The error I'm getting is not very descriptive, it will tell me
error: gradientDescent: product: nonconformant arguments (op1 is 1x97, op2 is 97x2)
I know the file is gradientDescent.m, but is there a way to get the line number of the error?
lasterror() contains a stack trace.
In my application, I'm getting the message "error: plot: properties must appear followed by a value", with no line number.
After I get the prompt back, I can example the stack trace like this:
octave:23> lasterror().stack
ans =
6x1 struct array containing the fields:
file
name
line
column
scope
context
octave:24> lasterror().stack.file
ans = /usr/share/octave/4.2.2/m/plot/draw/private/__plt__.m
ans = /usr/share/octave/4.2.2/m/plot/draw/plot.m
ans = /home/baccala/WAM/waveletauditory/SOM-Toolbox/som/vis_trajgui.m
ans = /home/baccala/WAM/waveletauditory/SOM-Toolbox/som/vis_trajgui.m
ans = /home/baccala/WAM/waveletauditory/SOM-Toolbox/som/vis_trajgui.m
ans = /home/baccala/WAM/waveletauditory/SOM-Toolbox/som/vis_trajgui.m
octave:25> lasterror().stack.line
ans = 96
ans = 223
ans = 616
ans = 567
ans = 548
ans = 253
octave:26>
Which tells me that the troublesome call to plot in on line 616 of vis_trajgui.m.
Related
It is possible to write a function directly in the octave shell?
A=147;
B=26.3;
C=5.4;
d=0.35*A;
function S=function_test(A,B,C,d)
S=2*A*B*C*d;
end
I tried this but if I wanted to know the value of "S", this error appears:
error: 'S' undefined near line 1, column 1
Yes it is possible. You does it correctly. But you missed indicating how you call the function. For me, no error occurs:
≫ function_test(1,2,3,4)
ans = 48
≫ res = function_test(1,2,3,4)
res = 48
≫ S = function_test(-1,3,5,7)
S = -210
≫
I want to run a MATLAB script M-file to reconstruct a point cloud in Octave. Therefore I had to rewrite some parts of the code to make it compatible with Octave. Actually the M-file works fine in Octave (I don't get any errors) and also the plotted point cloud looks good at first glance, but it seems that the variables are only half the size of the original MATLAB variables. In the attached screenshots you can see what I mean.
Octave:
MATLAB:
You can see that the dimension of e.g. M in Octave is 1311114x3 but in MATLAB it is 2622227x3. The actual number of rows in my raw file is 2622227 as well.
Here you can see an extract of the raw file (original data) that I use.
Rotation angle Measured distance
-0,090 26,295
-0,342 26,294
-0,594 26,294
-0,846 26,295
-1,098 26,294
-1,368 26,296
-1,620 26,296
-1,872 26,296
In MATLAB I created my output variable as follows.
data = table;
data.Rotationangle = cell2mat(raw(:, 1));
data.Measureddistance = cell2mat(raw(:, 2));
As there is no table function in Octave I wrote
data = cellfun(#(x)str2num(x), strrep(raw, ',', '.'))
instead.
Octave also has no struct2array function, so I had to replace it as well.
In MATLAB I wrote.
data = table2array(data);
In Octave this was a bit more difficult to do. I had to create a struct2array function, which I did by means of this bug report.
%% Create a struct2array function
function retval = struct2array (input_struct)
%input check
if (~isstruct (input_struct) || (nargin ~= 1))
print_usage;
endif
%convert to cell array and flatten/concatenate output.
retval = [ (struct2cell (input_struct)){:}];
endfunction
clear b;
b.a = data;
data = struct2array(b);
Did I make a mistake somewhere and could someone help me to solve this problem?
edit:
Here's the part of my script where I'm using raw.
delimiter = '\t';
startRow = 5;
formatSpec = '%s%s%[^\n\r]';
fileID = fopen(filename,'r');
dataArray = textscan(fileID, formatSpec, 'Delimiter', delimiter, 'HeaderLines' ,startRow-1, 'ReturnOnError', false, 'EndOfLine', '\r\n');
fclose(fileID);
%% Convert the contents of columns containing numeric text to numbers.
% Replace non-numeric text with NaN.
raw = repmat({''},length(dataArray{1}),length(dataArray)-1);
for col=1:length(dataArray)-1
raw(1:length(dataArray{col}),col) = mat2cell(dataArray{col}, ones(length(dataArray{col}), 1));
end
numericData = NaN(size(dataArray{1},1),size(dataArray,2));
for col=[1,2]
% Converts text in the input cell array to numbers. Replaced non-numeric
% text with NaN.
rawData = dataArray{col};
for row=1:size(rawData, 1)
% Create a regular expression to detect and remove non-numeric prefixes and
% suffixes.
regexstr = '(?<prefix>.*?)(?<numbers>([-]*(\d+[\.]*)+[\,]{0,1}\d*[eEdD]{0,1}[-+]*\d*[i]{0,1})|([-]*(\d+[\.]*)*[\,]{1,1}\d+[eEdD]{0,1}[-+]*\d*[i]{0,1}))(?<suffix>.*)';
try
result = regexp(rawData(row), regexstr, 'names');
numbers = result.numbers;
% Detected commas in non-thousand locations.
invalidThousandsSeparator = false;
if numbers.contains('.')
thousandsRegExp = '^\d+?(\.\d{3})*\,{0,1}\d*$';
if isempty(regexp(numbers, thousandsRegExp, 'once'))
numbers = NaN;
invalidThousandsSeparator = true;
end
end
% Convert numeric text to numbers.
if ~invalidThousandsSeparator
numbers = strrep(numbers, '.', '');
numbers = strrep(numbers, ',', '.');
numbers = textscan(char(numbers), '%f');
numericData(row, col) = numbers{1};
raw{row, col} = numbers{1};
end
catch
raw{row, col} = rawData{row};
end
end
end
You don't see any raw in my workspaces because I clear all temporary variables before I reconstruct my point cloud.
Also my original data in row 1311114 and 1311115 look normal.
edit 2:
As suggested here is a small example table to clarify what I want and what MATLAB does with the table2array function in my case.
data =
-0.0900 26.2950
-0.3420 26.2940
-0.5940 26.2940
-0.8460 26.2950
-1.0980 26.2940
-1.3680 26.2960
-1.6200 26.2960
-1.8720 26.2960
With the struct2array function I used in Octave I get the following array.
data =
-0.090000 26.295000
-0.594000 26.294000
-1.098000 26.294000
-1.620000 26.296000
-2.124000 26.295000
-2.646000 26.293000
-3.150000 26.294000
-3.654000 26.294000
If you compare the Octave array with my original data, you can see that every second row is skipped. This seems to be the reason for 1311114 instead of 2622227 rows.
edit 3:
I tried to solve my problem with the suggestions of #Tasos Papastylianou, which unfortunately was not successful.
First I did the variant with a struct.
data = struct();
data.Rotationangle = [raw(:,1)];
data.Measureddistance = [raw(:,2)];
data = cell2mat( struct2cell (data ).' )
But this leads to the following structure in my script. (Unfortunately the result is not what I would like to have as shown in edit 2. Don't be surprised, I only used a small part of my raw file to accelerate the run of my script, so here are only 769 lines.)
[766,1] = -357,966
[767,1] = -358,506
[768,1] = -359,010
[769,1] = -359,514
[1,2] = 26,295
[2,2] = 26,294
[3,2] = 26,294
[4,2] = 26,296
Furthermore I get the following error.
error: unary operator '-' not implemented for 'cell' operands
error: called from
Cloud_reconstruction at line 137 column 11
Also the approach with the dataframe octave package didn't work. When I run the following code it leads to the error you can see below.
dataframe2array = #(df) cell2mat( struct(df).x_data );
pkg load dataframe;
data = dataframe();
data.Rotationangle = [raw(:, 1)];
data.Measureddistance = [raw(:, 2)];
dataframe2array(data)
error:
warning: Trying to overwrite colum names
warning: called from
df_matassign at line 147 column 13
subsasgn at line 172 column 14
Cloud_reconstruction at line 106 column 20
warning: Trying to overwrite colum names
warning: called from
df_matassign at line 176 column 13
subsasgn at line 172 column 14
Cloud_reconstruction at line 106 column 20
warning: Trying to overwrite colum names
warning: called from
df_matassign at line 147 column 13
subsasgn at line 172 column 14
Cloud_reconstruction at line 107 column 23
warning: Trying to overwrite colum names
warning: called from
df_matassign at line 176 column 13
subsasgn at line 172 column 14
Cloud_reconstruction at line 107 column 23
error: RHS(_,2): but RHS has size 768x1
error: called from
df_matassign at line 179 column 11
subsasgn at line 172 column 14
Cloud_reconstruction at line 107 column 23
Both error messages refer to the following part of my script where I'm doing the reconstruction of the point cloud in cylindrical coordinates.
distLaserCenter = 47; % Distance between the pipe centerline and the blind zone in mm
m = size(data,1); % Find the length of the first dimension of data
zincr = 0.4/360; % z increment in mm per deg
data(:,1) = -data(:,1);
for i = 1:m
data(i,2) = data(i,2) + distLaserCenter;
if i == 1
data(i,3) = 0;
elseif abs(data(i,1)-data(i-1)) < 100
data(i,3) = data(i-1,3) + zincr*(data(i,1)-data(i-1));
else abs(data(i,1)-data(i-1)) > 100;
data(i,3) = data(i-1,3) + zincr*(data(i,1)-(data(i-1)-360));
end
end
To give some background information for a better understanding. The script is used to reconstruct a pipe as a point cloud. The surface of the pipe was scanned from inside with a laser and the laser measured several points (distance from laser to the inner wall of the pipe) at each deg of rotation. I hope this helps to understand what I want to do with my script.
Not sure exactly what you're trying to do, but here's a toy example of how a struct could be used in an equivalent manner to a table:
matlab:
data = table;
data.A = [1;2;3;4;5];
data.B = [10;20;30;40;50];
table2array(data)
octave:
data = struct();
data.A = [1;2;3;4;5];
data.B = [10;20;30;40;50];
cell2mat( struct2cell (data ).' )
Note the transposition operation (.') before passing the result to cell2mat, since in a table, the 'fieldnames' are arranged horizontally in columns, whereas the struct2cell ends up arranging what used to be the 'fieldnames' as rows.
You might also be interested in the dataframe octave package, which performs similar functions to matlab's table (or in fact, R's dataframe object): https://octave.sourceforge.io/dataframe/ (you can install this by typing pkg install -forge dataframe in your console)
Unfortunately, the way to display the data as an array is still not ideal (see: https://stackoverflow.com/a/55417141/4183191), but you can easily convert that into a tiny function, e.g.
dataframe2array = #(df) cell2mat( struct(df).x_data );
Your code can then become:
pkg load dataframe;
data = dataframe();
data.A = [1;2;3;4;5];
data.B = [10;20;30;40;50];
dataframe2array(data)
I am trying to make an animation from a graph and save the result as GIF or video.
The graph and the animation work well in MATLAB but I cannot save it as GIF.
imread gives this error:
Magick: "gswin32c" "-q" "-dBATCH" "-dSAFER" "-dMaxBitmap=50000000" "-
dNOPAUSE" "-sDEVICE=ppmraw" "-dTextAlphaBits=4" "-dG
raphicsAlphaBits=4" "-r72x72" "-dFirstPage=1" "-dLastPage=1" "-
sOutputFile=C:\Users ...
I tried the solution from here, but that error pops up.
This is my code:
clear all;
clc;
for m = 1:10
n = m.*100;
x = linspace(0,1500,1500);
x2 = linspace(n,1000+n,500);
y2 = [((20e-6.*n + 0.008).*(sin(pi/1000.*(x2-n))).^2) ];
y1 = zeros(1,n);
y3 = zeros(1,1000-n);
y7 = [y1 y2 y3];
y8 = y7 + 0;
y1 = (sin(pi/150*x)).^2;
y3 = exp((x/400)-5);
y5 = (y1.*y3)+y8;
plot( x,y5);
drawnow;
#pause(0.01);
endfor
im = imread ("animation.pdf", "Index", "all");
imwrite (im, "animation.gif", "DelayTime", .5);
EDIT:
This is the complete error. Directory name redacted for privacy.
Magick: "gswin32c" "-q" "-dBATCH" "-dSAFER" "-dMaxBitmap=50000000" "-dNOPAUSE" "-sDEVICE=ppmraw"
"-dTextAlphaBits=4" "-dGraphicsAlphaBits=4" "-r72x72" "-dFirstPage=1" "-dLastPage=1" "-sOutputFil
e=C:\Users\XXXXXXXXXXXXXXXXXXXXXXXXXX" "--" "C:\Users\XXXXXXXXXXXXXXXXXXXXXXXXXX" "-c
" "quit" [No such file or directory].
error: Magick++ exception: Magick: Postscript delegate failed (F:\XXXXXXXXXXXXXXXXXXXXXXXXXX\animation.pdf) reported by coders/pdf.c:434 (ReadPDFImage)
error: called from
__imread__ at line 78 column 10
imageIO at line 118 column 26
imread at line 106 column 30
test_animation2 at line 6 column 4
I had the same problem.
For me, the solution was to install or reinstall the GhostScript program.
This was the error message I received:
Magick: "gswin32c" "-q" "-dBATCH" "-dSAFER" "-dMaxBitmap=50000000" "-dNOPAUSE" "-sDEVICE=ppmraw"
"-dTextAlphaBits=4" "-dGraphicsAlphaBits=4" "-r72x72" "-dFirstPage=1" "-dLastPage=1" "-sOutputFil
e=C:\Users\xxxxxx\AppData\Local\Temp\gmncleNd" "--" "C:\Users\xxxxxx\AppData\Local\Temp\gmEh1Xv4" "
-c" "quit" [No such file or directory].
error: Magick++ exception: Magick: Postscript delegate failed (C:\Users\xxxxxx\Desktop\TexML2.0\IN
entrada\in.pdf) reported by coders/pdf.c:434 (ReadPDFImage)
error: called from
_imread_ at line 80 column 10
imageIO at line 118 column 28
imread at line 106 column 33
currently I'm using nonlin_curvefit function from GNU Octave's 'optim' package to fit data with . But this time I did also need the uncertainty of the returned parameters to determine the quality of the fit. After reading through the documentation I tied using the function curvefit_stat.
However whenever I alwas get errors using this functiona and I can't make any sense of the error message. I'm using Octave 4.2.2 from Ubuntu 18.04's default repository.
Standalone minimal example and error messages below. Startparameters init_cvg usually produces good result, while using init_dvg usually results in poor fits:
1;
x = linspace(-2*pi, 2*pi, 600);
ydata = 3.4*sin(1.6*x) + rand(size(x))*1.3;
f = #(p, x) p(1)*sin(p(2).*x);
function y = testfun(p ,x)
y = p(1).*sin(p(2).*x);
endfunction
init_cvg = [1; 1.1];
init_dvg = [1; 1.0];
[pc, mod_valc, cvgc, outpc] = nonlin_curvefit(f, init_cvg, x, ydata);
[pd, mod_vald, cvgd, outpd] = nonlin_curvefit(f, init_dvg, x, ydata);
hold off
plot(x, yd, "b.");
hold on;
plot(x, mod_valc, "r-");
plot(x, mod_vald, "color", [0.9 0.4 0.3]);
settings = optimset("ret_covp", true);
covpc = curvefit_stat(f, pc, x, ydata, settings);
covpd = curvefit_stat(f, pd, x, ydata, settings);
puts("sqrt(diag(covpc))")
sqrt(diag(covpc))
puts("sqrt(diag(covpd))")
sqrt(diag(covpd))
The first error message occurs when I use f as a model function, the second occurs when I use testfun instead:
>> curvefit_stat_TEST
error: label of objective function must be specified
error: called from
__residmin_stat__ at line 566 column 7
curvefit_stat at line 56 column 7
curvefit_stat_TEST at line 25 column 7
>> curvefit_stat_TEST
error: 'p' undefined near line 8 column 7
error: called from
testfun at line 8 column 5
curvefit_stat_TEST at line 25 column 7
>>
Could somebody confirm this error ?
I would appreciate any help.
I found the problem.
I needed to add "abjf_type", "wls" as arguments to optimset.
When I try to run predict() on the dataset, it keeps giving me error -
Error in eval(expr, envir, enclos) : object 'LoanRange' not found
Here is the part of dataset -
LoanRange Loan.Type N WAFICO WALTV WAOrigRev WAPTValue
1 0-99999 Conventional 109 722.5216 63.55385 6068.239 0.6031879
2 0-99999 FHA 30 696.6348 80.00100 7129.650 0.5623650
3 0-99999 VA 13 698.6986 74.40525 7838.894 0.4892977
4 100000-149999 Conventional 860 731.2333 68.25817 6438.330 0.5962638
5 100000-149999 FHA 285 673.2256 82.42225 8145.068 0.5211495
6 100000-149999 VA 125 704.1686 87.71306 8911.461 0.5020074
7 150000-199999 Conventional 1291 738.7164 70.08944 8125.979 0.6045117
8 150000-199999 FHA 403 672.0891 84.65318 10112.192 0.5199632
9 150000-199999 VA 195 694.1885 90.77495 10909.393 0.5250807
10 200000-249999 Conventional 1162 740.8614 70.65027 8832.563 0.6111419
11 200000-249999 FHA 348 667.6291 85.13457 11013.856 0.5374226
12 200000-249999 VA 221 702.9796 91.76759 11753.642 0.5078298
13 250000-299999 Conventional 948 742.0405 72.22742 9903.160 0.6106858
Following is the code used for predicting count data N after determining the overdispersion-
model2=glm(N~Loan.Type+WAFICO+WALTV+WAOrigRev+WAPTValue, family=quasipoisson(link = "log"), data = DF)
summary(model2)
This is what I have done to create a sequence of count and use predict function-
countaxis <- seq (0,1500,150)
Y <- predict(model2, list(N=countaxis, type = "response")
At this step, I get the error -
Error in eval(expr, envir, enclos) : object 'LoanRange' not found
Can someone please point me where is the problem here.
Think about what exactly you are trying to predict. You are providing the predict function values of N (via countaxis), but in fact the way you set up your model, N is your response variable and the remaining variables are the predictors. That's why R is asking for LoanRange. It actually needs values for LoanRange, Loan.Type, ..., WAPTValue in order to predict N. So you need to feed predict inputs that let the model try to predict N.
For example, you could do something like this:
# create some fake data to predict N
newdata1 = data.frame(rbind(c("0-99999", "Conventional", 722.5216, 63.55385, 6068.239, 0.6031879),
c("150000-199999", "VA", 12.5216, 3.55385, 60.239, 0.0031879)))
colnames(newdata1) = c("LoanRange" ,"Loan.Type", "WAFICO" ,"WALTV" , "WAOrigRev" ,"WAPTValue")
# ensure that numeric variables are indeed numeric and not factors
newdata1$WAFICO = as.numeric(as.character(newdata1$WAFICO))
newdata1$WALTV = as.numeric(as.character(newdata1$WALTV))
newdata1$WAPTValue = as.numeric(as.character(newdata1$WAPTValue))
newdata1$WAOrigRev = as.numeric(as.character(newdata1$WAOrigRev))
# make predictions - this will output values of N
predict(model2, newdata = newdata1, type = "response")