Making predictions with Azure Machine learning with new data that contains headers (like pd.Dataframe) - json

Question

My question is somehow related to https://learn.microsoft.com/en-us/answers/questions/217305/data-input-format-call-the-service-for-azure-ml-ti.html - however, the provided solution does not seem to work.
I am constructing a simple model with heart-disease dataset but I wrap it into Pipeline as I use some featurization steps (scaling, encoding etc.) The full script below:
import pandas as pd
import numpy as np
from sklearn.preprocessing import MinMaxScaler
from sklearn.compose import ColumnTransformer
from sklearn.preprocessing import OneHotEncoder
from sklearn.pipeline import Pipeline
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer
from sklearn.linear_model import LogisticRegression
%matplotlib inline
import matplotlib.pyplot as plt
import seaborn as sns
import joblib
import pickle
# data input
df = pd.read_csv('heart.csv')
# numerical variables
num_cols = ['age',
'trestbps',
'chol',
'thalach',
'oldpeak'
]
# categorical variables
cat_cols = ['sex',
'cp',
'fbs',
'restecg',
'exang',
'slope',
'ca',
'thal']
# changing format of the categorical variables
df[cat_cols] = df[cat_cols].apply(lambda x: x.astype('object'))
# target variable
y = df['target']
# features
X = df.drop(['target'], axis=1)
# data split:
# random seed
np.random.seed(42)
# splitting the data
X_train, X_test, y_train, y_test = train_test_split(X, y,
test_size=0.2,
stratify=y)
# double check
X_train.shape, X_test.shape, y_train.shape, y_test.shape
# pipeline for numerical data
num_preprocessing = Pipeline([('num_imputer', SimpleImputer(strategy='mean')), # imputing with mean
('minmaxscaler', MinMaxScaler())]) # scaling
# pipeline for categorical data
cat_preprocessing = Pipeline([('cat_imputer', SimpleImputer(strategy='constant', fill_value='missing')), # filling missing values
('onehot', OneHotEncoder(drop='first', handle_unknown='error'))]) # One Hot Encoding
# preprocessor - combining pipelines
preprocessor = ColumnTransformer([
('categorical', cat_preprocessing, cat_cols),
('numerical', num_preprocessing, num_cols)
])
# initial model parameters
log_ini_params = {'penalty': 'l2',
'tol': 0.0073559740277086005,
'C': 1.1592424247511928,
'fit_intercept': True,
'solver': 'liblinear'}
# model - Pipeline
log_clf = Pipeline([('preprocessor', preprocessor),
('clf', LogisticRegression(**log_ini_params))])
log_clf.fit(X_train, y_train)
# dumping the model
f = 'model/log.pkl'
with open(f, 'wb') as file:
pickle.dump(log_clf, file)
# loading it
loaded_model = joblib.load(f)
# double check on a single datapoint
new_data = pd.DataFrame({'age': 71,
'sex': 0,
'cp': 0,
'trestbps': 112,
'chol': 203,
'fbs': 0,
'restecg': 1,
'thalach': 185,
'exang': 0,
'oldpeak': 0.1,
'slope': 2,
'ca': 0,
'thal': 2}, index=[0])
loaded_model.predict(new_data)
...and it works just fine. Then I deploy the model to the Azure Web Service using these steps:
I create the score.py file
import joblib
from azureml.core.model import Model
import json
def init():
global model
model_path = Model.get_model_path('log') # logistic
print('Model Path is ', model_path)
model = joblib.load(model_path)
def run(data):
try:
data = json.loads(data)
result = model.predict(data['data'])
# any data type, as long as it is JSON serializable.
return {'data' : result.tolist() , 'message' : 'Successfully classified heart diseases'}
except Exception as e:
error = str(e)
return {'data' : error , 'message' : 'Failed to classify heart diseases'}
I deploy the model:
from azureml.core import Workspace
from azureml.core.webservice import AciWebservice
from azureml.core.webservice import Webservice
from azureml.core.model import InferenceConfig
from azureml.core.environment import Environment
from azureml.core import Workspace
from azureml.core.model import Model
from azureml.core.conda_dependencies import CondaDependencies
ws = Workspace.from_config()
model = Model.register(workspace = ws,
model_path ='model/log.pkl',
model_name = 'log',
tags = {'version': '1'},
description = 'Heart disease classification',
)
# to install required packages
env = Environment('env')
cd = CondaDependencies.create(pip_packages=['pandas==1.1.5', 'azureml-defaults','joblib==0.17.0'], conda_packages = ['scikit-learn==0.23.2'])
env.python.conda_dependencies = cd
# Register environment to re-use later
env.register(workspace = ws)
print('Registered Environment')
myenv = Environment.get(workspace=ws, name='env')
myenv.save_to_directory('./environ', overwrite=True)
aciconfig = AciWebservice.deploy_configuration(
cpu_cores=1,
memory_gb=1,
tags={'data':'heart disease classifier'},
description='Classification of heart diseases',
)
inference_config = InferenceConfig(entry_script='score.py', environment=myenv)
service = Model.deploy(workspace=ws,
name='hd-model-log',
models=[model],
inference_config=inference_config,
deployment_config=aciconfig,
overwrite = True)
service.wait_for_deployment(show_output=True)
url = service.scoring_uri
print(url)
The deployment is fine:
Succeeded
ACI service creation operation finished, operation "Succeeded"
But I can not make any predictions with the new data. I try to use:
import pandas as pd
new_data = pd.DataFrame([[71, 0, 0, 112, 203, 0, 1, 185, 0, 0.1, 2, 0, 2],
[80, 0, 0, 115, 203, 0, 1, 185, 0, 0.1, 2, 0, 0]],
columns=['age', 'sex', 'cp', 'trestbps', 'chol', 'fbs', 'restecg', 'thalach', 'exang', 'oldpeak', 'slope', 'ca', 'thal'])
Following the answer from this topic (https://learn.microsoft.com/en-us/answers/questions/217305/data-input-format-call-the-service-for-azure-ml-ti.html) I transform the data:
test_sample = json.dumps({'data': new_data.to_dict(orient='records')})
And try to make some predictions:
import json
import requests
data = test_sample
headers = {'Content-Type':'application/json'}
r = requests.post(url, data=data, headers = headers)
print(r.status_code)
print(r.json())
However, I encounter an error:
200
{'data': "Expected 2D array, got 1D array instead:\narray=[{'age': 71, 'sex': 0, 'cp': 0, 'trestbps': 112, 'chol': 203, 'fbs': 0, 'restecg': 1, 'thalach': 185, 'exang': 0, 'oldpeak': 0.1, 'slope': 2, 'ca': 0, 'thal': > 2}\n {'age': 80, 'sex': 0, 'cp': 0, 'trestbps': 115, 'chol': 203, 'fbs': 0, 'restecg': 1, 'thalach': 185, 'exang': 0, 'oldpeak': 0.1, 'slope': 2, 'ca': 0, 'thal': 0}].\nReshape your data either using array.reshape(-1, > 1) if your data has a single feature or array.reshape(1, -1) if it contains a single sample.", 'message': 'Failed to classify heart diseases'}
How is it possible to adjust the input data to this form of predictions and add other output like predict_proba so I could store them in a separate output dataset?
I know this error is somehow related either with the "run" part of the score.py file or the last code cell that calls the webservice, but I'm unable to find it.
Would really appreciate some help.

Answer 1

I believe I managed to solve the problem - even though I encountered some serious issues. :)
As described here here - I edited the score.py script:
import joblib
from azureml.core.model import Model
import numpy as np
import json
import pandas as pd
import numpy as np
from inference_schema.schema_decorators import input_schema, output_schema
from inference_schema.parameter_types.numpy_parameter_type import NumpyParameterType
from inference_schema.parameter_types.pandas_parameter_type import PandasParameterType
from inference_schema.parameter_types.standard_py_parameter_type import StandardPythonParameterType
data_sample = PandasParameterType(pd.DataFrame({'age': pd.Series([0], dtype='int64'),
'sex': pd.Series(['example_value'], dtype='object'),
'cp': pd.Series(['example_value'], dtype='object'),
'trestbps': pd.Series([0], dtype='int64'),
'chol': pd.Series([0], dtype='int64'),
'fbs': pd.Series(['example_value'], dtype='object'),
'restecg': pd.Series(['example_value'], dtype='object'),
'thalach': pd.Series([0], dtype='int64'),
'exang': pd.Series(['example_value'], dtype='object'),
'oldpeak': pd.Series([0.0], dtype='float64'),
'slope': pd.Series(['example_value'], dtype='object'),
'ca': pd.Series(['example_value'], dtype='object'),
'thal': pd.Series(['example_value'], dtype='object')}))
input_sample = StandardPythonParameterType({'data': data_sample})
result_sample = NumpyParameterType(np.array([0]))
output_sample = StandardPythonParameterType({'Results':result_sample})
def init():
global model
# Example when the model is a file
model_path = Model.get_model_path('log') # logistic
print('Model Path is ', model_path)
model = joblib.load(model_path)
#input_schema('Inputs', input_sample)
#output_schema(output_sample)
def run(Inputs):
try:
data = Inputs['data']
result = model.predict_proba(data)
return result.tolist()
except Exception as e:
error = str(e)
return error
In the deployment step I adjusted the CondaDependencies:
# to install required packages
env = Environment('env')
cd = CondaDependencies.create(pip_packages=['pandas==1.1.5', 'azureml-defaults','joblib==0.17.0', 'inference-schema==1.3.0'], conda_packages = ['scikit-learn==0.22.2.post1'])
env.python.conda_dependencies = cd
# Register environment to re-use later
env.register(workspace = ws)
print('Registered Environment')
as
a) It is necessary to include inference-schema in the Dependencies file
b) I downgraded scikit-learn to scikit-learn==0.22.2.post1 version because of this issue
Now, when I feed the model with new data:
new_data = {
"Inputs": {
"data": [
{
"age": 71,
"sex": "0",
"cp": "0",
"trestbps": 112,
"chol": 203,
"fbs": "0",
"restecg": "1",
"thalach": 185,
"exang": "0",
"oldpeak": 0.1,
"slope": "2",
"ca": "0",
"thal": "2"
}
]
}
}
And use it for prediction:
import json
import requests
data = new_data
headers = {'Content-Type':'application/json'}
r = requests.post(url, str.encode(json.dumps(data)), headers = headers)
print(r.status_code)
print(r.json())
I get:
200 [[0.02325369841858338, 0.9767463015814166]]
Uff! Maybe someone will benefit from my painful learning path! :)

Answer 2

The main issue is with the conversion of categorical variables. The traditional method of handling categorical variable is using OneHotEncoder
# changing format of the categorical variables
df[cat_cols] = df[cat_cols].apply(lambda x: x.astype('object'))
The transforming data need to apply like mentioned below:
from sklearn.preprocessing import MinMaxScaler
cat_col =['sex',
'cp',
'fbs',
'restecg',
'exang',
'slope',
'ca',
'thal']
df_2 = pd.get_dummies(data[cat_col], drop_first = True)
[0,1]'s will be formed after applying dummies, then
new_data = pd.DataFrame([[71, 0, 0, 112, 203, 0, 1, 185, 0, 0.1, 2, 0, 2],
[80, 0, 0, 115, 203, 0, 1, 185, 0, 0.1, 2, 0, 0]],
columns=['age', 'sex', 'cp', 'trestbps', 'chol', 'fbs', 'restecg', 'thalach', 'exang', 'oldpeak', 'slope', 'ca', 'thal'])
This can be applied with fewer changes in the syntax.
Edit:
new_data = {
"Inputs": {
"data": [
{
"age": 71,
"sex": "0",
"cp": "0",
"trestbps": 112,
"chol": 203,
"fbs": "0",
"restecg": "1",
"thalach": 185,
"exang": "0",
"oldpeak": 0.1,
"slope": "2",
"ca": "0",
"thal": "2"
}
]
}
}