{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Detector distortion corrections\n", "\n", "This tutorial shows how to correct images for spatial distortion. Some tutorial examples rely on files available in http://www.silx.org/pub/pyFAI/testimages/ and will be downloaded during this tutorial. The required minimum version of pyFAI is 0.12.0.\n", "\n", "## Detector definitions\n", "\n", "PyFAI features an impressive list of 64 detector definitions contributed often by manufacturers and some other reverse engineerd by scientists. \n", "Each of them is defined as an invividual class which contains a way to calculate the mask (invalid pixels, gaps,…) and a method to calculate the pixel positions in Cartesian coordinates. \n" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "pyFAI version: 0.18.0\n", "Number of detectors registered: 189 with 64 unique detectors\n", "\n", "List of all supported detectors\n", "Detector Quantum 210\t Spline= None\t PixelSize= 5.100e-05, 5.100e-05 m\n", "Detector Quantum 270\t Spline= None\t PixelSize= 6.480e-05, 6.480e-05 m\n", "Detector Quantum 315\t Spline= None\t PixelSize= 5.100e-05, 5.100e-05 m\n", "Detector Quantum 4\t Spline= None\t PixelSize= 8.200e-05, 8.200e-05 m\n", "Detector Aarhus\t Spline= None\t PixelSize= 2.489e-05, 2.489e-05 m\n", "Detector ApexII\t PixelSize= 1.200e-04, 1.200e-04 m\n", "Detector aca1300\t PixelSize= 3.750e-06, 3.750e-06 m\n", "Detector CirPAD\t PixelSize= 1.300e-04, 1.300e-04 m\n", "Undefined detector\n", "Detector Dexela 2923\t PixelSize= 7.500e-05, 7.500e-05 m\n", "Detector Eiger 16M\t PixelSize= 7.500e-05, 7.500e-05 m\n", "Detector Eiger 1M\t PixelSize= 7.500e-05, 7.500e-05 m\n", "Detector Eiger 4M\t PixelSize= 7.500e-05, 7.500e-05 m\n", "Detector Eiger 500k\t PixelSize= 7.500e-05, 7.500e-05 m\n", "Detector Eiger 9M\t PixelSize= 7.500e-05, 7.500e-05 m\n", "Detector FReLoN\t Spline= None\t PixelSize= 5.000e-05, 5.000e-05 m\n", "Detector Fairchild\t PixelSize= 1.500e-05, 1.500e-05 m\n", "Detector HF-130k\t Spline= None\t PixelSize= 1.500e-04, 1.500e-04 m\n", "Detector HF-1M\t Spline= None\t PixelSize= 1.500e-04, 1.500e-04 m\n", "Detector HF-262k\t Spline= None\t PixelSize= 1.500e-04, 1.500e-04 m\n", "Detector HF-2.4M\t Spline= None\t PixelSize= 1.500e-04, 1.500e-04 m\n", "Detector HF-4M\t Spline= None\t PixelSize= 1.500e-04, 1.500e-04 m\n", "Detector HF-9.4M\t Spline= None\t PixelSize= 1.500e-04, 1.500e-04 m\n", "Detector Imxpad S10\t PixelSize= 1.300e-04, 1.300e-04 m\n", "Detector Imxpad S140\t PixelSize= 1.300e-04, 1.300e-04 m\n", "Detector Imxpad S70\t PixelSize= 1.300e-04, 1.300e-04 m\n", "Detector MAR 345\t PixelSize= 1.000e-04, 1.000e-04 m\n", "Detector MAR 555\t Spline= None\t PixelSize= 1.390e-04, 1.390e-04 m\n", "Detector Maxipix 1x1\t PixelSize= 5.500e-05, 5.500e-05 m\n", "Detector Maxipix 2x2\t PixelSize= 5.500e-05, 5.500e-05 m\n", "Detector Maxipix 5x1\t PixelSize= 5.500e-05, 5.500e-05 m\n", "Detector Mythen 1280\t Spline= None\t PixelSize= 8.000e-03, 5.000e-05 m\n", "Detector Perkin detector\t PixelSize= 2.000e-04, 2.000e-04 m\n", "Detector Pilatus 100k\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus 1M\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus 200k\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus 2M\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus 300k\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus 300kw\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus 6M\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus CdTe 1M\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus CdTe 2M\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus CdTe 300k\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pilatus CdTe 300kw\t PixelSize= 1.720e-04, 1.720e-04 m\n", "Detector Pixium 4700\t PixelSize= 3.080e-04, 3.080e-04 m\n", "Detector Picam v1\t Spline= None\t PixelSize= 1.400e-06, 1.400e-06 m\n", "Detector Picam v2\t Spline= None\t PixelSize= 1.120e-06, 1.120e-06 m\n", "Detector Rayonix133\t PixelSize= 6.400e-05, 6.400e-05 m\n", "Detector Rayonix LX170\t PixelSize= 4.427e-05, 4.427e-05 m\n", "Detector Rayonix LX255\t PixelSize= 4.427e-05, 4.427e-05 m\n", "Detector Rayonix MX170\t PixelSize= 4.427e-05, 4.427e-05 m\n", "Detector Rayonix MX225\t PixelSize= 7.324e-05, 7.324e-05 m\n", "Detector Rayonix MX225HS\t PixelSize= 7.813e-05, 7.813e-05 m\n", "Detector Rayonix MX300\t PixelSize= 7.324e-05, 7.324e-05 m\n", "Detector Rayonix MX300HS\t PixelSize= 7.813e-05, 7.813e-05 m\n", "Detector Rayonix MX325\t PixelSize= 7.935e-05, 7.935e-05 m\n", "Detector Rayonix MX340HS\t PixelSize= 8.854e-05, 8.854e-05 m\n", "Detector Rayonix MX425HS\t PixelSize= 4.427e-05, 4.427e-05 m\n", "Detector Rayonix SX165\t PixelSize= 3.950e-05, 3.950e-05 m\n", "Detector Rayonix SX200\t PixelSize= 4.800e-05, 4.800e-05 m\n", "Detector Rayonix SX30HS\t PixelSize= 1.563e-05, 1.563e-05 m\n", "Detector Rayonix SX85HS\t PixelSize= 4.427e-05, 4.427e-05 m\n", "Detector Titan 2k x 2k\t PixelSize= 6.000e-05, 6.000e-05 m\n", "Detector Xpad S540 flat\t PixelSize= 1.300e-04, 1.300e-04 m\n" ] } ], "source": [ "import time, os\n", "start_time = time.time()\n", "\n", "#Nota: If you are behind a proxy/firewall this can help you\n", "#os.environ[\"http_proxy\"] = \"http://proxy.company.com:3128\"\n", "\n", "import pyFAI, pyFAI.detectors\n", "print(\"pyFAI version: %s\"% pyFAI.version)\n", "all_detectors = list(set(pyFAI.detectors.ALL_DETECTORS.values()))\n", "#Sort detectors according to their name\n", "all_detectors.sort(key=lambda i:i.__name__)\n", "nb_det = len(all_detectors)\n", "print(\"Number of detectors registered: %i with %i unique detectors\"%(len(pyFAI.detectors.ALL_DETECTORS),nb_det))\n", "print()\n", "print(\"List of all supported detectors\")\n", "for i in all_detectors:\n", " print(i())" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Defining a detector from a spline file \n", "For optically coupled CCD detectors, the geometrical distortion is often described by a two-dimensional cubic spline (as in FIT2D) which can be imported into the relevant detector instance and used to calculate the actual pixel position in space (and masked pixels).\n", "\n", "At the ESRF, mainly FReLoN detectors [J.-C. Labiche, ESRF Newsletter 25, 41 (1996)] are used with spline files describing the distortion of the fiber optic taper.\n", "\n", "Let's download such a file and create a detector from it. Users at ESRF may declare a proxy to connect to the internet. " ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/tmp/pyFAI_testdata_kieffer/halfccd.spline\n" ] } ], "source": [ "import os\n", "from silx.resources import ExternalResources\n", "downloader = ExternalResources(\"pyFAI\", \"http://www.silx.org/pub/pyFAI/testimages\", \"PYFAI_DATA\")\n", "spline_file = downloader.getfile(\"halfccd.spline\")\n", "print(spline_file)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Detector FReLoN\t Spline= /tmp/pyFAI_testdata_kieffer/halfccd.spline\t PixelSize= 4.842e-05, 4.684e-05 m\n", "Shape: 1025, 2048\n" ] } ], "source": [ "hd = pyFAI.detectors.FReLoN(splineFile=spline_file)\n", "print(hd)\n", "print(\"Shape: %i, %i\"% hd.shape)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*Note:* the unusual shape of this detector. This is probably a human error when calibrating the detector distortion in FIT2D.\n", "\n", "### Visualizing the mask\n", "Every detector object contains a mask attribute, defining pixels which are invalid. \n", "For FReLoN detector (a spline-files-defined detectors), all pixels having an offset such that the pixel falls out of the initial detector are considered as invalid. \n", "\n", "Masked pixel have non-null values can be displayed like this: " ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Populating the interactive namespace from numpy and matplotlib\n" ] } ], "source": [ "%pylab nbagg\n", "from pyFAI.gui import jupyter" ] }, { "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 = $('
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');\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 = $('
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')\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": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "halfccd_img = downloader.getfile(\"halfccd.edf\")\n", "import fabio\n", "raw = fabio.open(halfccd_img).data\n", "cor = dis.correct(raw, dummy=raw.min())\n", "\n", "#Then display raw and corrected imagesimages \n", "fig, ax = subplots(2, figsize=(8,8))\n", "\n", "jupyter.display(raw, label=\"Raw Image\", ax=ax[0])\n", "jupyter.display(cor, label=\"Corrected image\", ax=ax[1])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**Nota:** in this case the image size (1024 lines) does not match the detector's number of lines (1025) hence pyFAI complains about it. \n", "Here, pyFAI patched the image on an empty image of the right size so that the processing can occur. \n", "\n", "In this example, the size of the pixels and the shape of the detector are preserved, discarding all pixels falling outside the detector's grid. \n", "\n", "One may want all pixels' intensity to be preserved in the transformation. By allowing the output array to be large enough to accomodate all pixels, the total intensity can be kept. For this, just enable the \"resize\" option in the constructor of *Distortion*:" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "WARNING:pyFAI.ext._distortion:Patching image of shape 2048x1024 on expected size of 2048x1025\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Distortion correction csr on device None for detector shape (1045, 2052):\n", "Detector FReLoN\t Spline= /tmp/pyFAI_testdata_kieffer/halfccd.spline\t PixelSize= 4.842e-05, 4.684e-05 m\n", "After correction, the image has a different shape (1045, 2052)\n" ] } ], "source": [ "dis1 = Distortion(hd, resize=True)\n", "cor = dis1.correct(raw)\n", "print(dis1)\n", "print(\"After correction, the image has a different shape\", cor.shape)" ] }, { "cell_type": "code", "execution_count": 12, "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": [ "" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "xpad_file = downloader.getfile(\"LaB6_18.57keV_frame_13.edf\")\n", "xpad = pyFAI.detector_factory(\"Xpad_flat\")\n", "print(xpad)\n", "xpad_dis = Distortion(xpad, resize=True)\n", "\n", "raw = fabio.open(xpad_file).data\n", "cor = xpad_dis.correct(raw)\n", "print(\"Shape as input and output:\", raw.shape, cor.shape)\n", "print(\"Conservation of the total intensity:\", raw.sum(dtype=\"float64\"), cor.sum(dtype=\"float64\"))\n", "\n", "#then display images side by side\n", "fig, ax = subplots(1, 2, figsize=(8,8))\n", "jupyter.display(raw, label=\"Raw Image\", ax=ax[0])\n", "jupyter.display(cor, label=\"Corrected image\", ax=ax[1])\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### WOS XPad detector\n", "\n", "This is a new **WAXS opened for SAXS** pixel detector from ImXPad (available at ESRF-BM02/D2AM CRG beamline). \n", "It looks like two of *XPad_flat* detectors side by side with some modules shifted in order to create a hole to accomodate a flight-tube which gathers the SAXS photons to a second detector further away.\n", "\n", "The detector definition for this specific detector has directly been put down using the metrology informations from the manufacturer and saved as a NeXus detector definition file. \n" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "NexusDetector detector from NeXus file: /tmp/pyFAI_testdata_kieffer/WOS.h5\t PixelSize= 1.300e-04, 1.300e-04 m\n", "Shape as input: (598, 1154) and output: (710, 1302)\n", "Conservation of the total intensity: 4.4436e+08 vs 4.4436e+08 \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 = $('