diff --git a/README.Rmd b/README.Rmd index 69b337d..a02188d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -77,7 +77,6 @@ soy <- analyze_objects(img, marker = "id") soy$statistics ``` - # Disease severity ```{r fig.width=12, fig.height=3} diff --git a/README.md b/README.md index e8b1883..dd296f4 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,7 @@ will help you to: - Measure disease severity; - Count the number of lesions; - Obtain the shape of lesions; +- Produce Standard Area Diagrams; - Count objects in an image; - Get object features (area, perimeter, radius, circularity, eccentricity, solidity); @@ -79,12 +80,12 @@ grains. ``` r library(pliman) # |=======================================================| -# | Tools for Plant Image Analysis (pliman 0.3.0) | +# | Tools for Plant Image Analysis (pliman 1.0.0) | # | Author: Tiago Olivoto | # | Type 'vignette('pliman_start')' for a short tutorial | # | Visit 'https://bit.ly/pliman' for a complete tutorial | # |=======================================================| -img <- image_import(image_pliman("soybean_touch.jpg"), plot = TRUE) +img <-image_pliman("soybean_touch.jpg", plot = TRUE) soy <- analyze_objects(img, marker = "id") ``` @@ -104,10 +105,10 @@ soy$statistics # Disease severity ``` r -img <- image_import(image_pliman("sev_leaf.jpg")) -healthy <- image_import(image_pliman("sev_healthy.jpg")) -symptoms <- image_import(image_pliman("sev_sympt.jpg")) -background <- image_import(image_pliman("sev_back.jpg")) +img <-image_pliman("sev_leaf.jpg") +healthy <-image_pliman("sev_healthy.jpg") +symptoms <-image_pliman("sev_sympt.jpg") +background <-image_pliman("sev_back.jpg") image_combine(img, healthy, symptoms, background, ncol = 4) ``` @@ -126,7 +127,7 @@ sev <- ``` r sev$severity # healthy symptomatic -# 1 89.21025 10.78975 +# 1 89.04464 10.95536 ``` `pliman` takes the advantage of several powerful functions from [EBImage diff --git a/cran-comments.md b/cran-comments.md index 973015f..4feb03e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,5 @@ ## Release summary -This is a minor release (0.1.0) that includes new functions, minor improvements. I changed the R dependency to R (>= 4.1) to fix the bug with EBImage installation. See `NEWS.md` for additional information +This is a major release (1.0.0) that includes new features, bug corrections, and minor improvements. Please, see `NEWS.md` for additional information. ## Test environments diff --git a/docs/articles/analyze_objects_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/analyze_objects_files/figure-html/unnamed-chunk-15-1.png index e562e78..6d889ec 100644 Binary files a/docs/articles/analyze_objects_files/figure-html/unnamed-chunk-15-1.png and b/docs/articles/analyze_objects_files/figure-html/unnamed-chunk-15-1.png differ diff --git a/docs/articles/phytopatometry.html b/docs/articles/phytopatometry.html index 77293dd..29f8552 100644 --- a/docs/articles/phytopatometry.html +++ b/docs/articles/phytopatometry.html @@ -218,7 +218,7 @@ 

 res$severity
 #>    healthy symptomatic
-#> 1 89.22702    10.77298
+#> 1 89.31286 10.68714

Alternatively, users can create a mask instead of showing the original image.

 
@@ -239,7 +239,7 @@ 

 
 res2$severity
 #>    healthy symptomatic
-#> 1 89.38145    10.61855
+#> 1 88.76553 11.23447

@@ -264,7 +264,7 @@ 

 res3$severity
 #>    healthy symptomatic
-#> 1 93.86121    6.138791
+#> 1 93.67464 6.325357

@@ -281,47 +281,49 @@ 

 res4$shape
 #>    id        x        y area perimeter radius_mean radius_min radius_max
-#> 1   1 222.3081 114.5996  964       169   22.089227  0.7860029  38.771399
-#> 2   2 190.6217 130.1407 1237       215   20.161685  1.5231191  38.614600
-#> 3   3 178.9569 213.9870 3623       401   49.834381  1.2007553  94.223459
-#> 4   4 210.7272 194.5332 1763       218   23.680281  1.6099284  42.079274
-#> 5   5 264.1000 193.6000  130        38    6.018896  4.2975384   7.843562
-#> 6   6 120.6235 202.3412   85        29    4.764471  3.2292510   6.038422
-#> 9   7 211.8550 329.1710  883       123   17.881273  7.3957916  30.236039
-#> 11  8 281.2918 324.8911  257        53    8.849646  5.4810590  12.473539
-#> 12  9 347.9697 335.9205  264        54    8.967773  5.6583696  12.404394
-#> 13 10 184.7270 385.5640 1835       163   24.942991 12.2947739  37.689913
-#> 14 11 334.4275 370.2971  138        38    6.264066  4.3421053   8.426848
-#> 15 12 250.6716 377.4925  134        37    6.359633  3.3393420   8.967802
-#> 17 13 173.4002 450.3011 2189       235   28.356667 12.5831867  46.526638
-#> 20 14 109.1137 465.0995  211        60    8.180511  2.9397657  12.695494
-#> 21 15 123.8044 493.3944  900       112   17.471221  9.3636198  27.623079
-#> 22 16 150.0802 521.2828 1259       140   20.796205 10.6625513  32.361860
+#> 1   1 222.2887 114.6310 1046       172   22.403190  0.3139535  39.374835
+#> 2   2 190.8768 130.8834 1347       216   20.618337  1.4972039  38.603648
+#> 3   3 178.9976 214.1491 3735       403   50.147839  1.9180034  94.976418
+#> 4   4 210.8096 194.4208 1849       223   24.197001  0.8860333  42.460061
+#> 5   5 264.3768 193.6232  138        41    6.227708  4.3878720   8.276311
+#> 6   6 120.4600 202.2900  100        32    5.221618  3.1290599   6.858645
+#> 8   7 146.3521 261.8310   71        27    4.327466  3.0669261   5.530933
+#> 9   8 211.9205 329.0709  931       126   18.465829  7.5120295  30.797631
+#> 11  9 281.2727 325.0945  275        57    9.105716  5.3219234  13.142541
+#> 12 10 347.9933 335.8395  299        58    9.626815  6.2538692  13.069068
+#> 14 11 184.7567 385.3610 1878       164   25.184601 12.8391252  38.360316
+#> 16 12 334.2756 370.2436  156        40    6.723178  4.4702489   9.210490
+#> 17 13 250.7273 377.2987  154        39    6.831217  3.6234680   9.383635
+#> 19 14 173.2269 450.1422 2279       239   28.795630 12.8861388  47.416545
+#> 22 15 110.3394 465.0547  274        67    9.195734  4.0853012  13.637749
+#> 23 16 123.6069 493.3826  954       115   17.962954  9.9391342  27.653985
+#> 24 17 149.9523 521.2032 1299       140   21.236081 11.1714857  33.014963
 #>     radius_sd radius_ratio major_axis eccentricity       theta
-#> 1  11.2270164    49.327300   89.89300    0.9792454  1.39707872
-#> 2   8.9219132    25.352318   71.92778    0.8922875  1.48882769
-#> 3  25.3707260    78.470162  190.81747    0.9785970  1.16748882
-#> 4  10.0311965    26.137358   80.87732    0.8466161  1.27686034
-#> 5   1.0072635     1.825129   15.53860    0.7091755  0.06423295
-#> 6   0.8153877     1.869914   12.38446    0.6869883  0.11255328
-#> 9   6.2846866     4.088276   55.94020    0.9273173  1.54037560
-#> 11  1.9280128     2.275753   24.41219    0.8268777 -0.47920887
-#> 12  1.9452800     2.192221   24.70499    0.8266683  0.97625044
-#> 13  7.4770722     3.065523   75.43400    0.9067328  1.20507406
-#> 14  1.1640319     1.940729   16.42445    0.7361303  0.69651290
-#> 15  1.5849202     2.685500   18.38356    0.8563692 -0.76948291
-#> 17  9.7481634     3.697524   87.82668    0.8528370  0.97944688
-#> 20  2.7392857     4.318539   23.27308    0.8029749  0.01837607
-#> 21  5.5031294     2.950043   53.56349    0.9133958 -0.29195811
-#> 22  5.9292863     3.035095   58.71686    0.8604024 -0.06439327
+#> 1  11.1755916   125.416141   89.39593    0.9764562  1.39887312
+#> 2   8.9447371    25.783828   72.72970    0.8858606  1.48010840
+#> 3  25.3211016    49.518378  190.85475    0.9780844  1.16589555
+#> 4  10.1569704    47.921519   81.19874    0.8422778  1.27653300
+#> 5   1.1417925     1.886179   16.41411    0.7348168  0.11792299
+#> 6   1.0337754     2.191919   13.98327    0.7386224  0.04303979
+#> 8   0.6500446     1.803413   11.07961    0.6600266  0.45878072
+#> 9   6.4114268     4.099775   57.35088    0.9266472  1.54032658
+#> 11  2.0710833     2.469510   25.46050    0.8337564 -0.43324218
+#> 12  2.0059656     2.089757   26.08633    0.8212703  0.97031268
+#> 14  7.4266357     2.987767   75.79999    0.9040359  1.20711232
+#> 16  1.3381902     2.060398   17.67801    0.7478441  0.71462492
+#> 17  1.7686239     2.589683   19.81144    0.8545446 -0.75923505
+#> 19  9.8830893     3.679655   89.44341    0.8566149  0.98824516
+#> 22  2.7702290     3.338248   27.25855    0.8466537  0.02324116
+#> 23  5.5284069     2.782333   54.63570    0.9103912 -0.28990693
+#> 24  6.0158994     2.955289   59.62924    0.8617372 -0.05496710
 res4$statistics
 #>        stat      value
-#> 1         n    16.0000
-#> 2  min_area    85.0000
-#> 3 mean_area   992.0000
-#> 4  max_area  3623.0000
-#> 5   sd_area   984.0002
-#> 6  sum_area 15872.0000
+#> 1 n 17.0000 +#> 2 min_area 71.0000 +#> 3 mean_area 987.3529 +#> 4 max_area 3735.0000 +#> 5 sd_area 1006.6055 +#> 6 sum_area 16785.0000

diff --git a/docs/articles/phytopatometry_files/figure-html/disease2-1.png b/docs/articles/phytopatometry_files/figure-html/disease2-1.png index 06d6663..a889ae1 100644 Binary files a/docs/articles/phytopatometry_files/figure-html/disease2-1.png and b/docs/articles/phytopatometry_files/figure-html/disease2-1.png differ diff --git a/docs/articles/phytopatometry_files/figure-html/disease3-1.png b/docs/articles/phytopatometry_files/figure-html/disease3-1.png index 1fe006f..4f17c01 100644 Binary files a/docs/articles/phytopatometry_files/figure-html/disease3-1.png and b/docs/articles/phytopatometry_files/figure-html/disease3-1.png differ diff --git a/docs/articles/phytopatometry_files/figure-html/disease4-2.png b/docs/articles/phytopatometry_files/figure-html/disease4-2.png index dfea0bf..350f737 100644 Binary files a/docs/articles/phytopatometry_files/figure-html/disease4-2.png and b/docs/articles/phytopatometry_files/figure-html/disease4-2.png differ diff --git a/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-2-1.png index 6e4fdaa..986d7c3 100644 Binary files a/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-3-1.png index 3d429e1..15dee74 100644 Binary files a/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/phytopatometry_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/pliman_start.html b/docs/articles/pliman_start.html index 4d5fde5..ce767e4 100644 --- a/docs/articles/pliman_start.html +++ b/docs/articles/pliman_start.html @@ -309,7 +309,7 @@ 

# $severity
 #    healthy symptomatic
-# 1 89.07971    10.92029
+# 1 89.23474    10.76526
 # 
 # $shape
 # NULL
diff --git a/docs/articles/pliman_start_files/figure-html/unnamed-chunk-4-2.png b/docs/articles/pliman_start_files/figure-html/unnamed-chunk-4-2.png
index 82f7bda..b5fff7d 100644
Binary files a/docs/articles/pliman_start_files/figure-html/unnamed-chunk-4-2.png and b/docs/articles/pliman_start_files/figure-html/unnamed-chunk-4-2.png differ
diff --git a/docs/index.html b/docs/index.html
index 3a486eb..66c45eb 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -174,6 +174,7 @@
 
  • Measure disease severity;
    • 
 
  • Count the number of lesions;
    • 
 
  • Obtain the shape of lesions;
    • 
+
  • Produce Standard Area Diagrams;
    • 
 
  • Count objects in an image;
    • 
 
  • Get object features (area, perimeter, radius, circularity, eccentricity, solidity);
    • 
 
  • Get the RGB values for each object in an image;
    • 
@@ -210,12 +211,12 @@ 
    
 
     library(pliman)
 # |=======================================================|
-# | Tools for Plant Image Analysis (pliman 0.3.0)         |
+# | Tools for Plant Image Analysis (pliman 1.0.0)         |
 # | Author: Tiago Olivoto                                 |
 # | Type 'vignette('pliman_start')' for a short tutorial  |
 # | Visit 'https://bit.ly/pliman' for a complete tutorial |
 # |=======================================================|
-img <- image_import(image_pliman("soybean_touch.jpg"), plot = TRUE)
+img <-image_pliman("soybean_touch.jpg", plot = TRUE)
 soy <- analyze_objects(img, marker = "id")
    
 
    
 
    @@ -232,10 +233,10 @@ 
    
 
    
 Disease severity
    
 
    -img <- image_import(image_pliman("sev_leaf.jpg"))
-healthy <- image_import(image_pliman("sev_healthy.jpg"))
-symptoms <- image_import(image_pliman("sev_sympt.jpg"))
-background <- image_import(image_pliman("sev_back.jpg"))
+img <-image_pliman("sev_leaf.jpg")
+healthy <-image_pliman("sev_healthy.jpg")
+symptoms <-image_pliman("sev_sympt.jpg")
+background <-image_pliman("sev_back.jpg")
 image_combine(img, healthy, symptoms, background, ncol = 4)
    
 
    
 
    @@ -248,7 +249,7 @@ 
    
 
     sev$severity
 #    healthy symptomatic
-# 1 89.21025    10.78975
    
+# 1 89.04464    10.95536
    
 
    pliman takes the advantage of several powerful functions from EBImage package. Thanks to Andrzej Oleś and collaborators for the impressive job done with EBImage!
    
 
    
 
    
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 9609674..30ecc7d 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -8,7 +8,7 @@ articles:
   phytopatometry: phytopatometry.html
   pliman_start: pliman_start.html
   segmentation: segmentation.html
-last_built: 2021-11-09T18:14Z
+last_built: 2021-11-09T19:19Z
 urls:
   reference: https://tiagoolivoto.github.io/pliman//reference
   article: https://tiagoolivoto.github.io/pliman//articles
diff --git a/docs/reference/figures/README-unnamed-chunk-5-1.png b/docs/reference/figures/README-unnamed-chunk-5-1.png
index ab1b89b..7b0d6ce 100644
Binary files a/docs/reference/figures/README-unnamed-chunk-5-1.png and b/docs/reference/figures/README-unnamed-chunk-5-1.png differ
diff --git a/docs/reference/figures/README-unnamed-chunk-6-1.png b/docs/reference/figures/README-unnamed-chunk-6-1.png
index 08e2941..a688f22 100644
Binary files a/docs/reference/figures/README-unnamed-chunk-6-1.png and b/docs/reference/figures/README-unnamed-chunk-6-1.png differ
diff --git a/docs/reference/rgb_to_hsv-1.png b/docs/reference/rgb_to_hsv-1.png
index dc11a67..f9cb693 100644
Binary files a/docs/reference/rgb_to_hsv-1.png and b/docs/reference/rgb_to_hsv-1.png differ
diff --git a/docs/reference/utils_file.html b/docs/reference/utils_file.html
index 85a5bf9..e51f6e1 100644
--- a/docs/reference/utils_file.html
+++ b/docs/reference/utils_file.html
@@ -354,11 +354,11 @@ 
    Examp
 # manipulate files
 dir <- tempdir()
 list.files(dir)
-#> [1] "downlit"          "file12ec373677fe" "file12ec75325b68"
+#> [1] "downlit"          "file15b42d1c622d" "file15b4c946339" 
 file.create(paste0(dir, "/test.txt"))
 #> [1] TRUE
 list.files(dir)
-#> [1] "downlit"          "file12ec373677fe" "file12ec75325b68" "test.txt"        
+#> [1] "downlit"          "file15b42d1c622d" "file15b4c946339"  "test.txt"        
 manipulate_files("test",
                  dir = paste0(dir, "\\"),
                 prefix = "chang_",
@@ -366,7 +366,7 @@ 
    Examp
                 overwrite = TRUE)
 #> Warning: Failed to copy 1 files.
 list.files(dir)
-#> [1] "downlit"          "file12ec373677fe" "file12ec75325b68" "test.txt"        
+#> [1] "downlit"          "file15b42d1c622d" "file15b4c946339"  "test.txt"        
 # }
    diff --git a/man/figures/README-unnamed-chunk-5-1.png b/man/figures/README-unnamed-chunk-5-1.png index ab1b89b..7b0d6ce 100644 Binary files a/man/figures/README-unnamed-chunk-5-1.png and b/man/figures/README-unnamed-chunk-5-1.png differ diff --git a/man/figures/README-unnamed-chunk-6-1.png b/man/figures/README-unnamed-chunk-6-1.png index 08e2941..a688f22 100644 Binary files a/man/figures/README-unnamed-chunk-6-1.png and b/man/figures/README-unnamed-chunk-6-1.png differ