From 8db4c0c68ebc1c17a5c4aecbae2d61cfba626cff Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Thu, 27 Oct 2022 13:46:37 +0200
Subject: [PATCH] MR comments, styling and refactors
---
...rk_analysis_all_gains_burst_mode_NBC.ipynb | 6 +--
.../Jungfrau/Jungfrau_darks_Summary_NBC.ipynb | 42 +++++++++----------
2 files changed, 24 insertions(+), 24 deletions(-)
diff --git a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
index c394e0c86..05bda3f95 100644
--- a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
@@ -34,7 +34,7 @@
"\n",
"# Parameters for calibration database and storing constants.\n",
"use_dir_creation_date = True # use dir creation date\n",
- "cal_db_interface = 'tcp://max-exfl016:8016' # calibrate db interface to connect to\n",
+ "cal_db_interface = 'tcp://max-exfl016:8016#8045' # calibrate db interface to connect to\n",
"cal_db_timeout = 300000 # timeout on caldb requests\n",
"local_output = True # output constants locally\n",
"db_output = False # output constants to database\n",
@@ -262,7 +262,7 @@
" condition=condition,\n",
" empty_constant=None,\n",
" cal_db_interface=cal_db_interface,\n",
- " creation_time=creation_time-timedelta(seconds=2) if creation_time else None,\n",
+ " creation_time=creation_time-timedelta(seconds=60) if creation_time else None,\n",
" strategy=\"pdu_prior_in_time\",\n",
" verbosity=1,\n",
" timeout=cal_db_timeout\n",
@@ -693,7 +693,7 @@
" for const in consts:\n",
" display(Markdown(f\" - {const} at {consts[const]['timestamp']}\"))\n",
" # saving locations of old constants for summary notebook\n",
- " with open(f\"{metadata_folder}/module_metadata_{mod}.yml\", \"w\") as fd:\n",
+ " with open(f\"{metadata_folder or out_folder}/module_metadata_{mod}.yml\", \"w\") as fd:\n",
" yaml.safe_dump(\n",
" {\n",
" \"module\": mod,\n",
diff --git a/notebooks/Jungfrau/Jungfrau_darks_Summary_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_darks_Summary_NBC.ipynb
index 5568147b7..55269def4 100644
--- a/notebooks/Jungfrau/Jungfrau_darks_Summary_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_darks_Summary_NBC.ipynb
@@ -127,7 +127,7 @@
"curr_constants = { c: initial_stacked_constants.copy() for c in dark_constants}\n",
"prev_constants = { c: initial_stacked_constants.copy() for c in dark_constants}\n",
"\n",
- "execulded_constants = [] # constants excluded from comparison plots.\n",
+ "exculded_constants = [] # constants excluded from comparison plots.\n",
"\n",
"# Loop over modules\n",
"for cname in dark_constants:\n",
@@ -160,7 +160,7 @@
" # Exclude constants from comparison plots, if the corresponding\n",
" # previous constants are not available for all modules.\n",
" if len(excluded_modules) == nmods:\n",
- " execulded_constants.append(cname)\n",
+ " exculded_constants.append(cname)\n",
" print(f\"No comparison plots for {cname}.\\n\")"
]
},
@@ -205,10 +205,11 @@
" \"Noise\": [(0., 5.), (0., 5.), (0., 5.)],\n",
" \"BadPixelsDark\": [(0., 5.), (0., 5.), (0., 5.)],\n",
"}\n",
- "\n",
+ "percentage_range = (0, 100)\n",
+ "perc_const_range = {c: [percentage_range]*3 for c in dark_constants}\n",
"gs = gridspec.GridSpec(2, 4)\n",
"\n",
- "axis = OrderedDict({\n",
+ "axes = {\n",
" \"ax0\": {\n",
" \"gs\": gs[0, 1:3],\n",
" \"shrink\": 0.7,\n",
@@ -216,6 +217,7 @@
" \"label\": \"ADCu\",\n",
" \"title\": \"{}\",\n",
" \"location\": \"right\",\n",
+ " \"range\": const_range,\n",
" },\n",
" \"ax1\": {\n",
" \"gs\": gs[1, :2],\n",
@@ -224,6 +226,7 @@
" \"label\": \"ADCu\",\n",
" \"location\": \"left\",\n",
" \"title\": \"Difference with previous {}\",\n",
+ " \"range\": diff_const_range,\n",
" },\n",
" \"ax2\": {\n",
" \"gs\": gs[1, 2:],\n",
@@ -231,8 +234,10 @@
" \"pad\": 0.02,\n",
" \"label\": \"%\",\n",
" \"location\": \"right\",\n",
- " \"title\": \"Difference with previous {} %\"},\n",
- " })"
+ " \"title\": \"Difference with previous {} %\",\n",
+ " \"range\": perc_const_range,\n",
+ " },\n",
+ " }"
]
},
{
@@ -273,20 +278,14 @@
" else:\n",
" fig = plt.figure(figsize=(20, 10))\n",
" \n",
- " for axname, axv in axis.items():\n",
- " # Add the min and max plot values for each axis.\n",
- " if axname == \"ax0\":\n",
- " vmin, vmax = const_range[cname][gain]\n",
- " elif axname == \"ax2\":\n",
- " vmin, vmax = 0, 100\n",
- " else:\n",
- " vmin, vmax = diff_const_range[cname][gain]\n",
+ " for axname, axv in axes.items():\n",
+ "\n",
" # Avoid difference plots if previous constants\n",
" # are missing for the detector.\n",
- " if cname in execulded_constants and axname != \"ax0\":\n",
+ " if cname in exculded_constants and axname != \"ax0\":\n",
" break\n",
" ax = fig.add_subplot(axv[\"gs\"])\n",
- "\n",
+ " vmin, vmax = axv[\"range\"][cname][gain]\n",
" geom.plot_data(\n",
" data_to_plot[axname],\n",
" vmin=vmin, vmax=vmax, ax=ax, \n",
@@ -323,9 +322,10 @@
"outputs": [],
"source": [
"if curr_constants[\"Offset\"].shape[-2] > 1:\n",
- " display(Markdown(\"## ## Summary across pixels per memory cells\"))\n",
+ " display(Markdown(\"## Summary across pixels per memory cells\"))\n",
"\n",
- " # Loop over modules and constants\n",
+ " # Plot mean and std of memcells for each module, gain, and constant\n",
+ " # across trains.\n",
" for const_name, const in curr_constants.items():\n",
" display(Markdown(f'### {const_name}'))\n",
"\n",
@@ -341,7 +341,7 @@
" figsize=(15, 6),\n",
" tight_layout={'pad': 0.2, 'w_pad': 1.3, 'h_pad': 1.3})\n",
" label = 'Fraction of bad pixels'\n",
- " ax = fig.add_subplot(111)\n",
+ " ax = fig.add_subplot(1, 1, 1)\n",
"\n",
" else:\n",
" datamean = np.nanmean(data, axis=(1, 2))\n",
@@ -349,7 +349,7 @@
" figsize=(15, 6),\n",
" tight_layout={'pad': 0.2, 'w_pad': 1.3, 'h_pad': 1.3})\n",
" label = f'{const_name} value [ADU], good pixels only'\n",
- " ax = fig.add_subplot(121)\n",
+ " ax = fig.add_subplot(1, 2, 1)\n",
"\n",
" d = []\n",
" for i, mod in enumerate(datamean):\n",
@@ -374,7 +374,7 @@
"\n",
" # Extra Sigma plot for Offset and Noise constants.\n",
" if const_name != 'BadPixelsDark':\n",
- " ax = fig.add_subplot(122)\n",
+ " ax = fig.add_subplot(1, 2, 2)\n",
" label = f'$\\sigma$ {const_name} [ADU], good pixels only'\n",
" d = []\n",
" for i, mod in enumerate(np.nanstd(data, axis=(1, 2))):\n",
--
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