{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Introduction to the tutorials\n", "\n", "## The iPython/Jupyter notebook\n", "\n", "The document you are seeing it may be a PDF or a web page or another format, but what is important is how it has been made ...\n", "\n", "According to this article in [Nature](http://www.nature.com/news/interactive-notebooks-sharing-the-code-1.16261) the Notebook, invented by iPython, and now part of the Jupyter project, is the revolution for data analysis which will allow reproducable science.\n", "\n", "This tutorial will introduce you to how to access to the notebook, how to use it and perform some basic data analysis with it and the pyFAI library.\n", "\n", "## Getting access to the notebook\n", "\n", "There are many cases ...\n", "\n", "### Inside ESRF\n", "The simplest case as the data analysis unit offers you a notebook server: just connect your web browser to http://scisoft13:8000 and authenticate with your ESRF credentials.\n", "\n", "### Outside ESRF with an ESRF account.\n", "The JupyterHub server is not directly available on the internet, but you can [login into the firewall](http://www.esrf.eu/Infrastructure/Computing/Networks/InternetAndTheFirewall/UsersManual/SSH) to forward the web server:\n", "\n", " ssh -XC -p5022 -L8000:scisoft13:8000 user@firewall.esrf.fr\n", "\n", "Once logged in ESRF, keep the terminal opened and browse on your local computer to http://localhost:8000 to authenticate with your ESRF credentials. Do not worry about confidentiality as the connection from your computer to the ESRF firewall is encrypted by the SSH connection.\n", "\n", "### Other cases\n", "In the most general case you will need to install the notebook on your local computer in addition to silx, pyFAI and FabIO to follow the tutorial. WinPython provides it under windows. Please refer to the installation procedure of pyFAI to install locally pyFAI on your computer. Anaconda provides also pyFAI and FabIO as packages.\n", "\n", "## Getting trained in using the notebook\n", "\n", "There are plenty of good tutorials on how to use the notebook.\n", "[This one](https://github.com/jupyter/mozfest15-training/blob/master/00-python-intro.ipynb) presents a quick overview of the Python programming language and explains how to use the notebook. Reading it is strongly encouraged before proceeding to the pyFAI itself.\n", "\n", "Anyway, the most important information is to use **Control-Enter** to evaluate a cell.\n", "\n", "In addition to this, we will need to download some files from the internet. \n", "The following cell contains a piece of code to download files using the silx library. You may have to adjust the proxy settings to be able to connect to internet, especially at ESRF, see the commented out code." ] }, { "cell_type": "markdown", "metadata": { "collapsed": true }, "source": [ "## Introduction to diffraction image analysis using the notebook\n", "\n", "All the tutorials in pyFAI are based on the notebook and if you wish to practice the exercises, you can download the notebook files (.ipynb) from [Github](https://github.com/silx-kit/pyFAI/tree/master/doc/source/usage/tutorial)\n", "\n", "### Load and display diffraction images\n", "\n", "First of all we will download an image and display it. Displaying it the right way is important as the orientation of the image imposes the azimuthal angle sign." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/mntdirect/_scisoft/users/jupyter/jupy35/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\n", " from ._conv import register_converters as _register_converters\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Using pyFAI version 0.15.0-beta4\n" ] } ], "source": [ "import os, time\n", "#Nota: comment out when outside ESRF\n", "os.environ[\"http_proxy\"] = \"http://proxy.esrf.fr:3128\"\n", "start_time = time.time()\n", "import pyFAI\n", "print(\"Using pyFAI version\", pyFAI.version)" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "from silx.resources import ExternalResources\n", "downloader = ExternalResources(\"pyFAI\", \"http://www.silx.org/pub/pyFAI/testimages/\", \"DATA\")" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/tmp/pyFAI_testdata_kieffer/moke.tif\n" ] } ], "source": [ "moke = downloader.getfile(\"moke.tif\")\n", "print(moke)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The *moke.tif* image we just downloaded is not a real diffraction image but it is a test pattern used in the tests of pyFAI. \n", "\n", "Prior to displaying it, we will use the Fable Input/Output library to read the content of the file:" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Populating the interactive namespace from numpy and matplotlib\n" ] } ], "source": [ "#initializes the visualization module to work with the jupyter notebook\n", "%pylab nbagg" ] }, { "cell_type": "code", "execution_count": 5, "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 = $('');\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": [ "Text(0.5,1,'Wrong orientation')" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "fig, ax = subplots(1,2, figsize=(10,5))\n", "ax[0].imshow(img, origin=\"lower\")\n", "ax[0].set_title(\"Proper orientation\")\n", "ax[1].imshow(img)\n", "ax[1].set_title(\"Wrong orientation\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Nota:** Displaying the image properly or not does not change the content of the image nor its representation in memory, it only changes its representation, which is important only for the user. **DO NOT USE** *numpy.flipud* or other array-manipulation which changes the memory representation of the image. This is likely to mess-up all your subsequent calculation.\n", "\n", "### 1D azimuthal integration\n", "\n", "To perform an azimuthal integration of this image, we need to create an **AzimuthalIntegrator** object we will call *ai*. \n", "Fortunately, the geometry is explained on the image." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Detector Detector\t Spline= None\t PixelSize= 1.000e-04, 1.000e-04 m\n", "SampleDetDist= 1.000000e-01m\tPONI= 0.000000e+00, 0.000000e+00m\trot1=0.000000 rot2= 0.000000 rot3= 0.000000 rad\n", "DirectBeamDist= 100.000mm\tCenter: x=0.000, y=0.000 pix\tTilt=0.000 deg tiltPlanRotation= 0.000 deg\n" ] } ], "source": [ "import pyFAI\n", "detector = pyFAI.detectors.Detector(pixel1=1e-4, pixel2=1e-4)\n", "ai = pyFAI.AzimuthalIntegrator(dist=0.1, detector=detector)\n", "# Short version ai = pyFAI.AzimuthalIntegrator(dist=0.1, pixel1=1e-4, pixel2=1e-4)\n", "print(ai)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Printing the *ai* object displays 3 lines:\n", "\n", " * The detector definition, here a simple detector with square, regular pixels with the right size\n", " * The detector position in space using the *pyFAI* coordinate system: dist, poni1, poni2, rot1, rot2, rot3\n", " * The detector position in space using the *FIT2D* coordinate system: direct_sample_detector_distance, center_X,\n", "center_Y, tilt and tilt_plan_rotation\n", "\n", "Right now, the geometry in the *ai* object is wrong. It may be easier to define it correctly using the *FIT2D* geometry which uses pixels for the center coordinates (but the sample-detector distance is in millimeters)." ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Help on method setFit2D in module pyFAI.geometry:\n", "\n", "setFit2D(directDist, centerX, centerY, tilt=0.0, tiltPlanRotation=0.0, pixelX=None, pixelY=None, splineFile=None) method of pyFAI.azimuthalIntegrator.AzimuthalIntegrator instance\n", " Set the Fit2D-like parameter set: For geometry description see\n", " HPR 1996 (14) pp-240\n", " \n", " Warning: Fit2D flips automatically images depending on their file-format.\n", " By reverse engineering we noticed this behavour for Tiff and Mar345 images (at least).\n", " To obtaine correct result you will have to flip images using numpy.flipud.\n", " \n", " :param direct: direct distance from sample to detector along the incident beam (in millimeter as in fit2d)\n", " :param tilt: tilt in degrees\n", " :param tiltPlanRotation: Rotation (in degrees) of the tilt plan arround the Z-detector axis\n", " * 0deg -> Y does not move, +X goes to Z<0\n", " * 90deg -> X does not move, +Y goes to Z<0\n", " * 180deg -> Y does not move, +X goes to Z>0\n", " * 270deg -> X does not move, +Y goes to Z>0\n", " \n", " :param pixelX,pixelY: as in fit2d they ar given in micron, not in meter\n", " :param centerX, centerY: pixel position of the beam center\n", " :param splineFile: name of the file containing the spline\n", "\n" ] } ], "source": [ "help(ai.setFit2D)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Detector Detector\t Spline= None\t PixelSize= 1.000e-04, 1.000e-04 m\n", "SampleDetDist= 1.000000e-01m\tPONI= 3.000000e-02, 3.000000e-02m\trot1=0.000000 rot2= 0.000000 rot3= 0.000000 rad\n", "DirectBeamDist= 100.000mm\tCenter: x=300.000, y=300.000 pix\tTilt=0.000 deg tiltPlanRotation= 0.000 deg\n" ] } ], "source": [ "ai.setFit2D(100, 300, 300)\n", "print(ai)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "With the *ai* object properly setup, we can perform the azimuthal integration using the *intergate1d* method.\n", "This methods takes only 2 mandatory parameters: the image to integrate and the number of bins. We will provide a few other to enforce the calculations to be performed in 2theta-space and in degrees:" ] }, { "cell_type": "code", "execution_count": 10, "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 = $('');\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": [ "Text(0,0.5,'Azimuthal angle chi (deg)')" ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "res2d = ai.integrate2d(img, 300, 360, unit=\"2th_deg\")\n", "\n", "#Display the integration result \n", "fig, ax = subplots(1,2, figsize=(10,5))\n", "jupyter.plot2d(res2d, label=\"moke\",ax=ax[0])\n", "\n", "#Example using pure matplotlib\n", "I, tth, chi = res2d\n", "ax[1].imshow(I, origin=\"lower\", extent=[tth.min(), tth.max(), chi.min(), chi.max()], aspect=\"auto\")\n", "ax[1].set_xlabel(\"2 theta (deg)\")\n", "ax[1].set_ylabel(\"Azimuthal angle chi (deg)\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The displayed images the \"caked\" image with the radial and azimuthal angles properly set on the axes. Search for the -180, -90, 360/0 and 180 mark on the transformed image.\n", "\n", "Like *integrate1d*, *integrate2d* offers the ability to save the intgrated image into an image file (EDF format by default) with again all metadata in the headers. \n", "\n", "### Radial integration\n", "\n", "Radial integration can directly be obtained from Caked images: " ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Column number 34\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": "stdout", "output_type": "stream", "text": [ "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0000.dat: 0.434s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0001.dat: 0.008s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0002.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0003.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0004.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0005.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0006.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0007.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0008.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0009.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0010.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0011.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0012.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0013.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0014.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0015.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0016.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0017.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0018.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0019.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0020.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0021.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0022.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0023.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0024.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0025.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0026.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0027.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0028.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0029.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0030.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0031.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0032.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0033.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0034.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0035.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0036.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0037.dat: 0.013s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0038.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0039.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0040.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0041.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0042.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0043.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0044.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0045.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0046.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0047.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0048.dat: 0.008s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0049.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/al2o3_0050.dat: 0.006s\n", "/tmp/pyFAI_testdata_kieffer/alumina/dark_0001.dat: 0.006s\n" ] } ], "source": [ "fig, ax = subplots()\n", "\n", "for one_file in all_edf:\n", " destination = os.path.splitext(one_file)[0]+\".dat\"\n", " image = fabio.open(one_file).data\n", " t0 = time.time()\n", " res = ai.integrate1d(image, 1000, filename=destination)\n", " print(\"%s: %.3fs\"%(destination, time.time()-t0))\n", " jupyter.plot1d(res, ax=ax)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "This was a simple integration of 50 files, saving the result into 2 column ASCII files.\n", "\n", "**Nota:** the first frame took 40x longer than the other. This highlights go crucial it is to re-use *azimuthal intgrator* objects when performance matters.\n", "\n", "## Conclusion\n", "Using the notebook is rather simple as it allows to mix comments, code, and images for visualization of scientific data.\n", "\n", "The basic use pyFAI's AzimuthalIntgrator has also been presented and may be adapted to you specific needs." ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Total execution time: 6.211s\n" ] } ], "source": [ "print(\"Total execution time: %.3fs\"%(time.time()-start_time))\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.5.3" } }, "nbformat": 4, "nbformat_minor": 1 }