pyadps 0.2.0b0__py3-none-any.whl → 0.3.0__py3-none-any.whl

{pyadps-0.2.0b0.dist-info → pyadps-0.3.0.dist-info}/METADATA

@@ -1,8 +1,7 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pyadps
-Version: 0.2.0b0
+Version: 0.3.0
 Summary: A Python package for ADCP data processing
-Home-page: https://example.com
 License: MIT
 Keywords: adcp,data-processing,oceanography
 Author: P. Amol
@@ -13,27 +12,39 @@ 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)
+Requires-Dist: matplotlib (>=3.8.4,<3.9.0)
 Requires-Dist: meson (>=1.4.1)
-Requires-Dist: netCDF4 (>=1.7.1)
-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: scipy (>=1.14.0)
-Requires-Dist: streamlit (>=1.36.0)
-Requires-Dist: wmm2020 (>=1.1.1)
-Project-URL: Documentation, https://example.com/docs
+Requires-Dist: netCDF4 (>=1.7.1,<1.8.0)
+Requires-Dist: numpy (>=1.26.4,<1.27.0)
+Requires-Dist: pandas (>=2.2.2,<2.3.0)
+Requires-Dist: plotly (>=5.22.0,<5.23.0)
+Requires-Dist: plotly-resampler (>=0.10.0,<0.11.0)
+Requires-Dist: pygeomag (>=1.1.0,<2.0.0)
+Requires-Dist: scipy (>=1.14.0,<1.15.0)
+Requires-Dist: streamlit (>=1.36.0,<1.37.0)
+Project-URL: Documentation, https://pyadps.readthedocs.io/en/latest/index.html
 Project-URL: Repository, https://github.com/p-amol/pyadps
+Project-URL: homepage, https://pyadps.readthedocs.io/en/latest/index.html
 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 +54,49 @@ 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 +107,51 @@ 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 +160,11 @@ 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-0.3.0.dist-info/RECORD

@@ -0,0 +1,35 @@
+pyadps/Home_Page.py,sha256=j_-3fsp1hkhpNEl5jE-CEQvClDGpMi1H3ZQPXfuKWBg,1782
+pyadps/__init__.py,sha256=bNCm6_WIhiwvaUeOZhRkyLZyzzUKfSH80Fslg0JPJyk,232
+pyadps/__main__.py,sha256=cIFUayxPnKl00oIR99L6IUEvc8trW7dijtfBQCAen5c,356
+pyadps/pages/01_Read_File.py,sha256=JY3NJ_uqA7QsIKZz5HjwIvaX6BzD_CFGDfL_P5axRQU,24694
+pyadps/pages/02_View_Raw_Data.py,sha256=wpTVe76oS9Jj2Q4x4yORLExpUjr_60xNi0V1EKhDI-8,6359
+pyadps/pages/03_Download_Raw_File.py,sha256=ebZu17STL3HhM8ExQvSWNfquI2CrmdJPxOeNjV-lvvU,12214
+pyadps/pages/04_Sensor_Health.py,sha256=2Qnwl7D46H-f8LmXLVZj5X36h8MjRwmVRK6Bs_wuB_k,33905
+pyadps/pages/05_QC_Test.py,sha256=6YjQTg_t0_Qll9xQ3SYieCBS2cDEMz9znovW3olPFwc,16566
+pyadps/pages/06_Profile_Test.py,sha256=Vir91oRIWApbO2elBm4I59rdf83NtspUmtzAyWdsIiY,34891
+pyadps/pages/07_Velocity_Test.py,sha256=K4vEiLPMXrU4JMLj-mIA1G4H5ORozMbHMiMov3ZZXP0,23008
+pyadps/pages/08_Write_File.py,sha256=cr8Ctwh8USTMHuRiR_JlHjKZelY6Yyx0g_DxWByd460,23742
+pyadps/pages/09_Add-Ons.py,sha256=lweofAxcvKLxzfCJl6vybmUmxWgcm4jEn5DjFaTHbpI,5986
+pyadps/pages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyadps/utils/__init__.py,sha256=JDIy5Yx6meDGxfLGyB5135TFWQc0lyNxu_cWrfSEDhU,485
+pyadps/utils/autoprocess.py,sha256=oQFmfMvCkZJHpCPvCl4bXOnGRfoOB8f2ZaGik5-9tq4,21095
+pyadps/utils/logging_utils.py,sha256=-b6rwnpF-g6ZSIj3PVyxiz4-blBKvKqh1HW1KRKpmyY,8492
+pyadps/utils/metadata/config.ini,sha256=TC7htzGwUukIXt_u3JR5ycyvOoDj_JxWgGY6khjNeck,2154
+pyadps/utils/metadata/demo.000,sha256=qxB3sgjABrpv4DNXkwjpbSxk5sc4UwAI8kgQX0--PM8,234468
+pyadps/utils/metadata/flmeta.json,sha256=wyoCCK1Nb7-U3NR2ZZxTfxH-vh_yzuOrg2T5f9goTNo,12439
+pyadps/utils/metadata/vlmeta.json,sha256=sdwCsCEDKDVpYaXG96qU9MQqjkq-585Eeu3be_bK7og,21606
+pyadps/utils/multifile.py,sha256=cXPYNJ3y-VkoeCtriR7TxBo0_mc34vUxK672ddXC6tM,10105
+pyadps/utils/plotgen.py,sha256=c7TUA9unErUxppYc14LZ2o_stzNMmmZ5X542iI5v1tA,26346
+pyadps/utils/profile_test.py,sha256=gnbS6ZsqKvv2tcHTj-Fi_VNOszbxDcPxl77_n4dLzSo,29237
+pyadps/utils/pyreadrdi.py,sha256=6ruA0QfVoMHd7vpLObjKj7dN1__a9ZCr9kIJduaOq28,38534
+pyadps/utils/readrdi.py,sha256=h6QXj5ynT-0u-PTaKEhpYAFFz5uE-zVHKG-_3yA5Meg,55829
+pyadps/utils/script.py,sha256=TKMCYe0HEz-2GFpNxKVzpg0p4MM-Cu2rcMZc51GgLn4,6534
+pyadps/utils/sensor_health.py,sha256=aHRaU4kMJZ9dGmYypKpCCgq-owWoNjvcl1I_9I7dG68,3973
+pyadps/utils/signal_quality.py,sha256=PjedVk38suwe3MSht_Z4yxNMqTFbGqE6MdlaJ3ypuUA,18506
+pyadps/utils/velocity_test.py,sha256=O8dgjv_5pxhJq6QuWHxysMjNzxSnob_2KPLInmO1kHI,6112
+pyadps/utils/writenc.py,sha256=KDolQ11Whh2bi4L2wfrgjXym5BWL8ikp0xvo4Pa0r4E,14455
+pyadps-0.3.0.dist-info/LICENSE,sha256=sfY_7DzQF5FxnO2T6ek74dfm5uBmwEp1oEg_WlzNsb8,1092
+pyadps-0.3.0.dist-info/METADATA,sha256=NXjYlGQqxSAe5FHHGKzkxxzYcnMcQ6mEI6IeuymNIBA,4569
+pyadps-0.3.0.dist-info/WHEEL,sha256=RaoafKOydTQ7I_I3JTrPCg6kUmTgtm4BornzOqyEfJ8,88
+pyadps-0.3.0.dist-info/entry_points.txt,sha256=-oZhbbJq8Q29uNVh5SmzOLp9OeFM9VUzHVxovfI4LXA,126
+pyadps-0.3.0.dist-info/RECORD,,

{pyadps-0.2.0b0.dist-info → pyadps-0.3.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.1
+Generator: poetry-core 2.0.0
 Root-Is-Purelib: true
 Tag: py3-none-any

{pyadps-0.2.0b0.dist-info → pyadps-0.3.0.dist-info}/entry_points.txt

@@ -1,4 +1,5 @@
 [console_scripts]
 run-auto=pyadps.utils.autoprocess:main
 run-pyadps=pyadps.__main__:main
+run-script=pyadps.utils.script:main
 

pyadps/pages/04_QC_Test.py

@@ -1,334 +0,0 @@
-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.subplots import make_subplots
-from plotly_resampler import FigureResampler
-from streamlit.runtime.state import session_state
-from utils.signal_quality import ev_check, false_target, pg_check, qc_check
-
-if "flead" not in st.session_state:
-    st.write(":red[Please Select Data!]")
-    st.stop()
-
-# `mask` holds the temporary changes in the page
-# `qcmask` holds the final changes in the page
-if "mask" not in st.session_state:
-    st.session_state.mask = np.copy(st.session_state.orig_mask)
-
-if not st.session_state.isQCMask:
-    st.write(":grey[Creating a new mask file ...]")
-    st.session_state.qc_mask = np.copy(st.session_state.orig_mask)
-    st.session_state.isSubmit = False
-else:
-    st.write(":grey[Working on a saved mask file ...]")
-    st.write(":orange[WARNING! QC test already completed. Reset to change settings.]")
-    reset_button1 = st.button("Reset Mask Data")
-    if reset_button1:
-        st.session_state.mask = np.copy(st.session_state.orig_mask)
-        st.session_state.qc_mask = np.copy(st.session_state.orig_mask)
-        st.write(":green[Mask data is reset to default]")
-
-if "isThresh" not in st.session_state:
-    st.session_state.isThresh = False
-
-# Load data
-flobj = st.session_state.flead
-vlobj = st.session_state.vlead
-velocity = st.session_state.velocity
-echo = st.session_state.echo
-correlation = st.session_state.correlation
-pgood = st.session_state.pgood
-ensembles = st.session_state.head.ensembles
-cells = flobj.field()["Cells"]
-fdata = flobj.fleader
-vdata = vlobj.vleader
-x = np.arange(0, ensembles, 1)
-y = np.arange(0, cells, 1)
-
-
-@st.cache_data
-def fillplot_plotly(data, colorscale="balance"):
-    fig = FigureResampler(go.Figure())
-    data1 = np.where(data == -32768, np.nan, data)
-    fig.add_trace(
-        go.Heatmap(z=data1[:, 0:-1], x=x, y=y, colorscale=colorscale, hoverongaps=False)
-    )
-    st.plotly_chart(fig)
-
-
-@st.cache_data
-def plot_noise(dep=0, rec=-1):
-    n = dep
-    m = rec
-    colorleft = [
-        "rgb(240, 255, 255)",
-        "rgb(115, 147, 179)",
-        "rgb(100, 149, 237)",
-        "rgb(15, 82, 186)",
-    ]
-    colorright = [
-        "rgb(250, 200, 152)",
-        "rgb(255, 165, 0)",
-        "rgb(255, 95, 31)",
-        "rgb(139, 64, 0)",
-    ]
-    fig = make_subplots(
-        rows=1,
-        cols=2,
-        subplot_titles=[
-            f"Deployment Ensemble ({x[n]+1})",
-            f"Recovery Ensemble ({x[m]+1})",
-        ],
-    )
-    for i in range(4):
-        fig.add_trace(
-            go.Scatter(
-                x=echo[i, :, n],
-                y=y,
-                name=f"Beam (D) {i+1}",
-                line=dict(color=colorleft[i]),
-            ),
-            row=1,
-            col=1,
-        )
-    for i in range(4):
-        fig.add_trace(
-            go.Scatter(
-                x=echo[i, :, m],
-                y=y,
-                name=f"Beam (R)  {i+1}",
-                line=dict(color=colorright[i]),
-            ),
-            row=1,
-            col=2,
-        )
-
-    fig.update_layout(height=600, width=800, title_text="Echo Intensity")
-    fig.update_xaxes(title="Echo (count)")
-    fig.update_yaxes(title="Cells")
-    st.plotly_chart(fig)
-    
-#########  NOISE FLOOR IDENTIFICATION ##############
-dn = rn = 1
-st.header("Noise Floor Identification", divider="blue")
-st.write(
-    """
-    If the ADCP has collected data from the air either 
-    before deployment or after recovery, this data can 
-    be used to estimate the echo intensity threshold. 
-    The plots below show the echo intensity from the first 
-    and last ensembles. The noise level is typically around 
-    30-40 counts throughout the entire profile.
-"""
-)
-dn = st.number_input("Deployment Ensemble", x[0] + 1, x[-1] + 1, x[0] + 1)
-# r = st.number_input("Recovery Ensemble", -1 * (x[-1] + 1), -1 * (x[0] + 1), -1)
-rn = st.number_input("Recovery Ensemble", x[0] + 1, x[-1] + 1, x[-1] + 1)
-dn = dn - 1
-rn = rn - 1
-
-plot_noise(dep=dn, rec=rn)
-
-
-################## QC Test ###################
-
-st.header("Quality Control Tests", divider="blue")
-st.write("")
-
-left, right = st.columns([1, 1])
-with left:
-    st.write(""" Teledyne RDI recommends these quality control tests, 
-                 some of which can be configured before deployment. 
-                 The pre-deployment values configured for the ADCP are listed 
-                 in the table below. The noise-floor identification graph above 
-                 can assist in determining the echo intensity threshold. 
-                 For more information about these tests, 
-                 refer to *Acoustic Doppler Current Profiler Principles of 
-                 Operation: A Practical Primer* by Teledyne RDI.""")
-    fdata = st.session_state.flead.field()
-    st.divider()
-    st.write(":blue-background[Additional Information:]")
-    st.write(f"Number of Pings per Ensemble: `{fdata["Pings"]}`")
-    st.write(f"Number of Beams: `{fdata["Beams"]}`")
-    st.divider()
-    st.write(":red-background[Thresholds used during deployment:]")
-    thresh = pd.DataFrame(
-        [
-            ["Correlation", fdata["Correlation Thresh"]],
-            ["Error Velocity", fdata["Error Velocity Thresh"]],
-            ["Echo Intensity", 0],
-            ["False Target", fdata["False Target Thresh"]],
-            ["Percentage Good", fdata["Percent Good Min"]],
-        ],
-        columns=["Threshold", "Values"],
-    )
-
-    st.write(thresh)
-
-with right:
-    with st.form(key="my_form"):
-        st.write("Would you like to apply new threshold?")
-
-        ct = st.number_input(
-            "Select Correlation Threshold",
-            0,
-            255,
-            fdata["Correlation Thresh"],
-        )
-
-        evt = st.number_input(
-            "Select Error Velocity Threshold",
-            0,
-            9999,
-            fdata["Error Velocity Thresh"],
-        )
-
-        et = st.number_input(
-            "Select Echo Intensity Threshold",
-            0,
-            255,
-            0,
-        )
-
-        ft = st.number_input(
-            "Select False Target Threshold",
-            0,
-            255,
-            fdata["False Target Thresh"],
-        )
-
-        option = st.selectbox(
-            "Would you like to use a three-beam solution?", (True, False)
-        )
-
-        pgt = st.number_input(
-            "Select Percent Good Threshold",
-            0,
-            100,
-            fdata["Percent Good Min"],
-        )
-        submit_button = st.form_submit_button(label="Submit")
-
-
-mask = st.session_state.mask
-with left:
-    if submit_button:
-        st.session_state.newthresh = pd.DataFrame(
-            [
-                ["Correlation", str(ct)],
-                ["Error Velocity", str(evt)],
-                ["Echo Intensity", str(et)],
-                ["False Target", str(ft)],
-                ["Three Beam", str(option)],
-                ["Percentage Good", str(pgt)],
-            ],
-            columns=["Threshold", "Values"],
-        )
-        st.session_state.isThresh = True
-        # st.write(st.session_state.newthresh)
-
-        mask = pg_check(pgood, mask, pgt, threebeam=option)
-        mask = qc_check(correlation, mask, ct)
-        mask = qc_check(echo, mask, et)
-        mask = ev_check(velocity[3, :, :], mask, evt)
-        mask = false_target(echo, mask, ft, threebeam=True)
-        st.session_state.mask = mask
-
-    if st.session_state.isThresh:
-        st.write(":green-background[Current Thresholds]")
-        st.write(st.session_state.newthresh)
-
-
-
-st.header("Mask File", divider="blue")
-st.write(
-"""
-Displayed the mask file. 
-Ensure to save any necessary changes or apply additional thresholds if needed.
-"""
-)
-
-
-if st.button("Display mask file"):
-    st.subheader("Default Mask File")
-    st.write(
-    """
-ADCP assigns missing values based on thresholds set before deployment.
-These values cannot be recovered and the default 
-"""
-)
-    fillplot_plotly(st.session_state.orig_mask, colorscale="greys")
-
-
-    st.subheader("Update Mask File")
-    st.write(
-    """
-Update, display and save the updated mask file after applying threshold.
-If thresholds are not saved, default mask file is used. 
-"""
-)
-# values, counts = np.unique(mask, return_counts=True)
-    fillplot_plotly(st.session_state.mask, colorscale="greys")
-
-############## SENSOR HEALTH ######################
-st.header("Sensor Health", divider="blue")
-st.write("The following details can be used to determine whether the additional sensors are functioning properly.")
-# ################## Pressure Sensor Check ###################
-# st.subheader("Pressure Sensor Check", divider="orange")
-#
-# st.subheader("Temperature Sensor Check", divider="orange")
-#
-# st.subheader("Tilt Sensor Check", divider="orange")
-################## Fix Orientation ###################
-st.subheader("Fix Orientation", divider="orange")
-
-
-if st.session_state.beam_direction == 'Up':
-    beamalt = 'Down' 
-else:
-    beamalt = 'Up'
-st.write(f"The current orientation of ADCP is `{st.session_state.beam_direction}`. Use the below option to correct the orientation.")
-
-beamdir_select = st.radio(f'Change orientation to {beamalt}', ['No', 'Yes'])
-if beamdir_select == 'Yes':
-    st.session_state.beam_direction = beamalt
-    st.write(f"The orientation changed to `{st.session_state.beam_direction}`")
-
-
-
-
-################## Save Button #############
-st.header("Save Data", divider="blue")
-col1, col2 = st.columns([1, 1])
-with col1:
-    save_mask_button = st.button(label="Save Mask Data")
-
-    if save_mask_button:
-        # st.session_state.mask = mask
-        st.session_state.qc_mask = np.copy(st.session_state.mask)
-        st.session_state.isQCMask = True
-        st.session_state.isProfileMask = False
-        st.session_state.isGridSave = False
-        st.session_state.isVelocityMask = False
-        st.write(":green[Mask file saved]")
-    else:
-        st.write(":red[Mask data not saved]")
-with col2:
-    reset_mask_button = st.button("Reset mask Data")
-    if reset_mask_button:
-        st.session_state.mask = np.copy(st.session_state.orig_mask)
-        st.session_state.isQCMask = False
-        st.session_state.isGrid = False
-        st.session_state.isProfileMask = False
-        st.session_state.isVelocityMask = False
-        st.write(":green[Mask data is reset to default]")
-
-
-
-
-
-
-
-