From ce2389009c00e8ffc5f3f34185d66fb956b1d22a Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Wed, 15 Nov 2023 10:42:34 +0100
Subject: [PATCH] Deprecate notebook parameter whether to save datasets, now
always enabled
---
.../REMI/REMI_Digitize_and_Transform.ipynb | 85 ++++++++-----------
1 file changed, 37 insertions(+), 48 deletions(-)
diff --git a/notebooks/REMI/REMI_Digitize_and_Transform.ipynb b/notebooks/REMI/REMI_Digitize_and_Transform.ipynb
index c6aa4f03f..b188101e9 100644
--- a/notebooks/REMI/REMI_Digitize_and_Transform.ipynb
+++ b/notebooks/REMI/REMI_Digitize_and_Transform.ipynb
@@ -13,12 +13,6 @@
"\n",
"calib_config_path = '/gpfs/exfel/exp/SQS/202101/p002535/usr/config_board2+4.yaml' # Path to correction and transform configuration\n",
"\n",
- "# These parameters are required by xfel-calibrate but ignored in this notebook.\n",
- "cycle = '' # Proposal cycle, currently not used.\n",
- "cal_db_timeout = 0 # Calibration DB timeout, currently not used.\n",
- "cal_db_interface = 'foo' # Calibration DB interface, currently not used.\n",
- "karabo_da = 'bar' # Karabo data aggregator name, currently not used\n",
- "\n",
"# Output parameters.\n",
"karabo_id = 'SQS_REMI_DLD6' # Karabo device ID root for virtual output device.\n",
"proposal = '' # Proposal, leave empty for auto detection based on in_folder\n",
@@ -26,11 +20,6 @@
"out_seq_len = 5000 # Number of trains per sequence file in output.\n",
"det_device_id = '{karabo_id}/DET/{det_name}' # Karabo device ID for virtual output device.\n",
"det_output_key = 'output' # Pipeline name for fast data output.\n",
- "save_raw_triggers = True # Whether to save trigger position in files.\n",
- "save_raw_edges = True # Whether to save digitized edge positions in files.\n",
- "save_raw_amplitudes = True # Whether to save analog pulse amplitudes in files.\n",
- "save_rec_signals = True # Whether to save reconstructed signals (u1-w2, mcp) in files.\n",
- "save_rec_hits = True # Whether to save reoncstructed hits (x,y,t,m) in files.\n",
"chunks_triggers = [500] # HDF chunk size for triggers.\n",
"chunks_edges = [500, 7, 50] # HDF chunk size for edges.\n",
"chunks_amplitudes = [500, 7, 50] # HDF chunk size for amplitudes.\n",
@@ -65,7 +54,19 @@
"mp_find_triggers = 0.5 # Parallelization for finding triggers.\n",
"mp_find_edges = 0.5 # Parallelization for digitizing analog signal.\n",
"mt_avg_trace = 2 # Parallelization for trace averaging.\n",
- "mp_rec_hits = 1.0 # Parallelization for hit reconstruction."
+ "mp_rec_hits = 1.0 # Parallelization for hit reconstruction.\n",
+ "\n",
+ "# DEPRECATED AND IGNORED\n",
+ "# Left for compatibility with webservice or legacy configuration.\n",
+ "cycle = '' # Proposal cycle, passed by webservice but not used.\n",
+ "karabo_da = 'bar' # Karabo data aggregator name, passed by webservice but not used\n",
+ "cal_db_timeout = 0 # Calibration DB timeout, passed by webservice but not used.\n",
+ "cal_db_interface = 'foo' # Calibration DB interface, passed by webservice but not used.\n",
+ "save_raw_triggers = True # Whether to save trigger position in files, ignored and always enabled.\n",
+ "save_raw_edges = True # Whether to save digitized edge positions in files, ignored and always enabled.\n",
+ "save_raw_amplitudes = True # Whether to save analog pulse amplitudes in files, ignored and always enabled.\n",
+ "save_rec_signals = True # Whether to save reconstructed signals (u1-w2, mcp) in files, ignored and always enabled.\n",
+ "save_rec_hits = True # Whether to save reoncstructed hits (x,y,t,m) in files, ignored and always enabled."
]
},
{
@@ -1328,17 +1329,10 @@
"\n",
"control_sources = [det_device_id.format(karabo_id=karabo_id, det_name=det_name.upper())\n",
" for det_name in remi['detector']]\n",
- "\n",
- "channels = []\n",
- "if save_raw_triggers or save_raw_edges:\n",
- " channels.append('raw')\n",
- "if save_rec_signals or save_rec_hits:\n",
- " channels.append('rec')\n",
- " \n",
"instrument_channels = [\n",
" f'{device_id}:{det_output_key}/{channel}'\n",
" for device_id in control_sources\n",
- " for channel in channels\n",
+ " for channel in ['raw', 'rec']\n",
"]"
]
},
@@ -1378,38 +1372,33 @@
" \n",
" cur_data = det_data[det_name]\n",
" \n",
- " if save_raw_triggers:\n",
- " cur_fast_data.create_key('raw.triggers', triggers[pulse_mask],\n",
- " maxshape=(None,) + triggers.shape[1:],\n",
- " chunks=tuple(chunks_triggers), **dataset_kwargs)\n",
+ " cur_fast_data.create_key('raw.triggers', triggers[pulse_mask],\n",
+ " maxshape=(None,) + triggers.shape[1:],\n",
+ " chunks=tuple(chunks_triggers), **dataset_kwargs)\n",
" \n",
- " if save_raw_edges:\n",
- " cur_fast_data.create_key('raw.edges', cur_data['edges'][pulse_mask],\n",
- " maxshape=(None,) + cur_data['edges'].shape[1:],\n",
- " chunks=tuple(chunks_edges if chunks_edges[-1] <= cur_max_hits\n",
- " else chunks_edges[:-1] + [cur_max_hits]),\n",
- " **dataset_kwargs)\n",
+ " cur_fast_data.create_key('raw.edges', cur_data['edges'][pulse_mask],\n",
+ " maxshape=(None,) + cur_data['edges'].shape[1:],\n",
+ " chunks=tuple(chunks_edges if chunks_edges[-1] <= cur_max_hits\n",
+ " else chunks_edges[:-1] + [cur_max_hits]),\n",
+ " **dataset_kwargs)\n",
" \n",
- " if save_raw_amplitudes:\n",
- " cur_fast_data.create_key('raw.amplitudes', cur_data['amplitudes'][pulse_mask],\n",
- " maxshape=(None,) + cur_data['amplitudes'].shape[1:],\n",
- " chunks=tuple(chunks_amplitudes if chunks_amplitudes[-1] <= cur_max_hits\n",
- " else chunks_amplitudes[:-1] + [cur_max_hits]),\n",
- " **dataset_kwargs)\n",
+ " cur_fast_data.create_key('raw.amplitudes', cur_data['amplitudes'][pulse_mask],\n",
+ " maxshape=(None,) + cur_data['amplitudes'].shape[1:],\n",
+ " chunks=tuple(chunks_amplitudes if chunks_amplitudes[-1] <= cur_max_hits\n",
+ " else chunks_amplitudes[:-1] + [cur_max_hits]),\n",
+ " **dataset_kwargs)\n",
" \n",
- " if save_rec_signals:\n",
- " cur_fast_data.create_key('rec.signals', cur_data['signals'][pulse_mask],\n",
- " maxshape=(None,) + cur_data['signals'].shape[1:],\n",
- " chunks=tuple(chunks_signals if chunks_signals[-1] <= cur_max_hits\n",
- " else chunks_signals[:-1] + [cur_max_hits]),\n",
- " **dataset_kwargs)\n",
+ " cur_fast_data.create_key('rec.signals', cur_data['signals'][pulse_mask],\n",
+ " maxshape=(None,) + cur_data['signals'].shape[1:],\n",
+ " chunks=tuple(chunks_signals if chunks_signals[-1] <= cur_max_hits\n",
+ " else chunks_signals[:-1] + [cur_max_hits]),\n",
+ " **dataset_kwargs)\n",
" \n",
- " if save_rec_hits:\n",
- " cur_fast_data.create_key('rec.hits', cur_data['hits'][pulse_mask],\n",
- " maxshape=(None,) + hits.shape[1:],\n",
- " chunks=tuple(chunks_hits if chunks_hits[-1] <= cur_max_hits\n",
- " else chunks_hits[:-1] + [cur_max_hits]),\n",
- " **dataset_kwargs)\n",
+ " cur_fast_data.create_key('rec.hits', cur_data['hits'][pulse_mask],\n",
+ " maxshape=(None,) + hits.shape[1:],\n",
+ " chunks=tuple(chunks_hits if chunks_hits[-1] <= cur_max_hits\n",
+ " else chunks_hits[:-1] + [cur_max_hits]),\n",
+ " **dataset_kwargs)\n",
" \n",
" cur_fast_data.create_index(raw=pulse_counts[train_mask], rec=pulse_counts[train_mask])\n",
" \n",
--
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