I am facing a setback while loading a .mat file in jupyter notebook. Here's the issue encountered:
#import mat4py
from scipy.io import loadmat
mat = loadmat('Dog_1_ictal_segment_1.mat')
Error: TypeError: Expecting miMATRIX type here, got 3225714032
The mat file is downloaded from UPenn and Mayo's competition hosted at Kaggle, https://www.kaggle.com/c/seizure-detection/data.
I don't have access to the original matlab file, and I am not sure if the same was saved under v7.3+ release. Can anyone please guide me on this?
On matlab try:
fid = fopen('Dog_1_ictal_segment_1.mat');
txt = char(fread(fid,[1,140],'*char'));
fclose(fid);
disp(txt)
I get MATLAB 5.0 MAT-file for Patient_8_ictal_segment_1.mat (same competition). When using -v7.3 the header should start with MATLAB 7.3 MAT-file. I was able to load the data to python with no error using your code.
Possibly your data is corrupt, try downloading it.
Related
Currently I am working a project that has have been using the pathlib library so I can work on my Windows desktop when I need too and on my MacBook Pro. Essentially be able to work between both operating systems. I have not have any issues at all until right now. Here is the set up:
I have a pipeline set up to automatically save a .joblib and a whole lot of .png files that will go to a directory called
output_dir = Path('../Trained_Models/Differential_gene_analysis/A Kidney Cancer Transcriptome Molecular Signature Identifies Tumors with Tumor Thrombus/Models train on TCGA data and test on Rodriguez data/Oct-XX-20XX')
For example, if I want to save a .joblib file under the name RandomForest_TumorThrombus_104.joblib,I would use the command
joblib.dump(model ,output_dir / 'RandomForest_TumorThrombus_104.joblib')
On my MacBook Pro, I have no issues when this is ran, but on Windows it gives me the following error
FileNotFoundError: [Errno 2] No such file or directory: '..\\Trained_Models\\Differential_gene_analysis\\A Kidney Cancer Transcriptome Molecular Signature Identifies Tumors with Tumor Thrombus\\Models train on TCGA data and test on Rodriguez data\\Oct-17-2022\\RandomForest_TumorThrombus_104.joblib'
I have tried to use the .resolve() method to get the absolute path but still gives me the same error. I have tried to experiment to try to see what is goin on such as using os.path.exists(). When using the os.path.exists() method I get True for the follwoing command:
os.path.exists(output_dir)
So it does indeed recognize that the directory exists. The next thing I tried was to rename the file to something like dddddd.joblib and that worked. But I find that only a few names for the file would allow me to save the files. During debug I found that the most recent Traceback occurs here:
with open(filename, 'wb') as f:```
I was wondering if anyone here had any idea what was going on here and how I can fix this issue? Please and Thank you.
The solution was to enable long paths on Windows.
I'm a beginner at OpenCV, and trying to run an open-source program.
http://asrl.utias.utoronto.ca/code/gpusurf/index.html
I currently have the Computer Vision Toolbox OpenCV Interface 20.1.0 installed and Computer Vision Toolbox 9.2.
I cannot run this simple open-source feature matching algorithm without encountering errors.
import cv2
import matplotlib.pyplot as plt
%matplotlib inline
% read images
img1 = cv2.imread('[INSERT PATH #1]');
img2 = cv2.imread('[INSERT PATH #2]');
img1 = cv2.cvtColor(img1, cv2.COLOR_BGR2GRAY);
img2 = cv2.cvtColor(img2, cv2.COLOR_BGR2GRAY);
%sift
sift = cv2.xfeatures2d.SIFT_create();
keypoints_1, descriptors_1 = sift.detectAndCompute(img1,None);
keypoints_2, descriptors_2 = sift.detectAndCompute(img2,None);
len(keypoints_1), len(keypoints_2)
The following message is returned:
Error: File: Keypoints.m Line: 1 Column: 8
The import statement 'import cv2' cannot be found or cannot be imported. Imported names must end with '.*' or be
fully qualified.
However, when I remove Line 1, I instead get the following error.
Error: File: Keypoints.m Line: 2 Column: 8
The import statement 'import matplotlib.pyplot' cannot be found or cannot be imported. Imported names must end
with '.*' or be fully qualified.
Finally, following the error message only results in a sequence of further errors from the cv2 library. Any ideas?
That's because the code you've used isn't MATLAB code, it's python code.
As per the website you've linked:
From within Matlab
The parallel implementation coded in Matlab can be run by using the surf_find_keypoints() function. The output keypoints can be sorted by strength using surf_best_n_keypoints(), and plotted using surf_plot_keypoints().
Check that you've downloaded the correct files and try again.
Furthermore, the Matlab OpenCV Interface is designed to integrate C++ OpenCV code, not python. Documentations here.
Yes, it is correct that this is Python code. I would recommend checking your dependencies/libraries. The PyCharm IDE is what I personally use since it takes care of all the libraries easily.
If you do end up trying out PyCharm click on the red icon when hovering on CV2. It’ll then give you a prompt to download the library.
Edit:
Using Python some setup can be done. Using pip:
Install opencv-python
pip install opencv-python
Install opencv-contrib-python
pip install opencv-contrib-python
Unfortunately, there is some issue with the sift feature since by default it is excluded from newer free versions of OpenCV.
sift = cv2.xfeatures2d.SIFT_create() not working even though have contrib installed
import cv2
Image_1 = cv2.imread("Image_1.png", cv2.IMREAD_COLOR)
Image_2 = cv2.imread("Image_2.jpg", cv2.IMREAD_COLOR)
Image_1 = cv2.cvtColor(Image_1, cv2.COLOR_BGR2GRAY)
Image_2 = cv2.cvtColor(Image_2, cv2.COLOR_BGR2GRAY)
sift = cv2.SIFT_create()
keypoints_1, descriptors_1 = sift.detectAndCompute(Image_1,None)
keypoints_2, descriptors_2 = sift.detectAndCompute(Image_2,None)
len(keypoints_1), len(keypoints_2)
The error I received:
"/Users/michael/Documents/PYTHON/Test Folder/venv/bin/python" "/Users/michael/Documents/PYTHON/Test Folder/Testing.py"
Traceback (most recent call last):
File "/Users/michael/Documents/PYTHON/Test Folder/Testing.py", line 9, in <module>
sift = cv2.SIFT_create()
AttributeError: module 'cv2.cv2' has no attribute 'SIFT_create'
Process finished with exit code 1
I have generated a box file from a png image then I followed this tutorial:
https://pretius.com/how-to-prepare-training-files-for-tesseract-ocr-and-improve-characters-recognition/ to generate custom traineddata file.
I encountered an error when I tried to use the generated traineddata alongside with Pytesseract.
and i got this kind of error:
raise TesseractError(proc.returncode, get_errors(error_string))
pytesseract.pytesseract.TesseractError: (-4, "read_params_file:
Can't open txt read_params_file: Can't open txt read_params_file: Can't open txt read_params_file: Can't open txt Error: LSTM requested, but not present!! Loading tesseract. mgr->GetComponent(TESSDATA_NORMPROTO, &fp)
:Error:Assert failed:in file adaptmatch.cpp, line 552")
I'm using Tesseract version 5.0
This is my config options
traineddata = f'+eng+lav+lav2'
config = f'-l {traineddata} --oem 1 --psm 3 {tessdata_dir}'
I followed the same tutorial and encountered the exact same error. At my first tries the ***.traineddata didn't generated well, and I findout that one file was missing (normproto). So I just cleaned all the generated files (except the corrected .box files) and rerun the train process, and everything worked fine on the second attempt.
I was making a math class note with some unicode characters (Simplified Chinese, in my case) in it. And when I was trying to convert it into PDF file, it popped out 500 error. The error message reads:
...
*************************************************
("E:\Program Files (x86)\MiKTeX 2.9\tex\latex\fontspec\fontspec.sty"
("E:\Program Files (x86)\MiKTeX 2.9\tex\latex\fontspec\fontspec-xetex.sty"
("E:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\fontenc.sty"
("E:\Program Files (x86)\MiKTeX 2.9\tex\latex\base\tuenc.def"))
("E:\Program Files (x86)\MiKTeX 2.9\tex\latex\fontspec\fontspec.cfg")
! Undefined control sequence.
<argument> \LaTeX3 error:
Erroneous variable \c__fontspec_shape_n_n_tl used!
l.3806 \emfontdeclare{ \emshape, \eminnershape }
?
! Emergency stop.
<argument> \LaTeX3 error:
Erroneous variable \c__fontspec_shape_n_n_tl used!
l.3806 \emfontdeclare{ \emshape, \eminnershape }
No pages of output.
Transcript written on notebook.log.
I guess the fontspec part went wrong, but I don't know how to solve it.
For your information, here is what I've done before I got the 500 error.
1.I've installed the pandoc, and I already have Miktex before;
2.I've changed the file
...\nbconvert\templates\latex\article.tplx
rewritten the article class to be ctexart;
3.I've changed the file
...\nbconvert\templates\latex\exporters\pdf.py
rewritten the latex command to be
latex_command = List([u"xelatex", u"{filename}"], config=True,
help="Shell command used to compile latex."
)
4.I've also tried this:"https://github.com/ipython/ipython/issues/7150", which tends to convert the ipynb file into latex file first, then into PDF. And this didn't work for me either. The main reason is that the config file can't be found by jupyter nbconvert command.
For your information, my OS is Win7 Ultimate x64, with Chrome for Anaconda3 jupyter notebook.
Thanks in advance for anyone who takes time to read my post. Any help would be appreciated.
I am trying to create .fits files using the matlab.io.fits functions, following the example given here: matlab.io.fits.createFile.
However, this gives me the following error:
>> import matlab.io.*
>> fptr = fits.createFile('myfile.fits');
??? Undefined variable "fits" or class "fits.createFile".
Importing the fits class directly also gives an error:
>> import matlab.io.fits
??? Import argument 'matlab.io.fits' cannot be found or cannot be imported
I get the same result in Matlab2009 and 2015.
What am I doing wrong? Do I need to install a specific class? I am new to Matlab, so it might be a very easy mistake, but some of my more Matlab proficient colleagues has not been able to solve the problem.
This error indicate that the function cannot be found. This is usually caused by the MATLAB path being corrupted. You can restore it with:
>> restoredefaultpath
>> rehash toolboxcache
You can figure out if the file is found by executing:
>> which -all matlab.io.fits.createFile
The file should be in <matlabroot>/toolbox/matlab/imagesci/+matlab/+io/+fits/createFile.m. If it is not there, you probably need to reinstall MATLAB.