From 3858361bcd4e6c09da42267c868f794d95742506 Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Fri, 23 Dec 2022 09:32:55 +0100
Subject: [PATCH] dicom to interfile conversion expects a default patient
position
---
mu_map/file/convert.py | 47 ++++++++++++++++++++++++------------------
1 file changed, 27 insertions(+), 20 deletions(-)
diff --git a/mu_map/file/convert.py b/mu_map/file/convert.py
index 0f3e2ef..bc87ca2 100644
--- a/mu_map/file/convert.py
+++ b/mu_map/file/convert.py
@@ -12,7 +12,11 @@ from mu_map.file.interfile import (
"""
Module for the conversion between the different formats.
"""
-def parse_position(position: str) -> Tuple[str, str]:
+
+
+def parse_position(
+ dcm: DICOM, default_orientation: str = "feet_in", default_rotation: str = "supine"
+) -> Tuple[str, str]:
"""
Parse the patient position from the DICOM patient position
field into the orientation and rotation as used by the Interfile
@@ -21,24 +25,25 @@ def parse_position(position: str) -> Tuple[str, str]:
:param position: the value of the patient position field in the DICOM header
:return: a tuple of patient orientation and rotation
"""
- if len(position) != 3:
- raise ValueError(f"Cannot parse patient position {position}")
-
- _orienation = position[:2]
- if _orienation == "FF":
- orientation = "feet_in"
- elif _orienation == "HF":
- orientation = "head_in"
-
- _rotation = position[2]
- if _orienation == "P":
- rotation = "prone"
- elif _rotation == "S":
- rotation = "supine"
-
- if rotation is None or orientation is None:
- raise ValueError(f"Cannot parse patient position {position}")
-
+ orientation = default_orientation
+ rotation = default_rotation
+
+ try:
+ position = dcm.PatientPosition
+
+ _orienation = position[:2]
+ if _orienation == "FF":
+ orientation = "feet_in"
+ elif _orienation == "HF":
+ orientation = "head_in"
+
+ _rotation = position[2]
+ if _orienation == "P":
+ rotation = "prone"
+ elif _rotation == "S":
+ rotation = "supine"
+ except:
+ pass
return orientation, rotation
@@ -50,7 +55,6 @@ def dicom_to_interfile(dcm: DICOM, image: np.ndarray) -> Interfile:
:param image: the image as a numpy array
:return: an Interfile as a combination of header and image
"""
- orientation, rotation = parse_position(dcm.PatientPosition)
header = TEMPLATE_HEADER_IMAGE.replace("{ROWS}", str(dcm.Rows))
header = header.replace("{SPACING_X}", f"{dcm.PixelSpacing[0]:.4f}")
@@ -60,8 +64,11 @@ def dicom_to_interfile(dcm: DICOM, image: np.ndarray) -> Interfile:
header = header.replace("{SPACING_Z}", f"{dcm.SliceThickness:.4f}")
header = header.replace("{OFFSET_X}", str(-0.5 * dcm.Rows * dcm.PixelSpacing[0]))
header = header.replace("{OFFSET_Y}", str(-0.5 * dcm.Columns * dcm.PixelSpacing[1]))
+
+ orientation, rotation = parse_position(dcm)
header = header.replace("{PATIENT_ORIENTATION}", orientation)
header = header.replace("{PATIENT_ROTATION}", rotation)
+
header = parse_interfile_header_str(header)
return Interfile(header, image.astype(np.float32))
--
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