Read in .xrdml data within a complex array
I'm trying to read several files of type ".xrdml" and combine them into a single dataframe with an intuitive label. The problem is that this file type has a large metadata.
I've tried the following
Required package
library(rxylib)
Things i tried
temp = list.files(pattern="*.xrdml")
xyz<-do.call(rbind,sapply(temp, read_xyData,verbose = TRUE,metaData = FALSE))
i ended up with a list, i can call each member of the list using for example xyz[[2]]
2Theta V2
[1,] 4.006565 3496
[2,] 4.019695 3417
[3,] 4.032826 3520
[4,] 4.045956 3516
[5,] 4.059086 3480
[6,] 4.072217 3343
[7,] 4.085347 3466
[8,] 4.098477 3552
[9,] 4.111607 3425
[10,] 4.124738 3384
if i try to flatten the list by using the unlist function, then the result becomes messy
what i will like to do is to read in all the files and combine them by column, each file has first column in common i.e 2Theta . i will also like to use the unique part of each file title to label V2
my files have titles like "BBHD-FASS_4-70_step01_40s_LM 11_5.xrdml". what i hope to be able to do at the end is to have a dataframe similar to the sample below
2Theta LM 6-26 LM 6-27 LM 6-28 LM 4-10 LM 4-11 LM 4-12
4.006565 3576 3535 3677 3576 3535 3677
4.019695 3526 3552 3662 3526 3552 3662
4.032826 3584 3581 3657 3584 3581 3657
4.045956 3489 3535 3539 3489 3535 3539
4.059086 3496 3507 3525 3496 3507 3525
4.072217 3335 3466 3628 3335 3466 3628
4.085347 3353 3456 3444 3353 3456 3444
4.098477 3430 3479 3588 3430 3479 3588
4.111607 3334 3547 3535 3334 3547 3535
4.124738 3424 3342 3439 3424 3342 3439
4.137868 3349 3384 3459 3349 3384 3459
4.150998 3318 3395 3413 3318 3395 3413
4.164129 3208 3490 3457 3208 3490 3457
4.177259 3357 3295 3519 3357 3295 3519
4.190389 3254 3372 3450 3254 3372 3450
Here are samples of my files sample files
Sadly, i've spent so much time already trying several things which didn't work.
I'll be very grateful for any help or guidance i can get on how to approach this problem.
r arraylist customization
add a comment |
I'm trying to read several files of type ".xrdml" and combine them into a single dataframe with an intuitive label. The problem is that this file type has a large metadata.
I've tried the following
Required package
library(rxylib)
Things i tried
temp = list.files(pattern="*.xrdml")
xyz<-do.call(rbind,sapply(temp, read_xyData,verbose = TRUE,metaData = FALSE))
i ended up with a list, i can call each member of the list using for example xyz[[2]]
2Theta V2
[1,] 4.006565 3496
[2,] 4.019695 3417
[3,] 4.032826 3520
[4,] 4.045956 3516
[5,] 4.059086 3480
[6,] 4.072217 3343
[7,] 4.085347 3466
[8,] 4.098477 3552
[9,] 4.111607 3425
[10,] 4.124738 3384
if i try to flatten the list by using the unlist function, then the result becomes messy
what i will like to do is to read in all the files and combine them by column, each file has first column in common i.e 2Theta . i will also like to use the unique part of each file title to label V2
my files have titles like "BBHD-FASS_4-70_step01_40s_LM 11_5.xrdml". what i hope to be able to do at the end is to have a dataframe similar to the sample below
2Theta LM 6-26 LM 6-27 LM 6-28 LM 4-10 LM 4-11 LM 4-12
4.006565 3576 3535 3677 3576 3535 3677
4.019695 3526 3552 3662 3526 3552 3662
4.032826 3584 3581 3657 3584 3581 3657
4.045956 3489 3535 3539 3489 3535 3539
4.059086 3496 3507 3525 3496 3507 3525
4.072217 3335 3466 3628 3335 3466 3628
4.085347 3353 3456 3444 3353 3456 3444
4.098477 3430 3479 3588 3430 3479 3588
4.111607 3334 3547 3535 3334 3547 3535
4.124738 3424 3342 3439 3424 3342 3439
4.137868 3349 3384 3459 3349 3384 3459
4.150998 3318 3395 3413 3318 3395 3413
4.164129 3208 3490 3457 3208 3490 3457
4.177259 3357 3295 3519 3357 3295 3519
4.190389 3254 3372 3450 3254 3372 3450
Here are samples of my files sample files
Sadly, i've spent so much time already trying several things which didn't work.
I'll be very grateful for any help or guidance i can get on how to approach this problem.
r arraylist customization
add a comment |
I'm trying to read several files of type ".xrdml" and combine them into a single dataframe with an intuitive label. The problem is that this file type has a large metadata.
I've tried the following
Required package
library(rxylib)
Things i tried
temp = list.files(pattern="*.xrdml")
xyz<-do.call(rbind,sapply(temp, read_xyData,verbose = TRUE,metaData = FALSE))
i ended up with a list, i can call each member of the list using for example xyz[[2]]
2Theta V2
[1,] 4.006565 3496
[2,] 4.019695 3417
[3,] 4.032826 3520
[4,] 4.045956 3516
[5,] 4.059086 3480
[6,] 4.072217 3343
[7,] 4.085347 3466
[8,] 4.098477 3552
[9,] 4.111607 3425
[10,] 4.124738 3384
if i try to flatten the list by using the unlist function, then the result becomes messy
what i will like to do is to read in all the files and combine them by column, each file has first column in common i.e 2Theta . i will also like to use the unique part of each file title to label V2
my files have titles like "BBHD-FASS_4-70_step01_40s_LM 11_5.xrdml". what i hope to be able to do at the end is to have a dataframe similar to the sample below
2Theta LM 6-26 LM 6-27 LM 6-28 LM 4-10 LM 4-11 LM 4-12
4.006565 3576 3535 3677 3576 3535 3677
4.019695 3526 3552 3662 3526 3552 3662
4.032826 3584 3581 3657 3584 3581 3657
4.045956 3489 3535 3539 3489 3535 3539
4.059086 3496 3507 3525 3496 3507 3525
4.072217 3335 3466 3628 3335 3466 3628
4.085347 3353 3456 3444 3353 3456 3444
4.098477 3430 3479 3588 3430 3479 3588
4.111607 3334 3547 3535 3334 3547 3535
4.124738 3424 3342 3439 3424 3342 3439
4.137868 3349 3384 3459 3349 3384 3459
4.150998 3318 3395 3413 3318 3395 3413
4.164129 3208 3490 3457 3208 3490 3457
4.177259 3357 3295 3519 3357 3295 3519
4.190389 3254 3372 3450 3254 3372 3450
Here are samples of my files sample files
Sadly, i've spent so much time already trying several things which didn't work.
I'll be very grateful for any help or guidance i can get on how to approach this problem.
r arraylist customization
I'm trying to read several files of type ".xrdml" and combine them into a single dataframe with an intuitive label. The problem is that this file type has a large metadata.
I've tried the following
Required package
library(rxylib)
Things i tried
temp = list.files(pattern="*.xrdml")
xyz<-do.call(rbind,sapply(temp, read_xyData,verbose = TRUE,metaData = FALSE))
i ended up with a list, i can call each member of the list using for example xyz[[2]]
2Theta V2
[1,] 4.006565 3496
[2,] 4.019695 3417
[3,] 4.032826 3520
[4,] 4.045956 3516
[5,] 4.059086 3480
[6,] 4.072217 3343
[7,] 4.085347 3466
[8,] 4.098477 3552
[9,] 4.111607 3425
[10,] 4.124738 3384
if i try to flatten the list by using the unlist function, then the result becomes messy
what i will like to do is to read in all the files and combine them by column, each file has first column in common i.e 2Theta . i will also like to use the unique part of each file title to label V2
my files have titles like "BBHD-FASS_4-70_step01_40s_LM 11_5.xrdml". what i hope to be able to do at the end is to have a dataframe similar to the sample below
2Theta LM 6-26 LM 6-27 LM 6-28 LM 4-10 LM 4-11 LM 4-12
4.006565 3576 3535 3677 3576 3535 3677
4.019695 3526 3552 3662 3526 3552 3662
4.032826 3584 3581 3657 3584 3581 3657
4.045956 3489 3535 3539 3489 3535 3539
4.059086 3496 3507 3525 3496 3507 3525
4.072217 3335 3466 3628 3335 3466 3628
4.085347 3353 3456 3444 3353 3456 3444
4.098477 3430 3479 3588 3430 3479 3588
4.111607 3334 3547 3535 3334 3547 3535
4.124738 3424 3342 3439 3424 3342 3439
4.137868 3349 3384 3459 3349 3384 3459
4.150998 3318 3395 3413 3318 3395 3413
4.164129 3208 3490 3457 3208 3490 3457
4.177259 3357 3295 3519 3357 3295 3519
4.190389 3254 3372 3450 3254 3372 3450
Here are samples of my files sample files
Sadly, i've spent so much time already trying several things which didn't work.
I'll be very grateful for any help or guidance i can get on how to approach this problem.
r arraylist customization
r arraylist customization
edited Nov 19 '18 at 18:08
user20650
17k43367
17k43367
asked Sep 2 '18 at 5:37
HammaoHammao
155313
155313
add a comment |
add a comment |
1 Answer
1
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votes
To get to the data you need to find the correct position in the list of data that is returned by read_xyData
. You can do this by looking at str(lst)
below. To get to the data use ...$dataset[[1]]$data_block
. (there may be extractor functions in the package but I have not checked)
# download data : link dead
#download.file("https://ucc93bf0aa50821e11b95c9530f5.dl.dropboxusercontent.com/zip_by_token_key?_download_id=9101556320431172280658295109635067362614982268430911643523348&_notify_domain=www.dropbox.com&dl=1&key=AV5mxk0trnetzASlH9_xJijTiGE55mUz0qa-x7JveZ7-Rdp3Z8i7GmwwQoWj8tUO14RKj51huhb5CuBdoxAC3WLuHvOMr7_bul691AmGpmwZgWWy0STezjFRnq0CVUR-iHNnZUHk9-t-i72nYODDpjXvo0PBhWTXwJuNWCSL4bnAauZREQtZwzNlspMF8PwZ37E9enf1WUUakLJwE43GbV2lAkuOTDghfcMmwokulIMEGA", destfile=temp<-tempfile())
unzip(temp, exdir=xdir<-tempdir())
nms <- list.files(xdir, pattern="xrdml", full.names=TRUE)
# grab the names to names columns later
cnms <- gsub(".*(LM \w+).*$", "\1", basename(nms))
library(rxylib)
# loop through files to read in
lst <- lapply(nms, read_xyData, verbose = TRUE, metaData = FALSE)
# grab the data
dats <- lapply(lst, function(x) x$dataset[[1]]$data_block)
# rename second column
dats <- lapply(seq_along(dats), function(x) {
colnames(dats[[x]])[2] <- cnms[x] ; dats[[x]]})
# merge
alldat <- Reduce(function(...) merge(..., by="2Theta"), dats)
Thanks for taking out time to help out with this... i added just a line of code to read in the file because the unzip failedpath = "~/MEGA/R/Spectral_Files/Spectral_Files/Data" nms <- list.files(path, pattern="xrdml", full.names=TRUE)
. Also the labelling doesn't work as expected because my files can different suffixes not only "LM". I tried modifying the gsub() but got error each time. It will be highly appreciated if you can help with this.
– Hammao
Nov 20 '18 at 20:40
you're welcome. re the names, you could trygsub(".*_(\w+ \w+).*$", "\1", basename(nms))
but I think it is better asking for help with this in a new question -- get the regrex folks eyes on it. (ps best to add a small sample of different potential names frombasename(nms)
to try and get all edge cases)
– user20650
Nov 20 '18 at 20:58
1
Thanks ... it worked for all file types, !!! I wish i have your type of knowledge in base r
– Hammao
Nov 20 '18 at 22:59
add a comment |
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To get to the data you need to find the correct position in the list of data that is returned by read_xyData
. You can do this by looking at str(lst)
below. To get to the data use ...$dataset[[1]]$data_block
. (there may be extractor functions in the package but I have not checked)
# download data : link dead
#download.file("https://ucc93bf0aa50821e11b95c9530f5.dl.dropboxusercontent.com/zip_by_token_key?_download_id=9101556320431172280658295109635067362614982268430911643523348&_notify_domain=www.dropbox.com&dl=1&key=AV5mxk0trnetzASlH9_xJijTiGE55mUz0qa-x7JveZ7-Rdp3Z8i7GmwwQoWj8tUO14RKj51huhb5CuBdoxAC3WLuHvOMr7_bul691AmGpmwZgWWy0STezjFRnq0CVUR-iHNnZUHk9-t-i72nYODDpjXvo0PBhWTXwJuNWCSL4bnAauZREQtZwzNlspMF8PwZ37E9enf1WUUakLJwE43GbV2lAkuOTDghfcMmwokulIMEGA", destfile=temp<-tempfile())
unzip(temp, exdir=xdir<-tempdir())
nms <- list.files(xdir, pattern="xrdml", full.names=TRUE)
# grab the names to names columns later
cnms <- gsub(".*(LM \w+).*$", "\1", basename(nms))
library(rxylib)
# loop through files to read in
lst <- lapply(nms, read_xyData, verbose = TRUE, metaData = FALSE)
# grab the data
dats <- lapply(lst, function(x) x$dataset[[1]]$data_block)
# rename second column
dats <- lapply(seq_along(dats), function(x) {
colnames(dats[[x]])[2] <- cnms[x] ; dats[[x]]})
# merge
alldat <- Reduce(function(...) merge(..., by="2Theta"), dats)
Thanks for taking out time to help out with this... i added just a line of code to read in the file because the unzip failedpath = "~/MEGA/R/Spectral_Files/Spectral_Files/Data" nms <- list.files(path, pattern="xrdml", full.names=TRUE)
. Also the labelling doesn't work as expected because my files can different suffixes not only "LM". I tried modifying the gsub() but got error each time. It will be highly appreciated if you can help with this.
– Hammao
Nov 20 '18 at 20:40
you're welcome. re the names, you could trygsub(".*_(\w+ \w+).*$", "\1", basename(nms))
but I think it is better asking for help with this in a new question -- get the regrex folks eyes on it. (ps best to add a small sample of different potential names frombasename(nms)
to try and get all edge cases)
– user20650
Nov 20 '18 at 20:58
1
Thanks ... it worked for all file types, !!! I wish i have your type of knowledge in base r
– Hammao
Nov 20 '18 at 22:59
add a comment |
To get to the data you need to find the correct position in the list of data that is returned by read_xyData
. You can do this by looking at str(lst)
below. To get to the data use ...$dataset[[1]]$data_block
. (there may be extractor functions in the package but I have not checked)
# download data : link dead
#download.file("https://ucc93bf0aa50821e11b95c9530f5.dl.dropboxusercontent.com/zip_by_token_key?_download_id=9101556320431172280658295109635067362614982268430911643523348&_notify_domain=www.dropbox.com&dl=1&key=AV5mxk0trnetzASlH9_xJijTiGE55mUz0qa-x7JveZ7-Rdp3Z8i7GmwwQoWj8tUO14RKj51huhb5CuBdoxAC3WLuHvOMr7_bul691AmGpmwZgWWy0STezjFRnq0CVUR-iHNnZUHk9-t-i72nYODDpjXvo0PBhWTXwJuNWCSL4bnAauZREQtZwzNlspMF8PwZ37E9enf1WUUakLJwE43GbV2lAkuOTDghfcMmwokulIMEGA", destfile=temp<-tempfile())
unzip(temp, exdir=xdir<-tempdir())
nms <- list.files(xdir, pattern="xrdml", full.names=TRUE)
# grab the names to names columns later
cnms <- gsub(".*(LM \w+).*$", "\1", basename(nms))
library(rxylib)
# loop through files to read in
lst <- lapply(nms, read_xyData, verbose = TRUE, metaData = FALSE)
# grab the data
dats <- lapply(lst, function(x) x$dataset[[1]]$data_block)
# rename second column
dats <- lapply(seq_along(dats), function(x) {
colnames(dats[[x]])[2] <- cnms[x] ; dats[[x]]})
# merge
alldat <- Reduce(function(...) merge(..., by="2Theta"), dats)
Thanks for taking out time to help out with this... i added just a line of code to read in the file because the unzip failedpath = "~/MEGA/R/Spectral_Files/Spectral_Files/Data" nms <- list.files(path, pattern="xrdml", full.names=TRUE)
. Also the labelling doesn't work as expected because my files can different suffixes not only "LM". I tried modifying the gsub() but got error each time. It will be highly appreciated if you can help with this.
– Hammao
Nov 20 '18 at 20:40
you're welcome. re the names, you could trygsub(".*_(\w+ \w+).*$", "\1", basename(nms))
but I think it is better asking for help with this in a new question -- get the regrex folks eyes on it. (ps best to add a small sample of different potential names frombasename(nms)
to try and get all edge cases)
– user20650
Nov 20 '18 at 20:58
1
Thanks ... it worked for all file types, !!! I wish i have your type of knowledge in base r
– Hammao
Nov 20 '18 at 22:59
add a comment |
To get to the data you need to find the correct position in the list of data that is returned by read_xyData
. You can do this by looking at str(lst)
below. To get to the data use ...$dataset[[1]]$data_block
. (there may be extractor functions in the package but I have not checked)
# download data : link dead
#download.file("https://ucc93bf0aa50821e11b95c9530f5.dl.dropboxusercontent.com/zip_by_token_key?_download_id=9101556320431172280658295109635067362614982268430911643523348&_notify_domain=www.dropbox.com&dl=1&key=AV5mxk0trnetzASlH9_xJijTiGE55mUz0qa-x7JveZ7-Rdp3Z8i7GmwwQoWj8tUO14RKj51huhb5CuBdoxAC3WLuHvOMr7_bul691AmGpmwZgWWy0STezjFRnq0CVUR-iHNnZUHk9-t-i72nYODDpjXvo0PBhWTXwJuNWCSL4bnAauZREQtZwzNlspMF8PwZ37E9enf1WUUakLJwE43GbV2lAkuOTDghfcMmwokulIMEGA", destfile=temp<-tempfile())
unzip(temp, exdir=xdir<-tempdir())
nms <- list.files(xdir, pattern="xrdml", full.names=TRUE)
# grab the names to names columns later
cnms <- gsub(".*(LM \w+).*$", "\1", basename(nms))
library(rxylib)
# loop through files to read in
lst <- lapply(nms, read_xyData, verbose = TRUE, metaData = FALSE)
# grab the data
dats <- lapply(lst, function(x) x$dataset[[1]]$data_block)
# rename second column
dats <- lapply(seq_along(dats), function(x) {
colnames(dats[[x]])[2] <- cnms[x] ; dats[[x]]})
# merge
alldat <- Reduce(function(...) merge(..., by="2Theta"), dats)
To get to the data you need to find the correct position in the list of data that is returned by read_xyData
. You can do this by looking at str(lst)
below. To get to the data use ...$dataset[[1]]$data_block
. (there may be extractor functions in the package but I have not checked)
# download data : link dead
#download.file("https://ucc93bf0aa50821e11b95c9530f5.dl.dropboxusercontent.com/zip_by_token_key?_download_id=9101556320431172280658295109635067362614982268430911643523348&_notify_domain=www.dropbox.com&dl=1&key=AV5mxk0trnetzASlH9_xJijTiGE55mUz0qa-x7JveZ7-Rdp3Z8i7GmwwQoWj8tUO14RKj51huhb5CuBdoxAC3WLuHvOMr7_bul691AmGpmwZgWWy0STezjFRnq0CVUR-iHNnZUHk9-t-i72nYODDpjXvo0PBhWTXwJuNWCSL4bnAauZREQtZwzNlspMF8PwZ37E9enf1WUUakLJwE43GbV2lAkuOTDghfcMmwokulIMEGA", destfile=temp<-tempfile())
unzip(temp, exdir=xdir<-tempdir())
nms <- list.files(xdir, pattern="xrdml", full.names=TRUE)
# grab the names to names columns later
cnms <- gsub(".*(LM \w+).*$", "\1", basename(nms))
library(rxylib)
# loop through files to read in
lst <- lapply(nms, read_xyData, verbose = TRUE, metaData = FALSE)
# grab the data
dats <- lapply(lst, function(x) x$dataset[[1]]$data_block)
# rename second column
dats <- lapply(seq_along(dats), function(x) {
colnames(dats[[x]])[2] <- cnms[x] ; dats[[x]]})
# merge
alldat <- Reduce(function(...) merge(..., by="2Theta"), dats)
edited Nov 20 '18 at 21:04
answered Nov 19 '18 at 18:07
user20650user20650
17k43367
17k43367
Thanks for taking out time to help out with this... i added just a line of code to read in the file because the unzip failedpath = "~/MEGA/R/Spectral_Files/Spectral_Files/Data" nms <- list.files(path, pattern="xrdml", full.names=TRUE)
. Also the labelling doesn't work as expected because my files can different suffixes not only "LM". I tried modifying the gsub() but got error each time. It will be highly appreciated if you can help with this.
– Hammao
Nov 20 '18 at 20:40
you're welcome. re the names, you could trygsub(".*_(\w+ \w+).*$", "\1", basename(nms))
but I think it is better asking for help with this in a new question -- get the regrex folks eyes on it. (ps best to add a small sample of different potential names frombasename(nms)
to try and get all edge cases)
– user20650
Nov 20 '18 at 20:58
1
Thanks ... it worked for all file types, !!! I wish i have your type of knowledge in base r
– Hammao
Nov 20 '18 at 22:59
add a comment |
Thanks for taking out time to help out with this... i added just a line of code to read in the file because the unzip failedpath = "~/MEGA/R/Spectral_Files/Spectral_Files/Data" nms <- list.files(path, pattern="xrdml", full.names=TRUE)
. Also the labelling doesn't work as expected because my files can different suffixes not only "LM". I tried modifying the gsub() but got error each time. It will be highly appreciated if you can help with this.
– Hammao
Nov 20 '18 at 20:40
you're welcome. re the names, you could trygsub(".*_(\w+ \w+).*$", "\1", basename(nms))
but I think it is better asking for help with this in a new question -- get the regrex folks eyes on it. (ps best to add a small sample of different potential names frombasename(nms)
to try and get all edge cases)
– user20650
Nov 20 '18 at 20:58
1
Thanks ... it worked for all file types, !!! I wish i have your type of knowledge in base r
– Hammao
Nov 20 '18 at 22:59
Thanks for taking out time to help out with this... i added just a line of code to read in the file because the unzip failed
path = "~/MEGA/R/Spectral_Files/Spectral_Files/Data" nms <- list.files(path, pattern="xrdml", full.names=TRUE)
. Also the labelling doesn't work as expected because my files can different suffixes not only "LM". I tried modifying the gsub() but got error each time. It will be highly appreciated if you can help with this.– Hammao
Nov 20 '18 at 20:40
Thanks for taking out time to help out with this... i added just a line of code to read in the file because the unzip failed
path = "~/MEGA/R/Spectral_Files/Spectral_Files/Data" nms <- list.files(path, pattern="xrdml", full.names=TRUE)
. Also the labelling doesn't work as expected because my files can different suffixes not only "LM". I tried modifying the gsub() but got error each time. It will be highly appreciated if you can help with this.– Hammao
Nov 20 '18 at 20:40
you're welcome. re the names, you could try
gsub(".*_(\w+ \w+).*$", "\1", basename(nms))
but I think it is better asking for help with this in a new question -- get the regrex folks eyes on it. (ps best to add a small sample of different potential names from basename(nms)
to try and get all edge cases)– user20650
Nov 20 '18 at 20:58
you're welcome. re the names, you could try
gsub(".*_(\w+ \w+).*$", "\1", basename(nms))
but I think it is better asking for help with this in a new question -- get the regrex folks eyes on it. (ps best to add a small sample of different potential names from basename(nms)
to try and get all edge cases)– user20650
Nov 20 '18 at 20:58
1
1
Thanks ... it worked for all file types, !!! I wish i have your type of knowledge in base r
– Hammao
Nov 20 '18 at 22:59
Thanks ... it worked for all file types, !!! I wish i have your type of knowledge in base r
– Hammao
Nov 20 '18 at 22:59
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