Write the model and dataset tutorials, update the dependencies, and various small bug fixes

examples/basic_ptycho_dataset.py

@@ -0,0 +1,69 @@
+from __future__ import division, print_function, absolute_import
+import numpy as np
+import torch as t
+from matplotlib import pyplot as plt
+from CDTools.datasets import CDataset
+from CDTools.tools import data as cdtdata
+
+
+__all__ = ['BasicPtychoDataset']
+
+
+class BasicPtychoDataset(CDataset):
+    """The standard dataset for a 2D ptychography scan"""
+
+    def __init__(self, translations, patterns, *args, **kwargs):
+        """Initialize the dataset from python objects"""
+
+        super(BasicPtychoDataset,self).__init__(*args, **kwargs)
+        self.translations = t.Tensor(translations).clone()
+        self.patterns = t.Tensor(patterns).clone()
+
+    def __len__(self):
+        return self.patterns.shape[0]
+
+    def _load(self, index):
+        return (index, self.translations[index]), self.patterns[index]
+
+
+    def to(self, *args, **kwargs):
+        """Sends the relevant data to the given device and dtype"""
+        super(BasicPtychoDataset,self).to(*args,**kwargs)
+        self.translations = self.translations.to(*args, **kwargs)
+        self.patterns = self.patterns.to(*args, **kwargs)
+
+
+    @classmethod
+    def from_cxi(cls, cxi_file):
+        """Generates a new CDataset from a .cxi file directly"""
+
+        # Generate a base dataset
+        dataset = CDataset.from_cxi(cxi_file)
+        # Mutate the class to this subclass (BasicPtychoDataset)
+        dataset.__class__ = cls
+
+        # Load the data that is only relevant for this class
+        patterns, axes = cdtdata.get_data(cxi_file)
+        translations = cdtdata.get_ptycho_translations(cxi_file)
+
+        # And now re-add it
+        dataset.translations = t.Tensor(translations).clone()
+        dataset.patterns = t.Tensor(patterns).clone()
+
+        return dataset
+
+    
+    def to_cxi(self, cxi_file):
+        """Saves out a BasicPtychoDataset as a .cxi file"""
+
+        super(BasicPtychoDataset,self).to_cxi(cxi_file)
+        cdtdata.add_data(cxi_file, self.patterns, axes=self.axes)
+        cdtdata.add_ptycho_translations(cxi_file, self.translations)
+
+
+    def inspect(self):
+        """Plots a random diffraction pattern"""
+
+        index = np.random.randint(len(self))
+        plt.figure()
+        plt.imshow(self.patterns[index,:,:].cpu().numpy())