Dev/decode my302 (#254)

This PR adds support for decoding digital data from the my320 test chip.
- Added BitOffset (strong type)
- Expand 24 to 32 bit 
- Python bindings for decoding my302
- Improved docs

docs/src/index.rst

@@ -22,21 +22,14 @@ AARE
 
 .. toctree::
     :caption: Python API
-    :maxdepth: 1
-    
-    pyFile
-    pycalibration
-    pyCtbRawFile
-    pyClusterFile
-    pyClusterVector
-    pyCluster
-    pyInterpolation
-    pyJungfrauDataFile
-    pyRawFile
-    pyRawMasterFile
-    pyVarClusterFinder
+    :maxdepth: 3
+    :hidden:
 
+    pycalibration
+    python/cluster/index
+    python/file/index
     pyFit
+    
 
 
 .. toctree::

docs/src/pyCtbRawFile.rst

@@ -1,11 +0,0 @@
-
-CtbRawFile
-============
-
-.. py:currentmodule:: aare
-
-.. autoclass:: CtbRawFile
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :inherited-members:

docs/src/python/cluster/index.rst

@@ -0,0 +1,11 @@
+Cluster & Interpolation
+==========================
+
+.. toctree::
+   :caption: Cluster & Interpolation
+   :maxdepth: 1
+
+   pyCluster
+   pyClusterVector
+   pyInterpolation
+   pyVarClusterFinder

docs/src/python/cluster/pyInterpolation.rst

@@ -21,8 +21,8 @@ Supported are the following :math:`\eta`-functions:
 
 .. py:currentmodule:: aare
 
-.. image:: ../figures/Eta2x2.png
-    :target: ../figures/Eta2x2.png
+.. image:: ../../../figures/Eta2x2.png
+    :target: ../../../figures/Eta2x2.png
     :width: 650px
     :align: center
     :alt: Eta2x2
@@ -35,8 +35,8 @@ Supported are the following :math:`\eta`-functions:
 
 .. autofunction:: calculate_eta2
 
-.. image:: ../figures/Eta2x2Full.png
-    :target: ../figures/Eta2x2Full.png
+.. image:: ../../../figures/Eta2x2Full.png
+    :target: ../../../figures/Eta2x2Full.png
     :width: 650px
     :align: center
     :alt: Eta2x2 Full 
@@ -49,8 +49,8 @@ Supported are the following :math:`\eta`-functions:
 
 .. autofunction:: calculate_full_eta2
 
-.. image:: ../figures/Eta3x3.png
-    :target: ../figures/Eta3x3.png
+.. image:: ../../../figures/Eta3x3.png
+    :target: ../../../figures/Eta3x3.png
     :width: 650px
     :align: center
     :alt: Eta3x3
@@ -63,8 +63,8 @@ Supported are the following :math:`\eta`-functions:
 
 .. autofunction:: calculate_eta3
 
-.. image:: ../figures/Eta3x3Cross.png
-    :target: ../figures/Eta3x3Cross.png
+.. image:: ../../../figures/Eta3x3Cross.png
+    :target: ../../../figures/Eta3x3Cross.png
     :width: 650px
     :align: center
     :alt: Cross Eta3x3

docs/src/python/file/index.rst

@@ -0,0 +1,14 @@
+File I/O
+===================
+
+.. toctree::
+   :caption: File I/O
+   :maxdepth: 1
+
+   pyClusterFile
+   pyCtbRawFile
+   pyFile
+   pyJungfrauDataFile
+   pyRawFile
+   pyRawMasterFile
+   pyTransform

docs/src/python/file/pyCtbRawFile.rst

@@ -0,0 +1,25 @@
+
+CtbRawFile
+============
+
+Read analog, digital and transceiver samples from a raw file containing
+data from the Chip Test Board. Uses :mod:`aare.transform` to decode the 
+data into a format that the user can work with. 
+
+.. code:: python
+
+    import aare
+    from aare.transform import Mythen302Transform
+    my302 = Mythen302Transform(offset = 4)
+
+    with aare.CtbRawFile(fname, transform = my302) as f:
+    for header, data in f:
+       #do something with the data
+
+.. py:currentmodule:: aare
+
+.. autoclass:: CtbRawFile
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :inherited-members:

docs/src/python/file/pyTransform.rst

@@ -0,0 +1,27 @@
+Transform
+===================
+
+The transform module takes data read by :class:`aare.CtbRawFile` and decodes it
+to a useful image format. Depending on detector it supports both analog
+and digital samples. 
+
+For convenience the following transform objects are defined with a short name
+
+.. code:: python
+
+    moench05 = Moench05Transform()
+    moench05_1g = Moench05Transform1g()
+    moench05_old = Moench05TransformOld()
+    matterhorn02 = Matterhorn02Transform()
+    adc_sar_04_64to16 = AdcSar04Transform64to16()
+    adc_sar_05_64to16 = AdcSar05Transform64to16()
+
+.. py:currentmodule:: aare
+
+.. automodule:: aare.transform
+    :members:
+    :undoc-members:
+    :private-members:
+    :special-members: __call__
+    :show-inheritance:
+    :inherited-members: