Error using textread to read data containing "INF" or "NaN" with float data

15 views (last 30 days)
I have a file with data showing date,time, and floating point data downloaded from an instrument. Some instances of the floating point data were recorded as "INF" meaning the data record was skipped or erroneous. See the sample data below:
"2012-02-15 06:34:00",965,0,1.367,-61.03,-4.838,8.64,281.8,-1.367,-56.2,"INF",-61.03,-3.471,-57.56,296.5,352.7
"2012-02-15 06:35:00",966,0.946,1.802,-60.79,-4.656,8.66,281.8,-0.856,-56.14,1.904,-59.85,-2.854,-56.99,296.8,352.9
"2012-02-15 06:36:00",967,1.325,1.926,-60.82,-5.14,8.67,281.8,-0.602,-55.68,1.454,-59.5,-3.214,-56.29,296.8,352.5
I have tried to read the data using the following line:
[d1,counter,SR01Up,SR01Dn,IR01Up,IR01Dn,NR01TC,NR01TK,NetRs,NetRl,Albedo,UpTot,DnTot,NetTot,IR01UpCo,IR01DnCo] = textread([direct filename], '%22c %u %f %f %f %f %f %f %f %f %f %f %f %f %f %f','headerlines',4,'delimiter',',');
When I do, I get the following error;
Error using dataread
Trouble reading floating point number from file (row 966, field 11) ==> "INF",-61.03,-3.471,-57.56,2
Error in textread (line 176)
Error in CR3000dataproc2 (line 89)
= textread([direct filename], '%22c %u %f %f %f %f %f %f %f %f %f %f %f %f %f %f
Kindly help resolve this...

Answers (4)

Matt Kindig
Matt Kindig on 26 Jul 2013
Try using textscan() with the 'TreatAsEmpty' option:
output = textscan([direct filename], '%22c %u %f %f %f %f %f %f %f %f %f %f %f %f %f %f','delimiter',',', 'EmptyValue', NaN,'TreatAsEmpty', '"INF"');
d1= output{1};
counter = output{2}; %etc.
All the "INF" should now be converted to NaN.
  1 Comment
dpb on 26 Jul 2013
NB the character format "%22c" will end up returning the trailing comma as well as the two surrounding '"' marks on the date field as the actual date field is only 19 characters wide w/ leading and trailing double quotes to surround an embedded space in the string.
fmt=['"%19c" %u' repmat('%f',1,14)];
will return just the actual date/time string w/o additional post-processing to use it.
With 'collectoutput', 1 the first record is returned w/ the above fmt as
'2012-02-15 06:34:00' [965] [1x14 double]
instead of as
'"2012-02-15 06:34:00",' [965] [1x14 double]
Just a nit, but eliminates one additional step later...

Sign in to comment.

dpb on 26 Jul 2013
Edited: dpb on 26 Jul 2013
Here's a case where the "red-haired stepchild" status of textread hurts--it can't accept a custom 'TreatAsEmpty' string property. Use textscan instead.
Unfortunately, textscan has its own quirks; the most irritating of which is it can't return anything except a cell array... :(
>> l='"2012-02-15 06:34:00",965,0,1.367,-61.03,-4.838,8.64,281.8,-1.367,-56.2,"INF",-61.03,-3.471,-57.56,296.5,352.7 ';
>> fmt=['%s %u' repmat('%f',1,14)];
>> textscan(l, fmt,'delimiter',',','treatasempty',{'"INF"'},'collectoutput',1)
ans =
{1x1 cell} [965] [1x14 double]

Vincent Odongo
Vincent Odongo on 27 Jul 2013
Sorry guys, Doesn't seem to work for me...
I used your suggestions as follows...
[d1,counter,SR01Up,SR01Dn,IR01Up,IR01Dn,NR01TC,NR01TK,NetRs,NetRl,Albedo,UpTot,DnTot,NetTot,IR01UpCo,IR01DnCo] = textscan([direct filename], '%22c %u %f %f %f %f %f %f %f %f %f %f %f %f %f %f','headerlines',4,'delimiter',',','EmptyValue', NaN,'TreatAsEmpty', '"INF"');
On running the script I get the following error; Error using textscan Too many output arguments.
The same errors appears when I use; [d1,counter,SR01Up,SR01Dn,IR01Up,IR01Dn,NR01TC,NR01TK,NetRs,NetRl,Albedo,UpTot,DnTot,NetTot,IR01UpCo,IR01DnCo] = textscan([direct filename], '%22c %u %f %f %f %f %f %f %f %f %f %f %f %f %f %f','headerlines',4,'delimiter',',','treatasempty',{'"INF"'},'collectoutput',1)
  1 Comment
per isakson
per isakson on 27 Jul 2013
cac = textscan([direct filename], '%22c %u %f %f %f %f %f %f %f %f %f %f %f
%f %f %f','headerlines',4,'delimiter',',','EmptyValue', NaN,'TreatAsEmpty',
and markup your text

Sign in to comment.

dpb on 27 Jul 2013
Edited: dpb on 28 Jul 2013
[d1,counter,...,IR01DnCo] = textscan([direct filename], ...
On running the script I get the following error; Error using textscan Too many output arguments.
Well, yes, as per the doc, textscan returns ONLY a cell output.
doc textscan
As I showed earlier for the typical line
l='"2012-02-15 06:34:00",965,
-61.03,-3.471,-57.56,296.5,352.7 ';
and the format string
fmt=['"%19c" %u' repmat('%f',1,14)];
C=textscan(l, fmt,'delimiter',',','treatasempty',{'"INF"'},'collectoutput',1)
C =
'2012-02-15 06:34:00' [965] [1x14 double]
Also as noted previously there's a problem w/ an earlier respondent's format of '%22c' for the date/time string in doesn't character-match the leading/trailing '"' and picks up the delimiter comma as well as the actual data in the string is only 19 characters long--it's wrapped in " for the embedded spaces (21 char's total). The length of 22 then gets the delimiter, too.


Find more on Large Files and Big Data in Help Center and File Exchange

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!