Restructured the documentation

docs/Data_Format.rst

@@ -132,15 +132,17 @@ dataset would be structured as:
 | iN-1, j0   | iN-1, j1   | iN-1, j2   | ....   | iN-1, jP-1   | iN-1, jP-1   |
 +------------+------------+------------+--------+--------------+--------------+
 
-    * If the same voltage sweep were performed twice at each location, the data would be represented as N x 2 P.
-      The data is still saved as a long (2*P) 1D array at each location. The number of spectroscopic dimensions
-      would change from just ['Voltage'] to ['Voltage', 'Cycle'] where the second spectroscopic dimension would
-      account for repetitions of this bias sweep.
-        * **The spectroscopic data would be stored as it would be recorded as volt_0-cycle_0, volt_1-cycle_0.....
-          volt_P-1-cycle_0, volt_0-cycle_1.....volt_P-1-cycle-1. Just like the positions**
-    * Now, if the bias was swept thrice from -1 to +1V and then thrice again from -2 to 2V, the data bacomes
-      N x 2 * 3 P. The data now has two position dimensions (X, Y) and three spectrosocpic dimensions ['Voltage',
-      'Cycle', 'Step']. The data is still saved as a (P * 2 * 3) 1D array at each location.
+* If the same voltage sweep were performed twice at each location, the data would be represented as N x 2 P.
+  The data is still saved as a long (2*P) 1D array at each location. The number of spectroscopic dimensions
+  would change from just ['Voltage'] to ['Voltage', 'Cycle'] where the second spectroscopic dimension would
+  account for repetitions of this bias sweep.
+
+  * **The spectroscopic data would be stored as it would be recorded as volt_0-cycle_0, volt_1-cycle_0.....
+    volt_P-1-cycle_0, volt_0-cycle_1.....volt_P-1-cycle-1. Just like the positions**
+
+* Now, if the bias was swept thrice from -1 to +1V and then thrice again from -2 to 2V, the data bacomes
+  N x 2 * 3 P. The data now has two position dimensions (X, Y) and three spectrosocpic dimensions ['Voltage',
+  'Cycle', 'Step']. The data is still saved as a (P * 2 * 3) 1D array at each location.
 
 -  A collection of ``k`` chosen spectra would also be considered
    ``main`` datasets since the data is still structured as
@@ -357,24 +359,18 @@ comfortably accomodates the pycroscopy format and offers several
 advantageous features.
 
 Information can be stored in HDF5 files in several ways:
-* ``Datasets`` allow the storageo of data matricies and these are the
-  vessels used for storing the ``main``, ``ancillary``, and any extra data
-  matricies
-* ``Datagroups`` are similar to folders in conventional
-  file systems and can be used to store any number of datasets or
+
+* ``Datasets`` allow the storageo of data matricies and these are the vessels used for storing the ``main``,
+  ``ancillary``, and any extra data matricies
+* ``Datagroups`` are similar to folders in conventional file systems and can be used to store any number of datasets or
   datagroups themselves
-* ``Attributes`` are small pieces of
-  information, such as experimental or analytical parameters, that are
-  stored in key-value pairs in the same way as dictionaries in python.
-  Both datagroups and datasets can store attributes.
-* While they are not
-  means to store data, ``Links`` or ``references`` can be used to
-  provide shortcuts and aliases to datasets and datagroups. This feature
-  is especially useful for avoiding duplication of datasets when two
-  ``main`` datasets use the same ancillary datasets.
-
-Among the `various
-benefits <http://extremecomputingtraining.anl.gov/files/2015/03/HDF5-Intro-aug7-130.pdf>`__
+* ``Attributes`` are small pieces of information, such as experimental or analytical parameters, that are stored in
+  key-value pairs in the same way as dictionaries in python.  Both datagroups and datasets can store attributes.
+* While they are not means to store data, ``Links`` or ``references`` can be used to provide shortcuts and aliases to
+  datasets and datagroups. This feature is especially useful for avoiding duplication of datasets when two ``main``
+  datasets use the same ancillary datasets.
+
+Among the `various benefits <http://extremecomputingtraining.anl.gov/files/2015/03/HDF5-Intro-aug7-130.pdf>`__
 that they offer, HDF5 files:
 
 * are readily compatible with high-performance computing facilities
@@ -479,9 +475,10 @@ time)
 
   * ``labels`` - list of strings for the column names like ['Bias', 'Cycle']
   * ``units`` – list of strings for units like ['V', ''].
-  Empty string for dimensionless quantities
+    Empty string for dimensionless quantities
 
 * Optional attributes:
+
   * Region references based on row names
 
 Attributes
@@ -557,7 +554,7 @@ Measurement data
 
    -  Datasets common to Channel\_000 and Channel\_001
 
--  ....
+-  ...
 
 Tool (analysis / processing)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

docs/gen_modules/pycroscopy.analysis.be_loop_model.rst → docs/_autosummary/_autosummary/pycroscopy.analysis.be_loop_model.rst

-pycroscopy.analysis.be_loop_model
-=================================
+pycroscopy\.analysis\.be\_loop\_model
+=====================================
 
 .. automodule:: pycroscopy.analysis.be_loop_model
 
@@ -9,15 +9,12 @@ pycroscopy.analysis.be_loop_model
 
    
    
+   .. rubric:: Classes
 
-   Classes
-   -------
-
+   .. autosummary::
    
-   .. autoclass:: BELoopModel
-      :members:
-   .. autoclass:: LoopOptimize
-      :members:
+      BELoopModel
+      LoopOptimize
    
    
 

docs/gen_modules/pycroscopy.analysis.be_sho_model.rst → docs/_autosummary/_autosummary/pycroscopy.analysis.be_sho_model.rst

-pycroscopy.analysis.be_sho_model
-================================
+pycroscopy\.analysis\.be\_sho\_model
+====================================
 
 .. automodule:: pycroscopy.analysis.be_sho_model
 
@@ -9,13 +9,11 @@ pycroscopy.analysis.be_sho_model
 
    
    
+   .. rubric:: Classes
 
-   Classes
-   -------
-
+   .. autosummary::
    
-   .. autoclass:: BESHOmodel
-      :members:
+      BESHOmodel
    
    
 

docs/_autosummary/_autosummary/pycroscopy.analysis.fit_methods.rst

+pycroscopy\.analysis\.fit\_methods
+==================================
+
+.. automodule:: pycroscopy.analysis.fit_methods
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      BE_Fit_Methods
+      Fit_Methods
+      forc_iv_fit_methods
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.analysis.guess_methods.rst

+pycroscopy\.analysis\.guess\_methods
+====================================
+
+.. automodule:: pycroscopy.analysis.guess_methods
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      r_square
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      GuessMethods
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/gen_modules/_autosummary/pycroscopy.analysis.model.rst → docs/_autosummary/_autosummary/pycroscopy.analysis.model.rst

-pycroscopy.analysis.model
-=========================
+pycroscopy\.analysis\.model
+===========================
 
 .. automodule:: pycroscopy.analysis.model
 
@@ -9,13 +9,11 @@ pycroscopy.analysis.model
 
    
    
+   .. rubric:: Classes
 
-   Classes
-   -------
-
+   .. autosummary::
    
-   .. autoclass:: Model
-      :members:
+      Model
    
    
 

docs/_autosummary/_autosummary/pycroscopy.analysis.optimize.rst

+pycroscopy\.analysis\.optimize
+==============================
+
+.. automodule:: pycroscopy.analysis.optimize
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      targetFuncFit
+      targetFuncGuess
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      Optimize
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.io.be_hdf_utils.rst

+pycroscopy\.io\.be\_hdf\_utils
+==============================
+
+.. automodule:: pycroscopy.io.be_hdf_utils
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      generateTestSpectroscopicData
+      getActiveUDVSsteps
+      getDataIndicesForUDVSstep
+      getForExcitWfm
+      getIndicesforPlotGroup
+      getSliceForExcWfm
+      getSpecSliceForUDVSstep
+      isReshapable
+      isSimpleDataset
+      maxReadPixels
+      reshapeToNsteps
+      reshapeToOneStep
+   
+   
+
+   
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.io.hdf_utils.rst

+pycroscopy\.io\.hdf\_utils
+==========================
+
+.. automodule:: pycroscopy.io.hdf_utils
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      buildReducedSpec
+      calc_chunks
+      checkAndLinkAncillary
+      checkIfMain
+      check_for_old
+      copyAttributes
+      copyRegionRefs
+      copy_main_attributes
+      createRefFromIndices
+      create_empty_dataset
+      create_spec_inds_from_vals
+      findDataset
+      findH5group
+      getAuxData
+      getDataSet
+      getH5DsetRefs
+      getH5GroupRefs
+      getH5RegRefIndices
+      get_all_main
+      get_attr
+      get_attributes
+      get_data_descriptor
+      get_dimensionality
+      get_formatted_labels
+      get_sort_order
+      get_source_dataset
+      get_unit_values
+      linkRefAsAlias
+      linkRefs
+      link_as_main
+      print_tree
+      reducingRefCopy
+      reshape_from_Ndims
+      reshape_to_Ndims
+      simpleRefCopy
+   
+   
+
+   
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/gen_modules/pycroscopy.io.io_hdf5.rst → docs/_autosummary/_autosummary/pycroscopy.io.io_hdf5.rst

-pycroscopy.io.io_hdf5
-=====================
+pycroscopy\.io\.io\_hdf5
+========================
 
 .. automodule:: pycroscopy.io.io_hdf5
 
@@ -9,13 +9,11 @@ pycroscopy.io.io_hdf5
 
    
    
+   .. rubric:: Classes
 
-   Classes
-   -------
-
+   .. autosummary::
    
-   .. autoclass:: ioHDF5
-      :members:
+      ioHDF5
    
    
 

docs/_autosummary/_autosummary/pycroscopy.io.io_utils.rst

+pycroscopy\.io\.io\_utils
+=========================
+
+.. automodule:: pycroscopy.io.io_utils
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      check_dtype
+      check_ssh
+      complex_to_float
+      compound_to_scalar
+      getAvailableMem
+      getTimeStamp
+      realToComplex
+      realToCompound
+      recommendCores
+      transformToReal
+      transformToTargetType
+      uiGetFile
+   
+   
+
+   
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.io.microdata.rst

+pycroscopy\.io\.microdata
+=========================
+
+.. automodule:: pycroscopy.io.microdata
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      MicroData
+      MicroDataGroup
+      MicroDataset
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/gen_modules/_autosummary/pycroscopy.io.translators.rst → docs/_autosummary/_autosummary/pycroscopy.io.translators.rst

-pycroscopy.io.translators
-=========================
+pycroscopy\.io\.translators
+===========================
 
 .. automodule:: pycroscopy.io.translators
 

docs/_autosummary/_autosummary/pycroscopy.processing.atom_finding.rst

+pycroscopy\.processing\.atom\_finding
+=====================================
+
+.. automodule:: pycroscopy.processing.atom_finding
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      apply_binarization_filter
+      apply_binarization_filter_select
+      apply_find
+      apply_gaussian_corr_filter
+      apply_invert_filter
+      apply_select_channel
+      apply_wiener_filter
+      cluster_2d_oleg
+      cluster_2d_oleg_return_geo_center
+      cluster_into_atomic_columns
+      fun_2d_gaussian
+      return_img
+      return_pos
+      run_PCA_atoms
+   
+   
+
+   
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.processing.cluster.rst

+pycroscopy\.processing\.cluster
+===============================
+
+.. automodule:: pycroscopy.processing.cluster
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      reorder_clusters
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      Cluster
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/gen_modules/pycroscopy.processing.decomposition.rst → docs/_autosummary/_autosummary/pycroscopy.processing.decomposition.rst

-pycroscopy.processing.decomposition
-===================================
+pycroscopy\.processing\.decomposition
+=====================================
 
 .. automodule:: pycroscopy.processing.decomposition
 
@@ -9,13 +9,11 @@ pycroscopy.processing.decomposition
 
    
    
+   .. rubric:: Classes
 
-   Classes
-   -------
-
+   .. autosummary::
    
-   .. autoclass:: Decomposition
-      :members:
+      Decomposition
    
    
 

docs/_autosummary/_autosummary/pycroscopy.processing.feature_extraction.rst

+pycroscopy\.processing\.feature\_extraction
+===========================================
+
+.. automodule:: pycroscopy.processing.feature_extraction
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      pickle_keypoints
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      FeatureExtractorParallel
+      FeatureExtractorSerial
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.processing.fft.rst

+pycroscopy\.processing\.fft
+===========================
+
+.. automodule:: pycroscopy.processing.fft
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      downSample
+      getNoiseFloor
+      get_fft_stack
+      harmonicsPassFilter
+      makeLPF
+      noiseBandFilter
+   
+   
+
+   
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.processing.giv_utils.rst

+pycroscopy\.processing\.giv\_utils
+==================================
+
+.. automodule:: pycroscopy.processing.giv_utils
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      bayesian_inference_dataset
+      bayesian_inference_unit
+      do_bayesian_inference
+      plot_bayesian_results
+      plot_bayesian_spot_from_h5
+   
+   
+
+   
+   
+   
+
+   
+   
+   
\ No newline at end of file

docs/_autosummary/_autosummary/pycroscopy.processing.gmode_utils.rst

+pycroscopy\.processing\.gmode\_utils
+====================================
+
+.. automodule:: pycroscopy.processing.gmode_utils
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::