Hello consider following code
# load the mnist training data CSV file into a list
training_data_file = open("Training_Set/mnist_train_100.csv", 'r')
training_data_list = training_data_file.readlines()
training_data_file.close()
for record in training_data_list:
all_values = record.split(',')
x_inputs = (np.asfarray(all_values[1:]) / 255.0 * 0.99) + 0.01
print("xinput=" + str(x_inputs))
print(len(training_data_list))
MyCompleteInput = np.array(x_inputs,len(training_data_list))
I want to put x_inputs and len(training_data_list) into an array so if I print the shape of the array I get an output of (784,100).
But if I run my code I get following error:
TypeError Traceback (most recent call last)
<ipython-input-38-b0f129f57bcb> in <module>()
11 print("xinput=" + str(x_inputs))
12 print(len(training_data_list))
---> 13 MyCompleteInput = np.array(x_inputs,len(training_data_list))
14
15
TypeError: data type not understood
Can somebody help me out? tnx
The line will be
MyCompleteInput = np.array((x_inputs,len(training_data_list)))
Do this and your error will be gone. You need to add another set of parantheses for specifying the size.
Related
I am trying to do feature selection using feature forward method.
Tried previously answered questions but didn't get any proper solution. My code is as follows:
def forward_selection_rf(data, target, number_of_features=14):
# adapt number of features to select: if requested number
# is greater than features availabe, go for 75% of the
# features instead
if number_of_features > len(data.columns):
print("SFS: Wanted " + str(number_of_features) + " from " + str(len(data.columns)) + " featurs. Sanifying to 75%")
number_of_features = 0.75
# Sequential Forward Selection(sfs)
sfs1 = sfs(RandomForestClassifier(
n_estimators=70,
criterion='gini',
max_depth=15,
min_samples_split=2,
min_samples_leaf=1,
min_weight_fraction_leaf=0.0,
max_features='auto',
max_leaf_nodes=None,
min_impurity_decrease=0.0,
min_impurity_split=None,
bootstrap=True,
oob_score=False,
n_jobs=-1,
random_state=0,
verbose=0,
warm_start=False,
class_weight='balanced'
),
n_features_to_select=14,
direction='forward',
scoring = 'roc_auc',
cv = 5,
n_jobs = 3)
sfs1.fit(data, target)
return sfs1
compiler gives runtime error as follows:
forward_selection_rf(X, y, number_of_features=14)
Traceback (most recent call last):
File "C:\Users\drash\AppData\Local\Temp\ipykernel_37980\1091017691.py", line 1, in <module>
forward_selection_rf(X, y, number_of_features=14)
File "C:\Users\drash\OneDrive\Desktop\Howto Health\untitled3.py", line 102, in forward_selection_rf
TypeError: __init__() got an unexpected keyword argument 'n_features_to_select'
In this example, the guide step is defined as follows
def guide(params):
# returns the Bernoulli probablility
alpha = pyro.param(
"alpha", torch.tensor(params[0]), constraint=constraints.positive
)
beta = pyro.param(
"beta", torch.tensor(params[1]), constraint=constraints.positive
)
return pyro.sample("beta_dist", dist.Beta(alpha, beta))
svi = pyro.infer.SVI(
model=conditioned_data_model,
guide=guide,
optim=pyro.optim.SGD({"lr": 0.001, "momentum": 0.8}),
loss=pyro.infer.Trace_ELBO(),
)
params_prior = [prior.concentration1, prior.concentration0]
# Iterate over all the data and store results
losses, alpha, beta = [], [], []
pyro.clear_param_store()
num_steps = 3000
for t in range(num_steps):
losses.append(svi.step(params_prior))
alpha.append(pyro.param("alpha").item())
beta.append(pyro.param("beta").item())
posterior_vi = dist.Beta(alpha[-1], beta[-1])
However, running the above step gives the following error, what does those hints of fix mean and how to fix it accordingly?
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Input In [9], in <cell line: 15>()
14 num_steps = 3000
15 for t in range(num_steps):
---> 16 losses.append(svi.step(params_prior))
17 alpha.append(pyro.param("alpha").item())
18 beta.append(pyro.param("beta").item())
ValueError: at site "data_dist", invalid log_prob shape
Expected [], actual [100, 1]
Try one of the following fixes:
- enclose the batched tensor in a with pyro.plate(...): context
- .to_event(...) the distribution being sampled
- .permute() data dimensions
For a long time I was able to add data and fit, then plot the curve with data. But recently I get this:
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
<ipython-input-6-6f645a2744bc> in <module>
1 poland = prepare_data(europe_data, 'Poland')
----> 2 plot_all(poland, max_y=400000)
3 poland
~/Pulpit/library.py in plot_all(country, max_x, max_y)
43 def plot_all(country, max_x = 1000, max_y = 500000):
44
---> 45 parameters_logistic = scipy.optimize.curve_fit(func_logistic, country['n'], country['all'])[0]
46 parameters_expo = scipy.optimize.curve_fit(func_expo, country['n'], country['all'])[0]
47
/usr/local/lib64/python3.6/site-packages/scipy/optimize/minpack.py in curve_fit(f, xdata, ydata, p0, sigma, absolute_sigma, check_finite, bounds, method, jac, **kwargs)
787 cost = np.sum(infodict['fvec'] ** 2)
788 if ier not in [1, 2, 3, 4]:
--> 789 raise RuntimeError("Optimal parameters not found: " + errmsg)
790 else:
791 # Rename maxfev (leastsq) to max_nfev (least_squares), if specified.
RuntimeError: Optimal parameters not found: Number of calls to function has reached maxfev = 800.
Here are all Python Jupyter Notebook files: https://files.fm/u/zj7cc6ne#sign_up
How to solve this?
scipy.optimize.curve_fit takes a keyword argument p0.
Initial guess for the parameters (length N). If None, then the initial
values will all be 1 (if the number of parameters for the function can
be determined using introspection, otherwise a ValueError is raised).
If the defaults 1 are too far of from the result the algorithm may not converge. Try to put some values that make sense for your problem.
I have question about the data type of the result returned by Sympy Poly.all_coeffs(). I have started to use Sympy just recently.
My Sympy transfer function is following:
Then I run this code:
n,d = fraction(Gs)
num = Poly(n,s)
den = Poly(d,s)
num_c = num.all_coeffs()
den_c = den.all_coeffs()
I get:
Then I run this code:
from scipy import signal
#nu = [5000000.0]
#de = [4.99, 509000.0]
nu = num_c
de = den_c
sys = signal.lti(nu, de)
w,mag,phase = signal.bode(sys)
plt.plot(w/(2*np.pi), mag)
and the result is:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-131-fb960684259c> in <module>
4 nu = num_c
5 de = den_c
----> 6 sys = signal.lti(nu, de)
But if I use those commented line 'nu' and 'de' straight python lists instead, the program works. So what is wrong here?
Why did you just show a bit the error? Why not the full message, maybe even the full traceback!
In [60]: sys = signal.lti(num_c, den_c)
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-60-21f71ecd8884> in <module>
----> 1 sys = signal.lti(num_c, den_c)
/usr/local/lib/python3.6/dist-packages/scipy/signal/ltisys.py in __init__(self, *system, **kwargs)
590 self._den = None
591
--> 592 self.num, self.den = normalize(*system)
593
594 def __repr__(self):
/usr/local/lib/python3.6/dist-packages/scipy/signal/filter_design.py in normalize(b, a)
1609 leading_zeros = 0
1610 for col in num.T:
-> 1611 if np.allclose(col, 0, atol=1e-14):
1612 leading_zeros += 1
1613 else:
<__array_function__ internals> in allclose(*args, **kwargs)
/usr/local/lib/python3.6/dist-packages/numpy/core/numeric.py in allclose(a, b, rtol, atol, equal_nan)
2169
2170 """
-> 2171 res = all(isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan))
2172 return bool(res)
2173
<__array_function__ internals> in isclose(*args, **kwargs)
/usr/local/lib/python3.6/dist-packages/numpy/core/numeric.py in isclose(a, b, rtol, atol, equal_nan)
2267 y = array(y, dtype=dt, copy=False, subok=True)
2268
-> 2269 xfin = isfinite(x)
2270 yfin = isfinite(y)
2271 if all(xfin) and all(yfin):
TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
Now look at the elements of the num_c list (same for den_c):
In [55]: num_c[0]
Out[55]: 500000.000000000
In [56]: type(_)
Out[56]: sympy.core.numbers.Float
The scipy code is doing numpy testing on the inputs. So it's first turned the lists into arrays:
In [61]: np.array(num_c)
Out[61]: array([500000.000000000], dtype=object)
This array contains sympy object(s). It can't cast that to numpy float with 'safe'. But an explicit astype uses unsafe as the default:
In [63]: np.array(num_c).astype(float)
Out[63]: array([500000.])
So lets convert both lists into valid numpy float arrays:
In [64]: sys = signal.lti(np.array(num_c).astype(float), np.array(den_c).astype(float))
In [65]: sys
Out[65]:
TransferFunctionContinuous(
array([100200.4008016]),
array([1.00000000e+00, 1.02004008e+05]),
dt: None
)
Conversion in a list comprehension also works:
sys = signal.lti([float(i) for i in num_c],[float(i) for i in den_c])
You likely need to conver sympy objects to floats / lists of floats.
I am doing N4 bias correction in .nii file in python(Windows).For this I am using SimpleITK.While taking input of the image, I am having issues in reading the file.
Code :
print("N4 bias correction runs.")
inputImage =sitk.ReadImage("C/Users/LENOVO/Desktop/Brats18_2013_1_1_t1.nii")
maskImage = sitk.OtsuThreshold(inputImage,0,1,200)
sitk.WriteImage(maskImage,"C/Users/LENOVO/Desktop/Brats18_2013_1_1_t1_Mask.nii")
inputImage = sitk.Cast(inputImage,sitk.sitkFloat32)
corrector = sitk.N4BiasFieldCorrectionImageFilter();
output = corrector.Execute(inputImage,maskImage)
sitk.WriteImage(output,"C/Users/LENOVO/Desktop/Brats18_2013_1_1_t1_Mask.nii")
print("Finished N4 Bias Field Correction.....")
Error :
RuntimeError
Traceback (most recent call last)
<ipython-input-26-0835d7f75708> in <module>()
1
2 print("N4 bias correction runs.")
----> 3 inputImage = sitk.ReadImage("C/Users/LENOVO/Desktop/Brats18_2013_1_1_t1.nii")
4
5 maskImage = sitk.OtsuThreshold(inputImage,0,1,200)
~\Anaconda3\lib\site-packages\SimpleITK\SimpleITK.py in ReadImage(*args)
8612
8613 """
-> 8614 return _SimpleITK.ReadImage(*args)
8615 class HashImageFilter(ProcessObject):
8616 """
RuntimeError: Exception thrown in SimpleITK ReadImage: C:\Users\dashboard\Miniconda3\conda-bld\simpleitk_1521730316398\work\Code\IO\src\sitkImageReaderBase.cxx:89:
sitk::ERROR: The file "C/Users/LENOVO/Desktop/Brats18_2013_1_1_t1.nii" does not exist.
If you're going to use the Unix-style paths, then you need a leading slash, so the file path should be:
"/C/Users/LENOVO/Desktop/Brats18_2013_1_1_t1.nii/"
Or you can use Windows-style paths, then it would be:
"c:\Users\LENOVO\Desktop\Brats18_2013_1_1_t1.nii"