added JF frame checker, small cleanup

src/cristallina/utils.py

@@ -3,11 +3,14 @@ import os
 import json
 import re
 from pathlib import Path
-from collections import defaultdict
 
-import requests
+import subprocess
+
+from collections import defaultdict
+import time
 import datetime
 from json import JSONDecodeError
+import requests
 
 import logging
 
@@ -311,6 +314,25 @@ def is_processed_JF_file(filepath, detector="JF16T03V01"):
         raise ValueError(f"{filepath} does not seem to be an Jungfrau file from the detector {detector}.")
     return "meta" in f["data"][detector].keys()
 
+def check_JF_frames(JF_file_path):
+    """ Simple check if all frames in a given Jungfrau .h5 file are OK or if
+        there are missing or invalid frames.
+        
+        Raises an error if invalid frames are found, else returns True.
+    """
+    pattern = r"\.(JF[0-9].*)\.h5"
+    m = re.search(pattern, str(fpath))
+    if m is None:
+        raise LookupError("Cannot match Jungfrau detector name from file path.")
+
+    JF_name = m.groups()[0]
+    
+    with SFDataFiles(JF_file_path) as data:
+        JF = data[JF_name]
+        if JF.nvalid != JF.ntotal:
+            raise ValueError("Jungfrau frames invalid, this should not happen.")
+        else:
+            return True
 
 def get_step_time(step: SFDataFiles):
     """Returns the start and end time as a unix timestamp (in seconds)
@@ -326,26 +348,26 @@ def get_step_time(step: SFDataFiles):
     ) / np.timedelta64(1, "s")
 
 
-# TODO: Clean this up
-import time
-import subprocess
-from pathlib import Path
 
 
-def wait_for_run(run_number, total_length=15):
+
+def wait_for_run(run_number, total_num_steps, snd_file_path="/tmp/CantinaBand3.wav"):
+    """ Busy wait loop until run has completed all steps. Plays sound 
+        when all files are written to disk.
+    """
     base_path = cr.utils.heuristic_extract_base_path()
     data_path = Path(base_path) / f"run{run_number:0>4}/data"
 
     while True:
         pvfiles = data_path.glob("acq*.PVDATA.h5")
         length = len(list(pvfiles))
-        if length == total_length:
+        if length == total_num_steps:
             break
         else:
             print(f"Waiting for run {run_number} to complete, only {length} steps so far ...")
         time.sleep(5)
 
-    subprocess.run(["paplay", "/tmp/CantinaBand3.wav"])
+    subprocess.run(["paplay", snd_file_path])
 
 
 class ROI: