Merge remote-tracking branch 'origin/master'

# Conflicts:
#	docs/conf.py
#	eyepy/io/__init__.py
#	eyepy/io/base.py
#	eyepy/io/he_vol.py

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+minimum_pre_commit_version: 1.20.0
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+    -   id: requirements-txt-fixer
+    -   id: fix-encoding-pragma
+    -   id: check-added-large-files
+    -   id: check-docstring-first
+-   repo: https://github.com/asottile/blacken-docs
+    rev: v1.3.0
+    hooks:
+    -   id: blacken-docs
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.4.2
+    hooks:
+    -   id: python-use-type-annotations
+-   repo: https://github.com/myint/docformatter
+    rev: v1.3.1
+    hooks:
+    -   id: docformatter
+-   repo: https://github.com/pre-commit/mirrors-isort
+    rev: v4.3.21
+    hooks:
+    -   id: isort
+-   repo: https://github.com/psf/black
+    rev: 19.10b0
+    hooks:
+    -   id: black

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.
-

docs/examples.rst

@@ -0,0 +1,8 @@
+========
+Examples
+========
+
+.. toctree::
+   :maxdepth: 2
+
+   examples/rigid_registration

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`

docs/usage.rst

@@ -4,4 +4,4 @@ Usage
 
 To use eyepy in a project::
 
-    import eyepy
+    import eyepy as ep

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

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
 
 

eyepy/io/__init__.py

@@ -1 +1,2 @@
+# -*- coding: utf-8 -*-
 from .he_vol import HeyexOct, read_vol

eyepy/io/he_xml.py

@@ -1,73 +1,76 @@
-import untangle
+# -*- coding: utf-8 -*-
 import numpy as np
+import untangle
+
 
 class SpectralisXMLReader(object):
     def __init__(self, path):
         self.obj = untangle.parse(path)
-        
+
     @property
     def version(self):
         self.obj.HEDX.BODY.SWVersion.Version.cdata
-        
+
     @property
     def octs(self):
         images = self.obj.HEDX.BODY.Patient.Study.Series.Image
-        return [i for i in images if i.ImageType.Type == 'OCT']
-    
+        return [i for i in images if i.ImageType.Type == "OCT"]
+
     @property
     def oct_filenames(self):
         octs = self.octs
         return self.get_oct_filenames(octs)
-    
+
     @property
     def localizer_filename(self):
         return self.get_localizer_filename()
+
     @property
     def oct_width(self):
         return int(self.octs[0].OphthalmicAcquisitionContext.Width.cdata)
-    
+
     @property
     def oct_height(self):
         return int(self.octs[0].OphthalmicAcquisitionContext.Height.cdata)
-    
+
     @property
     def oct_n(self):
         return int(len(self.octs))
-
-
-    def get_segmentations(self):    
-
-        self.segmentations = {}        
+
+    def get_segmentations(self):
+
+        self.segmentations = {}
         seg_types = [x.Name for x in self.octs[0].Segmentation.SegLine]
-        
+
         for seg_type in seg_types:
             self.segmentations[seg_type.cdata] = self.get_segmentation(seg_type.cdata)
-        
+
             self.segmentations[seg_type.cdata] *= 255
-            self.segmentations[seg_type.cdata] = self.segmentations[seg_type.cdata].astype(np.uint8)
+            self.segmentations[seg_type.cdata] = self.segmentations[
+                seg_type.cdata
+            ].astype(np.uint8)
         return self.segmentations
-
-
+
     def get_segmentation(self, name):
         seg = np.zeros((self.oct_n, self.oct_height, self.oct_width))
         for i in range(self.oct_n):
             for s in self.octs[i].Segmentation.SegLine:
                 if s.Name.cdata == name:
-                    seg_data = np.array(s.Array.cdata.split(' ')).astype('float')
+                    seg_data = np.array(s.Array.cdata.split(" ")).astype("float")
                     x = np.where(seg_data < 10000)
                     y = np.rint(seg_data[x]).astype(int)
                     seg[i, y, x] = 1
-                    #seg = (seg*255).astype(np.uint8)
-                    
+                    # seg = (seg*255).astype(np.uint8)
+
         return seg
-    
+
     def get_oct_filenames(self, octs):
         names = []
         for o in octs:
-            names.append(o.ImageData.ExamURL.cdata.split('\\')[-1])
+            names.append(o.ImageData.ExamURL.cdata.split("\\")[-1])
         return names
-    
+
     def get_localizer_filename(self):
         images = self.obj.HEDX.BODY.Patient.Study.Series.Image
-        path = [i for i in images if i.ImageType.Type == 'LOCALIZER'][0]
-        return path.ImageData.ExamURL.cdata.split('\\')[-1]
+        path = [i for i in images if i.ImageType.Type == "LOCALIZER"][0]
+        return path.ImageData.ExamURL.cdata.split("\\")[-1]

eyepy/preprocess/__init__.py

@@ -1 +1,10 @@
+# -*- coding: utf-8 -*-
 from .loggabor import mean_phase
+
+
+def center_crop(img, size):
+    center = img.shape[0] // 2, img.shape[1] // 2
+
+    height_range = center[0] - size[0] // 2, center[0] + size[0] // 2
+    width_range = center[1] - size[1] // 2, center[1] + size[1] // 2
+    return img[height_range[0] : height_range[1], width_range[0] : width_range[1], :]