Update nbs

fzhu2e · Jan 25, 2024 · 6f01cc7 · 6f01cc7
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diff --git a/cfr/climate.py b/cfr/climate.py
@@ -550,12 +550,14 @@ def plot(self, **kwargs):
 
             kwargs['title'] = f'{self.da.name}, {date_str}' 
 
-        if len(set(np.diff(self.da.lon))) > 1:
-            # the case when longitudes cross 0 degree
-            fd_plot = self.wrap_lon(mode='180')
-            kwargs['central_longitude'] = 0
-        else:
-            fd_plot = self
+        # if len(set(np.diff(self.da.lon))) > 1:
+        #     # the case when longitudes cross 0 degree
+        #     fd_plot = self.wrap_lon(mode='180')
+        #     kwargs['central_longitude'] = 0
+        # else:
+            # fd_plot = self
+
+        fd_plot = self
 
         _kwargs.update(kwargs)
 

diff --git a/cfr/reconjob.py b/cfr/reconjob.py
@@ -1045,7 +1045,7 @@ def run_graphem(self, save_recon=True, save_dirpath=None, save_filename=None,
             fit_kws (dict): the arguments for :py:meth: `GraphEM.solver.GraphEM.fit`
                 The most important one is "graph_method"; available options include "neighborhood", "glasso", and "hybrid", where
                 "hybrid" means run "neighborhood" first with default `cutoff_radius=1500` to infill the data matrix and then
-                ran "glasso" with default `sp_FF=3, sp_FP=3` to improve the result further.
+                ran "glasso" with default `sp_FF=3, sp_FP=3, sp_PP=3` to improve the result further.
 
         See also:
             cfr.graphem.solver.GraphEM.fit : fitting the GraphEM method
@@ -1074,6 +1074,7 @@ def run_graphem(self, save_recon=True, save_dirpath=None, save_filename=None,
                 'cutoff_radius': 1500,
                 'sp_FF': 3,
                 'sp_FP': 3,
+                'sp_PP': 3,
             }
             fit_kwargs.update(fit_kws)
             if fit_kwargs['graph_method'] in ['neighborhood', 'glasso']:
@@ -1098,7 +1099,7 @@ def run_graphem(self, save_recon=True, save_dirpath=None, save_filename=None,
                     field = self.graphem_solver.field_r[inst],
                     proxy = self.graphem_solver.proxy_r[inst,:])
 
-                G_L.glasso_adj(target_FF=fit_kwargs['sp_FF'], target_FP=fit_kwargs['sp_FP'])
+                G_L.glasso_adj(target_FF=fit_kwargs['sp_FF'], target_FP=fit_kwargs['sp_FP'], target_PP=fit_kwargs['sp_PP'])
                 fit_kwargs.update({'estimate_graph': False, 'graph': G_L.adj})
                 self.graphem_solver.fit(
                     self.graphem_params['field'],
@@ -1235,6 +1236,6 @@ def run_graphem_cfg(self, cfg_path, verbose=False):
             graph_method=self.configs['graph_method'],
             cutoff_radius=self.configs['cutoff_radius'],
             output_indices=self.configs['output_indices'],
-            sp_FF=self.configs['sp_FF'], sp_FP=self.configs['sp_FP'],
+            sp_FF=self.configs['sp_FF'], sp_FP=self.configs['sp_FP'], sp_PP=self.configs['sp_PP'],
             verbose=verbose,
         )
diff --git a/cfr/visual.py b/cfr/visual.py
@@ -336,8 +336,11 @@ def plot_field_map(field_var, lat, lon, levels=50, add_cyclic_point=True,
     if add_cyclic_point:
         if mode == 'latlon':
             field_var_c, lon_c = cutil.add_cyclic_point(field_var, lon)
+            # field_var_c, lon_c = acp(field_var, lon)
+
             if signif_values is not None:
                 signif_values_c, lon_c = cutil.add_cyclic_point(signif_values, lon)
+
             lat_c = lat
         elif mode == 'mesh':
             if len(np.shape(lat)) == 1:
@@ -409,7 +412,8 @@ def plot_field_map(field_var, lat, lon, levels=50, add_cyclic_point=True,
     if add_gridlines:
         ax.gridlines(edgecolor='gray', linestyle=':', crs=transform)
 
-    cmap = plt.get_cmap(cmap)
+    if cmap is not None:
+        cmap = plt.get_cmap(cmap)
     if cmap_under is not None:
         cmap.set_under(cmap_under)
     if cmap_over is not None:

diff --git a/docs/_images/notebooks_graphem-primer_15_0.png b/docs/_images/notebooks_graphem-primer_15_0.png
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diff --git a/docs/_images/notebooks_graphem-real-pages2k_14_0.png b/docs/_images/notebooks_graphem-real-pages2k_14_0.png
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diff --git a/docs/_images/notebooks_graphem-real-pages2k_36_0.png b/docs/_images/notebooks_graphem-real-pages2k_36_0.png
diff --git a/docs/_images/notebooks_graphem-real-pages2k_3_1.png b/docs/_images/notebooks_graphem-real-pages2k_3_1.png
diff --git a/docs/_images/notebooks_graphem-real-pages2k_42_0.png b/docs/_images/notebooks_graphem-real-pages2k_42_0.png
diff --git a/docs/_images/notebooks_graphem-real-pages2k_42_1.png b/docs/_images/notebooks_graphem-real-pages2k_42_1.png
diff --git a/docs/_images/notebooks_graphem-real-pages2k_42_2.png b/docs/_images/notebooks_graphem-real-pages2k_42_2.png
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diff --git a/docs/_images/notebooks_lmr-real-pages2k_19_0.png b/docs/_images/notebooks_lmr-real-pages2k_19_0.png
diff --git a/docs/_images/notebooks_lmr-real-pages2k_28_0.png b/docs/_images/notebooks_lmr-real-pages2k_28_0.png
diff --git a/docs/_images/notebooks_lmr-real-pages2k_29_0.png b/docs/_images/notebooks_lmr-real-pages2k_29_0.png
diff --git a/docs/_images/notebooks_lmr-real-pages2k_32_0.png b/docs/_images/notebooks_lmr-real-pages2k_32_0.png
diff --git a/docs/_images/notebooks_lmr-real-pages2k_5_0.png b/docs/_images/notebooks_lmr-real-pages2k_5_0.png
diff --git a/docsrc/notebooks/test-graphem-primer.ipynb → docs/_sources/notebooks/graphem-primer.ipynb b/docsrc/notebooks/test-graphem-primer.ipynb → docs/_sources/notebooks/graphem-primer.ipynb
diff --git a/docs/_sources/notebooks/graphem-real-pages2k.ipynb b/docs/_sources/notebooks/graphem-real-pages2k.ipynb
diff --git a/docs/_sources/notebooks/lmr-real-pages2k.ipynb b/docs/_sources/notebooks/lmr-real-pages2k.ipynb
diff --git a/docs/_sources/ug-graphem.rst b/docs/_sources/ug-graphem.rst
@@ -4,5 +4,6 @@ GraphEM
 .. toctree::
     :maxdepth: 1
 
+    notebooks/graphem-primer
     notebooks/graphem-real-pages2k
     notebooks/graphem-cli
diff --git a/docs/cg-overview.html b/docs/cg-overview.html
@@ -206,6 +206,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>

diff --git a/docs/cg-updating-docs.html b/docs/cg-updating-docs.html
@@ -205,6 +205,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>

diff --git a/docs/cg-working-with-codebase.html b/docs/cg-working-with-codebase.html
@@ -206,6 +206,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -203,6 +203,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>
@@ -667,6 +668,8 @@ <h2 id="P">P</h2>
         <li><a href="ug-api.html#cfr.proxy.ProxyRecord.plotly">(cfr.proxy.ProxyRecord method)</a>
 </li>
       </ul></li>
+      <li><a href="ug-api.html#cfr.proxy.ProxyDatabase.plotly_concise">plotly_concise() (cfr.proxy.ProxyDatabase method)</a>
+</li>
       <li><a href="ug-api.html#cfr.proxy.ProxyDatabase.plotly_count">plotly_count() (cfr.proxy.ProxyDatabase method)</a>
 </li>
       <li><a href="ug-api.html#cfr.climate.ClimateField.plotly_grid">plotly_grid() (cfr.climate.ClimateField method)</a>

diff --git a/docs/index.html b/docs/index.html
@@ -205,6 +205,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="notebooks/graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>

diff --git a/docs/notebooks/climate-io.html b/docs/notebooks/climate-io.html
@@ -207,6 +207,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>

diff --git a/docs/notebooks/climate-ops.html b/docs/notebooks/climate-ops.html
@@ -207,6 +207,7 @@
 </ul>
 </li>
 <li class="toctree-l1 has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-cli.html">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>

diff --git a/docs/notebooks/graphem-cli.html b/docs/notebooks/graphem-cli.html
@@ -207,6 +207,7 @@
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../ug-graphem.html">GraphEM</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-6" name="toctree-checkbox-6" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-6"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="graphem-primer.html">A primer on GraphEM</a></li>
 <li class="toctree-l2"><a class="reference internal" href="graphem-real-pages2k.html">Reconstructing the tropical Pacific SST with PAGES2k and GraphEM</a></li>
 <li class="toctree-l2 current active"><a class="current reference internal" href="#">Running GraphEM with the Command Line Interface (CLI)</a></li>
 </ul>