36 lines
1.3 KiB
Python
36 lines
1.3 KiB
Python
#!/bin/python
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import tarfile
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from tqdm import tqdm
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from eisgenerator import EisSpectra
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import csv
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import argparse
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if __name__ == "__main__":
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parser = argparse.ArgumentParser("KissExpiramentExtractMeta")
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parser.add_argument('--data', '-d', required=True, help="Data input tar file")
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parser.add_argument('--out', '-o', required=True, help="output file")
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args = parser.parse_args()
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with open(args.out, 'w', newline='') as outfile:
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csvwriter = csv.writer(outfile, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
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with tarfile.open(args.data, mode="r") as tar:
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master_labels = None
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rows = list()
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for file_info in tqdm(tar, desc="Extracting Metadata", total=len(list(tar))):
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if file_info.isfile():
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filestr = tar.extractfile(file_info).read()
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spectra = EisSpectra.loadFromString(filestr)
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if master_labels is None:
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master_labels = spectra.labelNames
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master_labels_copy = master_labels.copy()
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for i in range(len(master_labels_copy)):
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print(master_labels_copy[i])
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master_labels_copy[i] = master_labels_copy[i].strip(' "')
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csvwriter.writerow(master_labels_copy)
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elif master_labels != spectra.labelNames:
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print(f"Error: not all files in {args.data} have the same labelNames")
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exit(1)
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csvwriter.writerow(spectra.labels)
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tar.close()
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