I try to load PET/CT data (folder available in https://wwsi365-my.sharepoint.com/:f:/g/personal/s9956jm_ms_wwsi_edu_pl/EkoL7bs8rvxLq7-YHminlA0Bhc0PBY5_rG3zwMI2coHUAQ?e=TuekJa) - file can be opened via slicer for example so is not corrupted, but when I try to load it via simpleitk in python code below- I get error
code
dirOfExample
="C:\\Users\\1\\Downloads\\bad45Y\\bad45Y\\DICOM\\21071306"
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(dirOfExample)
reader.SetFileNames(dicom_names)
error
WARNING: In D:\a\1\sitk-build\ITK\Modules\IO\GDCM\src\itkGDCMSeriesFileNames.cxx, line 113
GDCMSeriesFileNames (00000000679B0CC0): No Series can be found, make sure your restrictions are not too strong
Thanks for help!
It looks like your DICOM files are down within some sub-directories of "21071306". The SimpleITK ImageSeriesReader is only going to look for DICOM image files within the directory that you give it. It does not do a recursive search of the sub-directories.
Related
I have an excel file that I want to open in R. I tried both of these commands after saving the excel file as a csv file or a text file.
read.table() or read.csv()
I think part of the problem is where the file is located. I have it saved on the desk top. What am I missing here?
Here is the R output
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> help.search("read.csv")
> read.csv("Rtrial.csv")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> read.table("tab")
To throw out another option, why not set the working directory (preferably via a script) to the desktop using setwd('C:\John\Desktop') and then read the files just using file names
Try
f <- file.choose()
to choose the file interactively and save the name in f.
Then run read.csv on the saved filename
d <- read.csv(f)
Sound like you just have an issue with the path. Include the full path, if you use backslashes they need to be escaped: "C:\\folder\\folder\\Desktop\\file.csv" or "C:/folder/folder/Desktop/file.csv".
myfile = read.csv("C:/folder/folder/Desktop/file.csv") # or read.table()
It may also be wise to avoid spaces and symbols in your file names, though I'm fairly certain spaces are OK.
I had to combine Maiasaura and Svun answers to get it to work: using setwd and escaping all the slashes and spaces.
setwd('C:\\Users\\firstname\ lastname\\Desktop\\folder1\\folder2\\folder3')
data = read.csv("file.csv")
data
This solved the issue for me.
Here is one way to do it. It uses the ability of R to construct file paths based on the platform and hence will work on both Mac OS and Windows. Moreover, you don't need to convert your xls file to csv, as there are many R packages that will help you read xls directly (e.g. gdata package).
# get user's home directory
home = setwd(Sys.getenv("HOME"));
# construct path to file
fpath = file.path(home, "Desktop", "RTrial.xls");
# load gdata library to read xls files
library(gdata);
# read xls file
Rtrial = read.xls(fpath);
Let me know if this works.
Save as in excel will keep the file open and lock it so you can't open it. Close the excel file or you won't be able to use it in R.
Give the full path and escape backslashes read.csv("c:\\users\\JoeUser\\Desktop\\JoesData.csv")
I have experienced that this error occurs when you either move the excel file to the destination other than where your r file is located or when you move your r file to the destination other than where your excel file is located.
Good Practice:
Keep your .r and .csv files in the same directory.
open your .r file from getting into its directory instead of opening the r file from rstuio's open file option.
You also have import Dataset option at Environment Block, just click there and get your required packages installed & from next time use this option to read datasets. You will not get this error again.
I also appreciate the above provided answers.
Another way of reading Excel including the new format xlsx could be the package speedR (https://r-forge.r-project.org/projects/speedr/). It is an interactive and visual data importer. Besides importing you can filter(subset) the existing objects from the R workspace.
My issue was very simple, the working directory was not the "Source" directory that was printed when the file ran. To fix this, you can use getwd() and setwd() to get your relative links working, or just use a full path when opening the csv.
print(getwd()) # Where does the code think it is?
setwd("~/Documents") # Where do I want my code to be?
dat = read.csv("~/Documents/Data Visualization/expDataAnalysis/one/ac1_survey.csv") #just make it work!
MAC OS It happened to me as well. I simply chose from the R toolbar MISC and then chose Change Working Directory. I was able to choose the directory that the .csv file was saved in. When I went back to the command line and typed getwd() the full directory was updated and correct and the read.csv function finally worked.
I had the same problem and when I checked the properties of the file on file explorer, it shows me the next message:
"Security: This file came from another computer and might be blocked to help protect this computer"
You click on the "Unblock" button and... you can access to the file from R without any problem, just using read.csv() function and from the directory specified as your working directory, even if is not the same as the file’s directory you are accessing to.
I just had this problem and I first switched to another directory and then switched back and the problem was fixed.
this work for me, accesing data from root. use double slash to access address.
dataset = read.csv('C:\\Users\\Desktop\\Machine Learning\\Data.csv')
Kindly check whether the file name has an extension for example:
abc.csv
if so remove the .csv extension.
set wd to the folder containing the file (~)
data<-read.csv("abc.csv")
Your data has been read the data object
In my case this very problem was raised by wrong spelling, lower case 'c:' instead of upper case 'C:' in the path. I corrected spelling and problem vanished.
You can add absolute path to the file
heisenberg <- read.csv(file="C:/Users/tiago/Desktop/sample_100000.csv")
If really want to run something like
heisenberg <- read.csv(file="sample_100000.csv")
then you'll have to change the working directory to match the place the .CSV file is at. More about it here.
How can others who run my R program read a file(eg: csv) used in my R code without having to change the working directory in setwd()?
I will suggest you use the here() function in the here package in your code like this:
library(here)
Data1 <- read_csv(here("test_data.csv"))
read.csv has a file argument and if I were to quote from the inbuilt R help about file:
If it does not contain an absolute path, the file name is relative to
the current working directory, getwd().
So, providing the absolute path of the file inside the file argument solves this problem.
In Windows
Suppose your file name is test.csv and it's located in D:\files\test_folder (you can get the location of any file from its properties in Windows)
For reading this file you run:
df<-read.csv('D:\\files\\test_folder\\test.csv')
or
df<-read.csv('D:/files/test_folder/test.csv')
Suggested reading: Why \\ instead of \ and Paths in programming languages
Haven't used R in Linux but maybe Getting a file path in Linux might help
Read from web
Just type in the web address of the dataset in the file attribute. Try:
df<-read.csv('https://raw.githubusercontent.com/AdiPersonalWorks/Random/master/student_scores%20-%20student_scores.csv')
Note: This link contains a list of 25 students with their study hours and marks. I myself used this dataset for one of my earlier tasks and its perfectly safe
I have an excel file that I want to open in R. I tried both of these commands after saving the excel file as a csv file or a text file.
read.table() or read.csv()
I think part of the problem is where the file is located. I have it saved on the desk top. What am I missing here?
Here is the R output
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> help.search("read.csv")
> read.csv("Rtrial.csv")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> read.table("tab")
To throw out another option, why not set the working directory (preferably via a script) to the desktop using setwd('C:\John\Desktop') and then read the files just using file names
Try
f <- file.choose()
to choose the file interactively and save the name in f.
Then run read.csv on the saved filename
d <- read.csv(f)
Sound like you just have an issue with the path. Include the full path, if you use backslashes they need to be escaped: "C:\\folder\\folder\\Desktop\\file.csv" or "C:/folder/folder/Desktop/file.csv".
myfile = read.csv("C:/folder/folder/Desktop/file.csv") # or read.table()
It may also be wise to avoid spaces and symbols in your file names, though I'm fairly certain spaces are OK.
I had to combine Maiasaura and Svun answers to get it to work: using setwd and escaping all the slashes and spaces.
setwd('C:\\Users\\firstname\ lastname\\Desktop\\folder1\\folder2\\folder3')
data = read.csv("file.csv")
data
This solved the issue for me.
Here is one way to do it. It uses the ability of R to construct file paths based on the platform and hence will work on both Mac OS and Windows. Moreover, you don't need to convert your xls file to csv, as there are many R packages that will help you read xls directly (e.g. gdata package).
# get user's home directory
home = setwd(Sys.getenv("HOME"));
# construct path to file
fpath = file.path(home, "Desktop", "RTrial.xls");
# load gdata library to read xls files
library(gdata);
# read xls file
Rtrial = read.xls(fpath);
Let me know if this works.
Save as in excel will keep the file open and lock it so you can't open it. Close the excel file or you won't be able to use it in R.
Give the full path and escape backslashes read.csv("c:\\users\\JoeUser\\Desktop\\JoesData.csv")
I have experienced that this error occurs when you either move the excel file to the destination other than where your r file is located or when you move your r file to the destination other than where your excel file is located.
Good Practice:
Keep your .r and .csv files in the same directory.
open your .r file from getting into its directory instead of opening the r file from rstuio's open file option.
You also have import Dataset option at Environment Block, just click there and get your required packages installed & from next time use this option to read datasets. You will not get this error again.
I also appreciate the above provided answers.
Another way of reading Excel including the new format xlsx could be the package speedR (https://r-forge.r-project.org/projects/speedr/). It is an interactive and visual data importer. Besides importing you can filter(subset) the existing objects from the R workspace.
My issue was very simple, the working directory was not the "Source" directory that was printed when the file ran. To fix this, you can use getwd() and setwd() to get your relative links working, or just use a full path when opening the csv.
print(getwd()) # Where does the code think it is?
setwd("~/Documents") # Where do I want my code to be?
dat = read.csv("~/Documents/Data Visualization/expDataAnalysis/one/ac1_survey.csv") #just make it work!
MAC OS It happened to me as well. I simply chose from the R toolbar MISC and then chose Change Working Directory. I was able to choose the directory that the .csv file was saved in. When I went back to the command line and typed getwd() the full directory was updated and correct and the read.csv function finally worked.
I had the same problem and when I checked the properties of the file on file explorer, it shows me the next message:
"Security: This file came from another computer and might be blocked to help protect this computer"
You click on the "Unblock" button and... you can access to the file from R without any problem, just using read.csv() function and from the directory specified as your working directory, even if is not the same as the file’s directory you are accessing to.
I just had this problem and I first switched to another directory and then switched back and the problem was fixed.
this work for me, accesing data from root. use double slash to access address.
dataset = read.csv('C:\\Users\\Desktop\\Machine Learning\\Data.csv')
Kindly check whether the file name has an extension for example:
abc.csv
if so remove the .csv extension.
set wd to the folder containing the file (~)
data<-read.csv("abc.csv")
Your data has been read the data object
In my case this very problem was raised by wrong spelling, lower case 'c:' instead of upper case 'C:' in the path. I corrected spelling and problem vanished.
You can add absolute path to the file
heisenberg <- read.csv(file="C:/Users/tiago/Desktop/sample_100000.csv")
If really want to run something like
heisenberg <- read.csv(file="sample_100000.csv")
then you'll have to change the working directory to match the place the .CSV file is at. More about it here.
I would like to open an Excel file saved as webpage using R and I keep getting error messages.
The desired steps are:
1) Upload the file into RStudio
2) Change the format into a data frame / tibble
3) Save the file as an xls
The message I get when I open the file in Excel is that the file format (excel webpage format) and extension format (xls) differ. I have tried the steps in this answer, but to no avail. I would be grateful for any help!
I don't expect anybody will be able to give you a definitive answer without a link to the actual file. The complication is that many services will write files as .xls or .xlsx without them being valid Excel format. This is done because Excel is so common and some non-technical people feel more confident working with Excel files than a csv file. Now, the files will have been stored in a format that Excel can deal with (hence your warning message), but R's libraries are more strict and don't see the actual file type they were expecting, so they fail.
That said, the below steps worked for me when I last encountered this problem. A service was outputting .xls files which were actually just HTML tables saved with an .xls file extension.
1) Download the file to work with it locally. You can script this of course, e.g. with download.file(), but this step helps eliminate other errors involved in working directly with a webpage or connection.
2) Load the full file with readHTMLTable() from the XML package
library(XML)
dTemp = readHTMLTable([filename], stringsAsFactors = FALSE)
This will return a list of dataframes. Your result set will quite likely be the second element or later (see ?readHTMLTable for an example with explanation). You will probably need to experiment here and explore the list structure as it may have nested lists.
3) Extract the relevant list element, e.g.
df = dTemp[2]
You also mention writing out the final data frame as an xls file which suggests you want the old-style format. I would suggest the package WriteXLS for this purpose.
I seriously doubt Excel is 'saved as a web page'. I'm pretty sure the file just sits on a server and all you have to do is go fetch it. Some kind of files (In particular Excel and h5) are binary rather than text files. This needs an added setting to warn R that it is a binary file and should be handled appropriately.
myurl <- "http://127.0.0.1/imaginary/file.xlsx"
download.file(url=myurl, destfile="localcopy.xlsx", mode="wb")
or, for use downloader, and ty something like this.
myurl <- "http://127.0.0.1/imaginary/file.xlsx"
download(myurl, destfile="localcopy.csv", mode="wb")
I'm trying to load an Excel workbook with a large number of tabs into R, do some analysis, and then export the results back into Excel. I'm using the openxlsx package because of some of the features of that package that are not easily accessible using other packages (such as the ability to create "comments" in the output file, color code the tabs, and work with 64-bit R).
When I try to read in the workbooks, I sometimes get the following error message (or something similar):
Error in unzip(xlsxFile, exdir = xmlDir) :
cannot open file 'C:/Users/MENDEL~1/AppData/Local/Temp/RtmpIb3WOf/_excelXMLRead/xl/worksheets/sheet5.xml': Permission denied
This error message doesn't always show up - but sometimes it will appear and the program crashes.
Does anyone have any ideas how to fix this problem? I don't know why the program sometimes thinks it doesn't have permission to access the sheets.
Thank you in advance!
I can think of two possible scenarios for this error:
Scenario 1:
C:/Users/MENDEL~1/AppData/Local/ (This looks like you are trying to read a temporary file)
Solution:
If that is the case try moving the file to a different location like desktop and make sure that you update your working directory accordingly.
Scenario 2
C:/Users/MENDEL~1/AppData/Local/Temp/RtmpIb3WOf/_excelXMLRead/xl/worksheets/sheet5.xml' (Looks like there is some issue with Sheet5 which is of type .xml and the openxlsx does not allow you to read .xml)
Solution:
Check if there is some issue with the format or contents of sheet5 in the file that you are trying to read.
For additional information check CRAN Documentation