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

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 ##############
@@ -166,8 +180,65 @@ date_df = pd.DataFrame(
 )
 
 st.session_state.date = pd.to_datetime(date_df)
-
-######### MASK DATA ##############
+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)
+
+
+# ---------- 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
@@ -176,16 +247,17 @@ st.session_state.date = 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")
@@ -262,10 +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)
@@ -283,4 +363,3 @@ with right:
     df = df.astype("str")
     st.write((df.style.map(color_bool2)))
     # st.dataframe(df)
-

pyadps/pages/02_View_Raw_Data.py

@@ -84,45 +84,81 @@ The ordinate (y-axis) for the heatmap is `bins` as the depth correction is not a
 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))
+    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))
-
-basic_options = [
-    "Pressure",
-    "Temperature",
-    "Salinity",
-    "Depth of Transducer",
-    "Heading",
-    "Pitch",
-    "Roll",
-]
-
+    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))
 
-st.header("Velocity, Echo Intensity, Correlation & Percent Good", divider="blue")
+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)
+    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))
-
+    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))
 

pyadps/pages/03_Download_Raw_File.py

@@ -51,9 +51,9 @@ def file_write(path, axis_option, add_attributes=True):
     st.session_state.rawfilename = tempdirname.name + "/rawfile.nc"
     
     if add_attributes:
-        wr.rawnc(path, st.session_state.rawfilename, st.session_state.date, axis_option, attributes=st.session_state.attributes)
+        wr.rawnc(path, st.session_state.rawfilename, st.session_state.date1, axis_option, attributes=st.session_state.attributes)
     else:
-        wr.rawnc(path, st.session_state.rawfilename, st.session_state.date,axis_option)
+        wr.rawnc(path, st.session_state.rawfilename, st.session_state.date1,axis_option)
 
 @st.cache_data
 def file_write_vlead(path, axis_option, add_attributes=True):
@@ -61,9 +61,9 @@ def file_write_vlead(path, axis_option, add_attributes=True):
     st.session_state.vleadfilename = tempvardirname.name + "/vlead.nc"
     
     if add_attributes:
-        wr.vlead_nc(path, st.session_state.vleadfilename, st.session_state.date, axis_option, attributes=st.session_state.attributes)
+        wr.vlead_nc(path, st.session_state.vleadfilename, st.session_state.date2, axis_option, attributes=st.session_state.attributes)
     else:
-        wr.vlead_nc(path, st.session_state.vleadfilename, st.session_state.date, axis_option)
+        wr.vlead_nc(path, st.session_state.vleadfilename, st.session_state.date2, axis_option)
 
 if "axis_option" not in st.session_state:
     st.session_state.axis_option = "ensemble"  # Default value