pyadps 0.1.0__tar.gz → 0.1.0b0__tar.gz

{pyadps-0.1.0 → pyadps-0.1.0b0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.1
 Name: pyadps
-Version: 0.1.0
+Version: 0.1.0b0
 Summary: A Python package for ADCP data processing
 Home-page: https://example.com
 License: MIT
@@ -12,7 +12,6 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
 Provides-Extra: tests
 Requires-Dist: cmake (>=3.30.2)
 Requires-Dist: matplotlib (>=3.8.4)
@@ -22,30 +21,18 @@ 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.
-
-- Documentation: <https://pyadps.readthedocs.io>
-- Source code: <https://github.com/p-amol/pyadps>
-- Bug reports: <https://github.com/p-amol/pyadps/issues>
+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.
 
 ## Table of Contents
 
@@ -55,49 +42,37 @@ considerations.
 
 ## 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
 
@@ -108,51 +83,44 @@ 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)
 
-#### Step 1: Install Conda
 
+
+### 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 Conda Environment
-
+#### Step 3: Activate the Environment
 ```bash
 conda activate adpsenv
 ```
 
-#### Step 4: Install pyadps Dependencies
-
-You can install packages with pip inside Conda environments.
-
+#### Step 4: Install Dependencies
+You can install packages with pip inside Conda environments. 
 ```bash
 pip install pyadps
 ```
 
-#### Step 5: Deactivate the Conda Environment
-
-When done working in the environment, deactivate the environment by running:
-
-```bash
+#### Step 5: Deactivate the Environment
+When done, deactivate the environment by running:
+```
 conda deactivate
 ```
 
@@ -161,11 +129,11 @@ 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-0.1.0 → pyadps-0.1.0b0}/README.md

@@ -1,20 +1,8 @@
 # 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.
-
-- Documentation: <https://pyadps.readthedocs.io>
-- Source code: <https://github.com/p-amol/pyadps>
-- Bug reports: <https://github.com/p-amol/pyadps/issues>
+`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.
 
 ## Table of Contents
 
@@ -24,49 +12,37 @@ considerations.
 
 ## 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
 
@@ -77,51 +53,44 @@ 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)
 
-#### Step 1: Install Conda
 
+
+### 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 Conda Environment
-
+#### Step 3: Activate the Environment
 ```bash
 conda activate adpsenv
 ```
 
-#### Step 4: Install pyadps Dependencies
-
-You can install packages with pip inside Conda environments.
-
+#### Step 4: Install Dependencies
+You can install packages with pip inside Conda environments. 
 ```bash
 pip install pyadps
 ```
 
-#### Step 5: Deactivate the Conda Environment
-
-When done working in the environment, deactivate the environment by running:
-
-```bash
+#### Step 5: Deactivate the Environment
+When done, deactivate the environment by running:
+```
 conda deactivate
 ```
 
@@ -130,11 +99,11 @@ 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-0.1.0 → pyadps-0.1.0b0}/pyproject.toml

@@ -1,19 +1,19 @@
 [tool.poetry]
 name = "pyadps"
-version = "0.1.0"
+version = "0.1.0-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"
 ]
 
 
@@ -23,23 +23,22 @@ 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"]
 
 [tool.poetry.scripts]
 run-pyadps = "pyadps.__main__:main"
-run-auto = "pyadps.utils.autoprocess:main"
-run-script = "pyadps.utils.script:main"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
+
+

pyadps-0.1.0b0/src/pyadps/Home_Page.py

@@ -0,0 +1,42 @@
+import streamlit as st
+
+
+def main():
+    st.set_page_config(
+        page_title="ADCP Data Processing Software",
+        page_icon=":world_map:️",
+        layout="wide",
+        initial_sidebar_state="auto",
+        menu_items={
+            "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 software for processing Teledyne RDI Acoustic Doppler Current Profiler (ADCP) PD0 files. Currently the software can process the data from Workhorse ADCPs.
+
+    ## Features
+
+    * Access RDI ADCP binary files using Python 3
+    * Convert RDI binary files to netcdf
+    * Process ADCP data 
+
+    ## Contribute
+    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.
+    We have a mailing list located at: adps-python@google-groups.com
+    
+    ## License
+    The project is licensed under the MIT license.
+
+    """
+
+
+if __name__ == "__main__":
+    main()

{pyadps-0.1.0 → pyadps-0.1.0b0}/src/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 +110,6 @@ 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"]
 
     st.session_state.fname = uploaded_file.name
     st.session_state.head = ds.fileheader
@@ -123,15 +119,6 @@ if uploaded_file is not None:
     st.session_state.echo = ds.echo.data
     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 +132,6 @@ 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 ##############
@@ -180,158 +164,8 @@ 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)
-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_kernal_VT = 5
-st.session_state.despike_cutoff_VT = 3
-
-# Tab4: Flatline
-st.session_state.isFlatlineCheck_VT = False
-st.session_state.flatline_kernal_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
@@ -340,17 +174,16 @@ 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")
@@ -427,18 +260,10 @@ 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)
@@ -456,3 +281,4 @@ with right:
     df = df.astype("str")
     st.write((df.style.map(color_bool2)))
     # st.dataframe(df)
+