pyadps 0.1.1__py3-none-any.whl → 0.2.0b0__py3-none-any.whl

pyadps/utils/writenc.py

@@ -17,6 +17,7 @@ from netCDF4 import date2num
 from pyadps.utils import readrdi as rd
 
 
+
 def pd2nctime(time, t0="hours since 2000-01-01"):
     """
     Function to convert pandas datetime format to netcdf datetime format.
@@ -67,14 +68,7 @@ def flead_ncatt(fl_obj, ncfile_id, ens=0):
             setattr(ncfile_id, format_key, format(value))
 
 
-def rawnc(
-    infile,
-    outfile,
-    time,
-    axis_option=None,
-    attributes=None,
-    t0="hours since 2000-01-01",
-):
+def rawnc(infile, outfile, time, axis_option=None, attributes=None, t0="hours since 2000-01-01"):
     """
     rawnc is a function to create netcdf file. Stores 3-D data types like
     velocity, echo, correlation, and percent good.
@@ -162,100 +156,28 @@ def rawnc(
 
         vshape = var.T.shape
         if i == 0:
-            if primary_axis == "ensemble":
+            if primary_axis == "time":
+                time[:] = np.arange(1, vshape[0] + 1, 1)
+            elif primary_axis == "ensemble":
                 ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+            else:
+                raise ValueError(f"Invalid axis_option: {axis_option}.")
 
         varid[i][0 : vshape[0], 0 : vshape[1], 0 : vshape[2]] = var.T
-
+        
     # Add global attributes if provided
     if attributes:
         for key, value in attributes.items():
-            setattr(
-                outnc, key, str(value)
-            )  # Convert to string to store in NetCDF metadata
+            setattr(outnc, key, str(value))  # Convert to string to store in NetCDF metadata
 
     # outnc.history = "Created " + time.ctime(time.time())
     flead_ncatt(flead, outnc)
+    
 
     outnc.close()
 
-def flead_nc(
-    infile,
-    outfile,
-    time,
-    axis_option=None,
-    attributes=None,
-    t0="hours since 2000-01-01",
-):
-    """
-    Function to create ncfile containing Variable Leader.
-
-    Args:
-        infile (string): Input file path including filename
-        outfile (string): Output file path including filename
-    """
-    outnc = nc4.Dataset(outfile, "w", format="NETCDF4")
-
-    # Dimensions
-    # Define the primary axis based on axis_option
-    if axis_option == "ensemble":
-        outnc.createDimension("ensemble", None)
-        primary_axis = "ensemble"
-        ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
-        ensemble.axis = "T"
-    elif axis_option == "time":
-        tsize = len(time)
-        outnc.createDimension("time", tsize)
-        primary_axis = "time"
-        time_var = outnc.createVariable("time", "i4", ("time",))
-        time_var.axis = "T"
-        time_var.units = t0
-        time_var.long_name = "time"
-
-        # Convert time_data to numerical format
-        nctime = pd2nctime(time, t0)
-        time_var[:] = nctime
-
-    else:
-        raise ValueError(f"Invalid axis_option: {axis_option}.")
-
-    # Variables
-
-    flead = rd.FixedLeader(infile)
-    fdict = flead.fleader
-    varid = [0] * len(fdict)
-
-    i = 0
-
-    for key, values in fdict.items():
-        format_item = key.replace(" ", "_")
-        varid[i] = outnc.createVariable(
-            format_item, "i4", primary_axis, fill_value=-32768
-        )
-        var = values
-        vshape = var.shape
-        if i == 0:
-            if primary_axis == "ensemble":
-                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
-
-        varid[i][0 : vshape[0]] = var
-        i += 1
-
-    # Add global attributes if provided
-    if attributes:
-        for key, value in attributes.items():
-            setattr(outnc, key, str(value))  # Store attributes as strings
 
-    outnc.close()
-
-def vlead_nc(
-    infile,
-    outfile,
-    time,
-    axis_option=None,
-    attributes=None,
-    t0="hours since 2000-01-01",
-):
+def vlead_nc(infile, outfile, time, axis_option=None, attributes=None, t0="hours since 2000-01-01"):
     """
     Function to create ncfile containing Variable Leader.
 
@@ -304,12 +226,16 @@ def vlead_nc(
         var = values
         vshape = var.shape
         if i == 0:
-            if primary_axis == "ensemble":
+            if primary_axis == "time":
+                time[:] = np.arange(1, vshape[0] + 1, 1)
+            elif primary_axis == "ensemble":
                 ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+            else:
+                raise ValueError(f"Invalid axis_option: {axis_option}.")
 
         varid[i][0 : vshape[0]] = var
         i += 1
-
+        
     # Add global attributes if provided
     if attributes:
         for key, value in attributes.items():
@@ -318,9 +244,7 @@ def vlead_nc(
     outnc.close()
 
 
-def finalnc(
-    outfile, depth, final_mask, final_echo, final_corr , final_pgood, time, data, t0="hours since 2000-01-01", attributes=None
-):
+def finalnc(outfile, depth, time, data, t0="hours since 2000-01-01", attributes=None):
     """
     Function to create the processed NetCDF file.
 
@@ -335,19 +259,15 @@ def finalnc(
 
     # Change velocity to cm/s
     data = data.astype(np.float64)
-    data[data > fill] /= 10
+    data[data > fill] /= 10 
 
     # Change depth to positive
-    # depth = abs(depth)
+    depth = abs(depth)
 
     # Reverse the arrays if depth in descending order
     if np.all(depth[:-1] >= depth[1:]):
         depth = depth[::-1]
         data = data[:, ::-1, :]
-        final_mask = final_mask[::-1, :]
-        final_echo = final_echo[:,::-1, :]
-        final_corr = final_corr[:,::-1, :]
-        final_pgood = final_pgood[:,::-1, :]
 
     ncfile = nc4.Dataset(outfile, mode="w", format="NETCDF4")
     # Check if depth is scalar or array
@@ -387,45 +307,6 @@ def finalnc(
     evel.units = "cm/s"
     evel.long_name = "error_velocity"
 
-    mvel = ncfile.createVariable("mask", np.float32, ("time", "depth"), fill_value=fill)
-    mvel.long_name = "Velocity Mask (1: bad value, 0: good value)"
-
-    echo1 = ncfile.createVariable("echo1", np.float32, ("time", "depth"), fill_value=-32768)
-    echo1.long_name = "Echo intensity Beam 1"
-
-    echo2 = ncfile.createVariable("echo2", np.float32, ("time", "depth"), fill_value=-32768)
-    echo2.long_name = "Echo intensity Beam 2"
-
-    echo3 = ncfile.createVariable("echo3", np.float32, ("time", "depth"), fill_value=-32768)
-    echo3.long_name = "Echo intensity Beam 3"
-
-    echo4 = ncfile.createVariable("echo4", np.float32, ("time", "depth"), fill_value=-32768)
-    echo4.long_name = "Echo intensity Beam 4"
-
-    corr1 = ncfile.createVariable("corr1", np.float32, ("time", "depth"), fill_value=-32768)
-    corr1.long_name = "Beam 1 correlation"
-
-    corr2 = ncfile.createVariable("corr2", np.float32, ("time", "depth"), fill_value=-32768)
-    corr2.long_name = "Beam 2 correlation"
-
-    corr3 = ncfile.createVariable("corr3", np.float32, ("time", "depth"), fill_value=-32768)
-    corr3.long_name = "Beam 3 correlation"
-
-    corr4 = ncfile.createVariable("corr4", np.float32, ("time", "depth"), fill_value=-32768)
-    corr4.long_name = "Beam 4 correlation"  
-
-    pgd1 = ncfile.createVariable("pgd1", np.float32, ("time", "depth"), fill_value=-32768)
-    pgd1.long_name = "Percent Good Beam 1"
-
-    pgd2 = ncfile.createVariable("pgd2", np.float32, ("time", "depth"), fill_value=-32768)
-    pgd2.long_name = "Percent Good Beam 2"
-
-    pgd3 = ncfile.createVariable("pgd3", np.float32, ("time", "depth"), fill_value=-32768)
-    pgd3.long_name = "Percent Good Beam 3"
-
-    pgd4 = ncfile.createVariable("pgd4", np.float32, ("time", "depth"), fill_value=-32768)
-    pgd4.long_name = "Percent Good Beam 4"   
-
     nctime = pd2nctime(time, t0)
     # write data
     z[:] = depth
@@ -434,25 +315,10 @@ def finalnc(
     vvel[:, :] = data[1, :, :].T
     wvel[:, :] = data[2, :, :].T
     evel[:, :] = data[3, :, :].T
-    mvel[:, :] = final_mask.T
-    echo1[:, :] = final_echo[0, :, :].T
-    echo2[:, :] = final_echo[1, :, :].T
-    echo3[:, :] = final_echo[2, :, :].T
-    echo4[:, :] = final_echo[3, :, :].T
-    corr1[:, :] = final_corr[0, :, :].T
-    corr2[:, :] = final_corr[1, :, :].T
-    corr3[:, :] = final_corr[2, :, :].T
-    corr4[:, :] = final_corr[3, :, :].T
-    pgd1[:, :] = final_pgood[0, :, :].T
-    pgd2[:, :] = final_pgood[1, :, :].T
-    pgd3[:, :] = final_pgood[2, :, :].T
-    pgd4[:, :] = final_pgood[3, :, :].T
-
+    
     # Add global attributes if provided
     if attributes:
         for key, value in attributes.items():
             setattr(ncfile, key, str(value))  # Store attributes as strings
 
-    ncfile.mask_applied = "True"
-
     ncfile.close()

{pyadps-0.1.1.dist-info → pyadps-0.2.0b0.dist-info}/METADATA

@@ -1,8 +1,8 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.1
 Name: pyadps
-Version: 0.1.1
+Version: 0.2.0b0
 Summary: A Python package for ADCP data processing
-Home-page: https://pyadps.readthedocs.io/en/latest/index.html
+Home-page: https://example.com
 License: MIT
 Keywords: adcp,data-processing,oceanography
 Author: P. Amol
@@ -22,30 +22,18 @@ 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)
-Project-URL: Documentation, https://pyadps.readthedocs.io/en/latest/index.html
+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 +43,37 @@ 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 +84,44 @@ 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 +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.dist-info/RECORD

@@ -0,0 +1,31 @@
+pyadps/Home_Page.py,sha256=gC0eFMtn85U_A4KcVlCEzXkB6a_J0WD3vpK691Kmyw8,1180
+pyadps/__init__.py,sha256=bNCm6_WIhiwvaUeOZhRkyLZyzzUKfSH80Fslg0JPJyk,232
+pyadps/__main__.py,sha256=cIFUayxPnKl00oIR99L6IUEvc8trW7dijtfBQCAen5c,356
+pyadps/pages/01_Read_File.py,sha256=nN05FfZZ1wWOY0T1HRKQ9e2SGoKcc1eQLnTQnmQlfQw,8904
+pyadps/pages/02_View_Raw_Data.py,sha256=-Txl4seQG_c1iAyKRDGONebOARmgEelTgYw19DajToo,3675
+pyadps/pages/03_Download_Raw_File.py,sha256=XBpn4Jt4f9XjZoELS7svJW8S5JBFJnKPUkuIgsHlz_w,8787
+pyadps/pages/04_QC_Test.py,sha256=RR6xos_jgTVrxve8GyrUxvWhEmxpLgbQ-Cx-xAazsls,10335
+pyadps/pages/05_Profile_Test.py,sha256=TBqxJ4TRM7TN5Y7UxXkVtyfS6isD7FWzyS4wuZw79XE,19570
+pyadps/pages/06_Velocity_Test.py,sha256=pBl56ITM-fTM5UnfB_qcYdzWNtmlhD5ZeGUGLwrBKj8,12066
+pyadps/pages/07_Write_File.py,sha256=hzhKxQXwoMa-WC7Co3ufkqPAS_iLkqea6I_OusDQUM4,16115
+pyadps/pages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyadps/utils/__init__.py,sha256=NJQy9tUDnAOvX9-c47LjBJzxYeICC4y-WBv44pOL09k,402
+pyadps/utils/autoprocess.py,sha256=DB0a8ycyEL1n0nNWsG-1lU0JmO5CtNQA_VXJsntIfek,9691
+pyadps/utils/cutbin.py,sha256=JioME3mo4wZKiJ7lOWqNo0MvxHNFYv2enirBoD0oh6E,15911
+pyadps/utils/metadata/config.ini,sha256=zbwByM9mIfLPPCkaJI7ShCmLbnAI9lkeImnVpkSCw2U,1821
+pyadps/utils/metadata/flmeta.json,sha256=diIB9nht_0uw9YJNSFGdZYGzeVbR-07zIZS9Nf4VPSE,14245
+pyadps/utils/metadata/vlmeta.json,sha256=_dkQlGkkUvpAIM7S6kEUenSaiCpOrwXg8n1aU3dDF3s,22535
+pyadps/utils/plotgen.py,sha256=ylYPxBmrtPc_ssgEwyUixc6p3QuNcTs88LgJHWk_Vag,7129
+pyadps/utils/profile_test.py,sha256=_eXh0JstTAxvYAEJEn1J_QpEJWeQBVIyZ7IPWipq3Vg,6168
+pyadps/utils/pyreadrdi.py,sha256=MX5xe5qKwFMF1RWeCQ3-vBDxm9nP0UbHsEJzSDewnuY,34807
+pyadps/utils/readrdi.py,sha256=ZQnkoVI1NUUjU7tVWx4gnLo7b2C3Lv4LnVPKm56qvqg,45028
+pyadps/utils/regrid.py,sha256=Hj2dYSk4RQgXWXvkil5s5GlhyF-gE4HvO9Y_yIWrfPM,10006
+pyadps/utils/script.py,sha256=yf3AZS3FMS2xk77rwezGA8WefwV03vIRQ6HraoeLuBA,4965
+pyadps/utils/signal_quality.py,sha256=E1lZWZfdUnbc5c02px5WWU8b12DnkeCo-gRHjIoe18s,4170
+pyadps/utils/velocity_test.py,sha256=sjQDgyC8TtOcmR8xW7crPhbt9ZAyp6Ej5o8bOdcWqxk,4707
+pyadps/utils/writenc.py,sha256=Oc6vtMec4YWitv_XQYBuiakvo3ZUACBL0uZSL9lGUm4,9793
+pyadps-0.2.0b0.dist-info/LICENSE,sha256=sfY_7DzQF5FxnO2T6ek74dfm5uBmwEp1oEg_WlzNsb8,1092
+pyadps-0.2.0b0.dist-info/METADATA,sha256=bcnpYpROIyXwlFdsDSTHRnryh1CokPj6bqi5jTY1LVw,4238
+pyadps-0.2.0b0.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+pyadps-0.2.0b0.dist-info/entry_points.txt,sha256=qS5lbmTJLC4Ys0nu4-2tJoBpAHxTREta30KFrDyTfsY,90
+pyadps-0.2.0b0.dist-info/RECORD,,

{pyadps-0.1.1.dist-info → pyadps-0.2.0b0.dist-info}/WHEEL

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

{pyadps-0.1.1.dist-info → pyadps-0.2.0b0.dist-info}/entry_points.txt

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