Added netcdf (#273)

* netcdf

* fixed comments

* one file

* added unit tests

* document

* added example

* edit readme

* lowercase

* added additional logic:

* changing how output works, adding tests for output (#274)

* added backticks

* missed ths comment

---------

Co-authored-by: Kyle Shores <[email protected]>

README.md

@@ -32,16 +32,40 @@ Run an example. Notice that the output, in csv format, is printed to the termina
 music_box -e Chapman
 ```
 
-You can also run your own configuration
+Output can be saved to a file in csv file when no `--output-format` is passed
 
 ```
-music_box -c my_config.json
+music_box -e Chapman -o output.csv
 ```
 
-Output can be saved to a file
+Output can be saved to a file as csv file when `--output-format` csv is passed
 
 ```
-music_box -e Chapman -o output.csv
+music_box --output-format csv -e Chapman -o output.csv
+```
+
+Output can be saved to a file as netcdf file when `--output-format` netcdf is passed
+
+```
+music_box --output-format netcdf -e Chapman -o output.nc
+```
+
+Output can be saved to a file in csv file to output.csv when no output path is given but `--output-format` is csv
+
+```
+music_box --output-format csv -e Chapman
+```
+
+Output can be saved to a file in netcdf file to output.nc when no output path is given but `--output-format` is netcdf
+
+```
+music_box --output-format netcdf -e Chapman
+```
+
+You can also run your own configuration
+
+```
+music_box -c my_config.json
 ```
 
 And, if you have gnuplot installed, some basic plots can be made to show some resulting concentrations

src/acom_music_box/__init__.py

@@ -13,3 +13,4 @@
 from .evolving_conditions import EvolvingConditions
 from .music_box import MusicBox
 from .examples import Examples
+from .data_output import DataOutput

src/acom_music_box/data_output.py

@@ -0,0 +1,156 @@
+import os
+import datetime
+import logging
+
+logger = logging.getLogger(__name__)
+
+class DataOutput:
+    """
+    A class to handle data output operations for a DataFrame, including converting to CSV
+    or NetCDF formats with appended units for columns. Designed for environmental data
+    with specific units and formats.
+
+    This class manages file paths, unit mappings, and data output formats based on
+    the provided arguments, ensuring valid paths and creating necessary directories.
+
+    Parameters
+    ----------
+    df : pandas.DataFrame
+        The DataFrame containing the data to output.
+    args : argparse.Namespace
+        Arguments specifying output path, format, and additional options.
+
+    Attributes
+    ----------
+    df : pandas.DataFrame
+        The DataFrame to be output.
+    args : argparse.Namespace
+        Command-line arguments or configurations specifying output options.
+    unit_mapping : dict
+        A dictionary mapping specific columns to their respective units.
+
+    Examples
+    --------
+    >>> import pandas as pd
+    >>> from argparse import Namespace
+    >>> df = pd.DataFrame({
+    ...     'ENV.temperature': [290, 295, 300],
+    ...     'ENV.pressure': [101325, 100000, 98500],
+    ...     'ENV.number_density_air': [102, 5096, 850960],
+    ...     'time': [0, 1, 2]
+    ... })
+    >>> args = Namespace(output='output.nc', output_format='netcdf')
+    >>> data_output = DataOutput(df, args)
+    >>> data_output.output()    
+    """
+
+    def __init__(self, df, args):
+        """
+        Initialize the DataOutput class with a DataFrame and configuration arguments.
+
+        Parameters
+        ----------
+        df : pandas.DataFrame
+            The DataFrame containing the data to be output.
+        args : argparse.Namespace
+            Arguments specifying the output configuration, such as file path and format.
+
+        Notes
+        -----
+        The `args` argument should have the following attributes:
+            - output : str
+                The path to save the output file.
+            - output_format : str, optional
+                Format of the output file, either 'csv' or 'netcdf'. Defaults to 'csv'.
+        """
+        self.df = df
+        self.args = args
+        self.unit_mapping = {
+            'ENV.temperature': 'K',
+            'ENV.pressure': 'Pa',
+            'ENV.number_density_air': 'kg -m3',
+            'time': 's'
+        }
+
+    def _get_default_filename(self):
+        """Generate a default filename based on the current datetime and output format."""
+        now = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
+        extension = 'csv' if self.args.output_format == 'csv' else 'nc' 
+        return f"music_box_{now}.{extension}"
+
+    def _ensure_output_path(self):
+        """Ensure the output path is valid and create directories if needed."""
+        if not self.args.output:
+            self.args.output = self._get_default_filename()
+
+        if os.path.isdir(self.args.output):
+            self.args.output = os.path.join(
+                self.args.output, self._get_default_filename())
+
+        dir_path = os.path.dirname(self.args.output)
+        if dir_path and not os.path.exists(dir_path):
+            os.makedirs(dir_path, exist_ok=True)
+            logger.info(f"Created directory: {dir_path}")
+
+    def _append_units_to_columns(self):
+        """Append units to DataFrame column names based on unit mapping."""
+        self.df.columns = [
+            f"{col}.{self.unit_mapping[col]}" if col in self.unit_mapping else
+            f"{col}.mol m-3" if col.startswith('CONC.') else col
+            for col in self.df.columns
+        ]
+
+    def _convert_to_netcdf(self):
+        """Convert DataFrame to xarray Dataset and save as NetCDF with attributes."""
+        ds = self.df.set_index(['time']).to_xarray()
+        for var in ds.data_vars:
+            if var.startswith('CONC.'):
+                ds[var].attrs = {'units': 'mol m-3'}
+
+        ds['ENV.temperature'].attrs = {'units': 'K'}
+        ds['ENV.pressure'].attrs = {'units': 'Pa'}
+        ds['ENV.number_density_air'].attrs = {'units': 'kg -m3'}
+        ds['time'].attrs = {'units': 's'}
+
+        ds.to_netcdf(self.args.output)
+
+    def _output_csv(self):
+        """Handles CSV output."""
+        self._append_units_to_columns()
+        if self.args.output:
+            self._ensure_output_path()
+            self.df.to_csv(self.args.output, index=False)
+            logger.info(f"CSV output written to: {self.args.output}")
+        else:
+            print(self.df.to_csv(index=False))
+
+    def _output_netcdf(self):
+        """Handles NetCDF output."""
+        if self.args.output:
+            self._ensure_output_path()
+        self._convert_to_netcdf()
+        logger.info(f"NetCDF output written to: {self.args.output}")
+
+    def _output_terminal(self):
+        """Handles output to terminal."""
+        self._append_units_to_columns()
+        print(self.df.to_csv(index=False))
+
+    def output(self):
+        """Main method to handle output based on the provided arguments."""
+        # Default output paths based on format
+        if self.args.output is None:
+            self.args.output = self._get_default_filename()
+
+        # Determine output type and call the respective method
+        if self.args.output_format is None or self.args.output_format == 'terminal':
+            self._output_terminal()
+        elif self.args.output_format is None or self.args.output_format == 'csv':
+            self._output_csv()
+        elif self.args.output_format == 'netcdf':
+            self._output_netcdf()
+        else:
+            error = f"Unsupported output format: {self.args.output_format}"
+            logger.error(error)
+            raise ValueError(error)
+

src/acom_music_box/main.py

@@ -8,7 +8,7 @@
 import tempfile
 import matplotlib.pyplot as plt
 import mplcursors
-from acom_music_box import MusicBox, Examples, __version__
+from acom_music_box import MusicBox, Examples, __version__, DataOutput
 
 
 def format_examples_help(examples):
@@ -36,6 +36,12 @@ def parse_arguments():
         type=str,
         help='Path to save the output file, including the file name. If not provided, result will be printed to the console.'
     )
+    parser.add_argument(
+        '--output-format',
+        choices=['csv', 'netcdf', 'terminal'],
+        default='terminal',
+        help="Specify output format: 'terminal' (default), 'csv', or 'netcdf'."
+    )
     parser.add_argument(
         '-v', '--verbose',
         action='count',
@@ -154,7 +160,6 @@ def on_add(sel):
 
     plt.show()
 
-
 def main():
     start = datetime.datetime.now()
 
@@ -176,6 +181,7 @@ def main():
         musicBoxConfigFile = args.config
 
     musicBoxOutputPath = args.output
+
     plot_species_list = args.plot.split(',') if args.plot else None
 
     if not musicBoxConfigFile:
@@ -189,10 +195,11 @@ def main():
     logger.debug(f"Configuration file = {musicBoxConfigFile}")
     myBox.loadJson(musicBoxConfigFile)
 
-    result = myBox.solve(musicBoxOutputPath)
+    result = myBox.solve(callback=None)
 
-    if musicBoxOutputPath is None:
-        print(result.to_csv(index=False))
+    # Create an instance of DataOutput
+    dataOutput = DataOutput(result, args)
+    dataOutput.output()
 
     if plot_species_list:
         if args.plot_tool == 'gnuplot':

src/acom_music_box/music_box.py

@@ -59,7 +59,7 @@ def add_evolving_condition(self, time_point, conditions):
             time=[time_point], conditions=[conditions])
         self.evolvingConditions.append(evolving_condition)
 
-    def solve(self, output_path=None, callback=None):
+    def solve(self, callback=None):
         """
         Solves the box model simulation and optionally writes the output to a file.
 
@@ -68,8 +68,8 @@ def solve(self, output_path=None, callback=None):
         the specified file.
 
         Args:
-            output_path (str, optional): The path to the file where the output will be written. If None, no output file is created. Defaults to None.
-            callback (function, optional): A callback function that is called after each time step. Defaults to None. The callback will take the most recent results, the current time, conditions, and the total simulation time as arguments.
+            callback (function, optional): A callback function that is called after each time step. Defaults to None. 
+            The callback will take the most recent results, the current time, conditions, and the total simulation time as arguments.
 
         Returns:
             list: A 2D list where each inner list represents the results of the simulation
@@ -194,25 +194,7 @@ def solve(self, output_path=None, callback=None):
                 # increments time
                 curr_time += time_step
                 pbar.update(time_step)
-        df = pd.DataFrame(output_array[1:], columns=output_array[0])
-        # outputs to file if output is present
-        if output_path is not None:
-
-            # Check if the output_path is a full path or just a file name
-            if os.path.dirname(output_path) == '':
-                # If output_path is just a filename, use the current directory
-                output_path = os.path.join(os.getcwd(), output_path)
-            elif not os.path.basename(output_path):
-                raise ValueError(f"Invalid output path: '{output_path}' does not contain a filename.")
-
-            # Ensure the directory exists
-            dir_path = os.path.dirname(output_path)
-            if dir_path and not os.path.exists(dir_path):
-                os.makedirs(dir_path, exist_ok=True)
-
-            df.to_csv(output_path, index=False)
-
-        return df
+        return pd.DataFrame(output_array[1:], columns=output_array[0])
 
     def loadJson(self, path_to_json):
         """

tests/integration/test_executable_data_output.py

@@ -0,0 +1,50 @@
+import subprocess
+import os
+import glob
+import pytest
+import tempfile
+
+@pytest.fixture
+def temp_dir():
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        yield tmpdirname
+
+def test_print_results_to_terminal(temp_dir):
+    result = subprocess.run(['music_box', '-e', 'Analytical'], capture_output=True, text=True, cwd=temp_dir)
+    assert len(result.stdout) > 0
+
+def test_create_netcdf_with_timestamp(temp_dir):
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'netcdf'], cwd=temp_dir)
+    assert glob.glob(os.path.join(temp_dir, "music_box_*.nc"))
+
+def test_create_csv_with_timestamp(temp_dir):
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'csv'], cwd=temp_dir)
+    assert glob.glob(os.path.join(temp_dir, "music_box_*.csv"))
+
+def test_create_named_csv(temp_dir):
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'csv', '-o', 'out.csv'], cwd=temp_dir)
+    assert os.path.exists(os.path.join(temp_dir, "out.csv"))
+
+def test_create_named_netcdf(temp_dir):
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'netcdf', '-o', 'out.nc'], cwd=temp_dir)
+    assert os.path.exists(os.path.join(temp_dir, "out.nc"))
+
+def test_create_directory_and_named_netcdf(temp_dir):
+    os.makedirs(os.path.join(temp_dir, "results"), exist_ok=True)
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'netcdf', '-o', 'results/out.nc'], cwd=temp_dir)
+    assert os.path.exists(os.path.join(temp_dir, "results/out.nc"))
+
+def test_create_directory_and_named_csv(temp_dir):
+    os.makedirs(os.path.join(temp_dir, "results"), exist_ok=True)
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'csv', '-o', 'results/out.csv'], cwd=temp_dir)
+    assert os.path.exists(os.path.join(temp_dir, "results/out.csv"))
+
+def test_create_directory_and_timestamped_csv(temp_dir):
+    os.makedirs(os.path.join(temp_dir, "results"), exist_ok=True)
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'csv', '-o', 'results/'], cwd=temp_dir)
+    assert glob.glob(os.path.join(temp_dir, "results/music_box_*.csv"))
+
+def test_create_directory_and_timestamped_netcdf(temp_dir):
+    os.makedirs(os.path.join(temp_dir, "results"), exist_ok=True)
+    subprocess.run(['music_box', '-e', 'Analytical', '--output-format', 'netcdf', '-o', 'results/'], cwd=temp_dir)
+    assert glob.glob(os.path.join(temp_dir, "results/music_box_*.nc"))