i am trying to import a .tif image into matlab with the following code
>> aa = imread('house.tif');
i get the error
Error using rtifc
TIFF library error: '_TIFFVSetField: C:\Users\user\Documents\MATLAB\house.tif: Null count
for "Tag 34022" (type 1, writecount -3, passcount 1).'.
Error in readtif (line 49)
[X, map, details] = rtifc(args);
Error in imread (line 434)
[X, map] = feval(fmt_s.read, filename, extraArgs{:});
as i am using matlab for the first time in my life i really have no idea what this error means. Please help is required in this matter.
MATLAB R2012b has a bug and it cannot read TIFF files properly. More information can be found here: http://www.mathworks.com/matlabcentral/newsreader/view_thread/326232
Probably Matlab does not support the specific type of tif. In Matlab's defence, tif is not an easy file-format to read. It supports plenty of compression schemes, multiple pages and who knows what. I'd convert the tif to png and go with that.
Update: A quick Google search revealed that "rtifc" is a Matlab mex-wrapper around libtiff. Your error appears to come from libtiff. If the latter can't read it, your tif will probably be problematic for a lot of other applications too.
Another thing you could try is use the implementation tiffread from François Nedelec's group at EMBL. http://www.embl.de/ExternalInfo/nedelec/misc/matlab/tiffread29.m. It's heavily used by biology folks all over the world. I've been using it for many years.
Related
The Matlab app imageLabeler is supposed to support the following format:
imageLabeler(imgStore)
I have an imgStore, defined as follows:
imds = imageDatastore(cellArrayOfImageFilenames);
imgStore = transform(imds, #(x)demosaic(x,'rggb'));
I have to do this, because my images are stored as bayer encoded images, and this is the only way I've figured out to get the imgStore to return these images as 3 channel RGB images. However, when I try and initalize imageLabeler, I get this error:
>> imageLabeler(imgStore)
Error using imageLabelerInternal
Expected input name to be one of these types:
char
Instead its type was matlab.io.datastore.TransformedDatastore.
Error in vision.internal.imageLabeler.imageLabelerInternal
Error in imageLabeler (line 58)
vision.internal.imageLabeler.imageLabelerInternal(varargin{:});
TLDR:
How do I get imageLabeler to handle my bayer encoded images?
The way to fix this, is with the imageDatastore 'ReadFcn' parameter. The documentation for imageDatastore explicity tells you to NOT do this, as it slows down Neural Network stuff. Here's the Matlab doc text:
Using ReadFcn to transform or pre-process 2-D images is not
recommended. For file formats recognized by imformats, specifying
ReadFcn slows down the performance of imageDatastore. For more
efficient ways to transform and pre-process images, see Preprocess
Images for Deep Learning (Deep Learning Toolbox).
So, all that said, here's the workaround:
imgStore = imageDatastore(cellArrayOfImageFilenames ...
, 'ReadFcn', #(x)demosaic(imread(x),'rggb')));
I am working with few Dicom files and when i try to use dicomread('filename.dcm') in MATLAB it gives the following error:
Error using dicomread>processOffsetTable (line 943)
The compressed pixel data is missing item delimiters.
Error in dicomread>processEncapsulatedPixels (line 858)
[offsetTable, offset] = processOffsetTable(metadata);
Error in dicomread>newDicomread (line 232)
X = processEncapsulatedPixels(metadata, frames);
Error in dicomread (line 86)
[X, map, alpha, overlays] = newDicomread(msgname, frames, useVRHeuristic);
I can view this same file in dicom viewing Softwares like onis, di com viewer, Sante Dicom etc.., but when i use dicomread I cannot see see them and get this error
I have so many images of this same format and cannot start from the beginning again, Is there any way I can use this file and view it.
Refer this online help.
It is common in DICOM world that not all data sets fully comply with DICOM. Most applications (you mentioned in your question) handle the non-compliant part with assumptions and workarounds based on experience and imagination.
Try setting TF to false to read these files.
Also note the list of supported transfer syntax:
Little-endian, implicit VR, uncompressed
Little-endian, explicit VR, uncompressed
Big-endian, explicit VR, uncompressed
JPEG (lossy or lossless)
JPEG2000 (lossy or lossless)
Run-length Encoding (RLE)
GE implicit VR, LE with uncompressed BE pixels (1.2.840.113619.5.2)
Check your input image is compressed with one of the above.
I want to use fig2texPS to export plots from MATLAB to LaTeX. I copied the the script to D:\Eigene Dokumente\MATLAB\fig2TexPS and added this folder as a path in MATLAB. Unfortunately, I receive the following error:
>> fig2texPS()
Undefined function 'find' for input arguments of type 'matlab.graphics.chart.primitive.Line'.
Error in fig2texPS (line 526)
lsh = double(find(handle(lshandles),'-class','graph2d.lineseries')); % find plots
PS: I use a version of the script which was updated in order to work with pdtlatex (http://pastebin.com/xK6KxxBT) that I found in the MATLAB Central File Exchange. The same error also occurs when I use the original script.
This might not be the answer you are looking for, but there is the marvelous matlab2tikz that does the job of conversion of figures quite nicely, which you could use as an alternative to fig2texPS.
I also use the function fig2texPS.m and it works very well. It might be an answer for your question to use an older version of Matlab. I am using 2013b and it works. While I have tried this function with Matlab 2015a, I was getting the same error message.
I hope my answer helps you with your problems.
I am new to Matlab and trying to save my current figure to file. So, I have followed the official documentation at http://www.mathworks.co.uk/help/matlab/ref/savefig.html#inputarg_h and entered the following into Matlab:
figure;
surf(peaks);
savefig('PeaksFile.fig');
close(gcf);
However, I get the following error:
Undefined function 'savefig' for input arguments of type 'char'.
If I type in:
help savefig
I get the following error:
savefig not found.
Any ideas on what's going on? I would have thought that savefig comes with all releases of Matlab rather than requiring any add-ons. The version of my Matlab is 2013a.
It looks as though savefig is not implemented in Matlab version earlier than 2013b (from some experimentation and a comment at the end of http://www.mathworks.com/matlabcentral/fileexchange/10889-savefig). Instead, use saveas(h,'filename.ext'), which is documented here http://www.mathworks.co.uk/help/matlab/ref/saveas.html and is certainly included in 2012a.
You're using R2013a, while savefig was released in R2013b. I can't test if the functionality is identical as I don't have R2013b (or newer) on this computer, but you might try the savefig-function on the File Exchange, or other alternatives available in the R2013a-release.
The two answers are great. Another option which I believe has been around for many, many years is to use the print command:
print -f1 -djpeg bob.jpg
The -f1 is the figure number and obviously bob.jpg is the filename to which you want to write. I have code going back to 2007 using that but I am sure it goes back earlier than that. So it should work with pretty much any version you are using.
For that matter, using print, you can write PS, EPS, TIFF, PNG as well as JPG.
Im trying to perform centerline extraction for cardiac CT images, and I am stuck. I need an example code that uses the "fast marching method". I got this code from mathworks.
I1=im2double(imread('se036.png'));
SpeedImage=I1*1000+0.001;
SourcePoint=[800;803];
DistanceMap= msfm(SpeedImage, SourcePoint);
figure
imshow(DistanceMap,[0 3400]) StartPoint=[9;14];
ShortestLine=shortestpath(DistanceMap,StartPoint,SourcePoint);
hold on
plot(ShortestLine(:,2),ShortestLine(:,1),'r')
But I get error message Undefined function 'msfm' for input arguments of type 'double'.
It appears you are trying to use the Matlab File Exchange submission Accurate Fast Marching but you haven't properly installed the code. The function file you downloaded, msfm.m, needs to be in a folder on your path or in the current working directory.