Hi Augusto!
A possible solution is provided below.
> Hello, well i have a problem and i don't even know in which list ask,
> so if anyone know a little about image processing and morphometrics
> and could enlighten me.
>
> My problem is as follow, i was trying to learn a little about
> morphometrics and was reading Morphometrics with R book.
> I was able to process a image of spermatozoids and retrieve their
> contours with EBimage package and was playing with the functions on
> the book.
> But each contour of the head of the spermatoidz image I'm looking is
> oriented to one side.
>
> Reading an article of Ostermeier et al he cite that "A method to
> consistently orient sperm was developed that was both objective and
> able to be automated."
>
> So i was wondering how is this done? Is there any magic word to start
> search for a solution on google so something like that?
>
> EBimage and other packages actually have a function to rotate image,
> so i was wondering if there is already a clever solution, like make
> the largest diameter be perpendicular to x axis, thing like this, or
> it need far more complex solutions?
The rot2() function in the sfsmisc package might be useful for you. The
following code is probably not as elegant as it could be, but it will hopefully
give you some ideas to find a robust solution:
install.packages("sfsmisc")
library(sfsmisc)
S1 <- sptz[[1]]
S1dist <- as.matrix(dist(S1))
#Largest diameter
S1distMax <- which(S1dist == max(S1dist), arr.ind = TRUE)
S1dims <- c(diff(S1[S1distMax[2,] ,]), max(S1dist))
#Angle from the vertical
phi <- asin(S1dims[1]/S1dims[3])
rotS1 <- rot2(S1, phi = phi)
par(mfrow = c(1, 2))
plot(S1, asp = 1)
plot(rotS1, asp = 1)
I hope this helps!
Sam
> Here is an example of 4 contours, also i post a link to the original
> image, i can post the rest of the script, but basically i use EBimage
> and ocontour function to get here.
>
> #
> par(mfrow=c(2,2))
> for(i in 1:4) {plot(sptz[[i]])}
>
> Thanks for the patience and any hint on where to look for a solution
> for problems like this is welcome.
>
> Reference
>
> Ostermeier GC, Sargeant GA, Yandell BS, Evenson DP, Parrish JJ. The
> relationship of bull fertility to sperm nuclear shape. J of Androl.
> 2001;22(4):595-603
>
> Original Image link:
>
> http://s9.postimage.org/sea4l288f/exe.jpg
>
> #Data of the Example
> > dput(sptz)
> list(structure(c(718L, 717L, 716L, 715L, 714L, 713L, 712L, 711L,
> 710L, 709L, 708L, 707L, 706L, 705L, 704L, 703L, 702L, 701L, 700L,
> 699L, 698L, 697L, 696L, 695L, 694L, 693L, 692L, 691L, 690L, 689L,
> 688L, 687L, 686L, 685L, 684L, 683L, 682L, 681L, 680L, 679L, 678L,
> 677L, 676L, 675L, 674L, 673L, 672L, 671L, 670L, 669L, 669L, 669L,
> 669L, 669L, 669L, 669L, 669L, 669L, 669L, 669L, 669L, 670L, 670L,
> 671L, 672L, 672L, 673L, 674L, 674L, 675L, 676L, 677L, 678L, 679L,
> 680L, 681L, 682L, 683L, 684L, 685L, 686L, 687L, 688L, 689L, 690L,
> 691L, 692L, 693L, 694L, 695L, 696L, 697L, 698L, 699L, 700L, 701L,
> 702L, 703L, 704L, 705L, 706L, 707L, 708L, 709L, 710L, 711L, 712L,
> 713L, 714L, 715L, 716L, 717L, 718L, 719L, 720L, 721L, 722L, 723L,
> 724L, 725L, 726L, 727L, 728L, 728L, 728L, 728L, 727L, 727L, 726L,
> 726L, 725L, 725L, 725L, 725L, 724L, 724L, 724L, 723L, 722L, 721L,
> 720L, 719L, 78L, 79L, 79L, 79L, 79L, 79L, 79L, 79L, 79L, 79L,
> 80L, 80L, 80L, 80L, 80L, 80L, 81L, 80L, 81L, 81L, 81L, 81L, 81L,
> 82L, 82L, 82L, 82L, 82L, 82L, 82L, 83L, 83L, 83L, 84L, 84L, 84L,
> 85L, 85L, 85L, 86L, 86L, 87L, 87L, 88L, 89L, 89L, 90L, 91L, 92L,
> 93L, 94L, 95L, 96L, 97L, 98L, 99L, 100L, 101L, 102L, 103L, 104L,
> 105L, 106L, 107L, 108L, 109L, 110L, 111L, 112L, 113L, 113L, 114L,
> 114L, 114L, 114L, 114L, 115L, 115L, 115L, 114L, 114L, 114L, 114L,
> 115L, 114L, 114L, 114L, 113L, 113L, 113L, 113L, 112L, 112L, 112L,
> 111L, 111L, 110L, 109L, 108L, 107L, 107L, 106L, 105L, 105L, 104L,
> 104L, 103L, 102L, 101L, 101L, 100L, 100L, 99L, 98L, 98L, 97L,
> 96L, 96L, 95L, 94L, 94L, 93L, 93L, 92L, 91L, 90L, 89L, 88L, 87L,
> 86L, 85L, 84L, 83L, 82L, 81L, 80L, 79L, 79L, 78L, 78L, 78L, 78L
> ), .Dim = c(142L, 2L)), structure(c(415L, 414L, 413L, 412L, 411L,
> 410L, 409L, 408L, 407L, 406L, 405L, 404L, 403L, 402L, 401L, 400L,
> 399L, 398L, 397L, 397L, 396L, 397L, 396L, 395L, 395L, 394L, 394L,
> 393L, 394L, 394L, 394L, 394L, 394L, 394L, 394L, 395L, 395L, 396L,
> 396L, 397L, 398L, 399L, 400L, 401L, 402L, 403L, 403L, 404L, 405L,
> 406L, 407L, 408L, 409L, 410L, 411L, 412L, 413L, 414L, 415L, 416L,
> 417L, 418L, 419L, 420L, 421L, 422L, 423L, 424L, 425L, 426L, 427L,
> 428L, 429L, 430L, 431L, 432L, 433L, 434L, 435L, 436L, 437L, 438L,
> 439L, 440L, 439L, 438L, 439L, 440L, 441L, 442L, 443L, 444L, 445L,
> 446L, 447L, 448L, 449L, 450L, 451L, 452L, 453L, 454L, 455L, 456L,
> 455L, 455L, 454L, 454L, 454L, 454L, 454L, 454L, 454L, 455L, 454L,
> 454L, 453L, 452L, 451L, 450L, 449L, 448L, 447L, 446L, 445L, 444L,
> 443L, 442L, 441L, 440L, 439L, 438L, 437L, 436L, 435L, 434L, 433L,
> 432L, 431L, 430L, 429L, 428L, 427L, 426L, 425L, 424L, 423L, 422L,
> 421L, 420L, 419L, 418L, 417L, 416L, 221L, 222L, 222L, 222L, 222L,
> 223L, 223L, 223L, 223L, 223L, 224L, 224L, 224L, 224L, 225L, 225L,
> 226L, 226L, 227L, 228L, 229L, 230L, 231L, 231L, 232L, 233L, 234L,
> 235L, 236L, 237L, 238L, 239L, 240L, 241L, 242L, 243L, 244L, 245L,
> 246L, 247L, 248L, 249L, 248L, 249L, 249L, 250L, 251L, 251L, 252L,
> 253L, 253L, 253L, 253L, 252L, 252L, 252L, 253L, 252L, 252L, 252L,
> 252L, 252L, 252L, 252L, 252L, 252L, 252L, 252L, 252L, 251L, 251L,
> 251L, 250L, 250L, 249L, 250L, 249L, 248L, 247L, 247L, 247L, 246L,
> 245L, 245L, 245L, 244L, 243L, 242L, 243L, 244L, 243L, 242L, 242L,
> 241L, 241L, 241L, 240L, 240L, 240L, 240L, 240L, 239L, 238L, 237L,
> 236L, 235L, 234L, 233L, 232L, 231L, 230L, 229L, 228L, 227L, 226L,
> 225L, 224L, 224L, 224L, 224L, 223L, 223L, 223L, 223L, 223L, 223L,
> 223L, 223L, 223L, 223L, 223L, 222L, 222L, 222L, 222L, 222L, 222L,
> 222L, 222L, 222L, 222L, 221L, 221L, 221L, 222L, 221L, 221L, 221L,
> 221L, 221L, 221L, 221L, 221L, 221L), .Dim = c(154L, 2L)), structure(c(395L,
> 394L, 393L, 393L, 393L, 393L, 393L, 392L, 391L, 390L, 390L, 390L,
> 390L, 391L, 392L, 393L, 394L, 395L, 396L, 397L, 398L, 399L, 400L,
> 401L, 402L, 402L, 403L, 403L, 403L, 403L, 404L, 405L, 406L, 407L,
> 408L, 409L, 410L, 411L, 412L, 413L, 414L, 414L, 415L, 416L, 416L,
> 417L, 418L, 419L, 420L, 421L, 422L, 423L, 424L, 425L, 426L, 427L,
> 428L, 429L, 430L, 431L, 432L, 433L, 434L, 435L, 436L, 437L, 437L,
> 438L, 439L, 440L, 441L, 441L, 442L, 443L, 444L, 445L, 446L, 446L,
> 447L, 448L, 449L, 449L, 449L, 450L, 449L, 450L, 450L, 449L, 449L,
> 449L, 449L, 448L, 447L, 446L, 445L, 444L, 443L, 442L, 441L, 440L,
> 439L, 438L, 437L, 436L, 435L, 434L, 433L, 432L, 431L, 430L, 429L,
> 428L, 427L, 426L, 425L, 424L, 423L, 422L, 421L, 420L, 419L, 418L,
> 417L, 416L, 415L, 414L, 413L, 412L, 411L, 410L, 409L, 408L, 407L,
> 406L, 405L, 404L, 403L, 402L, 401L, 400L, 399L, 398L, 397L, 396L,
> 540L, 541L, 542L, 543L, 544L, 545L, 546L, 547L, 548L, 549L, 550L,
> 551L, 552L, 553L, 554L, 555L, 556L, 556L, 557L, 558L, 559L, 560L,
> 561L, 562L, 563L, 564L, 565L, 566L, 567L, 568L, 568L, 569L, 569L,
> 568L, 568L, 568L, 569L, 568L, 569L, 568L, 569L, 570L, 570L, 571L,
> 572L, 573L, 573L, 573L, 574L, 574L, 574L, 575L, 575L, 575L, 575L,
> 576L, 577L, 576L, 577L, 576L, 576L, 576L, 577L, 577L, 577L, 578L,
> 577L, 576L, 576L, 576L, 575L, 574L, 573L, 574L, 574L, 573L, 572L,
> 571L, 570L, 569L, 568L, 567L, 566L, 565L, 564L, 563L, 562L, 561L,
> 560L, 559L, 558L, 557L, 556L, 556L, 555L, 554L, 554L, 554L, 553L,
> 552L, 552L, 551L, 551L, 550L, 549L, 549L, 549L, 548L, 548L, 547L,
> 547L, 546L, 546L, 546L, 546L, 545L, 545L, 544L, 544L, 543L, 543L,
> 543L, 543L, 543L, 542L, 542L, 542L, 542L, 542L, 541L, 541L, 541L,
> 541L, 541L, 540L, 540L, 540L, 540L, 540L, 540L, 540L, 540L, 540L,
> 540L), .Dim = c(144L, 2L)), structure(c(34L, 33L, 32L, 31L, 30L,
> 29L, 28L, 27L, 26L, 25L, 24L, 23L, 22L, 21L, 20L, 19L, 18L, 17L,
> 16L, 15L, 14L, 13L, 12L, 11L, 10L, 9L, 8L, 7L, 6L, 5L, 4L, 3L,
> 2L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
> 0L, 0L, 0L, 0L, 0L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
> 11L, 12L, 13L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L,
> 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L,
> 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 47L, 48L,
> 49L, 49L, 50L, 50L, 50L, 51L, 51L, 51L, 51L, 51L, 51L, 51L, 51L,
> 50L, 50L, 50L, 49L, 49L, 48L, 47L, 46L, 45L, 44L, 44L, 44L, 44L,
> 43L, 42L, 41L, 40L, 39L, 38L, 37L, 36L, 35L, 362L, 363L, 363L,
> 364L, 364L, 365L, 365L, 365L, 366L, 366L, 366L, 366L, 367L, 367L,
> 368L, 368L, 369L, 370L, 371L, 372L, 373L, 373L, 374L, 375L, 375L,
> 376L, 377L, 377L, 378L, 379L, 380L, 381L, 382L, 382L, 382L, 383L,
> 384L, 385L, 386L, 387L, 388L, 389L, 390L, 391L, 392L, 393L, 394L,
> 395L, 396L, 397L, 398L, 399L, 400L, 401L, 400L, 401L, 401L, 401L,
> 401L, 401L, 402L, 402L, 402L, 401L, 401L, 402L, 402L, 402L, 402L,
> 402L, 401L, 401L, 400L, 401L, 401L, 401L, 400L, 400L, 401L, 400L,
> 401L, 401L, 401L, 400L, 400L, 399L, 399L, 398L, 398L, 397L, 397L,
> 396L, 395L, 394L, 393L, 393L, 392L, 392L, 391L, 391L, 391L, 390L,
> 389L, 388L, 387L, 386L, 385L, 384L, 383L, 382L, 381L, 380L, 379L,
> 378L, 377L, 376L, 375L, 374L, 373L, 372L, 371L, 370L, 369L, 369L,
> 369L, 368L, 367L, 366L, 365L, 364L, 364L, 363L, 362L, 362L, 362L,
> 362L, 362L, 362L), .Dim = c(138L, 2L)))
>
> --
> Grato
> Augusto C. A. Ribas
>
> Site Pessoal: http://recologia.wordpress.com/
> Lattes: http://lattes.cnpq.br/7355685961127056
Samuel Brown
Postgraduate Student
Bio-Protection Research Centre
PO Box 84
Lincoln University
Lincoln 7647
Canterbury
New Zealand
[email protected]
http://www.the-praise-of-insects.blogspot.com
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