From f5f73a4a4786b754867bd7e0c5cd79a4b94f6035 Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Thu, 22 Dec 2022 14:57:50 +0100
Subject: [PATCH] refactoring of dicom module
---
mu_map/file/dicom.py | 16 +++++++++-------
mu_map/file/interfile_to_dicom.py | 8 ++++----
2 files changed, 13 insertions(+), 11 deletions(-)
diff --git a/mu_map/file/dicom.py b/mu_map/file/dicom.py
index 2fed122..e3cd5ab 100644
--- a/mu_map/file/dicom.py
+++ b/mu_map/file/dicom.py
@@ -6,7 +6,11 @@ from typing import Tuple
import numpy as np
import pydicom
-dcm_type = pydicom.dataset.FileDataset
+
+"""
+Alias for the main dicom datatype.
+"""
+DICOM = pydicom.dataset.FileDataset
"""
Since DICOM images only allow images stored in short integer format,
@@ -58,7 +62,7 @@ class DICOMTime(Enum):
"""
return f"{self.name}Time"
- def to_datetime(self, dicom: dcm_type) -> datetime:
+ def to_datetime(self, dicom: DICOM) -> datetime:
"""
Get the datetime according to this DICOMTime type.
"""
@@ -94,7 +98,7 @@ def parse_age(patient_age: str) -> int:
return int(_num)
-def load_dcm(filename: str) -> Tuple[pydicom.dataset.FileDataset, np.ndarray]:
+def load_dcm(filename: str) -> Tuple[DICOM, np.ndarray]:
"""
Load a DICOM image, the data as a numpy array and apply normalization of the Siemens SPECT/CT
Scanner.
@@ -144,9 +148,7 @@ def scale_image(image: np.ndarray, initial_scale=10000000) -> Tuple[np.ndarray,
return image, scale
-def update_dcm(
- dcm: pydicom.dataset.FileDataset, image: np.ndarray
-) -> pydicom.dataset.FileDataset:
+def update_dcm(dcm: DICOM, image: np.ndarray) -> DICOM:
"""
Update the image data in a DICOM file. This function scales the image, converts
it to unsigned integers with 16 bits and updates the pixel data in the DICOM file.
@@ -176,7 +178,7 @@ def update_dcm(
return dcm
-def change_uid(dcm: pydicom.dataset.FileDataset) -> pydicom.dataset.FileDataset:
+def change_uid(dcm: DICOM) -> DICOM:
"""
Change the UIDs (SeriesInstance and SOPInstance) in a DICOM header so that
it becomes its own unique file. Note that this method does not guarantee
diff --git a/mu_map/file/interfile_to_dicom.py b/mu_map/file/interfile_to_dicom.py
index b4ce0b1..830d49b 100644
--- a/mu_map/file/interfile_to_dicom.py
+++ b/mu_map/file/interfile_to_dicom.py
@@ -8,22 +8,22 @@ 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",
+ 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"
+ "--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",
+ 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",
+ help="the output file - defaults to the Interfile input with a dcm extension",
)
parser.add_argument(
"--description",
--
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