diff --git a/pkgdown.yml b/pkgdown.yml index 108d1df..3f71214 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 2.19.2 pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2023-09-22T23:42Z +last_built: 2023-09-24T01:02Z urls: reference: https://yuhangtom.github.io/wire/reference article: https://yuhangtom.github.io/wire/articles diff --git a/reference/index.html b/reference/index.html index d23ce2e..d9ef41b 100644 --- a/reference/index.html +++ b/reference/index.html @@ -92,6 +92,16 @@

All functionsinside_polygon() + +
Identify the inside polygon of a set of points
+
+ + x3p_boundary_points() +
+
Identify boundary of a 3d topographic scan in x3p format
+
+ x3p_image_autosize()
Plot x3p object as an image with auto-adjusted size
@@ -100,6 +110,11 @@

All functionsx3p_subsamples
Subsampled wire cuts data
+

+ + x3p_surface_polygon() +
+
Add a polygon of the scan shape as mask
diff --git a/reference/inside_polygon.html b/reference/inside_polygon.html new file mode 100644 index 0000000..e03db29 --- /dev/null +++ b/reference/inside_polygon.html @@ -0,0 +1,100 @@ + +Identify the inside polygon of a set of points — inside_polygon • wire + Skip to contents + + +
+
+
+

Identify the inside polygon of a set of points

+ +
inside_polygon.Rd
+
+ +
+

Uses concentric mirroring onto a radius around the center point, applies an +alpha hull to that shape, and mirrors the result back.

+
+ +
+

Usage

+ 
inside_polygon(x, y, concavity, center = NULL)
+
+ +
+

Arguments

+
x
+

numeric vector of x positions

+ + +
y
+

numeric vector of y positions

+ + +
concavity
+

strictly positive parameter. Smaller values approach the +inside of the boundary +more closely. Large values concentrate on the inner center of the area

+ + +
center
+

numeric vector of length 2, consisting of (x,y) coordinate for +centering x and y values. +If center is NULL, the half ranges of x and y are used.

+ +
+
+

Value

+ + +

dataframe of x and y positions describing the inside of the area +described by the input x and y, variable id describes the order of the points

+
+ +
+ + +
+

Developed by Yuhang Lin, Heike Hofmann.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/reference/x3p_boundary_points.html b/reference/x3p_boundary_points.html new file mode 100644 index 0000000..f1996e9 --- /dev/null +++ b/reference/x3p_boundary_points.html @@ -0,0 +1,88 @@ + +Identify boundary of a 3d topographic scan in x3p format — x3p_boundary_points • wire + Skip to contents + + +
+
+
+

Identify boundary of a 3d topographic scan in x3p format

+ +
x3p_boundary_points.Rd
+
+ +
+

Identify boundary of a 3d topographic scan in x3p format

+
+ +
+

Usage

+ 
x3p_boundary_points(x3p, sample)
+
+ +
+

Arguments

+
x3p
+

topographic scan in x3p format

+ + +
sample
+

positive integer value specifying the sampling ratio: +every sample value in x and y direction will be included. +Higher values result in faster results but cruder assessments of the boundary.

+ +
+
+

Value

+ + +

data frame of boundary points, variables are named x and y

+ + +
+ +
+ + +
+

Developed by Yuhang Lin, Heike Hofmann.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/reference/x3p_surface_polygon.html b/reference/x3p_surface_polygon.html new file mode 100644 index 0000000..828335a --- /dev/null +++ b/reference/x3p_surface_polygon.html @@ -0,0 +1,106 @@ + +Add a polygon of the scan shape as mask — x3p_surface_polygon • wire + Skip to contents + + +
+
+
+

Add a polygon of the scan shape as mask

+ +
x3p_surface_polygon.Rd
+
+ +
+

Add a polygon of the scan shape as mask

+
+ +
+

Usage

+ 
x3p_surface_polygon(
+  x3p,
+  colour = "red",
+  sample = 10,
+  center = NULL,
+  concavity = 1.5
+)
+
+ +
+

Arguments

+
x3p
+

x3p file

+ + +
colour
+

colour for the polygon

+ + +
sample
+

strictly positive integer value specifying the amount of +downsampling to be used (see x3p_sample) to calculate the boundary points +of the polygon. Larger values of sample will result in faster response times +but results in less accurate polygons.

+ + +
center
+

point on the center of the scan. If NULL, a center will be +derived from the boundary points

+ + +
concavity
+

strictly positive value used in concaveman::concaveman

+ +
+
+

Value

+ + +

x3p object with mask

+
+ +
+ + +
+

Developed by Yuhang Lin, Heike Hofmann.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/search.json b/search.json index d085569..4dc40f1 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://yuhangtom.github.io/wire/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 wire authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://yuhangtom.github.io/wire/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yuhang Lin. Author, maintainer. Heike Hofmann. Author.","code":""},{"path":"https://yuhangtom.github.io/wire/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Lin Y, Hofmann H (2023). wire: Package (One Line, Title Case). 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rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. 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vertical direction — get_x3p_bin_rotate","text":"","code":"get_x3p_bin_rotate( x3p_inner_impute, freqs = c(0, 0.3, 0.7, 1), method = \"MLE\", ntheta = 720, min_score_cut = 2, ifplot = FALSE, loess_span = 0.2 )"},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_bin_rotate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rotate imputed x3p object to vertical direction — get_x3p_bin_rotate","text":"x3p_inner_impute imputed x3p object freqs length 4 vector values corresponding color frequency (turned quantiles differenced values) used x3ptools::x3p_bin_stripes method choice MLE quantile computing rotation angle ntheta number bins along theta used imager::hough_line min_score_cut tuning parameter minimum scores required hough transformation ifplot whether graphs displayed loess_span parameter controls degree smoothing, available method = MLE","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary data frame for the inner polygon — get_x3p_inner_df","title":"Summary data frame for the inner polygon — get_x3p_inner_df","text":"Create summary data frame inner polygon x3p object.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary data frame for the inner polygon — get_x3p_inner_df","text":"","code":"get_x3p_inner_df(x3p, mask_col = \"#FF0000\", concavity = 1.5)"},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary data frame for the inner polygon — get_x3p_inner_df","text":"x3p x3p object mask_col colour polygon concavity strictly positive value used concaveman::concaveman","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_impute.html","id":null,"dir":"Reference","previous_headings":"","what":"Impute the inner polygon — get_x3p_inner_impute","title":"Impute the inner polygon — get_x3p_inner_impute","text":"Obtained x3p object imputing inner polygon.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_impute.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Impute the inner polygon — get_x3p_inner_impute","text":"","code":"get_x3p_inner_impute( x3p, mask_col = \"#FF0000\", concavity = 1.5, ifsave = FALSE, dir_name = NULL, ifplot = FALSE )"},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_impute.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Impute the inner polygon — get_x3p_inner_impute","text":"x3p x3p object mask_col colour polygon concavity strictly positive value used concaveman::concaveman ifsave whether imputation procedure gif going saved dir_name required ifsave TRUE ifplot whether graphs displayed","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_nomiss_res.html","id":null,"dir":"Reference","previous_headings":"","what":"Removing missing values and the quadratic trend from inner polygon — get_x3p_inner_nomiss_res","title":"Removing missing values and the quadratic trend from inner polygon — get_x3p_inner_nomiss_res","text":"Obtained x3p object removing missing values quadratic trend inner polygon.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_nomiss_res.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Removing missing values and the quadratic trend from inner polygon — get_x3p_inner_nomiss_res","text":"","code":"get_x3p_inner_nomiss_res(x3p, mask_col = \"#FF0000\", concavity = 1.5)"},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_inner_nomiss_res.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Removing missing values and the quadratic trend from inner polygon — get_x3p_inner_nomiss_res","text":"x3p x3p object mask_col colour polygon concavity strictly positive value used concaveman::concaveman","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_rotate_angle_MLE.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the rotation angle using MLE — get_x3p_rotate_angle_MLE","title":"Compute the rotation angle using MLE — get_x3p_rotate_angle_MLE","text":"Compute rotation angle using MLE hough transformation.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_rotate_angle_MLE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the rotation angle using MLE — get_x3p_rotate_angle_MLE","text":"","code":"get_x3p_rotate_angle_MLE( x3p, ntheta = 720, min_score_cut = 2, ifplot = FALSE, loess_span = 0.2 )"},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_rotate_angle_MLE.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the rotation angle using MLE — get_x3p_rotate_angle_MLE","text":"x3p x3p object ntheta number bins along theta used imager::hough_line min_score_cut tuning parameter minimum scores required hough transformation ifplot whether graphs displayed loess_span parameter controls degree smoothing","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_rotate_angle_quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the rotation angle using quantile — get_x3p_rotate_angle_quantile","title":"Compute the rotation angle using quantile — get_x3p_rotate_angle_quantile","text":"Compute rotation angle using quantile hough transformation.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_rotate_angle_quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the rotation angle using quantile — get_x3p_rotate_angle_quantile","text":"","code":"get_x3p_rotate_angle_quantile( x3p, ntheta = 720, min_score_cut = 2, ifplot = FALSE )"},{"path":"https://yuhangtom.github.io/wire/reference/get_x3p_rotate_angle_quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the rotation angle using quantile — get_x3p_rotate_angle_quantile","text":"x3p x3p object ntheta number bins along theta used imager::hough_line min_score_cut tuning parameter minimum scores required hough transformation ifplot whether graphs displayed","code":""},{"path":"https://yuhangtom.github.io/wire/reference/inside_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify the inside polygon of a set of points — inside_polygon","title":"Identify the inside polygon of a set of points — inside_polygon","text":"Uses concentric mirroring onto radius around center point, applies alpha hull shape, mirrors result back.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/inside_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify the inside polygon of a set of points — inside_polygon","text":"","code":"inside_polygon(x, y, concavity, center = NULL)"},{"path":"https://yuhangtom.github.io/wire/reference/inside_polygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify the inside polygon of a set of points — inside_polygon","text":"x numeric vector x positions y numeric vector y positions concavity strictly positive parameter. Smaller values approach inside boundary closely. Large values concentrate inner center area center numeric vector length 2, consisting (x,y) coordinate centering x y values. center NULL, half ranges x y used.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/inside_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify the inside polygon of a set of points — inside_polygon","text":"dataframe x y positions describing inside area described input x y, variable id describes order points","code":""},{"path":"https://yuhangtom.github.io/wire/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://yuhangtom.github.io/wire/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_boundary_points.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify boundary of a 3d topographic scan in x3p format — x3p_boundary_points","title":"Identify boundary of a 3d topographic scan in x3p format — x3p_boundary_points","text":"Identify boundary 3d topographic scan x3p format","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_boundary_points.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify boundary of a 3d topographic scan in x3p format — x3p_boundary_points","text":"","code":"x3p_boundary_points(x3p, sample)"},{"path":"https://yuhangtom.github.io/wire/reference/x3p_boundary_points.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify boundary of a 3d topographic scan in x3p format — x3p_boundary_points","text":"x3p topographic scan x3p format sample positive integer value specifying sampling ratio: every sample value x y direction included. Higher values result faster results cruder assessments boundary.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_boundary_points.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify boundary of a 3d topographic scan in x3p format — x3p_boundary_points","text":"data frame boundary points, variables named x y","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_image_autosize.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot x3p object as an image with auto-adjusted size — x3p_image_autosize","title":"Plot x3p object as an image with auto-adjusted size — x3p_image_autosize","text":"Plot x3p object image auto-adjusted size based x3ptools::x3p_image.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_image_autosize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot x3p object as an image with auto-adjusted size — x3p_image_autosize","text":"","code":"x3p_image_autosize(x3p, ifhtml = FALSE, zoom = 0.6, ...)"},{"path":"https://yuhangtom.github.io/wire/reference/x3p_image_autosize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot x3p object as an image with auto-adjusted size — x3p_image_autosize","text":"x3p x3p object ifhtml logical, whether image put html zoom numeric value indicating amount zoom ... parameter values except size zoom used x3ptools::x3p_image","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_subsamples.html","id":null,"dir":"Reference","previous_headings":"","what":"Subsampled wire cuts data — x3p_subsamples","title":"Subsampled wire cuts data — x3p_subsamples","text":"list wire cuts data set subsampling factor 10 original wire cuts x3p.","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_subsamples.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subsampled wire cuts data — x3p_subsamples","text":"","code":"x3p_subsamples"},{"path":"https://yuhangtom.github.io/wire/reference/x3p_subsamples.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subsampled wire cuts data — x3p_subsamples","text":"list list x3p objects","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_surface_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a polygon of the scan shape as mask — x3p_surface_polygon","title":"Add a polygon of the scan shape as mask — x3p_surface_polygon","text":"Add polygon scan shape mask","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_surface_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a polygon of the scan shape as mask — x3p_surface_polygon","text":"","code":"x3p_surface_polygon( x3p, colour = \"red\", sample = 10, center = NULL, concavity = 1.5 )"},{"path":"https://yuhangtom.github.io/wire/reference/x3p_surface_polygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a polygon of the scan shape as mask — x3p_surface_polygon","text":"x3p x3p file colour colour polygon sample strictly positive integer value specifying amount downsampling used (see x3p_sample) calculate boundary points polygon. Larger values sample result faster response times results less accurate polygons. center point center scan. NULL, center derived boundary points concavity strictly positive value used concaveman::concaveman","code":""},{"path":"https://yuhangtom.github.io/wire/reference/x3p_surface_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a polygon of the scan shape as mask — x3p_surface_polygon","text":"x3p object mask","code":""}] diff --git a/sitemap.xml b/sitemap.xml index f3e3d9b..0c84c39 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -45,13 +45,22 @@ https://yuhangtom.github.io/wire/reference/index.html + + https://yuhangtom.github.io/wire/reference/inside_polygon.html + https://yuhangtom.github.io/wire/reference/pipe.html + + https://yuhangtom.github.io/wire/reference/x3p_boundary_points.html + https://yuhangtom.github.io/wire/reference/x3p_image_autosize.html https://yuhangtom.github.io/wire/reference/x3p_subsamples.html + + https://yuhangtom.github.io/wire/reference/x3p_surface_polygon.html +