From 1c824d4696813b8ce8baf922043edd57fad2698d Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Thu, 24 Mar 2022 07:15:09 +0100
Subject: [PATCH] separate header and new plots changes from this MR
---
...Jungfrau_Gain_Correct_and_Verify_NBC.ipynb | 84 ++++++-------------
1 file changed, 25 insertions(+), 59 deletions(-)
diff --git a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
index cc1fc79d8..4a8438abe 100644
--- a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
@@ -242,7 +242,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Retrieving calibration constants"
+ "### Retrieving calibration constants ###"
]
},
{
@@ -477,7 +477,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Correcting RAW data"
+ "### Correcting RAW data ###"
]
},
{
@@ -572,7 +572,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### Processing time summary"
+ "### Processing time summary ###"
]
},
{
@@ -660,6 +660,15 @@
"gain = jf_raw.get_array(\"data.gain\")[:, :, cell_idx_preview, ...].values"
]
},
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "### Single Train Preview ###\n",
+ "\n",
+ "A single image from the first train"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -689,13 +698,6 @@
" cb.set_label(\"Counts\")"
]
},
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Signal vs Gain Bit Value"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -722,7 +724,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## RAW Preview"
+ "### Mean RAW Preview ###\n",
+ "\n",
+ "The per pixel mean of the sequence file of RAW data"
]
},
{
@@ -731,7 +735,6 @@
"metadata": {},
"outputs": [],
"source": [
- "display(Markdown((f\"### The per pixel mean of sequence {first_seq} of the RAW data\")))\n",
"fig = plt.figure(figsize=(18, 20))\n",
"ax = fig.add_subplot(111)\n",
"raw_mean = np.mean(raw, axis=1)\n",
@@ -746,32 +749,13 @@
"plt.show()"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "display(Markdown((f\"### A single image from train {tid}\")))\n",
- "\n",
- "fig = plt.figure(figsize=(18, 20))\n",
- "ax = fig.add_subplot(111)\n",
- "geom.plot_data_fast(\n",
- " raw_train,\n",
- " ax=ax,\n",
- " vmin=min(0.75*np.median(raw_train[raw_train > 0]), 2000),\n",
- " vmax=max(1.5*np.median(raw_train[raw_train > 0]), 16000),\n",
- " cmap=\"jet\",\n",
- " colorbar={'shrink': 0.5, 'pad': 0.02}\n",
- ")\n",
- "plt.show()"
- ]
- },
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "## CORRECTED Preview"
+ "### Mean CORRECTED Preview ###\n",
+ "\n",
+ "The per pixel mean of the sequence file of CORR data"
]
},
{
@@ -780,8 +764,6 @@
"metadata": {},
"outputs": [],
"source": [
- "display(Markdown((f\"### The per pixel mean of sequence {first_seq} of the CORR data\")))\n",
- "\n",
"fig = plt.figure(figsize=(20, 25))\n",
"ax = fig.add_subplot(111)\n",
"corrected_mean = np.mean(corrected, axis=1)\n",
@@ -862,7 +844,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Maximum GAIN Preview"
+ "### Maximum GAIN Preview ###\n",
+ "\n",
+ "The per pixel maximum of the first train of the GAIN data"
]
},
{
@@ -889,8 +873,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Bad Pixels\n",
- "\n",
+ "## Bad Pixels ##\n",
"The mask contains dedicated entries for all pixels and memory cells as well as all three gains stages. Each mask entry is encoded in 32 bits as:"
]
},
@@ -913,7 +896,9 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "### Single Image Bad Pixels"
+ "### Single Image Bad Pixels ###\n",
+ "\n",
+ "A single image bad pixel map for the first image of the first train"
]
},
{
@@ -935,25 +920,6 @@
")\n",
"plt.show()"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "display(Markdown(f\"#### Bad pixels fraction for cellId {sc_start} across sequence {first_seq}\"))\n",
- "\n",
- "fig = plt.figure(figsize=(18, 20))\n",
- "ax = fig.add_subplot(111)\n",
- "geom.plot_data_fast(\n",
- " np.mean(mask>0, axis=1),\n",
- " ax=ax,\n",
- " vmin=0, vmax=1, cmap=\"jet\",\n",
- " colorbar={'shrink': 0.5, 'pad': 0.02},\n",
- ")\n",
- "plt.show()"
- ]
}
],
"metadata": {
--
GitLab