Commit 360a5a28 authored by Unknown's avatar Unknown
Browse files

Doc updates

parent 3e895b38
...@@ -9,15 +9,20 @@ pycroscopy\.processing\.svd\_utils ...@@ -9,15 +9,20 @@ pycroscopy\.processing\.svd\_utils
.. autosummary:: .. autosummary::
doSVD
get_component_slice get_component_slice
rebuild_svd rebuild_svd
simplifiedKPCA simplified_kpca
.. rubric:: Classes
.. autosummary::
SVD
......
...@@ -14,6 +14,8 @@ pycroscopy\.viz\.be\_viz\_utils ...@@ -14,6 +14,8 @@ pycroscopy\.viz\.be\_viz\_utils
jupyter_visualize_beps_sho jupyter_visualize_beps_sho
jupyter_visualize_loop_sho_raw_comparison jupyter_visualize_loop_sho_raw_comparison
jupyter_visualize_parameter_maps jupyter_visualize_parameter_maps
plot_1d_spectrum
plot_2d_spectrogram
plot_loop_guess_fit plot_loop_guess_fit
plot_loop_sho_raw_comparison plot_loop_sho_raw_comparison
visualize_sho_results visualize_sho_results
......
pycroscopy\.viz\.jupyter\_utils
===============================
.. automodule:: pycroscopy.viz.jupyter_utils
.. rubric:: Functions
.. autosummary::
simple_ndim_visualizer
\ No newline at end of file
...@@ -9,6 +9,7 @@ pycroscopy\.viz\.plot\_utils ...@@ -9,6 +9,7 @@ pycroscopy\.viz\.plot\_utils
.. autosummary:: .. autosummary::
cbar_for_line_plot
cmap_from_rgba cmap_from_rgba
cmap_hot_desaturated cmap_hot_desaturated
cmap_jet_white_center cmap_jet_white_center
...@@ -17,9 +18,6 @@ pycroscopy\.viz\.plot\_utils ...@@ -17,9 +18,6 @@ pycroscopy\.viz\.plot\_utils
get_cmap_object get_cmap_object
make_linear_alpha_cmap make_linear_alpha_cmap
make_scalar_mappable make_scalar_mappable
plotScree
plot_1d_spectrum
plot_2d_spectrogram
plot_cluster_dendrogram plot_cluster_dendrogram
plot_cluster_h5_group plot_cluster_h5_group
plot_cluster_results_separate plot_cluster_results_separate
...@@ -32,10 +30,10 @@ pycroscopy\.viz\.plot\_utils ...@@ -32,10 +30,10 @@ pycroscopy\.viz\.plot\_utils
plot_loops plot_loops
plot_map plot_map
plot_map_stack plot_map_stack
plot_scree
rainbow_plot rainbow_plot
save_fig_filebox_button save_fig_filebox_button
set_tick_font_size set_tick_font_size
single_img_cbar_plot
......
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.Cluster`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.Cluster``
.. only:: html .. 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 .. raw:: html
...@@ -19,4 +19,4 @@ Examples using ``pycroscopy.Cluster`` ...@@ -19,4 +19,4 @@ Examples using ``pycroscopy.Cluster``
.. only:: not html .. only:: not html
* :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py` * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
...@@ -5,13 +5,13 @@ Examples using ``pycroscopy.MicroDataGroup`` ...@@ -5,13 +5,13 @@ Examples using ``pycroscopy.MicroDataGroup``
.. raw:: html .. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip=""> <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
.. only:: html .. 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 .. raw:: html
...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataGroup`` ...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataGroup``
.. only:: not html .. 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 .. raw:: html
...@@ -57,6 +57,24 @@ Examples using ``pycroscopy.MicroDataGroup`` ...@@ -57,6 +57,24 @@ Examples using ``pycroscopy.MicroDataGroup``
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py` * :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 .. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017"> <div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
......
...@@ -5,13 +5,13 @@ Examples using ``pycroscopy.MicroDataset`` ...@@ -5,13 +5,13 @@ Examples using ``pycroscopy.MicroDataset``
.. raw:: html .. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip=""> <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
.. only:: html .. 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 .. raw:: html
...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataset`` ...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.MicroDataset``
.. only:: not html .. 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 .. raw:: html
...@@ -57,6 +57,24 @@ Examples using ``pycroscopy.MicroDataset`` ...@@ -57,6 +57,24 @@ Examples using ``pycroscopy.MicroDataset``
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py` * :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 .. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017"> <div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
......
Examples using ``pycroscopy.doSVD`` Examples using ``pycroscopy.SVD``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. raw:: html .. raw:: html
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.doSVD`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.doSVD``
.. only:: html .. 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 .. raw:: html
...@@ -19,4 +19,4 @@ Examples using ``pycroscopy.doSVD`` ...@@ -19,4 +19,4 @@ Examples using ``pycroscopy.doSVD``
.. only:: not html .. only:: not html
* :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py` * :ref:`sphx_glr_auto_examples_data_analysis_plot_spectral_unmixing.py`
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.getAuxData`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.getAuxData``
.. only:: html .. 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 .. raw:: html
...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.getAuxData`` ...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.getAuxData``
.. only:: not html .. 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 .. raw:: html
......
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.get_attr`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: html .. 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 .. raw:: html
...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.get_attr`` ...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: not html .. 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 .. raw:: html
......
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.print_tree`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.print_tree``
.. only:: html .. 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 .. raw:: html
...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.print_tree`` ...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.print_tree``
.. only:: not html .. 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 .. raw:: html
......
...@@ -5,13 +5,13 @@ Examples using ``pycroscopy.io.hdf_utils.getH5DsetRefs`` ...@@ -5,13 +5,13 @@ Examples using ``pycroscopy.io.hdf_utils.getH5DsetRefs``
.. raw:: html .. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip=""> <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
.. only:: html .. 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 .. raw:: html
...@@ -19,4 +19,22 @@ Examples using ``pycroscopy.io.hdf_utils.getH5DsetRefs`` ...@@ -19,4 +19,22 @@ Examples using ``pycroscopy.io.hdf_utils.getH5DsetRefs``
.. only:: not html .. 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`
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.ioHDF5`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.ioHDF5``
.. only:: html .. 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 .. raw:: html
...@@ -19,17 +19,17 @@ Examples using ``pycroscopy.ioHDF5`` ...@@ -19,17 +19,17 @@ Examples using ``pycroscopy.ioHDF5``
.. only:: not html .. 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 .. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip=""> <div class="sphx-glr-thumbcontainer" tooltip="**Chris R. Smith** -- cq6@ornl.gov License: MIT">
.. only:: html .. 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 .. raw:: html
...@@ -37,7 +37,7 @@ Examples using ``pycroscopy.ioHDF5`` ...@@ -37,7 +37,7 @@ Examples using ``pycroscopy.ioHDF5``
.. only:: not html .. 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 .. raw:: html
...@@ -75,6 +75,24 @@ Examples using ``pycroscopy.ioHDF5`` ...@@ -75,6 +75,24 @@ Examples using ``pycroscopy.ioHDF5``
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py` * :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 .. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017"> <div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
......
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_cluster_h5_group`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_cluster_h5_group``
.. only:: html .. 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 .. raw:: html
...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.plot_utils.plot_cluster_h5_group`` ...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.plot_utils.plot_cluster_h5_group``
.. only:: not html .. 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 .. raw:: html
......
...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_line_family`` ...@@ -9,9 +9,9 @@ Examples using ``pycroscopy.plot_utils.plot_line_family``
.. only:: html .. 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 .. raw:: html
...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.plot_utils.plot_line_family`` ...@@ -19,7 +19,7 @@ Examples using ``pycroscopy.plot_utils.plot_line_family``
.. only:: not html .. only:: not html
* :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`