)
+    fig.colorbar(cs)
+    st.pyplot(fig)
+
+
+@st.cache_data
+def fillplot_plotly(data, colorscale="balance", title="Data", xaxis="time"):
+    if xaxis == "time":
+        xdata = st.session_state.date
+    elif xaxis == "ensemble":
+        xdata = x
+    else:
+        xdata = x
+    fig = FigureResampler(go.Figure())
+    data1 = np.where(data == -32768, np.nan, data)
+    fig.add_trace(
+        go.Heatmap(
+            z=data1[:, 0:-1],
+            x=xdata,
+            y=y,
+            colorscale=colorscale,
+            hoverongaps=False,
+        )
+    )
+    fig.update_layout(
+        xaxis=dict(showline=True, mirror=True),
+        yaxis=dict(showline=True, mirror=True),
+        title_text=title,
+    )
+    st.plotly_chart(fig)
+
+
+@st.cache_data
+def lineplot(data, title, xaxis="time"):
+    if xaxis == "time":
+        df = pd.DataFrame({"date": st.session_state.date, title: data})
+        fig = px.line(df, x="date", y=title)
+    else:
+        df = pd.DataFrame({"ensemble": x, title: data})
+        fig = px.line(df, x="ensemble", y=title)
+
+    st.plotly_chart(fig)
+
+
+# Introduction
+st.header("View Raw Data", divider="orange")
+st.write(
+    """
+Displays all variables available in the raw file. No processing has been carried out. 
+Data might be missing because of the quality-check criteria used before deployment.\n 
+Either `time` or `ensemble` axis can be chosen as the abscissa (x-axis).
+The ordinate (y-axis) for the heatmap is `bins` as the depth correction is not applied. 
+"""
+)
+xbutton = st.radio("Select an x-axis to plot", ["time", "ensemble"], horizontal=True)
+
+
+tab1, tab2, tab3, tab4 = st.tabs(["Primary Data", "Variable Leader", "Fixed Leader", "Advanced"])
+
+with tab3:
+# Fixed Leader Plots
+    st.header("Fixed Leader", divider="blue")
+    fbutton = st.radio("Select a dynamic variable to plot:", fdata.keys(), horizontal=True)
+    lineplot(fdata[fbutton], fbutton, xaxis=str(xbutton))
+
+with tab2:
+# Variable Leader Plots
+    st.header("Variable Leader", divider="blue")
+    vbutton = st.radio("Select a dynamic variable to plot:", vdata.keys(), horizontal=True)
+    lineplot(vdata[vbutton], vbutton, xaxis=str(xbutton))
+
+with tab1:
+    st.header("Velocity, Echo Intensity, Correlation & Percent Good", divider="blue")
+
+
+    def call_plot(varname, beam, xaxis="time"):
+        if varname == "Velocity":
+            fillplot_plotly(velocity[beam - 1, :, :], title=varname, xaxis=xaxis)
+        elif varname == "Echo":
+            fillplot_plotly(echo[beam - 1, :, :], title=varname, xaxis=xaxis)
+        elif varname == "Correlation":
+            fillplot_plotly(correlation[beam - 1, :, :], title=varname, xaxis=xaxis)
+        elif varname == "Percent Good":
+            fillplot_plotly(pgood[beam - 1, :, :], title=varname, xaxis=xaxis)
+
+
+    var_option = st.selectbox(
+        "Select a data type", ("Velocity", "Echo", "Correlation", "Percent Good")
+    )
+    beam = st.radio("Select beam", (1, 2, 3, 4), horizontal=True)
+    call_plot(var_option, beam, xaxis=str(xbutton))
+
+
+with tab4:
+    st.header("Advanced Data", divider="blue")
+    adv_option = st.selectbox(
+        "Select a data type", ("Bit Result", 
+                            "ADC Channel", 
+                            "Error Status Word 1", 
+                            "Error Status Word 2",
+                            "Error Status Word 3",
+                            "Error Status Word 4"))
+    if adv_option == "Bit Result": 
+        bitdata = st.session_state.vlead.bitresult()
+        st.subheader("BIT Result", divider="orange")
+        st.write("""
+        This field contains the results of Workhorse ADCPs builtin test functions.
+        A zero indicates a successful BIT result.
+        """)
+        bitbutton = st.radio("Select a dynamic variable to plot:", bitdata.keys(), horizontal=True)
+        lineplot(bitdata[bitbutton], bitbutton, xaxis=str(xbutton))
+
+    elif adv_option == "ADC Channel":
+        adcdata = st.session_state.vlead.adc_channel()
+        st.subheader("ADC Channel", divider="orange")
+        adcbutton = st.radio("Select a dynamic variable to plot:", adcdata.keys(), horizontal=True)
+        lineplot(adcdata[adcbutton], adcbutton, xaxis=str(xbutton))
+    elif adv_option == "Error Status Word 1":
+        errordata1 = st.session_state.vlead.error_status_word(esw=1)
+        st.subheader("Error Status Word", divider="orange")
+        errorbutton = st.radio("Select a dynamic variable to plot:", errordata1.keys(), horizontal=True)
+        lineplot(errordata1[errorbutton], errorbutton, xaxis=str(xbutton))
+    elif adv_option == "Error Status Word 2":
+        errordata2 = st.session_state.vlead.error_status_word(esw=2)
+        errorbutton = st.radio("Select a dynamic variable to plot:", errordata2.keys(), horizontal=True)
+        lineplot(errordata2[errorbutton], errorbutton, xaxis=str(xbutton))
+    elif adv_option == "Error Status Word 3":
+        errordata3 = st.session_state.vlead.error_status_word(esw=3)
+        errorbutton = st.radio("Select a dynamic variable to plot:", errordata3.keys(), horizontal=True)
+        lineplot(errordata3[errorbutton], errorbutton, xaxis=str(xbutton))
+    elif adv_option == "Error Status Word 4":
+        errordata4 = st.session_state.vlead.error_status_word(esw=4)
+        errorbutton = st.radio("Select a dynamic variable to plot:", errordata4.keys(), horizontal=True)
+        lineplot(errordata4[errorbutton], errorbutton, xaxis=str(xbutton))
+