Improved BOZ flat field

• adds low and high threshold on product and ratio of ROIs to calculate flat field correction
• adds default flat field guess for the fit as parameters
• implement hexagonal lattice for DSSC pixels
• breaks left/right symmetry for flat field fitting since zone plate can be slightly rotated
• implements a refine fit with regularization for flat field calculation
• implements dask auto rechunking

Closes #53 (closed) #55 (closed)

src/toolbox_scs/routines/boz.py

@@ -92,8 +92,8 @@ class parameters():
             self.module, drop_intra_darks=True, persist=True)
 
         # make sure to rechunk the arrays
-        self.arr = self.arr.rechunk((100, -1, -1, -1))
-        self.arr_dark = self.arr_dark.rechunk((100, -1, -1, -1))
+        self.arr = self.arr.rechunk(('auto', -1, -1, -1))
+        self.arr_dark = self.arr_dark.rechunk(('auto', -1, -1, -1))
 
     def set_mask(self, arr):
         """Set mask of bad pixels.
@@ -473,7 +473,7 @@ def histogram_module(arr, mask=None):
     if mask is not None:
         w = da.repeat(da.repeat(da.array(mask[None, None, :, :]),
                 arr.shape[1], axis=1), arr.shape[0], axis=0)
-        w = w.rechunk((100, -1, -1, -1))
+        w = w.rechunk(arr.chunks)
         return da.bincount(arr.ravel(), w.ravel(), minlength=512).compute()
     else:
         return da.bincount(arr.ravel(), minlength=512).compute()
@@ -1246,7 +1246,7 @@ def nl_fit(params, domain):
     p0 = np.array([0]*N)
 
     # flat flat_field
-    ff = compute_flat_field_correction(params.rois, params.get_flat_field())
+    ff = compute_flat_field_correction(params.rois, params)
 
     fixed_p = (domain, params.nl_alpha, params.arr_dark, params.arr, params.tid,
         fitrois, params.get_mask(), ff, params.sat_level)