Merge branch 'feature/trigger_devel' of github.com:nu-radio/NuRadioMC…

… into feature/trigger_devel
nu-radio · Sep 18, 2023 · eb9a237 · eb9a237
2 parents d2cb3a6 + dee70b0
commit eb9a237
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Showing 16 changed files with 261 additions and 127 deletions.
diff --git a/NuRadioMC/utilities/Veff.py b/NuRadioMC/utilities/Veff.py
@@ -644,7 +644,7 @@ def get_Veff_Aeff_array(data):
     * array of unique trigger names
 
     Examples
-    ---------
+    --------
 
     To plot the full sky effective volume for 'all_triggers' do
 

diff --git a/NuRadioReco/detector/ARA/ara_detector_db.json b/NuRadioReco/detector/ARA/ara_detector_db.json
@@ -1,4 +1,3 @@
-{
 {
 	"_default": {},
 	"channels": {

diff --git a/NuRadioReco/detector/RNO_G/RNO_single_station.json b/NuRadioReco/detector/RNO_G/RNO_single_station.json
@@ -194,7 +194,6 @@
       "ant_rotation_phi": 90.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
-      "cab_time_delay": 19.8,
       "reference_channel": 0,
       "channel_id": 12,
       "station_id": 11
@@ -211,7 +210,6 @@
       "ant_rotation_phi": 90.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
-      "cab_time_delay": 19.8,
       "reference_channel": 0,
       "channel_id": 13,
       "station_id": 11
@@ -228,23 +226,21 @@
       "ant_rotation_phi": 90.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
-      "cab_time_delay": 19.8,
       "reference_channel": 0,
       "channel_id": 14,
       "station_id": 11
     },
     "15": {
       "amp_type": "rno_surface",
       "ant_comment": "second arm south-east from DAQ, north-east position in arm, pointing side-downwards",
-      "ant_orientation_phi": 240.0,
+      "ant_orientation_phi": 120.0,
       "ant_orientation_theta": 135.0,
       "ant_position_x": -10.276,
       "ant_position_y": -4.2,
       "ant_position_z": -2.0,
-      "ant_rotation_phi": 330.0,
+      "ant_rotation_phi": 210.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
-      "cab_time_delay": 19.8,
       "reference_channel": 0,
       "channel_id": 15,
       "station_id": 11
@@ -258,10 +254,9 @@
       "ant_position_x": -9.526,
       "ant_position_y": -5.5,
       "ant_position_z": -2.0,
-      "ant_rotation_phi": 330.0,
+      "ant_rotation_phi": 210.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
-      "cab_time_delay": 19.8,
       "reference_channel": 0,
       "channel_id": 16,
       "station_id": 11
@@ -270,12 +265,12 @@
     "17": {
       "amp_type": "rno_surface",
       "ant_comment": "second arm south-east from DAQ, south-west position in arm, pointing side-downwards",
-      "ant_orientation_phi": 60.0,
+      "ant_orientation_phi": 300.0,
       "ant_orientation_theta": 135.0,
       "ant_position_x": -8.776,
       "ant_position_y": -6.8,
       "ant_position_z": -2,
-      "ant_rotation_phi": 330.0,
+      "ant_rotation_phi": 210.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
       "reference_channel": 0,
@@ -286,12 +281,12 @@
     "18": {
       "amp_type": "rno_surface",
       "ant_comment": "third arm south-west from DAQ, south-east position in arm, pointing side-downwards",
-      "ant_orientation_phi": 120.0,
+      "ant_orientation_phi": 240.0,
       "ant_orientation_theta": 135.0,
       "ant_position_x": 8.776,
       "ant_position_y": -6.8,
       "ant_position_z": -2.0,
-      "ant_rotation_phi": 210.0,
+      "ant_rotation_phi": 330.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
       "reference_channel": 0,
@@ -306,7 +301,7 @@
       "ant_position_x": 9.526,
       "ant_position_y": -5.5,
       "ant_position_z": -2.0,
-      "ant_rotation_phi": 210.0,
+      "ant_rotation_phi": 330.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
       "reference_channel": 0,
@@ -316,12 +311,12 @@
     "20": {
       "amp_type": "rno_surface",
       "ant_comment": "third arm south-west from DAQ, north-west position in arm, pointing side-downwards",
-      "ant_orientation_phi": 300.0,
+      "ant_orientation_phi": 60.0,
       "ant_orientation_theta": 135.0,
-      "ant_position_x": -10.276,
-      "ant_position_y": 4.2,
+      "ant_position_x": 10.276,
+      "ant_position_y": -4.2,
       "ant_position_z": -2.0,
-      "ant_rotation_phi": 210.0,
+      "ant_rotation_phi": 330.0,
       "ant_rotation_theta": 90.0,
       "ant_type": "createLPDA_100MHz_InfFirn_n1.4",
       "reference_channel": 0,
@@ -381,7 +376,8 @@
       "pos_northing": 0.0,
       "pos_site": "summit",
       "station_id": 11,
-      "station_type": null
+      "station_type": null,
+      "reference_station": 11
     }
   }
 }
diff --git a/NuRadioReco/detector/antenna_models_hash.json b/NuRadioReco/detector/antenna_models_hash.json
@@ -16,7 +16,6 @@
   "dip7cm_z200m_InFirn_RG.pkl": "49ea79abe0784f216ffc4c88db540785a38b87d9",
   "dip7cm_InfAir.pkl": "407ab67708d750c1c0e6bb83f4a3b41168fc7d1b",
   "dip7cm_z270mm_InAir.pkl": "a669d71b79d653c4ea8eb6ab3cbb17bb9026ff9d",
-	"dip7cm_z260mm_InFirn_RG.pkl": "d72fe75ae0f16f9e40d69796aa015e528735d2ec",
   "dip7cm_z1m_InAir.pkl": "1c5e4f65bd15b227fb2eebe1e61c1813509ebd97",
   "dip7cm_z1m_InAir_RG_NearHorizontalHD.pkl": "6a08c240e8162b8193da91e1528d301f9a017e3a",
   "dip7cm_z1m_InAir_RG_NearHorizontalHD2.pkl": "e880c00f3087ed3b3f8276d78645b4ea13217721",
@@ -42,16 +41,13 @@
   "createLPDA_100MHz_z1cm_InAir_RG.pkl": "9202fa4842792b241366b38cd9a358c03f83acbd",
 	"XFDTD_Hpol_150mmHole_n1.78.pkl": "cfa1e1d1ddbd146ca3b89c580e137e22300551c4",
 	"XFDTD_Vpol_CrossFeed_150mmHole_n1.78.pkl": "5d87513779cf2cb5d3309a9bb89dbb163d656114",
-        "trislot_RNOG.pkl": "29ef63bc9f25da743dd85d33e5645fc6330f6675",
-        "RNOG_vpol_v1_n1.73.pkl": "4bd0b5941b31c6c39fd6b438f005075b025fee8d",
-        "RNOG_vpol_v1_n1.4.pkl": "1b8be66b64f241d26e34567167318aa85c396f2a", 
-        "RNOG_vpol_4inch_half_1.73.pkl":
-        "f08d263233503f79e5be10c18bc7587b8b421c1d", 
-        "RNOG_vpol_4inch_center_1.73.pkl":
-        "5f429ed9ed08175a7f75fd44422367d2278bf2e1", 
-        "RNOG_vpol_4inch_wall_1.73.pkl":
-        "da24017eb80f7a68348a674be2c527457fe19992", 
-        "RNOG_quadslot_v1_1.74.pkl":
-        "e9c4946dd2176489249c862f32ef272ab627dc28", 
-        "RNOG_quadslot_v2_1.74.pkl": "b99d69578f8e7c006dcce3de51e26c4f463872b8"
+  "trislot_RNOG.pkl": "29ef63bc9f25da743dd85d33e5645fc6330f6675",
+  "RNOG_vpol_v1_n1.73.pkl": "4bd0b5941b31c6c39fd6b438f005075b025fee8d",
+  "RNOG_vpol_v1_n1.4.pkl": "1b8be66b64f241d26e34567167318aa85c396f2a", 
+  "RNOG_vpol_4inch_half_n1.73.pkl": "f08d263233503f79e5be10c18bc7587b8b421c1d", 
+  "RNOG_vpol_4inch_center_n1.73.pkl": "5f429ed9ed08175a7f75fd44422367d2278bf2e1", 
+  "RNOG_vpol_4inch_wall_n1.73.pkl": "da24017eb80f7a68348a674be2c527457fe19992", 
+  "RNOG_quadslot_v1_n1.74.pkl": "e9c4946dd2176489249c862f32ef272ab627dc28", 
+  "RNOG_quadslot_v2_n1.74.pkl": "b99d69578f8e7c006dcce3de51e26c4f463872b8",
+  "SKALA_InfFirn": "69b3007da083bb722a4494af97221917973ab297"
 }
diff --git a/NuRadioReco/framework/trigger.py b/NuRadioReco/framework/trigger.py
@@ -27,8 +27,8 @@ def deserialize(triggers_pkl):
             trigger  = EnvelopePhasedTrigger(None, None, None, None)
         elif(trigger_type == 'rnog_surface_trigger'):
             trigger = RNOGSurfaceTrigger(None, None, None, None)
-        elif(trigger_type == 'time_over_threshold'):
-            trigger = TimeOverThresholdTrigger(None, None, None, None)
+        elif(trigger_type == 'gru_time_over_threshold'):
+            trigger = GruTimeOverThresholdTrigger(None, None, None)
         else:
             raise ValueError("unknown trigger type")
         trigger.deserialize(data_pkl)

diff --git a/NuRadioReco/modules/analogToDigitalConverter.py b/NuRadioReco/modules/analogToDigitalConverter.py
@@ -296,7 +296,7 @@ def get_digital_trace(self, station, det, channel,
         if trigger_filter is not None:
 
             trace_fft = np.fft.rfft(trace)
-            if(len(trace_fft) != trigger_filter):
+            if len(trace_fft) != len(trigger_filter):
                 raise ValueError("Wrong filter length to apply to traces")
 
             trace = np.fft.irfft(trace_fft * trigger_filter)

diff --git a/NuRadioReco/modules/io/RNO_G/readRNOGDataMattak.py b/NuRadioReco/modules/io/RNO_G/readRNOGDataMattak.py
@@ -15,6 +15,35 @@
 from NuRadioReco.utilities import units
 import mattak.Dataset
 
+import string
+import random
+
+
+def create_random_directory_path(prefix="/tmp/", n=7):
+    """
+    Produces a path for a temporary directory with a n letter random suffix
+    
+    Parameters
+    ----------
+    
+    prefix: str
+        Path prefix, i.e., root directory. (Defaut: /tmp/)
+        
+    n: int
+        Number of letters for the random suffix. (Default: 7)
+        
+    Returns
+    -------
+    
+    path: str
+        Return path (e.g, /tmp/readRNOGData_XXXXXXX)
+    """
+    # generating random strings
+    res = ''.join(random.choices(string.ascii_lowercase + string.digits, k=n))
+    path = os.path.join(prefix, "readRNOGData_" + res)
+
+    return path
+
 
 def baseline_correction(wfs, n_bins=128, func=np.median):
     """
@@ -152,6 +181,8 @@ def __init__(self, run_table_path=None, log_level=logging.INFO):
 
         # Initialize run table for run selection
         self.__run_table = None
+
+        self.__temporary_dirs = []
 
         if run_table_path is None:
             try:
@@ -310,15 +341,31 @@ def begin(self,
                 if not all_files_in_directory(dir_file):
                     self.logger.error(f"Incomplete directory: {dir_file}. Skip ...")
                     continue
-
-                try:
-                    dataset = mattak.Dataset.Dataset(station=0, run=0, data_dir=dir_file, verbose=verbose, **mattak_kwargs)
-                except (ReferenceError, KeyError) as e:
-                    self.logger.error(f"The following exeption was raised reading in the run: {dir_file}. Skip that run ...:\n", exc_info=e)
-                    continue
             else:
-                raise NotImplementedError("The option to read in files is not implemented yet")
+                # Providing direct paths to a Mattak combined.root file is not supported by the mattak library yet. 
+                # It only accepts directry paths in which it will look for a file called `combined.root` (or waveforms.root if 
+                # it is not a combined file). To work around this: Create a tmp directory under `/tmp/`, link the file you want to
+                # read into this directory with the the name `combined.root`, use this path to read the run.
+
+                path = create_random_directory_path()
+                self.logger.debug(f"Create temporary directory: {path}")
+                if os.path.exists(path):
+                    raise ValueError(f"Temporary directory {path} already exists.")
+
+                os.mkdir(path)
+                self.__temporary_dirs.append(path)  # for housekeeping
+
+                self.logger.debug(f"Create symlink for {dir_file}")
+                os.symlink(dir_file, os.path.join(path, "combined.root"))
+
+                dir_file = path  # set path to e.g. /tmp/NuRadioReco_XXXXXXX/combined.root
+
 
+            try:
+                dataset = mattak.Dataset.Dataset(station=0, run=0, data_dir=dir_file, verbose=verbose, **mattak_kwargs)
+            except (ReferenceError, KeyError) as e:
+                self.logger.error(f"The following exeption was raised reading in the run: {dir_file}. Skip that run ...:\n", exc_info=e)
+                continue
 
             # filter runs/datasets based on 
             if select_runs and self.__run_table is not None and not self.__select_run(dataset):
@@ -515,7 +562,8 @@ def get_events_information(self, keys=["station", "run", "eventNumber"]):
 
         if not do_read:
             # ... or when it does not have the desired information
-            first_event_info = next(iter(self._events_information))
+            first_event_info = self._events_information[list(self._events_information.keys())[0]]
+
             for key in keys:
                 if key not in list(first_event_info.keys()):
                     do_read = True
@@ -556,8 +604,7 @@ def _check_for_valid_information_in_event_info(self, event_info):
         is_valid: bool
             Returns True if all information valid, false otherwise
         """
-
-
+
         if math.isinf(event_info.triggerTime):
             self.logger.error(f"Event {event_info.eventNumber} (st {event_info.station}, run {event_info.run}) "
                                      "has inf trigger time. Skip event...")
@@ -567,7 +614,7 @@ def _check_for_valid_information_in_event_info(self, event_info):
 
         if (event_info.sampleRate == 0 or event_info.sampleRate is None) and self._overwrite_sampling_rate is None:
             self.logger.error(f"Event {event_info.eventNumber} (st {event_info.station}, run {event_info.run}) "
-                              f"has a sampling rate of {event_info.sampleRate:.2f} GHz. Event is skipped ... "
+                              f"has a sampling rate of {event_info.sampleRate} GHz. Event is skipped ... "
                               f"You can avoid this by setting 'overwrite_sampling_rate' in the begin() method.")
             self.__invalid += 1
             return False
@@ -788,4 +835,10 @@ def end(self):
                 f"\n\tRead {self.__n_runs} runs, skipped {self.__skipped_runs} runs.")
         else:
             self.logger.info(
-                f"\n\tRead {self.__counter} events (skipped {self.__skipped} events, {self.__invalid} invalid events)")
+                f"\n\tRead {self.__counter} events   (skipped {self.__skipped} events, {self.__invalid} invalid events)")
+
+        # Clean up links and temporary directories.
+        for d in self.__temporary_dirs:
+            self.logger.debug(f"Remove temporary folder: {d}")
+            os.unlink(os.path.join(d, "combined.root"))
+            os.rmdir(d)
diff --git a/NuRadioReco/modules/measured_noise/RNO_G/noiseImporter.py b/NuRadioReco/modules/measured_noise/RNO_G/noiseImporter.py
@@ -73,10 +73,13 @@ def begin(self, noise_folders, file_pattern="*",
 
         if not isinstance(noise_folders, list):
             noise_folders = [noise_folders]
-
+                    
         # find all subfolders
         noise_files = []
         for noise_folder in noise_folders:
+            if noise_folder == "":
+                continue
+
             noise_files += glob.glob(f"{noise_folder}/**/{file_pattern}root", recursive=True)
         self.__noise_folders = np.unique([os.path.dirname(e) for e in noise_files])       
 

diff --git a/NuRadioReco/modules/measured_noise/channelMeasuredNoiseAdder.py b/NuRadioReco/modules/measured_noise/channelMeasuredNoiseAdder.py
@@ -44,7 +44,7 @@ def begin(self, filenames=None, folder=None, file_pattern="*",
             including subdirectories. (Default: None)
             
         file_pattern: str
-            Use glob.glob(f"{folder}/**/{file_pattern}.nur", recursive=True) to search for files. (Default: "*")
+            Use ``glob.glob(f"{folder}/**/{file_pattern}.nur", recursive=True)`` to search for files. (Default: "*")
         
         random_seed: int, default: None
             Seed for the random number generator. By default, no seed is set.
-Original file line number
+Diff line change
@@ Expand Up / @@ -644,7 +644,7 @@ def get_Veff_Aeff_array(data): @@
         * array of unique trigger names
         Examples
-        ---------
+        --------
         To plot the full sky effective volume for 'all_triggers' do
@@ Expand Down @@