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Add the option to have an image path inside index file #349

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Merged
Arkkienkeli merged 1 commit into from
Jan 2, 2024
Merged

Add the option to have an image path inside index file #349

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5 changes: 4 additions & 1 deletion deepprofiler/dataset/image_dataset.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import numpy as np
import pandas as pd
import os

import deepprofiler.dataset.pixels
import deepprofiler.dataset.utils
Expand Down Expand Up @@ -61,7 +62,9 @@ def __init__(self, metadata, sampling_field, channels, dataRoot, keyGen, config)

def get_image_paths(self, r):
key = self.keyGen(r)
image = [self.root + "/" + r[ch] for ch in self.channels]
list_images = [r[ch] for ch in self.channels]
paths = [(os.path.split(r[ch]))[0] for ch in self.channels]
image = [list_images[ch] if os.path.isdir(paths[ch]) else self.root + "/" + list_images[ch] for ch in range(len(paths))]
outlines = self.outlines
if outlines is not None:
outlines = self.outlines + r["Outlines"]
Expand Down