pydicomrt 0.4.0__tar.gz

pydicomrt-0.4.0/.gitignore

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+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
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+# Abstra
+# Abstra is an AI-powered process automation framework.
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+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the enitre vscode folder
+# .vscode/
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+# Ruff stuff:
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+example/

pydicomrt-0.4.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 HigumaLu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pydicomrt-0.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pydicomrt
+Version: 0.4.0
+Summary: Add your description here
+Author-email: Higumalu <higuma.lu@gmail.com>
+License: MIT
+License-File: LICENSE
+Requires-Python: >=3.8
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: opencv-python>=4.10.0
+Requires-Dist: pydicom>=2.0.0
+Requires-Dist: scipy>=1.10.3
+Requires-Dist: simpleitk>=2.5.0
+Description-Content-Type: text/markdown
+
+# pydicomRT
+pydicomRT 是一個用於處理放射治療結構集（RTSTRUCT）DICOM文件的Python庫。它提供了創建、修改和驗證RTSTRUCT數據集的功能，以及在RTSTRUCT和體積掩碼之間進行轉換的工具。
+
+## 功能特點
+- 創建RTSTRUCT數據集
+- 添加和管理感興趣區域(ROI)
+- 將3D掩碼轉換為DICOM輪廓
+- 將DICOM輪廓轉換為3D掩碼
+- 驗證RTSTRUCT數據集的合規性
+- 處理和排序DICOM圖像序列
+- 坐標轉換工具
+## 安裝
+### 依賴項
+- Python >= 3.8
+- pydicom >= 2.0.0
+- numpy == 1.26.4
+- opencv-python >= 4.10.0
+- scipy >= 1.10.3
+### 使用pip安裝
+```
+pip install pydicomrt
+```
+
+從源碼安裝
+```
+git clone https://github.com/yourusername/pydicomRT.git
+cd pydicomRT
+pip install .
+
+```
+
+## 使用示例
+### 創建RTSTRUCT數據集並添加ROI
+
+```python
+
+import numpy as np
+from pydicomrt.rs.make_contour_sequence import add_contour_sequence_from_mask3d
+from pydicomrt.rs.add_new_roi import create_roi_into_rs_ds
+from pydicomrt.rs.builder import create_rtstruct_dataset
+from pydicomrt.utils.image_series_loader import load_sorted_image_series
+
+# 加載圖像序列
+ds_list = load_sorted_image_series("path/to/dicom/images")
+
+# 創建空的RTSTRUCT數據集
+rs_ds = create_rtstruct_dataset(ds_list)
+
+# 創建ROI（感興趣區域）
+rs_ds = create_roi_into_rs_ds(rs_ds, [0, 255, 0], 1, "CTV", "CTV")
+
+# 創建3D掩碼
+mask = np.zeros((len(ds_list), 512, 512))
+mask[100:200, 100:400, 100:400] = 1
+mask[120:180, 200:300, 200:300] = 0
+
+# 將3D掩碼添加到RTSTRUCT數據集
+rs_ds = add_contour_sequence_from_mask3d(rs_ds, ds_list, 1, mask)
+
+# 保存RTSTRUCT數據集
+rs_ds.save_as("path/to/output.dcm", write_like_original=False)
+```
+
+
+### 從RTSTRUCT數據集中提取輪廓信息
+```python
+from pydicomrt.rs.parser import get_roi_number_to_name, get_contour_dict
+
+# 獲取ROI映射
+roi_map = get_roi_number_to_name(rs_ds)
+print(roi_map)  # 輸出: {1: 'CTV'}
+
+# 獲取輪廓字典
+ctr_dict = get_contour_dict(rs_ds)
+
+```
+
+### 驗證RTSTRUCT數據集
+```python
+from pydicomrt.rs.checker import check_rs_iod
+
+# 檢查RTSTRUCT數據集是否符合IOD規範
+result = check_rs_iod(rs_ds)
+print(result)  # 輸出: {'result': True, 'content': []}
+
+```
+
+
+## 模塊結構
+- rs : 放射治療結構集相關功能
+  
+  - builder : 創建RTSTRUCT數據集
+  - add_new_roi : 添加新的ROI
+  - make_contour_sequence : 創建輪廓序列
+  - parser : 解析RTSTRUCT數據集
+  - checker : 驗證RTSTRUCT數據集
+  - rs_to_volume : RTSTRUCT與體積數據轉換
+- utils : 實用工具
+  
+  - image_series_loader : 加載和排序DICOM圖像序列
+  - coordinate_transform : 坐標轉換工具
+  - validate_dcm_info : 驗證DICOM信息
+## 貢獻
+歡迎提交問題和拉取請求。
+
+## 許可證
+請參閱LICENSE文件。
+
+## 作者
+- Higumalu ( higuma.lu@gmail.com )

pydicomrt-0.4.0/README.md

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+# pydicomRT
+pydicomRT 是一個用於處理放射治療結構集（RTSTRUCT）DICOM文件的Python庫。它提供了創建、修改和驗證RTSTRUCT數據集的功能，以及在RTSTRUCT和體積掩碼之間進行轉換的工具。
+
+## 功能特點
+- 創建RTSTRUCT數據集
+- 添加和管理感興趣區域(ROI)
+- 將3D掩碼轉換為DICOM輪廓
+- 將DICOM輪廓轉換為3D掩碼
+- 驗證RTSTRUCT數據集的合規性
+- 處理和排序DICOM圖像序列
+- 坐標轉換工具
+## 安裝
+### 依賴項
+- Python >= 3.8
+- pydicom >= 2.0.0
+- numpy == 1.26.4
+- opencv-python >= 4.10.0
+- scipy >= 1.10.3
+### 使用pip安裝
+```
+pip install pydicomrt
+```
+
+從源碼安裝
+```
+git clone https://github.com/yourusername/pydicomRT.git
+cd pydicomRT
+pip install .
+
+```
+
+## 使用示例
+### 創建RTSTRUCT數據集並添加ROI
+
+```python
+
+import numpy as np
+from pydicomrt.rs.make_contour_sequence import add_contour_sequence_from_mask3d
+from pydicomrt.rs.add_new_roi import create_roi_into_rs_ds
+from pydicomrt.rs.builder import create_rtstruct_dataset
+from pydicomrt.utils.image_series_loader import load_sorted_image_series
+
+# 加載圖像序列
+ds_list = load_sorted_image_series("path/to/dicom/images")
+
+# 創建空的RTSTRUCT數據集
+rs_ds = create_rtstruct_dataset(ds_list)
+
+# 創建ROI（感興趣區域）
+rs_ds = create_roi_into_rs_ds(rs_ds, [0, 255, 0], 1, "CTV", "CTV")
+
+# 創建3D掩碼
+mask = np.zeros((len(ds_list), 512, 512))
+mask[100:200, 100:400, 100:400] = 1
+mask[120:180, 200:300, 200:300] = 0
+
+# 將3D掩碼添加到RTSTRUCT數據集
+rs_ds = add_contour_sequence_from_mask3d(rs_ds, ds_list, 1, mask)
+
+# 保存RTSTRUCT數據集
+rs_ds.save_as("path/to/output.dcm", write_like_original=False)
+```
+
+
+### 從RTSTRUCT數據集中提取輪廓信息
+```python
+from pydicomrt.rs.parser import get_roi_number_to_name, get_contour_dict
+
+# 獲取ROI映射
+roi_map = get_roi_number_to_name(rs_ds)
+print(roi_map)  # 輸出: {1: 'CTV'}
+
+# 獲取輪廓字典
+ctr_dict = get_contour_dict(rs_ds)
+
+```
+
+### 驗證RTSTRUCT數據集
+```python
+from pydicomrt.rs.checker import check_rs_iod
+
+# 檢查RTSTRUCT數據集是否符合IOD規範
+result = check_rs_iod(rs_ds)
+print(result)  # 輸出: {'result': True, 'content': []}
+
+```
+
+
+## 模塊結構
+- rs : 放射治療結構集相關功能
+  
+  - builder : 創建RTSTRUCT數據集
+  - add_new_roi : 添加新的ROI
+  - make_contour_sequence : 創建輪廓序列
+  - parser : 解析RTSTRUCT數據集
+  - checker : 驗證RTSTRUCT數據集
+  - rs_to_volume : RTSTRUCT與體積數據轉換
+- utils : 實用工具
+  
+  - image_series_loader : 加載和排序DICOM圖像序列
+  - coordinate_transform : 坐標轉換工具
+  - validate_dcm_info : 驗證DICOM信息
+## 貢獻
+歡迎提交問題和拉取請求。
+
+## 許可證
+請參閱LICENSE文件。
+
+## 作者
+- Higumalu ( higuma.lu@gmail.com )

pydicomrt-0.4.0/pyproject.toml

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+[project]
+name = "pydicomrt"
+version = "0.4.0"
+description = "Add your description here"
+readme = "README.md"
+authors = [
+    { name = "Higumalu", email = "higuma.lu@gmail.com" }
+]
+requires-python = ">=3.8"
+license = {text = "MIT"}
+dependencies = [
+    "pydicom>=2.0.0",
+    "numpy>=1.26.4",
+    "opencv-python>=4.10.0",
+    "scipy>=1.10.3",
+    "simpleitk>=2.5.0",
+]
+
+[project.scripts]
+pydicomrt = "pydicomrt:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

pydicomrt-0.4.0/src/pydicomrt/__init__.py

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+def main() -> None:
+    print("Hello from pydicomrt!")

pydicomrt-0.4.0/src/pydicomrt/ct/ct_ds_iod.py

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+from pydicom.uid import UID
+
+
+CT_IMAGE_IOD = {
+    "PatientID": {},
+    "PatientName": {},
+    "PatientBirthDate": {},
+    "PatientSex": {},
+    "StudyInstanceUID": {},
+    "StudyID": {},
+    "StudyDate": {},
+    "StudyTime": {},
+    "AccessionNumber": {},
+    "SeriesInstanceUID": {"type": UID},
+    "SeriesNumber": {},
+    "Modality": {"value": "CT"},
+    "Manufacturer": {},
+    "FrameOfReferenceUID": {"type": UID},
+    "SOPClassUID": {"type": UID},
+    "SOPInstanceUID": {"type": UID},
+    "InstanceNumber": {},
+
+    "SliceThickness": {},
+    "ImagePositionPatient": {},
+    "ImageOrientationPatient": {},
+    "PixelSpacing": {},
+
+    "Rows": {},
+    "Columns": {},
+
+    "ImageType": {},
+    "BitsAllocated": {},
+    "BitsStored": {},
+    "HighBit": {},
+    "RescaleIntercept": {},
+    "RescaleSlope": {},
+
+    "PixelData": {},
+
+}

pydicomrt-0.4.0/src/pydicomrt/dose/builder.py

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+import os
+import numpy as np
+import SimpleITK as sitk
+
+from datetime import datetime
+from pydicom.tag import Tag
+from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
+from pydicom.sequence import Sequence
+from pydicom.uid import generate_uid
+from pydicom.uid import ImplicitVRLittleEndian
+
+
+DICOM_UID_PREFIX = os.getenv('DICOM_UID_PREFIX', "1.2.826.0.1.3680043.8.498.")  # PYDICOM_ROOT_UID
+
+def generate_base_dataset() -> FileDataset:
+    file_name = "bear_dose"
+    file_meta = get_file_meta()
+    ds = FileDataset(file_name, {}, file_meta=file_meta, preamble=b"\0" * 128)
+    add_required_elements_to_ds(ds)
+    add_sequence_lists_to_ds(ds)
+    return ds
+
+def get_file_meta() -> FileMetaDataset:
+    file_meta = FileMetaDataset()
+    file_meta.FileMetaInformationGroupLength = 190
+    file_meta.FileMetaInformationVersion = b"\x00\x01"
+    file_meta.TransferSyntaxUID = ImplicitVRLittleEndian
+    file_meta.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.481.2"
+    file_meta.MediaStorageSOPInstanceUID = (
+        generate_uid(prefix=DICOM_UID_PREFIX)
+    )
+    file_meta.ImplementationClassUID = DICOM_UID_PREFIX + "1"
+    # TODO file_meta.ImplementationVersionName = ""
+    return file_meta
+
+def add_required_elements_to_ds(ds: FileDataset):
+    dt = datetime.now()
+    # Append data elements required by the DICOM standarad
+    ds.SpecificCharacterSet = "ISO_IR 192"
+    ds.InstanceCreationDate = dt.strftime("%Y%m%d")
+    ds.InstanceCreationTime = dt.strftime("%H%M%S")
+    ds.Modality = "RTDOSE"
+    ds.Manufacturer = "higumalu"
+    ds.ManufacturerModelName = "modelv1"
+    ds.InstitutionName = "higumalu"
+    # Set the transfer syntax
+    ds.is_little_endian = True
+    ds.is_implicit_VR = True
+    # Set values already defined in the file meta
+    ds.SOPClassUID = ds.file_meta.MediaStorageSOPClassUID
+    ds.SOPInstanceUID = ds.file_meta.MediaStorageSOPInstanceUID
+
+    ds.ApprovalStatus = "UNAPPROVED"
+
+def add_sequence_lists_to_ds(ds: FileDataset):
+    ds.ReferencedRTPlanSequence = Sequence()
+
+# ---------------------------------------------------------------------------------------- #
+
+def add_patient_information(ds: FileDataset, reference_ds: Dataset):
+    ds.PatientName = getattr(reference_ds, "PatientName", "Unknown")
+    ds.PatientID = getattr(reference_ds, "PatientID", "Unknown")
+    ds.PatientBirthDate = getattr(reference_ds, "PatientBirthDate", "")
+    ds.PatientSex = getattr(reference_ds, "PatientSex", "")
+    ds.PatientAge = getattr(reference_ds, "PatientAge", "")
+    ds.PatientSize = getattr(reference_ds, "PatientSize", "")
+    ds.PatientWeight = getattr(reference_ds, "PatientWeight", "")
+    return ds
+
+def add_study_information(ds: FileDataset, reference_ds: Dataset):
+    dt = datetime.now()
+    ds.StudyInstanceUID = getattr(reference_ds, "StudyInstanceUID", generate_uid(prefix=DICOM_UID_PREFIX))
+    ds.StudyDate = getattr(reference_ds, "StudyDate", dt.strftime("%Y%m%d"))
+    ds.StudyTime = getattr(reference_ds, "StudyTime", dt.strftime("%H%M%S"))
+    ds.StudyID = getattr(reference_ds, "StudyID", "")
+    ds.AccessionNumber = getattr(reference_ds, "AccessionNumber", "")
+    ds.ReferringPhysicianName = getattr(reference_ds, "ReferringPhysicianName", "")
+    return ds
+
+def add_series_information(ds: FileDataset, reference_ds: Dataset, series_number: int = 1):
+    dt = datetime.now()
+    ds.Modality = "RTDOSE"
+    ds.SeriesInstanceUID = generate_uid(prefix=DICOM_UID_PREFIX)
+    ds.SeriesDate = dt.strftime("%Y%m%d")
+    ds.SeriesTime = dt.strftime("%H%M%S")
+    ds.SeriesDescription = getattr(reference_ds, "SeriesDescription", "") + "_dose" + dt.strftime("%Y%m%d%H%M%S")
+    ds.SeriesNumber = getattr(reference_ds, "SeriesNumber", series_number)
+    ds.OperatorsName = getattr(reference_ds, "OperatorsName", "")
+    return ds
+
+def add_frame_of_reference_information(ds: FileDataset, reference_ds: Dataset):
+    ds.FrameOfReferenceUID = getattr(reference_ds, "FrameOfReferenceUID", generate_uid(prefix=DICOM_UID_PREFIX))
+    ds.PositionReferenceIndicator = getattr(reference_ds, "PositionReferenceIndicator", "")
+    return ds
+
+# ---------------------------------------------------------------------------------------- #
+
+def cp_information_from_ds(
+    ds: FileDataset,
+    reference_ds: Dataset,
+    ):
+    ds = add_patient_information(ds, reference_ds)
+    ds = add_study_information(ds, reference_ds)
+    ds = add_series_information(ds, reference_ds)
+    ds = add_frame_of_reference_information(ds, reference_ds)
+    return ds
+
+# ---------------------------------------------------------------------------------------- #
+
+def add_dose_grid_to_ds(
+    ds: FileDataset,
+    dose_sitk_image: sitk.Image,
+    ):
+    scaling = 1e-7
+    array = sitk.GetArrayFromImage(dose_sitk_image)
+    size = list(dose_sitk_image.GetSize())
+    spacing = list(dose_sitk_image.GetSpacing())
+    direction = list(dose_sitk_image.GetDirection())
+    origin = list(dose_sitk_image.GetOrigin())
+
+    ds.SamplesPerPixel = 1
+    ds.PhotometricInterpretation = "MONOCHROME2"
+    ds.BitsAllocated = 32
+    ds.BitsStored = 32
+    ds.HighBit = 31
+    ds.PixelRepresentation = True
+    ds.DoseUnits = "GY"
+    ds.DoseType = "EFFECTIVE"
+    ds.DoseSummationType = "PLAN"
+    ds.NumberOfFrames = size[2]
+    ds.FrameIncrementPointer = Tag(0x3004, 0x000C)
+
+    ds.ImagePositionPatient = origin
+    ds.ImageOrientationPatient = direction
+    ds.PixelSpacing = spacing[0:2]
+    ds.SliceThickness = spacing[2]
+    ds.Columns = size[0]
+    ds.Rows = size[1]
+    ds.GridFrameOffsetVector = [ov * spacing[2] for ov in range(size[2])]
+    ds.DoseGridScaling = scaling
+    ds.PixelData = (array // scaling).astype(np.uint32).tobytes()
+    return ds
+
+
+# -------------------------------- example --------------------------------------------------- #
+
+if __name__ == "__main__":
+    import pydicom
+    import SimpleITK as sitk
+    dose_sitk_image = sitk.ReadImage("example/data/DF_001/RD_003/CT_001_dose.dcm")
+    ds = pydicom.dcmread("example/data/DF_001/RD_003/CT_001.dcm")
+
+    dose_ds = generate_base_dataset()
+    dose_ds = cp_information_from_ds(dose_ds, ds)
+    dose_ds = add_dose_grid_to_ds(dose_ds, dose_sitk_image)
+    dose_ds.save_as("example/data/DF_001/RD_003/dose.dcm")