add simple cell phantom and phantom base class

cellsino/elements/__init__.py

@@ -1,3 +1,3 @@
-from .sphere import Sphere
+from .el_sphere import Sphere
 
 available = [Sphere]

cellsino/phantoms/base_phantom.py

@@ -0,0 +1,22 @@
+class BasePhantom(object):
+    def __init__(self, elements=[]):
+        self.elements = elements
+
+    def __iter__(self):
+        for el in self.elements:
+            yield el
+
+    def append(self, element):
+        self.elements.append(element)
+
+    def transform(self, x=0, y=0, z=0, rot_main=0, rot_in_plane=0,
+                  rot_perp_plane=0):
+        ph = BasePhantom()
+        for el in self:
+            ph.append(el.transform(x=x,
+                                   y=y,
+                                   z=z,
+                                   rot_main=rot_main,
+                                   rot_in_plane=rot_in_plane,
+                                   rot_perp_plane=rot_perp_plane))
+        return ph

cellsino/phantoms/ph_simple_cell.py

@@ -0,0 +1,56 @@
+from .base_phantom import BasePhantom
+from ..elements import Sphere
+
+
+class SimpleCell(BasePhantom):
+    def __init__(self,
+                 cytoplasm_index=1.365,
+                 nucleus_index=1.360,
+                 nucleoli_index=1.387,
+                 medium_index=1.335,
+                 cytoplasm_fl=0,
+                 nucleus_fl=3,
+                 nucleus_shell_fl=10,
+                 nucleoli_fl=0):
+        """Simple cell phantom with cytoplasm, nucleus, and 2 nucleoli
+
+        Configuration:
+        - cytoplasm_index sphere (no fl) containing
+          - nucleus sphere (shell fluorescence) containing
+            - 2 small nucleoli (full fluorescence)
+        """
+        nleoi1 = Sphere(radius=1.5e-6,
+                        position=(-.25, 2, 2),
+                        fl_intensity=nucleoli_fl-nucleus_fl,
+                        n_object=medium_index+(nucleoli_index-nucleus_index),
+                        medium_index=medium_index,
+                        )
+
+        nleoi2 = Sphere(radius=1.5e-6,
+                        position=(+.25, -1, 2),
+                        fl_intensity=nucleoli_fl-nucleus_fl,
+                        n_object=medium_index+(nucleoli_index-nucleus_index),
+                        medium_index=medium_index,
+                        )
+
+        nuclus = Sphere(radius=4e-6,
+                        position=(0, 1, 1),
+                        fl_intensity=nucleus_shell_fl,
+                        n_object=medium_index+(nucleus_index-cytoplasm_index),
+                        medium_index=medium_index,
+                        )
+
+        nuclus_shell = Sphere(radius=3.8e-6,
+                              position=(0, 1, 1),
+                              fl_intensity=nucleus_fl-nucleus_shell_fl,
+                              n_object=medium_index,
+                              medium_index=medium_index,
+                              )
+
+        cyto = Sphere(radius=5.5e-6,
+                      position=(0, 0, 0),
+                      fl_intensity=cytoplasm_fl,
+                      n_object=cytoplasm_index,
+                      medium_index=medium_index,
+                      )
+        self.elements = [nleoi1, nleoi2, nuclus, nuclus_shell, cyto]