reorganize the directory structure

DAmonitor/base.py

@@ -93,7 +93,7 @@ def load_inv_bkg_ana(files):
     return datasets
 
 
-def query_dataset(dataset):
+def query_dataset(dataset, meta_exclude=None):
     if dataset.groups:
         for grp in dataset.groups:
             print(grp)
@@ -107,7 +107,8 @@ def query_dataset(dataset):
                     print(text + text2.rstrip(","))
             else:
                 for var in dataset.groups[grp].variables:
-                    text += f"{var}, "
+                    if meta_exclude is None or meta_exclude not in var:
+                        text += f"{var}, "
                 print(text.rstrip(","))
     else:
         text = ""
@@ -116,12 +117,13 @@ def query_dataset(dataset):
         print(text.rstrip(","))
 
 
-def query_data(data):
+def query_data(data, meta_exclude=None):
     text = ""
     if data.data:
         data = data.data
     for var in data:
-        text += f"{var}, "
+        if meta_exclude is None or meta_exclude not in var:
+            text += f"{var}, "
     print(text.rstrip(","))
 
 

DAmonitor/obs/__init__.py

@@ -1,7 +1,7 @@
-from .ioda import ioda
+from .obsSpace import obsSpace
 from .fit_rate import fit_rate
 
 __all__ = [
-    'ioda',
+    'obsSpace',
     'fit_rate',
 ]

DAmonitor/obs/ioda.py → DAmonitor/obs/obsSpace.py

@@ -16,10 +16,10 @@ def __getattr__(self, name):
             raise AttributeError(f"No variable '{name}_{self.varname}' found.") from e
 
 
-class ioda:
+class obsSpace:
     def __init__(self, filepath):
         """
-        Initialize an IODA object and load the NetCDF file.
+        Initialize an obsSpace object and load the NetCDF file.
 
         Parameters:
         - filepath (str): Path to the NetCDF file.
@@ -39,8 +39,8 @@ def __init__(self, filepath):
         #
         self._get_metadata()
 
-        # Remove groups, provide direct access to varaibles, such as ioda.t, ioda.q, ioda.u, ioda.v, etc
-        for var in ["airTemperature", "windEastward", "windNorthward", "specificHumidity"]:
+        # Remove groups, provide direct access to varaibles, such as obsSpace.t, obsSpace.q, obsSpace.u, obsSpace.v, etc
+        for var in ["airTemperature", "windEastward", "windNorthward", "specificHumidity", "brightnessTemperature"]:
             self._get_data_by_varname(var)
 
     def get_valid_subset(data, item, condition={"EffectiveQC2": 0}):
@@ -64,8 +64,9 @@ def _get_data_by_varname(self, varname):
         for grp in dataset.groups:
             if dataset.groups[grp].groups:
                 for nestgrp in dataset.groups[grp].groups:  # DiagnosticFlags
-                    data[nestgrp] = dataset.groups[grp].groups[nestgrp].variables[varname][:]
-                    only_has_metadata = False
+                    if varname in dataset.groups[grp].groups[nestgrp].variables:
+                        data[nestgrp] = dataset.groups[grp].groups[nestgrp].variables[varname][:]
+                        only_has_metadata = False
             else:
                 if grp == "MetaData":
                     for var in dataset.groups['MetaData'].variables:
@@ -74,7 +75,7 @@ def _get_data_by_varname(self, varname):
                 elif grp == "ObsError" and varname == "specificHumidity":
                     data["ObsError"] = dataset.groups["ObsError"].variables["relativeHumidity"][:]
                     only_has_metadata = False
-                elif varname == "brightnessTemperature" and (grp == "ObsValue" or grp == "ObsValueAdj"):
+                elif varname == "brightnessTemperature" and (grp == "ObsValue" or grp == "ObsValueAdj") and "brightnessTemperature" in dataset.groups[grp].variables:
                     data[grp] = dataset.groups[grp].variables["radiance"][:]
                     only_has_metadata = False
                 elif varname in dataset.groups[grp].variables:
@@ -92,9 +93,11 @@ def _get_data_by_varname(self, varname):
             self.v = _ObsDF(data)
         elif varname == "specificHumidity":
             self.q = _ObsDF(data)
+        elif varname == "brightnessTemperature":
+            self.bt = _ObsDF(data)
 
     def __getitem__(self, key):
-        # Enable ioda["t"]
+        # Enable obsSpace["t"]
         if key in ["t", "airTemperature"]:
             return self.t
         elif key in ["u", "windEastward"]:
@@ -103,11 +106,13 @@ def __getitem__(self, key):
             return self.u
         elif key in ["q", "specificHumidity"]:
             return self.q
+        elif key in ["bt", "brightnessTemperature"]:
+            return self.bt
         raise KeyError(f"Key '{key}' not found.")
 
     def __getattr__(self, name):
-        # Enable myioda.t (only called if attribute not found normally)
+        # Enable obsSpace.t
         try:
             return self.__getitem__(name)
         except KeyError:
-            raise AttributeError(f"'ioda' object has no attribute or variable '{name}'")
+            raise AttributeError(f"'obsSpace' object has no attribute or variable '{name}'")

DAmonitor/shapes.py

@@ -6,6 +6,7 @@
 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")

docs/_toc.yml

@@ -1,5 +1,6 @@
 # Table of contents
 # Learn more at https://jupyterbook.org/customize/toc.html
+# ****  Be sure to remove the trailing .ipynb or .md  ****
 
 format: jb-book
 root: intro
@@ -10,7 +11,9 @@ parts:
   - file: example
   - file: markdown-notebooks
 
-- caption: demo
+- caption: DA monitor
   chapters:
   - file: notebook_docs/mpas_plotting
     title: mpas-jedi plotting
+  - file: notebook_docs/obs_exploring
+    title: obs exploring

docs/build_book.sh

@@ -4,16 +4,11 @@ doc_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
 #### add new notebooks to the notebooks array
 declare -A notebooks
 notebooks["mpas_plotting.ipynb"]="mpas_plotting.ipynb"
+notebooks["obs_exploring.ipynb"]="obs_exploring.ipynb"
 
 
 ### users usually do not need to make changes below this line
 ### ========================================================================
-doc_repo=$1
-if [[ -z "${doc_repo}" ]]; then
-  echo "Usage: build_book.sh <doc_repo>"
-  exit 1
-fi
-
 set -x
 ### always start from a clean notebook_docs/ directory
 rm -rf ${doc_dir}/notebook_docs
@@ -28,10 +23,30 @@ done
 jupyter-book clean ${doc_dir}
 jupyter-book build ${doc_dir}
 
-### push book to doc_repo
+### push book to book_repo
+# save the origin URL and restore after ghp-import, which has to use the origin remote
 save_origin=$(git remote get-url origin)
 
-git remote set-url origin ${doc_repo}
-ghp-import -n -p -f ${doc_dir}/_build/html
+# get the remote url for current branch and set it as book_repo
+remote=$(git rev-parse --abbrev-ref --symbolic-full-name @{u} | cut -d'/' -f1)
+book_repo=$(git remote get-url ${remote})
+#book_repo= # use this line to overwrite the automatically-detected book_repo
+
+if [[ "${book_repo}" ==  *"NOAA-GSL/pyDAmonitor" ]] \
+   || [[ "${book_repo}" ==  *"pyDAmonitor/pyDAmonitor" ]]; then
+      echo "ERROR: current branch tracks the authoritative repository:"
+      echo "  ${book_repo}"
+      echo "users can ONLY push books to their own forks"
+      exit 1
+fi
 
+# change origin, ghp-import and then restore origin 
+git remote set-url origin ${book_repo}
+ghp-import -n -p -f ${doc_dir}/_build/html
 git remote set-url origin ${save_origin}
+
+### print out helper information
+set +x
+account=$(echo "${book_repo}" | awk -F'[:/]' '{print $(NF-1)}')
+echo -e "\nVisit https://${account}.github.io/pyDAmonitor to check the results"
+echo " (Github action may take a few minutes to render the updated pages)"

docs/intro.md

@@ -9,11 +9,7 @@ MarkDown files can be used to add additional documentation.
 # Table of Contents
 
 - [mpas_plotting Notebook](notebook_docs/mpas_plotting)
-- place holder
-- place holder
-- place holder
-- place holder
-- place holder
+- [obs exploring](notebook_docs/obs_exploring)
 - place holder
 - place holder
 - place holder