From 4ef0e02b0eb394a1e443b2c055c1cdf8303232b3 Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Thu, 22 Dec 2022 15:48:50 +0100
Subject: [PATCH] move file conversion into one script
---
mu_map/file/convert.py | 98 +++++++++++++++++++++++++++++++
mu_map/file/dicom_to_interfile.py | 56 ------------------
mu_map/file/interfile_to_dicom.py | 45 --------------
3 files changed, 98 insertions(+), 101 deletions(-)
create mode 100644 mu_map/file/convert.py
delete mode 100644 mu_map/file/dicom_to_interfile.py
delete mode 100644 mu_map/file/interfile_to_dicom.py
diff --git a/mu_map/file/convert.py b/mu_map/file/convert.py
new file mode 100644
index 0000000..7e72656
--- /dev/null
+++ b/mu_map/file/convert.py
@@ -0,0 +1,98 @@
+import numpy as np
+
+from mu_map.file.dicom import DICOM
+from mu_map.file.interfile import (
+ Interfile,
+ parse_interfile_header_str,
+ TEMPLATE_HEADER_IMAGE,
+)
+
+"""
+Module for the conversion between the different formats.
+"""
+
+
+def dicom_to_interfile(dcm: DICOM, image: np.ndarray) -> Interfile:
+ """
+ Convert a DICOM image to Interfile format.
+
+ :param dcm: the DICOM image
+ :param image: the image as a numpy array
+ :return: an Interfile as a combination of header and image
+ """
+ header = TEMPLATE_HEADER_IMAGE.replace("{ROWS}", str(dcm.Rows))
+ header = header.replace("{SPACING_X}", f"{dcm.PixelSpacing[0]:.4f}")
+ header = header.replace("{COLUMNS}", str(dcm.Columns))
+ header = header.replace("{SPACING_Y}", f"{dcm.PixelSpacing[1]:.4f}")
+ header = header.replace("{SLICES}", str(dcm.NumberOfSlices))
+ 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]))
+ header = parse_interfile_header_str(header)
+ return Interfile(header, image.astype(np.float32))
+
+
+if __name__ == "__main__":
+ import argparse
+ import os
+
+ import pydicom
+
+ from mu_map.file.dicom import change_uid, load_dcm, update_dcm, EXTENSION_DICOM
+ from mu_map.file.interfile import write_interfile, load_interfile_img
+
+ def main_interfile(args):
+ args.out = args.file if args.out is None else args.out
+
+ dcm, image = load_dcm(args.file)
+ interfile = dicom_to_interfile(dcm, image)
+ write_interfile(args.out, interfile)
+
+ def main_dicom(args):
+ args.out = args.file if args.out is None else args.out
+ args.out = os.path.splitext(args.out)[0]
+ args.out = f"{args.out}{EXTENSION_DICOM}"
+
+ image = load_interfile_img(args.file)
+ reference = pydicom.dcmread(args.reference)
+ dcm = update_dcm(reference.copy(), image)
+ dcm = change_uid(dcm)
+
+ if args.description:
+ dcm.SeriesDescription = args.description
+
+ pydicom.dcmwrite(args.out, dcm)
+
+ parser = argparse.ArgumentParser(
+ description="convert images between different formats",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
+ parser.add_argument(
+ "file",
+ type=str,
+ help="the file to be converted (a DICOM image or an Interfile header)",
+ )
+ parser.add_argument(
+ "--out",
+ type=str,
+ help="the filename for the output file. If not specified it defaults to the input name with different extensions.",
+ )
+ subparsers = parser.add_subparsers(help="file to convert to")
+
+ parser_dcm = subparsers.add_parser("dicom", help="convert to a DICOM file")
+ parser_dcm.add_argument(
+ "--reference",
+ type=str,
+ required=True,
+ help="reference DICOM file to use for the header",
+ )
+ parser_dcm.add_argument(
+ "--description", type=str, help="update the series description"
+ )
+ parser_dcm.set_defaults(func=main_dicom)
+
+ parser_inter = subparsers.add_parser("interfile", help="convert to an Interfile")
+ parser_inter.set_defaults(func=main_interfile)
+
+ args = parser.parse_args()
+ args.func(args)
diff --git a/mu_map/file/dicom_to_interfile.py b/mu_map/file/dicom_to_interfile.py
deleted file mode 100644
index 98a4c4e..0000000
--- a/mu_map/file/dicom_to_interfile.py
+++ /dev/null
@@ -1,56 +0,0 @@
-from typing import Dict, Tuple
-
-import numpy as np
-from pydicom.dataset import FileDataset as DCMImage
-
-from mu_map.file.interfile import TEMPLATE_HEADER_IMAGE, parse_interfile_header_str
-
-
-def to_interfile(dcm: DCMImage, image: np.ndarray) -> Tuple[Dict[str, str], np.ndarray]:
- """
- Convert a DICOM image to INTERFILE format.
-
- :param dcm: the DICOM image
- :param image: the image as a numpy array
- :return: the header and image in INTERFILE format
- """
- header = TEMPLATE_HEADER_IMAGE.replace("{ROWS}", str(dcm.Rows))
- header = header.replace("{SPACING_X}", f"{dcm.PixelSpacing[0]:.4f}")
- header = header.replace("{COLUMNS}", str(dcm.Columns))
- header = header.replace("{SPACING_Y}", f"{dcm.PixelSpacing[1]:.4f}")
- header = header.replace("{SLICES}", str(dcm.NumberOfSlices))
- 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]))
- header = parse_interfile_header_str(header)
- return header, image.astype(np.float32)
-
-
-if __name__ == "__main__":
- import argparse
- import os
-
- from mu_map.file.dicom import load_dcm
- from mu_map.file.interfile import write_interfile
-
- parser = argparse.ArgumentParser(
- description="convert a DICOM image to the INTERFILE format"
- )
- parser.add_argument(
- "--dcm", type=str, required=True, help="the DICOM image to convert"
- )
- parser.add_argument(
- "--out",
- type=str,
- help="the filename for the resulting INTERFILE format. If not specified it defaults to the input name with different extensions.",
- )
- args = parser.parse_args()
-
- args.out = args.dcm if args.out is None else args.out
- args.out = os.path.splitext(args.out)[
- 0
- ] # make sure the output file does not have an extension
-
- dcm, image = load_dcm(args.dcm)
- header, image = to_interfile(dcm, image)
- write_interfile(args.out, header, image)
diff --git a/mu_map/file/interfile_to_dicom.py b/mu_map/file/interfile_to_dicom.py
deleted file mode 100644
index 830d49b..0000000
--- a/mu_map/file/interfile_to_dicom.py
+++ /dev/null
@@ -1,45 +0,0 @@
-import argparse
-import os
-
-import numpy as np
-import pydicom
-
-from mu_map.file.dicom import update_dcm, change_uid
-from mu_map.file.interfile import load_interfile_img
-
-parser = argparse.ArgumentParser(
- description="convert an Interfile image to a DICOM image",
- formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-)
-parser.add_argument(
- "--inter", type=str, required=True, help="the Interfile image to be converted"
-)
-parser.add_argument(
- "--dcm",
- type=str,
- required=True,
- help="a DICOM reference image - data and according fields are exchanged from the Interfile image",
-)
-parser.add_argument(
- "--out",
- type=str,
- help="the output file - defaults to the Interfile input with a dcm extension",
-)
-parser.add_argument(
- "--description",
- type=str,
- help="if provided the series description will be updated",
-)
-args = parser.parse_args()
-
-if args.out is None:
- args.out = os.path.splitext(args.inter)[0] + ".dcm"
-
-image = load_interfile_img(args.inter)
-
-dcm = pydicom.dcmread(args.dcm)
-dcm = update_dcm(dcm.copy(), image)
-dcm = change_uid(dcm)
-if args.description:
- dcm.SeriesDescription = args.description
-pydicom.dcmwrite(args.out, dcm)
--
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