Another commit

MedVisBonn · Nov 12, 2019 · 64e1d1b · 64e1d1b
1 parent 7ce9ebd
commit 64e1d1b
Show file tree

Hide file tree

Showing 36 changed files with 485 additions and 2,616 deletions.
diff --git a/LICENSE b/LICENSE
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-
diff --git a/docs/conf.py b/docs/conf.py
@@ -20,10 +20,12 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
 
 import eyepy
 
+sys.path.insert(0, os.path.abspath(".."))
+
+
 # -- General configuration ---------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -32,22 +34,22 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode", "nbsphinx"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'eyepy'
+project = u"eyepy"
 copyright = u"2019, Olivier Morelle"
 author = u"Olivier Morelle"
 
@@ -70,10 +72,10 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -84,7 +86,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -95,13 +97,13 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'eyepydoc'
+htmlhelp_basename = "eyepydoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -110,15 +112,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -128,21 +127,15 @@
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'eyepy.tex',
-     u'eyepy Documentation',
-     u'Olivier Morelle', 'manual'),
+    (master_doc, "eyepy.tex", u"eyepy Documentation", u"Olivier Morelle", "manual")
 ]
 
 
 # -- Options for manual page output ------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'eyepy',
-     u'eyepy Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "eyepy", u"eyepy Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------
@@ -151,13 +144,13 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'eyepy',
-     u'eyepy Documentation',
-     author,
-     'eyepy',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "eyepy",
+        u"eyepy Documentation",
+        author,
+        "eyepy",
+        "One line description of project.",
+        "Miscellaneous",
+    )
 ]
-
-
-
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -4,7 +4,5 @@ Examples
 
 .. toctree::
    :maxdepth: 2
-
-   examples/rigid_registration
 
-
+   examples/rigid_registration
diff --git a/docs/examples/rigid_registration.ipynb b/docs/examples/rigid_registration.ipynb
diff --git a/docs/index.rst b/docs/index.rst
@@ -8,11 +8,13 @@ Welcome to eyepy's documentation!
    readme
    installation
    usage
+   examples
    modules
    contributing
    authors
    history
 
+
 Indices and tables
 ==================
 * :ref:`genindex`

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -4,4 +4,4 @@ Usage
 
 To use eyepy in a project::
 
-    import eyepy
+    import eyepy as ep
diff --git a/eyepy/__init__.py b/eyepy/__init__.py
@@ -6,6 +6,4 @@
 __email__ = "oli4morelle@gmail.com"
 __version__ = "0.1.0"
 
-from . import io
-from . import preprocess
-from . import register
+from . import io, preprocess, register
diff --git a/eyepy/cli.py b/eyepy/cli.py
@@ -8,12 +8,11 @@
 def main():
     """Console script for eyepy."""
     parser = argparse.ArgumentParser()
-    parser.add_argument('_', nargs='*')
+    parser.add_argument("_", nargs="*")
     args = parser.parse_args()
 
     print("Arguments: " + str(args._))
-    print("Replace this message by putting your code into "
-          "eyepy.cli.main")
+    print("Replace this message by putting your code into " "eyepy.cli.main")
     return 0
 
 

diff --git a/eyepy/io/__init__.py b/eyepy/io/__init__.py
@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 from .he_vol import VolReader
diff --git a/eyepy/io/base.py b/eyepy/io/base.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import abc
 
 
@@ -7,20 +8,21 @@ def __init__(self):
 
     @abc.abstractmethod
     def read(self, filepath):
-        """Returns an OCT object"""
+        """Returns an OCT object."""
         pass
 
     @abc.abstractmethod
     def read_meta(self, filepath):
-        """Returns only the OCT meta data"""
+        """Returns only the OCT meta data."""
         pass
 
     @abc.abstractmethod
     def read_bscans(self, filepath):
-        """Returns only the B-scans"""
+        """Returns only the B-scans."""
         pass
 
     @abc.abstractmethod
     def read_nir(self, filepath):
-        """Returns only the near-infrared fundus reflectance (NIR) acquired by an scanning laser ophthalmoscope (SLO)"""
+        """Returns only the near-infrared fundus reflectance (NIR) acquired by
+        an scanning laser ophthalmoscope (SLO)"""
         pass