From 95a90653d096cb8b62ba9ae74f6a372c9139fc39 Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Wed, 4 Jan 2023 12:51:27 +0100
Subject: [PATCH] update mu map dataset to load dicom images in same stacking
direction
---
mu_map/dataset/default.py | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/mu_map/dataset/default.py b/mu_map/dataset/default.py
index 385ca93..bb57235 100644
--- a/mu_map/dataset/default.py
+++ b/mu_map/dataset/default.py
@@ -17,7 +17,8 @@ from mu_map.data.remove_bed import (
from mu_map.data.review_mu_map import discard_slices
from mu_map.data.split import split_csv
from mu_map.dataset.transform import Transform
-from mu_map.dataset.util import align_images, load_dcm_img
+from mu_map.dataset.util import align_images
+from mu_map.file.dicom import load_dcm_img
from mu_map.logging import get_logger
@@ -97,9 +98,13 @@ class MuMapDataset(Dataset):
_id = row[headers.id]
mu_map_file = os.path.join(self.dir_images, row[headers.file_mu_map])
- mu_map = load_dcm_img(mu_map_file)
+ mu_map = load_dcm_img(mu_map_file, direction=1)
+
+ recon_file = os.path.join(self.dir_images, row[self.header_recon])
+ recon = load_dcm_img(recon_file, direction=1)
+
if self.discard_mu_map_slices:
- mu_map = discard_slices(row, mu_map)
+ mu_map, recon = discard_slices(row, mu_map, recon)
if self.bed_contours:
if _id in self.bed_contours:
bed_contour = self.bed_contours[_id]
@@ -107,8 +112,6 @@ class MuMapDataset(Dataset):
else:
logger.warning(f"Could not find bed contour for id {_id}")
- recon_file = os.path.join(self.dir_images, row[self.header_recon])
- recon = load_dcm_img(recon_file)
if self.align:
recon, mu_map = align_images(recon, mu_map)
--
GitLab