From 48229114275b99f355ac433eab29066443daceb7 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Mon, 24 Oct 2022 22:53:18 +0200
Subject: [PATCH] update extra-geom, cfelpyutils, update plot, and dont remove
module YAML files
---
...rk_analysis_all_gains_burst_mode_NBC.ipynb | 2 +-
.../Jungfrau/Jungfrau_darks_Summary_NBC.ipynb | 59 +++++++++++--------
setup.py | 4 +-
3 files changed, 39 insertions(+), 26 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 a98cb8230..c394e0c86 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
@@ -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\"{out_folder}/module_metadata_{mod}.yml\", \"w\") as fd:\n",
+ " with open(f\"{metadata_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 05b5b2033..0e3818a73 100644
--- a/notebooks/Jungfrau/Jungfrau_darks_Summary_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_darks_Summary_NBC.ipynb
@@ -4,9 +4,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Jungfrau Dark Summary #\n",
+ "# Jungfrau Dark Summary\n",
"\n",
- "Author: European XFEL Detector Group, Version: 1.0\n",
+ "Author: European XFEL Detector Department, Version: 1.0\n",
"\n",
"Summary for process dark constants and a comparison with previously injected constants with the same conditions."
]
@@ -77,13 +77,12 @@
"dark_constants = [\"Offset\", \"Noise\", \"BadPixelsDark\"]\n",
"\n",
"prev_const_metadata = {}\n",
- "for fn in out_folder.glob(\"module_metadata_*.yml\"):\n",
+ "for fn in Path(metadata_folder or out_folder).glob(\"module_metadata_*.yml\"):\n",
" with fn.open(\"r\") as fd:\n",
" fdict = yaml.safe_load(fd)\n",
" module = fdict[\"module\"]\n",
" mod_mapping[module] = fdict[\"pdu\"]\n",
" prev_const_metadata[module] = fdict[\"old-constants\"]\n",
- " fn.unlink()\n",
"\n",
"metadata.save()"
]
@@ -180,6 +179,12 @@
" \"BadPixelsDark\": [(0., 5.), (0., 5.), (0., 5.)],\n",
"}\n",
"\n",
+ "diff_const_range = {\n",
+ " \"Offset\": [(0, 500), (0, 500), (0, 500)],\n",
+ " \"Noise\": [(0., 5.), (0., 5.), (0., 5.)],\n",
+ " \"BadPixelsDark\": [(0., 5.), (0., 5.), (0., 5.)],\n",
+ "}\n",
+ "\n",
"gs = gridspec.GridSpec(2, 4)\n",
"\n",
"axis = OrderedDict({\n",
@@ -187,14 +192,16 @@
" \"gs\": gs[0, 1:3],\n",
" \"shrink\": 0.9,\n",
" \"pad\": 0.05,\n",
- " \"label\": \"ADUs\",\n",
+ " \"label\": \"ADCu\",\n",
" \"title\": '{}',\n",
+ " 'location': 'right',\n",
" },\n",
" \"ax1\": {\n",
" \"gs\": gs[1, :2],\n",
" \"shrink\": 0.6,\n",
" \"pad\": 0.05,\n",
- " \"label\": \"ADUs\",\n",
+ " \"label\": \"ADCu\",\n",
+ " 'location': 'left',\n",
" \"title\": 'Difference with previous {}',\n",
" },\n",
" \"ax2\": {\n",
@@ -202,6 +209,7 @@
" \"shrink\": 0.6,\n",
" \"pad\": 0.05,\n",
" \"label\": \"%\",\n",
+ " 'location': 'right',\n",
" \"title\": 'Difference with previous {} %'},\n",
" })"
]
@@ -227,8 +235,8 @@
" # the difference with the previous constant\n",
" # and the fraction of that difference.\n",
" mean_const = np.nanmean(const, axis=3)\n",
- " mean_diff = np.nanmean(const, axis=3) - np.nanmean(prev_constants[cname], axis=3)\n",
- " mean_frac = (mean_diff / mean_const) * 100\n",
+ " mean_diff = np.abs(np.nanmean(const, axis=3) - np.nanmean(prev_constants[cname], axis=3)) # noqa\n",
+ " mean_frac = np.abs(mean_diff / mean_const) * 100\n",
" \n",
" for gain in range(gainstages):\n",
" plot_data = {\n",
@@ -247,37 +255,40 @@
" # 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 = get_range(plot_data[axname], 2)\n",
+ " vmin, vmax = diff_const_range[cname][gain]\n",
" ax = fig.add_subplot(axv[\"gs\"])\n",
"\n",
" geom.plot_data_fast(\n",
" plot_data[axname],\n",
" vmin=vmin, vmax=vmax, ax=ax, \n",
" colorbar={\n",
- " 'shrink': axv[\"shrink\"],\n",
- " 'pad': axv[\"pad\"],\n",
- " },\n",
+ " \"shrink\": axv[\"shrink\"],\n",
+ " \"pad\": axv[\"pad\"],\n",
+ " \"location\": axv[\"location\"]},\n",
" )\n",
"\n",
" colorbar = ax.images[0].colorbar\n",
- " colorbar.set_label(axv[\"label\"])\n",
+ " colorbar.set_label(axv[\"label\"], fontsize=15)\n",
" colorbar.ax.tick_params(labelsize=15)\n",
- " ax.tick_params(labelsize=15)\n",
+ " ax.tick_params(labelsize=1)\n",
" ax.set_title(axv[\"title\"].format(\n",
" f\"{cname} {gain_names[gain]}\"), fontsize=15)\n",
- " ax.set_xlabel('Columns', fontsize=15)\n",
- " ax.set_ylabel('Rows', fontsize=15)\n",
+ " \n",
+ " if axname == \"ax0\":\n",
+ " ax.set_xlabel('Columns', fontsize=15)\n",
+ " ax.set_ylabel('Rows', fontsize=15)\n",
+ " ax.tick_params(labelsize=15)\n",
+ " else:\n",
+ " ax.tick_params(labelsize=0)\n",
+ " # Remove axes labels for comparison plots.\n",
+ " ax.set_xlabel('')\n",
+ " ax.set_ylabel('')\n",
" plt.show()"
]
},
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Summary across pixels per memory cells"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -285,6 +296,8 @@
"outputs": [],
"source": [
"if curr_constants[\"Offset\"].shape[-2] > 1:\n",
+ " display(Markdown(\"## ## Summary across pixels per memory cells\"))\n",
+ "\n",
" # Loop over modules and constants\n",
" for const_name, const in curr_constants.items():\n",
" display(Markdown(f'### {const_name}'))\n",
diff --git a/setup.py b/setup.py
index aae7823b4..d7324fd81 100644
--- a/setup.py
+++ b/setup.py
@@ -58,14 +58,14 @@ install_requires = [
"markupsafe==2.0.1",
"astcheck==0.2.5",
"astsearch==0.2.0",
- "cfelpyutils==1.0.1",
+ "cfelpyutils==2.0.6",
"calibration_client==10.0.0",
"dill==0.3.0",
"docutils==0.17.1",
"dynaconf==3.1.4",
"env_cache==0.1",
"extra_data==1.12.0",
- "extra_geom==1.6.0",
+ "extra_geom==1.8.0",
"gitpython==3.1.0",
"h5py==3.5.0",
"iminuit==1.3.8",
--
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