From 6d06707e1e0456108764e3afd9f13f79b0720e78 Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Tue, 2 Mar 2021 10:02:12 +0100
Subject: [PATCH] Skipping thresholds, gain separation bp for fixed gain mode
---
.../Characterize_AGIPD_Gain_Darks_NBC.ipynb | 76 +++++++++++--------
1 file changed, 45 insertions(+), 31 deletions(-)
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index dfbeb5b60..58aaf3e52 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -462,11 +462,12 @@
"outputs": [],
"source": [
"# Add a badpixel due to bad gain separation\n",
- "for g in range(2):\n",
- " # Bad pixels during bad gain separation.\n",
- " # Fraction of pixels in the module with separation lower than \"thresholds_gain_sigma\".\n",
- " bad_sep = (gain_g[qm][..., g+1] - gain_g[qm][..., g]) / np.sqrt(gainstd_g[qm][..., g+1]**2 + gainstd_g[qm][..., g]**2)\n",
- " badpix_g[qm][...,g+1][(bad_sep)<thresholds_gain_sigma]|= BadPixels.GAIN_THRESHOLDING_ERROR.value"
+ "if not fixed_gain_mode:\n",
+ " for g in range(2):\n",
+ " # Bad pixels during bad gain separation.\n",
+ " # Fraction of pixels in the module with separation lower than \"thresholds_gain_sigma\".\n",
+ " bad_sep = (gain_g[qm][..., g+1] - gain_g[qm][..., g]) / np.sqrt(gainstd_g[qm][..., g+1]**2 + gainstd_g[qm][..., g]**2)\n",
+ " badpix_g[qm][...,g+1][(bad_sep)<thresholds_gain_sigma]|= BadPixels.GAIN_THRESHOLDING_ERROR.value"
]
},
{
@@ -482,13 +483,14 @@
"metadata": {},
"outputs": [],
"source": [
- "thresholds_g = {}\n",
- "for qm in gain_g.keys():\n",
- " thresholds_g[qm] = np.zeros((gain_g[qm].shape[0], gain_g[qm].shape[1], gain_g[qm].shape[2], 5))\n",
- " thresholds_g[qm][...,0] = (gain_g[qm][...,1]+gain_g[qm][...,0])/2\n",
- " thresholds_g[qm][...,1] = (gain_g[qm][...,2]+gain_g[qm][...,1])/2\n",
- " for i in range(3):\n",
- " thresholds_g[qm][...,2+i] = gain_g[qm][...,i]"
+ "if not fixed_gain_mode:\n",
+ " thresholds_g = {}\n",
+ " for qm in gain_g.keys():\n",
+ " thresholds_g[qm] = np.zeros((gain_g[qm].shape[0], gain_g[qm].shape[1], gain_g[qm].shape[2], 5))\n",
+ " thresholds_g[qm][...,0] = (gain_g[qm][...,1]+gain_g[qm][...,0])/2\n",
+ " thresholds_g[qm][...,1] = (gain_g[qm][...,2]+gain_g[qm][...,1])/2\n",
+ " for i in range(3):\n",
+ " thresholds_g[qm][...,2+i] = gain_g[qm][...,i]"
]
},
{
@@ -503,9 +505,10 @@
" res[qm] = {\n",
" 'Offset': offset_g[qm],\n",
" 'Noise': noise_g[qm],\n",
- " 'ThresholdsDark': thresholds_g[qm],\n",
" 'BadPixelsDark': badpix_g[qm]\n",
- " }"
+ " }\n",
+ " if not fixed_gain_mode:\n",
+ " res[qm]['ThresholdsDark'] = thresholds_g[qm]"
]
},
{
@@ -545,7 +548,10 @@
"outputs": [],
"source": [
"# Retrieve existing constants for comparison\n",
- "clist = [\"Offset\", \"Noise\", \"ThresholdsDark\", \"BadPixelsDark\"]\n",
+ "if fixed_gain_mode:\n",
+ " clist = [\"Offset\", \"Noise\", \"BadPixelsDark\"]\n",
+ "else:\n",
+ " clist = [\"Offset\", \"Noise\", \"ThresholdsDark\", \"BadPixelsDark\"]\n",
"old_const = {}\n",
"old_mdata = {}\n",
"detinst = getattr(Detectors, dinstance)\n",
@@ -776,19 +782,20 @@
"metadata": {},
"outputs": [],
"source": [
- "# Plot only three gain threshold maps.\n",
- "bp_thresh = OrderedDict()\n",
- "for mod, con in badpix_g.items():\n",
- " bp_thresh[mod] = np.zeros((con.shape[0], con.shape[1], con.shape[2], 5), dtype=con.dtype)\n",
- " bp_thresh[mod][...,:2] = con[...,:2]\n",
- " bp_thresh[mod][...,2:] = con\n",
+ "if not fixed_gain_mode:\n",
+ " # Plot only three gain threshold maps.\n",
+ " bp_thresh = OrderedDict()\n",
+ " for mod, con in badpix_g.items():\n",
+ " bp_thresh[mod] = np.zeros((con.shape[0], con.shape[1], con.shape[2], 5), dtype=con.dtype)\n",
+ " bp_thresh[mod][...,:2] = con[...,:2]\n",
+ " bp_thresh[mod][...,2:] = con\n",
"\n",
"\n",
- "create_constant_overview(thresholds_g, \"Threshold (ADU)\", max_cells, 4000, 10000, 5,\n",
- " badpixels=[bp_thresh, np.nan],\n",
- " gmap=['HG-MG Threshold', 'MG-LG Threshold', 'High gain', 'Medium gain', 'low gain'],\n",
- " marker=['d','d','','','']\n",
- " )"
+ " create_constant_overview(thresholds_g, \"Threshold (ADU)\", max_cells, 4000, 10000, 5,\n",
+ " badpixels=[bp_thresh, np.nan],\n",
+ " gmap=['HG-MG Threshold', 'MG-LG Threshold', 'High gain', 'Medium gain', 'low gain'],\n",
+ " marker=['d','d','','','']\n",
+ " )"
]
},
{
@@ -883,14 +890,21 @@
" \"New constant\", \"Old constant \",\n",
" \"New constant\", \"Old constant \"]\n",
"\n",
- "for const in ['Offset', 'Noise', 'ThresholdsDark']:\n",
- " if const != 'ThresholdsDark':\n",
- " table = [['','High gain', 'High gain', 'Medium gain', 'Medium gain', 'Low gain', 'Low gain']]\n",
- " else:\n",
+ "if fixed_gain_mode:\n",
+ " constants = ['Offset', 'Noise']\n",
+ "else:\n",
+ " ['Offset', 'Noise', 'ThresholdsDark']\n",
+ "\n",
+ "for const in constants:\n",
+ " \n",
+ " if const == 'ThresholdsDark':\n",
" table = [['','HG-MG threshold', 'HG-MG threshold', 'MG-LG threshold', 'MG-LG threshold']]\n",
- " for qm in res.keys():\n",
+ " else: \n",
+ " table = [['','High gain', 'High gain', 'Medium gain', 'Medium gain', 'Low gain', 'Low gain']]\n",
"\n",
+ " for qm in res.keys():\n",
" data = np.copy(res[qm][const])\n",
+ " \n",
" if const == 'ThresholdsDark':\n",
" data[...,0][res[qm]['BadPixelsDark'][...,0]>0] = np.nan\n",
" data[...,1][res[qm]['BadPixelsDark'][...,1]>0] = np.nan\n",
--
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