add rytov and base propagators

cellsino/propagators/__init__.py

@@ -0,0 +1,5 @@
+from .rytov import Rytov
+
+available = [Rytov]
+
+dictionary = {"rytov": Rytov}

cellsino/propagators/base_propagator.py

@@ -0,0 +1,35 @@
+import abc
+
+import numpy as np
+
+from ..elements import Sphere
+
+
+class BasePropagator(object):
+    __metaclass__ = abc.ABCMeta
+
+    def __init__(self, phantom, wavelength, pixel_size, grid_size):
+        """Base propagator
+
+        Notes
+        -----
+        - The origin of the coordinate system is the center of the grid.
+          For even grid sizes, the origin is between two pixels. For odd
+          grid sizes the origin coincides with the center pixel.
+        """
+        self.phantom = phantom
+        self.wavelength = wavelength
+        self.pixel_size = pixel_size
+        self.grid_size = grid_size
+        self.center = np.array(self.grid_size) / 2 - .5
+
+    def propagate(self):
+        field = np.ones(self.grid_size, dtype=np.complex256)
+        for element in self.phantom:
+            if isinstance(element, Sphere):
+                field *= self.propagate_sphere(element)
+        return field
+
+    @abc.abstractmethod
+    def propagate_sphere(self, sphere):
+        pass

cellsino/propagators/rytov.py

@@ -0,0 +1,18 @@
+import qpsphere
+
+from .base_propagator import BasePropagator
+
+
+class Rytov(BasePropagator):
+    """Rytov approximation"""
+
+    def propagate_sphere(self, sphere):
+        center = self.center + sphere.points[0]/self.pixel_size
+        qpi = qpsphere.models.rytov(radius=sphere.radius,
+                                    sphere_index=sphere.object_index,
+                                    medium_index=sphere.medium_index,
+                                    wavelength=self.wavelength,
+                                    pixel_size=self.pixel_size,
+                                    grid_size=self.grid_size,
+                                    center=center)
+        return qpi.field

setup.py

@@ -24,7 +24,8 @@
     license="MIT",
     description=description,
     long_description=open('README.rst').read() if exists('README.rst') else '',
-    install_requires=["qpimage",
+    install_requires=["h5py>=2.7.0",
+                      "qpimage",
                       "qpsphere",
                       "numpy>=1.12.0",
                       ],