Doc updates

docs/_autosummary/_autosummary/pycroscopy.processing.svd_utils.rst

@@ -9,15 +9,20 @@ pycroscopy\.processing\.svd\_utils
 
    .. autosummary::
    
-      doSVD
       get_component_slice
       rebuild_svd
-      simplifiedKPCA
+      simplified_kpca
    
    
 
    
    
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      SVD
+   
    
 
    

docs/_autosummary/_autosummary/pycroscopy.viz.be_viz_utils.rst

@@ -14,6 +14,8 @@ pycroscopy\.viz\.be\_viz\_utils
       jupyter_visualize_beps_sho
       jupyter_visualize_loop_sho_raw_comparison
       jupyter_visualize_parameter_maps
+      plot_1d_spectrum
+      plot_2d_spectrogram
       plot_loop_guess_fit
       plot_loop_sho_raw_comparison
       visualize_sho_results

docs/_autosummary/_autosummary/pycroscopy.viz.jupyter_utils.rst

+pycroscopy\.viz\.jupyter\_utils
+===============================
+
+.. automodule:: pycroscopy.viz.jupyter_utils
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      simple_ndim_visualizer
+   
+   
+
+   
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.viz.plot_utils.rst

@@ -9,6 +9,7 @@ pycroscopy\.viz\.plot\_utils
 
    .. autosummary::
    
+      cbar_for_line_plot
       cmap_from_rgba
       cmap_hot_desaturated
       cmap_jet_white_center
@@ -17,9 +18,6 @@ pycroscopy\.viz\.plot\_utils
       get_cmap_object
       make_linear_alpha_cmap
       make_scalar_mappable
-      plotScree
-      plot_1d_spectrum
-      plot_2d_spectrogram
       plot_cluster_dendrogram
       plot_cluster_h5_group
       plot_cluster_results_separate
@@ -32,10 +30,10 @@ pycroscopy\.viz\.plot\_utils
       plot_loops
       plot_map
       plot_map_stack
+      plot_scree
       rainbow_plot
       save_fig_filebox_button
       set_tick_font_size
-      single_img_cbar_plot
    
    
 

docs/_autosummary/backreferences/pycroscopy.Cluster.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.Cluster``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,4 +19,4 @@ Examples using ``pycroscopy.Cluster``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`

docs/_autosummary/backreferences/pycroscopy.MicroDataGroup.examples

@@ -5,13 +5,13 @@ Examples using ``pycroscopy.MicroDataGroup``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="">
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_microdata_example_thumb.png
+    .. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+        :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
 
 .. raw:: html
 
@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataGroup``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+    * :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
 
 .. raw:: html
 
@@ -57,6 +57,24 @@ Examples using ``pycroscopy.MicroDataGroup``
 
     * :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
 
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
+
+.. only:: html
+
+    .. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
+
+        :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`
+
+.. raw:: html
+
+    </div>
+
+.. only:: not html
+
+    * :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`
+
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">

docs/_autosummary/backreferences/pycroscopy.MicroDataset.examples

@@ -5,13 +5,13 @@ Examples using ``pycroscopy.MicroDataset``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="">
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_microdata_example_thumb.png
+    .. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+        :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
 
 .. raw:: html
 
@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataset``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+    * :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
 
 .. raw:: html
 
@@ -57,6 +57,24 @@ Examples using ``pycroscopy.MicroDataset``
 
     * :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
 
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
+
+.. only:: html
+
+    .. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
+
+        :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`
+
+.. raw:: html
+
+    </div>
+
+.. only:: not html
+
+    * :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`
+
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">

docs/_autosummary/backreferences/pycroscopy.doSVD.examples → docs/_autosummary/backreferences/pycroscopy.SVD.examples

 
 
-Examples using ``pycroscopy.doSVD``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Examples using ``pycroscopy.SVD``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. raw:: html
 
@@ -9,9 +9,9 @@ Examples using ``pycroscopy.doSVD``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,4 +19,4 @@ Examples using ``pycroscopy.doSVD``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`

docs/_autosummary/backreferences/pycroscopy.hdf_utils.getAuxData.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.getAuxData``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.getAuxData``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 

docs/_autosummary/backreferences/pycroscopy.hdf_utils.get_attr.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 

docs/_autosummary/backreferences/pycroscopy.hdf_utils.print_tree.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.print_tree``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.print_tree``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 

docs/_autosummary/backreferences/pycroscopy.io.hdf_utils.getH5DsetRefs.examples

@@ -5,13 +5,13 @@ Examples using ``pycroscopy.io.hdf_utils.getH5DsetRefs``
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="">
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_microdata_example_thumb.png
+    .. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+        :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
 
 .. raw:: html
 
@@ -19,4 +19,22 @@ Examples using ``pycroscopy.io.hdf_utils.getH5DsetRefs``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+    * :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
+
+.. only:: html
+
+    .. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
+
+        :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`
+
+.. raw:: html
+
+    </div>
+
+.. only:: not html
+
+    * :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`

docs/_autosummary/backreferences/pycroscopy.ioHDF5.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.ioHDF5``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,17 +19,17 @@ Examples using ``pycroscopy.ioHDF5``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
-    <div class="sphx-glr-thumbcontainer" tooltip="">
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_microdata_example_thumb.png
+    .. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+        :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
 
 .. raw:: html
 
@@ -37,7 +37,7 @@ Examples using ``pycroscopy.ioHDF5``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_microdata_example.py`
+    * :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_5_microdata.py`
 
 .. raw:: html
 
@@ -75,6 +75,24 @@ Examples using ``pycroscopy.ioHDF5``
 
     * :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
 
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
+
+.. only:: html
+
+    .. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_01_5_microdata_thumb.png
+
+        :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`
+
+.. raw:: html
+
+    </div>
+
+.. only:: not html
+
+    * :ref:`sphx_glr_auto_tutorials_plot_tutorial_01_5_microdata.py`
+
 .. raw:: html
 
     <div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">

docs/_autosummary/backreferences/pycroscopy.plot_utils.plot_cluster_h5_group.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_cluster_h5_group``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,7 +19,7 @@ Examples using ``pycroscopy.plot_utils.plot_cluster_h5_group``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 

docs/_autosummary/backreferences/pycroscopy.plot_utils.plot_line_family.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_line_family``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,7 +19,7 @@ Examples using ``pycroscopy.plot_utils.plot_line_family``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 

docs/_autosummary/backreferences/pycroscopy.plot_utils.plot_loops.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_loops``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,4 +19,4 @@ Examples using ``pycroscopy.plot_utils.plot_loops``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`

docs/_autosummary/backreferences/pycroscopy.plot_utils.plot_map_stack.examples

@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_map_stack``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,4 +19,4 @@ Examples using ``pycroscopy.plot_utils.plot_map_stack``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`

docs/_autosummary/backreferences/pycroscopy.plot_utils.plotScree.examples → docs/_autosummary/backreferences/pycroscopy.plot_utils.plot_scree.examples

 
 
-Examples using ``pycroscopy.plot_utils.plotScree``
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Examples using ``pycroscopy.plot_utils.plot_scree``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 .. raw:: html
 
@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plotScree``
 
 .. only:: html
 
-    .. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
+    .. figure:: /auto_examples/data_analysis/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
 
-        :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+        :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
 
 .. raw:: html
 
@@ -19,4 +19,4 @@ Examples using ``pycroscopy.plot_utils.plotScree``
 
 .. only:: not html
 
-    * :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
+    * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`