pyadps 0.1.1__py3-none-any.whl → 0.2.1b0__py3-none-any.whl

pyadps/Home_Page.py

@@ -8,22 +8,16 @@ def main():
         layout="wide",
         initial_sidebar_state="auto",
         menu_items={
-            "Get Help": "https://github.com/p-amol/pyadps",
-            "Report a bug": "https://github.com/p-amol/pyadps/issues",
+            "Get Help": "http://github.com/p-amol/adps",
+            "Report a bug": "http://github.com/adps/issues",
             "About": "# Python ADCP Data Processing Software (PyADPS)",
         },
     )
 
     """
     # **Python ADCP Data Processing Software (pyadps)**
-  
-    `pyadps` is a Python package for processing moored Acoustic Doppler Current Profiler (ADCP) data. It provides various functionalities such as data reading, quality control tests, NetCDF file creation, and visualization.
+    `pyadps` is a software for processing Teledyne RDI Acoustic Doppler Current Profiler (ADCP) PD0 files. Currently the software can process the data from Workhorse ADCPs.
 
-    This software offers both a graphical interface (Streamlit) for those new to Python and direct Python package access for experienced users. Please note that pyadps is primarily designed for Teledyne RDI workhorse ADCPs. Other company's ADCP files are not compatible, and while some other RDI models may work, they might require additional considerations.
-
-    * Documentation: https://pyadps.readthedocs.io
-    * Source code: https://github.com/p-amol/pyadps
-    * Bug reports: https://github.com/p-amol/pyadps/issues
     ## Features
 
     * Access RDI ADCP binary files using Python 3
@@ -31,8 +25,8 @@ def main():
     * Process ADCP data 
 
     ## Contribute
-    Issue Tracker: https://github.com/p-amol/pyadps/issues
-    Source Code: https://github.com/p-amol/pyadps
+    Issue Tracker: http://github.com/adps/issues
+    Source Code: http://github.com/p-amol/adps
 
     ## Support
     If you are having issues, please let us know.

pyadps/pages/01_Read_File.py

@@ -1,15 +1,12 @@
 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
@@ -113,7 +110,7 @@ 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
@@ -124,14 +121,6 @@ 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
@@ -145,9 +134,6 @@ 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 ##############
@@ -182,157 +168,10 @@ 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.date3 = pd.to_datetime(date_df)
-st.session_state.ensemble_axis = np.arange(0, st.session_state.head.ensembles, 1)
-st.session_state.axis_option = "time"
-
-
-# ---------- Initialize all options -------------
-# ------------------------
-# Page: Download Raw File
-# ------------------------
-# Widgets
-st.session_state.add_attributes_DRW = "No"
-st.session_state.axis_option_DRW = "time"
-st.session_state.rawnc_download_DRW = False
-st.session_state.vleadnc_download_DRW = False
-st.session_state.rawcsv_option_DRW = "Velocity"
-st.session_state.rawcsv_beam_DRW = 1
-st.session_state.rawcsv_download_DRW = False
-
-# ------------------
-# Page: Sensor Test
-# ------------------
-st.session_state.isSensorTest = False
-st.session_state.isFirstSensorVisit = True
-
-# -- Tab 1: Depth Correction
-st.session_state.isDepthModified_ST = False
-# Widgets
-# Options: "Fixed Value", "File Upload"
-st.session_state.depthoption_ST = "Fixed Value"
-st.session_state.isFixedDepth_ST = False
-st.session_state.fixeddepth_ST = 0
-st.session_state.isUploadDepth_ST = False
-
-# -- Tab 2: Salinity Correction
-st.session_state.isSalinityModified_ST = False
-# Widgets
-st.session_state.salinityoption_ST = "Fixed Value"
-st.session_state.isFixedSalinity_ST = False
-st.session_state.fixedsalinity_ST = 35
-st.session_state.isUploadSalinity_ST = False
-
-# -- Tab 3: Temperature Correction
-st.session_state.isTemperatureModified_ST = False
-# Widgets
-st.session_state.temperatureoption_ST = "Fixed Value"
-st.session_state.isFixedTemperature_ST = False
-st.session_state.fixedtemperature_ST = 0
-st.session_state.isUploadTemperature_ST = False
-
-# -- Tab 7: Pitch, Roll, Velocity Correction
-st.session_state.isRollCheck_ST = False
-st.session_state.isPitchCheck_ST = False
-st.session_state.isVelocityModifiedSound_ST = False
-# Widgets
-st.session_state.roll_cutoff_ST = 359
-st.session_state.pitch_cutoff_ST = 359
-
-# ------------------
-# Page: QC Test
-# ------------------
-# Global Test
-st.session_state.isQCTest = False
-st.session_state.isFirstQCVisit = True
-
-# Tab 2: Apply QC
-st.session_state.isQCCheck_QCT = False
-# Widgets
-st.session_state.ct_QCT = 64
-st.session_state.et_QCT = 0
-st.session_state.evt_QCT = 2000
-st.session_state.ft_QCT = 50
-st.session_state.is3beam_QCT = True
-st.session_state.pgt_QCT = 0
-
-# Data Modifications
-st.session_state.isBeamModified_QCT = False
-# Widgets
-st.session_state.beam_direction_QCT = st.session_state.beam_direction
-
-# ------------------
-# Page: Profile Test
-# ------------------
-st.session_state.isProfileTest = False
-st.session_state.isFirstProfileVisit = True
-
-# Tab1: Trim Ends
-st.session_state.isTrimEndsCheck_PT = False
-# Widgets
-st.session_state.start_ens_PT = 0
-st.session_state.end_ens_PT = st.session_state.head.ensembles
-
-# Tab2: Cutbins - Sidelobe
-st.session_state.isCutBinSideLobeCheck_PT = False
-st.session_state.extra_cells_PT = 0
-st.session_state.water_depth_PT = 0
-
-# Tab3: Cutbins - Manual
-st.session_state.isCutBinManualCheck_PT = False
-
-# Tab4: Regrid
-st.session_state.isRegridCheck_PT = False
-st.session_state.end_cell_option_PT = "Cell"
-st.session_state.interpolate_PT = "nearest"
-st.session_state.manualdepth_PT = 0
-
-# ------------------
-# Page: Velocity Test
-# ------------------
-# Global Test
-st.session_state.isVelocityTest = False
-# Check if visiting the page first time
-st.session_state.isFirstVelocityVisit = True
-# Local Tests:
-# Tab1: Magnetic Declination
-st.session_state.isMagnetCheck_VT = False
-# OPTIONS: pygeomag, API, Manual
-st.session_state.magnet_method_VT = "pygeomag"
-st.session_state.magnet_lat_VT = 0
-st.session_state.magnet_lon_VT = 0
-st.session_state.magnet_year_VT = 2025
-st.session_state.magnet_depth_VT = 0
-st.session_state.magnet_user_input_VT = 0
-
-# Tab2: Velocity Cutoff
-st.session_state.isCutoffCheck_VT = False
-st.session_state.maxuvel_VT = 250
-st.session_state.maxvvel_VT = 250
-st.session_state.maxwvel_VT = 15
-
-# Tab3: Despike
-st.session_state.isDespikeCheck_VT = False
-st.session_state.despike_kernel_VT = 5
-st.session_state.despike_cutoff_VT = 3
-
-# Tab4: Flatline
-st.session_state.isFlatlineCheck_VT = False
-st.session_state.flatline_kernel_VT = 5
-st.session_state.flatline_cutoff_VT = 3
-
-# ------------------
-# Page: Write File
-# ------------------
-st.session_state.isWriteFile = True
-st.session_state.isAttributes = False
-st.session_state.mask_data_WF = "Yes"
-# FileTypes: NetCDF, CSV
-st.session_state.file_type_WF = "NetCDF"
-st.session_state.isProcessedNetcdfDownload_WF = True
-st.session_state.isProcessedCSVDownload_WF = False
-
-# MASK DATA
+
+
+
+######### 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
@@ -341,17 +180,16 @@ st.session_state.isProcessedCSVDownload_WF = False
 # WARNING: Never Change `st.session_state.orig_mask` in the code!
 #
 if "orig_mask" not in st.session_state:
-    ds = st.session_state.ds
-    st.session_state.orig_mask = default_mask(ds)
+    st.session_state.orig_mask = default_mask(
+        st.session_state.flead, st.session_state.velocity
+    )
 
-# ----------------------
-# 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
+# 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
 
 ########## FILE HEADER ###############
 st.header("File Header", divider="blue")
@@ -428,18 +266,10 @@ 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": new_dict.keys(),
-            "Values": new_dict.values(),
+            "Fields": st.session_state.flead.field().keys(),
+            "Values": st.session_state.flead.field().values(),
         }
     )
     st.dataframe(df, use_container_width=True)
@@ -457,3 +287,4 @@ with right:
     df = df.astype("str")
     st.write((df.style.map(color_bool2)))
     # st.dataframe(df)
+

pyadps/pages/02_View_Raw_Data.py

@@ -84,81 +84,45 @@ 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))
+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")
+basic_options = [
+    "Pressure",
+    "Temperature",
+    "Salinity",
+    "Depth of Transducer",
+    "Heading",
+    "Pitch",
+    "Roll",
+]
 
 
-    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)
+st.header("Velocity, Echo Intensity, Correlation & Percent Good", divider="blue")
 
 
-    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))
+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))
+