# HDBScan-based clustering algorithm using the hdbscan library to assign cluster labels
# to multidimensional data with runtime and memory tracking, and support for saving results.
#
# **Importing and Using the HDBScan Class in a Python Program**
#
# import pandas as pd
#
# from geoanalytics.clustering import HDBScan
#
# df = pd.read_csv('input.csv')
#
# hdb = HDBScan(df)
#
# labels_df = hdb.run(min_sample=5, min_cluster_size=10)
#
# hdb.getRuntime()
#
# hdb.getMemoryUSS()
#
# hdb.getMemoryRSS()
#
# hdb.save('HDBScanLabels.csv')
#
__copyright__ = """
Copyright (C) 2022 Rage Uday Kiran
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
"""
import time
import psutil
import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
import hdbscan as hdbscan
import pandas as pd
[docs]
class HDBScan:
"""
**About this algorithm**
:**Description**:
HDBSCAN (Hierarchical Density-Based Spatial Clustering of Applications with Noise)
is an advanced density-based clustering algorithm. It extends DBSCAN by converting
it into a hierarchical clustering algorithm and then using a technique to extract a flat
clustering based on the stability of clusters. This wrapper enables runtime and memory
usage tracking, and allows exporting results to CSV.
:**Parameters**:
- Dataset (pandas DataFrame) must be provided during object initialization.
- Clustering hyperparameters are passed to the run() method.
:**Attributes**:
- **df** (*pd.DataFrame*) -- The input data with 'x', 'y' coordinates and features.
- **labelsDF** (*pd.DataFrame*) -- DataFrame containing 'x', 'y', and assigned cluster labels.
- **startTime, endTime** (*float*) -- Runtime tracking.
- **memoryUSS, memoryRSS** (*float*) -- Memory usage of the clustering process in kilobytes.
**Execution methods**
**Calling from a Python program**
.. code-block:: python
import pandas as pd
from geoanalytics.clustering import HDBScan
df = pd.read_csv("input.csv")
hdb = HDBScan(df)
labels_df = hdb.run(min_sample=5, min_cluster_size=10)
hdb.getRuntime()
hdb.getMemoryUSS()
hdb.getMemoryRSS()
hdb.save('HDBScanLabels.csv')
**Credits**
This implementation was created by Raashika and revised by M.Charan Teja under the guidance of Professor Rage Uday Kiran.
"""
def __init__(self, dataframe):
self.df = dataframe.copy()
self.df.columns = ['x', 'y'] + list(self.df.columns[2:])
self.labelsDF = None
self.startTime = None
self.endTime = None
self.memoryUSS = None
self.memoryRSS = None
[docs]
def getRuntime(self):
"""
Prints the total runtime of the clustering algorithm.
"""
print("Total Execution time of proposed Algorithm:", self.endTime - self.startTime, "seconds")
[docs]
def getMemoryUSS(self):
"""
Prints the memory usage (USS) of the process in kilobytes.
"""
print("Memory (USS) of proposed Algorithm in KB:", self.memoryUSS)
[docs]
def run(self, min_sample = 5, min_cluster_size = 10):
"""
Executes HDBScan clustering algorithm.
:param min_sample: int, minimum samples required for a dense region (default: 5)
:param min_cluster_size: int, minimum size of clusters to extract (default: 10)
:return: labelsDF (pd.DataFrame) with columns ['x', 'y', 'labels']
"""
self.startTime = time.time()
data = self.df.drop(['x', 'y'], axis=1)
data = data.to_numpy()
hdbs = hdbscan.HDBSCAN(min_samples=min_sample, min_cluster_size=min_cluster_size, core_dist_n_jobs=1).fit(data)
label = self.df[['x', 'y']]
self.labelsDF = label.assign(labels=hdbs.labels_)
self.endTime = time.time()
process = psutil.Process()
self.memoryUSS = process.memory_full_info().uss / 1024
self.memoryRSS = process.memory_full_info().rss / 1024
return self.labelsDF
[docs]
def save(self, outputFileLabels='HDBScanLabels.csv'):
"""
Saves the clustering result with labels to a CSV file.
:param outputFileLabels: str, filename for saving labels (default: 'HDBScanLabels.csv')
"""
if self.labelsDF is not None:
try:
self.labelsDF.to_csv(outputFileLabels, index=False)
print(f"Labels saved to: {outputFileLabels}")
except Exception as e:
print(f"Failed to save labels: {e}")
else:
print("No labels to save. Please execute run() method first.")