feat: add capability to track progress of sinogram generation

CHANGELOG

@@ -1,3 +1,5 @@
+0.2.0
+ - feat: add capability to track progress of sinogram generation
 0.1.0
  - add basic example to docs 
  - drawing refractive index and fluorescence phantoms

cellsino/phantoms/__init__.py

@@ -1,3 +1,7 @@
 from .ph_simple_cell import SimpleCell
 
-available = [SimpleCell]
+phan_dict = {
+    "simple cell": SimpleCell,
+}
+
+available = sorted(phan_dict.keys())

cellsino/propagators/__init__.py

@@ -1,9 +1,9 @@
 from .pp_rytov import Rytov
 from .pp_projection import Projection
 
-dictionary = {
+prop_dict = {
     "projection": Projection,
     "rytov": Rytov,
 }
 
-available = sorted(dictionary.keys())
+available = sorted(prop_dict.keys())

cellsino/sinogram.py

@@ -5,17 +5,25 @@
 import qpimage
 
 from .fluorescence import Fluorescence
-from .propagators import dictionary as pp_dict
+from .propagators import prop_dict
+from .phantoms import phan_dict
 
 
 class Sinogram(object):
     def __init__(self, phantom, wavelength, pixel_size, grid_size):
-        self.phantom = phantom
+        if isinstance(phantom, str):
+            self.phantom = phan_dict[phantom]()
+        else:
+            self.phantom = phantom
         self.wavelength = wavelength
         self.pixel_size = pixel_size
         self.grid_size = grid_size
 
-    def compute(self, angles, path=None, propagator="rytov"):
+    def compute(self, angles, path=None, propagator="rytov",
+                count=None, max_count=None):
+        if max_count is not None:
+            max_count.value += angles.size
+
         if isinstance(angles, int):
             angles = np.linspace(0, 2*np.pi, angles, endpoint=False)
 
@@ -38,10 +46,10 @@ def compute(self, angles, path=None, propagator="rytov"):
         for ii, ang in enumerate(angles):
             ph = self.phantom.transform(rot_main=ang)
 
-            pp = pp_dict[propagator](phantom=ph,
-                                     grid_size=self.grid_size,
-                                     pixel_size=self.pixel_size,
-                                     wavelength=self.wavelength)
+            pp = prop_dict[propagator](phantom=ph,
+                                       grid_size=self.grid_size,
+                                       pixel_size=self.pixel_size,
+                                       wavelength=self.wavelength)
             qpi = pp.propagate()
             fluor = Fluorescence(phantom=ph,
                                  grid_size=self.grid_size,
@@ -61,6 +69,9 @@ def compute(self, angles, path=None, propagator="rytov"):
                 sino_fields[ii] = qpi.field
                 sino_fluor[ii] = fluor
 
+            if count is not None:
+                count.value += 1
+
         if write:
             return path
         else: