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DarrylBryson
DarrylBryson

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Auto Generate Lab Measurement Dataset

#python #datascience #devops #sampledata

Auto Generate Lab Measurement Dataset

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A typical data source found in most industrial work places are lab measurements. This type of data usually has a well defined structure and is a mixture of categorical and numeric data types. Measurement ranges and file format can vary greatly between use cases. This article covers how to generate a simple dataset that can be customized to simulate a wide range of use cases.

Contents

  1. Data Structure
  2. Packages
    • Faker
    • xml.etree.ElementTree
    • Pandas
  3. Generate Dataset
  4. Convert Dataset to XML
  5. Convert Dataset to Pandas DataFrame
  6. Save File
    • csv
    • xml
    • parquet

Sample Data Structure

Field DataType Min Max
machine_id string
test_id uuid
technician string
test_routine categorical
batched categorical
loc_1 dictionary
loc_1_x_offset decimal -15 15
loc_1_y_offset decimal -1 1
loc_1_z_offset int 2500 5000
loc_2 dictionary
loc_2_x_offset decimal -15 15
loc_2_y_offset decimal -1 1
loc_2_z_offset int 2500 5000

Packages

Faker: Is a python package for creating, as the name implies, fake data. This library not only generates random numbers and strings but more complex elements like addresses, and names.

from faker import Faker
fake = Faker()
Faker.seed(0)
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xml.etree.ElementTree: Is a base library of Python that is a simple and efficient way of querying, parsing, and creating XML data.

import xml.etree.ElementTree as ET
from xml.dom import minidom
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Pandas: Is the goto library for working with table-like data.

import pandas as pd
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# base imports
import uuid
import os
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Generate Dataset

The structure of the dataset is represented by a dictionary and uses Faker to fill in the data values. This allows for simple modifications when moving between use cases.

def generate_measurement_record():
    base_equipment_name='Machine'
    equipment_cnt = 25
    n = fake.pyint(min_value=1, max_value=equipment_cnt)

    measurement_record = {
        'machine_id': '_'.join([base_equipment_name, f'{n:02}'])
        ,'test_id':str(uuid.uuid4().hex)
        ,'technician':fake.name()
        ,'test_routine':fake.random_sample(elements=('a', 'b', 'c', 'd', 'e', 'f'))
        ,'batched':fake.random_sample(elements=('Yes', 'No', 'N/A'), length=1)[0]
        ,'loc_1':{
            'x_offset':fake.pydecimal(left_digits=2, right_digits=2, min_value=-15, max_value=15)
            ,'y_offset':fake.pydecimal(left_digits=1, right_digits=6, min_value=-1, max_value=1)
            ,'z_offset':fake.pyint(min_value=2500, max_value=5000)
        }
        ,'loc_2':{
            'x_offset':fake.pydecimal(left_digits=2, right_digits=2, min_value=-15, max_value=15)
            ,'y_offset':fake.pydecimal(left_digits=1, right_digits=6, min_value=-1, max_value=1)
            ,'z_offset':fake.pyint(min_value=2500, max_value=5000)
        }
    }
    return measurement_record
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Repeatedly calling this function generates new records with random data that can be collected in a list up to a desired size.

records_cnt = 5

measurement_record = None
measurement_list=[]

for _ in range(records_cnt):
    measurement_record = generate_measurement_record()
    measurement_list.append(measurement_record) # List of nested dictionaries
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Convert Dataset to XML

Next we'll need a function that will handle converting the records stored as dictionaries to xml. Then apply the function to each record in the list.

import xml.etree.ElementTree as ET

def dict_to_xml(d, r=None):
    file_id = str(uuid.uuid4().hex)
    if r is None:
        r = ET.Element('DataFile')
        r.set('id', file_id)
    if isinstance(d, dict):
        for k, v in d.items():
            s = ET.SubElement(r, k)
            dict_to_xml(v, s)
    elif isinstance(d, tuple) or isinstance(d, list):
        val = '/'.join(str(v) for v in d)
        r.text = val
    elif isinstance(d, str):
        r.text = d
    else:
        r.text = str(d)
    return r
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# Convert each record
xml_dataset = ET.Element('DataFiles')
for rcd in measurement_list:
    file_id = str(uuid.uuid4().hex)
    child = ET.SubElement(xml_dataset,'DataFile')
    child.set('id', file_id)

    # Convert to xml
    element= dict_to_xml(rcd,child)
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The resulting xml file can be viewed with:

from xml.dom import minidom

xml= ET.tostring(xml_dataset, encoding='unicode', method='xml')
xml= minidom.parseString(xml)
xml= xml.toprettyxml(indent='  ')

print(xml)
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<?xml version="1.0" ?>
<DataFiles>
  <DataFile id="33c768494e484df9b954c4c7bae2ce68">
    <machine_id>Machine_10</machine_id>
    <test_id>3c0c95f773bf426585a3a68642d2d41a</test_id>
    <technician>Brett Kerr</technician>
    <test_routine>c/f/a/b</test_routine>
    <batched>Yes</batched>
    <loc_1>
      <x_offset>8.63</x_offset>
      <y_offset>0.39661</y_offset>
      <z_offset>3736</z_offset>
    </loc_1>
    <loc_2>
      <x_offset>-4.94</x_offset>
      <y_offset>0.964363</y_offset>
      <z_offset>3182</z_offset>
    </loc_2>
  </DataFile>
</DataFiles>
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Convert Dataset to Pandas DataFrame

Pandas can directly create a DataFrame from a dictionary if the dictionary is not nested. So, the first step of conversion is to create a function to flatten the measurement dictionary structure:

import collections.abc

def flatten(d, parent_key='', sep='_'):
    items = []
    for k, v in d.items():
        new_key = parent_key + sep + k if parent_key else k
        if isinstance(v, collections.MutableMapping):
            items.extend(flatten(v, new_key, sep=sep).items())
        else:
            items.append((new_key, v))
    return dict(items)
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Next, create a new list of the flattened records:

measurement_flat_list= []

for rcd in measurement_list:
    measurement_flat_list.append(flatten(rcd)) # List of single depth dictionaries
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Finally, convert the list to a dataframe:

measurement_df = pd.DataFrame(measurement_flat_list)
measurement_df.head()
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machine_id test_id technician test_routine batched loc_1_x_offset loc_1_y_offset loc_1_z_offset loc_2_x_offset loc_2_y_offset loc_2_z_offset
0 Machine_02 ffbb9f35d5484deebab0598926194203 Stephanie Leblanc [f, d, c, e, a] Yes 14.86 0.607854 3627 0.63 0.86374 3828
1 Machine_20 fb824a88e0f145169b411a2180c5671c Kevin Rogers [b, a] N/A -6.14 0.390133 3198 -4.54 0.105494 3099
2 Machine_23 25d73f925ba14df5a09a11ef8fb3a68d Robert Walters [e, a, f, d, c] N/A 12.73 0.410212 2874 -3.14 0.634917 2588
3 Machine_07 a3fb30a0fe8f4000aa72eb182230d236 Cathy Martinez [f, a] N/A -14.69 0.650746 2915 12.33 0.231556 2794
4 Machine_21 02a27172e035464fbdf680c476312b03 Jeffrey Brown [a, e, f, c] No -8.33 0.94833 4426 12.72 0.731588 3333

Save Dataset Files

  • XML
  • CSV
  • Parquet 
# xml
destPath = 'sample_lab_measurement.xml'
# Convert to string
xml_str= ET.tostring(xml_dataset, encoding='unicode', method='xml')

# Pretty print string 
xml_str= minidom.parseString(xml_str)
xml_str= xml_str.toprettyxml(indent='  ')

# Write file
with open(destPath, 'w') as f:  # Write in file as utf-8
    f.write(xml_str)
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# csv
destPath = 'sample_lab_measurement.csv'
measurement_df.to_csv(destPath, index = False, header=True)
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# parquet
destPath = 'sample_lab_measurement.parquet'
measurement_df.to_parquet(destPath, index = False)
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