From d80575c99d53bffe8ed26d774fd80ab80f43a43c Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Thu, 1 Sep 2022 12:07:25 +0200
Subject: [PATCH] fix mu map dataset and add options for display
---
mu_map/data/datasets.py | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/mu_map/data/datasets.py b/mu_map/data/datasets.py
index 64fd191..7d0d6c7 100644
--- a/mu_map/data/datasets.py
+++ b/mu_map/data/datasets.py
@@ -70,7 +70,7 @@ class MuMapDataset(Dataset):
def __getitem__(self, index: int):
row = self.table.iloc[index]
- recon_file = os.path.join(self.dir_images, row[header.file_recon_nac_nsc])
+ recon_file = os.path.join(self.dir_images, row[headers.file_recon_nac_nsc])
mu_map_file = os.path.join(self.dir_images, row[headers.file_mu_map])
recon = pydicom.dcmread(recon_file).pixel_array
@@ -105,9 +105,15 @@ if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Visualize the images of a MuMapDataset", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("dataset_dir", type=str, help="the directory from which the dataset is loaded")
parser.add_argument("--unaligned", action="store_true", help="do not perform center alignment of reconstruction an mu-map slices")
+ parser.add_argument("--show_bed", action="store_true", help="do not remove the bed contour from the mu map")
+ parser.add_argument("--full_mu_map", action="store_true", help="do not remove broken slices of the mu map")
args = parser.parse_args()
- dataset = MuMapDataset(args.dataset_dir, align=not args.unaligned)
+ align = not args.unaligned
+ discard_mu_map_slices = not args.full_mu_map
+ bed_contours_file = None if args.show_bed else DEFAULT_BED_CONTOURS_FILENAME
+
+ dataset = MuMapDataset(args.dataset_dir, align=align, discard_mu_map_slices=discard_mu_map_slices, bed_contours_file=bed_contours_file)
wname = "Dataset"
cv.namedWindow(wname, cv.WINDOW_NORMAL)
--
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