I am trying to call R packages from python (python 2.7.9) and trying to call Apriori function.
import rpy2
from rpy2 import *
import rpy2.interactive as r
arules = r.packages.importr("arules")
from rpy2.robjects.vectors import ListVector
od = r.OrderedDict()
od["supp"] = 0.0005
od["conf"] = 0.7
od["target"] = 'rules'
result = ListVector(od)
dataset = 'c:/Apriori/testcase.txt'
my_rules = arules.apriori(dataset, parameter=result)
print('my_rules',my_rules)
I am failing in rules. The error is below:
AttributeError: 'module' object has no attribute 'packages'
Please help
from rpy2.robjects.packages import importr
arules = importr("arules")
Related
I am trying to upload the image from the local system within the same directory. Post uploading, when I am passing through open cv split and merge for b,g, and r colors, i get the error ValueError: not enough values to unpack (expected 3, got 0)
Error :
this is the error that is showing is there any possibility to debug in the streamlit where I can track changes at different lines of code? (As in the image path,) when executed in a google collab as individual ipynb files run properly and I get by required classification
ValueError: not enough values to unpack (expected 3, got 0)
Traceback:
File "C:\Users\ADARSH\anaconda3\lib\site-packages\streamlit\runtime\scriptrunner\script_runner.py", line 564, in _run_script
exec(code, module.__dict__)
File "C:\Users\ADARSH\streamlit\deploy_test.py", line 76, in <module>
main()
File "C:\Users\ADARSH\streamlit\deploy_test.py", line 68, in main
mask = imageToTensor('image')
File "C:\Users\ADARSH\streamlit\deploy_test.py", line 44, in imageToTensor
b,g,r = cv2.split(bgr_img)
My entire streamlit app code
from pathlib import Path
import cv2
import numpy as np
import pandas as pd
import os
import cv2
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import random
from sklearn.utils import shuffle
from tqdm import tqdm_notebook
import streamlit as st
from PIL import Image as impo
from fastai import *
from fastai.vision import *
from torchvision.models import *
class MyImageItemList(ImageList):
def open(self, fn:PathOrStr)->Image:
img = readCroppedImage(fn.replace('/./','').replace('//','/'))
# This ndarray image has to be converted to tensor before passing on as fastai Image, we can use pil2tensor
return vision.Image(px=pil2tensor(img, np.float32))
def read_image(name):
image = st.file_uploader("Upload an "+ name, type=["png", "jpg", "jpeg",'tif'])
if image is not None:
im = impo.open(image)
im.filename = image.name
return image
def imageToTensor(image):
sz = 68
bgr_img = cv2.imread(image)
b,g,r = cv2.split(bgr_img)
rgb_img = cv2.merge([r,g,b])
# crop to center to the correct size and convert from 0-255 range to 0-1 range
H,W,C = rgb_img.shape
rgb_img = rgb_img[(H-sz)//2:(sz +(H-sz)//2),(H-sz)//2:(sz +(H-sz)//2),:] / 256
return vision.Image(px=pil2tensor(rgb_img, np.float32))
def learn_infernce():
return load_learner('./')
def get_prediction(image):
if st.button('Classify'):
pred, pred_idx, probs = learn_inference.predict(image)
classes = ['negative', 'tumor']
st.write(f'Prediction: {pred}; Probability: {probs[pred_idx]:.04f}')
else:
st.write(f'Click the button to classify')
def main():
st.set_page_config(page_title='Cancer detection', page_icon=None, layout='centered', initial_sidebar_state='auto')
image = read_image('image')
mask = imageToTensor('image')
if mask is not None:
get_prediction('mask')
if __name__ == "__main__":
main()
In your main function you are passing 'str' instead of variables, and also I think your read_image is not well structured.
What you should do is to first save the uploaded file in a directory and fetch the file from that directory and pass it to imageToTensor() as a parameter. That's one work around which will give you a total control over the file. Otherwise you will get other error messages after the first error is fixed.
You can automate some few lines of code in a separate python file to delete the uploaded file from the directory with a given duration.
Note: Keep an eye on the imports because I skipped them to keep the code short
class MyImageItemList(ImageList):
def open(self, fn:PathOrStr)->Image:
img = readCroppedImage(fn.replace('/./','').replace('//','/'))
# This ndarray image has to be converted to tensor before passing on as fastai Image, we can use pil2tensor
return vision.Image(px=pil2tensor(img, np.float32))
# Refactured read_image()
def get_uploaded_image():
upload = st.file_uploader("Upload an image", type=["png", "jpg", "jpeg",'tif'])
if upload is not None:
st.write(upload.name)
# Create a directory and save the image file before proceeding.
file_path = os.path.join("data/uploadedImages/", upload.name)
with open(file_path, "wb") as user_file:
user_file.write(upload.getbuffer())
return file_path # fixed indentation
def imageToTensor(image):
sz = 68
bgr_img = cv2.imread(image)
b,g,r = cv2.split(bgr_img)
rgb_img = cv2.merge([r,g,b])
# crop to center to the correct size and convert from 0-255 range to 0-1 range
H,W,C = rgb_img.shape
rgb_img = rgb_img[(H-sz)//2:(sz +(H-sz)//2),(H-sz)//2:(sz +(H-sz)//2),:] / 256
return vision.Image(px=pil2tensor(rgb_img, np.float32))
def learn_infernce():
return load_learner('./')
def get_prediction(image):
if st.button('Classify'):
pred, pred_idx, probs = learn_inference.predict(image)
classes = ['negative', 'tumor']
st.write(f'Prediction: {pred}; Probability: {probs[pred_idx]:.04f}')
else:
st.write(f'Click the button to classify')
def main():
st.set_page_config(page_title='Cancer detection', page_icon=None, layout='centered', initial_sidebar_state='auto')
# Holds the saved file path
user_image = get_uploaded_image()
if user_image is not None:
# Pass the path to imageToTensor() as a parameter.
mask = imageToTensor(user_image)
get_prediction(mask)
if __name__ == "__main__":
main()
output:
I have created a simple ann like this:
`from keras.models import Sequential
import tensorflow
from tensorflow.python.keras.layers import Dense
from tensorflow.keras.wrappers.scikit_learn import KerasRegressor
model = Sequential()
model.add(Dense(20, input_dim=2, kernel_initializer='uniform', activation='relu'))
model.add(Dense(1))
model.compile(loss='mse', optimizer = 'adam', metrics= tf.keras.metrics.RootMeanSquaredError())
n_epochs = 1000
n_batch = 6
model.fit(x_train_norm, y_train, epochs=n_epochs, batch_size=n_batch, verbose = 1)
`
And when I try to save the model: (already installed h5py)
model.save("model.h5")
I get the next error message:
Layer ModuleWrapper has arguments ['module', 'method_name']
in `__init__` and therefore must override `get_config()`.
Example:
class CustomLayer(keras.layers.Layer):
def __init__(self, arg1, arg2):
super().__init__()
self.arg1 = arg1
self.arg2 = arg2
def get_config(self):
config = super().get_config()
config.update({
"arg1": self.arg1,
"arg2": self.arg2,
})
return config
I've read NotImplementedError: Layers with arguments in `__init__` must override `get_config`
but I don't know how to apply it to my problem because It's a very simple ann, I don't youse encoder like in the example above
This is a snippet of my code in PyTorch, my jupiter notebook stuck when I used num_workers > 0, I spent a lot on this problem without any answer. I do not have a GPU and I work only with a CPU.
class IndexedDataset(Dataset):
def __init__(self,data,targets, test=False):
self.dataset = data
if not test:
self.labels = targets.numpy()
self.mask = np.concatenate((np.zeros(NUM_LABELED), np.ones(NUM_UNLABELED)))
def __len__(self):
return len(self.dataset)
def __getitem__(self, idx):
image = self.dataset[idx]
return image, self.labels[idx]
def display(self, idx):
plt.imshow(self.dataset[idx], cmap='gray')
plt.show()
train_set = IndexedDataset(train_data, train_target, test = False)
test_set = IndexedDataset(test_data, test_target, test = True)
train_loader = DataLoader(train_set, batch_size=BATCH_SIZE, num_workers=2)
test_loader = DataLoader(test_set, batch_size=BATCH_SIZE, num_workers=2)
Any help, appreciated.
When num_workers is greater than 0, PyTorch uses multiple processes for data loading.
Jupyter notebooks have known issues with multiprocessing.
One way to resolve this is not to use Jupyter notebooks - just write a normal .py file and run it via command-line.
Or try use what's suggested here: Jupyter notebook never finishes processing using multiprocessing (Python 3).
Since jupyter Notebook doesn't support python multiprocessing, there are two thin libraries, you should install one of them as mentioned here 1 and 2.
I prefer to solve my problem in two ways without using any external libraries:
By converting my file from .ipynb format to .py format and run it in the terminal and I write my code in the main() function as follows:
...
...
train_set = IndexedDataset(train_data, train_target, test = False)
train_loader = DataLoader(train_set, batch_size=BATCH_SIZE, num_workers=4)
if `__name__ == '__main__'`:
for images,label in train_loader:
print(images.shape)
With multiprocessing library as follows:
In try.ipynb:
import multiprocessing as mp
import processing as ps
...
...
train_set = IndexedDataset(train_data, train_target, test = False)
train_loader = DataLoader(train_set, batch_size=BATCH_SIZE)
if __name__=="__main__":
p = mp.Pool(8)
r = p.map(ps.getShape,train_loader)
print(r)
p.close()
In processing.py file:
def getShape(data):
for i in data:
return i[0].shape
My script gives different results if I run it on colab, jupyter notebook or directly. The colab result is wrong as the 3 equation are not coupled.
import sympy as sp
from IPython.display import *
sp.init_printing(use_latex=True)
t,M_x0,My0,M_z0,w,k_2=sp.symbols('t,M_x0,My0,M_z0,omega,k_2',real=True)
M_x=sp.Function('M_x',real=True)(t)
M_y=sp.Function('M_y',real=True)(t)
M_z=sp.Function('M_z',real=True)(t)
e1=sp.Eq(sp.Derivative(M_x,t),w*M_y)
e2=sp.Eq(sp.Derivative(M_y,t),-w*M_x)
e3=sp.Eq(sp.Derivative(M_z,t),0)
sys3 = [e1,e2,e3]
sol= sp.dsolve(sys3)
display('Systeme :',sys3)
display('Solution :',sol)
The handling of systems of ODEs has been rewritten on sympy master and will be very different in sympy 1.7. This is what I get with current master (which will become 1.7):
In [7]: sys3
Out[7]:
⎡d d d ⎤
⎢──(Mₓ(t)) = ω⋅M_y(t), ──(M_y(t)) = -ω⋅Mₓ(t), ──(M_z(t)) = 0⎥
⎣dt dt dt ⎦
In [8]: dsolve(sys3)
Out[8]: [Mₓ(t) = C₁⋅sin(ω⋅t) + C₂⋅cos(ω⋅t), M_y(t) = C₁⋅cos(ω⋅t) - C₂⋅sin(ω⋅t), M_z(t) = C₃]
So, I'm using a function from this website to (try) to make stick plots of some netCDF4 data. There is an excerpt of my code below. I got my data from here.
The stick_plot(time,u,v) function is EXACTLY as it appears in the website I linked which is why I did not show a copy of that function below.
When I run my code I get the following error. Any idea on how to get around this?
AttributeError: 'numpy.float64' object has no attribute 'toordinal'
The description of time from the netCDF4 file:
<type 'netCDF4._netCDF4.Variable'>
float64 time(time)
long_name: time
standard_name: time
units: days since 1900-01-01 00:00:00Z
axis: T
ancillary_variables: time_quality_flag
data_min: 2447443.375
data_max: 2448005.16667
unlimited dimensions:
current shape = (13484,)
filling off
Here is an excerpt of my code:
imports:
import matplotlib.pyplot as plot
import numpy as np
from netCDF4 import Dataset
import os
from matplotlib.dates import date2num
from datetime import datetime
trying to generate the plots:
path = '/Users/Kyle/Documents/Summer_Research/east_coast_currents/'
currents = [x for x in os.listdir('%s' %(path)) if '.DS' not in x]
for datum in currents:
working_data = Dataset('%s' %(path+datum), 'r', format = 'NETCDF4')
u = working_data.variables['u'][:][:100]
v = working_data.variables['v'][:][:100]
time = working_data.variables['time'][:][:100]
q = stick_plot(time,u,v)
ref = 1
qk = plot.quiverkey(q, 0.1, 0.85, ref,
"%s N m$^{-2}$" % ref,
labelpos='N', coordinates='axes')
_ = plot.xticks(rotation=70)
Joe Kington answered my question. The netCDF4 file read the times in as a datetime object. All I had to do was replace date2num(time) with time which fixed everything.