Develop Reference

Reading CT Scan dicom file

i am trying to read CT scan Dicom file using pydicom python library but i just can't get rid of this below error even when i install gdcm and pylibjpeg
RuntimeError: The following handlers are available to decode the pixel data however they are missing required dependencies: GDCM (req. ), pylibjpeg (req. )
Here is my code
!pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg
!pip install python-gdcm
import gdcm
import pylibjpeg
import numpy as np
import pydicom
from pydicom.pixel_data_handlers.util import apply_voi_lut
import matplotlib.pyplot as plt
%matplotlib inline
def read_xray(path, voi_lut = True, fix_monochrome = True):
dicom = pydicom.read_file(path)
# VOI LUT (if available by DICOM device) is used to transform raw DICOM data to "human-friendly" view
if voi_lut:
data = apply_voi_lut(dicom.pixel_array, dicom)
else:
data = dicom.pixel_array
# depending on this value, X-ray may look inverted - fix that:
if fix_monochrome and dicom.PhotometricInterpretation == "MONOCHROME1":
data = np.amax(data) - data
data = data - np.min(data)
data = data / np.max(data)
data = (data * 255).astype(np.uint8)
return data
img = read_xray('/content/ActiveTB/2018/09/17/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157438.869027/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157440.863887/1.2.392.200036.9116.2.6.1.44063.1797735841.1537154539.142332.dcm')
plt.figure(figsize = (12,12))
plt.imshow(img)
Here is the image link on which i am trying to run this code
https://drive.google.com/file/d/1-xuryA5VlglaumU2HHV7-p6Yhgd6AaCC/view?usp=sharing

Try running the following:
!pip install pylibjpeg
!pip install gdcm

In a similar problem as yours, we could see that the problem persists at the Pixel Data level. You need to install one or more optional libraries, so that you can handle the various compressions.
First, you should do:
$ pip uninstall pycocotools
$ pip install pycocotools --no-binary :all: --no-build-isolation
From here, you should do as follows:
$ pip install pylibjpeg pylibjpeg-libjpeg pydicom
Then, your code should look like this:
from pydicom import dcmread
import pylibjpeg
import gdcm
import numpy as np
import pydicom
from pydicom.pixel_data_handlers.util import apply_voi_lut
import matplotlib.pyplot as plt
%matplotlib inline
def read_xray(path, voi_lut = True, fix_monochrome = True):
dicom = dcmread(path)
# VOI LUT (if available by DICOM device) is used to transform raw DICOM data to "human-friendly" view
if voi_lut:
data = apply_voi_lut(dicom.pixel_array, dicom)
else:
data = dicom.pixel_array
# depending on this value, X-ray may look inverted - fix that:
if fix_monochrome and dicom.PhotometricInterpretation == "MONOCHROME1":
data = np.amax(data) - data
data = data - np.min(data)
data = data / np.max(data)
data = (data * 255).astype(np.uint8)
return data
img = read_xray('/content/ActiveTB/2018/09/17/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157438.869027/1.2.392.200036.9116.2.6.1.44063.1797735841.1537157440.863887/1.2.392.200036.9116.2.6.1.44063.1797735841.1537154539.142332.dcm')
plt.figure(figsize = (12,12))
plt.imshow(img)

Can't import pytagcloud in jupyter notebook but I installed the library using pip

I can't import pytagcloud in jupyter notebook. How do I solve this problem? I searched some tutorials and also installed other packages required but still doesn't work?
Do you have any suggestion?
Here is my code. Thanks.
import pytagcloud as pytagcloud
import codecs
from bs4 import BeautifulSoup
from konlpy.tag import Twitter
# utf-16 인코딩으로 파일을 열고 글자를 출력하기 --- (※1)
samsung = codecs.open("samsung.txt", encoding="utf-8")
line = samsung.readlines()
twitter = Twitter()
word_dic = {}
for line in line:
malist = twitter.pos(line)
for word in malist:
if word[1] == "Noun": # 명사 확인하기 --- (※3)
if not (word[0] in word_dic):
word_dic[word[0]] = 0
word_dic[word[0]] += 1 # 카운트하기
# 많이 사용된 명사 출력하기 --- (※4)
keys = sorted(word_dic.items(), key=lambda x:x[1], reverse=True)
for word, count in keys[:40]:
print("{0}({1}) ".format(word, count), end="")
print()
keys
import pytagcloud
taglist = pytagcloud.make_tags(keys, maxsize = 80)
taglist
pytagcloud.create_tag_image(taglist, 'wordcolud.jpg', size = (900,600), fontname = 'Nobile', rectangular = False)
%matplotlib inline
import matplotlib.pyplot as plt
from wordcloud import WordCloud as wordcloud
wordcloud = WordCloud(stopwords = stopwords)
wordcloud = wordcloud.generate_from_keys(keys)
wordcloud = WordCloud().generate(keys)
draw_wordcloud_from_rss(keys)
cmd:pytagcloud
cmd:pygame
cmd:simplejson
jupyter notebook: pytagcloud

I asked one of my colleagues and she gave the answer!
So the problem was simple. I installed all those libraries in 'cmd'
but I had to install them in "Anaconda prompt".
So, if you have same problem as mine, try this.
# Anaconda prompt
pip install pygame
pip install -U pytagcloud
pip install simplejson
jupyter notebook.
# Import.
I succeeded to import pygame, pytagcloud and simplejson libraries.
Yet, I have still errors in my code of the post above and there is more libraries to install(konply..etc). error is everywhere!
Anyway, I hope this helps someone.

Python - dot file to png file not found error

I am trying to convert dot file into a png or jpeg file where I can view the Random Forest Tree. I am following this tutorial: https://towardsdatascience.com/how-to-visualize-a-decision-tree-from-a-random-forest-in-python-using-scikit-learn-38ad2d75f21c.
I am getting error FileNotFoundError: [WinError 2] The system cannot find the file specified
I can see that tree.dot is there and I am able to open it. Trying to find why it is not reading it? Thanks.
from sklearn.datasets import load_iris
iris = load_iris()
# Model (can also use single decision tree)
from sklearn.ensemble import RandomForestClassifier
model = RandomForestClassifier(n_estimators=10)
# Train
model.fit(iris.data, iris.target)
# Extract single tree
estimator = model.estimators_[5]
from sklearn.tree import export_graphviz
# Export as dot file
export_graphviz(estimator, out_file='tree.dot',
feature_names = iris.feature_names,
class_names = iris.target_names,
rounded = True, proportion = False,
precision = 2, filled = True)
<<error occurs here>>
# Convert to png using system command (requires Graphviz)
from subprocess import call
call(['dot', '-Tpng', 'tree.dot', '-o', 'tree.png', '-Gdpi=600'])
# Display in jupyter notebook
from IPython.display import Image
Image(filename = 'tree.png')

I ran through docker - ubuntu image and ran: RUN apt-get install graphviz -y in the Dockerfile. It started to work. Then used dot -Tpng tree.dot -o tree.png

Export PDF of decisiontree

i'm using scikitlearn to introduce me to Machine Learning, i' m following this tutorial link to yt
but if i try to export the pdf decision tree i have this error:
i try to do: open -w review iris.pdf
and the result is :
Impossibile ottenere un descrittore di file che si riferisce alla console
if i compile from the terminal i have the error:
Traceback (most recent call last) File "fstraining.py", line 2, in <module>
import graphviz ImportError: No module named graphviz
Thanks for the attention

Once you have built your decision tree clf, simply:
from sklearn.externals.six import StringIO
from sklearn.tree import export_graphviz
import pydotplus
# Export resulting tree to DOT source code string
dot_data = export_graphviz(clf,
feature_names=col_names,
out_file=None,
filled=True,
rounded=True)
#Export to pdf
pydot_graph = pydotplus.graph_from_dot_data(dot_data)
pydot_graph.write_pdf('tree.pdf')
This answer is adapted from here:

Can't import package file (no module named...) (Python)

I am receving this error while I am try to run the code (from CMD):
ModuleNotFoundError: No module named 'numbers.hog'; numbers is not a package
Here is the hog.py file code...
from skimage import feature
class HOG:
def __init__(self, orientations = 9, pixelsPerCell = (8, 8),
cellsPerBlock = (3, 3), normalize = False):
self.orienations = orientations
self.pixelsPerCell = pixelsPerCell
self.cellsPerBlock = cellsPerBlock
self.normalize = normalize
def describe(self, image):
hist = feature.hog(image,
orientations = self.orienations,
pixels_per_cell = self.pixelsPerCell,
cells_per_block = self.cellsPerBlock,
normalize = self.normalize)
return hist
...and the main (train.py) which return the error.
from sklearn.svm import LinearSVC
from numbers.hog import HOG
from numbers import dataset
import argparse
import pickle as cPickle
ap = argparse.ArgumentParser()
ap.add_argument("-d", "--dataset", required = True,
help = "path to the dataset file")
ap.add_argument("-m", "--model", required = True,
help = "path to where the model will be stored")
args = vars(ap.parse_args())
(digits, target) = dataset.load_digits(args["dataset"])
data = []
hog = HOG(orientations = 18, pixelsPerCell = (10, 10),
cellsPerBlock = (1, 1), normalize = True)
for image in digits:
image = dataset.deskew(image, 20)
image = dataset.center_extent(image, (20, 20))
hist = hog.describe(image)
data.append(hist)
model = LinearSVC(random_state = 42)
model.fit(data, target)
f = open(args["model"], "w")
f.write(cPickle.dumps(model))
f.close()
I don't uderstand why it gives me error on module package. numbers is a package, why it don't import it as well (as it seems) ?
UPDATE: tried to put from .hog import HOG and then execute from CMD..It prints:
No module named '__main__.hog'; '__main__' is not a package
Is it crazy ? hog.py is in the main package together with the other files. As you can see, it also contains HOG class.... Can't understand.. Some one can reproduce the error ?
In the IDE console it prints:
usage: train.py [-h] -d DATASET -m MODEL
train.py: error: the following arguments are required: -d/--dataset, -m/--model
This should be correct as soon as it is executed in IDE because the program MUST run in CMD.
UPDATE 2: for who is interested, this is the project https://github.com/VAUTPL/Number_Detection

Change from numbers.hog import HOG to from hog import HOG and change from numbers import dataset to import dataset.
You are already in the "numbers" package so you don't have to precise it again when you import it.
When you type from numbers import dataset, Python will look for a package numbers (inside the actual package) that contains a dataset.py file.
If your train.py was outside the numbers package then you have to put the package name (numbers) before.

Important
numbers is a python standard package
https://docs.python.org/2/library/numbers.html
Check if you are not really importing that package or rename your package to a more specific name.
Also:
It might looks like python doesnt recognize your package.
Open a python shell and write:
import sys
print sys.path
Check if your number path is there.
If it's not there you have to add it.
sys.path.insert(0, "/path/to/your/package_or_module")

Your train.py file is already in the package "numbers", so you don't have to import numbers.
Try this instead:
from hog import HOG
I saw in comment that it gives you "error (red line)".
Can you be more precise, because I don't see errors there.