Commit d703117e authored by syz's avatar syz
Browse files

Merge remote-tracking branch 'origin/cades_dev' into cades_dev_local

# Conflicts:
#	setup.py
parents 972bc0e5 f314598f
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.getH5DsetRefs``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_02_writing_to_h5_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -19,7 +19,7 @@ Examples using ``pycroscopy.hdf_utils.getH5DsetRefs``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -27,9 +27,9 @@ Examples using ``pycroscopy.hdf_utils.getH5DsetRefs``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_05_data_processing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
......@@ -37,4 +37,40 @@ Examples using ``pycroscopy.hdf_utils.getH5DsetRefs``
.. only:: not html
* :ref:`sphx_glr_auto_examples_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="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath**">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
Examples using ``pycroscopy.hdf_utils.get_all_main``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
......@@ -27,9 +27,9 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_02_writing_to_h5_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -37,7 +37,7 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_02_writing_to_h5.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
......@@ -45,9 +45,9 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_03_multidimensional_data_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
......@@ -55,7 +55,7 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
......@@ -63,9 +63,9 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_04_parallel_computing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_04_parallel_computing_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_04_parallel_computing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_04_parallel_computing.py`
.. raw:: html
......@@ -73,7 +73,7 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_04_parallel_computing.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_04_parallel_computing.py`
.. raw:: html
......@@ -81,9 +81,9 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_05_data_processing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
......@@ -91,4 +91,94 @@ Examples using ``pycroscopy.hdf_utils.get_attr``
.. only:: not html
* :ref:`sphx_glr_auto_examples_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="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath, Chris R. Smith**">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_04_parallel_computing_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_04_parallel_computing.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_04_parallel_computing.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath**">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
Examples using ``pycroscopy.hdf_utils.get_attributes``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
Examples using ``pycroscopy.hdf_utils.get_data_descriptor``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
Examples using ``pycroscopy.hdf_utils.get_dimensionality``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.get_formatted_labels``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_03_multidimensional_data_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
......@@ -19,4 +19,40 @@ Examples using ``pycroscopy.hdf_utils.get_formatted_labels``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.get_sort_order``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_03_multidimensional_data_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
......@@ -19,4 +19,40 @@ Examples using ``pycroscopy.hdf_utils.get_sort_order``
.. only:: not html
* :ref:`sphx_glr_auto_examples_tutorial_03_multidimensional_data.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_03_multidimensional_data.py`
Examples using ``pycroscopy.hdf_utils.get_source_dataset``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
Examples using ``pycroscopy.hdf_utils.get_unit_values``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="11/11/2017">
.. only:: html
.. figure:: /auto_examples/user_tutorials/images/thumb/sphx_glr_plot_tutorial_01_interacting_w_h5_files_thumb.png
:ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_user_tutorials_plot_tutorial_01_interacting_w_h5_files.py`
......@@ -9,9 +9,9 @@ Examples using ``pycroscopy.hdf_utils.linkRefs``
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_tutorial_05_data_processing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_examples_tutorial_05_data_processing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
......@@ -19,4 +19,22 @@ Examples using ``pycroscopy.hdf_utils.linkRefs``
.. only:: not html
* :ref:`sphx_glr_auto_examples_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="**Suhas Somnath**">
.. only:: html
.. figure:: /auto_tutorials/images/thumb/sphx_glr_plot_tutorial_05_data_processing_thumb.png
:ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_tutorials_plot_tutorial_05_data_processing.py`
......@@ -5,13 +5,13 @@ Examples using ``pycroscopy.hdf_utils.print_tree``
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="Conventionally, the h5py package is used to create, read, write, and modify h5 files.">
<div class="sphx-glr-thumbcontainer" tooltip="S. Somnath\ :sup:`1,2`, R. K. Vasudevan\ :sup:`1,3` * :sup:`1` Institute for Functional Imagin...">
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_load_dataset_example_thumb.png
.. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
:ref:`sphx_glr_auto_examples_load_dataset_example.py`
:ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
.. raw:: html
......@@ -19,17 +19,17 @@ Examples using ``pycroscopy.hdf_utils.print_tree``
.. only:: not html
* :ref:`sphx_glr_auto_examples_load_dataset_example.py`
* :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="S. Somnath\ :sup:`1,2`, R. K. Vasudevan\ :sup:`1,3` * :sup:`1` Institute for Functional Imagin...">
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_examples/images/thumb/sphx_glr_plot_spectral_unmixing_thumb.png
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_01_translator_thumb.png
:ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_translator.py`
.. raw:: html
......@@ -37,7 +37,61 @@ Examples using ``pycroscopy.hdf_utils.print_tree``
.. only:: not html
* :ref:`sphx_glr_auto_examples_plot_spectral_unmixing.py`
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_01_translator.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_02_writing_to_h5_thumb.png
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_02_writing_to_h5.py`
.. raw:: html
<div class="sphx-glr-thumbcontainer" tooltip="**Suhas Somnath** 8/8/2017">
.. only:: html
.. figure:: /auto_examples/dev_tutorials/images/thumb/sphx_glr_plot_tutorial_03_multidimensional_data_thumb.png
:ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html
</div>
.. only:: not html
* :ref:`sphx_glr_auto_examples_dev_tutorials_plot_tutorial_03_multidimensional_data.py`
.. raw:: html