使用Pandas对大文件进行切片、删除重复项并合并到输出中

Question

所以，我有一个有12.5亿个特性的地理包。该文件实际上并不包含几何图形，并且只有一个属性' id‘，它是唯一的id。有很多重复的东西，我想删除重复的'id‘，只保留唯一的值。由于存在大量的数据( geopackage包含19 GB)，我选择了切片。我尝试了多进程，但这不起作用，而且它会有问题，因为我必须跟踪唯一的'id‘，而多进程不允许这样做(至少据我所知)。

我所拥有的：

import fiona
import geopandas as gpd
import pandas as pd
# import numpy as np

slice_count = 200
start = 0
end = slice_count
fname = "path/Output.gpkg"

file_gpd = gpd.read_file(fname, rows=slice(start, end))
chunk = pd.DataFrame(file_gpd)
chunks = pd.DataFrame()
only_ids = pd.DataFrame(columns=['id'])
loop = True
while loop:
    try:
        # Dropping duplicates in current dataset
        chunk = chunk.drop_duplicates(subset=['id'])

        # Extract only unique IDS from chunk variable to save memory 
        only_ids_in_chunk = pd.DataFrame()
        only_ids_in_chunk['id'] = chunk['id']

        only_ids = only_ids.append(only_ids_in_chunk)
        only_ids = only_ids.drop_duplicates(subset=['id'])

        # If we want to make another file which have all values unique
        # we must store somewhere what we have in chunk variable, to be able to load new chunk
        # Because we must not have all chunks in memory at the same time

        del chunk

        # Load next chunk

        start += slice_count
        end += slice_count
        file_gpd = gpd.read_file(fname, rows=slice(start, end))
        chunk = pd.DataFrame(file_gpd)
        if len(chunk) == 0:
            print(len(only_ids))
            loop = False
        else:
            pass
    except Exception:
        loop = False
        print("Iteration is stopped")

我得到了一个无限循环。我认为使用if语句可以发现块的长度何时等于0，或者切片何时结束。

Answer 1

所以，这是最终的脚本。我遇到的问题是，当您使用geopandas对geopackage文件进行切片时，当您看到结尾时，它会从头开始并且不会停止。因此，我在代码末尾添加了if语句来涵盖这一点。

import fiona
import geopandas as gpd
import pandas as pd
import logging
import time

slice_count = 20000000
start = 0
end = slice_count
fname = "/Output.gpkg"

chunk = gpd.read_file(fname, rows=slice(start, end), ignore_geometry=True)

chunks = pd.DataFrame()
only_ids = pd.DataFrame(columns=['id'])
loop = True
chunk_num = 1
while loop:
    start_time = time.time()
    # Dropping duplicates in current dataset
    chunk = chunk.drop_duplicates(subset=['id'])
        
    only_ids = only_ids.append(chunk)
    only_ids = only_ids.drop_duplicates(subset=['id'])

    # delete chunk to save memory
    del chunk

    # Load next chunk
    start += slice_count
    end += slice_count
    chunk = gpd.read_file(fname, rows=slice(start, end), ignore_geometry=True)
    
    FORMAT = '%(asctime)s:%(name)s:%(levelname)s - %(message)s'
    logging.basicConfig(format=FORMAT, level=logging.INFO)
    logging.info(f"Chunk {chunk_num} done")
    print(f"Duration: {time.time() - start_time}")
    chunk_num += 1

    if len(chunk) != slice_count:
        chunk = chunk.drop_duplicates(subset=['id'])
        only_ids = only_ids.append(chunk)
        only_ids = only_ids.drop_duplicates(subset=['id'])
        del chunk
        break

only_ids.to_csv('output.csv')