I'm using H5Py to manipulate some large files and am continuously receiving the following error(s):
OSError: Unable to open file (file is already open for read-only)
During handling of the above exception, another exception occurred:
OSError: Unable to create file (file exists)
The code that I have looks like this:
def something_h5py(args, data_file, dir_file):
# skip if the direction file already exists
if os.path.exists(data_file):
f = h5py.File(data_file, 'r')
if (args.y and 'ycoordinates' in f.keys()) or 'xcoordinates' in f.keys():
f.close()
print ("%s is already set up" % data_file)
return
f = h5py.File(data_file, 'a')
Right above the error message the print statement also returns its message to stdout, but that would mean that the file was closed and therefore there shouldn't be an open file somewhere (which I thought was initially the error).
What else could be causing this problem? Thanks.
Related
I am having the following code:
%% Methods
function obj = loadDataGroundTruth(obj)
dataFile = [obj.Configuration.dir.datafiles,'.csv'] ;
% Open the data file
fid = fopen(dataFile,'r+'); %# open csv file for reading
% Scan data file until get to the segments part
bIdFound = false ;
while ((~feof(fid)) & (~bIdFound))
line = fgets(fid); %# read line by line
stringId = sscanf(line,'%s'); %# sscanf can read only numeric data :(
% Stop when we reach the trajectories section
if strcmp(stringId, 'Segments')
bIdFound = true ;
end
end
% Exit if there is not trajectories section in the file
if (~bIdFound)
% Close file descriptor
fclose(fid);
error('This data file does not contain motion information') ;
end
which is supposed to lead the .csv files and do some work with them. However, I get the error specified in the title. Full trace can be seen below:
Error using feof
Invalid file identifier. Use fopen to generate a valid file identifier.
Error in vicon.DataLoaderVICON/loadDataGroundTruth (line 99)
while ((~feof(fid)) & (~bIdFound))
Error in vicon.DataLoaderVICON (line 82)
obj.loadDataGroundTruth() ;
Error in vicon.DataLoaderVICONEdges (line 39)
obj = obj#vicon.DataLoaderVICON(varargin{:})
Error in sequence.SequenceVICON (line 51)
obj.DataLoader = vicon.DataLoaderVICONEdges(directory,...
Error in Lshape0001 (line 21)
seq = sequence.SequenceVICON(SEQUENCE_NAME,...
The problem I suspect though is in this line:
while ((~feof(fid)) & (~bIdFound))
Before anyone tells me to do so: I've already launched Matlab 2017b with sudo rights (Ubuntu 16.04) and I've added the entire folder to the path (with its subfolders).
Thanks in advance.
Okay, figured out, thanks to contributions of user obchardon.
I've noticed that the path had somehow ./ included in it as well, which shouldn't have been the case. The file I was trying to run probably was written in a Windows machine, and thus had different symbols/notation in the path. Once I printed the path it was trying to load the file from, I've noticed that it should not have ./. I removed that from the path and it worked.
I am really a new person in MATLAB and I need use it to finish my homework.
First, I try to open a txt file to get data.
So, I do like this:
folder='C:\Users\yshi20\Desktop\COSC6335\proj_1';
file='transactionDB.txt';
myData=fullfile(folder,file);
[Datafile, message] = fopen('transactionDB.txt', 'r');
But the datafile value always show -1 which means it failed to open.
So, I use this to check why I cannot open it:
if Datafile < 0
disp(message);
c = [];
else
Data = fread(Datafile, 5, 'uint8=>char')'
end
But the result says: No such file or directory.
But I checked many times, and I am sure the file name is correct and the location folder is correct, so, how to solve the problem?
You're using the wrong variable. You need to use myData in fopen.
[Datafile, message] = fopen(myData, 'r');
myData stores the complete path to your file whereas in your original code, you're using relative referencing which means that it's going to look for the file in the current working directory. A -1 code means that it can't find the file... and rightfully so given your error. It can't find the file in the current working directory. As such, make sure you change your fopen statement so that the correct path to your file is specified.
I am writing a script that can execute a batch file, which needs to open a file in the same folder first. My current code is:
from subprocess import Popen
p = Popen("Mad8dl.bat <RUNTHISTO.txt>", cwd=r"C:\...\test")
stdout, stderr = p.communicate()
where the ... is just the path to the folder. However, everytime I run it I get the syntax error:
The syntax of the command is incorrect
Any help regarding the syntax would be greatly appreciated.
First, you should probably remove the < and > angle brackets from your code; just pass the filename, without any brackets, to your batch file. (Unless your filename really does contain < and > characters, in which case I really want to know how you managed it since those characters are forbidden in filenames in Windows).
Second, your code should look like:
from subprocess import Popen, PIPE
p = Popen(["Mad8dl.bat", "RUNTHISTOO.txt"], cwd=r"C:\...\test", stdout=PIPE, stderr=PIPE)
stdout, stderr = p.communicate()
Note the list containing the components of the call, rather than a single string. Also note that you need to specify stdout=PIPE and stderr=PIPE in your Popen() call if you want to use communicate() later on.
I'm trying to solve the bilateral problem on Spotify's Tech Puzzles. http://www.spotify.com/us/jobs/tech/bilateral-projects/ I have something that is working on my computer that reads input from a file input.txt, and it outputs to ouput.txt. My problem is that I cannot figure out how to make my code work when I submit it where it must read from stdin. I have looked at several other posts and I don't see anything that makes sense to me. I see some people just use raw_input - but this produces a user prompt?? Not sure what to do. Here is the protion of my code that is suposed to read the input, and write the output. Any suggestions on how this might need changed? Also how would I test the code once it is changed to read from stdin? How can I put test data in stdin? The error i get back from spotify says Run Time Error - NameError.
import sys
# Read input
Input = []
for line in sys.stdin.readlines():
if len(line) <9:
teamCount = int(line)
if len(line) > 8:
subList = []
a = line[0:4]
b = line[5:9]
subList.append(a)
subList.append(b)
Input.append(subList)
##### algorithm here
#write output
print listLength
for empWin in win:
print empWin
You are actually doing ok.
for line in sys.stdin.readlines():
will read lines from stdin. It can however be shortened to:
for line in sys.stdin:
I don't use Windows, but to test your solution from a command line, you should run it like this:
python bilateral.py < input.txt > output.txt
If I run your code above like that, I see the error message
Traceback (most recent call last):
File "bilateral.py", line 20, in <module>
print listLength
NameError: name 'listLength' is not defined
which by accident (because I guess you didn't send in that) was the error the Spotify puzzle checker discovered. You have probably just misspelled a variable somewhere.
I am using Matlab to create a new file by calling
fid = fopen(filename,'w')
since filename doesn't exist, it should create a new file and give me a valid file descriptor. Instead it returns -1. If I run the code again however, I get fid = 3.
This is being run on ubuntu but it apparently works fine on windows and I can't figure out why.
-Mike
not sure if this helps, but note that if the folder doesn't exist, fopen with 'w' can't create the file and so returns -1.
You should check out the two-output-argument form of fopen in the doc here. This allows you to do stuff like
[fh, failmessage] = fopen( fname, 'wt' );
if fh == -1
error( 'Failed to open %s: %s', fname, failmessage );
end