drawtext               package:EBImage               R Documentation

_D_r_a_w_i_n_g _p_r_i_m_i_t_i_v_e_s _o_n _i_m_a_g_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     The family of functions to draw primitives on images. At the
     moment, there is only one functions out of the planned family to
     draw text.

_U_s_a_g_e:

       ## S4 methods for signatures 'img=Image,xy=numeric,label=character' 
       ## and 'img=Image,xy=matrix,label=character' and
       ## S4 method for signature 'Image, list, list':
       drawtext(img, xy, labels, font, col, ...)
         
       drawfont(family=switch(.Platform$OS.type, windows="Arial", "helvetica"), 
                style="n", size=14, weight=200, antialias=TRUE)

_A_r_g_u_m_e_n_t_s:

     img: An object of 'Image'. With indexed images, please ensure that
          the color range is in '[0,1]'.

      xy: (x,y) coordinates of labels. For single frames a matrix with 
          the first column being 'x' and second 'y' or a corresponding
          numeric  vector as it would be used to construct such a
          matrix. For multiple frames, a list of corresponding
          matrices/vectors. 

  labels: A character vector of labels to be output. For multiple
          frames a list of such characters. 

    font: An S3 object of class 'DrawFont' as returned by  'drawfont'.
          If omitted, the 'drawfont' functions is called internally to
          obtain the default values. 

     col: A character vector of font colors. One per frame, recycled
          between frames if required. 

     ...: Reserved. 

  family: A character value for the font family to use. On Linux/UNIX
          machines one can try to use 'helvetica', 'times', 'courier' 
          and 'symbol'. On Windows machines, one can specify installed
          TrueType fonts, like 'Arial'.

   style: A character value for the font style to use. Can be specified
          by providing the first letter only. Supported are: 'normal' 
          (default), 'italic', 'oblique'. 

    size: A numeric value for the font size.

  weight: A numeric value for the font weight (bold font). Supported
          values between 100 and 900.

antialias: A logical value for whether the font should be 
          anti-aliased. 

_V_a_l_u_e:

     An object of 'Image' even if the supplied 'img' was of  any
     derived class. If supplied was an 'IndexedImage', ensure  that it
     was normalized to the range $[0,1]$ before calling 'drawtext': the
     function is for annotation purposes only and using it with
     'IndexedImage''s is likely to destroy indexing information!

_A_u_t_h_o_r(_s):

     Oleg Sklyar, osklyar@ebi.ac.uk, 2007

_S_e_e _A_l_s_o:

     ' Image '

_E_x_a_m_p_l_e_s:

     ## FIXME: This example is currently excluded from MacOS builds as it fails in 
     ## ImageMagick string assertion. Although I tried to find the reason for
     ## the problem, I do not have a test environment (MacOS). Please test it and
     ## report what goes wrong here and at which stage.

     if ( length(grep("apple", Sys.getenv("R_PLATFORM"))) == 0 ) {
       ## load images
       f <- paste( system.file(package="EBImage"), "images/Gene1_G.tif", sep="/" )
       ii = normalize(readImage(f), separate=TRUE)
       ## segment
       mask = thresh(ii, 25, 25, 0.02)
       mk3 = morphKern(3)
       mk5 = morphKern(5)
       mask = dilate(erode(closing(mask, mk5), mk3), mk5)
       ## index objects in images and remove bad ones
       io = watershed( distmap(mask), 1.5, 1)
       ft = hullFeatures(io)
       mf = moments(io, ii)   ## need these for intensity and size
       for ( i in seq_along(ft) ) ft[[i]] = cbind(ft[[i]], mf[[i]])
       io = rmObjects(io, lapply(ft, function(x) 
              which(x[,"h.s"] < 150 | x[,"int"] < 50 | 0.3 * x[,"h.p"] < x[,"h.edge"] )
            ))
       ft = hullFeatures(io)
       ## get centres of objects (list, for ii is a stack of 4)
       xy <- lapply(ft, function(x) x[,1:2])
       # create labels for objects (list, for ii is a stack of 4)
       labels <- lapply(xy, function(x) as.character(1:nrow(x)))
       ## set font properties: semi bold
       f <- drawfont()
       f$weight=600
       ## draw annotations, recycle 2 colours between 4 images
       annot <- drawtext(channel(ii,"rgb"), xy, labels, font=f, col=c("#F0B769","#ACEE3F"))
       if (interactive()) display(annot)
     }

