pyDAmonitor 0.1.0__py3-none-any.whl

DAmonitor/base.py

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+import os
+import sys
+import subprocess
+from netCDF4 import Dataset
+import pandas as pd
+
+
+def source(bash_file, optional=False):
+    """
+    Source a Bash file and capture the environment variables
+    """
+    # check if bash_file exists
+    command = f"source {bash_file} && env"
+    proc = subprocess.Popen(
+        ["bash", "-c", command], stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True
+    )
+    stdout, stderr = proc.communicate()
+    if proc.returncode != 0:
+        if optional:
+            return  # do nothing for optional config files
+        else:
+            raise Exception(f"Error sourcing bash file: {stderr}")
+    env_vars = {}
+    for line in stdout.splitlines():
+        key, _, value = line.partition("=")
+        env_vars[key] = value
+    # Update the current environment
+    os.environ.update(env_vars)
+
+
+def get_run_directory():
+    """Get the run directory, handling both scripts and Jupyter Notebooks."""
+    if "ipykernel" in sys.modules:  # Running in a Jupyter Notebook
+        return os.getcwd()
+    else:  # Running as a script
+        return os.path.dirname(os.path.abspath(__file__))
+
+
+def get_inv_bkg_ana_files(expdir, cdate):
+    source(f"{expdir}/exp.setup")
+    NET = os.getenv("NET")
+    RUN = NET
+    WGF = os.getenv("WGF")
+    TAG = os.getenv("TAG")
+    COMROOT = os.getenv("COMROOT")
+    DATAROOT = os.getenv("DATAROOT")
+    with open(f"{expdir}/VERSION", "r") as file:
+        VERSION = file.readline().strip()
+    # print(NET, RUN, WGF, TAG, VERSION, COMROOT, DATAROOT)
+
+    # find the correct invariant.nc
+    jedivar_log = (
+        f"{COMROOT}/{NET}/{VERSION}/logs/{RUN}.{cdate[:8]}/{cdate[8:10]}/{WGF}/{RUN}_jedivar_{TAG}_{cdate}.log"
+    )
+    end_str = "./invariant.nc"
+    with open(f"{jedivar_log}", "r") as file:
+        for line in file:
+            line = line.strip()
+            if line.endswith(end_str):
+                inv_file = line[:-len(end_str)].split(":", 1)[1].strip()[len("ln -snf"):].strip()
+                break
+    # print(inv_file)
+
+    # find the background file from the prep_ic log file
+    prep_ic_log = (
+        f"{COMROOT}/{NET}/{VERSION}/logs/{RUN}.{cdate[:8]}/{cdate[8:10]}/{WGF}/{RUN}_prep_ic_{TAG}_{cdate}.log"
+    )
+    start_str = "warm start from"
+    with open(f"{prep_ic_log}", "r") as file:
+        for line in file:
+            if line.startswith(start_str):
+                bkg_file = line[len(start_str):].strip()
+                break
+    # print(bkg_file)
+
+    # find the analysis file from the UMBRELLA_PREP_IC
+    ana_file = f"{DATAROOT}/{cdate[:8]}/{RUN}_prep_ic_{cdate[8:10]}_{VERSION}/{WGF}/mpasin.nc"
+    # print(ana_file)
+
+    files = {
+        "inv": inv_file,
+        "bkg": bkg_file,
+        "ana": ana_file,
+    }
+    return files
+
+
+def load_inv_bkg_ana(files):
+    datasets = {}
+    datasets["inv"] = Dataset(files["inv"], "r")
+    datasets["bkg"] = Dataset(files["bkg"], "r")
+    datasets["ana"] = Dataset(files["ana"], "r")
+    return datasets
+
+
+def query_dataset(dataset, meta_exclude=None):
+    if dataset.groups:
+        for grp in dataset.groups:
+            print(grp)
+            text = "    "
+            if dataset.groups[grp].groups:
+                for nestgrp in dataset.groups[grp].groups:
+                    print(text + nestgrp)
+                    text2 = "    "
+                    for var in dataset.groups[grp].groups[nestgrp].variables:
+                        text2 += f"{var}, "
+                    print(text + text2.rstrip(", "))
+            else:
+                for var in dataset.groups[grp].variables:
+                    if meta_exclude is None or meta_exclude not in var:
+                        text += f"{var}, "
+                print(text.rstrip(", "))
+
+    if dataset.variables:
+        text = ""
+        for var in dataset.variables:
+            text += f"{var}, "
+        print(text.rstrip(", "))
+
+
+def query_data(data, meta_exclude=None):
+    text = ""
+    if data.data:
+        data = data.data
+    for var in data:
+        if meta_exclude is None or meta_exclude not in var:
+            text += f"{var}, "
+    print(text.rstrip(", "))
+
+
+def query_obj(obj):
+    return [attr for attr in dir(obj) if not callable(getattr(obj, attr)) and not attr.startswith("_")]
+
+
+def to_dataframe(obsDF):
+    obsDF = obsDF
+    if hasattr(obsDF, "data"):
+        obsDF = obsDF.data
+    return pd.DataFrame(obsDF)
+
+
+def load_figs(*paths):
+    from IPython.display import Image, display
+    imgs = [Image(path) for path in paths]
+    display(*imgs)
+
+
+def aircraft_reject_list_to_df(filepath):
+    dcReject = {}
+    with open(filepath, 'r') as myfile:
+        for line in myfile:
+            if line.strip() and not line.strip().startswith(";"):
+                fields = line.split()
+                if len(fields) >= 17:
+                    tailID = fields[0]  # ID?
+                    if tailID in dcReject:
+                        print(f"duplicate entry: {tailID}")
+                    #
+                    size = len(fields)
+                    fail_reason = ""
+                    for pos in range(17, size):
+                        fail_reason = fail_reason + fields[pos]
+
+                    dcAircraft = {
+                        "tailID": fields[0],
+                        "flagT": fields[1],
+                        "flagW": fields[2],
+                        "flagR": fields[3],
+                        "FSL": fields[4],
+                        "MDCRS": fields[5],
+                        "N": fields[6],
+                        "bs_T": fields[7],  # bs=bias
+                        "std_T": fields[8],
+                        "bs_S": fields[9],  # wind speed ?
+                        "std_S": fields[10],
+                        "bs_D": fields[11],  # wind direction?
+                        "std_D": fields[12],
+                        "bs_W": fields[13],
+                        "std_W": fields[14],
+                        "bs_RH": fields[15],
+                        "std_RH": fields[16],
+                        "fail_reason": fail_reason,
+                    }
+                    #
+                    dcReject[tailID] = dcAircraft
+                else:
+                    print(f"warning: less than 17 columns\n{line}")
+    return pd.DataFrame(dcReject).T.reset_index(drop=True)  # transpose and then drop customized row names

DAmonitor/shapes.py

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+# from holoviews import opts
+import os
+import geoviews as gv
+import geoviews.feature as gf
+import cartopy.crs as ccrs
+import geopandas as gp
+
+pyDAmonitor_ROOT = os.getenv("pyDAmonitor_ROOT")
+
+# common border lines
+coast_lines = gf.coastline(projection=ccrs.PlateCarree(), line_width=1, scale="50m")
+state_lines = gf.states(projection=ccrs.PlateCarree(), line_width=1, line_color='gray', scale="50m")
+counties_gdf = gp.read_file(f"{pyDAmonitor_ROOT}/data/shapes_county/cb_2018_us_county_500k.shp")  # https://www2.census.gov/geo/tiger/GENZ2018/shp/cb_2018_us_county_500k.zip
+county_lines = gv.Polygons(counties_gdf, crs=ccrs.PlateCarree()).opts(fill_alpha=0, line_color='gray', line_width=0.5)
+# county_lines # show the county_lines plot. This step is slow as we will plot many polygons

pydamonitor-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: pyDAmonitor
+Version: 0.1.0
+Summary: Safeguard invaluable DA investments by vigilantly monitoring DA performance
+Author: Junjun Hu, Aiden Pape, Ethan Wiese, Haidao Lin, Sijie Pan, Chunhua Zhou, Liaofan Lin, Terra Ladwig
+Author-email: Guoqing Ge <Guoqing.Ge@noaa.gov>
+Project-URL: Homepage, https://pydamonitor.github.io/docs/intro.html
+Project-URL: Source, https://github.com/pyDAmonitor/pyDAmonitor
+Project-URL: Wiki, https://github.com/pyDAmonitor/pyDAmonitor/wiki
+Project-URL: Tracker, https://github.com/pyDAmonitor/pyDAmonitor/issues
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+[pyDAmonitor Book](https://pyDAmonitor.github.io/docs): showcase plots and results
+
+# pyDAmonitor
+Safeguarding invaluable DA investments by vigilantly monitoring DA performance both in real-time and retrospective scenarios.
+
+# Installation
+```
+git clone https://github.com/pyDAmonitor/pyDAmonitor.git
+conda env create -f pyDAmonitor/environment.yaml
+conda activate pyDAmonitor
+```
+Note: The `pyDAmonitor` Python environment is already installed on `Jet/Hera/Ursa/Gaea/Orion/Hercules/Derecho` and can be loaded with `source pyDAmonitor/ush/load_pyDAmonitor.sh`.  
+Sample data is also staged on these machines for a quick start. If you need the sample data on other platforms, feel free to reach out.
+
+# Details
+Data assimilation (DA) is a critical component of modern weather forecasting and earth system modeling, it enables the integration of atmospheric observations into models to increase forecast accuracy. 
+
+pyDAmonitor automatically reads JEDI (or GSI) diagnostic files and create a comprehensive set of statistics, plots, and maps of key assimilation metrics like OmB (Observation minus Background) and OmA (Observation minus Analysis), innovation distribution, etc. It aims to facilitate and speed up analysis of DA performance in both real-time and retrospective scenarios.
+
+# Links:
+[pyDAmonitor Book](https://pyDAmonitor.github.io/docs): showcase plots and results
+
+[work with pyDAmonitor](https://github.com/pyDAmonitor/pyDAmonitor/wiki/work-with-pyDAmonitor)  
+
+Check [wiki](https://github.com/pyDAmonitor/pyDAmonitor/wiki) for more information

pydamonitor-0.1.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+DAmonitor/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+DAmonitor/base.py,sha256=JtAjGzn_PicyeYMbuFCG-qQOctSKfOrB2GMfk0S2u8M,6301
+DAmonitor/shapes.py,sha256=1wzzkhyoiVQKNnDWfkOS6hhm19d8DHpqrmYF_PLDcrQ,786
+pydamonitor-0.1.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+pydamonitor-0.1.0.dist-info/METADATA,sha256=liJFbABpUuV8_o3GBVPBt2f6dPcFcB4BjF1_goPn5Ak,2233
+pydamonitor-0.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+pydamonitor-0.1.0.dist-info/top_level.txt,sha256=S0XAbUMibf0CXOj26PtTcTgEghtxuHCIgQRsirHfOvE,10
+pydamonitor-0.1.0.dist-info/RECORD,,

pydamonitor-0.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

pydamonitor-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,201 @@
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pydamonitor-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+DAmonitor