pyadps 0.2.0b0__tar.gz → 0.3.0b0__tar.gz

{pyadps-0.2.0b0 → pyadps-0.3.0b0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pyadps
-Version: 0.2.0b0
+Version: 0.3.0b0
 Summary: A Python package for ADCP data processing
 Home-page: https://example.com
 License: MIT
@@ -22,18 +22,30 @@ 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
 
-`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 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.
 
-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.
+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>
 
 ## Table of Contents
 
@@ -43,37 +55,49 @@ This software offers both a graphical interface (`Streamlit`) for those new to P
 
 ## Installation
 
-We recommend installing the package within a virtual environment. At present, the package is compatible exclusively with Python version 3.12.
-You can create a Python environment using tools like `venv` or `conda`. Below are instructions for both methods.
+We recommend installing the package within a virtual environment.
+At present, the package is compatible exclusively with Python version 3.12.
+You can create a Python environment using tools like `venv` or `conda`.
+Below are instructions for both methods.
 
 ### 1. Using `venv` (Built-in Python Tool)
 
 #### Step 1: Install Python version 3.12 (if not already installed)
+
 Ensure you have Python installed. You can download the latest version from [python.org](https://www.python.org/downloads/).
 
-#### Step 2: Create a Virtual Environment 
+#### Step 2: Create a Virtual Environment
+
 - Open your terminal or command prompt.
 - Navigate to your project folder:
+
 ```bash
 cd /path/to/your/project
 ```
-- Run the following command to create a virtual environment (replace adpsenv with your preferred environment name):
+
+- Run the following command to create a virtual environment
+(replace adpsenv with your preferred environment name):
 
 ```bash
 python -m venv adpsenv
 ```
 
 #### Step 3: Activate the Environment
+
 - On Windows:
+
 ```bash
 adpsenv\Scripts\activate
 ```
 
 - On macOS/Linux:
+
 ```bash
 source adpsenv/bin/activate
 ```
-You’ll see the environment name in your terminal prompt indicating the environment is active.
+
+You’ll see the environment name in your terminal prompt
+indicating the environment is active.
 
 #### Step 4: Install Dependencies
 
@@ -84,44 +108,51 @@ pip install pyadps
 ```
 
 #### Step 5: Deactivate the Environment
+
 When you’re done working in the environment, deactivate it by running:
 
 ```bash
 deactivate
 ```
 
-
-
-
-### 2. Using `conda` (Anaconda/Miniconda):
+### 2. Using `conda` (Anaconda/Miniconda)
 
 #### Step 1: Install Conda
+
 First, you need to have Conda installed on your system. You can either install:
 
 - [Anaconda (Full Distribution)](https://www.anaconda.com/products/individual)
 - [Miniconda (Lightweight Version)](https://docs.conda.io/en/latest/miniconda.html)
 
 #### Step 2: Create a Conda Environment with Python 3.12
-Once Conda is installed, open a terminal or command prompt and run the following to create a new environment (replace `adpsenv` with your preferred environment name):
+
+Once Conda is installed, open a terminal or command prompt and run
+the following to create a new environment (replace `adpsenv` with
+your preferred environment name):
 
 ```bash
 conda create --name adpsenv python=3.12
 ```
 
-#### Step 3: Activate the Environment
+#### Step 3: Activate the Conda Environment
+
 ```bash
 conda activate adpsenv
 ```
 
-#### Step 4: Install Dependencies
-You can install packages with pip inside Conda environments. 
+#### Step 4: Install pyadps Dependencies
+
+You can install packages with pip inside Conda environments.
+
 ```bash
 pip install pyadps
 ```
 
-#### Step 5: Deactivate the Environment
-When done, deactivate the environment by running:
-```
+#### Step 5: Deactivate the Conda Environment
+
+When done working in the environment, deactivate the environment by running:
+
+```bash
 conda deactivate
 ```
 
@@ -130,11 +161,11 @@ conda deactivate
 ### Streamlit web interface
 
 Open a terminal or command prompt, activate the environment, and run the command.
+
 ```bash
 run-pyadps
 ```
 
-
 ## License
 
 This project is licensed under the MIT License. See the LICENSE file for details.

{pyadps-0.2.0b0 → pyadps-0.3.0b0}/README.md

@@ -1,8 +1,20 @@
 # 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.
-
-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.
+`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.
+
+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>
 
 ## Table of Contents
 
@@ -12,37 +24,49 @@ This software offers both a graphical interface (`Streamlit`) for those new to P
 
 ## Installation
 
-We recommend installing the package within a virtual environment. At present, the package is compatible exclusively with Python version 3.12.
-You can create a Python environment using tools like `venv` or `conda`. Below are instructions for both methods.
+We recommend installing the package within a virtual environment.
+At present, the package is compatible exclusively with Python version 3.12.
+You can create a Python environment using tools like `venv` or `conda`.
+Below are instructions for both methods.
 
 ### 1. Using `venv` (Built-in Python Tool)
 
 #### Step 1: Install Python version 3.12 (if not already installed)
+
 Ensure you have Python installed. You can download the latest version from [python.org](https://www.python.org/downloads/).
 
-#### Step 2: Create a Virtual Environment 
+#### Step 2: Create a Virtual Environment
+
 - Open your terminal or command prompt.
 - Navigate to your project folder:
+
 ```bash
 cd /path/to/your/project
 ```
-- Run the following command to create a virtual environment (replace adpsenv with your preferred environment name):
+
+- Run the following command to create a virtual environment
+(replace adpsenv with your preferred environment name):
 
 ```bash
 python -m venv adpsenv
 ```
 
 #### Step 3: Activate the Environment
+
 - On Windows:
+
 ```bash
 adpsenv\Scripts\activate
 ```
 
 - On macOS/Linux:
+
 ```bash
 source adpsenv/bin/activate
 ```
-You’ll see the environment name in your terminal prompt indicating the environment is active.
+
+You’ll see the environment name in your terminal prompt
+indicating the environment is active.
 
 #### Step 4: Install Dependencies
 
@@ -53,44 +77,51 @@ pip install pyadps
 ```
 
 #### Step 5: Deactivate the Environment
+
 When you’re done working in the environment, deactivate it by running:
 
 ```bash
 deactivate
 ```
 
-
-
-
-### 2. Using `conda` (Anaconda/Miniconda):
+### 2. Using `conda` (Anaconda/Miniconda)
 
 #### Step 1: Install Conda
+
 First, you need to have Conda installed on your system. You can either install:
 
 - [Anaconda (Full Distribution)](https://www.anaconda.com/products/individual)
 - [Miniconda (Lightweight Version)](https://docs.conda.io/en/latest/miniconda.html)
 
 #### Step 2: Create a Conda Environment with Python 3.12
-Once Conda is installed, open a terminal or command prompt and run the following to create a new environment (replace `adpsenv` with your preferred environment name):
+
+Once Conda is installed, open a terminal or command prompt and run
+the following to create a new environment (replace `adpsenv` with
+your preferred environment name):
 
 ```bash
 conda create --name adpsenv python=3.12
 ```
 
-#### Step 3: Activate the Environment
+#### Step 3: Activate the Conda Environment
+
 ```bash
 conda activate adpsenv
 ```
 
-#### Step 4: Install Dependencies
-You can install packages with pip inside Conda environments. 
+#### Step 4: Install pyadps Dependencies
+
+You can install packages with pip inside Conda environments.
+
 ```bash
 pip install pyadps
 ```
 
-#### Step 5: Deactivate the Environment
-When done, deactivate the environment by running:
-```
+#### Step 5: Deactivate the Conda Environment
+
+When done working in the environment, deactivate the environment by running:
+
+```bash
 conda deactivate
 ```
 
@@ -99,11 +130,11 @@ conda deactivate
 ### Streamlit web interface
 
 Open a terminal or command prompt, activate the environment, and run the command.
+
 ```bash
 run-pyadps
 ```
 
-
 ## License
 
 This project is licensed under the MIT License. See the LICENSE file for details.

{pyadps-0.2.0b0 → pyadps-0.3.0b0}/pyproject.toml

@@ -1,19 +1,19 @@
 [tool.poetry]
 name = "pyadps"
-version = "0.2.0-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-0.2.0b0 → 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 ##############
@@ -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)
-