diff --git a/notebooks/ePix100/Correction_ePix100_NBC.ipynb b/notebooks/ePix100/Correction_ePix100_NBC.ipynb index 30d0586b3039ddd3ddbefed3c7e6da98f1b27753..89fa139226537207b3b447893c3a26c57333ccb5 100644 --- a/notebooks/ePix100/Correction_ePix100_NBC.ipynb +++ b/notebooks/ePix100/Correction_ePix100_NBC.ipynb @@ -24,15 +24,15 @@ "metadata": {}, "outputs": [], "source": [ - "in_folder = \"/gpfs/exfel/exp/MID/202330/p900329/raw\" # input folder, required\n", + "in_folder = \"/gpfs/exfel/exp/HED/202102/p002739/raw\" # input folder, required\n", "out_folder = \"\" # output folder, required\n", "metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n", "sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n", "sequences_per_node = 1 # number of sequence files per cluster node if run as slurm job, set to 0 to not run SLURM parallel\n", - "run = 106 # which run to read data from, required\n", + "run = 38 # which run to read data from, required\n", "\n", "# Parameters for accessing the raw data.\n", - "karabo_id = \"MID_EXP_EPIX-1\" # karabo karabo_id\n", + "karabo_id = \"HED_IA1_EPX100-1\" # karabo karabo_id\n", "karabo_da = \"EPIX01\" # data aggregators\n", "db_module = \"\" # module id in the database\n", "receiver_template = \"RECEIVER\" # detector receiver template for accessing raw data files\n", @@ -628,8 +628,11 @@ " \"data.image.pixels\", data=data, chunks=dataset_chunk)\n", " outp_source.create_key(\n", " \"data.trainId\", data=seq_dc.train_ids, chunks=min(50, len(seq_dc.train_ids)))\n", - " outp_source.create_key(\n", - " \"data.pulseId\", data=list(seq_dc[instrument_src]['data.pulseId'].ndarray().squeeze()), chunks=min(50, len(seq_dc.train_ids)))\n", + " \n", + " if np.isin('data.pulseId', list(seq_dc[instrument_src].keys())): # some runs are missing 'data.pulseId'\n", + " outp_source.create_key(\n", + " \"data.pulseId\", data=list(seq_dc[instrument_src]['data.pulseId'].ndarray().squeeze()), chunks=min(50, len(seq_dc.train_ids)))\n", + " \n", " if pattern_classification:\n", " # Add main corrected `data.image.pixels` dataset and store corrected data.\n", " outp_source.create_key(\n",