pydartdiags 0.0.42__tar.gz → 0.5.0__tar.gz

pydartdiags-0.5.0/PKG-INFO

@@ -0,0 +1,49 @@
+Metadata-Version: 2.2
+Name: pydartdiags
+Version: 0.5.0
+Summary: Observation Sequence Diagnostics for DART
+Home-page: https://github.com/NCAR/pyDARTdiags.git
+Author: Helen Kershaw
+Author-email: Helen Kershaw <hkershaw@ucar.edu>
+Project-URL: Homepage, https://github.com/NCAR/pyDARTdiags.git
+Project-URL: Issues, https://github.com/NCAR/pyDARTdiags/issues
+Project-URL: Documentation, https://ncar.github.io/pyDARTdiags
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: numpy>=1.26
+Requires-Dist: plotly>=5.22.0
+Requires-Dist: pyyaml>=6.0.2
+Requires-Dist: matplotlib>=3.9.4
+Dynamic: author
+Dynamic: home-page
+Dynamic: requires-python
+
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![codecov](https://codecov.io/gh/NCAR/pyDARTdiags/graph/badge.svg?token=VK55SQZSVD)](https://codecov.io/gh/NCAR/pyDARTdiags)
+[![PyPI version](https://badge.fury.io/py/pydartdiags.svg)](https://pypi.org/project/pydartdiags/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+# pyDARTdiags
+
+pyDARTdiags is a Python library for observation space diagnostics for the Data Assimilation Research Testbed ([DART](https://github.com/NCAR/DART)).
+
+pyDARTdiags is under initial development, so please use caution.
+The MATLAB [observation space diagnostics](https://docs.dart.ucar.edu/en/latest/guide/matlab-observation-space.html) are available through [DART](https://github.com/NCAR/DART).
+
+
+pyDARTdiags can be installed through pip: https://pypi.org/project/pydartdiags/  
+Documentation : https://ncar.github.io/pyDARTdiags/
+
+## Contributing
+Contributions are welcome! If you have a feature request, bug report, or a suggestion, please open an issue on our GitHub repository.
+Please read our [Contributors Guide](https://github.com/NCAR/pyDARTdiags/blob/main/CONTRIBUTING.md) if you would like to contribute to
+pyDARTdiags.
+
+## License
+
+pyDARTdiags is released under the Apache License 2.0. For more details, see the LICENSE file in the root directory of this source tree or visit [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0).

pydartdiags-0.5.0/README.md

@@ -0,0 +1,24 @@
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![codecov](https://codecov.io/gh/NCAR/pyDARTdiags/graph/badge.svg?token=VK55SQZSVD)](https://codecov.io/gh/NCAR/pyDARTdiags)
+[![PyPI version](https://badge.fury.io/py/pydartdiags.svg)](https://pypi.org/project/pydartdiags/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+# pyDARTdiags
+
+pyDARTdiags is a Python library for observation space diagnostics for the Data Assimilation Research Testbed ([DART](https://github.com/NCAR/DART)).
+
+pyDARTdiags is under initial development, so please use caution.
+The MATLAB [observation space diagnostics](https://docs.dart.ucar.edu/en/latest/guide/matlab-observation-space.html) are available through [DART](https://github.com/NCAR/DART).
+
+
+pyDARTdiags can be installed through pip: https://pypi.org/project/pydartdiags/  
+Documentation : https://ncar.github.io/pyDARTdiags/
+
+## Contributing
+Contributions are welcome! If you have a feature request, bug report, or a suggestion, please open an issue on our GitHub repository.
+Please read our [Contributors Guide](https://github.com/NCAR/pyDARTdiags/blob/main/CONTRIBUTING.md) if you would like to contribute to
+pyDARTdiags.
+
+## License
+
+pyDARTdiags is released under the Apache License 2.0. For more details, see the LICENSE file in the root directory of this source tree or visit [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0).

{pydartdiags-0.0.42 → pydartdiags-0.5.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pydartdiags"
-version = "0.0.42"
+version = "0.5.0"
 authors = [
   { name="Helen Kershaw", email="hkershaw@ucar.edu" },
 ]
@@ -20,7 +20,8 @@ dependencies = [
     "pandas>=2.2.0",
     "numpy>=1.26",
     "plotly>=5.22.0",
-    "pyyaml>=6.0.2"
+    "pyyaml>=6.0.2",
+    "matplotlib>=3.9.4"
 ]
 
 [project.urls]

{pydartdiags-0.0.42 → pydartdiags-0.5.0}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name="pydartdiags",
-    version="0.0.41",
+    version="0.0.43",
     packages=find_packages(where="src"),
     package_dir={"": "src"},
     author="Helen Kershaw",

pydartdiags-0.5.0/src/pydartdiags/matplots/matplots.py

@@ -0,0 +1,243 @@
+# SPDX-License-Identifier: Apache-2.0
+from pydartdiags.stats import stats
+import matplotlib.pyplot as plt
+
+# HK @todo color scheme class
+dacolors = ["green", "magenta", "orange", "red"]
+
+
+def plot_profile(obs_seq, levels, type, bias=True, rmse=True, totalspread=True):
+    """
+    plot_profile on the levels for prior and  posterior if present
+       - bias
+       - rmse
+       - totalspread
+
+    Args:
+        obs_seq, levels, type, bias=True, rmse=True, totalspread=True
+
+    Example:
+
+        type = 'RADIOSONDE_U_WIND_COMPONENT'
+        hPalevels = [0.0, 100.0,  150.0, 200.0, 250.0, 300.0, 400.0, 500.0, 700, 850, 925, 1000]
+        levels = [i * 100 for i in hPalevels]
+
+        plot_profile(obs_seq, levels, type, bias=True, rmse=True, totalspread=True)
+
+    """
+
+    # calculate stats and add to dataframe
+    stats.diag_stats(obs_seq.df)
+    qc0 = obs_seq.select_by_dart_qc(0)  # filter only qc=0
+
+    # filter by type
+    qc0 = qc0[qc0["type"] == type]
+    all_df = obs_seq.df[obs_seq.df["type"] == type]
+
+    # grand statistics
+    grand = stats.grand_statistics(qc0)
+
+    # add level bins to the dataframe
+    stats.bin_by_layer(all_df, levels)  # have to count used vs possible
+    stats.bin_by_layer(qc0, levels)
+
+    # aggregate by layer
+    df_pvu = stats.possible_vs_used_by_layer(all_df)  # possible vs used
+    df = stats.layer_statistics(qc0)  # bias, rmse, totalspread for plotting
+
+    fig, ax1 = plt.subplots()
+
+    # convert to hPa HK @todo only for Pressure (Pa)
+    df["midpoint"] = df["midpoint"].astype(float)
+    df["midpoint"] = df["midpoint"] / 100.0
+
+    df_pvu["midpoint"] = df_pvu["midpoint"].astype(float)
+    df_pvu["midpoint"] = df_pvu["midpoint"] / 100.0
+
+    # Add horizontal stripes alternating between gray and white to represent the vertical levels
+    left = df["vlevels"].apply(lambda x: x.left / 100.0)  # todo convert to HPa
+    right = df["vlevels"].apply(lambda x: x.right / 100.0)
+    for i in range(len(left)):
+        color = "gray" if i % 2 == 0 else "white"
+        ax1.axhspan(left.iloc[i], right.iloc[i], color=color, alpha=0.3)
+
+    # Plot the 'bias' data on the first y-axis
+    if bias:
+        ax1.plot(
+            df["prior_bias"],
+            df["midpoint"],
+            color=dacolors[0],
+            marker=".",
+            linestyle="-",
+            label="prior bias",
+        )
+        bias_prior = grand.loc[0, "prior_bias"]
+        if "posterior_bias" in df.columns:
+            ax1.plot(
+                df["posterior_bias"],
+                df["midpoint"],
+                color=dacolors[0],
+                marker=".",
+                linestyle="--",
+                label="posterior bias",
+            )
+            bias_posterior = grand.loc[0, "posterior_bias"]
+    if rmse:
+        ax1.plot(
+            df["prior_rmse"],
+            df["midpoint"],
+            color=dacolors[1],
+            marker=".",
+            linestyle="-",
+            label="prior RMSE",
+        )
+        rmse_prior = grand.loc[0, "prior_rmse"]
+        if "posterior_rmse" in df.columns:
+            ax1.plot(
+                df["posterior_rmse"],
+                df["midpoint"],
+                color=dacolors[1],
+                marker=".",
+                linestyle="--",
+                label="posterior RMSE",
+            )
+            rmse_posterior = grand.loc[0, "posterior_rmse"]
+    if totalspread:
+        ax1.plot(
+            df["prior_totalspread"],
+            df["midpoint"],
+            color=dacolors[2],
+            marker=".",
+            linestyle="-",
+            label="prior totalspread",
+        )
+        totalspread_prior = grand.loc[0, "prior_totalspread"]
+        if "posterior_totalspread" in df.columns:
+            totalspread_posterior = grand.loc[0, "posterior_totalspread"]
+            ax1.plot(
+                df["posterior_totalspread"],
+                df["midpoint"],
+                color=dacolors[2],
+                marker=".",
+                linestyle="--",
+                label="posterior totalspread",
+            )
+
+    ax1.set_ylabel("hPa")
+    ax1.tick_params(axis="y")
+    ax1.set_yticks(df["midpoint"])
+    # ax1.set_yticklabels(df['midpoint'])
+
+    ax3 = ax1.twiny()
+    ax3.set_xlabel("# obs (o=possible; +=assimilated)", color=dacolors[-1])
+    ax3.tick_params(axis="x", colors=dacolors[-1])
+    ax3.plot(
+        df_pvu["possible"],
+        df_pvu["midpoint"],
+        color=dacolors[-1],
+        marker="o",
+        linestyle="",
+        markerfacecolor="none",
+        label="possible",
+    )
+    ax3.plot(
+        df_pvu["used"],
+        df_pvu["midpoint"],
+        color=dacolors[-1],
+        marker="+",
+        linestyle="",
+        label="possible",
+    )
+    ax3.set_xlim(left=0)
+
+    ax1.invert_yaxis()
+    ax1.set_title(type)
+    datalabel = "bias," + " " + "rmse," + " " + "totalspread"
+    ax1.set_xlabel(datalabel)
+
+    lines1, labels1 = ax1.get_legend_handles_labels()
+    ax1.legend(lines1, labels1, loc="upper left", bbox_to_anchor=(1.05, 1))
+
+    ax1.text(
+        0.5, -0.15, obs_seq.file, ha="center", va="center", transform=ax1.transAxes
+    )
+
+    # Add a text box with information below the legend
+    textstr = "Grand statistics:\n"
+    if bias:
+        textstr += f"- prior_bias: {bias_prior:.7f}\n"
+    if rmse:
+        textstr += f"- rmse_prior: {rmse_prior:.7f}\n"
+    if totalspread:
+        textstr += f"- totalspread_prior: {totalspread_prior:.7f}\n"
+    if "posterior_bias" in df.columns:
+        if bias:
+            textstr += f"- posterior_bias: {bias_posterior:.7f}\n"
+        if rmse:
+            textstr += f"- rmse_posterior: {rmse_posterior:.7f}\n"
+        if totalspread:
+            textstr += f"- totalspread_posterior: {totalspread_posterior:.7f}\n"
+
+    props = dict(boxstyle="round", facecolor="wheat", alpha=0.5)
+    ax1.text(
+        1.05,
+        0.5,
+        textstr,
+        transform=ax1.transAxes,
+        fontsize=10,
+        verticalalignment="top",
+        bbox=props,
+    )
+
+    plt.show()
+
+    return fig
+
+
+def plot_rank_histogram(obs_seq, levels, type, ens_size):
+
+    qc0 = obs_seq.select_by_dart_qc(0)  # filter only qc=0
+    qc0 = qc0[qc0["type"] == type]  # filter by type
+    stats.bin_by_layer(qc0, levels)  # bin by level
+
+    midpoints = qc0["midpoint"].unique()
+
+    for level in sorted(midpoints):
+
+        df = qc0[qc0["midpoint"] == level]
+
+        df = stats.calculate_rank(qc0)
+
+        if "posterior_rank" in df.columns:
+            fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 6))
+        else:
+            fig, ax1 = plt.subplots()
+
+        # Plot the prior rank histogram
+        bins = list(range(1, ens_size + 2))
+        ax1.hist(
+            df["prior_rank"], bins=bins, color="blue", alpha=0.5, label="prior rank"
+        )
+        ax1.set_title("Prior Rank Histogram")
+        ax1.set_xlabel("Observation Rank (among ensemble members)")
+        ax1.set_ylabel("Count")
+
+        # Plot the posterior rank histogram if it exists
+        if "posterior_rank" in df.columns:
+            ax2.hist(
+                df["posterior_rank"],
+                bins=bins,
+                color="green",
+                alpha=0.5,
+                label="posterior rank",
+            )
+            ax2.set_title("Posterior Rank Histogram")
+            ax2.set_xlabel("Observation Rank (among ensemble members)")
+            ax2.set_ylabel("Count")
+
+        fig.suptitle(f"{type} at Level {level}", fontsize=14)
+
+        plt.tight_layout(rect=[0, 0.03, 1, 0.95])
+        plt.show()
+
+    return fig