PixelSpacing incorrectly taken into account

Hi all,

Thanks for all your work, rt-utils is a great tool !

I am working with a MR image and sometimes, depending of the aquisitiion we need to apply a rotation so that the images are "axialized".
The result is that the pixelSpacing has a different value for x and y and the rtstruct generated is incorrect.

Here is a python script that allows to create a SEG and a RT
Please set force=True in rt_utils when loading the dcm with pydicom, I had to create dcm file to have a self content script

import glob
import os
import pydicom_seg
import pydicom
import SimpleITK as sitk
import numpy as np
from rt_utils import RTStructBuilder
import json
  
# To update based on the path
dcm_dir = "C:\\Temp\\dicom_file_new"
seg_filename = "C:\\Temp\\segmentation.dcm"
rt_filename = "C:\\Temp\\segmentationRT.dcm"
template_filename = "C:\\Temp\\template.json"
isotrop = False

def process_image(image_data):
    out = np.where(image_data == 180, 1, 0).astype(np.uint16)
    return out
    
def create_input_dicom(dicom_dir, isotrop):
    os.makedirs(dicom_dir, exist_ok=True)

    header = '{"00080005": {"Value": ["ISO_IR 192"], "vr": "CS"}, "00080008": {"vr": "CS"}, "00080012": {"Value": ["20230721"], "vr": "DA"}, "00080013": {"Value": ["035751"], "vr": "TM"}, "00080014": {"Value": ["3.0.0"], "vr": "UI"}, "00080016": {"Value": ["1.2.840.10008.5.1.4.1.1.4"], "vr": "UI"}, "00080018": {"Value": ["2.25.115231125129161360422423700315339076734"], "vr": "UI"}, "00080020": {"Value": ["20150516"], "vr": "DA"}, "00080021": {"Value": ["20230721"], "vr": "DA"}, "00080022": {"Value": ["20150516"], "vr": "DA"}, "00080023": {"Value": ["20230721"], "vr": "DA"}, "00080030": {"vr": "TM"}, "00080031": {"Value": ["035751"], "vr": "TM"}, "00080032": {"vr": "TM"}, "00080033": {"Value": ["084601"], "vr": "TM"}, "00080050": {"Value": ["15060734050"], "vr": "SH"}, "00080060": {"Value": ["MR"], "vr": "CS"}, "00080070": {"Value": ["UNKNOWN"], "vr": "LO"}, "00080080": {"vr": "LO"}, "00080081": {"vr": "ST"}, "00080090": {"vr": "PN"}, "00081010": {"vr": "SH"}, "00081030": {"Value": ["PREPROCESS"], "vr": "LO"}, "0008103E": {"Value": ["PREPROCESS"], "vr": "LO"}, "00081040": {"vr": "LO"}, "00081048": {"vr": "PN"}, "00081050": {"vr": "PN"}, "00081060": {"vr": "PN"}, "00081070": {"vr": "PN"}, "00081090": {"Value": ["UNKNOWN"], "vr": "LO"}, "00081110": {"Value": [{"00081150": {"Value": ["1.2.840.10008.3.1.2.3.1"], "vr": "UI"}, "00081155": {"Value": ["1.2.124.113532.10.160.226.57.20150312.142717.6605503"], "vr": "UI"}}], "vr": "SQ"}, "00081111": {"Value": [{"00081150": {"Value": ["1.2.840.10008.3.1.2.3.3"], "vr": "UI"}, "00081155": {"Value": ["1.2.840.113619.6.322.240598304242724185143032673684777965063"], "vr": "UI"}}], "vr": "SQ"}, "00081120": {"Value": [{"00081150": {"Value": ["1.2.840.10008.3.1.2.1.1"], "vr": "UI"}, "00081155": {"Value": ["1.2.124.113532.10.160.160.59.20100828.175520.3010744"], "vr": "UI"}}], "vr": "SQ"}, "00100010": {"Value": [{"Alphabetic": "ANNON"}], "vr": "PN"}, "00100020": {"Value": ["ANNON"], "vr": "LO"}, "00100021": {"vr": "LO"}, "00100030": {"Value": ["20230101"], "vr": "DA"}, "00100032": {"vr": "TM"}, "00100040": {"vr": "CS"}, "00101010": {"vr": "AS"}, "00101030": {"vr": "DS"}, "00102110": {"vr": "LO"}, "00102160": {"vr": "SH"}, "00102180": {"vr": "SH"}, "001021B0": {"vr": "LT"}, "00104000": {"vr": "LT"}, "00120062": {"vr": "CS"}, "00180010": {"Value": ["15    g"], "vr": "LO"}, "00180020": {"Value": ["SE"], "vr": "CS"}, "00180021": {"Value": ["SK"], "vr": "CS"}, "00180022": {"vr": "CS"}, "00180023": {"Value": ["3D"], "vr": "CS"}, "00180025": {"Value": ["N"], "vr": "CS"}, "00180050": {"Value": [0.48828125], "vr": "DS"}, "00180080": {"Value": [600.0], "vr": "DS"}, "00180081": {"Value": [12.319], "vr": "DS"}, "00180083": {"Value": [1.0], "vr": "DS"}, "00180084": {"Value": [127.765418], "vr": "DS"}, "00180085": {"Value": ["1H"], "vr": "SH"}, "00180086": {"Value": [1], "vr": "IS"}, "00180087": {"Value": [3.0], "vr": "DS"}, "00180091": {"Value": [25], "vr": "IS"}, "00180093": {"Value": [100.0], "vr": "DS"}, "00180094": {"Value": [90.0], "vr": "DS"}, "00180095": {"Value": [244.141], "vr": "DS"}, "00181000": {"vr": "LO"}, "00181020": {"Value": ["3.0.0"], "vr": "LO"}, "00181030": {"vr": "LO"}, "00181040": {"Value": ["IV"], "vr": "LO"}, "00181088": {"Value": [0], "vr": "IS"}, "00181090": {"Value": [0], "vr": "IS"}, "00181094": {"Value": [0], "vr": "IS"}, "00181100": {"Value": [250.0], "vr": "DS"}, "00181250": {"vr": "SH"}, "00181310": {"Value": [0, 256, 256, 0], "vr": "US"}, "00181314": {"Value": [90.0], "vr": "DS"}, "00181315": {"Value": ["N"], "vr": "CS"}, "00181316": {"Value": [1.57316], "vr": "DS"}, "00185100": {"Value": ["HFS"], "vr": "CS"}, "0020000D": {"Value": ["2.25.255069905384861154924841019137563439343"], "vr": "UI"}, "0020000E": {"Value": ["2.25.205287721952789789408662186088058372087"], "vr": "UI"}, "00200010": {"vr": "SH"}, "00200011": {"Value": [350], "vr": "IS"}, "00200012": {"Value": [1], "vr": "IS"}, "00200013": {"Value": [1], "vr": "IS"}, "00200032": {"Value": [-92.620185852051, -157.00784301758, -132.19627380371], "vr": "DS"}, "00200037": {"Value": [1.0, 0.0, 0.0, 0.0, 1.0, 0.0], "vr": "DS"}, "00200052": {"Value": ["2.25.115231125129161360422423700315339076734"], "vr": "UI"}, "00200060": {"vr": "CS"}, "00201002": {"Value": [320], "vr": "IS"}, "00201040": {"vr": "LO"}, "00201041": {"Value": [-132.19627], "vr": "DS"}, "00280002": {"Value": [1], "vr": "US"}, "00280004": {"Value": ["MONOCHROME2"], "vr": "CS"}, "00280010": {"Value": [512], "vr": "US"}, "00280011": {"Value": [192], "vr": "US"}, "00280030": {"Value": [1.0, 2.0], "vr": "DS"}, "00280100": {"Value": [16], "vr": "US"}, "00280101": {"Value": [16], "vr": "US"}, "00280102": {"Value": [15], "vr": "US"}, "00280103": {"Value": [1], "vr": "US"}, "00280106": {"Value": [0], "vr": "SS"}, "00280107": {"Value": [739], "vr": "SS"}, "00281050": {"Value": [148.0], "vr": "DS"}, "00281051": {"Value": [11.0], "vr": "DS"}, "00281052": {"Value": [0.0], "vr": "DS"}, "00281053": {"Value": [1.0], "vr": "DS"}, "00281054": {"Value": ["US"], "vr": "LO"}, "00282110": {"Value": ["00"], "vr": "CS"}, "00321033": {"vr": "LO"}, "00380500": {"vr": "LO"}, "00400244": {"Value": ["20150516"], "vr": "DA"}, "00400245": {"Value": ["082225"], "vr": "TM"}, "00400253": {"Value": ["7246.1431760945"], "vr": "SH"}, "00400254": {"vr": "LO"}}'
    resZ = 0.48828125
    
    for i in range(512):
        ds = pydicom.dataset.Dataset.from_json(header)
        ds[0x0020, 0x0032].value[2] = ds[0x0020, 0x0032].value[2] + i * resZ
        ds.SOPInstanceUID = pydicom.uid.generate_uid(prefix=None)
        
        arr = np.zeros([512, 192]).astype(np.int16)
        arr[100:400, 30:150] = 150
        if i < 256:
            arr[50:200, 60:90] = 180
        else :
            arr[50:200, 60:90] = 130
        ds.PixelData = arr.tobytes()
        ds.is_little_endian = True
        ds.is_implicit_VR = True
        
        if isotrop:
            ds.PixelSpacing = [1, 1]
        ds.save_as(os.path.join(dicom_dir, f'MR{i:05}.dcm'))
        
#####################################
# Create the input dicom image
#####################################
create_input_dicom(dcm_dir, isotrop)

#####################################
# Read the original dicom image
#####################################
reader = sitk.ImageSeriesReader()
dcm_files = reader.GetGDCMSeriesFileNames(dcm_dir)
reader.SetFileNames(dcm_files)
image = reader.Execute()

#####################################
# Create dicom SEG object
#####################################
segmentation_data = process_image(sitk.GetArrayFromImage(image))
segmentation = sitk.GetImageFromArray(segmentation_data)
segmentation.CopyInformation(image)

# Write the template to file
template_json = '{"ContentCreatorName": "Reader1", "ClinicalTrialSeriesID": "Session1", "ClinicalTrialTimePointID": "1", "SeriesDescription": "Segmentation", "SeriesNumber": "300", "InstanceNumber": "1", "BodyPartExamined": "", "segmentAttributes": [[{"labelID": 1,    "SegmentDescription": "test",    "SegmentAlgorithmType": "SEMIAUTOMATIC",    "SegmentAlgorithmName": "Test",    "SegmentedPropertyCategoryCodeSequence": {"CodeValue": "123037004",     "CodingSchemeDesignator": "SCT",     "CodeMeaning": "Anatomical Structure"},    "SegmentedPropertyTypeCodeSequence": {"CodeValue": "91750005",     "CodingSchemeDesignator": "SCT",     "CodeMeaning": "1st Diagonal Coronary Artery"}}]], "ContentLabel": "SEGMENTATION", "ContentDescription": "Image segmentation", "ClinicalTrialCoordinatingCenterName": "dcmqi"}'
with open(template_filename, "w") as write_file:
    json.dump(json.loads(template_json), write_file)
    
template = pydicom_seg.template.from_dcmqi_metainfo(template_filename)
writer = pydicom_seg.MultiClassWriter(
    template=template,
    skip_empty_slices=False,  # Don't encode slices with only zeros
    skip_missing_segment=False,  # If a segment definition is missing in the
                                 # template, then raise an error instead of
                                 # skipping it.
)

dcm_files = glob.glob(dcm_dir + '\\*')
source_images = [pydicom.dcmread(x, stop_before_pixels=True, force=True) for x in dcm_files]
dcm = writer.write(segmentation, source_images)
dcm.save_as(seg_filename)

#####################################
# Compute the RT struct
#####################################
# Swap axis from Z, Y, X to X, Y, Z
segmentation_data = np.swapaxes(segmentation_data, 0, 2)
segmentation_data = np.swapaxes(segmentation_data, 0, 1)

roi_mask = np.where(segmentation_data == 1, True, False)
rtstruct = RTStructBuilder.create_new(dicom_series_path=dcm_dir)
rtstruct.add_roi(mask=roi_mask, name='seg test', color='cc0000')
rtstruct.save(rt_filename)

• When I set isotrop=True -> the x, y resolution is the same and the RT struct creation is fine.
  with MITK:

• When I set isotrop=False -> the x, y resolution is not the same and the RT is not at the correct place
  with MITK: