update docs

docs/conf.py

@@ -32,8 +32,8 @@
 sys.path.append(op.abspath('extensions'))
 
 # Mock all dependencies
-install_requires = ["h5py", "numpy", "scipy", "skimage",
-                    "skimage.restoration"]
+install_requires = ["h5py", "numpy", "qpimage",
+                    "skimage.external"]
 
 for mod_name in install_requires:
     sys.modules[mod_name] = mock.Mock()

docs/sec_code_reference.rst

@@ -5,4 +5,3 @@ Code reference
 .. toctree::
   :maxdepth: 2
 
-  userapi

docs/sec_getting_started.rst

@@ -6,4 +6,5 @@ Getting started
   :maxdepth: 2
 
   installation
+  userapi
   examples

docs/userapi.rst

@@ -1,5 +1,42 @@
 ========
 User API
 ========
+Qpformat supports several file formats
+(:py:class:`qpformat.file_formats.formats`), which are
+divided into :py:class:`qpformat.file_formats.SingleData`
+(the experimental data file format contains only one phase image)
+and :py:class:`qpformat.file_formats.SeriesData` (the experimental
+data file format supports multiple phase images).
+From these base classes, all data file formats are derived. The idea
+is that experimental data is not loaded into memory until the
+`get_qpimage` method is called which returns a
+:py:class:`qpimage.QPImage` object.
 
+Basic Usage
+-----------
+The file format type is determined automatically by qpformat.
+If the file format is implemented in qpformat, experimental
+data can be loaded with the :py:func:`qpformat.load_data` method.
 
+.. code-block:: python
+
+   # Obtain a qpformat.file_formats.SingleData object
+   # (the data is not loaded into memory, only the meta data is read)
+   ds = qpformat.load_data(path="/path/to/SID PHA_xxx.tif")
+   # Get the quantitative phase data (a qpimage.QPImage is returned)
+   qpi = ds.get_qpimage()
+
+
+SingleData
+----------
+.. autoclass:: qpformat.file_formats.SeriesData
+    :inherited-members:
+
+SeriesData
+----------
+.. autoclass:: qpformat.file_formats.SeriesData
+    :members:
+
+Constants
+---------
+.. autodata:: qpformat.file_formats.formats

qpformat/file_formats/__init__.py

@@ -1,7 +1,7 @@
 import os
 import os.path as op
 
-from .dataset import SeriesData
+from .dataset import SeriesData, SingleData
 from .series_hdf5_qpimage import SeriesHdf5Qpimage
 from .series_zip_tif_phasics import SeriesZipTifPhasics
 from .single_hdf5_qpimage import SingleHdf5Qpimage