re-wrote take_pedestal

slic/daq/diacounter.py

@@ -8,7 +8,7 @@ from ..utils.printing import printable_dict_of_dicts
 from .acquisition import Acquisition
 from .basecounter import BaseCounter
 from .utils import can_create_file, SwissFELPaths
-from .pedestals import find_last_pedestal
+from .pedestals import find_last_pedestal, take_pedestal
 
 
 
@@ -122,6 +122,15 @@ class DIACounter(BaseCounter):
     def get_last_pedestal(self):
         return find_last_pedestal(self.active_clients, self.paths.pede)
 
+    def take_pedestal(self, analyze=True, n_pulses=1000, n_bad_modules=0, freq=25, user=None):
+        instrument = self.instrument
+        pgroup = self.pgroup
+        api_address = self.api_address
+        raw_dir = self.paths.raw
+        res_dir = self.paths.res
+        exptime = EXPTIME[instrument]
+        return take_pedestal(instrument, pgroup, api_address, raw_dir, res_dir, analyze, n_pulses, n_bad_modules, freq, exptime, user)
+
     def __repr__(self):
         clients = self.active_clients
         clients = ", ".join(clients)

slic/daq/pedestals.py

@@ -2,11 +2,14 @@ import os
 from glob import glob
 from datetime import datetime
 from collections import defaultdict
+from jungfrau_utils.scripts.jungfrau_run_pedestals import run as ju_record_raw_pedestal
+
 
 
 TIMESTAMP_FORMAT = "%Y%m%d_%H%M"
 
 
+
 def find_last_pedestal(clients, directory="."):
     clients = set(clients)
     clients = clients - {"bsread"}
@@ -36,7 +39,6 @@ def find_last_pedestal(clients, directory="."):
     return res
 
 
-
 def extract_timestamp(fn):
     fn = strip_folder(fn)
     base = fn.split(".")[0]
@@ -56,61 +58,58 @@ def strip_folder(fn):
 
 
 
+def take_pedestal(instrument, pgroup, api_address, raw_dir, res_dir, analyze_locally, n_pulses, n_bad_modules, freq, exptime, user):
+    make_missing_dir(raw_dir)
+    make_missing_dir(res_dir)
 
+    now = datetime.now().strftime(TIMESTAMP_FORMAT)
+    file_base = "pedestal_" + now
 
+    raw_file_base = raw_dir + file_base
+    res_file_base = res_dir + file_base
 
-
-
-
-
-def take_pedestal(self, n_frames, analyze=True, n_bad_modules=0, update_config=True, freq=25):
-    from jungfrau_utils.scripts.jungfrau_run_pedestals import run as jungfrau_utils_run
-    directory = "/sf/%s/data/p%d/raw/JF_pedestals/" % (self.instrument, self.pgroup)
-    if not os.path.exists(directory):
-        print("Directory %s not existing, AND I CAN NOT CREATE IT, CALL DIMA" % directory)
-        #os.makedirs(directory)
-
-    res_dir = directory.replace("/raw/", "/res/")
-    if not os.path.exists(res_dir):
-        print("Directory %s not existing, creating it" % res_dir)
-        os.makedirs(res_dir)
-        os.chmod(res_dir, 0o775)
-    filename = "pedestal_%s" % datetime.now().strftime("%Y%m%d_%H%M")
     period = 1 / freq
-    jungfrau_utils_run(self.api_address, filename, directory, self.pgroup, period, self.detector_config["exptime"],
-                                 n_frames, 1, analyze, n_bad_modules, self.instrument)
-
-    if update_config:
-        self.pede_file = (directory + filename).replace("raw/", "res/").replace(".h5", ".res.h5")
-        print("Pedestal file updated to %s" % self.pede_file)
-    return self.pede_file
-
-#TODO: ?!?
-    if analyze:
-        pedestals_taken = Path(directory).glob(filename + "*")
-        print(
-            "Analysis of pedestal data is outsourced to batch farm, user credentials required."
-        )
-        user = input("enter user name for analysis on sf batch farm: ")
-        commandstr = [
-            f"ssh {user}@sf-cn-1 source /sf/{self.instrument}/bin/anaconda_env"
-        ]
-        for ped in pedestals_taken:
-            commandstr.append(
-                f"sbatch jungfrau_create_pedestals --filename {ped.as_posix()} --directory {res_dir} --verbosity 4"
-            )
-        os.system("\;".join(commandstr))
-
-
-
-
-
-
-
-
-
+    trigger = 1
 
+    ju_record_raw_pedestal(api_address, file_base, raw_dir, pgroup, period, exptime, n_pulses, trigger, analyze_locally, n_bad_modules, instrument)
 
+    if not analyze_locally:
+        analyze_pedestal_on_cluster(instrument, raw_file_base, res_dir, user)
+
+    return res_file_base
+
+
+def make_missing_dir(d):
+    if os.path.exists(d):
+        return
+
+    msg = "Directory \"{}\" does not exist, creating it...".format(d)
+    print(msg)
+
+    os.makedirs(d)
+    os.chmod(d, 0o775)
+
+
+def analyze_pedestal_on_cluster(instrument, raw_file_base, res_dir, user=None):
+    pedestals_taken = raw_file_base + "*"
+    pedestals_taken = glob(pedestals_taken)
+
+    if not pedestals_taken:
+        return
+
+    if user is None:
+        print("Analysis of raw pedestal data on SF computing nodes requires user credentials.")
+        user = input("Enter user name: ")
+
+    cmd = f"ssh {user}@sf-cn-1 source /sf/{instrument}/bin/anaconda_env"
+    commands = [cmd]
+
+    for ped in pedestals_taken:
+        cmd = f"sbatch jungfrau_create_pedestals --filename {ped} --directory {res_dir} --verbosity 4"
+        commands.append(cmd)
+
+    cmd = "\;".join(commands)
+    os.system(cmd)