diff --git a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb index a91f1fe78d6ccef2da245dc561c9553702e800a9..8c54074317466833ab19617bed2d042fecbe7947 100644 --- a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb +++ b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb @@ -21,15 +21,15 @@ "source": [ "in_folder = \"/gpfs/exfel/exp/DETLAB/202230/p900276/raw\" # the folder to read data from, required\n", "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/gotthard2\" # the folder to output to, required\n", - "run = 10 # run to process, required # TODO: test runs up to run 18. Last 3 runs can be checked.\n", + "run = 10 # run to process, required\n", "sequences = [-1] # sequences to correct, set to [-1] for all, range allowed\n", "sequences_per_node = 1 # number of sequence files per node if notebook executed through xfel-calibrate, set to 0 to not run SLURM parallel\n", "\n", "# Parameters used to access raw data.\n", "karabo_id = \"DET_LAB_G2\" # karabo prefix of Jungfrau devices\n", "karabo_da = [\"DA01\"] # data aggregators\n", - "receiver = \"GOT01\"\n", - "control_template = \"CTRL{:02d}\"\n", + "receiver_template = \"GOT{:02d}\" # receiver template used to read INSTRUMENT keys.\n", + "control_template = \"CTRL{:02d}\" # control template used to read CONTROL keys.\n", "instrument_source_template = '{}/DET/{}:daqOutput' # template for source name (filled with karabo_id & receiver_id). e.g. 'SPB_IRDA_JF4M/DET/JNGFR01:daqOutput'\n", "ctrl_source_template = '{}/DET/{}' # template for control source name (filled with karabo_id_control)\n", "karabo_id_control = \"\" # if control is on a different ID, set to empty string if it is the same a karabo-id\n", @@ -97,8 +97,10 @@ "\n", "run_dc = RunDirectory(in_folder / f'r{run:04d}')\n", "\n", - "instrument_src = instrument_source_template.format(karabo_id, \"{}\")\n", - "ctrl_src = ctrl_source_template.format(karabo_id_control, control_template)\n", + "instrument_src = instrument_source_template.format(\n", + " karabo_id, receiver_template)\n", + "ctrl_src = ctrl_source_template.format(\n", + " karabo_id_control, control_template)\n", "\n", "print(f\"Run is: {run}\")\n", "print(f\"Process modules: {karabo_da}\")\n", @@ -221,8 +223,8 @@ "metadata": {}, "outputs": [], "source": [ - "for k_da in karabo_da:\n", - " instr_mod_src = instrument_src.format(receiver)\n", + "for mod in karabo_da:\n", + " instr_mod_src = instrument_src.format(int(mod[-2:]))\n", " data_path = \"INSTRUMENT/\"+instr_mod_src+\"/data\"\n", "\n", " for raw_file in seq_files:\n", @@ -264,7 +266,7 @@ " chunks=((1,) + dshape[1:]), # 1 chunk == 1 image\n", " dtype=np.float32,\n", " )\n", - " step_timer.done_step(\"Storing data\")\n" + " step_timer.done_step(\"Storing data\")" ] }, { diff --git a/setup.py b/setup.py index 3e80af1ee68f1976ba8d9d8f236d2a5b9518306d..7331ed67c6c0945d1d49a1133284ad22237c0a09 100644 --- a/setup.py +++ b/setup.py @@ -28,8 +28,6 @@ ext_modules = [ "cal_tools.gotthard2.gotthard2algs", ["src/cal_tools/gotthard2/gotthard2algs.pyx"], include_dirs=[numpy.get_include()], - extra_compile_args=["-fopenmp", "-march=native"], - extra_link_args=["-fopenmp"], ), ]