I have a folder named:
'LIDC-IDRI'
inside this folder I have some other folders named:
'LIDC-IDRI-0001','LIDC-IDRI-0002','LIDC-IDRI-0003', ...
each of these subfolders contains a number of images.
What I want to do is to iterate through all images inside all subfolders and display them using 'imshow' function, can anyone help me do that?
Any help would be appreciated.
#honar.cs, based on your problem statement, I have tried to solve your problem.
Here I want to display all the png and jpg images present inside LIDC-IDRI-0001, LIDC-IDRI-0002, LIDC-IDRI-0003, LIDC-IDRI-0004 directories.
File structure »
H:\RISHIKESHAGRAWANI\PROJECTS\SOF\DISPLAYIMAGES
└───LIDC-IDRI
│ show_images.md
│ show_images.py
│ show_images_temp.py
│
├───LIDC-IDRI-0001
│ download.jpg
│ Hacker.jpg
│
├───LIDC-IDRI-0002
│ images.jpg
│
├───LIDC-IDRI-0003
│ internet.jpg
│ Internet.png
│
└───LIDC-IDRI-0004
RishikeshAgrawani-Hygull-Python.jpg
wallpaper-strange-funny-weird-crazy-absurd-awesome-592.jpg
waterfalls.jpg
Requirements »
numpy - pip install numpy
matplotlib - pip install matplotlib
Pillow - pip install Pillow
» Python code (Python 3.6)
show_images.py
import os
import json
import glob
import numpy as np
import matplotlib.image as mpimg
import matplotlib.pyplot as plt
image_formats = ["png", "jpg"]; # Let suppose we want to display png & jpg images (specify more if you want)
def show_images(image_file_name):
print("Displaying ", image_file_name)
img=mpimg.imread(image_file_name)
imgplot = plt.imshow(img)
plt.show()
def get_image_paths(current_dir):
files = os.listdir(current_dir);
paths = []; # To store relative paths of all png and jpg images
for file in files:
file = file.strip()
if os.path.isdir(file) and 'LIDC-IDRI-' in file:
for image_format in image_formats:
image_paths = glob.glob(os.path.join(".", file, "*." + image_format))
if image_paths:
paths.extend(image_paths);
return paths
if __name__ == "__main__":
image_paths = get_image_paths(".");
print(json.dumps(image_paths, indent=4))
# Display all images inside image_paths
for image_path in image_paths:
show_images(image_path);
print('\n')
How to run?
Open terminal and navigate inside LIDC-IDRI directory using cd command and run the below command.
python show_images.py
Output on console »
Images will be opened one by one (once you close 1st image, 2nd image will be displayed and so on).
[
".\\LIDC-IDRI-0001\\download.jpg",
".\\LIDC-IDRI-0001\\Hacker.jpg",
".\\LIDC-IDRI-0002\\images.jpg",
".\\LIDC-IDRI-0003\\Internet.png",
".\\LIDC-IDRI-0003\\internet.jpg",
".\\LIDC-IDRI-0004\\RishikeshAgrawani-Hygull-Python.jpg",
".\\LIDC-IDRI-0004\\wallpaper-strange-funny-weird-crazy-absurd-awesome-592.jpg",
".\\LIDC-IDRI-0004\\waterfalls.jpg"
]
Related
I have a structure like below:
src/py_meta/
handlers/
internals/
__init__.py
main.py
tests/
__init__.py
test_main.py
pyproject.toml
test_main.py
"""Test the main function
"""
import requests
from src.py_meta import main as py_meta
from src.py_meta.internals.metadata import MetaData
image = requests.get(
"https://file-examples.com/storage/fea8fc38fd63bc5c39cf20b/2017/10/file_example_JPG_500kB.jpg",
timeout=6,
)
with open("demo_file.jpg", "wb") as f:
f.write(image.content)
def test_read():
"""Tests for a MetaData object returned."""
assert isinstance(py_meta.read("demo_file.jpg"), MetaData)
I then get a ModuleNotFound error on the import statements
from src.py_meta import main as py_meta
from src.py_meta.internals.metadata import MetaData
# I have tried without the src.
And relevent contents of pyproject.toml
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
------------------------------------
[tool.pytest.ini_options]
pythonpath = "src"
addopts = ["--import-mode=importlib"]
[tool.pylint.ini_options]
pythonpath = "src"
Full code is on github: https://github.com/pyscripter99/python-metadata
I have tried pytest documentation
also followed the python guide. I expect the imports to work without any issues from pylint or pytest, along with future usage as a python package
I am currently doing an assignment on deep learning by downloading the assignment files from github.
import numpy as np
import matplotlib.pyplot as plt
import h5py
import scipy
from PIL import Image
from scipy import ndimage
from lr_utils import load_dataset
%matplotlib inline
You are given a dataset ("data.h5") containing: - a training set of m_train images labeled as cat (y=1) or non-cat (y=0) - a test set of m_test images labeled as cat or non-cat - each image is of shape (num_px, num_px, 3) where 3 is for the 3 channels (RGB). Thus, each image is square (height = num_px) and (width = num_px).
# Loading the data (cat/non-cat)
train_set_x_orig, train_set_y, test_set_x_orig, test_set_y, classes = load_dataset()
I ran the setup.sh file too but the error doesn't seem to go away.
lr_utils.py file:
import numpy as np
import h5py
def load_dataset():
train_dataset = h5py.File('datasets/train_catvnoncat.h5', "r")
train_set_x_orig = np.array(train_dataset["train_set_x"][:]) # your train set features
train_set_y_orig = np.array(train_dataset["train_set_y"][:]) # your train set labels
test_dataset = h5py.File('datasets/test_catvnoncat.h5', "r")
test_set_x_orig = np.array(test_dataset["test_set_x"][:]) # your test set features
test_set_y_orig = np.array(test_dataset["test_set_y"][:]) # your test set labels
classes = np.array(test_dataset["list_classes"][:]) # the list of classes
train_set_y_orig = train_set_y_orig.reshape((1, train_set_y_orig.shape[0]))
test_set_y_orig = test_set_y_orig.reshape((1, test_set_y_orig.shape[0]))
return train_set_x_orig, train_set_y_orig, test_set_x_orig, test_set_y_orig, classes
Kindly help!
I solved the issue by downloading uncorrupted .h5 files and putting them in the folder datasets/ in the same directory.
The files you downloaded are corrupted. You can visit https://github.com/abdur75648/Deep-Learning-Specialization-Coursera to download the uncorrupted files.
you can download uncorrupted files from here :
https://www.kaggle.com/datasets/muhammeddalkran/catvnoncat
and replace it in the directory of the corrupted files
I am trying to save a variable with data-type of "IPython.core.display.SVG" as a PNG file in Jupyter Notebook environment.
First I tried:
with open('./file.png','wb+') as outfile:
outfile.write(my_svg.data)
And I got the error:
TypeError: a bytes-like object is required, not 'str'
Next, I tried:
with open('./file.png','wb+') as outfile:
outfile.write(my_svg.data.encode('utf-8'))
But, I cannot open "file.png". The operating system gives error:
The file “file.png” could not be opened. It may be damaged or use a file format that Preview doesn’t recognize.
I can save "my_svg" with "svg" extension as below:
with open('./file.svg','wb+') as outfile:
outfile.write(my_svg.data.encode('utf-8'))
But, when I want to convert "file.svg" into "file.png" by:
import cairosvg
cairosvg.svg2png(url="./file.svg", write_to="./file.png")
I get the error:
ValueError: unknown locale: UTF-8
This is how I get "IPython.core.display.SVG" data-type in Jupyter Notebook:
from rdkit import Chem
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
smile_1 = 'C(C(N)=O)c(c)c'
smile_2 = 'o(cn)c(c)c'
m1 = Chem.MolFromSmiles(smile_1,sanitize=False)
Chem.SanitizeMol(m1, sanitizeOps=(Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_KEKULIZE^Chem.SanitizeFlags.SANITIZE_SETAROMATICITY))
m2 = Chem.MolFromSmiles(smile_2,sanitize=False)
Chem.SanitizeMol(m2, sanitizeOps=(Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_KEKULIZE^Chem.SanitizeFlags.SANITIZE_SETAROMATICITY))
mols = [m1, m2]
legends = ["smile_1", "smile_2"]
molsPerRow=2
subImgSize=(200, 200)
nRows = len(mols) // molsPerRow
if len(mols) % molsPerRow:
nRows += 1
fullSize = (molsPerRow * subImgSize[0], nRows * subImgSize[1])
d2d = rdMolDraw2D.MolDraw2DSVG(fullSize[0], fullSize[1], subImgSize[0], subImgSize[1])
d2d.drawOptions().prepareMolsBeforeDrawing=False
d2d.DrawMolecules(list(mols), legends=legends)
d2d.FinishDrawing()
SVG(d2d.GetDrawingText())
Environment:
macOS 11.2.3
python 3.6
RDKit version 2020.09.1
Any help is greatly appreciated.
Instead of creating an SVG with rdkit and trying to convert it to a PNG, why not just create a PNG directly?
from rdkit.Chem import Draw
from rdkit import Chem
# create rdkit mol
smile = 'CCCC'
mol = Chem.MolFromSmiles(smile)
# create png
d2d = Draw.MolDraw2DCairo(200, 200)
d2d.DrawMolecule(mol)
d2d.FinishDrawing()
png_data = d2d.GetDrawingText()
# save png to file
with open('mol_image.png', 'wb') as png_file:
png_file.write(png_data)
I am not sure why MolDraw2DCairo is not working for you but using the package you mention (cairosvg) you could extend your code sample quite easily:
# extra imports
import cairosvg
import tempfile
# replace molecule drawing part
d2d = rdMolDraw2D.MolDraw2DSVG(fullSize[0], fullSize[1], subImgSize[0], subImgSize[1])
d2d.drawOptions().prepareMolsBeforeDrawing=False
d2d.DrawMolecules(list(mols), legends=legends)
d2d.FinishDrawing()
svg_text = d2d.GetDrawingText()
# save to png file
with tempfile.NamedTemporaryFile(delete=True) as tmp:
tmp.write(svg_text.encode())
tmp.flush()
cairosvg.svg2png(url=tmp.name, write_to="./mol_img.png")
I am trying to extract a geographic coordinates in UTM format from a .pdf file with python3 in Ubuntu operative system, with the follow code:
from pathlib import Path
import textract
import numpy as np
import re
import os
import pdfminer
def main(_file):
try:
text = textract.process(_file, method="pdfminer")
except textract.exceptions.ShellError as ex:
print(ex)
return
with open("%s.csv" % Path(_file).name[: -len(Path(_file).suffix)],
"w+") as _file:
# find orders and DNIs
coords = re.compile(r"\d?\.?\d+\.+\d+\,\d{2}")
results = re.findall(coords, text.decode())
if results:
_file.write("|".join(results))
if __name__ == "__main__":
_file = "/home/cristian33/python_proj/folder1/buscarco.pdf"
main(_file)
when I run it give me the follow error:
The command pdf2txt.py /home/cristian33/python_proj/folder1/buscarco.pdf failed because the executable
pdf2txt.py is not installed on your system. Please make
sure the appropriate dependencies are installed before using
textract:
http://textract.readthedocs.org/en/latest/installation.html
somebody knows why is that error?
thanks
How can I read all images from datasets and store it in another location using opencv.
You can use glob to read the files in a folder.
import glob
import cv2
for file in glob.glob('source/*.png'):
img = cv2.imread(file)
filename = 'destination/'+file.split('source\\')[1]
cv2.imwrite(filename, img)
Split function of python can be used to obtain the image-name which is then written to the destination folder.
NOTE- If the folders are not in the current working directory please specify the absolute path. For more on absolute and relative paths refer here.
import os
import cv2
SOURCE_FOLDER = "a"
DESTINATION_FOLDER = "b"
for image_file_name in os.listdir(SOURCE_FOLDER):
# get full path to image file
image_path = os.path.join(SOURCE_FOLDER, image_file_name)
# read image
img = cv2.imread(image_path)
# store image in another folder
image_write_path = os.path.join(DESTINATION_FOLDER, image_file_name)
cv2.imwrite(image_write_path, img)