Python disable_validate_slice_increment示例

示例#1

文件： debug_directory.py 项目： icometrix/dicom2nifti

    def test_convert_directory(self):

        tmp_output_dir = tempfile.mkdtemp()
        try:
            settings.enable_resampling()
            settings.set_resample_spline_interpolation_order(1)
            settings.set_resample_padding(-1000)
            settings.disable_validate_slice_increment()
            settings.disable_validate_orthogonal()
            convert_directory.convert_directory("/Users/abrys/Downloads/dicom_CT_UNKNOWN_3",
                                                "/Users/abrys/Downloads")

        finally:
            shutil.rmtree(tmp_output_dir)

示例#2

    def test_convert_directory(self):

        tmp_output_dir = tempfile.mkdtemp()
        try:
            settings.enable_resampling()
            settings.set_resample_spline_interpolation_order(1)
            settings.set_resample_padding(-1000)
            settings.disable_validate_slice_increment()
            settings.disable_validate_orthogonal()
            convert_directory.convert_directory("/Users/abrys/Downloads/test",
                                                "/Users/abrys/Downloads")

        finally:
            shutil.rmtree(tmp_output_dir)

示例#3

文件： create_ground_truth.py 项目： marcellamontagnese/dicom2nifti

def generate_inconsistent_slice_incement():
    settings.disable_validate_orthogonal()
    settings.disable_validate_slice_increment()
    settings.enable_resampling()
    settings.set_resample_padding(0)
    settings.set_resample_spline_interpolation_order(1)

    dicom_directory = os.path.join(
        os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'tests',
        'data', 'failing', 'sliceincrement', '002')

    output_file = dicom_directory + '_ground_truth.nii.gz'
    reoriented_file = dicom_directory + '_ground_truth_reoriented.nii.gz'
    generate_ground_truth(dicom_directory, output_file, reoriented_file)

    settings.disable_resampling()
    settings.enable_validate_slice_increment()
    settings.enable_validate_orientation()

示例#4

文件： test_generic.py 项目： icometrix/dicom2nifti

    def test_inconsistent_slice_increment_resampling(self):
        tmp_output_dir = tempfile.mkdtemp()
        try:
            settings.disable_validate_orthogonal()
            settings.disable_validate_slice_increment()
            settings.enable_resampling()
            settings.set_resample_padding(0)
            settings.set_resample_spline_interpolation_order(1)
            results = convert_generic.dicom_to_nifti(read_dicom_directory(test_data.FAILING_SLICEINCREMENT_2),
                                                     os.path.join(tmp_output_dir, 'test.nii.gz'))
            assert_compare_nifti(results['NII_FILE'],
                                 ground_thruth_filenames(test_data.FAILING_SLICEINCREMENT_2)[0])
            self.assertTrue(isinstance(results['NII'], nibabel.nifti1.Nifti1Image))

        finally:
            settings.disable_resampling()
            settings.enable_validate_slice_increment()
            settings.enable_validate_orientation()
            shutil.rmtree(tmp_output_dir)

示例#5

文件： create_ground_truth.py 项目： icometrix/dicom2nifti

def generate_inconsistent_slice_incement():
    settings.disable_validate_orthogonal()
    settings.disable_validate_slice_increment()
    settings.enable_resampling()
    settings.set_resample_padding(0)
    settings.set_resample_spline_interpolation_order(1)

    dicom_directory = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))),
                                   'tests',
                                   'data',
                                   'failing',
                                   'sliceincrement',
                                   '002')

    output_file = dicom_directory + '_ground_truth.nii.gz'
    reoriented_file = dicom_directory + '_ground_truth_reoriented.nii.gz'
    generate_ground_truth(dicom_directory, output_file, reoriented_file)

    settings.disable_resampling()
    settings.enable_validate_slice_increment()
    settings.enable_validate_orientation()

示例#6

    def test_inconsistent_slice_increment_resampling(self):
        tmp_output_dir = tempfile.mkdtemp()
        try:
            settings.disable_validate_orthogonal()
            settings.disable_validate_slice_increment()
            settings.enable_resampling()
            settings.set_resample_padding(0)
            settings.set_resample_spline_interpolation_order(1)
            results = convert_generic.dicom_to_nifti(
                read_dicom_directory(test_data.FAILING_SLICEINCREMENT_2),
                os.path.join(tmp_output_dir, 'test.nii.gz'))
            assert_compare_nifti(
                results['NII_FILE'],
                ground_thruth_filenames(test_data.FAILING_SLICEINCREMENT_2)[0])
            self.assertTrue(
                isinstance(results['NII'], nibabel.nifti1.Nifti1Image))

        finally:
            settings.disable_resampling()
            settings.enable_validate_slice_increment()
            settings.enable_validate_orientation()
            shutil.rmtree(tmp_output_dir)

示例#7

文件： dicom2Nifti.py 项目： prashul/VarianMedicalProject

def convertDicom2Nifti( inputFiles,outputDirectory ):
    mapOfFileNames = {}
    settings.disable_validate_orientation()
    settings.disable_validate_orthogonal()
    settings.disable_validate_slice_increment()

示例#8

import asyncio
from pydicom import dcmread
from pydicom.tag import Tag
import dicom2nifti
import os
import pathlib
from pydcmq import *
import dicom2nifti.settings as settings

settings.disable_validate_orthogonal()
settings.disable_validate_slice_increment()
settings.enable_resampling()
settings.set_resample_spline_interpolation_order(1)
settings.set_resample_padding(-1024)


async def dcmhandler(channel, ds, uri, routing_key):
    print(f"dcm2niix: converting {uri} ({ds.SeriesDescription})")
    outdir = f"{os.environ['HOME']}/.dcmq/nii/{ds.StudyInstanceUID}"
    pathlib.Path(outdir).mkdir(parents=True, exist_ok=True)
    count = 0
    with os.scandir(uri) as it:
        for series in it:
            if series.is_dir():
                with os.scandir(series) as it2:
                    for instance in it2:
                        if instance.is_file():
                            dcmfilename = instance.name
                            break
                refds = dcmread(os.path.join(uri, series.name, dcmfilename))
                try: