pydartdiags 0.0.3a0__tar.gz → 0.0.4__tar.gz

{pydartdiags-0.0.3a0 → pydartdiags-0.0.4}/PKG-INFO

@@ -1,9 +1,10 @@
 Metadata-Version: 2.3
 Name: pydartdiags
-Version: 0.0.3a0
+Version: 0.0.4
 Summary: Observation Sequence Diagnostics for DART
 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
 Author-email: Helen Kershaw <hkershaw@ucar.edu>
 License-File: LICENSE
 Classifier: License :: OSI Approved :: Apache Software License
@@ -15,30 +16,34 @@ Requires-Dist: pandas>=2.2.0
 Requires-Dist: plotly>=5.22.0
 Description-Content-Type: text/markdown
 
-# pyDARTdiag
+# pyDARTdiags
 
-pyDARTdiag is a python library for obsevation space diagnostics for the Data Assimilation Research Testbed ([DART](https://github.com/NCAR/DART)).
+pyDARTdiags is a python library for obsevation space diagnostics for the Data Assimilation Research Testbed ([DART](https://github.com/NCAR/DART)).
 
-pyDARTdiag is under initial development, so please use caution.
+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).
 
-* obs\_sequence to DataFrame
+
+pyDARTdiags can be installed through pip.  We recommend installing pydartdiags in a virtual enviroment:
+
+
+```
+python3 -m venv dartdiags
+source dartdiags/bin/activate
+pip install pydartdiags
+```
 
 ## Example importing the obs\_sequence and plots modules
 
 ```python
-import sys
-import os
-sys.path.append(os.path.abspath("/Users/hkershaw/DART/Projects/Diagnostics/pyDART/src/obs_sequence"))
-
-import obs_sequence as dart_os
-import plots as dart_plots
+from pydartdiags.obs_sequence import obs_sequence as obs_seq
+from pydartdiags.plots import plots
 ```
 
 ## Examining the dataframe
 
 ```python
-obs_seq = dart_os.obs_sequence('obs_seq.final.ascii')
+obs_seq = obs_seq.obs_sequence('obs_seq.final.ascii')
 obs_seq.df.head()
 ```
 
@@ -196,9 +201,10 @@ obs_seq.df.head()
 </div>
 
 
+Find the numeber of assimilated (used) observations vs. possible observations by type
 
 ```python
-dart_os.possible_vs_used(obs_seq.df)
+obs_seq.possible_vs_used(obs_seq.df)
 ```
 
 <table border="1" class="dataframe">
@@ -349,17 +355,14 @@ dart_os.possible_vs_used(obs_seq.df)
 
 ## Example plotting
 
-
-
 ### rank histogram
 
 * Select only observations that were assimliated (QC === 0).
 * plot the rank histogram
 
 ```python
-
-df_qc0 = dart_os.select_by_dart_qc(obs_seq.df, 0)  # only qc 0
-df_profile, figrmse, figbias = dart_plots.plot_profile(df_qc0, plevels)
+df_qc0 = obs_seq.select_by_dart_qc(obs_seq.df, 0) 
+plots.plot_rank_histogram(df_qc0)
 ```
 ![Rank Histogram](docs/images/rankhist.png)
 
@@ -374,8 +377,8 @@ df_profile, figrmse, figbias = dart_plots.plot_profile(df_qc0, plevels)
 hPalevels = [0.0, 100.0,  150.0, 200.0, 250.0, 300.0, 400.0, 500.0, 700, 850, 925, 1000]# float("inf")] # Pa?
 plevels = [i * 100 for i in hPalevels]
 
-df_qc0 = dart_os.select_by_dart_qc(obs_seq.df, 0)  # only qc 0
-df_profile, figrmse, figbias = dart_plots.plot_profile(df_qc0, plevels)
+df_qc0 = obs_seq.select_by_dart_qc(obs_seq.df, 0)  # only qc 0
+df_profile, figrmse, figbias = plots.plot_profile(df_qc0, plevels)
 ```
 
 ![RMSE Plot](docs/images/rmse.png)

{pydartdiags-0.0.3a0 → pydartdiags-0.0.4}/README.md

@@ -1,27 +1,31 @@
-# pyDARTdiag
+# pyDARTdiags
 
-pyDARTdiag is a python library for obsevation space diagnostics for the Data Assimilation Research Testbed ([DART](https://github.com/NCAR/DART)).
+pyDARTdiags is a python library for obsevation space diagnostics for the Data Assimilation Research Testbed ([DART](https://github.com/NCAR/DART)).
 
-pyDARTdiag is under initial development, so please use caution.
+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).
 
-* obs\_sequence to DataFrame
+
+pyDARTdiags can be installed through pip.  We recommend installing pydartdiags in a virtual enviroment:
+
+
+```
+python3 -m venv dartdiags
+source dartdiags/bin/activate
+pip install pydartdiags
+```
 
 ## Example importing the obs\_sequence and plots modules
 
 ```python
-import sys
-import os
-sys.path.append(os.path.abspath("/Users/hkershaw/DART/Projects/Diagnostics/pyDART/src/obs_sequence"))
-
-import obs_sequence as dart_os
-import plots as dart_plots
+from pydartdiags.obs_sequence import obs_sequence as obs_seq
+from pydartdiags.plots import plots
 ```
 
 ## Examining the dataframe
 
 ```python
-obs_seq = dart_os.obs_sequence('obs_seq.final.ascii')
+obs_seq = obs_seq.obs_sequence('obs_seq.final.ascii')
 obs_seq.df.head()
 ```
 
@@ -179,9 +183,10 @@ obs_seq.df.head()
 </div>
 
 
+Find the numeber of assimilated (used) observations vs. possible observations by type
 
 ```python
-dart_os.possible_vs_used(obs_seq.df)
+obs_seq.possible_vs_used(obs_seq.df)
 ```
 
 <table border="1" class="dataframe">
@@ -332,17 +337,14 @@ dart_os.possible_vs_used(obs_seq.df)
 
 ## Example plotting
 
-
-
 ### rank histogram
 
 * Select only observations that were assimliated (QC === 0).
 * plot the rank histogram
 
 ```python
-
-df_qc0 = dart_os.select_by_dart_qc(obs_seq.df, 0)  # only qc 0
-df_profile, figrmse, figbias = dart_plots.plot_profile(df_qc0, plevels)
+df_qc0 = obs_seq.select_by_dart_qc(obs_seq.df, 0) 
+plots.plot_rank_histogram(df_qc0)
 ```
 ![Rank Histogram](docs/images/rankhist.png)
 
@@ -357,8 +359,8 @@ df_profile, figrmse, figbias = dart_plots.plot_profile(df_qc0, plevels)
 hPalevels = [0.0, 100.0,  150.0, 200.0, 250.0, 300.0, 400.0, 500.0, 700, 850, 925, 1000]# float("inf")] # Pa?
 plevels = [i * 100 for i in hPalevels]
 
-df_qc0 = dart_os.select_by_dart_qc(obs_seq.df, 0)  # only qc 0
-df_profile, figrmse, figbias = dart_plots.plot_profile(df_qc0, plevels)
+df_qc0 = obs_seq.select_by_dart_qc(obs_seq.df, 0)  # only qc 0
+df_profile, figrmse, figbias = plots.plot_profile(df_qc0, plevels)
 ```
 
 ![RMSE Plot](docs/images/rmse.png)

pydartdiags-0.0.4/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

pydartdiags-0.0.4/docs/build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 1e397e888b34fea22bbbc9a10b6321e0
+tags: 645f666f9bcd5a90fca523b33c5a78b7

pydartdiags-0.0.4/docs/build/html/_sources/index.rst.txt

@@ -0,0 +1,40 @@
+.. pydartdiags documentation master file, created by
+   sphinx-quickstart on Mon Aug  5 15:37:19 2024.
+
+.. self adds index.rst to the toctree
+
+pyDARTdiags
+===========
+
+.. toctree::
+    :maxdepth: 3
+    :hidden:
+    
+    self
+    quickstart
+    obs_sequence
+    plots
+
+pyDARTdiags is a python library for obsevation space diagnostics for the Data Assimilation Research Testbed (`DART <https://github.com/NCAR/DART>`_).
+
+
+.. note::
+
+    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>`_.
+
+
+Contributing
+============
+
+Contributions are welcome! If you have a feature request, bug report, or a suggestion, please open an issue on our GitHub repository.
+
+License
+=======
+
+DartLabPlot 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-0.0.4/docs/build/html/_sources/obs_sequence.rst.txt

@@ -0,0 +1,8 @@
+module: obs_sequence
+====================
+
+.. automodule:: obs_sequence
+   :members:
+   :member-order: bysource
+
+

pydartdiags-0.0.4/docs/build/html/_sources/plots.rst.txt

@@ -0,0 +1,6 @@
+module: plots
+====================
+
+.. automodule:: plots
+   :members:
+   :member-order: bysource

pydartdiags-0.0.4/docs/build/html/_sources/quickstart.rst.txt

@@ -0,0 +1,380 @@
+Quickstart
+==========
+
+Installation
+------------
+
+pyDARTdiags can be installed through pip.  We recommend installing pydartdiags in a virtual enviroment:
+
+
+.. code-block :: text
+
+    python3 -m venv dartdiags
+    source dartdiags/bin/activate
+    pip install pydartdiags
+
+
+
+Read an obs_sequence file
+-------------------------
+
+Read an observation sequence file into a DataFrama
+
+.. code-block :: python
+
+    obs_seq = obs_seq.obs_sequence('obs_seq.final.ascii')
+    
+
+Examine the DataFrame
+---------------------
+
+.. code-block :: python
+
+    obs_seq.df.head()
+
+.. raw :: html
+
+    <table border="1" class="dataframe">
+    <thead>
+        <tr style="text-align: right;">
+        <th></th>
+        <th>obs_num</th>
+        <th>observation</th>
+        <th>prior_ensemble_mean</th>
+        <th>prior_ensemble_spread</th>
+        <th>prior_ensemble_member_1</th>
+        <th>prior_ensemble_member_2</th>
+        <th>prior_ensemble_member_3</th>
+        <th>prior_ensemble_member_4</th>
+        <th>prior_ensemble_member_5</th>
+        <th>prior_ensemble_member_6</th>
+        <th>...</th>
+        <th>latitude</th>
+        <th>vertical</th>
+        <th>vert_unit</th>
+        <th>type</th>
+        <th>seconds</th>
+        <th>days</th>
+        <th>time</th>
+        <th>obs_err_var</th>
+        <th>bias</th>
+        <th>sq_err</th>
+        </tr>
+    </thead>
+    <tbody>
+        <tr>
+        <th>0</th>
+        <td>1</td>
+        <td>230.16</td>
+        <td>231.310652</td>
+        <td>0.405191</td>
+        <td>231.304725</td>
+        <td>231.562874</td>
+        <td>231.333915</td>
+        <td>231.297690</td>
+        <td>232.081416</td>
+        <td>231.051063</td>
+        <td>...</td>
+        <td>0.012188</td>
+        <td>23950.0</td>
+        <td>pressure (Pa)</td>
+        <td>ACARS_TEMPERATURE</td>
+        <td>75603</td>
+        <td>153005</td>
+        <td>2019-12-01 21:00:03</td>
+        <td>1.00</td>
+        <td>1.150652</td>
+        <td>1.324001</td>
+        </tr>
+        <tr>
+        <th>1</th>
+        <td>2</td>
+        <td>18.40</td>
+        <td>15.720527</td>
+        <td>0.630827</td>
+        <td>14.217207</td>
+        <td>15.558196</td>
+        <td>15.805599</td>
+        <td>16.594644</td>
+        <td>14.877743</td>
+        <td>16.334438</td>
+        <td>...</td>
+        <td>0.012188</td>
+        <td>23950.0</td>
+        <td>pressure (Pa)</td>
+        <td>ACARS_U_WIND_COMPONENT</td>
+        <td>75603</td>
+        <td>153005</td>
+        <td>2019-12-01 21:00:03</td>
+        <td>6.25</td>
+        <td>-2.679473</td>
+        <td>7.179578</td>
+        </tr>
+        <tr>
+        <th>2</th>
+        <td>3</td>
+        <td>1.60</td>
+        <td>-4.932073</td>
+        <td>0.825899</td>
+        <td>-5.270562</td>
+        <td>-5.955998</td>
+        <td>-4.209766</td>
+        <td>-5.105016</td>
+        <td>-4.669405</td>
+        <td>-4.365305</td>
+        <td>...</td>
+        <td>0.012188</td>
+        <td>23950.0</td>
+        <td>pressure (Pa)</td>
+        <td>ACARS_V_WIND_COMPONENT</td>
+        <td>75603</td>
+        <td>153005</td>
+        <td>2019-12-01 21:00:03</td>
+        <td>6.25</td>
+        <td>-6.532073</td>
+        <td>42.667980</td>
+        </tr>
+        <tr>
+        <th>3</th>
+        <td>4</td>
+        <td>264.16</td>
+        <td>264.060532</td>
+        <td>0.035584</td>
+        <td>264.107192</td>
+        <td>264.097270</td>
+        <td>264.073212</td>
+        <td>264.047718</td>
+        <td>264.074140</td>
+        <td>264.019895</td>
+        <td>...</td>
+        <td>0.010389</td>
+        <td>56260.0</td>
+        <td>pressure (Pa)</td>
+        <td>ACARS_TEMPERATURE</td>
+        <td>75603</td>
+        <td>153005</td>
+        <td>2019-12-01 21:00:03</td>
+        <td>1.00</td>
+        <td>-0.099468</td>
+        <td>0.009894</td>
+        </tr>
+        <tr>
+        <th>4</th>
+        <td>5</td>
+        <td>11.60</td>
+        <td>10.134115</td>
+        <td>0.063183</td>
+        <td>10.067956</td>
+        <td>10.078798</td>
+        <td>10.120263</td>
+        <td>10.084885</td>
+        <td>10.135112</td>
+        <td>10.140610</td>
+        <td>...</td>
+        <td>0.010389</td>
+        <td>56260.0</td>
+        <td>pressure (Pa)</td>
+        <td>ACARS_U_WIND_COMPONENT</td>
+        <td>75603</td>
+        <td>153005</td>
+        <td>2019-12-01 21:00:03</td>
+        <td>6.25</td>
+        <td>-1.465885</td>
+        <td>2.148818</td>
+        </tr>
+    </tbody>
+    </table>
+    <p>5 rows × 97 columns</p>
+
+
+
+Find the numeber of assimilated (used) observations vs. possible observations by type
+
+.. code-block :: python
+
+    obs_seq.possible_vs_used(obs_seq.df)
+
+.. raw :: html
+
+    <table border="1" class="dataframe">
+    <thead>
+        <tr style="text-align: right;">
+        <th></th>
+        <th>type</th>
+        <th>possible</th>
+        <th>used</th>
+        </tr>
+    </thead>
+    <tbody>
+        <tr>
+        <th>0</th>
+        <td>ACARS_TEMPERATURE</td>
+        <td>175429</td>
+        <td>128040</td>
+        </tr>
+        <tr>
+        <th>1</th>
+        <td>ACARS_U_WIND_COMPONENT</td>
+        <td>176120</td>
+        <td>126946</td>
+        </tr>
+        <tr>
+        <th>2</th>
+        <td>ACARS_V_WIND_COMPONENT</td>
+        <td>176120</td>
+        <td>127834</td>
+        </tr>
+        <tr>
+        <th>3</th>
+        <td>AIRCRAFT_TEMPERATURE</td>
+        <td>21335</td>
+        <td>13663</td>
+        </tr>
+        <tr>
+        <th>4</th>
+        <td>AIRCRAFT_U_WIND_COMPONENT</td>
+        <td>21044</td>
+        <td>13694</td>
+        </tr>
+        <tr>
+        <th>5</th>
+        <td>AIRCRAFT_V_WIND_COMPONENT</td>
+        <td>21044</td>
+        <td>13642</td>
+        </tr>
+        <tr>
+        <th>6</th>
+        <td>AIRS_SPECIFIC_HUMIDITY</td>
+        <td>6781</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>7</th>
+        <td>AIRS_TEMPERATURE</td>
+        <td>19583</td>
+        <td>7901</td>
+        </tr>
+        <tr>
+        <th>8</th>
+        <td>GPSRO_REFRACTIVITY</td>
+        <td>81404</td>
+        <td>54626</td>
+        </tr>
+        <tr>
+        <th>9</th>
+        <td>LAND_SFC_ALTIMETER</td>
+        <td>21922</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>10</th>
+        <td>MARINE_SFC_ALTIMETER</td>
+        <td>9987</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>11</th>
+        <td>MARINE_SFC_SPECIFIC_HUMIDITY</td>
+        <td>4196</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>12</th>
+        <td>MARINE_SFC_TEMPERATURE</td>
+        <td>8646</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>13</th>
+        <td>MARINE_SFC_U_WIND_COMPONENT</td>
+        <td>8207</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>14</th>
+        <td>MARINE_SFC_V_WIND_COMPONENT</td>
+        <td>8207</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>15</th>
+        <td>RADIOSONDE_SPECIFIC_HUMIDITY</td>
+        <td>14272</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>16</th>
+        <td>RADIOSONDE_SURFACE_ALTIMETER</td>
+        <td>601</td>
+        <td>0</td>
+        </tr>
+        <tr>
+        <th>17</th>
+        <td>RADIOSONDE_TEMPERATURE</td>
+        <td>29275</td>
+        <td>22228</td>
+        </tr>
+        <tr>
+        <th>18</th>
+        <td>RADIOSONDE_U_WIND_COMPONENT</td>
+        <td>36214</td>
+        <td>27832</td>
+        </tr>
+        <tr>
+        <th>19</th>
+        <td>RADIOSONDE_V_WIND_COMPONENT</td>
+        <td>36214</td>
+        <td>27975</td>
+        </tr>
+        <tr>
+        <th>20</th>
+        <td>SAT_U_WIND_COMPONENT</td>
+        <td>107212</td>
+        <td>82507</td>
+        </tr>
+        <tr>
+        <th>21</th>
+        <td>SAT_V_WIND_COMPONENT</td>
+        <td>107212</td>
+        <td>82647</td>
+        </tr>
+    </tbody>
+    </table>
+    <p>
+
+
+plot a rank histogram
+----------------------
+
+* Select only observations that were assimilated (QC === 0).
+* Plot the rank histogram
+
+.. code-block :: python
+
+    df_qc0 = obs_seq.select_by_dart_qc(obs_seq.df, 0) 
+    plots.plot_rank_histogram(df_qc0)
+
+.. image:: images/rankhist.png
+   :alt: Rank Histogram
+
+plot profiles of RMSE and Bias
+------------------------------
+
+* Choose levels
+* Select only observations that were assimilated (QC === 0).
+* Plot the profiles
+
+.. code-block :: python
+
+    hPalevels = [0.0, 100.0,  150.0, 200.0, 250.0, 300.0, 400.0, 500.0, 700, 850, 925, 1000]  # Pa?
+    plevels = [i * 100 for i in hPalevels]
+
+    df_qc0 = obs_seq.select_by_dart_qc(obs_seq.df, 0)  # only qc 0
+    df_profile, figrmse, figbias = plots.plot_profile(df_qc0, plevels)
+
+.. image:: images/rmse.png
+   :alt: RMSE Plot
+
+.. image:: images/bias.png
+   :alt: Bias Plot
+