demo/demo.md
In KeachMurakami/dualband:
library(tidyverse)
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, cache = T, out.width = "50%")
# load core functions and libraries
library(dualband)
library(imager)
library(EBImage)
library(pri)
set_read_img("jpg")
Demo
Load images
(img_files <- dir("sample_data/", full.names = T))
## [1] "sample_data//img1.jpg" "sample_data//img2.jpg"
img_demo <-
img_files %>%
read_imgs %>%
.^3 # correct gamma value
dualband::show(img_demo, browser = F, all = F)
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
Divide images into small pieces
To divide images, the locations should be approximated.
location_demo <-
tribble(
~ x, ~ y, ~ size, ~ location,
474, 501, 100, "a",
1497, 933, 100, "b"
)
location_demo
## # A tibble: 2 x 4
## x y size location
## <dbl> <dbl> <dbl> <chr>
## 1 474 501 100 a
## 2 1497 933 100 b
The images are divided into a list of small images---called pieces.
piece_demo <-
location_demo %>%
split(.$location) %>%
map(~ divide_piece(., img_demo))
piece_demo %>%
map(dualband::show, browser = F)
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## $a
## NULL
##
## $b
## NULL
Detect markers
Determine a center of the marker with set_center. A binarised piece
can be checked as the side-effect (.check = T). This function appends
attributes related to binarisation, eroding, and geomery of
white-reflectance to the input image. That is, only attributes will be
changed. Returns NULL when the .check = T.
piece_demo %>%
map(~ set_center(., .check = T, browser = F,
white_ratio = .95, erode_size = 1, occupancy = .001))
## $a
## NULL
##
## $b
## NULL
piece_demo_1 <-
piece_demo %>%
map(~ set_center(., .check = F, browser = F,
white_ratio = .95, erode_size = 1, occupancy = .001))
- white_ratio (0--1)
- bright pixels within top
X% are regarded as the white regions.
- erode_size (int)
- if the white regions are separated, the regions may be merged by
increasing this factor.
- occupancy (0--1)
- smaller regions can be removed by increasing this factor
although the smaller regions do not count as long as a true
white region is the largest.
Set ROIs
Determine the ROIs with set_masks. A masked piece can be checked as
the side-effect (.check = T). This function appends attributes related
to ROIS to the input image. That is, only attributes will be changed.
Returns NULL when the .check = T.
piece_demo_1 %>%
map(~ set_masks(., .check = T, browser = F,
ref_white_ratio = 1/5, margin_white_ratio = 1.2, outer_white_ratio = 2))
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## $a
## NULL
##
## $b
## NULL
piece_demo_2 <-
piece_demo_1 %>%
map(~ set_masks(., .check = F, browser = F,
ref_white_ratio = 1/5, margin_white_ratio = 1.2, outer_white_ratio = 2))
sizes <-
c(ref = .5, white = 1, margin = 1.2, outer = 2)
colors <-
c(ref = "grey50", white = "white", margin = "black", outer = "orange")
rectangles <-
map2(rev(sizes), rev(colors),
~ annotate(geom = "rect", xmin = -.x, xmax = .x, ymin = -.x, ymax = .x, fill = .y))
tibble() %>%
ggplot(aes()) +
theme_minimal() +
rectangles +
coord_fixed()
- ref_white_ratio (0--1)
- grey / white
- margin_white_ratio ( > 1)
- black / white
- outer_white_ratio ( > margin_white_ratio)
- orange / white
Summarise marker data
Statistics can be summarised by extract_reflectance.
piece_demo_2 %>%
map(extract_reflectance)
## $a
## file median_marker mean_marker median_target mean_target median_refl
## 1 img1 0.1838584 0.1827335 0.03448369 0.04125444 0.1875557
## 2 img2 0.1800806 0.1815917 0.03448369 0.04144903 0.1914903
## mean_refl z
## 1 0.2257629 1
## 2 0.2282540 2
##
## $b
## file median_marker mean_marker median_target mean_target median_refl
## 1 img1 0.3756928 0.3722550 0.1654869 0.1711268 0.4404845
## 2 img2 0.3576146 0.3561011 0.1619660 0.1642440 0.4529066
## mean_refl z
## 1 0.4597030 1
## 2 0.4612286 2
Check mapping
Map reference (i.e. reflectance standard) and target (i.e. leaf) regions
on the input image.
masked_pieces_demo <-
piece_demo_2 %>%
# adjust mapping colors and pixel values
map(check_mask, map_rgb = c(marker = 1, target = 3), map_int = c(marker = 10, target = 10))
masked_full_demo <-
map_full(list_pieces = masked_pieces_demo, full_size_img = img_demo)
dualband::show(masked_full_demo, browser = F)
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
Session information
devtools::session_info()
## Session info --------------------------------------------------------------
## setting value
## version R version 3.3.1 (2016-06-21)
## system x86_64, darwin13.4.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz Asia/Tokyo
## date 2018-02-28
## Packages ------------------------------------------------------------------
## package * version date
## abind 1.4-5 2016-07-21
## assertthat 0.2.0 2017-04-11
## backports 1.0.4 2016-10-24
## bindr 0.1 2016-11-13
## bindrcpp * 0.2 2017-06-17
## BiocGenerics 0.20.0 2017-04-20
## bmp 0.2 2013-08-10
## broom 0.4.3 2017-11-20
## cellranger 1.1.0 2016-07-27
## cli 1.0.0 2017-11-05
## codetools 0.2-14 2015-07-15
## colorspace 1.2-6 2015-03-11
## crayon 1.3.4 2017-09-16
## devtools 1.12.0 2016-06-24
## digest 0.6.13 2017-12-14
## dplyr * 0.7.4 2017-09-28
## dualband * 0.1.0 2018-02-28
## EBImage * 4.16.0 2017-04-20
## evaluate 0.10.1 2017-06-24
## fftwtools 0.9-8 2017-03-25
## forcats * 0.2.0 2017-01-23
## ggplot2 * 2.2.1.9000 2018-02-13
## glue 1.2.0 2017-10-29
## gtable 0.2.0 2016-02-26
## haven 1.1.0 2017-07-09
## hms 0.3 2016-11-22
## htmltools 0.3.6 2017-04-28
## httr 1.3.1 2017-08-20
## imager * 0.40.2 2017-04-24
## jpeg 0.1-8 2014-01-23
## jsonlite 1.5 2017-06-01
## knitr 1.17 2017-08-10
## labeling 0.3 2014-08-23
## lattice 0.20-33 2015-07-14
## lazyeval 0.2.1 2017-10-29
## locfit 1.5-9.1 2013-04-20
## lubridate 1.7.1 2017-11-03
## magrittr * 1.5 2014-11-22
## memoise 1.0.0 2016-01-29
## mnormt 1.5-4 2016-03-09
## modelr 0.1.1 2017-07-24
## munsell 0.4.3 2016-02-13
## nlme 3.1-128 2016-05-10
## pkgconfig 2.0.1 2017-03-21
## plyr * 1.8.4 2016-06-08
## png 0.1-7 2013-12-03
## pri * 0.1.0 2017-11-19
## psych 1.6.6 2016-06-28
## purrr * 0.2.4 2017-10-18
## R6 2.2.2 2017-06-17
## Rcpp 0.12.14 2017-11-23
## readbitmap 0.1-4 2014-09-05
## readr * 1.1.1 2017-05-16
## readxl 1.0.0 2017-04-18
## reshape2 1.4.3 2017-12-11
## rlang 0.1.6.9003 2018-02-13
## rmarkdown 1.6 2017-06-15
## rprojroot 1.2 2017-01-16
## rstudioapi 0.7 2017-09-07
## rvest 0.3.2 2016-06-17
## scales 0.5.0.9000 2017-12-23
## stringi 1.1.6 2017-11-17
## stringr * 1.3.0 2018-02-19
## tibble * 1.3.4 2017-08-22
## tidyr * 0.8.0 2018-01-29
## tidyverse * 1.2.1 2017-11-14
## tiff 0.1-5 2013-09-04
## withr 2.1.1.9000 2017-12-23
## xml2 1.1.1 2017-01-24
## yaml 2.1.14 2016-11-12
## source
## CRAN (R 3.3.0)
## cran (@0.2.0)
## cran (@1.0.4)
## cran (@0.1)
## CRAN (R 3.3.2)
## Bioconductor
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## cran (@1.1.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## cran (@0.6.13)
## cran (@0.7.4)
## Github (KeachMurakami/dualband@c320f18)
## Bioconductor
## cran (@0.10.1)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## Github (thomasp85/ggplot2@7859a29)
## cran (@1.2.0)
## CRAN (R 3.3.1)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## cran (@0.3.6)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## cran (@1.5)
## cran (@1.17)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## cran (@0.2.1)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## cran (@2.0.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.0)
## Github (KeachMurakami/pri@8673b65)
## CRAN (R 3.3.0)
## cran (@0.2.4)
## cran (@2.2.2)
## cran (@0.12.14)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## cran (@1.4.3)
## Github (tidyverse/rlang@616fd4d)
## CRAN (R 3.3.2)
## cran (@1.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## Github (hadley/scales@d767915)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## cran (@1.3.4)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.0)
## Github (jimhester/withr@df18523)
## cran (@1.1.1)
## cran (@2.1.14)
KeachMurakami/dualband documentation built on May 6, 2019, 12:23 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(tidyverse)
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, cache = T, out.width = "50%")
# load core functions and libraries
library(dualband)
library(imager)
library(EBImage)
library(pri)
set_read_img("jpg")
Demo
Load images
(img_files <- dir("sample_data/", full.names = T))
## [1] "sample_data//img1.jpg" "sample_data//img2.jpg"
img_demo <-
img_files %>%
read_imgs %>%
.^3 # correct gamma value
dualband::show(img_demo, browser = F, all = F)
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
Divide images into small pieces
To divide images, the locations should be approximated.
location_demo <-
tribble(
~ x, ~ y, ~ size, ~ location,
474, 501, 100, "a",
1497, 933, 100, "b"
)
location_demo
## # A tibble: 2 x 4
## x y size location
## <dbl> <dbl> <dbl> <chr>
## 1 474 501 100 a
## 2 1497 933 100 b
The images are divided into a list of small images---called pieces.
piece_demo <-
location_demo %>%
split(.$location) %>%
map(~ divide_piece(., img_demo))
piece_demo %>%
map(dualband::show, browser = F)
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## $a
## NULL
##
## $b
## NULL
Detect markers
Determine a center of the marker with set_center. A binarised piece
can be checked as the side-effect (.check = T). This function appends
attributes related to binarisation, eroding, and geomery of
white-reflectance to the input image. That is, only attributes will be
changed. Returns NULL when the .check = T.
piece_demo %>%
map(~ set_center(., .check = T, browser = F,
white_ratio = .95, erode_size = 1, occupancy = .001))
## $a
## NULL
##
## $b
## NULL
piece_demo_1 <-
piece_demo %>%
map(~ set_center(., .check = F, browser = F,
white_ratio = .95, erode_size = 1, occupancy = .001))
- white_ratio (0--1)
- bright pixels within top
X%are regarded as the white regions.
- bright pixels within top
- erode_size (int)
- if the white regions are separated, the regions may be merged by increasing this factor.
- occupancy (0--1)
- smaller regions can be removed by increasing this factor although the smaller regions do not count as long as a true white region is the largest.
Set ROIs
Determine the ROIs with set_masks. A masked piece can be checked as
the side-effect (.check = T). This function appends attributes related
to ROIS to the input image. That is, only attributes will be changed.
Returns NULL when the .check = T.
piece_demo_1 %>%
map(~ set_masks(., .check = T, browser = F,
ref_white_ratio = 1/5, margin_white_ratio = 1.2, outer_white_ratio = 2))
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
## $a
## NULL
##
## $b
## NULL
piece_demo_2 <-
piece_demo_1 %>%
map(~ set_masks(., .check = F, browser = F,
ref_white_ratio = 1/5, margin_white_ratio = 1.2, outer_white_ratio = 2))
sizes <-
c(ref = .5, white = 1, margin = 1.2, outer = 2)
colors <-
c(ref = "grey50", white = "white", margin = "black", outer = "orange")
rectangles <-
map2(rev(sizes), rev(colors),
~ annotate(geom = "rect", xmin = -.x, xmax = .x, ymin = -.x, ymax = .x, fill = .y))
tibble() %>%
ggplot(aes()) +
theme_minimal() +
rectangles +
coord_fixed()
- ref_white_ratio (0--1)
- grey / white
- margin_white_ratio ( > 1)
- black / white
- outer_white_ratio ( > margin_white_ratio)
- orange / white
Summarise marker data
Statistics can be summarised by extract_reflectance.
piece_demo_2 %>%
map(extract_reflectance)
## $a
## file median_marker mean_marker median_target mean_target median_refl
## 1 img1 0.1838584 0.1827335 0.03448369 0.04125444 0.1875557
## 2 img2 0.1800806 0.1815917 0.03448369 0.04144903 0.1914903
## mean_refl z
## 1 0.2257629 1
## 2 0.2282540 2
##
## $b
## file median_marker mean_marker median_target mean_target median_refl
## 1 img1 0.3756928 0.3722550 0.1654869 0.1711268 0.4404845
## 2 img2 0.3576146 0.3561011 0.1619660 0.1642440 0.4529066
## mean_refl z
## 1 0.4597030 1
## 2 0.4612286 2
Check mapping
Map reference (i.e. reflectance standard) and target (i.e. leaf) regions on the input image.
masked_pieces_demo <-
piece_demo_2 %>%
# adjust mapping colors and pixel values
map(check_mask, map_rgb = c(marker = 1, target = 3), map_int = c(marker = 10, target = 10))
masked_full_demo <-
map_full(list_pieces = masked_pieces_demo, full_size_img = img_demo)
dualband::show(masked_full_demo, browser = F)
## Only the first frame of the image stack is displayed.
## To display all frames use 'all = TRUE'.
Session information
devtools::session_info()
## Session info --------------------------------------------------------------
## setting value
## version R version 3.3.1 (2016-06-21)
## system x86_64, darwin13.4.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz Asia/Tokyo
## date 2018-02-28
## Packages ------------------------------------------------------------------
## package * version date
## abind 1.4-5 2016-07-21
## assertthat 0.2.0 2017-04-11
## backports 1.0.4 2016-10-24
## bindr 0.1 2016-11-13
## bindrcpp * 0.2 2017-06-17
## BiocGenerics 0.20.0 2017-04-20
## bmp 0.2 2013-08-10
## broom 0.4.3 2017-11-20
## cellranger 1.1.0 2016-07-27
## cli 1.0.0 2017-11-05
## codetools 0.2-14 2015-07-15
## colorspace 1.2-6 2015-03-11
## crayon 1.3.4 2017-09-16
## devtools 1.12.0 2016-06-24
## digest 0.6.13 2017-12-14
## dplyr * 0.7.4 2017-09-28
## dualband * 0.1.0 2018-02-28
## EBImage * 4.16.0 2017-04-20
## evaluate 0.10.1 2017-06-24
## fftwtools 0.9-8 2017-03-25
## forcats * 0.2.0 2017-01-23
## ggplot2 * 2.2.1.9000 2018-02-13
## glue 1.2.0 2017-10-29
## gtable 0.2.0 2016-02-26
## haven 1.1.0 2017-07-09
## hms 0.3 2016-11-22
## htmltools 0.3.6 2017-04-28
## httr 1.3.1 2017-08-20
## imager * 0.40.2 2017-04-24
## jpeg 0.1-8 2014-01-23
## jsonlite 1.5 2017-06-01
## knitr 1.17 2017-08-10
## labeling 0.3 2014-08-23
## lattice 0.20-33 2015-07-14
## lazyeval 0.2.1 2017-10-29
## locfit 1.5-9.1 2013-04-20
## lubridate 1.7.1 2017-11-03
## magrittr * 1.5 2014-11-22
## memoise 1.0.0 2016-01-29
## mnormt 1.5-4 2016-03-09
## modelr 0.1.1 2017-07-24
## munsell 0.4.3 2016-02-13
## nlme 3.1-128 2016-05-10
## pkgconfig 2.0.1 2017-03-21
## plyr * 1.8.4 2016-06-08
## png 0.1-7 2013-12-03
## pri * 0.1.0 2017-11-19
## psych 1.6.6 2016-06-28
## purrr * 0.2.4 2017-10-18
## R6 2.2.2 2017-06-17
## Rcpp 0.12.14 2017-11-23
## readbitmap 0.1-4 2014-09-05
## readr * 1.1.1 2017-05-16
## readxl 1.0.0 2017-04-18
## reshape2 1.4.3 2017-12-11
## rlang 0.1.6.9003 2018-02-13
## rmarkdown 1.6 2017-06-15
## rprojroot 1.2 2017-01-16
## rstudioapi 0.7 2017-09-07
## rvest 0.3.2 2016-06-17
## scales 0.5.0.9000 2017-12-23
## stringi 1.1.6 2017-11-17
## stringr * 1.3.0 2018-02-19
## tibble * 1.3.4 2017-08-22
## tidyr * 0.8.0 2018-01-29
## tidyverse * 1.2.1 2017-11-14
## tiff 0.1-5 2013-09-04
## withr 2.1.1.9000 2017-12-23
## xml2 1.1.1 2017-01-24
## yaml 2.1.14 2016-11-12
## source
## CRAN (R 3.3.0)
## cran (@0.2.0)
## cran (@1.0.4)
## cran (@0.1)
## CRAN (R 3.3.2)
## Bioconductor
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## cran (@1.1.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## cran (@0.6.13)
## cran (@0.7.4)
## Github (KeachMurakami/dualband@c320f18)
## Bioconductor
## cran (@0.10.1)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## Github (thomasp85/ggplot2@7859a29)
## cran (@1.2.0)
## CRAN (R 3.3.1)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## cran (@0.3.6)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## cran (@1.5)
## cran (@1.17)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## cran (@0.2.1)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## cran (@2.0.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.0)
## Github (KeachMurakami/pri@8673b65)
## CRAN (R 3.3.0)
## cran (@0.2.4)
## cran (@2.2.2)
## cran (@0.12.14)
## CRAN (R 3.3.0)
## CRAN (R 3.3.2)
## CRAN (R 3.3.2)
## cran (@1.4.3)
## Github (tidyverse/rlang@616fd4d)
## CRAN (R 3.3.2)
## cran (@1.2)
## CRAN (R 3.3.2)
## CRAN (R 3.3.0)
## Github (hadley/scales@d767915)
## CRAN (R 3.3.2)
## CRAN (R 3.3.1)
## cran (@1.3.4)
## CRAN (R 3.3.1)
## CRAN (R 3.3.1)
## CRAN (R 3.3.0)
## Github (jimhester/withr@df18523)
## cran (@1.1.1)
## cran (@2.1.14)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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