BS data now found correctly
This commit is contained in:
John Henry Beale
+344
-174
@@ -12,6 +12,7 @@ import sys
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import time
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import zmq
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import re
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import glob
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from pathlib import Path
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from loguru import logger
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@@ -23,7 +24,7 @@ import receive_msg
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#sys.path.insert(0, os.path.expanduser('/sf/cristallina/applications/mx/jungfraujoch_openapi_python/sf_datafiles'))
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#from sfdata import SFDataFiles
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#define log file place:
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LOG_FILENAME = time.strftime("/sf/cristallina/data/p23083/res/clara_%Y%m.log")
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LOG_FILENAME = time.strftime("/sf/cristallina/data/p23523/res/clara_%Y%m.log")
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logger.add(LOG_FILENAME, level="INFO", rotation="100MB")
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@@ -72,54 +73,71 @@ def to_json(obj):
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"""
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return json.dumps(obj, default=lambda obj: obj.__dict__, indent=4)
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def wait_for_dataset(h5file, dataset_path, timeout=60, check_interval=0.1):
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def wait_for_dataset(
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filepath,
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dataset_path,
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timeout=60,
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check_interval=0.1
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):
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"""
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Wait until an HDF5 dataset exists and contains data.
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Parameters
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----------
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h5file : h5py.File
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Open HDF5 file handle
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dataset_path : str
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Path to dataset inside HDF5 file
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timeout : float
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Max wait time in seconds
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check_interval : float
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Time between checks in seconds
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Wait until an HDF5 dataset becomes readable.
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Handles:
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- incomplete HDF5 metadata
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- delayed writer flushes
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- unstable object headers
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- live DAQ writing
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Returns
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-------
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dataset
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The HDF5 dataset object
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Raises
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------
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TimeoutError
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If dataset does not become available in time
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np.ndarray
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Dataset contents
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"""
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start = time.time()
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attempt = 0
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while True:
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try:
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if dataset_path in h5file:
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ds = h5file[dataset_path]
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# Optional: ensure dataset is populated
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if ds.shape[0] > 0:
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return ds
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h5file = None
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try:
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h5file = h5py.File(filepath, "r")
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data = h5file[dataset_path][:]
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h5file.close()
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return data
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except Exception as e:
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logger.info(f"Waiting for dataset {dataset_path}: {e}")
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attempt += 1
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if attempt % 100 == 0:
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logger.info(
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f"Still waiting for dataset "
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f"{dataset_path} "
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f"in {filepath}: {e}"
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)
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try:
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h5file.close()
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except:
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pass
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if time.time() - start > timeout:
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raise TimeoutError(
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f"Timeout waiting for dataset {dataset_path}"
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f"Timeout waiting for dataset "
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f"{dataset_path}"
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)
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time.sleep(check_interval)
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# --------class with functions-----
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@@ -443,202 +461,340 @@ class CollectedH5:
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return output_file_path
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def find_matching_bsdata(self, pulseids_JF, data_dir):
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"""
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Search all BSDATA files and find pulse ID matches
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with the current Jungfrau acquisition.
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"""
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matched_results = []
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bsdata_files = sorted(
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glob.glob(
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os.path.join(data_dir, "acq*.BSDATA.h5")
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)
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)
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logger.info(
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f"Searching {len(bsdata_files)} BSDATA files"
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)
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for bsfile in bsdata_files:
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logger.info(f"Checking BSDATA file: {bsfile}")
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try:
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bsdata = h5py.File(bsfile, "r")
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pulseids_BS = wait_for_dataset(
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bsdata,
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"/SAR-CVME-TIFALL6:EvtSet/pulse_id",
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timeout=60,
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check_interval=0.1
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)[:]
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evt_set = wait_for_dataset(
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bsdata,
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"/SAR-CVME-TIFALL6:EvtSet/data",
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timeout=60,
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check_interval=0.1
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)[:]
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inters, ind_JF, ind_BS = np.intersect1d(
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pulseids_JF,
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pulseids_BS,
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return_indices=True
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)
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logger.info(
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f"{os.path.basename(bsfile)} "
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f"matched {len(inters)} pulse IDs"
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)
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if len(inters) > 0:
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matched_results.append(
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(
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evt_set,
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ind_JF,
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ind_BS,
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bsfile
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)
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)
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bsdata.close()
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except Exception as e:
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logger.info(
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f"Could not process BSDATA file "
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f"{bsfile}: {e}"
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)
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logger.info(
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f"Found {len(matched_results)} "
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f"matching BSDATA files"
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)
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return matched_results
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def create_list_file(self):
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"""
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Function to generate a list file with the path of the input H5 file
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:return:None
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"""
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import glob
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print('writing list files')
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#Assemble path for raw data
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# Assemble path for raw data
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pgroup = str(self.message["experiment_group"])
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raw = "raw"
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data = "data"
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filen = str(self.message["filename"])
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file_path = slash / filen
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# write to cell file in output folder
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run_number = self.message["run_number"]
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acq_number = self.message["file_number"]
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name = f'run{run_number:04}_acq{acq_number:04}'
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#f = open(name + ".list", "w")
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#f.write(str(file_path))
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#f.close()
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bsdata_name = Path(filen[:-15]+'.BSDATA.h5')
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jf_path = file_path
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bsdata_path = slash / bsdata_name
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logger.info("Waiting for bs_data to exist")
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start_t = time.time()
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while not bsdata_path.exists():
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current_t = time.time()
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elapsed_t = current_t-start_t
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if elapsed_t > 600:
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print("Wait for BSdata exceeds 10 minutes. Exiting loop")
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break
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time.sleep(1)
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try:
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time.sleep(10)
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#bsdata = SFDataFiles(bsdata_path)
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bsdata = h5py.File(bsdata_path, "r") #r"/sf/cristallina/data/p21630/raw/run0065-lov_movestop_normal_1/data/acq0001.BSDATA.h5"
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except Exception as e:
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print(f"didn't open bsdata due to error {e}") #_logger.error(f"Cannot open {data_file} (due to {e})")
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return
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pulseids_BS = wait_for_dataset(
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bsdata,
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"/SAR-CVME-TIFALL6:EvtSet/pulse_id",
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timeout=600,
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check_interval=0.1
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)[:]
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evt_set = wait_for_dataset(
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bsdata,
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"/SAR-CVME-TIFALL6:EvtSet/data",
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timeout=600,
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check_interval=0.1
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)[:]
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jf_path= file_path
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master_path = slash / Path(filen[:-19]+'_master.h5')
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master_path = slash / Path(filen[:-19] + '_master.h5')
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print(master_path)
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file_exists = os.path.exists(master_path)
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st = time.perf_counter()
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while not file_exists:
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time.sleep(1)
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file_exists = os.path.exists(master_path)
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if time.perf_counter()-st > 1800:
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print('Wait for acq master exceeded 30 minutes!!!')
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break
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time.sleep(1)
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file_exists = os.path.exists(master_path)
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if time.perf_counter() - st > 1800:
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print('Wait for acq master exceeded 30 minutes!!!')
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break
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try:
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try:
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print(f"JF file path = {jf_path}, file_path = {file_path}")
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print(os.path.exists(jf_path))
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x = h5py.File(jf_path, "r")
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#data = SFDataFiles(bsdata_path, jf_path)
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pulseids_JF = wait_for_dataset(
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jf_path,
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"/entry/xfel/pulseID",
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timeout=600,
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check_interval=0.1
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)
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except Exception as e:
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print(f"didn't open {jf_path} due to error {e}") #_logger.error(f"Cannot open {data_file} (due to {e})")
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print(f"didn't open {jf_path} due to error {e}")
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return
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pulseids_JF = wait_for_dataset(
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x,
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"/entry/xfel/pulseID",
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timeout=600,
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check_interval=0.1
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)[:]
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n_pulse_id = len(pulseids_JF) #- maybe not needed ?
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index_dark = []
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index_light = []
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blanks = []
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#print(evt_set)
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index_dark = set()
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index_light = set()
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blanks = set()
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_inters, ind_JF, ind_BS = np.intersect1d(pulseids_JF, pulseids_BS, return_indices=True)
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#evt_set = evt_set[ind_BS]
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#print(len(evt_set))
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#print(min(ind_BS),max(ind_BS),len(ind_BS))
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# -----------------------------------------------------------------
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# Wait for expected BSDATA file for this acquisition
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# -----------------------------------------------------------------
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for idx_JF, idx_BS in zip(ind_JF, ind_BS):
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events = evt_set[idx_BS]
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trigger_event = int(self.message["user_data"]["trigger_event"])
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data_dir = os.path.dirname(str(file_path))
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if trigger_event == 63:
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if events[trigger_event] and events[200]:
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index_dark.append(idx_JF)
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bsdata_name = Path(
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filen[:-15] + '.BSDATA.h5'
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)
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elif events[200]:
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index_light.append(idx_JF)
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bsdata_path = slash / bsdata_name
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else:
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blanks.append(idx_JF)
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logger.info(
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f"Waiting for BSDATA file: {bsdata_path}"
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)
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else:
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start_t = time.time()
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if events[trigger_event] and events[200]:
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index_light.append(idx_JF)
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while not bsdata_path.exists():
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elif events[200]:
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index_dark.append(idx_JF)
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elapsed_t = time.time() - start_t
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else:
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blanks.append(idx_JF)
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if elapsed_t > 600:
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logger.info(
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"Wait for BSDATA exceeded 10 minutes"
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)
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#for i in range(n_pulse_id):
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break
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# p = pulseids_JF[i]
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# q = pulseids_BS[i]
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# if p != q:
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# #event_i = np.where(pulseids_JF == q)[0] for normal detector
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# event_i = np.where(pulseids_BS == p)[0][0]#[::2] #[0][0]
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# #event_i = i
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# else:
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# event_i=i#
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time.sleep(0.1)
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# events=evt_set[event_i]
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#print(events)
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#print(len(events))
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#print(event_i)
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#print(p,q)
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#print(i)
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logger.info(
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"Expected BSDATA file appeared"
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)
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# trigger_event = int(self.message["user_data"]["trigger_event"])
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# -----------------------------------------------------------------
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# Search ALL BSDATA files for matching pulse IDs
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# -----------------------------------------------------------------
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# if self.message["user_data"]["trigger_flag"]:
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# if events[trigger_event] and events[200]:
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# index_light.append(i)
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bsdata_files = sorted(
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glob.glob(
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os.path.join(data_dir, "acq*.BSDATA.h5")
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)
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)
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# elif events[200]:
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# index_dark.append(i)
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logger.info(
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f"Found {len(bsdata_files)} BSDATA files"
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)
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# else:
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# blanks.append(i)
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for bsfile in bsdata_files:
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logger.info(f"Checking BSDATA file: {bsfile}")
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try:
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pulseids_BS = wait_for_dataset(
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bsfile,
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"/SAR-CVME-TIFALL6:EvtSet/pulse_id",
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timeout=30,
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check_interval=0.1
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)[:]
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evt_set = wait_for_dataset(
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bsfile,
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"/SAR-CVME-TIFALL6:EvtSet/data",
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timeout=30,
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check_interval=0.1
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)[:]
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# ---------------------------------------------------------
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# Match pulse IDs
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# ---------------------------------------------------------
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inters, ind_JF, ind_BS = np.intersect1d(
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pulseids_JF,
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pulseids_BS,
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return_indices=True
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)
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logger.info(
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f"{os.path.basename(bsfile)} "
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f"matched {len(inters)} pulse IDs"
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)
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trigger_event = int(
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self.message["user_data"]["trigger_event"]
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)
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# ---------------------------------------------------------
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# Sort light / dark / blank
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# ---------------------------------------------------------
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for idx_JF, idx_BS in zip(ind_JF, ind_BS):
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events = evt_set[idx_BS]
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if trigger_event == 63:
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if events[trigger_event] and events[200]:
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index_dark.add(idx_JF)
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elif events[200]:
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index_light.add(idx_JF)
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else:
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blanks.add(idx_JF)
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else:
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if events[trigger_event] and events[200]:
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index_light.add(idx_JF)
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elif events[200]:
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index_dark.add(idx_JF)
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else:
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blanks.add(idx_JF)
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except Exception as e:
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logger.info(
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f"Could not process BSDATA file "
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f"{bsfile}: {e}"
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)
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bsdata.close()
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x.close()
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acq_dark = []
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acq_light = []
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acq_blank = []
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acq_blank = []
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delim = "//"
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if index_dark:
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for frame_number in index_dark:
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acq_dark.append(f"{jf_path} {delim}{frame_number}")
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file_off = name+'_off.list'
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logger.info(f"List of dark frames : {file_off} , {len(index_dark)} frames")
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for frame_number in sorted(index_dark):
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acq_dark.append(
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f"{jf_path} {delim}{frame_number}"
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)
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file_off = name + '_off.list'
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logger.info(
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f"List of dark frames : "
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f"{file_off} , {len(index_dark)} frames"
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)
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with open(file_off, "w") as f_list:
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for frame in acq_dark:
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print(f"{frame}", file = f_list)
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print(f"{frame}", file=f_list)
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if index_light:
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for frame_number in index_light:
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acq_light.append(f"{jf_path} {delim}{frame_number}")
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file_on = name+'_on.list'
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logger.info(f"List of light frames : {file_on} , {len(index_light)} frames")
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for frame_number in sorted(index_light):
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acq_light.append(
|
||||
f"{jf_path} {delim}{frame_number}"
|
||||
)
|
||||
|
||||
file_on = name + '_on.list'
|
||||
|
||||
logger.info(
|
||||
f"List of light frames : "
|
||||
f"{file_on} , {len(index_light)} frames"
|
||||
)
|
||||
|
||||
with open(file_on, "w") as f_list:
|
||||
|
||||
for frame in acq_light:
|
||||
print(f"{frame}", file = f_list)
|
||||
|
||||
print(f"{frame}", file=f_list)
|
||||
|
||||
if blanks:
|
||||
for frame_number in blanks:
|
||||
acq_blank.append(f"{jf_path} {delim}{frame_number}")
|
||||
file_blank = name+'_blank.list'
|
||||
with open(file_blank, "w") as f_list:
|
||||
for frame in acq_blank:
|
||||
print(f"{frame}", file = f_list)
|
||||
|
||||
|
||||
for frame_number in sorted(blanks):
|
||||
|
||||
acq_blank.append(
|
||||
f"{jf_path} {delim}{frame_number}"
|
||||
)
|
||||
|
||||
file_blank = name + '_blank.list'
|
||||
|
||||
with open(file_blank, "w") as f_list:
|
||||
|
||||
for frame in acq_blank:
|
||||
|
||||
print(f"{frame}", file=f_list)
|
||||
|
||||
return None
|
||||
|
||||
def create_slurm_script(self,trigger, geometry_file_path):
|
||||
@@ -766,12 +922,25 @@ class CollectedH5:
|
||||
# sub.run(["sbatch", "run_SLURM"])
|
||||
|
||||
try:
|
||||
slurm_out = sub.run(["sbatch", "run_SLURM_" + trigger ], capture_output=True)
|
||||
time.sleep(1)
|
||||
txt = slurm_out.stdout.decode().split()
|
||||
# grep the slurm number
|
||||
slurm_out = sub.run(
|
||||
["sbatch", "run_SLURM_" + trigger],
|
||||
capture_output=True,
|
||||
text=True
|
||||
)
|
||||
|
||||
logger.info(f"sbatch stdout: {slurm_out.stdout}")
|
||||
logger.info(f"sbatch stderr: {slurm_out.stderr}")
|
||||
|
||||
txt = slurm_out.stdout.split()
|
||||
|
||||
if len(txt) == 0:
|
||||
raise RuntimeError(
|
||||
f"sbatch returned empty stdout. stderr={slurm_out.stderr}"
|
||||
)
|
||||
|
||||
logger.info(f"submitted batch job number: {txt[-1]}")
|
||||
self.message["SlurmJobID_" + trigger] = str(txt[-1])
|
||||
|
||||
except Exception as e:
|
||||
logger.info("Could not submit SLURM job: {}".format(e))
|
||||
|
||||
@@ -855,7 +1024,8 @@ if __name__ == "__main__":
|
||||
context = zmq.Context()
|
||||
subscriber = context.socket(zmq.SUB)
|
||||
#subscriber.connect("tcp://sf-broker-01.psi.ch:5555")
|
||||
subscriber.connect("tcp://sf-daqtest-01.psi.ch:5401")
|
||||
#subscriber.connect("tcp://sf-daqtest-01.psi.ch:5401")
|
||||
subscriber.connect("tcp://sf-daq-2.psi.ch:5401")
|
||||
subscriber.setsockopt_string(zmq.SUBSCRIBE, "")
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user