renaming

docs/source/datasets.rst

@@ -1,7 +1,7 @@
 Datasets
 ========
 
-.. automodule:: CDTools.datasets
+.. automodule:: cdtools.datasets
    :members:
    :private-members:
 

docs/source/examples.rst

@@ -94,11 +94,5 @@ First is :code:`analysis.synthesize_reconstructions`. This function takes a stac
 
 Second is :code:`analysis.calc_consistency_prtf`. This function compares the power into various spatial frequencies between a stack of individual reconstructions and a synthesized reconstruction, in analogy with the phase retrieval transfer function. It then outputs a curve analogous to the PRTF, that shows at what spatial frequencies the reconstructions have converged consistently. This result is then plotted as well.
 
-Much of this functionality is duplicated by the analysis script, which will perform much of the same analysis on any saved reconstruction ensemble saved in this format.
-
-.. code-block:: bash
-		
-   $ python -m CDTools.scripts.synthesize example_reconstructions/gold_balls_ensemble.pickle
-
 
 

docs/source/installation.rst

@@ -6,7 +6,7 @@ Step 1: Download
 
 The source code for CDTools is hosted on it's `MIT github page`_. Access to the MIT github page can be granted to any member of the MIT community - if you are not a member, access can be arranged through a guest account on MIT's GitHub enterprise server.
 
-.. _`MIT github page`: https://github.mit.edu/Scattering/CDTools
+.. _`MIT github page`: https://github.mit.edu/Scattering/cdtools
 
 It is recommended that you clone the repository, rather than just downloading the contents, as it remains under development. Cloning the repository will allow you to easily get access to new updates, bug fixes, etc.
 

docs/source/intro.rst

@@ -12,14 +12,14 @@ CDTools is a python library for ptychography and CDI reconstructions, using an A
 .. code-block:: python
 
    # imports
-   import CDTools
+   import cdtools
    from matplotlib import pyplot as plt
 		
    # Load the file
-   dataset = CDTools.datasets.Ptycho2DDataset.from_cxi('ptycho_data.cxi')
+   dataset = cdtools.datasets.Ptycho2DDataset.from_cxi('ptycho_data.cxi')
 
    # Generate a model from the data
-   model = CDTools.models.SimplePtycho.from_dataset(dataset)
+   model = cdtools.models.SimplePtycho.from_dataset(dataset)
 
    # Run a reconstruction
    for loss in model.Adam_optimize(20, dataset):

docs/source/models.rst

@@ -1,7 +1,7 @@
 Models
 ======
 
-.. automodule:: CDTools.models
+.. automodule:: cdtools.models
    :members:
    :private-members:
 

docs/source/tools/analysis.rst

@@ -1,5 +1,5 @@
 Analysis
 ========
 
-.. automodule:: CDTools.tools.analysis
+.. automodule:: cdtools.tools.analysis
    :members:

docs/source/tools/data.rst

@@ -1,5 +1,5 @@
 Data
 ====
 
-.. automodule:: CDTools.tools.data
+.. automodule:: cdtools.tools.data
    :members:

docs/source/tools/image_processing.rst

@@ -1,5 +1,5 @@
 Image Processing
 ================
 
-.. automodule:: CDTools.tools.image_processing
+.. automodule:: cdtools.tools.image_processing
    :members:

docs/source/tools/initializers.rst

@@ -1,5 +1,5 @@
 Initializers
 ============
 
-.. automodule:: CDTools.tools.initializers
+.. automodule:: cdtools.tools.initializers
    :members:

docs/source/tools/interactions.rst

@@ -1,5 +1,5 @@
 Interactions
 ============
 
-.. automodule:: CDTools.tools.interactions
+.. automodule:: cdtools.tools.interactions
    :members:

docs/source/tools/losses.rst

@@ -1,5 +1,5 @@
 Losses
 ======
 
-.. automodule:: CDTools.tools.losses
+.. automodule:: cdtools.tools.losses
    :members:

docs/source/tools/measurements.rst

@@ -1,5 +1,5 @@
 Measurements
 ============
 
-.. automodule:: CDTools.tools.measurements
+.. automodule:: cdtools.tools.measurements
    :members:

docs/source/tools/plotting.rst

@@ -1,5 +1,5 @@
 Plotting
 ========
 
-.. automodule:: CDTools.tools.plotting
+.. automodule:: cdtools.tools.plotting
    :members:

docs/source/tools/propagators.rst

@@ -1,5 +1,5 @@
 Propagators
 ===========
 
-.. automodule:: CDTools.tools.propagators
+.. automodule:: cdtools.tools.propagators
    :members: