From e0d463db1a500764ce57b815a1b94e23d9d62ced Mon Sep 17 00:00:00 2001
From: Tamino Huxohl <thuxohl@techfak.uni-bielefeld.de>
Date: Wed, 14 Dec 2022 13:55:12 +0100
Subject: [PATCH] move function of data/dicom_util to file/dicom
---
mu_map/data/dicom_util.py | 50 -----------------------
mu_map/data/prepare.py | 2 +-
mu_map/file/dicom.py | 85 ++++++++++++++++++++++++++++++++++++---
3 files changed, 81 insertions(+), 56 deletions(-)
delete mode 100644 mu_map/data/dicom_util.py
diff --git a/mu_map/data/dicom_util.py b/mu_map/data/dicom_util.py
deleted file mode 100644
index a627857..0000000
--- a/mu_map/data/dicom_util.py
+++ /dev/null
@@ -1,50 +0,0 @@
-from datetime import datetime
-from enum import Enum
-
-import pydicom
-
-
-class DICOMTime(Enum):
- Study = 1
- Series = 2
- Acquisition = 3
- Content = 4
-
- def date_field(self):
- return f"{self.name}Date"
-
- def time_field(self):
- return f"{self.name}Time"
-
- def to_datetime(self, dicom: pydicom.dataset.FileDataset) -> datetime:
- _date = dicom[self.date_field()].value
- _time = dicom[self.time_field()].value
- return datetime(
- year=int(_date[0:4]),
- month=int(_date[4:6]),
- day=int(_date[6:8]),
- hour=int(_time[0:2]),
- minute=int(_time[2:4]),
- second=int(_time[4:6]),
- # microsecond=int(_time.split(".")[1]),
- )
-
-
-def parse_age(patient_age: str) -> int:
- """
- Parse an age string as defined in the DICOM standard into an integer representing the age in years.
-
- :param patient_age: age string as defined in the DICOM standard
- :return: the age in years as a number
- """
- assert (
- type(patient_age) == str
- ), f"patient age needs to be a string and not {type(patient_age)}"
- assert (
- len(patient_age) == 4
- ), f"patient age [{patient_age}] has to be four characters long"
- _num, _format = patient_age[:3], patient_age[3]
- assert (
- _format == "Y"
- ), f"currently, only patient ages in years [Y] is supported, not [{_format}]"
- return int(_num)
diff --git a/mu_map/data/prepare.py b/mu_map/data/prepare.py
index 702769e..58b89a8 100644
--- a/mu_map/data/prepare.py
+++ b/mu_map/data/prepare.py
@@ -8,7 +8,7 @@ import numpy as np
import pandas as pd
import pydicom
-from mu_map.data.dicom_util import DICOMTime, parse_age
+from mu_map.file.dicom import DICOMTime, parse_age
from mu_map.logging import add_logging_args, get_logger_by_args
diff --git a/mu_map/file/dicom.py b/mu_map/file/dicom.py
index 10f4084..2fed122 100644
--- a/mu_map/file/dicom.py
+++ b/mu_map/file/dicom.py
@@ -1,3 +1,5 @@
+from datetime import datetime
+from enum import Enum
import random
from typing import Tuple
@@ -29,6 +31,69 @@ Default extension of dicom files.
EXTENSION_DICOM = ".dcm"
+class DICOMTime(Enum):
+ """
+ Class for parsing dates and times defined in a DICOM header
+ into a python datetime type. It maps the four datetime fields
+ [Study, Series, Acquisition, Content] of the DICOM header into
+ an enumeration type.
+
+ Usage: DICOMTime.Series.to_datetime(dcm)
+ """
+
+ Study = 1
+ Series = 2
+ Acquisition = 3
+ Content = 4
+
+ def date_field(self) -> str:
+ """
+ Get the name of the date field according to this DICOMTime type.
+ """
+ return f"{self.name}Date"
+
+ def time_field(self) -> str:
+ """
+ Get the name of the time field according to this DICOMTime type.
+ """
+ return f"{self.name}Time"
+
+ def to_datetime(self, dicom: dcm_type) -> datetime:
+ """
+ Get the datetime according to this DICOMTime type.
+ """
+ _date = dicom[self.date_field()].value
+ _time = dicom[self.time_field()].value
+ return datetime(
+ year=int(_date[0:4]),
+ month=int(_date[4:6]),
+ day=int(_date[6:8]),
+ hour=int(_time[0:2]),
+ minute=int(_time[2:4]),
+ second=int(_time[4:6]),
+ )
+
+
+def parse_age(patient_age: str) -> int:
+ """
+ Parse an age string as defined in the DICOM standard into an integer representing the age in years.
+
+ :param patient_age: age string as defined in the DICOM standard
+ :return: the age in years as a number
+ """
+ assert (
+ type(patient_age) == str
+ ), f"patient age needs to be a string and not {type(patient_age)}"
+ assert (
+ len(patient_age) == 4
+ ), f"patient age [{patient_age}] has to be four characters long"
+ _num, _format = patient_age[:3], patient_age[3]
+ assert (
+ _format == "Y"
+ ), f"currently, only patient ages in years [Y] is supported, not [{_format}]"
+ return int(_num)
+
+
def load_dcm(filename: str) -> Tuple[pydicom.dataset.FileDataset, np.ndarray]:
"""
Load a DICOM image, the data as a numpy array and apply normalization of the Siemens SPECT/CT
@@ -69,7 +134,7 @@ def scale_image(image: np.ndarray, initial_scale=10000000) -> Tuple[np.ndarray,
is smaller than the maximum uint16 number
:return: the image scaled and converted to uint16 as well as the used scaling factor
"""
- if image.min() < 0.0:
+ if image.min() < 0.0:
raise ValueError("Cannot scale images with negative values!")
scale = initial_scale
@@ -121,15 +186,25 @@ def change_uid(dcm: pydicom.dataset.FileDataset) -> pydicom.dataset.FileDataset:
:param dcm: the DICOM file to be udpated
:return: the DICOM file with updated UIDs
"""
- dcm.SeriesInstanceUID = UID_PREFIX + str(random.randint(10000000000000, 99999999999999))
- dcm.SOPInstanceUID = UID_PREFIX + str(random.randint(10000000000000, 99999999999999))
+ dcm.SeriesInstanceUID = UID_PREFIX + str(
+ random.randint(10000000000000, 99999999999999)
+ )
+ dcm.SOPInstanceUID = UID_PREFIX + str(
+ random.randint(10000000000000, 99999999999999)
+ )
return dcm
+
if __name__ == "__main__":
import argparse
- parser = argparse.ArgumentParser(description="Dump the header of a DICOM image", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
- parser.add_argument("file", type=str, help="the DICOM file of which the header is dumped")
+ parser = argparse.ArgumentParser(
+ description="Dump the header of a DICOM image",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
+ parser.add_argument(
+ "file", type=str, help="the DICOM file of which the header is dumped"
+ )
args = parser.parse_args()
dcm = pydicom.dcmread(args.file)
--
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