pyadps 0.1.0__py3-none-any.whl → 0.1.0b0__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.
@@ -67,16 +68,9 @@ 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 main(infile, outfile, attributes=None):
     """
-    rawnc is a function to create netcdf file. Stores 3-D data types like
+    Main function to create netcdf file. Stores 3-D data types like
     velocity, echo, correlation, and percent good.
 
     Args:
@@ -96,33 +90,14 @@ def rawnc(
     beam_list = flead.fleader["Beams"]
 
     # 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}.")
-
+    outnc.createDimension("ensemble", None)
     outnc.createDimension("cell", max(cell_list))
     outnc.createDimension("beam", max(beam_list))
 
     # Variables
     # Dimension Variables
+    ensemble = outnc.createVariable("ensemble", "u4", ("ensemble",))
+    ensemble.axis = "T"
     cell = outnc.createVariable("cell", "i2", ("cell",))
     cell.axis = "Z"
     beam = outnc.createVariable("beam", "i2", ("beam",))
@@ -143,9 +118,9 @@ def rawnc(
     for i, item in enumerate(varlist):
         if item == "Velocity":
             varid[i] = outnc.createVariable(
-                item, "i2", (primary_axis, "cell", "beam"), fill_value=-32768
+                item, "i2", ("ensemble", "cell", "beam"), fill_value=-32768
             )
-            # varid[i].missing_value = -32768
+            varid[i].missing_value = -32768
             vel = getattr(rd, item)
             var = vel(infile).data
             # var = rd.variables(infile, item)
@@ -154,7 +129,7 @@ def rawnc(
             # Unsigned integers might be assigned for future netcdf versions
             format_item = item.replace(" ", "")  # For percent good
             varid[i] = outnc.createVariable(
-                format_item, "i2", (primary_axis, "cell", "beam")
+                format_item, "i2", ("ensemble", "cell", "beam")
             )
             datatype = getattr(rd, format_item)
             var = np.array(datatype(infile).data, dtype="int16")
@@ -162,32 +137,22 @@ def rawnc(
 
         vshape = var.T.shape
         if i == 0:
-            if primary_axis == "ensemble":
-                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
-
+            ensemble[:] = np.arange(1, vshape[0] + 1, 1)
         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 vlead_nc(
-    infile,
-    outfile,
-    time,
-    axis_option=None,
-    attributes=None,
-    t0="hours since 2000-01-01",
-):
+def vlead_nc(infile, outfile, attributes=None):
     """
     Function to create ncfile containing Variable Leader.
 
@@ -198,29 +163,12 @@ def vlead_nc(
     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}.")
+    outnc.createDimension("ensemble", None)
 
     # Variables
+    # Dimension Variables
+    ensemble = outnc.createVariable("ensemble", "i4", ("ensemble",))
+    ensemble.axis = "T"
 
     vlead = rd.VariableLeader(infile)
     vdict = vlead.vleader
@@ -231,17 +179,16 @@ def vlead_nc(
     for key, values in vdict.items():
         format_item = key.replace(" ", "_")
         varid[i] = outnc.createVariable(
-            format_item, "i4", primary_axis, fill_value=-32768
+            format_item, "i4", "ensemble", fill_value=-32768
         )
         var = values
         vshape = var.shape
         if i == 0:
-            if primary_axis == "ensemble":
-                ensemble[:] = np.arange(1, vshape[0] + 1, 1)
+            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():
@@ -250,9 +197,7 @@ def vlead_nc(
     outnc.close()
 
 
-def finalnc(
-    outfile, depth, final_mask, 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.
 
@@ -263,21 +208,6 @@ def finalnc(
         data (numpy array): Velocity (beam, depth, time)
         t0 (string): Time unit and origin
     """
-    fill = -32768
-
-    # Change velocity to cm/s
-    data = data.astype(np.float64)
-    data[data > fill] /= 10
-
-    # Change depth to positive
-    # 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, :]
-
     ncfile = nc4.Dataset(outfile, mode="w", format="NETCDF4")
     # Check if depth is scalar or array
     if np.isscalar(depth):
@@ -291,22 +221,21 @@ def finalnc(
     z = ncfile.createVariable("depth", np.float32, ("depth"))
     z.units = "m"
     z.long_name = "depth"
-    z.positive = "down"
 
     t = ncfile.createVariable("time", np.float32, ("time"))
     t.units = t0
     t.long_name = "time"
 
     # Create 2D variables
-    uvel = ncfile.createVariable("u", np.float32, ("time", "depth"), fill_value=fill)
+    uvel = ncfile.createVariable("u", np.float32, ("time", "depth"), fill_value=-32768)
     uvel.units = "cm/s"
     uvel.long_name = "zonal_velocity"
 
-    vvel = ncfile.createVariable("v", np.float32, ("time", "depth"), fill_value=fill)
+    vvel = ncfile.createVariable("v", np.float32, ("time", "depth"), fill_value=-32768)
     vvel.units = "cm/s"
     vvel.long_name = "meridional_velocity"
 
-    wvel = ncfile.createVariable("w", np.float32, ("time", "depth"), fill_value=fill)
+    wvel = ncfile.createVariable("w", np.float32, ("time", "depth"), fill_value=-32768)
     wvel.units = "cm/s"
     wvel.long_name = "vertical_velocity"
 
@@ -316,24 +245,18 @@ 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)"
-
     nctime = pd2nctime(time, t0)
     # write data
-    z[:] = depth
+    z[:] = depth * -1
     t[:] = nctime
     uvel[:, :] = data[0, :, :].T
     vvel[:, :] = data[1, :, :].T
     wvel[:, :] = data[2, :, :].T
     evel[:, :] = data[3, :, :].T
-    mvel[:, :] = final_mask.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-0.1.0.dist-info → pyadps-0.1.0b0.dist-info}/METADATA

@@ -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-0.1.0b0.dist-info/RECORD

@@ -0,0 +1,29 @@
+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=ndBslgOHxbk6U6AMKL2uEnwCFL7rukpx8CqfM-_LXz8,8788
+pyadps/pages/02_View_Raw_Data.py,sha256=-Txl4seQG_c1iAyKRDGONebOARmgEelTgYw19DajToo,3675
+pyadps/pages/03_Download_Raw_File.py,sha256=YdGnlx6ZsJ_vAEK8086sCIHewvi9gg0d2yWl7s7qeNU,8216
+pyadps/pages/04_QC_Test.py,sha256=uawHLN9X7X7ykOZtI_viMMG-OlEEerm2X8uJFyWiRzo,8363
+pyadps/pages/05_Profile_Test.py,sha256=wQ_jXaaaEPCdb4yWzITHuGlkbGdw97ZnlK_4ppF7XS4,12114
+pyadps/pages/06_Velocity_Test.py,sha256=8AtUC3V7BJPuxVe1gMkrdwG0_XZwE0DE4bRCW86Luto,9666
+pyadps/pages/07_Write_File.py,sha256=7SBx4IDV4Oi6CBPvTzV7dJCvjGOimr6FwSEksk_rQBk,13481
+pyadps/pages/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pyadps/utils/__init__.py,sha256=EyjpjGiv-IEL7Q09pBvVJ6O7rnRyUdb1dkNlOFTn_xQ,362
+pyadps/utils/cutbin.py,sha256=JioME3mo4wZKiJ7lOWqNo0MvxHNFYv2enirBoD0oh6E,15911
+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=1Ot8_1z9VUfX4bmVp-_P_QStrnbkVDwLth2pQQCJTrM,5652
+pyadps/utils/pyreadrdi.py,sha256=MX5xe5qKwFMF1RWeCQ3-vBDxm9nP0UbHsEJzSDewnuY,34807
+pyadps/utils/readrdi.py,sha256=jRtzMsaAd_raDD5fmAjVXK5M18QgukmW7SmmACI98o0,44975
+pyadps/utils/regrid.py,sha256=Oh1s4g83EWOvCfOkFiEpNoEI3ARwMukjlmVCi834KYM,3269
+pyadps/utils/script.py,sha256=yf3AZS3FMS2xk77rwezGA8WefwV03vIRQ6HraoeLuBA,4965
+pyadps/utils/signal_quality.py,sha256=E1lZWZfdUnbc5c02px5WWU8b12DnkeCo-gRHjIoe18s,4170
+pyadps/utils/velocity_test.py,sha256=keNd2DNBF0E0FhkqGHXM-zapA5xCEvvh8eyBd3xacvU,3555
+pyadps/utils/writenc.py,sha256=fJi7KSUS5AqZt-YNVsfM74Q0Dq54FUiPyMkNFRc83MQ,7663
+pyadps-0.1.0b0.dist-info/LICENSE,sha256=sfY_7DzQF5FxnO2T6ek74dfm5uBmwEp1oEg_WlzNsb8,1092
+pyadps-0.1.0b0.dist-info/METADATA,sha256=EYXVTygVzbyau6IJ4ro7iWq0Yv_3YobAO4KPoNeQp4c,4187
+pyadps-0.1.0b0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pyadps-0.1.0b0.dist-info/entry_points.txt,sha256=jFrXjOakSOPFOv2iDeYx_fI9FxdL1wXQ6FghECFpsvg,51
+pyadps-0.1.0b0.dist-info/RECORD,,

{pyadps-0.1.0.dist-info → pyadps-0.1.0b0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.0
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pyadps-0.1.0b0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+run-pyadps=pyadps.__main__:main
+