{"id":19011,"date":"2022-11-05T02:34:34","date_gmt":"2022-11-04T21:04:34","guid":{"rendered":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/"},"modified":"2022-11-05T02:34:34","modified_gmt":"2022-11-04T21:04:34","slug":"solved-3d-image-visualisation-with-numpy-vtk","status":"publish","type":"post","link":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/","title":{"rendered":"[Solved] 3d image visualisation with numpy\/vtk"},"content":{"rendered":"<p> [ad_1]<br \/>\n<\/p>\n<div id=\"answer-15760163\" class=\"answer js-answer accepted-answer js-accepted-answer\" data-answerid=\"15760163\" data-parentid=\"15633067\" data-score=\"3\" data-position-on-page=\"1\" data-highest-scored=\"1\" data-question-has-accepted-highest-score=\"1\" itemprop=\"acceptedAnswer\" itemscope itemtype=\"https:\/\/schema.org\/Answer\">\n<div class=\"post-layout\">\n<div class=\"votecell post-layout--left\"><\/div>\n<div class=\"answercell post-layout--right\">\n<div class=\"s-prose js-post-body\" itemprop=\"text\">\n<p>I finally find out what was wrong<br \/>\nhere&#8217;s my new code<\/p>\n<pre><code>import vtk\nimport numpy as np\nimport os\nimport matplotlib.pyplot as plt\nimport PIL\nimport Image\n\nDEBUG =False\ndirectory=\"splitted_mri\/\"\n\nl = []\n\nk=0 #add the next picture in a differente level of depth\/z-positions\nfor file in os.listdir(directory):\n    img = directory + file\n    if DEBUG : print img\n    l.append(img)\n# the os.listdir function do not give the files in the right order \n#so we need to sort them\nl=sorted(l)\n\ntemp = Image.open(l[0])\nh, w = temp.size\nd = len(l)*5 #with our sample each images will be displayed 5times to get a better view\nif DEBUG : print 'width, height, depth : ',w,h,d\n\nstack = np.zeros((w,d,h),dtype=np.uint8)\n\nfor i in l:\n    im = Image.open(i)\n    temp = np.asarray(im, dtype=int)\n    for i in range(5):\n        stack[:,k+i,:]= temp\n    k+=5\n    #~ stack[:,k,:]= temp\n    #~ k+=1\n\nif DEBUG :\n    res = np.amax(stack)\n    print 'max value',res\n    res1 = np.amin(stack)\nprint 'min value',res1\n\n#convert the stack in the right dtype\nstack = np.require(stack,dtype=np.uint8)\n\nif DEBUG :#check if the image have not been modified\ntest = stack [:,0,:]\nplt.imshow(test,cmap='gray')\nplt.show()\n\nif DEBUG : print 'stack shape &amp; dtype' ,stack.shape,',',stack.dtype\n\ndataImporter = vtk.vtkImageImport()\ndata_string = stack.tostring()\n\ndataImporter.CopyImportVoidPointer(data_string, len(data_string))\ndataImporter.SetDataScalarTypeToUnsignedChar()\ndataImporter.SetNumberOfScalarComponents(1)\n\n#vtk uses an array in the order : height, depth, width which is \n#different of numpy (w,h,d) \nw, d, h = stack.shape\ndataImporter.SetDataExtent(0, h-1, 0, d-1, 0, w-1)\ndataImporter.SetWholeExtent(0, h-1, 0, d-1, 0, w-1)\n\nalphaChannelFunc = vtk.vtkPiecewiseFunction()\ncolorFunc = vtk.vtkColorTransferFunction()\nfor i in range(256):\n    alphaChannelFunc.AddPoint(i, 0.2)\n    colorFunc.AddRGBPoint(i,i\/255.0,i\/255.0,i\/255.0)\n# for our test sample, we set the black opacity to 0 (transparent) so as\n#to see the sample  \nalphaChannelFunc.AddPoint(0, 0.0)\ncolorFunc.AddRGBPoint(0,0,0,0)\n\nvolumeProperty = vtk.vtkVolumeProperty()\nvolumeProperty.SetColor(colorFunc)\n#volumeProperty.ShadeOn()\nvolumeProperty.SetScalarOpacity(alphaChannelFunc)\n\n# This class describes how the volume is rendered (through ray tracing).\ncompositeFunction = vtk.vtkVolumeRayCastCompositeFunction()\n# We can finally create our volume. We also have to specify the data for\n# it, as well as how the data will be rendered.\nvolumeMapper = vtk.vtkVolumeRayCastMapper()\n# function to reduce the spacing between each image\nvolumeMapper.SetMaximumImageSampleDistance(0.01)\n\nvolumeMapper.SetVolumeRayCastFunction(compositeFunction)\nvolumeMapper.SetInputConnection(dataImporter.GetOutputPort())\n\n# The class vtkVolume is used to pair the preaviusly declared volume as \n#well as the properties to be used when rendering that volume.\nvolume = vtk.vtkVolume()\nvolume.SetMapper(volumeMapper)\nvolume.SetProperty(volumeProperty)\n\n# With almost everything else ready, its time to initialize the renderer and window,\n# as well as creating a method for exiting the application\nrenderer = vtk.vtkRenderer()\nrenderWin = vtk.vtkRenderWindow()\nrenderWin.AddRenderer(renderer)\nrenderInteractor = vtk.vtkRenderWindowInteractor()\nrenderInteractor.SetRenderWindow(renderWin)\n\n# We add the volume to the renderer ...\nrenderer.AddVolume(volume)\n# ... set background color to white ...\nrenderer.SetBackground(1, 1, 1)\n# ... and set window size.\nrenderWin.SetSize(550, 550)\nrenderWin.SetMultiSamples(4)\n# A simple function to be called when the user decides to quit the application.\ndef exitCheck(obj, event):\n    if obj.GetEventPending() != 0:\n        obj.SetAbortRender(1)\n\n# Tell the application to use the function as an exit check.\nrenderWin.AddObserver(\"AbortCheckEvent\", exitCheck)\n\n#to auit, press q\nrenderInteractor.Initialize()\n# Because nothing will be rendered without any input, we order the first\n# render manually before control is handed over to the main-loop.\nrenderWin.Render()\nrenderInteractor.Start()\n<\/code><\/pre>\n<\/p><\/div>\n<div class=\"mt24\"><\/div>\n<\/div>\n<p>            <span class=\"d-none\" itemprop=\"commentCount\">1<\/span> <\/p><\/div>\n<\/div>\n<p>[ad_2]<\/p>\n<p>solved 3d image visualisation with numpy\/vtk <\/p>\n","protected":false},"excerpt":{"rendered":"<p>[ad_1] I finally find out what was wrong here&#8217;s my new code import vtk import numpy as np import os import matplotlib.pyplot as plt import PIL import Image DEBUG =False directory=&#8221;splitted_mri\/&#8221; l = [] k=0 #add the next picture in a differente level of depth\/z-positions for file in os.listdir(directory): img = directory + file if &#8230; <a title=\"[Solved] 3d image visualisation with numpy\/vtk\" class=\"read-more\" href=\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\" aria-label=\"More on [Solved] 3d image visualisation with numpy\/vtk\">Read more<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[320],"tags":[1999,349,4558],"class_list":["post-19011","post","type-post","status-publish","format-standard","hentry","category-solved","tag-3d","tag-python","tag-visualization"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.5 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>[Solved] 3d image visualisation with numpy\/vtk - JassWeb<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"[Solved] 3d image visualisation with numpy\/vtk - JassWeb\" \/>\n<meta property=\"og:description\" content=\"[ad_1] I finally find out what was wrong here&#8217;s my new code import vtk import numpy as np import os import matplotlib.pyplot as plt import PIL import Image DEBUG =False directory=&quot;splitted_mri\/&quot; l = [] k=0 #add the next picture in a differente level of depth\/z-positions for file in os.listdir(directory): img = directory + file if ... Read more\" \/>\n<meta property=\"og:url\" content=\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\" \/>\n<meta property=\"og:site_name\" content=\"JassWeb\" \/>\n<meta property=\"article:published_time\" content=\"2022-11-04T21:04:34+00:00\" \/>\n<meta name=\"author\" content=\"Kirat\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Kirat\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\"},\"author\":{\"name\":\"Kirat\",\"@id\":\"https:\/\/jassweb.com\/solved\/#\/schema\/person\/65c9c7b7958150c0dc8371fa35dd7c31\"},\"headline\":\"[Solved] 3d image visualisation with numpy\/vtk\",\"datePublished\":\"2022-11-04T21:04:34+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\"},\"wordCount\":28,\"publisher\":{\"@id\":\"https:\/\/jassweb.com\/solved\/#organization\"},\"keywords\":[\"3d\",\"python\",\"visualization\"],\"articleSection\":[\"Solved\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\",\"url\":\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\",\"name\":\"[Solved] 3d image visualisation with numpy\/vtk - JassWeb\",\"isPartOf\":{\"@id\":\"https:\/\/jassweb.com\/solved\/#website\"},\"datePublished\":\"2022-11-04T21:04:34+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/jassweb.com\/solved\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"[Solved] 3d image visualisation with numpy\/vtk\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/jassweb.com\/solved\/#website\",\"url\":\"https:\/\/jassweb.com\/solved\/\",\"name\":\"JassWeb\",\"description\":\"Build High-quality Websites\",\"publisher\":{\"@id\":\"https:\/\/jassweb.com\/solved\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/jassweb.com\/solved\/?s={search_term_string}\"},\"query-input\":{\"@type\":\"PropertyValueSpecification\",\"valueRequired\":true,\"valueName\":\"search_term_string\"}}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/jassweb.com\/solved\/#organization\",\"name\":\"Jass Web\",\"url\":\"https:\/\/jassweb.com\/solved\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/jassweb.com\/solved\/#\/schema\/logo\/image\/\",\"url\":\"https:\/\/jassweb.com\/wp-content\/uploads\/2021\/02\/jass-website-logo-1.png\",\"contentUrl\":\"https:\/\/jassweb.com\/wp-content\/uploads\/2021\/02\/jass-website-logo-1.png\",\"width\":693,\"height\":132,\"caption\":\"Jass Web\"},\"image\":{\"@id\":\"https:\/\/jassweb.com\/solved\/#\/schema\/logo\/image\/\"}},{\"@type\":\"Person\",\"@id\":\"https:\/\/jassweb.com\/solved\/#\/schema\/person\/65c9c7b7958150c0dc8371fa35dd7c31\",\"name\":\"Kirat\",\"image\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/jassweb.com\/solved\/#\/schema\/person\/image\/\",\"url\":\"https:\/\/jassweb.com\/solved\/wp-content\/litespeed\/avatar\/1261af3c9451399fa1336d28b98ea3bb.jpg?ver=1775193939\",\"contentUrl\":\"https:\/\/jassweb.com\/solved\/wp-content\/litespeed\/avatar\/1261af3c9451399fa1336d28b98ea3bb.jpg?ver=1775193939\",\"caption\":\"Kirat\"},\"sameAs\":[\"http:\/\/jassweb.com\"],\"url\":\"https:\/\/jassweb.com\/solved\/author\/jaspritsinghghumangmail-com\/\"}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"[Solved] 3d image visualisation with numpy\/vtk - JassWeb","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/","og_locale":"en_US","og_type":"article","og_title":"[Solved] 3d image visualisation with numpy\/vtk - JassWeb","og_description":"[ad_1] I finally find out what was wrong here&#8217;s my new code import vtk import numpy as np import os import matplotlib.pyplot as plt import PIL import Image DEBUG =False directory=\"splitted_mri\/\" l = [] k=0 #add the next picture in a differente level of depth\/z-positions for file in os.listdir(directory): img = directory + file if ... Read more","og_url":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/","og_site_name":"JassWeb","article_published_time":"2022-11-04T21:04:34+00:00","author":"Kirat","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Kirat","Est. reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/#article","isPartOf":{"@id":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/"},"author":{"name":"Kirat","@id":"https:\/\/jassweb.com\/solved\/#\/schema\/person\/65c9c7b7958150c0dc8371fa35dd7c31"},"headline":"[Solved] 3d image visualisation with numpy\/vtk","datePublished":"2022-11-04T21:04:34+00:00","mainEntityOfPage":{"@id":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/"},"wordCount":28,"publisher":{"@id":"https:\/\/jassweb.com\/solved\/#organization"},"keywords":["3d","python","visualization"],"articleSection":["Solved"],"inLanguage":"en-US"},{"@type":"WebPage","@id":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/","url":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/","name":"[Solved] 3d image visualisation with numpy\/vtk - JassWeb","isPartOf":{"@id":"https:\/\/jassweb.com\/solved\/#website"},"datePublished":"2022-11-04T21:04:34+00:00","breadcrumb":{"@id":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/jassweb.com\/solved\/solved-3d-image-visualisation-with-numpy-vtk\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/jassweb.com\/solved\/"},{"@type":"ListItem","position":2,"name":"[Solved] 3d image visualisation with numpy\/vtk"}]},{"@type":"WebSite","@id":"https:\/\/jassweb.com\/solved\/#website","url":"https:\/\/jassweb.com\/solved\/","name":"JassWeb","description":"Build High-quality Websites","publisher":{"@id":"https:\/\/jassweb.com\/solved\/#organization"},"potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/jassweb.com\/solved\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Organization","@id":"https:\/\/jassweb.com\/solved\/#organization","name":"Jass Web","url":"https:\/\/jassweb.com\/solved\/","logo":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/jassweb.com\/solved\/#\/schema\/logo\/image\/","url":"https:\/\/jassweb.com\/wp-content\/uploads\/2021\/02\/jass-website-logo-1.png","contentUrl":"https:\/\/jassweb.com\/wp-content\/uploads\/2021\/02\/jass-website-logo-1.png","width":693,"height":132,"caption":"Jass Web"},"image":{"@id":"https:\/\/jassweb.com\/solved\/#\/schema\/logo\/image\/"}},{"@type":"Person","@id":"https:\/\/jassweb.com\/solved\/#\/schema\/person\/65c9c7b7958150c0dc8371fa35dd7c31","name":"Kirat","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/jassweb.com\/solved\/#\/schema\/person\/image\/","url":"https:\/\/jassweb.com\/solved\/wp-content\/litespeed\/avatar\/1261af3c9451399fa1336d28b98ea3bb.jpg?ver=1775193939","contentUrl":"https:\/\/jassweb.com\/solved\/wp-content\/litespeed\/avatar\/1261af3c9451399fa1336d28b98ea3bb.jpg?ver=1775193939","caption":"Kirat"},"sameAs":["http:\/\/jassweb.com"],"url":"https:\/\/jassweb.com\/solved\/author\/jaspritsinghghumangmail-com\/"}]}},"_links":{"self":[{"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/posts\/19011","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/comments?post=19011"}],"version-history":[{"count":0,"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/posts\/19011\/revisions"}],"wp:attachment":[{"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/media?parent=19011"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/categories?post=19011"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/jassweb.com\/solved\/wp-json\/wp\/v2\/tags?post=19011"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}