From 79abd4e69727876006265632c4385bacef68f7da Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Mon, 16 May 2022 12:06:28 +0200
Subject: [PATCH] Add chunking to LPD correct output data
---
notebooks/LPD/LPD_Correct_Fast.ipynb | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/notebooks/LPD/LPD_Correct_Fast.ipynb b/notebooks/LPD/LPD_Correct_Fast.ipynb
index b27a64e2b..5e29c6fac 100644
--- a/notebooks/LPD/LPD_Correct_Fast.ipynb
+++ b/notebooks/LPD/LPD_Correct_Fast.ipynb
@@ -53,6 +53,8 @@
"\n",
"# Output options\n",
"overwrite = True # set to True if existing data should be overwritten\n",
+ "chunks_data = 32 # HDF chunk size for pixel data in number of frames.\n",
+ "chunks_ids = 32 # HDF chunk size for cellId and pulseId datasets.\n",
"\n",
"# Parallelization options\n",
"sequences_per_node = 1 # Sequence files to process per node\n",
@@ -423,9 +425,12 @@
" outp_source = outp_file.create_instrument_source(outp_source_name)\n",
" \n",
" outp_source.create_index(image=image_counts)\n",
- " outp_source.create_key('image.data', data=out_data)\n",
- " outp_source.create_key('image.cellId', data=in_cell)\n",
- " outp_source.create_key('image.pulseId', data=in_pulse)\n",
+ " outp_source.create_key('image.data', data=out_data,\n",
+ " chunks=(chunks_data, 256, 256))\n",
+ " outp_source.create_key('image.cellId', data=in_cell,\n",
+ " chunks=(chunks_ids,))\n",
+ " outp_source.create_key('image.pulseId', data=in_pulse,\n",
+ " chunks=(chunks_ids,))\n",
" write_compressed_frames(\n",
" out_gain, outp_file, f'INSTRUMENT/{outp_source_name}/image/gain', comp_threads=8)\n",
" write_compressed_frames(\n",
--
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