don't compress saved arrays for speed; add better option for rendering debugging arrays

lib/imaging.py

@@ -38,7 +38,8 @@ class ImagingData:
 
         arrays_file = io.fresh_filename(T.joinpath("arrays.npz"), overwrite)
         if printflag: print("[imaging] save arrays")
-        np.savez_compressed(arrays_file, **self.arrays)
+        #np.savez_compressed(arrays_file, **self.arrays)
+        np.savez(arrays_file, **self.arrays)
 
         config_file = io.fresh_filename(T.joinpath("config.toml"), overwrite)
         if printflag: print("[imaging] save camera config")
@@ -190,9 +191,9 @@ class FluorescenceData(ImagingData):
         N_bkgd = compute_mot_number(
             self.arrays["background"].astype(np.float64),
             **compute_mot_number_params,
-            k=0
+            k=None
         ) if subtract_bkgd and "background" in self.arrays.keys() else 0.0
-        for label, array in self.arrays.items():
+        for k, (label, array) in enumerate(self.arrays.items()):
             dtype_info = np.iinfo(array.dtype)
             if array.max() >= (dtype_info.max - dtype_info.bits):
                 print(
@@ -200,7 +201,7 @@ class FluorescenceData(ImagingData):
             N = compute_mot_number(
                 array.astype(np.float64),
                 **compute_mot_number_params,
-                k=1
+                k=None
             )
             sx, sy = lls_fit_gaussian(array, _dA)
             self.results = dict() if self.results is None else self.results
@@ -215,15 +216,16 @@ class FluorescenceData(ImagingData):
         return self
 
 def compute_mot_number(image, QE, gain, exposure_time, solid_angle,
-        detuning, intensity_parameter, k=0):
+        detuning, intensity_parameter, k=None):
     H, W = image.shape
     K_h = 3.0
     slice_h = pd.S[int(H / K_h) : int((K_h - 1) * H / K_h)]
     K_w = 3.0
     slice_w = pd.S[int(W / K_w) : int((K_w - 1) * W / K_w)]
     im = image[slice_h, slice_w]
-    #pd.Plotter().imshow(image).savefig(f"image_{k}.png").close()
-    #pd.Plotter().imshow(im).savefig(f"img_{k}.png").close()
+    if k is not None:
+        pd.Plotter().imshow(image).savefig(f"image_{k}.png").close()
+        pd.Plotter().imshow(im).savefig(f"img_{k}.png").close()
     electron_rate = im.astype(np.float64).sum()
     photon_rate = (
         electron_rate