{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Calibration of a 2 theta arm with a Pilatus 100k detector\n", "\n", "The aim of this document is to explain how to use pyFAI.goniometer for calibrating the position of the detector from the goniometer encoders.\n", "\n", "Those data have been acquired at ROBL (ESRF-BM20 German CRG) in winter 2017 by Christoph Henning using a Pilatus 100k detector and LaB6 as calibrant. One hundred and twenty one images have been acquired with the detector moving between 5 and 65 degree with a step size of half a degree. The motor position is registered in the filename.\n", "\n", "A prior manual calibration (using pyFAI-calib) has been performed on four images locate at 31.5, 33.5, 35 and 35.5 degrees. Those images were the first with two rings. The control points extrated during this initial calibration has been used as a starting point for this calibration. Then more images have been added to make the model more robust.\n", "\n", "The raw data files are available at: http://www.silx.org/pub/pyFAI/gonio/Pilatus-100k-LaB6/\n", "\n", "## Initialization and loading of the libraries\n", "\n", "Initialization of the plotting library, matplotlib, to be used with the jupyter notebook" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Populating the interactive namespace from numpy and matplotlib\n", "Using pyFAI version 0.18.0\n" ] } ], "source": [ "%pylab nbagg\n", "\n", "import time, pyFAI\n", "start_time = time.time()\n", "print(\"Using pyFAI version\", pyFAI.version)" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "['LaB6_gonio_BM20', 'del_45.0_0001p.cbf', 'del_08.5_0001p.cbf', 'del_20.5_0001p.cbf', 'minimum-mask.edf', 'del_09.0_0001p.cbf', 'del_53.0_0001p.cbf', 'del_60.0_0001p.cbf', 'del_63.5_0001p.cbf', 'del_56.5_0001p.cbf', 'del_12.5_0001p.cbf', 'del_53.5_0001p.cbf', 'del_42.5_0001p.cbf', 'del_16.5_0001p.cbf', 'del_05.5_0001p.cbf', 'del_47.0_0001p.cbf', 'del_39.0_0001p.cbf', 'del_47.5_0001p.cbf', 'del_57.0_0001p.cbf', 'del_35.5_0001p.poni', 'del_07.5_0001p.cbf', 'del_41.5_0001p.cbf', 'del_51.0_0001p.cbf', 'del_33.0_0001p.cbf', 'del_22.0_0001p.cbf', 'del_43.5_0001p.cbf', 'del_64.5_0001p.cbf', 'del_35.0_0001p.cbf', 'del_13.5_0001p.cbf', 'del_08.0_0001p.cbf', 'del_29.0_0001p.cbf', 'del_45.5_0001p.cbf', 'del_63.0_0001p.cbf', 'del_61.5_0001p.cbf', 'del_31.5_0001p.npt', 'del_11.0_0001p.cbf', 'del_46.5_0001p.cbf', 'del_11.5_0001p.cbf', 'del_56.0_0001p.cbf', 'del_18.0_0001p.cbf', 'del_06.5_0001p.cbf', 'del_46.0_0001p.cbf', 'del_58.5_0001p.cbf', 'del_35.5_0001p.npt', 'del_30.0_0001p.cbf', 'del_15.5_0001p.cbf', 'del_36.5_0001p.cbf', 'del_13.0_0001p.cbf', 'del_55.0_0001p.cbf', 'del_27.5_0001p.cbf', 'del_31.5_0001p.cbf', 'del_24.0_0001p.cbf', 'del_38.0_0001p.cbf', 'del_48.5_0001p.cbf', 'del_16.0_0001p.cbf', 'del_52.5_0001p.cbf', 'del_38.5_0001p.cbf', 'del_54.5_0001p.cbf', 'del_48.0_0001p.cbf', 'del_31.0_0001p.cbf', 'del_28.5_0001p.cbf', 'del_21.5_0001p.cbf', 'del_06.0_0001p.cbf', 'del_25.5_0001p.cbf', 'del_40.5_0001p.cbf', 'del_44.5_0001p.cbf', 'del_39.5_0001p.cbf', 'del_35.5_0001p.cbf', 'del_62.0_0001p.cbf', 'del_36.0_0001p.cbf', 'del_57.5_0001p.cbf', 'del_28.0_0001p.cbf', 'del_17.5_0001p.cbf', 'del_24.5_0001p.cbf', 'del_35.0_0001p.poni', 'del_50.5_0001p.cbf', 'del_18.5_0001p.cbf', 'del_27.0_0001p.cbf', 'del_19.5_0001p.cbf', 'del_21.0_0001p.cbf', 'del_17.0_0001p.cbf', 'del_50.0_0001p.cbf', 'del_44.0_0001p.cbf', 'del_30.5_0001p.cbf', 'del_51.5_0001p.cbf', 'del_62.5_0001p.cbf', 'del_05.0_0001p.cbf', 'del_26.5_0001p.cbf', 'del_31.5_0001p.poni', 'del_23.5_0001p.cbf', 'del_33.5_0001p.poni', 'del_37.5_0001p.cbf', 'del_19.0_0001p.cbf', 'del_29.5_0001p.cbf', 'del_10.0_0001p.cbf', 'del_40.0_0001p.cbf', 'del_58.0_0001p.cbf', 'del_49.5_0001p.cbf', 'del_09.5_0001p.cbf', 'del_15.0_0001p.cbf', 'del_43.0_0001p.cbf', 'del_60.5_0001p.cbf', 'del_34.0_0001p.cbf', 'del_20.0_0001p.cbf', 'deviation-mask.edf', 'del_41.0_0001p.cbf', 'del_07.0_0001p.cbf', 'del_54.0_0001p.cbf', 'del_33.5_0001p.npt', 'del_33.5_0001p.cbf', 'del_32.0_0001p.cbf', 'del_59.5_0001p.cbf', 'del_14.0_0001p.cbf', 'del_32.5_0001p.cbf', 'del_59.0_0001p.cbf', 'del_65.0_0001p.cbf', 'del_25.0_0001p.cbf', 'del_61.0_0001p.cbf', 'del_34.5_0001p.cbf', 'del_52.0_0001p.cbf', 'del_22.5_0001p.cbf', 'del_10.5_0001p.cbf', 'del_42.0_0001p.cbf', 'del_64.0_0001p.cbf', 'del_14.5_0001p.cbf', 'del_26.0_0001p.cbf', 'del_49.0_0001p.cbf', 'del_35.0_0001p.npt', 'del_55.5_0001p.cbf', 'del_23.0_0001p.cbf', 'del_12.0_0001p.cbf', 'del_37.0_0001p.cbf']\n" ] } ], "source": [ "#Download all images\n", "\n", "import os\n", "from silx.resources import ExternalResources\n", "\n", "#Nota: This may be useful if you are behind a firewall\n", "#os.environ[\"http_proxy\"] = \"http://proxy.esrf.fr:3128\"\n", "\n", "downloader = ExternalResources(\"pyFAI\", \"http://www.silx.org/pub/pyFAI/testimages\", \"PYFAI_DATA\")\n", "all_files = downloader.getdir(\"LaB6_gonio_BM20.tar.bz2\")\n", "print([os.path.basename(i) for i in all_files])\n" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "#Loading of a few libraries\n", "\n", "import os\n", "import random\n", "import fabio\n", "import pyFAI\n", "from pyFAI.goniometer import GeometryTransformation, GoniometerRefinement, Goniometer\n", "from pyFAI.gui import jupyter" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Display of an image and its headers" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "List of images: /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_05.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_05.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_06.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_06.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_07.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_07.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_08.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_08.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_09.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_09.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_10.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_10.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_11.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_11.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_12.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_12.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_13.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_13.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_14.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_14.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_15.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_15.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_16.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_16.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_17.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_17.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_18.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_18.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_19.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_19.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_20.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_20.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_21.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_21.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_22.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_22.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_23.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_23.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_24.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_24.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_25.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_25.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_26.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_26.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_27.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_27.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_28.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_28.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_29.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_29.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_30.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_30.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_31.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_31.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_32.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_32.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_33.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_33.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_34.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_34.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_35.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_35.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_36.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_36.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_37.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_37.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_38.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_38.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_39.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_39.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_40.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_40.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_41.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_41.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_42.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_42.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_43.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_43.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_44.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_44.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_45.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_45.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_46.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_46.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_47.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_47.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_48.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_48.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_49.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_49.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_50.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_50.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_51.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_51.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_52.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_52.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_53.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_53.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_54.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_54.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_55.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_55.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_56.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_56.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_57.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_57.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_58.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_58.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_59.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_59.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_60.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_60.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_61.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_61.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_62.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_62.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_63.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_63.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_64.0_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_64.5_0001p.cbf, /tmp/pyFAI_testdata_kieffer/LaB6_gonio_BM20/del_65.0_0001p.cbf.\n", "\n", "Image headers:\n", "_array_data.header_convention: PILATUS_1.2\n", "_array_data.header_contents: # Detector: PILATUS 2M, 24-0111\r\n", "# 2016-05-17T18:12:57.232113\r\n", "# Pixel_size 172e-6 m x 172e-6 m\r\n", "# Silicon sensor, thickness 0.000450 m\r\n", "# Exposure_time 9.9977 s\r\n", "# Exposure_period 9.9977 s\r\n", "# Tau = 1.991e-07 s\r\n", "# Count_cutoff 1071182 counts\r\n", "# Threshold_setting: 4024.0 eV\r\n", "# Gain_setting: low gain (vrf = -0.300)\r\n", "# N_excluded_pixels = 1\r\n", "# Excluded_pixels: badpix_mask.tif\r\n", "# Flat_field: FF_p2m0111_E26000_T13000_vrf_m0p30.tif\r\n", "# Trim_file: p2m0111_E26000_T13000_vrf_m0p30.bin\r\n", "# Image_path: /ramdisk/\r\n", "# Wavelength 0.7749 A\r\n", "# Start_angle 0.00 deg.\r\n", "# Angle_increment 0.00 deg.\r\n", "# Omega 0.00 deg.\r\n", "# Omega_increment 0.00 deg.\r\n", "# Phi 0.00 deg.\r\n", "# Phi_increment 0.00 deg.\r\n", "# Kappa 0.0 deg.\r\n", "# Oscillation_axis PHI\r\n", "# Detector_distance 0.157 m\r\n", "# Detector_Voffset 0.0 m\r\n", "# Beam_xy (542.41, 732.4) pixels\r\n", "# Flux 0 counts\r\n", "# Temperature 0.00 K\r\n", "# Blower 0.0 C\r\n", "# Lakeshore 0.00 K\n", "Content-Type: application/octet-stream;\n", "conversions: x-CBF_BYTE_OFFSET\n", "Content-Transfer-Encoding: BINARY\n", "X-Binary-Size: 95035\n", "X-Binary-ID: 1\n", "X-Binary-Element-Type: signed 32-bit integer\n", "X-Binary-Element-Byte-Order: LITTLE_ENDIAN\n", "Content-MD5: darooj/7FEQRNdNzNDo0XQ==\n", "X-Binary-Number-of-Elements: 94965\n", "X-Binary-Size-Fastest-Dimension: 487\n", "X-Binary-Size-Second-Dimension: 195\n", "X-Binary-Size-Padding: 4095\n" ] }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('
');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stderr", "output_type": "stream", "text": [ "WARNING:matplotlib.legend:No handles with labels found to put in legend.\n", "WARNING:matplotlib.legend:No handles with labels found to put in legend.\n", "WARNING:matplotlib.legend:No handles with labels found to put in legend.\n" ] } ], "source": [ "#Display all images with associated calibration:\n", "nimg = len(gonioref.single_geometries)\n", "fig,ax = subplots(nimg, 1, figsize=(8,nimg*3))\n", "for i, sg in enumerate(gonioref.single_geometries.values()):\n", " jupyter.display(sg=sg, ax=ax[i])" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Cost function before refinement: 4.676280279481871e-05\n", "[0.8 0.02 0.04 0. 0. 0.01745329]\n", " fun: 3.4745458906298305e-09\n", " jac: array([ 1.55798347e-08, 6.20440474e-08, -8.86844706e-09, 9.38192904e-09,\n", " 4.54171479e-08, 5.30001824e-06])\n", " message: 'Optimization terminated successfully.'\n", " nfev: 145\n", " nit: 18\n", " njev: 18\n", " status: 0\n", " success: True\n", " x: array([ 0.80587963, 0.01626972, 0.04374852, -0.00299843, -0.00217847,\n", " 0.01745329])\n", "Cost function after refinement: 3.4745458906298305e-09\n", "GonioParam(dist=0.8058796325498109, poni1=0.016269720089887214, poni2=0.04374852459791066, rot1=-0.00299843026796996, rot2_offset=-0.002178469918866194, rot2_scale=0.017453292519943295)\n", "maxdelta on: dist (0) 0.8 --> 0.8058796325498109\n" ] }, { "data": { "text/plain": [ "array([ 0.80587963, 0.01626972, 0.04374852, -0.00299843, -0.00217847,\n", " 0.01745329])" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Initial refinement of the goniometer model with 5 dof\n", "gonioref.refine2()" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [], "source": [ "# This function adds new images to the pool of data used for the refinement.\n", "# A set of new control points are extractred and a refinement step is performed at each iteration\n", "# The last image of the serie is displayed \n", "\n", "def optimize_with_new_images(list_images, pts_per_deg=1):\n", " sg = None\n", " for fname in list_images:\n", " print()\n", " basename = os.path.basename(fname)\n", " base = os.path.splitext(basename)[0]\n", " fimg = fabio.open(fname)\n", " if base in gonioref.single_geometries:\n", " continue\n", " print(base)\n", " sg = gonioref.new_geometry(base, image=fimg.data, metadata=base,\n", " calibrant=LaB6)\n", " print(sg.extract_cp(pts_per_deg=pts_per_deg))\n", " print(\"*\"*50)\n", " gonioref.refine2()\n", " if sg: \n", " sg.geometry_refinement.set_param(gonioref.get_ai(sg.get_position()).param)\n", " jupyter.display(sg=sg)\n" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "\n", "del_32.5_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# c ring 7: 36 points\n", "\n", "del_30.5_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# d ring 6: 36 points\n", "\n", "\n", "del_39.0_0001p\n", "ControlPoints instance containing 2 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 2 groups of points:\n", "# e ring 10: 15 points\n", "# f ring 11: 30 points\n", "\n", "del_36.0_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# g ring 9: 36 points\n", "\n", "del_34.0_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# h ring 8: 36 points\n", "\n", "\n", "del_34.5_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# i ring 8: 36 points\n", "\n", "del_33.0_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# j ring 7: 36 points\n", "\n", "del_31.0_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# k ring 6: 36 points\n", "\n", "del_36.5_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# l ring 9: 36 points\n", "\n", "\n", "del_32.0_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# m ring 7: 36 points\n", "\n", "del_38.0_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# n ring 10: 30 points\n", "\n", "del_37.0_0001p\n", "ControlPoints instance containing 2 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 2 groups of points:\n", "# o ring 9: 36 points\n", "# p ring 10: 30 points\n", "\n", "del_38.5_0001p\n", "ControlPoints instance containing 2 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 2 groups of points:\n", "# q ring 10: 30 points\n", "# r ring 11: 30 points\n", "\n", "del_30.0_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# s ring 6: 36 points\n", "\n", "del_37.5_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# t ring 10: 30 points\n", "\n", "del_39.5_0001p\n", "ControlPoints instance containing 1 group of point:\n", "LaB6 Calibrant with 97 reflections at wavelength 7.7490120575e-11\n", "Containing 1 groups of points:\n", "# u ring 11: 30 points\n", "**************************************************\n", "Cost function before refinement: 3.813327532311906e-09\n", "[ 0.80587963 0.01626972 0.04374852 -0.00299843 -0.00217847 0.01745329]\n", " fun: 3.812335448053385e-09\n", " jac: array([-2.22773900e-08, -2.33643926e-06, -5.14150986e-07, 4.15150166e-07,\n", " -1.88629408e-06, -1.01147741e-04])\n", " message: 'Optimization terminated successfully.'\n", " nfev: 10\n", " nit: 1\n", " njev: 1\n", " status: 0\n", " success: True\n", " x: array([ 0.80587964, 0.0162702 , 0.04374863, -0.00299852, -0.00217808,\n", " 0.01745329])\n", "Cost function after refinement: 3.812335448053385e-09\n", "GonioParam(dist=0.805879637162137, poni1=0.016270203827866713, poni2=0.04374863104808195, rot1=-0.0029985162209439967, rot2_offset=-0.0021780793792502335, rot2_scale=0.017453292519943295)\n", "maxdelta on: poni1 (1) 0.016269720089887214 --> 0.016270203827866713\n" ] }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('
');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Append all other images\n", "\n", "all_images = [i for i in all_files if i.endswith(\".cbf\")]\n", "random.shuffle(all_images)\n", "optimize_with_new_images(all_images)" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "First & last rings\n", "Total number of images: 121\n" ] }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('
');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Integrate the whole set of images in a single run:\n", "\n", "res = multigeo.integrate1d(images, npt)\n", "jupyter.plot1d(res)\n" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [], "source": [ "# Save the goniometer configuration with 1 angle\n", "\n", "gonioref.save(\"ROBL_v1.json\")" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "1.1942389076112182e-08 1.1942389076112182e-08\n", "Cost function before refinement: 1.1942389076112182e-08\n", "[ 0.80589541 0.01621863 0.04325154 -0.00259669 0. -0.00221956\n", " 0.01745653]\n", " fun: 4.771332375726204e-09\n", " jac: array([ 7.51745395e-08, 3.65634497e-08, -3.23285264e-08, 2.71254135e-08,\n", " -1.14617673e-07, 2.69500796e-08, -2.99239233e-06])\n", " message: 'Optimization terminated successfully.'\n", " nfev: 112\n", " nit: 12\n", " njev: 12\n", " status: 0\n", " success: True\n", " x: array([ 8.05907458e-01, 1.62095935e-02, 4.16735154e-02, -1.32101442e-03,\n", " -1.35396963e-04, -2.22709995e-03, 1.74566297e-02])\n", "Cost function after refinement: 4.771332375726204e-09\n", "GonioParam(dist=0.8059074581036026, poni1=0.01620959350506622, poni2=0.041673515394250335, rot1=-0.0013210144198282034, rot1_scale=-0.0001353969630508145, rot2_offset=-0.0022270999476141687, rot2_scale=0.01745662973261901)\n", "maxdelta on: poni2 (2) 0.04325154482302155 --> 0.041673515394250335\n" ] } ], "source": [ "#Can the refinement be improved by freeing another degree of freedom ? what about rot1 ?\n", "\n", "goniotrans2 = GeometryTransformation(param_names = [\"dist\", \"poni1\", \"poni2\", \n", " \"rot1\", \"rot1_scale\",\n", " \"rot2_offset\", \"rot2_scale\"],\n", " dist_expr=\"dist\", \n", " poni1_expr=\"poni1\",\n", " poni2_expr=\"poni2\", \n", " rot1_expr=\"rot1_scale * pos + rot1\", \n", " rot2_expr=\"rot2_scale * pos + rot2_offset\", \n", " rot3_expr=\"0.0\")\n", "\n", "param2 = (gonioref.nt_param(*gonioref.param))._asdict()\n", "param2[\"rot1_scale\"] = 0\n", "\n", "gonioref2 = GoniometerRefinement(param2, \n", " pos_function = get_angle,\n", " trans_function=goniotrans2,\n", " detector=pilatus,\n", " wavelength=wavelength)\n", "gonioref2.single_geometries = gonioref.single_geometries.copy()\n", "\n", "print(gonioref2.chi2(), gonioref.chi2())\n", "gonioref2.refine2()\n", "gonioref2.save(\"ROBL_v2.json\")" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "First & last rings\n" ] }, { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. 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');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('tabindex', 0)\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "\n", "}\n", "\n", "mpl.figure.prototype._key_event_extra = function(event, name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager)\n", " manager = IPython.keyboard_manager;\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\n", "\n", "\n", "mpl.find_output_cell = function(html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i=0; i= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] == html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "}\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel != null) {\n", " IPython.notebook.kernel.comm_manager.register_target('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "" ] }, "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Create a MultiGeometry integrator from the refined geometry and display the integrated image:\n", "\n", "multigeo2 = gonioref2.get_mg(angles)\n", "multigeo2.radial_range=(4, 66)\n", "print(multigeo2)\n", "\n", "res2 = multigeo2.integrate1d(images, npt)\n", "\n", "#Display the 2 curves with a zoom\n", "fig = figure(figsize=(10,5))\n", "ax = fig.add_subplot(1,2,1)\n", "ax.plot(*res2, label=\"rot1 & rot2 rotation\")\n", "ax.plot(*res, label=\"rot2 only rotation\")\n", "ax.set_xlabel(res.unit.label)\n", "ax.set_ylabel(\"Intensity\")\n", "ax.set_title(\"Azimuthal integration of 121 images merged\")\n", "ax.legend()\n", "ay = fig.add_subplot(1,2,2)\n", "ay.plot(*res2, label=\"rot1 & rot2 rotation\")\n", "ay.plot(*res, label=\"rot2 only rotation\")\n", "ay.set_xlabel(res.unit.label)\n", "ay.set_ylabel(\"Intensity\")\n", "ay.set_xlim(10.5,11)\n", "ay.set_title(\"Zoom on first peak\")\n", "ay.legend()\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "With the first model, the refinement was not perfect on the very low angles and indicates a miss-fit. Relaxing the constrains on *rot1* allowed to spot a non (perfect) orthogonality between the goniometer axis and the incident beam. Releasing the distances is also possible, for example to cope with the sample not perfectly mounted on the center of the goniometer. \n", "\n", "## Evaluation of the peak-profile\n", "\n", "For every peak, as listed in the calibrant's definition, the peak height can be extracted and the nearest minimum evaluated. The the full width at half maximum can be measured an ploted as function of the scattering angle. \n", "The FWHM can be fitted against Caglioti's formula: \n", "\n", "FWHM² = U tan² $\\theta$ + V tan $\\theta$ + W" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [], "source": [ "# Line profile function...\n", "#Peak profile\n", "\n", "from scipy.interpolate import interp1d\n", "from scipy.optimize import bisect\n", "\n", "def calc_fwhm(integrate_result, calibrant):\n", " \"calculate the tth position and FWHM for each peak\"\n", " delta = integrate_result.intensity[1:] - integrate_result.intensity[:-1]\n", " maxima = numpy.where(numpy.logical_and(delta[:-1]>0, delta[1:]<0))[0]\n", " minima = numpy.where(numpy.logical_and(delta[:-1]<0, delta[1:]>0))[0]\n", " maxima += 1\n", " minima += 1\n", " tth = []\n", " FWHM = []\n", " for tth_rad in calibrant.get_2th():\n", " tth_deg = tth_rad*integrate_result.unit.scale\n", " if (tth_deg<=integrate_result.radial[0]) or (tth_deg>=integrate_result.radial[-1]):\n", " continue\n", " idx_theo = abs(integrate_result.radial-tth_deg).argmin()\n", " id0_max = abs(maxima-idx_theo).argmin()\n", " id0_min = abs(minima-idx_theo).argmin()\n", " I_max = integrate_result.intensity[maxima[id0_max]]\n", " I_min = integrate_result.intensity[minima[id0_min]]\n", " tth_maxi = integrate_result.radial[maxima[id0_max]]\n", " I_thres = (I_max + I_min)/2.0\n", " if minima[id0_min]>maxima[id0_max]:\n", " if id0_min == 0:\n", " min_lo = integrate_result.radial[0]\n", " else:\n", " min_lo = integrate_result.radial[minima[id0_min-1]]\n", " min_hi = integrate_result.radial[minima[id0_min]]\n", " else:\n", " if id0_min == len(minima) -1:\n", " min_hi = integrate_result.radial[-1]\n", " else:\n", " min_hi = integrate_result.radial[minima[id0_min+1]]\n", " min_lo = integrate_result.radial[minima[id0_min]]\n", "\n", " f = interp1d(integrate_result.radial, integrate_result.intensity-I_thres)\n", " tth_lo = bisect(f, min_lo, tth_maxi)\n", " tth_hi = bisect(f, tth_maxi, min_hi)\n", " FWHM.append(tth_hi-tth_lo)\n", " tth.append(tth_deg)\n", " return tth, FWHM\n" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('
')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\n", " for(var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('