{"id":13094,"date":"2021-05-22T10:01:35","date_gmt":"2021-05-22T15:01:35","guid":{"rendered":"https:\/\/rud.is\/b\/?p=13094"},"modified":"2021-05-22T10:01:35","modified_gmt":"2021-05-22T15:01:35","slug":"a-swiftr-brief-interlude-while-awaiting-cdcfluview-cran-checks","status":"publish","type":"post","link":"https:\/\/rud.is\/b\/2021\/05\/22\/a-swiftr-brief-interlude-while-awaiting-cdcfluview-cran-checks\/","title":{"rendered":"A {swiftr} Brief Interlude While Awaiting {cdcfluview} CRAN Checks"},"content":{"rendered":"

My {cdcfluview} package started tossing erros on CRAN just over a week ago when the CDC added an extra parameter to one of the hidden API endpoints that the package wraps. After a fairly hectic set of days since said NOTE came, I had time this morning to poke at a fix. There are alot<\/em> of tests, so after successful debugging session I was awaiting CRAN checks on various remotes as well as README builds and figured I’d keep up some practice with another, nascent, package of mine, {swiftr}, which makes it dead simple to build R functions from Swift code, in similar fashion to what Rcpp::cppFunction()<\/code> does for C\/C++ code.<\/p>\n

macOS comes with a full set of machine learning\/AI libraries\/frameworks that definitely have “batteries included” (i.e. you can almost just make one function call to get 90-95% what you want without even training new models). One of which is text extraction from Apple’s computer Vision<\/code> framework<\/a>. I thought it’d be a fun and quick “wait mode” distraction to wrap the VNRecognizeTextRequest()<\/code> function and use it from R.<\/p>\n

To show how capable the default model is, I pulled a semi-complex random image from DDG’s image search:<\/p>\n

\"Yellow<\/center><\/p>\n

Let’s build the function (you need to be on macOS for this; exposition inine):<\/p>\n

library(swiftr) # github.com\/hrbrmstr\/swiftr\n\nswift_function(\n  code = '\nimport Foundation\nimport CoreImage\nimport Cocoa\nimport Vision\n\n@_cdecl (\"detect_text\")\npublic func detect_text(path: SEXP) -> SEXP {\n\n   \/\/ turn R string into Swift String so we can use it\n   let fileName = String(cString: R_CHAR(STRING_ELT(path, 0)))\n\n   var res: String = \"\"\n   var out: SEXP = R_NilValue\n\n  \/\/ get image into the right format\n  if let ciImage = CIImage(contentsOf: URL(fileURLWithPath:fileName)) {\n\n    let context = CIContext(options: nil)\n    if let img = context.createCGImage(ciImage, from: ciImage.extent) {\n\n      \/\/ setup comptuer vision request\n      let requestHandler = VNImageRequestHandler(cgImage: img)\n\n      \/\/ start recognition\n      let request = VNRecognizeTextRequest()\n      do {\n        try requestHandler.perform([request])\n\n        \/\/ if we have results\n        if let observations = request.results as? [VNRecognizedTextObservation] {\n\n          \/\/ paste them together\n          let recognizedStrings = observations.compactMap { observation in\n            observation.topCandidates(1).first?.string\n          }\n          res = recognizedStrings.joined(separator: \"\\\\n\")\n        }\n      } catch {\n        debugPrint(\"\\\\(error)\")\n      }\n    }\n  }\n\n  res.withCString { cstr in out = Rf_mkString(cstr) }\n\n  return(out)\n}\n')\n<\/code><\/pre>\n
The detect_text()<\/code> is now available in R, so let’s see how it performs on that image of signs:<\/p>\n
detect_text(path.expand(\"~\/Data\/signs.jpeg\")) %>% \n  stringi::stri_split_lines() %>% \n  unlist()\n##  [1] \"BEWILDERED\" \"UNCLEAR\"    \"nAZEU\"      \"UNCERTAIN\"  \"VISA\"       \"INSURE\"    \n##  [7] \"ATED\"       \"MUDDLED\"    \"LOsT\"       \"DISTRACTED\" \"PERPLEXED\"  \"CONFUSED\"  \n## [13] \"PUZZLED\" \n<\/code><\/pre>\n
It works super-fast and gets far more correct than I would have expected.<\/p>\n
Toy examples aside, it also works pretty well (as one would expect) on “real” text images, such as this example from the Tesseract test suite:<\/p>\n
\"tesseract<\/a><\/p>\n
detect_text(path.expand(\"~\/Data\/tesseract\/news.3B\/0\/8200_006.3B.tif\")) %>% \n  stringi::stri_split_lines() %>% \n  unlist()\n##  [1] \"Tobacco chiefs still refuse to see the truth abou\"                           \n##  [2] \"even of America's least conscionable\"                                        \n##  [3] \"The tobacco industry would like to promote\"                                  \n##  [4] \"men sat together in Washington last\"                                         \n##  [5] \"under the conditions they are used.'\"                                        \n##  [6] \"week to do what they do best: blow\"                                          \n##  [7] \"the specter of prohibition.\"                                                 \n##  [8] \"panel\\\" of toxicologists as \\\"not hazardous\"                                 \n##  [9] \"smoke at the truth about cigarettes.\"                                        \n## [10] \"'If cigarettes are too dangerous to be sold,\"                                \n## [11] \"then ban them. Some smokers will obey the\"                                   \n## [12] \"People not paid by the tobacco companies\"                                    \n## [13] \"aren't so sure. The list includes several\"                                   \n## [14] \"The CEOs of the nation's largest tobacco\"                                    \n## [15] \"firms told congressional panel that nicotine\"                                \n## [16] \"law, but many will not. People will be selling\"                              \n## [17] \"iS not addictive, that they are unconvinced\"                                 \n## [18] \"cigarettes out of the trunks of cars, cigarettes\"                            \n## [19] \"substances the government does not allow in\"                                 \n## [20] \"foods or classifies as potentially toxic. They\"                              \n## [21] \"that smoking causes lung cancer or any other\"                                \n## [22] \"made by who knows who, made of who knows include ammonia, a pesticide called\"\n## [23] \"illness, and that smoking is no more harmful\"                                \n## [24] \"what,\\\" said James Johnston of R.J. Reynolds.\"                               \n## [25] \"than drinking coffee or eating Twinkies.\"                                    \n## [26] \"It's a ruse. He knows cigarettes are not\"                                    \n## [27] \"methoprene, and ethyl furoate, which has\"                                    \n## [28] \"They said these things with straight taces.\"                                 \n## [29] \"going to be banned, at leasi not in his lifetime.\"                           \n## [30] \"caused liver damage in rats.\"                                                \n## [31] \"The list \\\"begs a number of important\"                                       \n## [32] \"They said them in the face of massive\"                                       \n## [33] \"STEVE WILSON\"                                                                \n## [34] \"What he really fears are new taxes, stronger\"                                \n## [35] \"questions about the safety of these additives,\\\"\"                            \n## [36] \"scientific evidence that smoking is responsible\"                             \n## [37] \"anti-smoking campaigns, further smoking\"                                     \n## [38] \"said a joint statement from the American\"                                    \n## [39] \"for more than 400,000 deaths every year.\"                                    \n## [40] \"restrictions, limits on secondhand smoke and\"                                \n## [41] \"Rep. Henry Waxman, D-Calif., put that\"                                       \n## [42] \"Republic Columnist\"                                                          \n## [43] \"Lung, Cancer and Heart associations. The\"                                    \n## [44] \"limits on tar and nicotine.\"                                                 \n## [45] \"statement added that substances safe to eat\"                                 \n## [46] \"frightful statistic another way:\"                                            \n## [47] \"Collectively, these steps can accelerate the\"                                \n## [48] \"\\\"Imagine our nation's outrage if two fully\"                                 \n## [49] \"He and the others played dumb for the\"                                       \n## [50] \"current 5 percent annual decline in cigarette\"                               \n## [51] \"aren't necessarily safe to inhale.\"                                          \n## [52] \"The 50-page list can be obtained free by\"                                    \n## [53] \"loaded jumbo jets crashed each day, killing all\"                             \n## [54] \"entire six hours, but really didn't matter.\"                                 \n## [55] \"use and turn the tobacco business from highly\"                               \n## [56] \"calling 1-800-852-8749.\"                                                     \n## [57] \"aboard. That's the same number of Americans\"                                 \n## [58] \"The game i nearly over, and the tobacco\"                                     \n## [59] \"profitable to depressed.\"                                                    \n## [60] \"Johnson's comment about cigarettes \\\"made\"                                   \n## [61] \"Here are just the 44 ingredients that start\"                                 \n## [62] \"that cigarettes kill every 24 hours.'\"                                       \n## [63] \"executives know it.\"                                                         \n## [64] \"with the letter \\\"A\\\":\"                                                      \n## [65] \"The CEOs were not impressed.\"                                                \n## [66] \"The hearing marked a turning point in the\"                                   \n## [67] \"of who knows what\\\" was comical.\"                                            \n## [68] \"Acetanisole, acetic acid, acetoin,\"                                          \n## [69] \"\\\"We have looked at the data.\"                                               \n## [70] \"It does\"                                                                     \n## [71] \"nation's growing aversion to cigarettes. No\"                                 \n## [72] \"The day before the hearing, the tobacco\"                                     \n## [73] \"acetophenone,6-acetoxydihydrotheaspirane,\"                                   \n## [74] \"not convince me that smoking causes death,\\\"\"                                \n## [75] \"2-acetyl-3-ethylpyrazine, 2-acetyl-5-\"                                       \n## [76] \"said Andrew Tisch of the Lorillard Tobacco\"                                  \n## [77] \"longer hamstrung by tobacco-state seniority\"                                 \n## [78] \"companies released a long-secret list of 599\"                                \n## [79] \"Co.\"                                                                         \n## [80] \"and the deep-pocketed tobacco lobby,\"                                        \n## [81] \"methylfuran, acetylpyrazine, 2-acetylpyridine,\"                              \n## [82] \"Congress is taking aim at cigarette makers.\"                                 \n## [83] \"additives used in cigarettes. The companies\"                                 \n## [84] \"said all are certified by an \\\"independent\"                                  \n## [85] \"3-acetylpyridine, 2-acetylthiazole, aconitic\"   \n<\/code><\/pre>\n
(You can compare that on your own with the Tesseract results<\/a>.)<\/p>\n
FIN<\/h3>\n
{cdcfluview} checks are done, and the fixed functions are back on CRAN! Just in time to close out this post.<\/p>\n
If you’re on macOS, definitely check out the various ML\/AI frameworks Apple has to offer via Swift and have some fun playing with integrating them into R (or build some small, command line utilities if you want to keep Swift and R apart).<\/p>\n","protected":false},"excerpt":{"rendered":"
My {cdcfluview} package started tossing erros on CRAN just over a week ago when the CDC added an extra parameter to one of the hidden API endpoints that the package wraps. After a fairly hectic set of days since said NOTE came, I had time this morning to poke at a fix. There are alot […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":3,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":""},"categories":[780,91,830],"tags":[],"class_list":["post-13094","post","type-post","status-publish","format-standard","hentry","category-macos","category-r","category-swift"],"yoast_head":"\nA {swiftr} Brief Interlude While Awaiting {cdcfluview} CRAN Checks - rud.is<\/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:\/\/rud.is\/b\/2021\/05\/22\/a-swiftr-brief-interlude-while-awaiting-cdcfluview-cran-checks\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A {swiftr} Brief Interlude While Awaiting {cdcfluview} CRAN Checks - rud.is\" \/>\n<meta property=\"og:description\" content=\"My {cdcfluview} package started tossing erros on CRAN just over a week ago when the CDC added an extra parameter to one of the hidden API endpoints that the package wraps. 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