R - 根据不同的角度和原点旋转数据框中的坐标
R - Rotate coordinates in dataframe based on varying angles and origin
我有一个数据框 data 有几列，包括 ID Image（重复几行）和 X CenterX_um 和 Y CenterY_um 坐标（每行不同).
我想根据每个 ID 特定的角度和原点旋转 X、Y 坐标。我在单独的数据框 rotation_info.
上也有此信息
我试过 rearrr::rotate_2d 功能，但它不允许我指定角度和原点。相反，它希望对所有人使用相同的角度和原点。
有什么线索吗？
这是每个数据帧的子集：
data <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-03_roi1", "P112_SOD1_scene-03_roi1", "P112_SOD1_scene-08_roi1", "P112_SOD1_scene-08_roi1",
"P112_SOD1_scene-14_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1", "P112_WT_scene-13_roi1"),
Area_pixel2 = c(6172L, 2804L, 4133L, 1547L, 9224L, 5133L, 4311L, 2740L, 2610L, 3802L, 5129L, 4106L),
Area_um2 = c(318.03702442715, 144.48733254921, 212.96938139297, 79.715372130394, 475.30355044005, 264.49838729497, 222.14154444352,
141.18947617148, 134.49070540422, 195.91328043941, 264.29227127136, 211.57809823361),
CenterX_um = c(1149.8904493589, 1126.4609300602, 1100.8211294593, 1024.1176019595, 993.32875148771, 964.51498442025, 874.9485394368,
843.03397382692, 1457.7886911485, 1359.4372824824, 1549.4154976822, 1614.8843949665),
CenterY_um = c(65.734010569428, 87.806098466489, 121.24362888879, 344.12182158201, 349.1125830895, 378.36327230154, 222.10103046474,
236.8534704986, 524.97197144378, 536.26329031132, 101.93303030628, 103.3766130805),
Circularity = c(0.70514719268137, 0.73725777209061, 0.55904614141807, 0.64491724919754, 0.72628772170604, 0.68836548793912,
0.80455000787307, 0.75794971514553, 0.58945714820048, 0.75891540252167, 0.63520099709918, 0.79151119246911),
Compactness = c(0.66065335617958, 0.64189735971181, 0.53383026406418, 0.53076228622962, 0.76004630952984, 0.72584335956662,
0.81606076244974, 0.77264654886067, 0.51250290104024, 0.78515382913133, 0.66035724052464, 0.80977712999347)),
row.names = c(1L, 2L, 3L, 1505L, 1506L, 1507L, 8500L, 8501L, 15689L, 15690L, 30001L, 30002L), class = "data.frame")
data
# Image Area_pixel2 Area_um2 CenterX_um CenterY_um Circularity Compactness
#1 P112_SOD1_scene-01_roi1 6172 318.03702 1149.8904 65.73401 0.7051472 0.6606534
#2 P112_SOD1_scene-01_roi1 2804 144.48733 1126.4609 87.80610 0.7372578 0.6418974
#3 P112_SOD1_scene-01_roi1 4133 212.96938 1100.8211 121.24363 0.5590461 0.5338303
#1505 P112_SOD1_scene-03_roi1 1547 79.71537 1024.1176 344.12182 0.6449172 0.5307623
#1506 P112_SOD1_scene-03_roi1 9224 475.30355 993.3288 349.11258 0.7262877 0.7600463
#1507 P112_SOD1_scene-03_roi1 5133 264.49839 964.5150 378.36327 0.6883655 0.7258434
#8500 P112_SOD1_scene-08_roi1 4311 222.14154 874.9485 222.10103 0.8045500 0.8160608
#8501 P112_SOD1_scene-08_roi1 2740 141.18948 843.0340 236.85347 0.7579497 0.7726465
#15689 P112_SOD1_scene-14_roi1 2610 134.49071 1457.7887 524.97197 0.5894571 0.5125029
#15690 P112_SOD1_scene-14_roi1 3802 195.91328 1359.4373 536.26329 0.7589154 0.7851538
#30001 P112_WT_scene-13_roi1 5129 264.29227 1549.4155 101.93303 0.6352010 0.6603572
#30002 P112_WT_scene-13_roi1 4106 211.57810 1614.8844 103.37661 0.7915112 0.8097771
rotation_info <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-08_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1"
), Angle = c(199.289658091447, 202.184697711029, 158.990932730799,
180.612494033135, 15.223442470483), CC_X = c(989.039056641, 970.652055588,
1104.355063245, 781.334044746, 1034.893059267), CC_Y = c(792.457045383,
798.359045721, 940.915053885, 747.057042783, 709.829040651)), row.names = c(NA,
-5L), class = "data.frame")
rotation_info
# Image Angle CC_X CC_Y
#1 P112_SOD1_scene-01_roi1 199.28966 989.0391 792.4570
#2 P112_SOD1_scene-03_roi1 202.18470 970.6521 798.3590
#3 P112_SOD1_scene-08_roi1 158.99093 1104.3551 940.9151
#4 P112_SOD1_scene-14_roi1 180.61249 781.3340 747.0570
#5 P112_WT_scene-13_roi1 15.22344 1034.8931 709.8290
我的想法是首先基于 Image 合并两个数据帧，以便为每一行复制角度和原点（这很有效），然后将 rearrr::rotate_2d 函数应用于每个排。这是我 运行 遇到麻烦的时候，因为它需要所有行的相同角度和原点。
# Merge rotation info into data
data <- merge(data, rotation_info, by="Image", all.x=TRUE)
# Rotate based on angle ("Angle") and origin ("CC_X", "CC_Y")
data <- rotate_2d(data, degrees = data$Angle, x_col = "CenterX_um", y_col = "CenterY_um",
origin = c(data$CC_X, data$CC_Y) , suffix = "", overwrite = TRUE)
欢迎任何其他方法。我不一定需要我的数据框中的旋转信息（实际上我打算在之后删除它）。
提前致谢！
似乎 rearrr::rotate_2d() 并不是真正设计用于以您尝试的方式从源数据中获取 degrees 和 origin 参数。如果这样做，它将每隔 Angle 围绕每个 origin.
旋转每个点
相反，我使用 purrr::group_map() 按 Image 拆分数据，并使用单个 degrees 和 origin 参数分别对每个数据进行操作（由 mean(., na.rm = T) 尽管您可以使用 unique() 或 min() 或其他任何东西来获取单个值而不是重复值的向量）。
见底部的图，我分别用红色和蓝色显示原始点和旋转点，每个点的原点都带有 *.
library(tidyverse)
library(rearrr)
data <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-03_roi1", "P112_SOD1_scene-03_roi1", "P112_SOD1_scene-08_roi1", "P112_SOD1_scene-08_roi1",
"P112_SOD1_scene-14_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1", "P112_WT_scene-13_roi1"),
Area_pixel2 = c(6172L, 2804L, 4133L, 1547L, 9224L, 5133L, 4311L, 2740L, 2610L, 3802L, 5129L, 4106L),
Area_um2 = c(318.03702442715, 144.48733254921, 212.96938139297, 79.715372130394, 475.30355044005, 264.49838729497, 222.14154444352,
141.18947617148, 134.49070540422, 195.91328043941, 264.29227127136, 211.57809823361),
CenterX_um = c(1149.8904493589, 1126.4609300602, 1100.8211294593, 1024.1176019595, 993.32875148771, 964.51498442025, 874.9485394368,
843.03397382692, 1457.7886911485, 1359.4372824824, 1549.4154976822, 1614.8843949665),
CenterY_um = c(65.734010569428, 87.806098466489, 121.24362888879, 344.12182158201, 349.1125830895, 378.36327230154, 222.10103046474,
236.8534704986, 524.97197144378, 536.26329031132, 101.93303030628, 103.3766130805),
Circularity = c(0.70514719268137, 0.73725777209061, 0.55904614141807, 0.64491724919754, 0.72628772170604, 0.68836548793912,
0.80455000787307, 0.75794971514553, 0.58945714820048, 0.75891540252167, 0.63520099709918, 0.79151119246911),
Compactness = c(0.66065335617958, 0.64189735971181, 0.53383026406418, 0.53076228622962, 0.76004630952984, 0.72584335956662,
0.81606076244974, 0.77264654886067, 0.51250290104024, 0.78515382913133, 0.66035724052464, 0.80977712999347)),
row.names = c(1L, 2L, 3L, 1505L, 1506L, 1507L, 8500L, 8501L, 15689L, 15690L, 30001L, 30002L), class = "data.frame")
rotation_info <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-08_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1"),
Angle = c(199.289658091447, 202.184697711029, 158.990932730799, 180.612494033135, 15.223442470483),
CC_X = c(989.039056641, 970.652055588, 1104.355063245, 781.334044746, 1034.893059267),
CC_Y = c(792.457045383, 798.359045721, 940.915053885, 747.057042783, 709.829040651)),
row.names = c(NA, -5L), class = "data.frame")
# Merge rotation info into data
data2 <- merge(data, rotation_info, by="Image", all.x=TRUE)
# rotate each image by its respective origin and angle
data3 <- data2 %>%
group_by(Image) %>%
group_map(
~ rotate_2d(
data = .,
degrees = mean(.[["Angle"]], na.rm = T),
x_col = "CenterX_um",
y_col = "CenterY_um",
origin = c(mean(.[["CC_X"]], na.rm = T), mean(.[["CC_Y"]], na.rm = T)),
keep_original = TRUE
),
.keep = T
) %>%
bind_rows()
# visualize rotated result vs original
data3 %>%
select(Image, CC_X:CC_Y, starts_with("Center")) %>%
group_by(Image) %>%
mutate(point_id = row_number()) %>%
ungroup() %>%
pivot_longer(
cols = -c(Image, point_id, CC_X, CC_Y),
names_to = c("axis", "units", "rotation"),
names_prefix = "Center",
names_sep = "_",
values_to = "position"
) %>%
replace_na(list(rotation = "original")) %>%
pivot_wider(names_from = axis, values_from = position) %>%
ggplot(aes(X, Y, color = rotation)) +
geom_point() +
geom_path() +
geom_point(aes(CC_X, CC_Y), size = 4, color = "black", shape = 8) +
facet_wrap(~Image, scales = "free")
#> Warning: Expected 3 pieces. Missing pieces filled with `NA` in 2 rows [1, 2].
由 reprex package (v2.0.1)
于 2022-01-27 创建
我有一个数据框 data 有几列，包括 ID Image（重复几行）和 X CenterX_um 和 Y CenterY_um 坐标（每行不同).
我想根据每个 ID 特定的角度和原点旋转 X、Y 坐标。我在单独的数据框 rotation_info.
我试过 rearrr::rotate_2d 功能，但它不允许我指定角度和原点。相反，它希望对所有人使用相同的角度和原点。
有什么线索吗？
这是每个数据帧的子集：
data <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-03_roi1", "P112_SOD1_scene-03_roi1", "P112_SOD1_scene-08_roi1", "P112_SOD1_scene-08_roi1",
"P112_SOD1_scene-14_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1", "P112_WT_scene-13_roi1"),
Area_pixel2 = c(6172L, 2804L, 4133L, 1547L, 9224L, 5133L, 4311L, 2740L, 2610L, 3802L, 5129L, 4106L),
Area_um2 = c(318.03702442715, 144.48733254921, 212.96938139297, 79.715372130394, 475.30355044005, 264.49838729497, 222.14154444352,
141.18947617148, 134.49070540422, 195.91328043941, 264.29227127136, 211.57809823361),
CenterX_um = c(1149.8904493589, 1126.4609300602, 1100.8211294593, 1024.1176019595, 993.32875148771, 964.51498442025, 874.9485394368,
843.03397382692, 1457.7886911485, 1359.4372824824, 1549.4154976822, 1614.8843949665),
CenterY_um = c(65.734010569428, 87.806098466489, 121.24362888879, 344.12182158201, 349.1125830895, 378.36327230154, 222.10103046474,
236.8534704986, 524.97197144378, 536.26329031132, 101.93303030628, 103.3766130805),
Circularity = c(0.70514719268137, 0.73725777209061, 0.55904614141807, 0.64491724919754, 0.72628772170604, 0.68836548793912,
0.80455000787307, 0.75794971514553, 0.58945714820048, 0.75891540252167, 0.63520099709918, 0.79151119246911),
Compactness = c(0.66065335617958, 0.64189735971181, 0.53383026406418, 0.53076228622962, 0.76004630952984, 0.72584335956662,
0.81606076244974, 0.77264654886067, 0.51250290104024, 0.78515382913133, 0.66035724052464, 0.80977712999347)),
row.names = c(1L, 2L, 3L, 1505L, 1506L, 1507L, 8500L, 8501L, 15689L, 15690L, 30001L, 30002L), class = "data.frame")
data
# Image Area_pixel2 Area_um2 CenterX_um CenterY_um Circularity Compactness
#1 P112_SOD1_scene-01_roi1 6172 318.03702 1149.8904 65.73401 0.7051472 0.6606534
#2 P112_SOD1_scene-01_roi1 2804 144.48733 1126.4609 87.80610 0.7372578 0.6418974
#3 P112_SOD1_scene-01_roi1 4133 212.96938 1100.8211 121.24363 0.5590461 0.5338303
#1505 P112_SOD1_scene-03_roi1 1547 79.71537 1024.1176 344.12182 0.6449172 0.5307623
#1506 P112_SOD1_scene-03_roi1 9224 475.30355 993.3288 349.11258 0.7262877 0.7600463
#1507 P112_SOD1_scene-03_roi1 5133 264.49839 964.5150 378.36327 0.6883655 0.7258434
#8500 P112_SOD1_scene-08_roi1 4311 222.14154 874.9485 222.10103 0.8045500 0.8160608
#8501 P112_SOD1_scene-08_roi1 2740 141.18948 843.0340 236.85347 0.7579497 0.7726465
#15689 P112_SOD1_scene-14_roi1 2610 134.49071 1457.7887 524.97197 0.5894571 0.5125029
#15690 P112_SOD1_scene-14_roi1 3802 195.91328 1359.4373 536.26329 0.7589154 0.7851538
#30001 P112_WT_scene-13_roi1 5129 264.29227 1549.4155 101.93303 0.6352010 0.6603572
#30002 P112_WT_scene-13_roi1 4106 211.57810 1614.8844 103.37661 0.7915112 0.8097771
rotation_info <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-08_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1"
), Angle = c(199.289658091447, 202.184697711029, 158.990932730799,
180.612494033135, 15.223442470483), CC_X = c(989.039056641, 970.652055588,
1104.355063245, 781.334044746, 1034.893059267), CC_Y = c(792.457045383,
798.359045721, 940.915053885, 747.057042783, 709.829040651)), row.names = c(NA,
-5L), class = "data.frame")
rotation_info
# Image Angle CC_X CC_Y
#1 P112_SOD1_scene-01_roi1 199.28966 989.0391 792.4570
#2 P112_SOD1_scene-03_roi1 202.18470 970.6521 798.3590
#3 P112_SOD1_scene-08_roi1 158.99093 1104.3551 940.9151
#4 P112_SOD1_scene-14_roi1 180.61249 781.3340 747.0570
#5 P112_WT_scene-13_roi1 15.22344 1034.8931 709.8290
我的想法是首先基于 Image 合并两个数据帧，以便为每一行复制角度和原点（这很有效），然后将 rearrr::rotate_2d 函数应用于每个排。这是我 运行 遇到麻烦的时候，因为它需要所有行的相同角度和原点。
# Merge rotation info into data
data <- merge(data, rotation_info, by="Image", all.x=TRUE)
# Rotate based on angle ("Angle") and origin ("CC_X", "CC_Y")
data <- rotate_2d(data, degrees = data$Angle, x_col = "CenterX_um", y_col = "CenterY_um",
origin = c(data$CC_X, data$CC_Y) , suffix = "", overwrite = TRUE)
欢迎任何其他方法。我不一定需要我的数据框中的旋转信息（实际上我打算在之后删除它）。
提前致谢！
似乎 rearrr::rotate_2d() 并不是真正设计用于以您尝试的方式从源数据中获取 degrees 和 origin 参数。如果这样做，它将每隔 Angle 围绕每个 origin.
相反，我使用 purrr::group_map() 按 Image 拆分数据，并使用单个 degrees 和 origin 参数分别对每个数据进行操作（由 mean(., na.rm = T) 尽管您可以使用 unique() 或 min() 或其他任何东西来获取单个值而不是重复值的向量）。
见底部的图，我分别用红色和蓝色显示原始点和旋转点，每个点的原点都带有 *.
library(tidyverse)
library(rearrr)
data <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-03_roi1", "P112_SOD1_scene-03_roi1", "P112_SOD1_scene-08_roi1", "P112_SOD1_scene-08_roi1",
"P112_SOD1_scene-14_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1", "P112_WT_scene-13_roi1"),
Area_pixel2 = c(6172L, 2804L, 4133L, 1547L, 9224L, 5133L, 4311L, 2740L, 2610L, 3802L, 5129L, 4106L),
Area_um2 = c(318.03702442715, 144.48733254921, 212.96938139297, 79.715372130394, 475.30355044005, 264.49838729497, 222.14154444352,
141.18947617148, 134.49070540422, 195.91328043941, 264.29227127136, 211.57809823361),
CenterX_um = c(1149.8904493589, 1126.4609300602, 1100.8211294593, 1024.1176019595, 993.32875148771, 964.51498442025, 874.9485394368,
843.03397382692, 1457.7886911485, 1359.4372824824, 1549.4154976822, 1614.8843949665),
CenterY_um = c(65.734010569428, 87.806098466489, 121.24362888879, 344.12182158201, 349.1125830895, 378.36327230154, 222.10103046474,
236.8534704986, 524.97197144378, 536.26329031132, 101.93303030628, 103.3766130805),
Circularity = c(0.70514719268137, 0.73725777209061, 0.55904614141807, 0.64491724919754, 0.72628772170604, 0.68836548793912,
0.80455000787307, 0.75794971514553, 0.58945714820048, 0.75891540252167, 0.63520099709918, 0.79151119246911),
Compactness = c(0.66065335617958, 0.64189735971181, 0.53383026406418, 0.53076228622962, 0.76004630952984, 0.72584335956662,
0.81606076244974, 0.77264654886067, 0.51250290104024, 0.78515382913133, 0.66035724052464, 0.80977712999347)),
row.names = c(1L, 2L, 3L, 1505L, 1506L, 1507L, 8500L, 8501L, 15689L, 15690L, 30001L, 30002L), class = "data.frame")
rotation_info <- structure(list(Image = c("P112_SOD1_scene-01_roi1", "P112_SOD1_scene-03_roi1",
"P112_SOD1_scene-08_roi1", "P112_SOD1_scene-14_roi1", "P112_WT_scene-13_roi1"),
Angle = c(199.289658091447, 202.184697711029, 158.990932730799, 180.612494033135, 15.223442470483),
CC_X = c(989.039056641, 970.652055588, 1104.355063245, 781.334044746, 1034.893059267),
CC_Y = c(792.457045383, 798.359045721, 940.915053885, 747.057042783, 709.829040651)),
row.names = c(NA, -5L), class = "data.frame")
# Merge rotation info into data
data2 <- merge(data, rotation_info, by="Image", all.x=TRUE)
# rotate each image by its respective origin and angle
data3 <- data2 %>%
group_by(Image) %>%
group_map(
~ rotate_2d(
data = .,
degrees = mean(.[["Angle"]], na.rm = T),
x_col = "CenterX_um",
y_col = "CenterY_um",
origin = c(mean(.[["CC_X"]], na.rm = T), mean(.[["CC_Y"]], na.rm = T)),
keep_original = TRUE
),
.keep = T
) %>%
bind_rows()
# visualize rotated result vs original
data3 %>%
select(Image, CC_X:CC_Y, starts_with("Center")) %>%
group_by(Image) %>%
mutate(point_id = row_number()) %>%
ungroup() %>%
pivot_longer(
cols = -c(Image, point_id, CC_X, CC_Y),
names_to = c("axis", "units", "rotation"),
names_prefix = "Center",
names_sep = "_",
values_to = "position"
) %>%
replace_na(list(rotation = "original")) %>%
pivot_wider(names_from = axis, values_from = position) %>%
ggplot(aes(X, Y, color = rotation)) +
geom_point() +
geom_path() +
geom_point(aes(CC_X, CC_Y), size = 4, color = "black", shape = 8) +
facet_wrap(~Image, scales = "free")
#> Warning: Expected 3 pieces. Missing pieces filled with `NA` in 2 rows [1, 2].
由 reprex package (v2.0.1)
于 2022-01-27 创建