CSV-file used for this script: ~/Data/CoordSys_FLT1-7_50x.csv
This script formats the output of the resulting CSV-file from applying a template computing ISO25178 parameters in ConfoMap. The script will:
All files will be saved in a subfolder “Data” within the directory of the present Rmd file, i.e. “~/Data”.
library(openxlsx)
library(tools)
library(R.utils)imp.info <- file.info(params$data)
imp.data <- read.csv(params$data, header=FALSE, skip=3, stringsAsFactors=FALSE, na.strings="*****")The imported file is: “~/Data/CoordSys_FLT1-7_50x.csv”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2018-09-27 16:39:21”, “2019-01-03 10:18:43” and “2019-01-03 10:18:43”.
keep.col <- c(1:2, 4:5, 7:9, 11:13, 15:53)
data.keep <- imp.data[keep.col]
str(data.keep)'data.frame': 20 obs. of 49 variables:
$ V1 : chr "27/09/2018" "27/09/2018" "27/09/2018" "27/09/2018" ...
$ V2 : chr "15:20:31" "15:20:53" "15:22:14" "15:23:44" ...
$ V4 : chr "FLT1-7_LSM_50x-0.95_replica1_20180903_Topo" "FLT1-7_LSM_50x-0.95_replica2_20180903_Topo" "FLT1-7_LSM_50x-0.95_replica3_20180903_Topo" "FLT1-7_LSM_50x-0.95_replica4_20180903_Topo" ...
$ V5 : chr "03/09/2018 16:10" "03/09/2018 16:18" "03/09/2018 16:25" "03/09/2018 16:34" ...
$ V7 : num 255 255 255 255 255 ...
$ V8 : int 991 991 991 991 991 991 991 991 991 991 ...
$ V9 : num 0.258 0.258 0.258 0.258 0.258 ...
$ V11: num 255 255 255 255 255 ...
$ V12: int 991 991 991 991 991 991 991 991 991 991 ...
$ V13: num 0.258 0.258 0.258 0.258 0.258 ...
$ V15: num 26.7 29.6 28.7 28.7 28.4 ...
$ V16: int 65532 65532 65531 65532 65532 65532 65531 65532 65532 65532 ...
$ V17: num 0.407 0.451 0.438 0.438 0.433 ...
$ V18: num 0 0 0 0 0 0 0 0 0 0 ...
$ V19: num 1.49 1.39 1.25 1.33 1.29 ...
$ V20: num -0.00297 0.09683 0.13965 0.09766 0.08338 ...
$ V21: num 4.42 4.28 3.76 4.33 3.86 ...
$ V22: num 6.07 6.21 5.92 6.24 6.01 ...
$ V23: num 7.14 5.94 4.06 6.39 4.75 ...
$ V24: num 13.2 12.15 9.98 12.62 10.76 ...
$ V25: num 1.123 1.069 0.983 1.03 1.006 ...
$ V26: num 0.293 0.258 0.183 0.167 0.183 ...
$ V27: num 1.72 1.64 1.55 1.61 1.57 ...
$ V28: num 3.04 2.82 2.53 2.65 2.57 ...
$ V29: num 14.4 14.6 13.7 14.6 14.1 ...
$ V30: num 0.761 0.812 0.741 0.827 0.777 ...
$ V31: num 87.2 85.5 94.2 94.2 69.3 ...
$ V32: logi NA NA NA NA NA NA ...
$ V33: logi NA NA NA NA NA NA ...
$ V34: num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ V35: num 1.81 1.72 1.61 1.68 1.64 ...
$ V36: num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ V37: num 1.2 1.14 1.1 1.12 1.12 ...
$ V38: num 1.63 1.55 1.47 1.52 1.49 ...
$ V39: num 0.187 0.174 0.144 0.158 0.15 ...
$ V40: num 2.51 2.46 2.35 2.42 2.4 ...
$ V41: num 1.4 1.25 1.07 1.15 1.07 ...
$ V42: num 1.48 1.37 1.15 1.29 1.2 ...
$ V43: num 10.9 10.5 10.4 10.6 10.4 ...
$ V44: num 87.1 87 87.7 87.8 88 ...
$ V45: num 1.2 1.14 NA 1.1 NA ...
$ V46: num 2.71 1.67 NA 2.83 NA ...
$ V47: num 98.1 92.2 NA 98.9 NA ...
$ V48: num 112.8 93.9 61.8 82.5 72.4 ...
$ V49: num 90 90 90 90 90 ...
$ V50: num 0.00361 0.00598 -0.00684 -0.00647 0.00911 ...
$ V51: num 110.3 73.2 73.7 58.2 77 ...
$ V52: num -0.00452 0.0028 0.00173 -0.00307 0.00726 ...
$ V53: num -90 -90 -90 -90 -90 ...head.keep <- strsplit(readLines(params$data, n=3)[2], ",")[[1]][keep.col]
head.keep <- c("Analysis date","Analysis time", head.keep[-(1:2)])
names(data.keep) <- gsub("\\.+", "\\.", make.names(head.keep))
names(data.keep) <- gsub("\\.$", "", names(data.keep))
names(data.keep) [1] "Analysis.date"
[2] "Analysis.time"
[3] "Name.of.the.studiable"
[4] "Date.of.the.measurement"
[5] "Axis.length.X"
[6] "Axis.size.X"
[7] "Axis.spacing.X"
[8] "Axis.length.Y"
[9] "Axis.size.Y"
[10] "Axis.spacing.Y"
[11] "Axis.length.Z"
[12] "Axis.size.Z"
[13] "Axis.spacing.Z"
[14] "NMP.ratio.Z"
[15] "Sq"
[16] "Ssk"
[17] "Sku"
[18] "Sp"
[19] "Sv"
[20] "Sz"
[21] "Sa"
[22] "Smr.c.1.µm.under.the.highest.peak"
[23] "Smc.p.10"
[24] "Sxp.p.50.q.97.5"
[25] "Sal.s.0.2"
[26] "Str.s.0.2"
[27] "Std.Reference.angle.0"
[28] "Sdq"
[29] "Sdr"
[30] "Vm.p.10"
[31] "Vv.p.10"
[32] "Vmp.p.10"
[33] "Vmc.p.10.q.80"
[34] "Vvc.p.10.q.80"
[35] "Vvv.p.80"
[36] "Sk.Gaussian.filter.0.08.mm.End.effects.managed"
[37] "Spk.Gaussian.filter.0.08.mm.End.effects.managed"
[38] "Svk.Gaussian.filter.0.08.mm.End.effects.managed"
[39] "Smr1.Gaussian.filter.0.08.mm.End.effects.managed"
[40] "Smr2.Gaussian.filter.0.08.mm.End.effects.managed"
[41] "Spq.Gaussian.filter.0.08.mm.End.effects.managed"
[42] "Svq.Gaussian.filter.0.08.mm.End.effects.managed"
[43] "Smq.Gaussian.filter.0.08.mm.End.effects.managed"
[44] "Distance.A"
[45] "Angle.X.axis.A"
[46] "Angle.Y.axis.A"
[47] "Distance.B"
[48] "Angle.X.axis.B"
[49] "Angle.Y.axis.B" col.var <- 5:length(data.keep)
names.var <- names(data.keep)[col.var]
units.var <- strsplit(readLines(params$data, n=3)[3], ",")[[1]][keep.col]
units.var <- units.var[col.var]
units.var <- c(units.var, "µm", "µm") ## in planing for X/Y shift! ##
units.var.table <- data.frame(variable=c(names(data.keep)[col.var],"Xshift","Yshift"), unit=units.var)
names(units.var) <- c(names.var,"Xshift","Yshift")
units.var.table variable unit
1 Axis.length.X µm
2 Axis.size.X points
3 Axis.spacing.X µm
4 Axis.length.Y µm
5 Axis.size.Y points
6 Axis.spacing.Y µm
7 Axis.length.Z µm
8 Axis.size.Z digits
9 Axis.spacing.Z nm
10 NMP.ratio.Z %
11 Sq µm
12 Ssk <no unit>
13 Sku <no unit>
14 Sp µm
15 Sv µm
16 Sz µm
17 Sa µm
18 Smr.c.1.µm.under.the.highest.peak %
19 Smc.p.10 µm
20 Sxp.p.50.q.97.5 µm
21 Sal.s.0.2 µm
22 Str.s.0.2 <no unit>
23 Std.Reference.angle.0 °
24 Sdq <no unit>
25 Sdr %
26 Vm.p.10 µm³/µm²
27 Vv.p.10 µm³/µm²
28 Vmp.p.10 µm³/µm²
29 Vmc.p.10.q.80 µm³/µm²
30 Vvc.p.10.q.80 µm³/µm²
31 Vvv.p.80 µm³/µm²
32 Sk.Gaussian.filter.0.08.mm.End.effects.managed µm
33 Spk.Gaussian.filter.0.08.mm.End.effects.managed µm
34 Svk.Gaussian.filter.0.08.mm.End.effects.managed µm
35 Smr1.Gaussian.filter.0.08.mm.End.effects.managed %
36 Smr2.Gaussian.filter.0.08.mm.End.effects.managed %
37 Spq.Gaussian.filter.0.08.mm.End.effects.managed <no unit>
38 Svq.Gaussian.filter.0.08.mm.End.effects.managed <no unit>
39 Smq.Gaussian.filter.0.08.mm.End.effects.managed <no unit>
40 Distance.A µm
41 Angle.X.axis.A °
42 Angle.Y.axis.A °
43 Distance.B µm
44 Angle.X.axis.B °
45 Angle.Y.axis.B °
46 Xshift µm
47 Yshift µmsplit.info <- strsplit(data.keep$Name.of.the.studiable,"_| > ")
data.final <- data.frame(do.call(rbind, split.info), data.keep[-3])Warning in (function (..., deparse.level = 1) : number of columns of result
is not a multiple of vector length (arg 1)data.final <- data.final[-(6:7)]
names(data.final)[1:5] <- c("Sample","Microscope","Objective","Replica","Acquisition.date")
str(data.final)'data.frame': 20 obs. of 53 variables:
$ Sample : Factor w/ 1 level "FLT1-7": 1 1 1 1 1 1 1 1 1 1 ...
$ Microscope : Factor w/ 2 levels "LSM","Sneox": 1 1 1 1 1 1 1 1 1 1 ...
$ Objective : Factor w/ 2 levels "50x-0.8","50x-0.95": 2 2 2 2 2 2 2 2 2 2 ...
$ Replica : Factor w/ 10 levels "replica1","replica10",..: 1 3 4 5 6 7 8 9 10 2 ...
$ Acquisition.date : Factor w/ 3 levels "20180903","20180905",..: 1 1 1 1 1 2 2 2 2 2 ...
$ Analysis.date : chr "27/09/2018" "27/09/2018" "27/09/2018" "27/09/2018" ...
$ Analysis.time : chr "15:20:31" "15:20:53" "15:22:14" "15:23:44" ...
$ Date.of.the.measurement : chr "03/09/2018 16:10" "03/09/2018 16:18" "03/09/2018 16:25" "03/09/2018 16:34" ...
$ Axis.length.X : num 255 255 255 255 255 ...
$ Axis.size.X : int 991 991 991 991 991 991 991 991 991 991 ...
$ Axis.spacing.X : num 0.258 0.258 0.258 0.258 0.258 ...
$ Axis.length.Y : num 255 255 255 255 255 ...
$ Axis.size.Y : int 991 991 991 991 991 991 991 991 991 991 ...
$ Axis.spacing.Y : num 0.258 0.258 0.258 0.258 0.258 ...
$ Axis.length.Z : num 26.7 29.6 28.7 28.7 28.4 ...
$ Axis.size.Z : int 65532 65532 65531 65532 65532 65532 65531 65532 65532 65532 ...
$ Axis.spacing.Z : num 0.407 0.451 0.438 0.438 0.433 ...
$ NMP.ratio.Z : num 0 0 0 0 0 0 0 0 0 0 ...
$ Sq : num 1.49 1.39 1.25 1.33 1.29 ...
$ Ssk : num -0.00297 0.09683 0.13965 0.09766 0.08338 ...
$ Sku : num 4.42 4.28 3.76 4.33 3.86 ...
$ Sp : num 6.07 6.21 5.92 6.24 6.01 ...
$ Sv : num 7.14 5.94 4.06 6.39 4.75 ...
$ Sz : num 13.2 12.15 9.98 12.62 10.76 ...
$ Sa : num 1.123 1.069 0.983 1.03 1.006 ...
$ Smr.c.1.µm.under.the.highest.peak : num 0.293 0.258 0.183 0.167 0.183 ...
$ Smc.p.10 : num 1.72 1.64 1.55 1.61 1.57 ...
$ Sxp.p.50.q.97.5 : num 3.04 2.82 2.53 2.65 2.57 ...
$ Sal.s.0.2 : num 14.4 14.6 13.7 14.6 14.1 ...
$ Str.s.0.2 : num 0.761 0.812 0.741 0.827 0.777 ...
$ Std.Reference.angle.0 : num 87.2 85.5 94.2 94.2 69.3 ...
$ Sdq : logi NA NA NA NA NA NA ...
$ Sdr : logi NA NA NA NA NA NA ...
$ Vm.p.10 : num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ Vv.p.10 : num 1.81 1.72 1.61 1.68 1.64 ...
$ Vmp.p.10 : num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ Vmc.p.10.q.80 : num 1.2 1.14 1.1 1.12 1.12 ...
$ Vvc.p.10.q.80 : num 1.63 1.55 1.47 1.52 1.49 ...
$ Vvv.p.80 : num 0.187 0.174 0.144 0.158 0.15 ...
$ Sk.Gaussian.filter.0.08.mm.End.effects.managed : num 2.51 2.46 2.35 2.42 2.4 ...
$ Spk.Gaussian.filter.0.08.mm.End.effects.managed : num 1.4 1.25 1.07 1.15 1.07 ...
$ Svk.Gaussian.filter.0.08.mm.End.effects.managed : num 1.48 1.37 1.15 1.29 1.2 ...
$ Smr1.Gaussian.filter.0.08.mm.End.effects.managed: num 10.9 10.5 10.4 10.6 10.4 ...
$ Smr2.Gaussian.filter.0.08.mm.End.effects.managed: num 87.1 87 87.7 87.8 88 ...
$ Spq.Gaussian.filter.0.08.mm.End.effects.managed : num 1.2 1.14 NA 1.1 NA ...
$ Svq.Gaussian.filter.0.08.mm.End.effects.managed : num 2.71 1.67 NA 2.83 NA ...
$ Smq.Gaussian.filter.0.08.mm.End.effects.managed : num 98.1 92.2 NA 98.9 NA ...
$ Distance.A : num 112.8 93.9 61.8 82.5 72.4 ...
$ Angle.X.axis.A : num 90 90 90 90 90 ...
$ Angle.Y.axis.A : num 0.00361 0.00598 -0.00684 -0.00647 0.00911 ...
$ Distance.B : num 110.3 73.2 73.7 58.2 77 ...
$ Angle.X.axis.B : num -0.00452 0.0028 0.00173 -0.00307 0.00726 ...
$ Angle.Y.axis.B : num -90 -90 -90 -90 -90 ...col.var2 <- 19:47
names(data.final)[col.var2] <- sapply(strsplit(names(data.final)[col.var2], ".", fixed=TRUE), `[[`, 1)
names(data.final) [1] "Sample" "Microscope"
[3] "Objective" "Replica"
[5] "Acquisition.date" "Analysis.date"
[7] "Analysis.time" "Date.of.the.measurement"
[9] "Axis.length.X" "Axis.size.X"
[11] "Axis.spacing.X" "Axis.length.Y"
[13] "Axis.size.Y" "Axis.spacing.Y"
[15] "Axis.length.Z" "Axis.size.Z"
[17] "Axis.spacing.Z" "NMP.ratio.Z"
[19] "Sq" "Ssk"
[21] "Sku" "Sp"
[23] "Sv" "Sz"
[25] "Sa" "Smr"
[27] "Smc" "Sxp"
[29] "Sal" "Str"
[31] "Std" "Sdq"
[33] "Sdr" "Vm"
[35] "Vv" "Vmp"
[37] "Vmc" "Vvc"
[39] "Vvv" "Sk"
[41] "Spk" "Svk"
[43] "Smr1" "Smr2"
[45] "Spq" "Svq"
[47] "Smq" "Distance.A"
[49] "Angle.X.axis.A" "Angle.Y.axis.A"
[51] "Distance.B" "Angle.X.axis.B"
[53] "Angle.Y.axis.B" data.final$Acquisition.date <- as.Date(as.character(data.final$Acquisition.date), format="%Y%m%d")
data.final$Analysis.date <- as.Date(data.final$Analysis.date, format="%d/%m/%Y")
data.final$Date.of.the.measurement <- as.POSIXct(data.final$Date.of.the.measurement, format="%d/%m/%Y %H:%M:%S")
str(data.final)'data.frame': 20 obs. of 53 variables:
$ Sample : Factor w/ 1 level "FLT1-7": 1 1 1 1 1 1 1 1 1 1 ...
$ Microscope : Factor w/ 2 levels "LSM","Sneox": 1 1 1 1 1 1 1 1 1 1 ...
$ Objective : Factor w/ 2 levels "50x-0.8","50x-0.95": 2 2 2 2 2 2 2 2 2 2 ...
$ Replica : Factor w/ 10 levels "replica1","replica10",..: 1 3 4 5 6 7 8 9 10 2 ...
$ Acquisition.date : Date, format: "2018-09-03" "2018-09-03" ...
$ Analysis.date : Date, format: "2018-09-27" "2018-09-27" ...
$ Analysis.time : chr "15:20:31" "15:20:53" "15:22:14" "15:23:44" ...
$ Date.of.the.measurement: POSIXct, format: NA NA ...
$ Axis.length.X : num 255 255 255 255 255 ...
$ Axis.size.X : int 991 991 991 991 991 991 991 991 991 991 ...
$ Axis.spacing.X : num 0.258 0.258 0.258 0.258 0.258 ...
$ Axis.length.Y : num 255 255 255 255 255 ...
$ Axis.size.Y : int 991 991 991 991 991 991 991 991 991 991 ...
$ Axis.spacing.Y : num 0.258 0.258 0.258 0.258 0.258 ...
$ Axis.length.Z : num 26.7 29.6 28.7 28.7 28.4 ...
$ Axis.size.Z : int 65532 65532 65531 65532 65532 65532 65531 65532 65532 65532 ...
$ Axis.spacing.Z : num 0.407 0.451 0.438 0.438 0.433 ...
$ NMP.ratio.Z : num 0 0 0 0 0 0 0 0 0 0 ...
$ Sq : num 1.49 1.39 1.25 1.33 1.29 ...
$ Ssk : num -0.00297 0.09683 0.13965 0.09766 0.08338 ...
$ Sku : num 4.42 4.28 3.76 4.33 3.86 ...
$ Sp : num 6.07 6.21 5.92 6.24 6.01 ...
$ Sv : num 7.14 5.94 4.06 6.39 4.75 ...
$ Sz : num 13.2 12.15 9.98 12.62 10.76 ...
$ Sa : num 1.123 1.069 0.983 1.03 1.006 ...
$ Smr : num 0.293 0.258 0.183 0.167 0.183 ...
$ Smc : num 1.72 1.64 1.55 1.61 1.57 ...
$ Sxp : num 3.04 2.82 2.53 2.65 2.57 ...
$ Sal : num 14.4 14.6 13.7 14.6 14.1 ...
$ Str : num 0.761 0.812 0.741 0.827 0.777 ...
$ Std : num 87.2 85.5 94.2 94.2 69.3 ...
$ Sdq : logi NA NA NA NA NA NA ...
$ Sdr : logi NA NA NA NA NA NA ...
$ Vm : num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ Vv : num 1.81 1.72 1.61 1.68 1.64 ...
$ Vmp : num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ Vmc : num 1.2 1.14 1.1 1.12 1.12 ...
$ Vvc : num 1.63 1.55 1.47 1.52 1.49 ...
$ Vvv : num 0.187 0.174 0.144 0.158 0.15 ...
$ Sk : num 2.51 2.46 2.35 2.42 2.4 ...
$ Spk : num 1.4 1.25 1.07 1.15 1.07 ...
$ Svk : num 1.48 1.37 1.15 1.29 1.2 ...
$ Smr1 : num 10.9 10.5 10.4 10.6 10.4 ...
$ Smr2 : num 87.1 87 87.7 87.8 88 ...
$ Spq : num 1.2 1.14 NA 1.1 NA ...
$ Svq : num 2.71 1.67 NA 2.83 NA ...
$ Smq : num 98.1 92.2 NA 98.9 NA ...
$ Distance.A : num 112.8 93.9 61.8 82.5 72.4 ...
$ Angle.X.axis.A : num 90 90 90 90 90 ...
$ Angle.Y.axis.A : num 0.00361 0.00598 -0.00684 -0.00647 0.00911 ...
$ Distance.B : num 110.3 73.2 73.7 58.2 77 ...
$ Angle.X.axis.B : num -0.00452 0.0028 0.00173 -0.00307 0.00726 ...
$ Angle.Y.axis.B : num -90 -90 -90 -90 -90 ...data.final[1:10,"Xshift"] <- abs(data.final[1:10,"Distance.A"] - data.final[1,"Distance.A"])
data.final[11:20,"Xshift"] <- abs(data.final[11:20,"Distance.A"] - data.final[11,"Distance.A"])
data.final[1:10,"Yshift"] <- abs(data.final[1:10,"Distance.B"] - data.final[1,"Distance.B"])
data.final[11:20,"Yshift"] <- abs(data.final[11:20,"Distance.B"] - data.final[11,"Distance.B"])
data.final[c("Microscope","Replica","Xshift","Yshift")] Microscope Replica Xshift Yshift
1 LSM replica1 0.000000 0.0000000
2 LSM replica2 18.851380 37.1220103
3 LSM replica3 50.999715 36.5725880
4 LSM replica4 30.307684 52.1073457
5 LSM replica5 40.398741 33.2768377
6 LSM replica6 29.622459 14.6376101
7 LSM replica7 88.725450 18.0713862
8 LSM replica8 33.304726 1.5727510
9 LSM replica9 33.303371 3.8570131
10 LSM replica10 51.091176 14.9367229
11 Sneox replica1 0.000000 0.0000000
12 Sneox replica2 60.038194 4.3587697
13 Sneox replica3 62.799900 0.7891714
14 Sneox replica4 50.233881 18.7775508
15 Sneox replica5 115.447874 21.4503753
16 Sneox replica6 11.487581 27.1006115
17 Sneox replica7 47.290797 30.4415355
18 Sneox replica8 5.006597 33.0559393
19 Sneox replica9 44.509733 55.4592711
20 Sneox replica10 129.299897 61.3739679comment(data.final) <- units.varType comment(data.final) to check the units of the columns.
Axis.length.X
"µm"
Axis.size.X
"points"
Axis.spacing.X
"µm"
Axis.length.Y
"µm"
Axis.size.Y
"points"
Axis.spacing.Y
"µm"
Axis.length.Z
"µm"
Axis.size.Z
"digits"
Axis.spacing.Z
"nm"
NMP.ratio.Z
"%"
Sq
"µm"
Ssk
"<no unit>"
Sku
"<no unit>"
Sp
"µm"
Sv
"µm"
Sz
"µm"
Sa
"µm"
Smr.c.1.µm.under.the.highest.peak
"%"
Smc.p.10
"µm"
Sxp.p.50.q.97.5
"µm"
Sal.s.0.2
"µm"
Str.s.0.2
"<no unit>"
Std.Reference.angle.0
"°"
Sdq
"<no unit>"
Sdr
"%"
Vm.p.10
"µm³/µm²"
Vv.p.10
"µm³/µm²"
Vmp.p.10
"µm³/µm²"
Vmc.p.10.q.80
"µm³/µm²"
Vvc.p.10.q.80
"µm³/µm²"
Vvv.p.80
"µm³/µm²"
Sk.Gaussian.filter.0.08.mm.End.effects.managed
"µm"
Spk.Gaussian.filter.0.08.mm.End.effects.managed
"µm"
Svk.Gaussian.filter.0.08.mm.End.effects.managed
"µm"
Smr1.Gaussian.filter.0.08.mm.End.effects.managed
"%"
Smr2.Gaussian.filter.0.08.mm.End.effects.managed
"%"
Spq.Gaussian.filter.0.08.mm.End.effects.managed
"<no unit>"
Svq.Gaussian.filter.0.08.mm.End.effects.managed
"<no unit>"
Smq.Gaussian.filter.0.08.mm.End.effects.managed
"<no unit>"
Distance.A
"µm"
Angle.X.axis.A
"°"
Angle.Y.axis.A
"°"
Distance.B
"µm"
Angle.X.axis.B
"°"
Angle.Y.axis.B
"°"
Xshift
"µm"
Yshift
"µm" str(data.final)'data.frame': 20 obs. of 55 variables:
$ Sample : Factor w/ 1 level "FLT1-7": 1 1 1 1 1 1 1 1 1 1 ...
$ Microscope : Factor w/ 2 levels "LSM","Sneox": 1 1 1 1 1 1 1 1 1 1 ...
$ Objective : Factor w/ 2 levels "50x-0.8","50x-0.95": 2 2 2 2 2 2 2 2 2 2 ...
$ Replica : Factor w/ 10 levels "replica1","replica10",..: 1 3 4 5 6 7 8 9 10 2 ...
$ Acquisition.date : Date, format: "2018-09-03" "2018-09-03" ...
$ Analysis.date : Date, format: "2018-09-27" "2018-09-27" ...
$ Analysis.time : chr "15:20:31" "15:20:53" "15:22:14" "15:23:44" ...
$ Date.of.the.measurement: POSIXct, format: NA NA ...
$ Axis.length.X : num 255 255 255 255 255 ...
$ Axis.size.X : int 991 991 991 991 991 991 991 991 991 991 ...
$ Axis.spacing.X : num 0.258 0.258 0.258 0.258 0.258 ...
$ Axis.length.Y : num 255 255 255 255 255 ...
$ Axis.size.Y : int 991 991 991 991 991 991 991 991 991 991 ...
$ Axis.spacing.Y : num 0.258 0.258 0.258 0.258 0.258 ...
$ Axis.length.Z : num 26.7 29.6 28.7 28.7 28.4 ...
$ Axis.size.Z : int 65532 65532 65531 65532 65532 65532 65531 65532 65532 65532 ...
$ Axis.spacing.Z : num 0.407 0.451 0.438 0.438 0.433 ...
$ NMP.ratio.Z : num 0 0 0 0 0 0 0 0 0 0 ...
$ Sq : num 1.49 1.39 1.25 1.33 1.29 ...
$ Ssk : num -0.00297 0.09683 0.13965 0.09766 0.08338 ...
$ Sku : num 4.42 4.28 3.76 4.33 3.86 ...
$ Sp : num 6.07 6.21 5.92 6.24 6.01 ...
$ Sv : num 7.14 5.94 4.06 6.39 4.75 ...
$ Sz : num 13.2 12.15 9.98 12.62 10.76 ...
$ Sa : num 1.123 1.069 0.983 1.03 1.006 ...
$ Smr : num 0.293 0.258 0.183 0.167 0.183 ...
$ Smc : num 1.72 1.64 1.55 1.61 1.57 ...
$ Sxp : num 3.04 2.82 2.53 2.65 2.57 ...
$ Sal : num 14.4 14.6 13.7 14.6 14.1 ...
$ Str : num 0.761 0.812 0.741 0.827 0.777 ...
$ Std : num 87.2 85.5 94.2 94.2 69.3 ...
$ Sdq : logi NA NA NA NA NA NA ...
$ Sdr : logi NA NA NA NA NA NA ...
$ Vm : num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ Vv : num 1.81 1.72 1.61 1.68 1.64 ...
$ Vmp : num 0.0974 0.0825 0.0647 0.0742 0.0656 ...
$ Vmc : num 1.2 1.14 1.1 1.12 1.12 ...
$ Vvc : num 1.63 1.55 1.47 1.52 1.49 ...
$ Vvv : num 0.187 0.174 0.144 0.158 0.15 ...
$ Sk : num 2.51 2.46 2.35 2.42 2.4 ...
$ Spk : num 1.4 1.25 1.07 1.15 1.07 ...
$ Svk : num 1.48 1.37 1.15 1.29 1.2 ...
$ Smr1 : num 10.9 10.5 10.4 10.6 10.4 ...
$ Smr2 : num 87.1 87 87.7 87.8 88 ...
$ Spq : num 1.2 1.14 NA 1.1 NA ...
$ Svq : num 2.71 1.67 NA 2.83 NA ...
$ Smq : num 98.1 92.2 NA 98.9 NA ...
$ Distance.A : num 112.8 93.9 61.8 82.5 72.4 ...
$ Angle.X.axis.A : num 90 90 90 90 90 ...
$ Angle.Y.axis.A : num 0.00361 0.00598 -0.00684 -0.00647 0.00911 ...
$ Distance.B : num 110.3 73.2 73.7 58.2 77 ...
$ Angle.X.axis.B : num -0.00452 0.0028 0.00173 -0.00307 0.00726 ...
$ Angle.Y.axis.B : num -90 -90 -90 -90 -90 ...
$ Xshift : num 0 18.9 51 30.3 40.4 ...
$ Yshift : num 0 37.1 36.6 52.1 33.3 ...
- attr(*, "comment")= Named chr "µm" "points" "µm" "µm" ...
..- attr(*, "names")= chr "Axis.length.X" "Axis.size.X" "Axis.spacing.X" "Axis.length.Y" ...head(data.final) Sample Microscope Objective Replica Acquisition.date Analysis.date
1 FLT1-7 LSM 50x-0.95 replica1 2018-09-03 2018-09-27
2 FLT1-7 LSM 50x-0.95 replica2 2018-09-03 2018-09-27
3 FLT1-7 LSM 50x-0.95 replica3 2018-09-03 2018-09-27
4 FLT1-7 LSM 50x-0.95 replica4 2018-09-03 2018-09-27
5 FLT1-7 LSM 50x-0.95 replica5 2018-09-03 2018-09-27
6 FLT1-7 LSM 50x-0.95 replica6 2018-09-05 2018-09-27
Analysis.time Date.of.the.measurement Axis.length.X Axis.size.X
1 15:20:31 <NA> 255.3021 991
2 15:20:53 <NA> 255.3021 991
3 15:22:14 <NA> 255.3021 991
4 15:23:44 <NA> 255.3021 991
5 15:25:11 <NA> 255.3021 991
6 15:26:39 <NA> 255.3021 991
Axis.spacing.X Axis.length.Y Axis.size.Y Axis.spacing.Y Axis.length.Z
1 0.2578809 255.3021 991 0.2578809 26.69617
2 0.2578809 255.3021 991 0.2578809 29.55225
3 0.2578809 255.3021 991 0.2578809 28.71343
4 0.2578809 255.3021 991 0.2578809 28.69171
5 0.2578809 255.3021 991 0.2578809 28.35742
6 0.2578809 255.3021 991 0.2578809 32.68677
Axis.size.Z Axis.spacing.Z NMP.ratio.Z Sq Ssk Sku
1 65532 0.4073760 0 1.488856 -0.002966167 4.421120
2 65532 0.4509590 0 1.394765 0.096825541 4.283292
3 65531 0.4381656 0 1.254221 0.139646542 3.760289
4 65532 0.4378275 0 1.334686 0.097659238 4.332912
5 65532 0.4327263 0 1.285165 0.083383595 3.856306
6 65532 0.4987909 0 1.330428 0.036058892 4.390863
Sp Sv Sz Sa Smr Smc Sxp
1 6.067744 7.135436 13.20318 1.1231597 0.2934793 1.717098 3.036436
2 6.209435 5.938815 12.14825 1.0689597 0.2582295 1.638551 2.821328
3 5.919792 4.064468 9.98426 0.9830528 0.1827719 1.549140 2.531217
4 6.238691 6.385407 12.62410 1.0295042 0.1666355 1.606979 2.647887
5 6.008881 4.750513 10.75939 1.0062460 0.1827491 1.572206 2.569892
6 6.212940 6.449916 12.66286 1.0174876 0.1195299 1.566732 2.659812
Sal Str Std Sdq Sdr Vm Vv Vmp
1 14.36117 0.7612099 87.23766 NA NA 0.09741393 1.814525 0.09741393
2 14.60693 0.8121991 85.49456 NA NA 0.08249605 1.721069 0.08249605
3 13.68591 0.7405756 94.24377 NA NA 0.06469333 1.613826 0.06469333
4 14.58735 0.8273841 94.24814 NA NA 0.07415077 1.681125 0.07415077
5 14.10994 0.7773487 69.25086 NA NA 0.06564710 1.637851 0.06564710
6 14.08142 0.7003128 87.00026 NA NA 0.07765946 1.644378 0.07765946
Vmc Vvc Vvv Sk Spk Svk Smr1 Smr2
1 1.200814 1.627802 0.1867230 2.511306 1.404585 1.484395 10.92020 87.09988
2 1.142106 1.547504 0.1735655 2.459655 1.249207 1.371687 10.49765 87.03377
3 1.096797 1.469758 0.1440681 2.345582 1.073786 1.150289 10.39377 87.65104
4 1.115129 1.522651 0.1584748 2.421481 1.146464 1.294831 10.62076 87.83815
5 1.119894 1.487974 0.1498769 2.395216 1.068226 1.195285 10.39062 88.01758
6 1.108574 1.481198 0.1631801 2.303756 1.178533 1.352933 10.99725 87.15786
Spq Svq Smq Distance.A Angle.X.axis.A Angle.Y.axis.A
1 1.204824 2.714175 98.10662 112.76451 90.00361 0.003613407
2 1.137717 1.667827 92.19343 93.91312 90.00598 0.005982943
3 NA NA NA 61.76479 89.99316 -0.006839691
4 1.096027 2.827947 98.87538 82.45682 89.99353 -0.006471170
5 NA NA NA 72.36576 90.00911 0.009113466
6 NA NA NA 83.14205 90.00726 0.007260577
Distance.B Angle.X.axis.B Angle.Y.axis.B Xshift Yshift
1 110.31013 -0.004515873 -90.00452 0.00000 0.00000
2 73.18812 0.002802429 -89.99720 18.85138 37.12201
3 73.73754 0.001728188 -89.99827 50.99971 36.57259
4 58.20278 -0.003070476 -90.00307 30.30768 52.10735
5 77.03329 0.007259025 -89.99274 40.39874 33.27684
6 124.94774 -0.008370959 -90.00837 29.62246 14.63761file.out <- file_path_sans_ext(row.names(imp.info))The files will be saved as “~/Data/CoordSys_FLT1-7_50x.[ext]”.
write.xlsx(list(data=data.final, units=units.var.table), file=paste0(file.out,".xlsx"))
xlsx.info <- file.info(paste0(file.out,".xlsx"))The exported XLSX-file is: “CoordSys_FLT1-7_50x.xlsx”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2019-01-03 10:28:47”, “2019-01-03 10:27:28” and “2019-01-03 10:27:28”.
saveObject(data.final, file=paste0(file.out,".Rbin"))
Rbin.info <- file.info(paste0(file.out,".Rbin"))The exported Rbin-file is: “CoordSys_FLT1-7_50x.Rbin”
Its modification, ‘last status change’ (= ‘creation’ on Windows) and last access times are, respectively: “2019-01-03 10:28:47”, “2019-01-03 10:28:47” and “2019-01-03 10:28:47”.
sessionInfo()R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] R.utils_2.7.0 R.oo_1.22.0 R.methodsS3_1.7.1 openxlsx_4.1.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 digest_0.6.18 magrittr_1.5 evaluate_0.12
[5] zip_1.0.0 stringi_1.2.4 rmarkdown_1.11 stringr_1.3.1
[9] xfun_0.4 yaml_2.2.0 compiler_3.5.2 htmltools_0.3.6
[13] knitr_1.21 END OF SCRIPT