Update the docstrings on all the tools files and start laying out the docs for real

examples/MIT_BNL_logo.py

@@ -9,7 +9,6 @@ import pickle
 from time import time
 import datetime
 
-import h5py
 import torch as t
 import numpy as np
 
@@ -18,8 +17,7 @@ import numpy as np
 # Please contact Abe Levitan (alevitan@mit) if you would like access
 filename = '/media/Data Bank/CSX_6_17/Processed_CXIs/79511_p.cxi'
 
-with h5py.File(filename,'r') as f:
-    dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(f)
+dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(filename)
 
 # In this dataset, the edges of the patterns are too noisy and are
 # masked off anyway. We can easily just remove this data instead of

examples/gold_ball_ensemble_ptycho.py

@@ -1,16 +1,13 @@
 from __future__ import division, print_function, absolute_import
 
 import CDTools
-import h5py
 import numpy as np
 import pickle
 from matplotlib import pyplot as plt
 
 filename = 'example_data/AuBalls_700ms_30nmStep_3_6SS_filter.cxi'
 
-with h5py.File(filename,'r') as f:
-    dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(f)
-
+dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(filename)
 
 results = []
 

examples/gold_ball_ptycho.py

@@ -1,15 +1,13 @@
 from __future__ import division, print_function, absolute_import
 
 import CDTools
-import h5py
 import numpy as np
 import pickle
 from matplotlib import pyplot as plt
 
 filename = 'example_data/AuBalls_700ms_30nmStep_3_6SS_filter.cxi'
 
-with h5py.File(filename,'r') as f:
-    dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(f)
+dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(filename)
 
 
 model = CDTools.models.FancyPtycho.from_dataset(dataset, n_modes=2)
@@ -30,6 +28,7 @@ for i, loss in enumerate(model.Adam_optimize(30, dataset, batch_size=100)):
 
 with open('example_reconstructions/gold_balls.pickle', 'wb') as f:
     pickle.dump(model.save_results(dataset),f)
+
     
 model.inspect(dataset)
 dataset.inspect()

examples/simple_ptycho.py

@@ -3,18 +3,12 @@ from __future__ import division, print_function, absolute_import
 import CDTools
 from CDTools.tools import cmath
 from CDTools.tools.plotting import *
-import h5py
-import torch as t
-import numpy as np
 from matplotlib import pyplot as plt
 import pickle
 
-
 filename = 'example_data/AuBalls_700ms_30nmStep_3_6SS_filter.cxi'
 
-with h5py.File(filename,'r') as f:
-    dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(f)
-
+dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(filename)
 
 model = CDTools.models.SimplePtycho.from_dataset(dataset)
 

examples/specular_pinhole_ptycho.py

@@ -18,9 +18,7 @@ import numpy as np
 # Please contact Abe Levitan (alevitan@mit) if you would like access
 filename = '/media/Data Bank/CSX_10_18/Processed_CXIs/110531_p.cxi'
 
-with h5py.File(filename,'r') as f:
-    dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(f)
-
+dataset = CDTools.datasets.Ptycho_2D_Dataset.from_cxi(filename)
 
 model = CDTools.models.FancyPtycho.from_dataset(dataset,
                                                 randomize_ang = np.pi/4,