update notebooks

PaNOSC-ViNYL · Oct 29, 2020 · babf67f · babf67f
1 parent 5fb555b
commit babf67f
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diff --git a/simex/SFX/crystFEL-docker.ipynb b/simex/SFX/crystFEL-docker.ipynb
diff --git a/simex/SFX/crystFEL.ipynb b/simex/SFX/crystFEL.ipynb
diff --git a/simex/SPI/diffrChaperonins.ipynb b/simex/SPI/diffrChaperonins.ipynb
@@ -2,9 +2,17 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "initializing ocelot...\n"
+     ]
+    }
+   ],
    "source": [
     "import os,shutil\n",
     "import h5py\n",
@@ -106,7 +114,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -150,20 +158,23 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "PDB file /gpfs/exfel/data/user/juncheng/M5.2DEMO/simex/SPI/3IYF.pdb could not be found. Attempting to query from protein database server.\n",
-      "Downloading PDB structure '3IYF'...\n",
-      "110.63360626716167 s\n"
+      "150.22291002096608 s\n",
+      "Successful!\n"
      ]
     }
    ],
    "source": [
     "from timeit import default_timer as timer\n",
     "start = timer()\n",
     "\n",
-    "diffractor.backengine()\n",
+    "status = diffractor.backengine()\n",
     "\n",
     "end = timer()\n",
-    "print(end - start,'s') # Time in seconds"
+    "print(end - start,'s') # Time in seconds\n",
+    "if (status == 0):\n",
+    "    print (\"Successful!\")\n",
+    "else:\n",
+    "    print (\"Error code:\",status)"
    ]
   },
   {
@@ -185,7 +196,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -203,7 +214,7 @@
        " <AxesSubplot:xlabel='$x$ (pixel)', ylabel='$y$ (pixel)'>)"
       ]
      },
-     "execution_count": 33,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -239,7 +250,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -281,15 +292,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
       "WARNING:pyFAI.DEPRECATION:function, AzimuthalIntegrator is deprecated since silx version 0.16! Use 'pyFAI.azimuthalIntegrator.AzimuthalIntegrator' instead.\n",
-      "  File \"/gpfs/exfel/data/user/juncheng/miniconda3/envs/simex0.5/lib/python3.7/site-packages/SimEx/Analysis/DiffractionAnalysis.py\", line 528, in azimuthalIntegration\n",
+      "  File \"/opt/SimEx-master/Sources/python/SimEx/Analysis/DiffractionAnalysis.py\", line 528, in azimuthalIntegration\n",
       "    wavelength=lmd*1e-9)\n",
       "WARNING:silx.opencl.common:Unable to import pyOpenCl. Please install it from: http://pypi.python.org/pypi/pyopencl\n"
      ]
@@ -320,19 +331,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 37,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "*************************\n",
+      "Photon number statistics per pattern\n",
       "avg = 1.05245e+06\n",
       "std = 5.53632e+04\n",
-      "avg_mean = 1.05245e+02\n",
-      "avg_max = 3.03735e+04\n",
-      "avg_min = 2.49232e-04\n",
+      "Photon number statistics per pixel\n",
+      "avg_mean_pixel = 1.05245e+02\n",
+      "avg_max_pixel = 3.03735e+04\n",
+      "avg_min_pixel = 2.49232e-04\n",
       "*************************\n"
      ]
     },
@@ -362,7 +375,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -371,7 +384,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
@@ -388,16 +401,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<matplotlib.image.AxesImage at 0x2b2427cb9dd0>"
+       "<matplotlib.image.AxesImage at 0x7ff82033b850>"
       ]
      },
-     "execution_count": 41,
+     "execution_count": 16,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -417,13 +430,20 @@
    "source": [
     "plt.imshow(diffr_data[0])"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 823852."
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "simex0.5",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "simex0.5"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -435,7 +455,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.8"
+   "version": "3.7.7"
   }
  },
  "nbformat": 4,