LakeBeD-US-CSE

#!/usr/bin/env python3 
# -*- coding: utf-8 -*-
"""
Attribution 4.0 International
=======================================================================
Creative Commons Corporation ("Creative Commons") is not a law firm and
does not provide legal services or legal advice. Distribution of
Creative Commons public licenses does not create a lawyer-client or
other relationship. Creative Commons makes its licenses and related
information available on an "as-is" basis. Creative Commons gives no
warranties regarding its licenses, any material licensed under their
terms and conditions, or any related information. Creative Commons
disclaims all liability for damages resulting from their use to the
fullest extent possible.
Using Creative Commons Public Licenses
Creative Commons public licenses provide a standard set of terms and
conditions that creators and other rights holders may use to share
original works of authorship and other material subject to copyright
and certain other rights specified in the public license below. The
following considerations are for informational purposes only, are not
exhaustive, and do not form part of our licenses.
	Considerations for licensors: Our public licenses are
	intended for use by those authorized to give the public
	permission to use material in ways otherwise restricted by
	copyright and certain other rights. Our licenses are
	irrevocable. Licensors should read and understand the terms
	and conditions of the license they choose before applying it.
	Licensors should also secure all rights necessary before
	applying our licenses so that the public can reuse the
	material as expected. Licensors should clearly mark any
	material not subject to the license. This includes other CC-
	licensed material, or material used under an exception or
	limitation to copyright. More considerations for licensors:
	wiki.creativecommons.org/Considerations_for_licensors
	Considerations for the public: By using one of our public
	licenses, a licensor grants the public permission to use the
	licensed material under specified terms and conditions. If
	the licensor's permission is not necessary for any reason--for
	example, because of any applicable exception or limitation to
	copyright--then that use is not regulated by the license. Our
	licenses grant only permissions under copyright and certain
	other rights that a licensor has authority to grant. Use of
	the licensed material may still be restricted for other
	reasons, including because others have copyright or other
	rights in the material. A licensor may make special requests,
	such as asking that all changes be marked or described.
	Although not required by our licenses, you are encouraged to
	respect those requests where reasonable. More considerations
	for the public:
	wiki.creativecommons.org/Considerations_for_licensees
=======================================================================
Creative Commons Attribution 4.0 International Public License
By exercising the Licensed Rights (defined below), You accept and agree
to be bound by the terms and conditions of this Creative Commons
Attribution 4.0 International Public License ("Public License"). To the
extent this Public License may be interpreted as a contract, You are
granted the Licensed Rights in consideration of Your acceptance of
these terms and conditions, and the Licensor grants You such rights in
consideration of benefits the Licensor receives from making the
Licensed Material available under these terms and conditions.
Section 1 -- Definitions.
	a. Adapted Material means material subject to Copyright and Similar
		Rights that is derived from or based upon the Licensed Material
		and in which the Licensed Material is translated, altered,
		arranged, transformed, or otherwise modified in a manner requiring
		permission under the Copyright and Similar Rights held by the
		Licensor. For purposes of this Public License, where the Licensed
		Material is a musical work, performance, or sound recording,
		Adapted Material is always produced where the Licensed Material is
		synched in timed relation with a moving image.
  	b. Adapter's License means the license You apply to Your Copyright
		and Similar Rights in Your contributions to Adapted Material in
		accordance with the terms and conditions of this Public License.
  	c. Copyright and Similar Rights means copyright and/or similar rights
		closely related to copyright including, without limitation,
		performance, broadcast, sound recording, and Sui Generis Database
		Rights, without regard to how the rights are labeled or
		categorized. For purposes of this Public License, the rights
		specified in Section 2(b)(1)-(2) are not Copyright and Similar
		Rights.
  	d. Effective Technological Measures means those measures that, in the
		absence of proper authority, may not be circumvented under laws
		fulfilling obligations under Article 11 of the WIPO Copyright
		Treaty adopted on December 20, 1996, and/or similar international
		agreements.
  	e. Exceptions and Limitations means fair use, fair dealing, and/or
		any other exception or limitation to Copyright and Similar Rights
		that applies to Your use of the Licensed Material.
	f. Licensed Material means the artistic or literary work, database,
		or other material to which the Licensor applied this Public
		License.
	g. Licensed Rights means the rights granted to You subject to the
		terms and conditions of this Public License, which are limited to
		all Copyright and Similar Rights that apply to Your use of the
		Licensed Material and that the Licensor has authority to license.
	h. Licensor means the individual(s) or entity(ies) granting rights
		under this Public License.
	i. Share means to provide material to the public by any means or
		process that requires permission under the Licensed Rights, such
		as reproduction, public display, public performance, distribution,
		dissemination, communication, or importation, and to make material
		available to the public including in ways that members of the
		public may access the material from a place and at a time
		individually chosen by them.
	j. Sui Generis Database Rights means rights other than copyright
		resulting from Directive 96/9/EC of the European Parliament and of
		the Council of 11 March 1996 on the legal protection of databases,
		as amended and/or succeeded, as well as other essentially
		equivalent rights anywhere in the world.
	k. You means the individual or entity exercising the Licensed Rights
		under this Public License. Your has a corresponding meaning.
Section 2 -- Scope.
  	a. License grant.
		1. Subject to the terms and conditions of this Public License,
			the Licensor hereby grants You a worldwide, royalty-free,
			non-sublicensable, non-exclusive, irrevocable license to
			exercise the Licensed Rights in the Licensed Material to:
			a. reproduce and Share the Licensed Material, in whole or
				in part; and
			b. produce, reproduce, and Share Adapted Material.
		2. Exceptions and Limitations. For the avoidance of doubt, where
			Exceptions and Limitations apply to Your use, this Public
			License does not apply, and You do not need to comply with
			its terms and conditions.
		3. Term. The term of this Public License is specified in Section
			6(a).
		4. Media and formats; technical modifications allowed. The
			Licensor authorizes You to exercise the Licensed Rights in
			all media and formats whether now known or hereafter created,
			and to make technical modifications necessary to do so. The
			Licensor waives and/or agrees not to assert any right or
			authority to forbid You from making technical modifications
			necessary to exercise the Licensed Rights, including
			technical modifications necessary to circumvent Effective
			Technological Measures. For purposes of this Public License,
			simply making modifications authorized by this Section 2(a)
			(4) never produces Adapted Material.
		5. Downstream recipients.
			a. Offer from the Licensor -- Licensed Material. Every
			   recipient of the Licensed Material automatically
			   receives an offer from the Licensor to exercise the
			   Licensed Rights under the terms and conditions of this
			   Public License.
			b. No downstream restrictions. You may not offer or impose
			   any additional or different terms or conditions on, or
			   apply any Effective Technological Measures to, the
			   Licensed Material if doing so restricts exercise of the
			   Licensed Rights by any recipient of the Licensed
			   Material.
		6. No endorsement. Nothing in this Public License constitutes or
			may be construed as permission to assert or imply that You
			are, or that Your use of the Licensed Material is, connected
			with, or sponsored, endorsed, or granted official status by,
			the Licensor or others designated to receive attribution as
			provided in Section 3(a)(1)(A)(i).
	b. Other rights.
		1. Moral rights, such as the right of integrity, are not
			licensed under this Public License, nor are publicity,
			privacy, and/or other similar personality rights; however, to
			the extent possible, the Licensor waives and/or agrees not to
			assert any such rights held by the Licensor to the limited
			extent necessary to allow You to exercise the Licensed
			Rights, but not otherwise.
		2. Patent and trademark rights are not licensed under this
			Public License.
		3. To the extent possible, the Licensor waives any right to
			collect royalties from You for the exercise of the Licensed
			Rights, whether directly or through a collecting society
			under any voluntary or waivable statutory or compulsory
			licensing scheme. In all other cases the Licensor expressly
			reserves any right to collect such royalties.
Section 3 -- License Conditions.
Your exercise of the Licensed Rights is expressly made subject to the
following conditions.
	a. Attribution.
		1. If You Share the Licensed Material (including in modified
			form), You must:
				a. retain the following if it is supplied by the Licensor
				with the Licensed Material:
					i. identification of the creator(s) of the Licensed
						Material and any others designated to receive
						attribution, in any reasonable manner requested by
						the Licensor (including by pseudonym if
						designated);
					ii. a copyright notice;
					iii. a notice that refers to this Public License;
					iv. a notice that refers to the disclaimer of
						warranties;
					v. a URI or hyperlink to the Licensed Material to the
						extent reasonably practicable;
			b. indicate if You modified the Licensed Material and
			   retain an indication of any previous modifications; and
			c. indicate the Licensed Material is licensed under this
			   Public License, and include the text of, or the URI or
			   hyperlink to, this Public License.
		2. You may satisfy the conditions in Section 3(a)(1) in any
			reasonable manner based on the medium, means, and context in
			which You Share the Licensed Material. For example, it may be
			reasonable to satisfy the conditions by providing a URI or
			hyperlink to a resource that includes the required
			information.
		3. If requested by the Licensor, You must remove any of the
			information required by Section 3(a)(1)(A) to the extent
			reasonably practicable.
		4. If You Share Adapted Material You produce, the Adapter's
			License You apply must not prevent recipients of the Adapted
			Material from complying with this Public License.
Section 4 -- Sui Generis Database Rights.
Where the Licensed Rights include Sui Generis Database Rights that
apply to Your use of the Licensed Material:
	a. for the avoidance of doubt, Section 2(a)(1) grants You the right
		to extract, reuse, reproduce, and Share all or a substantial
		portion of the contents of the database;
	b. if You include all or a substantial portion of the database
		contents in a database in which You have Sui Generis Database
		Rights, then the database in which You have Sui Generis Database
		Rights (but not its individual contents) is Adapted Material; and
	c. You must comply with the conditions in Section 3(a) if You Share
		all or a substantial portion of the contents of the database.
For the avoidance of doubt, this Section 4 supplements and does not
replace Your obligations under this Public License where the Licensed
Rights include other Copyright and Similar Rights.
Section 5 -- Disclaimer of Warranties and Limitation of Liability.
	a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
		EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
		AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
		ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
		IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
		WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
		PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
		ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
		KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
		ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
	b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
		TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
		NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
		INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
		COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
		USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
		ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
		DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
		IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
	c. The disclaimer of warranties and limitation of liability provided
		above shall be interpreted in a manner that, to the extent
		possible, most closely approximates an absolute disclaimer and
		waiver of all liability.
Section 6 -- Term and Termination.
	a. This Public License applies for the term of the Copyright and
		Similar Rights licensed here. However, if You fail to comply with
		this Public License, then Your rights under this Public License
		terminate automatically.
	b. Where Your right to use the Licensed Material has terminated under
		Section 6(a), it reinstates:
		1. automatically as of the date the violation is cured, provided
			it is cured within 30 days of Your discovery of the
			violation; or
		2. upon express reinstatement by the Licensor.
	For the avoidance of doubt, this Section 6(b) does not affect any
	right the Licensor may have to seek remedies for Your violations
	of this Public License.
	c. For the avoidance of doubt, the Licensor may also offer the
		Licensed Material under separate terms or conditions or stop
		distributing the Licensed Material at any time; however, doing so
		will not terminate this Public License.
	d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
		License.
Section 7 -- Other Terms and Conditions.
	a. The Licensor shall not be bound by any additional or different
		terms or conditions communicated by You unless expressly agreed.
  	b. Any arrangements, understandings, or agreements regarding the
		Licensed Material not stated herein are separate from and
		independent of the terms and conditions of this Public License.
Section 8 -- Interpretation.
	a. For the avoidance of doubt, this Public License does not, and
		shall not be interpreted to, reduce, limit, restrict, or impose
		conditions on any use of the Licensed Material that could lawfully
		be made without permission under this Public License.
  	b. To the extent possible, if any provision of this Public License is
		deemed unenforceable, it shall be automatically reformed to the
		minimum extent necessary to make it enforceable. If the provision
		cannot be reformed, it shall be severed from this Public License
		without affecting the enforceability of the remaining terms and
		conditions.
  	c. No term or condition of this Public License will be waived and no
		failure to comply consented to unless expressly agreed to by the
		Licensor.
	d. Nothing in this Public License constitutes or may be interpreted
		as a limitation upon, or waiver of, any privileges and immunities
		that apply to the Licensor or You, including from the legal
		processes of any jurisdiction or authority.
=======================================================================
Creative Commons is not a party to its public
licenses. Notwithstanding, Creative Commons may elect to apply one of
its public licenses to material it publishes and in those instances
will be considered the “Licensor.” The text of the Creative Commons
public licenses is dedicated to the public domain under the CC0 Public
Domain Dedication. Except for the limited purpose of indicating that
material is shared under a Creative Commons public license or as
otherwise permitted by the Creative Commons policies published at
creativecommons.org/policies, Creative Commons does not authorize the
use of the trademark "Creative Commons" or any other trademark or logo
of Creative Commons without its prior written consent including,
without limitation, in connection with any unauthorized modifications
to any of its public licenses or any other arrangements,
understandings, or agreements concerning use of licensed material. For
the avoidance of doubt, this paragraph does not form part of the
public licenses.
Creative Commons may be contacted at creativecommons.org.
File: preprocess.py
Author: Aanish Pradhan
Created: 2024-09-09
License: Creative Commons Attribution 4.0 International (CC BY 4.0)
Description: Converts the LakeBeD-US: Ecology Edition dataset (McAfee et.al. 
2024) into the LakeBeD-US: Computer Science Edition dataset.
"""
# IMPORT PACKAGES
from collections import defaultdict # Default value for absent keys in dict
import lakedata # LakeBeD-US Lake class, constants and methods
import numpy as np # Numerical operations
import os # Operating system interfaces
import pandas as pd # Dataframe manipulation
import re # Regular expressions
import sys # System-specific parameters and functions
import typing # Type hints

# METHODS
def parse(lakebed_path: str) -> None:
	"""
	Parses through the files in the high frequency and low frequency 
	subdirectories of the specified LakeBeD-US data directory and processes 
	each raw data file.
	Args:
		lakebed_path (str): Path of the unzipped LakeBeD-US directory
	"""
	
	os.chdir(lakebed_path)
	
	# Process low frequency data
	print("Processing low frequency data...\n")
	os.chdir("LowFrequency")
	low_frequency_data_files = [file for file in os.listdir() if os.path.isfile(file)]
	low_frequency_data_files.sort()
	print(f"Low frequency data files: {low_frequency_data_files}\n")
	for low_frequency_data_file in low_frequency_data_files:
		print(f"Processing {low_frequency_data_file}...")
		wrangle(pd.read_parquet(low_frequency_data_file), low_frequency_data_file)
		print(f"Processed {low_frequency_data_file}\n")
	print("Processed low frequency data.\n")

	os.chdir("..") # Navigate back to parent LakeBeD-US directory

	# Process the high frequency data
	print("Processing high frequency data...\n")
	os.chdir("HighFrequency")
	concatenate_partitions(os.listdir())
	high_frequency_data_files = [file for file in os.listdir() if os.path.isfile(file)]
	high_frequency_data_files.sort()
	print(f"High frequency data files: {high_frequency_data_files}\n")
	for high_frequency_data_file in high_frequency_data_files:
		print(f"Processing {high_frequency_data_file}...")
		wrangle(pd.read_parquet(high_frequency_data_file), high_frequency_data_file)
		print(f"Processed {high_frequency_data_file}\n")
	print("Processed high frequency data.\n")

	os.chdir("..")
	print("Processed all files. Done")

def concatenate_partitions(files: list) -> None:
	"""
	Determines if any partitions of raw files in the unzipped LakeBeD-US data 
	directory need to be concatenated into a single data file. Partitioned 
	files are detected via RegEx matching if their filename matches the 
	following patterns (omitting the brackets): [FILENAME]_[LETTER PARTITION] 
	or [FILENAME]_[LETTER PARTITION]_[NUMBER PARTITION]. Data files with letter 
	and number partitions are concatenated into a single, lettered partition 
	file first. Lettered partitions are then concatenated into a single 
	file. For example, "Lake_A_1", "Lake_A_2", etc., "Lake_B_1", "Lake_B_2", 
	etc., are first concatenated into "Lake_A" and "Lake_B" and then 
	concatenated into "Lake". The original partitions and intermediate files 
	are deleted after concatenation.
	
	Args:
		files (list): A list of partitioned data files in the current working 
			directory
	"""

	lake_partitions = defaultdict(lambda: defaultdict(list))
	pattern = re.compile(r"([A-Za-z]+)(_([A-Z])(_(\d+))?)?\.parquet")

	for file in files:
		if file.endswith('.parquet'):
			match = pattern.match(file)
			if match:
				lake = match.group(1)
				lettered_partition = match.group(3) or ""
				numbered_sub_partition = match.group(5)

				if numbered_sub_partition:
					lake_partitions[lake][lettered_partition].append(file)
				else:
					lake_partitions[lake][lettered_partition].append(file)

	actions = []

	for lake, partitions in lake_partitions.items():
		for partition_letter, files in partitions.items():
			if partition_letter:
				if len(files) > 1:
					output_file = f"{lake}_{partition_letter}.parquet"
					actions.append((files, output_file))
					concatenate(files, output_file)
					for f in files:
						if os.path.exists(f):
							print(f"Deleting {f} after concatenation.")
							os.remove(f)
						else:
							print(f"File {f} not found. Skipping deletion.")

	for lake, partitions in lake_partitions.items():
		if len(partitions) > 1 or "" not in partitions:
			output_file = f"{lake}.parquet"
			partition_files = [f"{lake}_{letter}.parquet" for letter in partitions if letter]
			if partition_files:
				actions.append((partition_files, output_file))
				concatenate(partition_files, output_file)
				for pf in partition_files:
					if os.path.exists(pf):
						print(f"Deleting {pf} after concatenation.")
						os.remove(pf)
					else:
						print(f"File {pf} not found. Skipping deletion.")

	print("Concatenation Actions:")
	for files, output in actions:
		print(f"Concatenated {files} into {output}")

def concatenate(files: list, output_name: str) -> None:
	"""
	Concatenates a list of Apache Parquet files into a single file and then 
	writes the file to disk.
	Args:
		files (list): List of Apache Parquet files to concatenate
		output_name (str): Name of the output file
	"""

	files.sort()
	print(f"Concatenating {files} into {output_name}")

	partitions = []
	for file in files:
		partitions.append(pd.read_parquet(file))
	concatenated_data = pd.concat(partitions, axis=0)
	concatenated_data.to_parquet(output_name)

	for partition in partitions:
		del(partition)
	del(partitions)

def wrangle(data: pd.DataFrame, filename: str) -> None:
	"""
	Performs wrangling of dataframe from an Apache Parquet file.
	Args:
		data (pandas.DataFrame): Dataframe containing raw data of, potentially, 
			multiple lakes
		filename (str): Name of the file from which "data" came
	"""
	
	# Data Imputation
	"""
	Some dataframes may have missing values in the "flag" column. In cases 
	where the "flag" code is missing, we assume that there is no error with the 
	observation and impute the missing values with a '0' indicating a normal 
	observation.
	"""
	data["flag"] = data["flag"].fillna(0) # 0 = No error with observation
	print(f"Finished imputing {filename}")

	# Data Formatting
	"""
	This step verifies that the columns in the original dataframe are all of 
	correct type. Missing values in the dataframe might be coded as "None" 
	values but this doesn't let us meaningfully perform operations on the data 
	(e.g. grouping and aggregating). Replacing "None" with numpy.nan values 
	allows for such operations to function.
	"""
	data.fillna(np.nan) # NaN permits arithmetic operations on the missing data 
	data["source"] = data["source"].astype(str)
	data["datetime"] = pd.to_datetime(data["datetime"], utc = True)
	data["lake_id"] = data["lake_id"].astype(str)
	data["depth"] = data["depth"].astype(float)
	data["variable"] = data["variable"].astype(str)
	data["unit"] = data["unit"].astype(str)
	data["observation"] = data["observation"].astype(float)
	data["flag"] = data["flag"].astype(int)
	print(f"Finished formatting {filename}")

	# Data Cleaning
	"""
	Some erroneous observations may be coded such that their depth value is 
	"-99". We omit these values. It should be noted that negative depth values 
	are not necessarily incorrect. Hence we only omit observations with this 
	specific value.
	Chlorophyll a (chla) can be reported in two units: micrograms per liter and 
	relative fluoresence units. We split observations measuring chlorophyll a 
	into two variables by their unit.
	"""
	data[data["depth"] != -99.0]

	data.loc[(data["variable"] == "chla") & (data["unit"] == "MicroGM-PER-L"), "variable"] = "chla_ugl"
	data.loc[(data["variable"] == "chla") & (data["unit"] == "RFU"), "variable"] = "chla_rfu"
	print(f"Finished cleaning {filename}\n")

	# Data Structuring
	"""
	A single dataframe could contain data from multiple lakes. We split these 
	dataframes into a list of dataframes such that each element contains data 
	from only one lake.
	
	The data for each lake is then converted into a LakeData object (see 
	LakeData.py). This LakeData object holds the data for the lake in different 
	forms and for one-dimensional and two-dimensional variables. Depending on 
	what kind of output data is desired, we provide an easy way to extend the 
	functionality of this script to fit new purposes.
	Data within a dataframe can be duplicated. We combine duplicates into a 
	single observation by some predefined criteria (see LakeData.py).
	A dataframe can contain data for variables that change with time or depth 
	and time. We separate these variables into two dataframes.
	The data originally comes in a long format where different columns for 
	different features are represented in one columns with multiple rows. We 
	pivot this form to a wide, tabular format where different columns 
	represent different variables and each row represents a different datetime 
	and depth. The pivoting is done by some predefined criteria 
	(see LakeData.py).
	
	The one- and two-dimensional wide formats of the data are written out as 
	Apache Parquet files into a folder containing the data for a single lake. 
	The output files' names match the following pattern (omitting the 
	brackets): [LAKE ABBREVIATION]_[PARENT FILENAME]_[DIMENSIONALITY]
	"""
	data = data.sort_values(["lake_id", "datetime", "depth", "flag"])
	lakes = split_by_lake(data)
	lakes = [convert(lake) for lake in lakes]

	for lake in lakes:
		print(f"Deduplicating {lake.lake_id} in {filename}...")
		lake.deduplicate()
		print(f"Deduplicated {lake.lake_id} in {filename}")

		print(f"Separating variables for {lake.lake_id} in {filename}...")
		lake.separate_variables()
		print(f"Separated variables for {lake.lake_id} in {filename}")

		print(f"Pivoting {lake.lake_id} in {filename}...")
		lake.long_to_wide()
		print(f"Finished pivoting {lake.lake_id} in {filename}\n")

	print(f"Finished structuring {filename}\n")

	# Data Output
	for lake in lakes:
		lake_dir = lake.lake_id

		# Create directory based on lake_id if it doesn't exist
		if not os.path.exists(lake_dir):
			os.makedirs(lake_dir)

		# Sanitize parent_filename to remove file extensions and any unwanted characters
		parent_filename_clean = os.path.splitext(os.path.basename(filename))[0]
		parent_filename_clean = parent_filename_clean.replace(" ", "_")  # Replace spaces with underscores for safety

		# Generate output filenames using parent filename
		output_1d_filename = f"{lake.lake_id}_{parent_filename_clean}_1D.parquet"
		output_2d_filename = f"{lake.lake_id}_{parent_filename_clean}_2D.parquet"

		# Save CSV files in the created directory with the unique names
		print(f"Writing {lake_dir} in {filename} to disk...")
		lake.wide_data["1D"].to_parquet(os.path.join(lake_dir, output_1d_filename))
		lake.wide_data["2D"].to_parquet(os.path.join(lake_dir, output_2d_filename))
		print(f"Wrote {lake_dir} in {filename} to disk\n")


def split_by_lake(data: pd.DataFrame) -> typing.List[pd.DataFrame]:
	"""
	Splits a single dataframe containing data from multiple lakes into a list 
	of multiple dataframes with unique lakes.
	Args:
		data (pandas.DataFrame): Dataframe (potentially) containing data from 
			multiple lakes
	Returns:
		lakes (list): List containing dataframes with data for each unique lake
	"""	

	lake_ids = data["lake_id"].unique()
	lakes = []
	for lake_id in lake_ids:
		lake = data[data["lake_id"] == lake_id].reset_index(drop = True)
		lakes.append(lake)
		
	return lakes

def convert(data: pd.DataFrame) -> lakedata.LakeData:
	"""
	Converts a Pandas dataframe with data for a lake into a LakeData object.
	Args:
		data (pandas.DataFrame): Dataframe containing data for a single lake
	Returns:
		lake (LakeData): LakeData object with lake_id and raw_data fields 
			populated
	"""
	lake_id = data["lake_id"].unique()
	if len(lake_id) > 1:
		print(f"Lake dataframe contains more than 1 lake in it.")
		sys.exit(1)

	raw_data = data.drop("lake_id", axis = 1)
	lake = lakedata.LakeData(lake_id[0], raw_data)

	return lake

if __name__ == "__main__":

	if len(sys.argv) != 2:
		print(f"Usage: {sys.argv[0]} <PATH TO LAKEBED-US DATA DIRECTORY>/")
		sys.exit(1)
	else:
		lakebed_path = sys.argv[1]
		if not os.path.isdir(lakebed_path):
			print(f"Error: The provided path '{lakebed_path}' is not a directory.")
			sys.exit(1)
		  
		print(f"LakeBeD-US path: {lakebed_path}/\n")
		parse(lakebed_path)