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import os, sys, inspect, shutil, warnings
from dataclasses import dataclass, field
import pandas as pd
currentdir = os.path.dirname(os.path.dirname(inspect.getfile(inspect.currentframe())))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir)
sys.path.append(currentdir)
from vouchervision.general_utils import import_csv, import_tsv, bcolors
from vouchervision.general_utils import Print_Verbose, print_main_warn, print_main_success, make_file_names_valid, make_images_in_dir_vertical
from vouchervision.utils_GBIF import generate_image_filename
from vouchervision.download_from_GBIF_all_images_in_file import download_all_images_from_GBIF_LM2
from PIL import Image
from tqdm import tqdm
from pathlib import Path
import fitz
def convert_pdf_to_jpg(source_pdf, destination_dir, dpi=100):
doc = fitz.open(source_pdf)
for page_num in range(len(doc)):
page = doc.load_page(page_num) # Load the current page
pix = page.get_pixmap(dpi=dpi) # Render page to an image
output_filename = f"{os.path.splitext(os.path.basename(source_pdf))[0]}__{10000 + page_num + 1}.jpg"
output_filepath = os.path.join(destination_dir, output_filename)
pix.save(output_filepath) # Save the image
length_doc = len(doc)
doc.close()
return length_doc
@dataclass
class Project_Info():
batch_size: int = 50
image_location: str = ''
dir_images: str = ''
project_data: object = field(init=False)
project_data_list: object = field(init=False)
path_csv_combined: str = ''
path_csv_occ: str = ''
path_csv_img: str = ''
csv_combined: str = ''
csv_occ: str = ''
csv_img: str = ''
Dirs: object = field(init=False)
has_valid_images: bool = True
def __init__(self, cfg, logger, dir_home, Dirs) -> None:
self.Dirs = Dirs
logger.name = 'Project Info'
logger.info("Gathering Images and Image Metadata")
self.logger = logger
self.batch_size = cfg['leafmachine']['project']['batch_size']
self.image_location = cfg['leafmachine']['project']['image_location']
self.valid_extensions = ['.jpg', '.JPG', '.jpeg', '.JPEG', '.png', '.PNG', '.bmp', '.BMP', '.tif', '.TIF', '.tiff', '.TIFF']
self.copy_images_to_project_dir(cfg['leafmachine']['project']['dir_images_local'], Dirs)
self.make_file_names_custom(Dirs.save_original, cfg, Dirs)
# If project is local, expect:
# dir with images
# path to images.csv
# path to occ.csv
# OR path to combined.csv
# if self.image_location in ['local','l','L','Local']:
self.__import_local_files(cfg, logger, Dirs)
# If project is GBIF, expect:
# Darwin Core Images (or multimedia.txt) and Occurrences file pair, either .txt or .csv
# elif self.image_location in ['GBIF','g','G','gbif']:
# self.__import_GBIF_files_post_download(cfg, logger, dir_home)
self.__make_project_dict(Dirs) #, self.batch_size)
# Make sure image file names are legal
make_file_names_valid(Dirs.save_original, cfg)
# Make all images vertical
make_images_in_dir_vertical(Dirs.save_original, cfg)
@property
def has_valid_images(self):
return self.check_for_images()
@property
def file_ext(self):
return f"{['.jpg', '.JPG', '.jpeg', '.JPEG', '.png', '.PNG', '.bmp', '.BMP', '.tif', '.TIF', '.tiff', '.TIFF']}"
def check_for_images(self):
for filename in os.listdir(self.dir_images):
if filename.endswith(tuple(self.valid_extensions)):
return True
return False
def remove_non_numbers(self, s):
return ''.join([char for char in s if char.isdigit()])
# def copy_images_to_project_dir(self, dir_images, Dirs):
# n_total = len(os.listdir(dir_images))
# for file in tqdm(os.listdir(dir_images), desc=f'{bcolors.HEADER} Copying images to working directory{bcolors.ENDC}',colour="white",position=0,total = n_total):
# # Copy og image to new dir
# # Copied image will be used for all downstream applications
# source = os.path.join(dir_images, file)
# destination = os.path.join(Dirs.save_original, file)
# shutil.copy(source, destination)
def copy_images_to_project_dir(self, dir_images, Dirs):
n_total = len(os.listdir(dir_images))
for file in tqdm(os.listdir(dir_images), desc=f'{bcolors.HEADER} Copying images to working directory{bcolors.ENDC}', colour="white", position=0, total=n_total):
source = os.path.join(dir_images, file)
# Check if file is a PDF
if file.lower().endswith('.pdf'):
# Convert PDF pages to JPG images
n_pages = convert_pdf_to_jpg(source, Dirs.save_original)
self.logger.info(f"Converted {n_pages} pages to JPG from PDF: {file}")
else:
# Copy non-PDF files directly
destination = os.path.join(Dirs.save_original, file)
shutil.copy(source, destination)
def make_file_names_custom(self, dir_images, cfg, Dirs):
n_total = len(os.listdir(dir_images))
for file in tqdm(os.listdir(dir_images), desc=f'{bcolors.HEADER} Creating Catalog Number from file name{bcolors.ENDC}',colour="green",position=0,total = n_total):
# Copy og image to new dir
# Copied image will be used for all downstream applications
# source = os.path.join(dir_images, file)
# destination = os.path.join(Dirs.save_original, file)
# shutil.copy(source, destination)
if cfg['leafmachine']['project']['catalog_numerical_only'] or cfg['leafmachine']['project']['prefix_removal'] or cfg['leafmachine']['project']['suffix_removal']:
name = Path(file).stem
ext = Path(file).suffix
if cfg['leafmachine']['project']['prefix_removal']:
name_cleaned = name.replace(cfg['leafmachine']['project']['prefix_removal'], "")
if cfg['leafmachine']['project']['suffix_removal']:
name_cleaned = name.replace(cfg['leafmachine']['project']['suffix_removal'], "")
if cfg['leafmachine']['project']['catalog_numerical_only']:
name_cleaned = self.remove_non_numbers(name)
name_new = ''.join([name_cleaned,ext])
i = 0
try:
os.rename(os.path.join(dir_images,file), os.path.join(dir_images,name_new))
except:
warnings.warn("WARNING: duplicate file names will result given the current selections for 'prefix_removal', 'suffix_removal', or 'catalog_numerical_only'. Change them before continuing.")
warnings.warn("The affected file name has not been changed.")
def __create_combined_csv(self):
self.csv_img = self.csv_img.rename(columns={"gbifID": "gbifID_images"})
self.csv_img = self.csv_img.rename(columns={"identifier": "url"})
# print(self.csv_img.head(5))
combined = pd.merge(self.csv_img, self.csv_occ, left_on='gbifID_images', right_on='gbifID')
# print(combined.head(5))
names_list = combined.apply(generate_image_filename, axis=1, result_type='expand')
# print(names_list.head(5))
# Select columns 7, 0, 1
selected_columns = names_list.iloc[:,[7,0,1]]
# Rename columns
selected_columns.columns = ['fullname','filename_image','filename_image_jpg']
# print(selected_columns.head(5))
self.csv_combined = pd.concat([selected_columns, combined], axis=1)
# print(self.csv_combined.head(5))
new_name = ''.join(['combined_', os.path.basename(self.path_csv_occ).split('.')[0], '_', os.path.basename(self.path_csv_img).split('.')[0], '.csv'])
self.path_csv_combined = os.path.join(os.path.dirname(self.path_csv_occ), new_name)
self.csv_combined.to_csv(self.path_csv_combined, mode='w', header=True, index=False)
return self.path_csv_combined
def __import_local_files(self, cfg, logger, Dirs):
# Images
if cfg['leafmachine']['project']['dir_images_local'] is None:
self.dir_images = None
else:
self.dir_images = Dirs.save_original
# CSV import
# Combined
try:
if cfg['leafmachine']['project']['path_combined_csv_local'] is None:
self.csv_combined = None
self.path_csv_combined = None
else:
self.path_csv_combined = cfg['leafmachine']['project']['path_combined_csv_local']
self.csv_combined = import_csv(self.path_csv_combined)
# Occurrence
if cfg['leafmachine']['project']['path_occurrence_csv_local'] is None:
self.csv_occ = None
self.path_csv_occ = None
else:
self.path_csv_occ = cfg['leafmachine']['project']['path_occurrence_csv_local']
self.csv_occ = import_csv(self.path_csv_occ)
# Images/metadata
if cfg['leafmachine']['project']['path_images_csv_local'] is None:
self.path_csv_img = None
self.path_csv_img = None
else:
self.path_csv_img = cfg['leafmachine']['project']['path_images_csv_local']
self.csv_img = import_csv(self.path_csv_img)
# Create combined if it's missing
if self.csv_combined is None:
if cfg['leafmachine']['project']['path_combined_csv_local'] is not None:
# Print_Verbose(cfg, 2, 'Combined CSV file not provided, creating it now...').bold()
logger.info('Combined CSV file not provided, creating it now...')
location = self.__create_combined_csv()
# Print_Verbose(cfg, 2, ''.join(['Combined CSV --> ',location])).green()
logger.info(''.join(['Combined CSV --> ',location]))
else:
# Print_Verbose(cfg, 2, 'Combined CSV file not available or provided. Skipped record import.').bold()
logger.info('Combined CSV file not available or provided. Skipped record import.')
else:
# Print_Verbose(cfg, 2, ''.join(['Combined CSV --> ',self.path_csv_combined])).green()
logger.info(''.join(['Combined CSV --> ',self.path_csv_combined]))
except:
pass
# Print_Verbose(cfg, 2, ''.join(['Image Directory --> ',self.dir_images])).green()
logger.info(''.join(['Image Directory --> ',Dirs.save_original]))
# def __import_GBIF_files_post_download(self, cfg, logger, dir_home):
# # Download the images from GBIF
# # This pulls from /LeafMachine2/configs/config_download_from_GBIF_all_images_in_file or filter
# print_main_warn('Downloading Images from GBIF...')
# logger.info('Downloading Images from GBIF...')
# self.cfg_images = download_all_images_from_GBIF_LM2(dir_home, cfg['leafmachine']['project']['GBIF_mode'])
# self.dir_images = self.cfg_images['dir_destination_images']
# self.path_csv = self.cfg_images['dir_destination_csv']
# print_main_success(''.join(['Images saved to --> ',self.dir_images]))
# logger.info(''.join(['Images saved to --> ',self.dir_images]))
# self.path_csv_combined = os.path.join(self.path_csv, self.cfg_images['filename_combined'])
# self.path_csv_occ = os.path.join(self.path_csv, self.cfg_images['filename_occ'])
# self.path_csv_img = os.path.join(self.path_csv, self.cfg_images['filename_img'])
# if 'txt' in (self.cfg_images['filename_occ'].split('.')[1] or self.cfg_images['filename_img'].split('.')[1]):
# self.csv_combined = import_tsv(self.path_csv_combined)
# # self.csv_occ = import_tsv(self.path_csv_occ)
# # self.csv_img = import_tsv(self.path_csv_img)
# else:
# self.csv_combined = import_csv(self.path_csv_combined)
# # self.csv_occ = import_csv(self.path_csv_occ)
# # self.csv_img = import_csv(self.path_csv_img)
def process_in_batches(self, cfg):
batch_size = cfg['leafmachine']['project']['batch_size']
self.project_data_list = []
keys = list(self.project_data.keys())
num_batches = len(keys) // batch_size + 1
for i in range(num_batches):
start = i * batch_size
end = (i + 1) * batch_size
batch_keys = keys[start:end]
batch = {key: self.project_data[key] for key in batch_keys}
self.project_data_list.append(batch)
return num_batches, len(self.project_data)
# Original
'''def __make_project_dict(self):
self.project_data = {}
for img in os.listdir(self.dir_images):
if (img.endswith(".jpg") or img.endswith(".jpeg")):
img_name = str(img.split('.')[0])
self.project_data[img_name] = {}
'''
# def __make_project_dict(self): # This DELETES the invalid file, not safe
# self.project_data = {}
# for img in os.listdir(self.dir_images):
# img_split, ext = os.path.splitext(img)
# if ext.lower() in self.valid_extensions:
# with Image.open(os.path.join(self.dir_images, img)) as im:
# _, ext = os.path.splitext(img)
# if ext != '.jpg':
# im = im.convert('RGB')
# im.save(os.path.join(self.dir_images, img_split) + '.jpg', quality=100)
# img += '.jpg'
# os.remove(os.path.join(self.dir_images, ''.join([img_split, ext])))
# img_name = os.path.splitext(img)[0]
# self.project_data[img_split] = {}
def __make_project_dict(self, Dirs):
self.project_data = {}
invalid_dir = None
for img in os.listdir(Dirs.save_original):
img_split, ext = os.path.splitext(img)
if ext in self.valid_extensions:
with Image.open(os.path.join(Dirs.save_original, img)) as im:
_, ext = os.path.splitext(img)
if ext not in ['.jpg']:
im = im.convert('RGB')
new_img_name = ''.join([img_split, '.jpg'])
im.save(os.path.join(Dirs.save_original, new_img_name), quality=100)
self.project_data[img_split] = {}
# move the original file to the INVALID_FILE directory
if invalid_dir is None:
invalid_dir = os.path.join(os.path.dirname(Dirs.save_original), 'INVALID_FILES')
os.makedirs(invalid_dir, exist_ok=True)
# skip if the file already exists in the INVALID_FILE directory
if not os.path.exists(os.path.join(invalid_dir, img)):
shutil.move(os.path.join(Dirs.save_original, img), os.path.join(invalid_dir, img))
img = new_img_name
img_name = os.path.splitext(img)[0]
self.project_data[img_split] = {}
else:
# if the file has an invalid extension, move it to the INVALID_FILE directory
if invalid_dir is None:
invalid_dir = os.path.join(os.path.dirname(Dirs.save_original), 'INVALID_FILES')
os.makedirs(invalid_dir, exist_ok=True)
# skip if the file already exists in the INVALID_FILE directory
if not os.path.exists(os.path.join(invalid_dir, img)):
shutil.move(os.path.join(Dirs.save_original, img), os.path.join(invalid_dir, img))
def add_records_to_project_dict(self):
for img in os.listdir(self.Dirs.save_original):
if (img.endswith(".jpg") or img.endswith(".jpeg")):
img_name = str(img.split('.')[0])
try:
self.project_data[img_name]['GBIF_Record'] = self.__get_data_from_combined(img_name)
except:
self.project_data[img_name]['GBIF_Record'] = None
def __get_data_from_combined(self, img_name):
df = pd.DataFrame(self.csv_combined)
row = df[df['filename_image'] == img_name].head(1).to_dict()
return row
class Project_Stats():
specimens = 0
rulers = 0
def __init__(self, cfg, logger, dir_home) -> None:
logger.name = 'Project Info'
logger.info("Gathering Images and Image Metadata") |