使用python在excel中转​​换dicom标签时出错

Question

我正在尝试将 .dcm 文件中的 dicom 标签转换并列出为 excel（使用 python），但某些标签在转换时显示错误（PatientName、PixelSpacing 等）。

一些标签在 excel 文件中显示为“无”，尽管它们包含/显示 Dicom 格式的数据（SliceThickness、SpacingBetweenSlices 等）。我该如何解决这个问题？

此外，我希望输出文件位于不同的文件夹中，而不使用 os.chdir() 命令。我尝试了几种方法，但无法弄清楚。

任何建议将不胜感激。

这是我的代码：

import xlsxwriter 
import sys 
import dicom 
import os.path

root = input("Enter Directory Name: ") path = os.path.join(root, "targetdirectory") i=1

for path, subdirs, files in os.walk(root):
    for name in files:

        os.rename(os.path.join(path, name), os.path.join(path,'MR000'+ str(i)+'.dcm'))
        i=i+1
        print (os.path.join(path, name))

         dcm_files = [] for root, dirs, files in os.walk(path):
    for names in files:
        if names.endswith(".dcm"):
            dcm_files.append(os.path.join(root, names))

for dcm_file in dcm_files:
    ds = dicom.read_file(dcm_file)
    workbook = xlsxwriter.Workbook(os.path.basename(dcm_file) + '.xlsx')
    worksheet = workbook.add_worksheet()
    a = os.getcwd ()
    print (a)


    data = (
            #["PatientName", ds.get("PatientName", "None")],
            ["PatientID", ds.get("PatientID", "None")],
            ["PatientBirthDate", ds.get("PatientBirthDate", "None")],
            ["PatientSex", ds.get("PatientSex", "None")],
            ["RepetitionTime", ds.get("RepetitionTime", "None")],
            ["EchoTime", ds.get("EchoTime", "None")],
            ["Modality", ds.get("Modality", "None")],
            ["Manufacturer", ds.get("Manufacturer", "None")],
            ["InstitutionName", ds.get("Institution Name", "None")],
            #["ReferringPhysicianName", ds.get("ReferringPhysicianName", "None")],
            ["StudyDescription", ds.get("StudyDescription", "None")],
            ["PatientAge", ds.get("PatientAge", "None")],
            ["SliceThickness", ds.get("SliceThickness(mm)", "None")],
            ["SpacingBetweenSlices", ds.get("SpacingBetweenSlices", "None")],
            ["SeriesNumber", ds.get("SeriesNumber", "None")],
            #["PixelSpacing", ds.get("PixelSpacing", "None")],
            ["RequestedProcedureID", ds.get("RequestedProcedureID", "None")],
            ["Rows", ds.get("Rows", "None")],
            ["Columns", ds.get("Columns", "None")]
            )

    row = 0
    col = 0

    for name, value in (data):
        worksheet.write(row, col,     name)
        worksheet.write(row + 1, col, value)
        col += 1

    workbook.close()

来自dicom标签的一些数据：

Columns: 256
InstitutionName: UIC MR2
PatientAge: 046Y
PatientBirthDate: 19630503
PatientID: 080524186
PatientName: PEREZ^GUILLERMINA
PatientPosition: HFS
PatientSex: F
PixelSpacing: ['0.9375', '0.9375']
Rows: 256
SliceThickness: 5
SpacingBetweenSlices: 10
StudyID: 586323788
StudyTime: 204546

谢谢。

Answer 1

我可以在代码中看到一些错误...例如“SliceThickness(mm)”不是正确的 dicom 关键字，并且“机构名称”有一个空格。我认为最好不要重复关键字。下面的代码将关键字列表设置在循环之外，并使用相同的名称来查找值。它会检查某些无法写入的类型（列表和 PersonName3）并转换它们。列表简单地变成一个字符串，元素之间有逗号；您可以尝试在不同的单元格或其他解决方案中写入。

import xlsxwriter 
import sys 
import dicom 
import os.path
from dicom.valuerep import PersonName3

keywords = ("PatientName",
            "PatientID",
            "PatientBirthDate",
            "PatientSex",
            "RepetitionTime",
            "EchoTime",
            "Modality",
            "Manufacturer",
            "InstitutionName",
            "ReferringPhysicianName",
            "StudyDescription",
            "PatientAge",
            "SliceThickness",
            "SpacingBetweenSlices",
            "SeriesNumber",
            "PixelSpacing",
            "RequestedProcedureID",
            "Rows",
            "Columns",
           )

# ...
# XXX fill in dcm_files list
dcm_files = [r"C:\temp\test.dcm"]   

for dcm_file in dcm_files:
    ds = dicom.read_file(dcm_file)
    workbook = xlsxwriter.Workbook(os.path.basename(dcm_file) + '.xlsx')
    worksheet = workbook.add_worksheet()

    row = 0
    col = 0

    for keyword in keywords:
        value = ds.get(keyword, "None")
        if isinstance(value, list):
            value = ", ".join([str(x) for x in value])
        elif isinstance(value, PersonName3):
            value = str(value)
        worksheet.write(row, col, keyword)
        worksheet.write(row + 1, col, value)
        col += 1

    workbook.close()

我更改了 dcm_files 部分只是为了进行更简单的测试；您可以放回完整列表的代码。

我不知道为什么 SpacingBetweenSlices 在您的代码中不起作用，但从我的测试文件中可以看出它很好。

至于输出到不同的文件夹，您应该可以使用 os.path.join 与您想要的位置和您创建的 xlsx 文件名。