This is simple to test if you get the error on your side:
import geopandas as gpd
gdf = gpd.read_file('https://hepgis.fhwa.dot.gov/fhwagis/AltFuels_Rounds1-5_2021-05-25.zip')
File "fiona/ogrext.pyx", line 540, in fiona.ogrext.Session.start
File "fiona/_shim.pyx", line 90, in fiona._shim.gdal_open_vector
fiona.errors.DriverError: '/vsimem/6101ab5f23764c15b5fe47aa52a049d6' not recognized as a supported file format.
Interestingly, I have received this error for other URLs recently and thought there was something wrong with the URL. But, now I suspect that something else is going on since it is happening with more than one URL. On the other hand, some URLs don't have this issue. One other interesting thing, this error only occurs sometimes. For instance, if I rerun that command it will work maybe 1 out of 20 times.
My Fiona version:
fiona 1.8.20 py39hea8b339_1 conda-forge
Any help would be much appreciated.
Investigating, the URL does not return a zip file. See code below, it actually returns a HTML input page...
import geopandas as gpd
import requests, io
from pathlib import Path
from zipfile import ZipFile, BadZipFile
import urllib
import fiona
url = "https://hepgis.fhwa.dot.gov/fhwagis/AltFuels_Rounds1-5_2021-05-25.zip"
try:
gdf = gpd.read_file(url)
except Exception:
f = Path.cwd().joinpath(urllib.parse.urlparse(url).path.split("/")[-1])
r = requests.get(url, stream=True, headers={"User-Agent": "XY"})
with open(f, "wb") as fd:
for chunk in r.iter_content(chunk_size=128):
fd.write(chunk)
try:
zfile = ZipFile(f)
zfile.extractall(f.stem)
except BadZipFile:
with open(f) as fh:
print(fh.read())
Related
I work with a Mac. I have been trying to make a multiple sequence alignment in Python using Muscle. This is the code I have been running:
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input="testunaligned.fasta", out="testunaligned.aln", clwstrict=True)
print(cline)
from Bio import AlignIO
align = AlignIO.read(open("testunaligned.aln"), "clustal")
print(align)
I keep getting the following error:
FileNotFoundError: [Errno 2] No such file or directory: 'testunaligned.aln'
Does anyone know how I could fix this? I am very new to Python and computer science in general, and I am totally at a loss. Thanks!
cline in your code is an instance of MuscleCommandline object that you initialized with all the parameters. After the initialization, this instance can run muscle, but it will only do that if you call it. That means you have to invoke cline()
When you simply print the cline object, it will return a string that corresponds to the command you can manually run on the command line to get the same result as when you invoke cline().
And here the working code:
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(
input="testunaligned.fasta",
out="testunaligned.aln",
clwstrict=True
)
print(cline)
cline() # this is where mucle runs
from Bio import AlignIO
align = AlignIO.read(open("testunaligned.aln"), "clustal")
print(align)
I am still learning python but got stuck here:
from pathlib import Path
import os
import shutil
p = Path.home()
shutil.copy(p / 'G:\souce.txt', p / 'G:\dest.text')
The error is:
shutil: shutil
Anomalous backslash in string: '\s'. String constant might be missing an r prefix.pylint(anomalous-
backslash-in-string)
Anomalous backslash in string: '\d'. String constant might be missing an r prefix.pylint(anomalous-
backslash-in-string)
Module 'shutil' has no 'copy' memberpylint(no-member)
Not able to go for the next step. So any suggestions please.
You can just do:
import shutil
shutil.copy('G:\souce.txt', 'G:\dest.text')
from pydotplus import graph_from_dot_data
from sklearn.tree import export_graphviz
from IPython.display import Image
dot_data = export_graphviz(tree,filled=True,rounded=True,class_names=['Setosa','Versicolor','Virginica'],feature_names=['petal length','petal width'],out_file=None)
graph = graph_from_dot_data(dot_data)
Image(graph.create_png())
Program terminated with status:
1. stderr follows: 'C:\Users\En' is not recognized as an internal or external command,
operable program or batch file.
it seems that it split my username into half.How do i overcome this?
I have a very similar example that I'm trying out, it's based on a ML how-to book which is working with a Taiwan Credit Card dataset predicting default risk. My setup is as follows:
from six import StringIO
from sklearn.tree import export_graphviz
from IPython.display import Image
import pydotplus
Then creating the decision tree plot is done in this way:
dot_data = StringIO()
export_graphviz(decision_tree=class_tree,
out_file=dot_data,
filled=True,
rounded=True,
feature_names = X_train.columns,
class_names = ['pay','default'],
special_characters=True)
graph = pydotplus.graph_from_dot_data(dot_data.getvalue())
Image(graph.create_png())
I think it's all coming from the out_file=dot_data argument but cannot figure out where the file path is created and stored as print(dot_data.getvalue()) did not show any pathname.
In my research I came across sklearn.plot_tree() which seems to do everything that the graphviz does. So I took the above exporet_graphviz arguments and were matching arguments were in the .plot_tree method I added them.
I ended up with the following which created the same image as was found in the text:
from sklearn import tree
plt.figure(figsize=(20, 10))
tree.plot_tree(class_tree,
filled=True, rounded=True,
feature_names = X_train.columns,
class_names = ['pay','default'],
fontsize=12)
plt.show()
I have been attempting to download a plot created using plotly on google colaboratory. So far this is what I have attempted:
I have tried changing
files.download('foo.svg')
to
files.download('foo')
and I still get no results. I navigated to the files on Google colab and nothing shows there
import numpy as np
import pandas as pd
from plotly.offline import iplot
import plotly.graph_objs as go
from google.colab import files
def enable_plotly_in_cell():
import IPython
from plotly.offline import init_notebook_mode
display(IPython.core.display.HTML('''<script src="/static/components/requirejs/require.js"></script>'''))
init_notebook_mode(connected=False)
#this actually shows the plot
enable_plotly_in_cell()
N = 500
x = np.linspace(0, 1, N)
y = np.random.randn(N)
df = pd.DataFrame({'x': x, 'y': y})
df.head()
data = [
go.Scatter(
x=df['x'], # assign x as the dataframe column 'x'
y=df['y']
)
]
iplot(data,image = 'svg', filename = 'foo')
files.download('foo.svg')
This is the error I am getting:
OSErrorTraceback (most recent call last)
<ipython-input-18-31523eb02a59> in <module>()
29 iplot(data,image = 'svg', filename = 'foo')
30
---> 31 files.download('foo.svg')
32
/usr/local/lib/python2.7/dist-packages/google/colab/files.pyc in download(filename)
140 msg = 'Cannot find file: {}'.format(filename)
141 if _six.PY2:
--> 142 raise OSError(msg)
143 else:
144 raise FileNotFoundError(msg) # pylint: disable=undefined-variable
OSError: Cannot find file: foo.svg
To save vector or raster images (e.g. SVGs or PNGs) from Plotly figures you need to have Kaleido (preferred) or Orca (legacy) installed, which is actually possible using the following commands in Colab:
Kaleido:
!pip install kaleido
Orca:
!pip install plotly>=4.0.0
!wget https://github.com/plotly/orca/releases/download/v1.2.1/orca-1.2.1-x86_64.AppImage -O /usr/local/bin/orca
!chmod +x /usr/local/bin/orca
!apt-get install xvfb libgtk2.0-0 libgconf-2-4
Once either of the above is done you can use the following code to make, show and export a figure (using plotly version 4):
import plotly.graph_objects as go
fig = go.Figure( go.Scatter(x=[1,2,3], y=[1,3,2] ) )
fig.show()
fig.write_image("image.svg")
fig.write_image("image.png")
The files can then be downloaded with:
from google.colab import files
files.download('image.svg')
files.download('image.png')
Try this, it does work for me:
import plotly.graph_objects as go
fig = go.Figure(...) # plot your fig
go.Figure.write_html(fig,"file.html") # write as html or image
files.download("file.html") # download your file and give me a vote my answer
I'm trying to run a code from github that uses Python to classify images but I'm getting an error.
here is the code:
import argparse as ap
import cv2
import imutils
import numpy as np
import os
from sklearn.svm import LinearSVC
from sklearn.externals import joblib
from scipy.cluster.vq import *
# Get the path of the testing set
parser = ap.ArgumentParser()
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument("-t", "--testingSet", help="Path to testing Set")
group.add_argument("-i", "--image", help="Path to image")
parser.add_argument('-v',"--visualize", action='store_true')
args = vars(parser.parse_args())
# Get the path of the testing image(s) and store them in a list
image_paths = []
if args["testingSet"]:
test_path = args["testingSet"]
try:
testing_names = os.listdir(test_path)
except OSError:
print "No such directory {}\nCheck if the file exists".format(test_path)
exit()
for testing_name in testing_names:
dir = os.path.join(test_path, testing_name)
class_path = imutils.imlist(dir)
image_paths+=class_path
else:
image_paths = [args["image"]]
and this is the error message I'm getting
usage: getClass.py [-h]
(- C:/Users/Lenovo/Downloads/iris/bag-of-words-master/dataset/test TESTINGSET | - C:/Users/Lenovo/Downloads/iris/bag-of-words-master/dataset/test/test_1.jpg IMAGE)
[- C:/Users/Lenovo/Downloads/iris/bag-of-words-master/dataset]
getClass.py: error: one of the arguments - C:/Users/Lenovo/Downloads/iris/bag-of-words-master/dataset/test/--testingSet - C:/Users/Lenovo/Downloads/iris/bag-of-words-master/dataset/test/test_1.jpg/--image is required
can you please help me with this? where and how should I write the file path?
This is an error your own program is issuing. The message is not about the file path but about the number of arguments. This line
group = parser.add_mutually_exclusive_group(required=True)
says that only one of your command-line arguments (-t, -i) is permitted. But it appears from the error message that you are supplying both --testingSet and --image on your command line.
Since you only have 3 arguments, I have to wonder if you really need argument groups at all.
To get your command line to work, drop the mutually-exclusive group and add the arguments to the parser directly.
parser.add_argument("-t", "--testingSet", help="Path to testing Set")
parser.add_argument("-i", "--image", help="Path to image")
parser.add_argument('-v',"--visualize", action='store_true')