From 17a780c5021482c35f32d10653051723a1a1a6e3 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Mon, 14 Feb 2022 15:00:18 +0100
Subject: [PATCH] process all trains, correct offset dtype, and save raw image
like before
---
notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb | 4 ++--
notebooks/pnCCD/Correct_pnCCD_NBC.ipynb | 3 +--
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
index a8d232b4f..13e9c89e6 100644
--- a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
+++ b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
@@ -58,7 +58,7 @@
"sigmaNoise = 10. # pixels whose signal value exceeds sigmaNoise*noise will be considered as cosmics and are masked\n",
"bad_pixel_offset_sigma = 4. # any pixel whose offset beyond this standard deviations is a bad pixel\n",
"bad_pixel_noise_sigma = 4. # any pixel whose noise beyond this standard deviations is a bad pixel\n",
- "max_trains = 500 # Maximum number of trains to use for dark processing.\n",
+ "max_trains = 0 # Maximum number of trains to use for dark processing. Set to 0 to process all trains.\n",
"min_trains = 1 # Minimum number of trains to proceed with dark processing.\n",
"\n",
"# Don't delete. myMDC sends this parameter by default.\n",
@@ -250,7 +250,7 @@
"data = data.astype(np.float32)\n",
"\n",
"noiseMap = np.std(data, axis=0, dtype=np.float64)\n",
- "offsetMap = np.mean(data, axis=0)\n",
+ "offsetMap = np.mean(data, axis=0, dtype=np.float64)\n",
"step_timer.done_step(f'Initial maps are created from {n_trains} trains.')"
]
},
diff --git a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
index e10a3f33a..f7bc8a917 100644
--- a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
+++ b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
@@ -786,8 +786,7 @@
" # Copy RAW non-calibrated sources.\n",
" with h5py.File(seq_f, 'r') as sfile:\n",
" h5_copy_except.h5_copy_except_paths(\n",
- " sfile, ofile,\n",
- " [\"INSTRUMENT/\"+instrument_src+\"/data/image\"],\n",
+ " sfile, ofile, [],\n",
" )\n",
" # TODO: to clear this up: why save corrected data in data/pixels rather than data/image.\n",
" write_datasets(corr_arrays, ofile)\n",
--
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