feat: add simulation of constant bg fluorescence

RI-imaging · Mar 26, 2019 · b1b2d7a · b1b2d7a
1 parent 47a5047
commit b1b2d7a
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -2,7 +2,7 @@
  - feat: new options for sinogram generation
    - measurement duration (or specific times per angle)
    - specify simulated imaging modalities
-   - simulate photobleaching
+   - simulate photobleaching and background fluorescence
 0.2.1
  - ref: migrate to flimage
 0.2.0

diff --git a/cellsino/fluorescence.py b/cellsino/fluorescence.py
@@ -7,7 +7,7 @@
 class Fluorescence(object):
 
     def __init__(self, phantom, grid_size, pixel_size, displacement=(0, 0),
-                 bleach_factor=1):
+                 bleach_factor=1, background=0):
         """Fluorescence projector
 
         Notes
@@ -27,6 +27,7 @@ def __init__(self, phantom, grid_size, pixel_size, displacement=(0, 0),
         #: bleaching factor (image is multiplied by this factor
         #: to simulate photobleaching)
         self.bleach_factor = bleach_factor
+        self.background = background
 
     def project(self):
         fluor = np.zeros(self.grid_size, dtype=float)
@@ -35,7 +36,7 @@ def project(self):
                 fluor += self.project_sphere(element)
 
         flifull = flimage.FLImage(
-                    data=fluor * self.bleach_factor,
+                    data=fluor * self.bleach_factor + self.background,
                     meta_data={
                         "pixel size": self.pixel_size,
                         }

diff --git a/cellsino/sinogram.py b/cellsino/sinogram.py
@@ -20,7 +20,8 @@ def __init__(self, phantom, wavelength, pixel_size, grid_size):
 
     def compute(self, angles, axis_roll=0, displacements=None,
                 times=3.0, mode=["field", "fluorescence"], propagator="rytov",
-                bleach_decay=0, path=None, count=None, max_count=None):
+                bleach_decay=0, fluorescence_background=0, path=None,
+                count=None, max_count=None):
         """Compute sinogram data
 
         Parameters
@@ -48,6 +49,8 @@ def compute(self, angles, axis_roll=0, displacements=None,
             :data:`cellsino.propagators.available`.
         bleach_decay: float
             Photobleaching decay constant [1/s]
+        fluorescence_background: float
+            Overall fluorescence background signal
         path: str or pathlib.Path
             If not None, the data will be written to this file and
             a :class:`pathlib.Path` object will be returned.
@@ -122,6 +125,7 @@ def compute(self, angles, axis_roll=0, displacements=None,
                                    pixel_size=self.pixel_size,
                                    displacement=displacements[ii],
                                    bleach_factor=bleach_factor,
+                                   background=fluorescence_background,
                                    ).project()
                 fli["time"] = times[ii]