diff --git a/docs/source/datasets.rst b/docs/source/datasets.rst index fade617..35300d4 100644 --- a/docs/source/datasets.rst +++ b/docs/source/datasets.rst @@ -1,7 +1,7 @@ Datasets ======== -.. automodule:: CDTools.datasets +.. automodule:: cdtools.datasets :members: :private-members: diff --git a/docs/source/examples.rst b/docs/source/examples.rst index 8654c0e..da49e99 100644 --- a/docs/source/examples.rst +++ b/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 - diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 23d3607..69a57d9 100644 --- a/docs/source/installation.rst +++ b/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. diff --git a/docs/source/intro.rst b/docs/source/intro.rst index b550ff0..cb5e0ea 100644 --- a/docs/source/intro.rst +++ b/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): diff --git a/docs/source/models.rst b/docs/source/models.rst index 5291f60..34b0ca8 100644 --- a/docs/source/models.rst +++ b/docs/source/models.rst @@ -1,7 +1,7 @@ Models ====== -.. automodule:: CDTools.models +.. automodule:: cdtools.models :members: :private-members: diff --git a/docs/source/tools/analysis.rst b/docs/source/tools/analysis.rst index 4afd115..ff858d1 100644 --- a/docs/source/tools/analysis.rst +++ b/docs/source/tools/analysis.rst @@ -1,5 +1,5 @@ Analysis ======== -.. automodule:: CDTools.tools.analysis +.. automodule:: cdtools.tools.analysis :members: diff --git a/docs/source/tools/data.rst b/docs/source/tools/data.rst index 91bee3f..e1c5116 100644 --- a/docs/source/tools/data.rst +++ b/docs/source/tools/data.rst @@ -1,5 +1,5 @@ Data ==== -.. automodule:: CDTools.tools.data +.. automodule:: cdtools.tools.data :members: diff --git a/docs/source/tools/image_processing.rst b/docs/source/tools/image_processing.rst index e4dec5b..e3f514d 100644 --- a/docs/source/tools/image_processing.rst +++ b/docs/source/tools/image_processing.rst @@ -1,5 +1,5 @@ Image Processing ================ -.. automodule:: CDTools.tools.image_processing +.. automodule:: cdtools.tools.image_processing :members: diff --git a/docs/source/tools/initializers.rst b/docs/source/tools/initializers.rst index 7be9fef..238c925 100644 --- a/docs/source/tools/initializers.rst +++ b/docs/source/tools/initializers.rst @@ -1,5 +1,5 @@ Initializers ============ -.. automodule:: CDTools.tools.initializers +.. automodule:: cdtools.tools.initializers :members: diff --git a/docs/source/tools/interactions.rst b/docs/source/tools/interactions.rst index 8e0c235..cc5802e 100644 --- a/docs/source/tools/interactions.rst +++ b/docs/source/tools/interactions.rst @@ -1,5 +1,5 @@ Interactions ============ -.. automodule:: CDTools.tools.interactions +.. automodule:: cdtools.tools.interactions :members: diff --git a/docs/source/tools/losses.rst b/docs/source/tools/losses.rst index 0dd25ec..6ec8162 100644 --- a/docs/source/tools/losses.rst +++ b/docs/source/tools/losses.rst @@ -1,5 +1,5 @@ Losses ====== -.. automodule:: CDTools.tools.losses +.. automodule:: cdtools.tools.losses :members: diff --git a/docs/source/tools/measurements.rst b/docs/source/tools/measurements.rst index 301236f..0c2a05e 100644 --- a/docs/source/tools/measurements.rst +++ b/docs/source/tools/measurements.rst @@ -1,5 +1,5 @@ Measurements ============ -.. automodule:: CDTools.tools.measurements +.. automodule:: cdtools.tools.measurements :members: diff --git a/docs/source/tools/plotting.rst b/docs/source/tools/plotting.rst index 53512bd..4c83905 100644 --- a/docs/source/tools/plotting.rst +++ b/docs/source/tools/plotting.rst @@ -1,5 +1,5 @@ Plotting ======== -.. automodule:: CDTools.tools.plotting +.. automodule:: cdtools.tools.plotting :members: diff --git a/docs/source/tools/propagators.rst b/docs/source/tools/propagators.rst index 12976bf..b213666 100644 --- a/docs/source/tools/propagators.rst +++ b/docs/source/tools/propagators.rst @@ -1,5 +1,5 @@ Propagators =========== -.. automodule:: CDTools.tools.propagators +.. automodule:: cdtools.tools.propagators :members: diff --git a/src/CDTools/__init__.py b/src/CDToolstemp/__init__.py similarity index 100% rename from src/CDTools/__init__.py rename to src/CDToolstemp/__init__.py diff --git a/src/CDTools/datasets/__init__.py b/src/CDToolstemp/datasets/__init__.py similarity index 100% rename from src/CDTools/datasets/__init__.py rename to src/CDToolstemp/datasets/__init__.py diff --git a/src/CDTools/datasets/base.py b/src/CDToolstemp/datasets/base.py similarity index 100% rename from src/CDTools/datasets/base.py rename to src/CDToolstemp/datasets/base.py diff --git a/src/CDTools/datasets/polarized_ptycho_2d_dataset.py b/src/CDToolstemp/datasets/polarized_ptycho_2d_dataset.py similarity index 100% rename from src/CDTools/datasets/polarized_ptycho_2d_dataset.py rename to src/CDToolstemp/datasets/polarized_ptycho_2d_dataset.py diff --git a/src/CDTools/datasets/ptycho_2d_dataset.py b/src/CDToolstemp/datasets/ptycho_2d_dataset.py similarity index 100% rename from src/CDTools/datasets/ptycho_2d_dataset.py rename to src/CDToolstemp/datasets/ptycho_2d_dataset.py diff --git a/src/CDTools/models/__init__.py b/src/CDToolstemp/models/__init__.py similarity index 100% rename from src/CDTools/models/__init__.py rename to src/CDToolstemp/models/__init__.py diff --git a/src/CDTools/models/base.py b/src/CDToolstemp/models/base.py similarity index 100% rename from src/CDTools/models/base.py rename to src/CDToolstemp/models/base.py diff --git a/src/CDTools/models/bragg_2d_ptycho.py b/src/CDToolstemp/models/bragg_2d_ptycho.py similarity index 100% rename from src/CDTools/models/bragg_2d_ptycho.py rename to src/CDToolstemp/models/bragg_2d_ptycho.py diff --git a/src/CDTools/models/complex_adam.py b/src/CDToolstemp/models/complex_adam.py similarity index 100% rename from src/CDTools/models/complex_adam.py rename to src/CDToolstemp/models/complex_adam.py diff --git a/src/CDTools/models/complex_lbfgs.py b/src/CDToolstemp/models/complex_lbfgs.py similarity index 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