Try to get rid of cryst data entirely

dap/algos/streakfind.py

@@ -54,20 +54,20 @@ def calc_streakfinder_analysis(results, data, pf_pixel_mask):
 
     if do_snr:
         # Changes data in-place
-        data = cryst_data.snr[0].copy()
+        data = cryst_data #.snr[0].copy()
 
     try:
         _calc_streakfinder_analysis(results, cryst_data)
     except Exception as error:  # Broad exception - we don't want to break anything here
         results["cbd_error"] = f"Error processing CBD data:\n{error}"
-    print(f"Deleting cryst data;\nmem used before {virtual_memory().used // pow(2, 30)} Gb ")
-    cryst_data.clear()
-    del cryst_data
+    # print(f"Deleting cryst data;\nmem used before {virtual_memory().used // pow(2, 30)} Gb ")
+    # cryst_data.clear()
+    # del cryst_data
     print(f"mem used after {virtual_memory().used // pow(2, 30)} Gb \n")
 
     return data
 
-def _generate_cryst_data(results, data, pf_pixel_mask) -> CrystData:
+def _generate_cryst_data(results, data, pf_pixel_mask):  # -> CrystData:
     params_required = [
         "cbd_whitefield_data_file",
         "cbd_std_data_file",
@@ -80,13 +80,13 @@ def _generate_cryst_data(results, data, pf_pixel_mask) -> CrystData:
 
     whitefield_data_file = results["cbd_whitefield_data_file"]
     std_data_file = results["cbd_std_data_file"]
-    scale_whitefield = results["cbd_scale_whitefield"]
+    # scale_whitefield = results["cbd_scale_whitefield"]
 
     # Using CXI Store specification as default
     whitefield_dataset = results.get("cbd_whitefield_dataset", "entry/crystallography/whitefield")
     std_dataset = results.get("cbd_std_dataset", "entry/crystallography/std")
 
-    num_threads = results.get("cbd_num_threads", DEFAULT_NUM_THREADS)
+    # num_threads = results.get("cbd_num_threads", DEFAULT_NUM_THREADS)
 
     with h5py.File(whitefield_data_file, "r") as hf:
         whitefield = hf[whitefield_dataset][:]
@@ -103,17 +103,16 @@ def _generate_cryst_data(results, data, pf_pixel_mask) -> CrystData:
             mask = hf[mask_dataset][:].astype(bool)
         mask *= pf_pixel_mask
 
-    data = CrystData(
-        data=data[np.newaxis, :],
-        mask=mask,
-        std=std,
-        whitefield=whitefield
+    snr = np.divide(
+        data * mask - whitefield,
+        std,
+        out=np.zeros_like(data),
+        where=(std==0.0)
     )
-    if scale_whitefield:
-        data = data.scale_whitefield(method='median', num_threads=num_threads)
-    
-    data = data.update_snr()
-    return data
+    del whitefield
+    del std
+    del mask
+    return snr
 
 def _calc_streakfinder_analysis(results, cryst_data: CrystData):
     do_streakfinder_analysis = results.get("do_streakfinder_analysis", False)