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| # COPE scripts | ||
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| ## EIP extraction | ||
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| The script `eip_prepare_for_cope.py` extracts EIP files in a source directory to a target directory. It renames a specific subdirectory (`CaptureOne/Settings153` to `CaptureOne/Settings131`) and moves the EIP files into the `_raw` image directory. | ||
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| ## Usage | ||
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| ``` | ||
| usage: eip_prepare_for_cope.py [-h] -s SOURCE -t TARGET | ||
| options: | ||
| -h, --help show this help message and exit | ||
| -s SOURCE, --source SOURCE | ||
| Source directory | ||
| -t TARGET, --target TARGET | ||
| Target directory | ||
| ``` | ||
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| in Goobi workflow this can be integrated in a script step like this: | ||
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| ```shell | ||
| /opt/digiverso/goobi/scripts/eip_prepare_for_cope.py -s {origpath} -t {origpath} | ||
| ``` | ||
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| ## COPE conversion | ||
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| The script `cope_folder.py` converts IIQ files from the source directory and uses COPE to convert them to tiff files located in the target directory. Optionally the given resolution value will be used. | ||
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| ## Usage | ||
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| ``` | ||
| usage: cope_folder.py [-h] -s SOURCE -t TARGET [-r RESOLUTION] | ||
| options: | ||
| -h, --help show this help message and exit | ||
| -s SOURCE, --source SOURCE | ||
| -t TARGET, --target TARGET | ||
| -r RESOLUTION, --resolution RESOLUTION | ||
| ``` | ||
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| The path to the cope binary can be given by an environment variable named `COPE_PATH`. | ||
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| In Goobi workflow a script step in the external queue can be used to run the script on a Windows workernode like this: | ||
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| ```CMD | ||
| C:\Windows\py.exe D:\intranda\cope_folder.py -s "//mediaSMB-isilonArchive/GoobiMetadata/{s3_origpath}" -t "//mediaSMB-isilonArchive/GoobiMetadata/{s3_origpath}" -r "{process.File Resolution}" | ||
| ``` | ||
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| #!/usr/bin/env python3 | ||
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| import logging | ||
| import os | ||
| import shutil | ||
| import subprocess | ||
| from argparse import ArgumentParser | ||
| from pathlib import Path | ||
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| loglevel = (os.environ.get('PYTHON_LOGLEVEL') or "DEBUG").upper() | ||
| numeric_level = getattr(logging, loglevel.upper(), None) | ||
| logging.basicConfig( | ||
| format='%(asctime)s %(levelname)-8s %(message)s', level=numeric_level) | ||
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| file_name_pattern = "*.IIQ" | ||
| path_cope = (os.environ.get('COPE_PATH') or Path( | ||
| "C:/cope.Win.13.1.15-name_cope131/COPE/Bin/COPE.exe")) | ||
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| cope_options = ["-bits=8"] | ||
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| def find_files(root_dir: Path, file_name_pattern: str) -> list[list]: | ||
| """find files matching file_name_pattern in direct subdirectories of root_dir | ||
| Args: | ||
| root_dir (Path): top level directory to perform search in | ||
| file_name_pattern (str): globbing expression to match for | ||
| Returns: | ||
| list[list]: a list of lists with the filename and the parent directory basename of matching files | ||
| """ | ||
| found_files = [] | ||
| for file in Path(root_dir).glob("*/"+file_name_pattern): | ||
| found_files.append([file, file.parent.stem]) | ||
| return (found_files) | ||
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| def get_parser(): | ||
| """provides argument parser""" | ||
| parser = ArgumentParser() | ||
| parser.add_argument("-s", "--source", dest="source", | ||
| required=True, type=str) | ||
| parser.add_argument("-t", "--target", dest="target", | ||
| required=True, type=str) | ||
| parser.add_argument("-r", "--resolution", dest="resolution", | ||
| required=False, type=int) | ||
| return parser | ||
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| if __name__ == "__main__": | ||
| parser = get_parser() | ||
| args = parser.parse_args() | ||
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| sourcedir = Path(args.source) | ||
| targetdir = Path(args.target) | ||
| resolution = args.resolution | ||
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| logging.debug(f"path to cope: {path_cope}") | ||
| logging.debug(f"source directory: {sourcedir}") | ||
| logging.debug(f"target directory: {targetdir}") | ||
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| if resolution: | ||
| logging.debug(f"resolution: {resolution}") | ||
| cope_options.append(f"-resolution={resolution}") | ||
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| if not os.path.isdir(sourcedir): | ||
| logging.error("source directory does not exist") | ||
| exit(1) | ||
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| if not os.path.isdir(targetdir): | ||
| os.mkdir(targetdir) | ||
| logging.info("target directory created, as it did not exist") | ||
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| logging.info("start processing...") | ||
| files = find_files(sourcedir, file_name_pattern) | ||
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| if not files: | ||
| logging.info("no matching files found in source directory") | ||
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| for file, base in files: | ||
| target = Path(targetdir) / (base + ".tif") | ||
| logging.info(f"processing {file}") | ||
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| cope_command = [Path(path_cope), file, target] + cope_options | ||
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| logging.debug(f"running {cope_command}") | ||
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| # execute cope | ||
| try: | ||
| subprocess.run(cope_command, check=True) | ||
| except FileNotFoundError: | ||
| logging.error(f"cope executable was not found: {path_cope}") | ||
| exit(1) | ||
| except Exception as err: | ||
| logging.error(f"Unexpected {err=}, {type(err)=}") | ||
| raise | ||
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| # cope does not appear to make much use of exit codes, thus we check the existence of the expected tiff file here | ||
| if not target.is_file(): | ||
| logging.error(f"tiff file expected but not found: {target}") | ||
| exit(1) | ||
| else: | ||
| logging.debug(f"removing source package {target.with_suffix('')}") | ||
| shutil.rmtree(target.with_suffix('')) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,65 @@ | ||
| #!/usr/bin/env python3 | ||
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| # This script extracts eip files in a source directory to a target directory, renames a specific subdirectory and moves the original eip files | ||
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| import os | ||
| import shutil | ||
| from argparse import ArgumentParser | ||
| from pathlib import Path | ||
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| def extract_and_rename_eip(source_dir, target_dir): | ||
| # Check if source directory exists | ||
| if not os.path.isdir(source_dir): | ||
| print("Source directory does not exist") | ||
| exit(1) | ||
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| # Create target directory if it does not exist | ||
| os.makedirs(target_dir, exist_ok=True) | ||
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| if source_dir.name.endswith("_master"): | ||
| raw_directory = Path.joinpath( | ||
| source_dir.parent, source_dir.name.replace("_master", "_raw")) | ||
| os.makedirs(raw_directory, exist_ok=True) | ||
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| for filename in os.listdir(source_dir): | ||
| if filename.endswith(".eip"): | ||
| file_path = os.path.join(source_dir, filename) | ||
| if os.path.isfile(file_path): | ||
| # Unzip eip to target directory | ||
| unzip_dir = os.path.join( | ||
| target_dir, os.path.splitext(filename)[0]) | ||
| shutil.unpack_archive(filename=file_path, | ||
| extract_dir=unzip_dir, format="zip") | ||
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| capture_one_dir = os.path.join(unzip_dir, "CaptureOne") | ||
| settings_old = os.path.join(capture_one_dir, "Settings153") | ||
| settings_new = os.path.join(capture_one_dir, "Settings131") | ||
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| # Check if CaptureOne directory exists | ||
| if not os.path.isdir(capture_one_dir): | ||
| print(f"{capture_one_dir} does not exist") | ||
| exit(1) | ||
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| # Rename setting directory to matching version for cope | ||
| if os.path.isdir(settings_old): | ||
| os.rename(settings_old, settings_new) | ||
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| os.rename(file_path, Path.joinpath(raw_directory, filename)) | ||
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| def get_parser(): | ||
| """provides argument parser""" | ||
| parser = ArgumentParser() | ||
| parser.add_argument("-s", "--source", dest="source", | ||
| required=True, type=str, help="Source directory") | ||
| parser.add_argument("-t", "--target", dest="target", | ||
| required=True, type=str, help="Target directory") | ||
| return parser | ||
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| if __name__ == "__main__": | ||
| parser = get_parser() | ||
| args = parser.parse_args() | ||
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| extract_and_rename_eip(Path(args.source), Path(args.target)) |
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