From 8ed516f0fd2862a0b04c7ff30020ff6beacef189 Mon Sep 17 00:00:00 2001 From: fefossa Date: Thu, 15 Jun 2023 08:12:39 -0400 Subject: [PATCH] option to have image path inside index file The user may want to give a full path to the image file instead of moving the images to inputs/images. --- deepprofiler/dataset/image_dataset.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/deepprofiler/dataset/image_dataset.py b/deepprofiler/dataset/image_dataset.py index abd0b65e..20031aae 100644 --- a/deepprofiler/dataset/image_dataset.py +++ b/deepprofiler/dataset/image_dataset.py @@ -1,5 +1,6 @@ import numpy as np import pandas as pd +import os import deepprofiler.dataset.pixels import deepprofiler.dataset.utils @@ -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"]