dbdicom 0.2.0__py3-none-any.whl → 0.3.16__py3-none-any.whl

dbdicom/sop_classes/mr_image.py

@@ -0,0 +1,338 @@
+import os
+
+import numpy as np
+import vreg
+import pydicom
+from pydicom.dataset import FileMetaDataset, Dataset, FileDataset
+from pydicom.sequence import Sequence
+from pydicom.uid import (
+    ExplicitVRLittleEndian,
+    generate_uid,
+    MRImageStorage,
+)
+
+from datetime import datetime
+
+import dbdicom.utils.image as image
+
+
+def pixel_data(ds):
+    """Read the pixel array from an MR image"""
+
+    array = ds.pixel_array
+    array = array.astype(np.float32)
+    if [0x2005, 0x100E] in ds: # 'Philips Rescale Slope'
+        slope = ds[(0x2005, 0x100E)].value
+        intercept = ds[(0x2005, 0x100D)].value
+        if (intercept == 0) and (slope == 1): 
+            array = array.astype(np.int16)
+        else:
+            array = array.astype(np.float32)
+            array -= intercept
+            array /= slope
+    else:
+        slope = float(getattr(ds, 'RescaleSlope', 1)) 
+        intercept = float(getattr(ds, 'RescaleIntercept', 0)) 
+        if (intercept == 0) and (slope == 1): 
+            array = array.astype(np.int16)
+        else:
+            array = array.astype(np.float32)
+            array *= slope
+            array += intercept
+    return np.transpose(array)
+
+
+def set_pixel_data(ds, array):
+
+    # Delete 'Philips Rescale Slope'
+    if (0x2005, 0x100E) in ds: 
+        del ds[0x2005, 0x100E] 
+    if (0x2005, 0x100D) in ds: 
+        del ds[0x2005, 0x100D]
+
+    ds.BitsAllocated = 16
+    ds.BitsStored = 16
+    ds.HighBit = 15
+
+    if array.dtype==np.int16:
+        array = image.clip(array) # remove nan and infs
+        ds.PixelRepresentation = 1
+        ds.RescaleSlope = 1
+        ds.RescaleIntercept = 0
+    elif array.dtype==np.uint16:
+        array = image.clip(array) # remove nan and infs
+        ds.PixelRepresentation = 0
+        ds.RescaleSlope = 1
+        ds.RescaleIntercept = 0
+    else:
+        array = image.clip(array) # remove nan and infs
+        array, slope, intercept = image.scale_to_range(array, ds.BitsStored)
+        ds.PixelRepresentation = 0
+        ds.RescaleSlope = 1 / slope
+        ds.RescaleIntercept = - intercept / slope
+
+    array = np.transpose(array)
+    ds.Rows = array.shape[0]
+    ds.Columns = array.shape[1]
+    ds.PixelData = array.tobytes()
+
+
+
+def default(): # from the RIDER dataset
+
+    # File meta info data elements
+    file_meta = FileMetaDataset()
+    file_meta.FileMetaInformationGroupLength = 190
+    file_meta.FileMetaInformationVersion = b'\x00\x01'
+    file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
+    file_meta.MediaStorageSOPInstanceUID = '1.3.6.1.4.1.9328.50.16.175333593952805976694548436931998383940'
+    file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
+    file_meta.ImplementationClassUID = '1.2.40.0.13.1.1'
+    file_meta.ImplementationVersionName = 'dcm4che-1.4.27'
+
+    # Create the main dataset
+    ds = FileDataset(
+        filename_or_obj=None,
+        dataset=Dataset(),
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+    )
+
+    ds.is_implicit_VR = True
+    ds.is_little_endian = True
+
+    # Main data elements
+    ds.SpecificCharacterSet = 'ISO_IR 100'
+    ds.ImageType = ['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']
+    ds.SOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
+    ds.SOPInstanceUID = pydicom.uid.generate_uid()
+    ds.StudyDate = '19040321'
+    ds.ContentDate = '19040321'
+    ds.StudyTime = ''
+    ds.AcquisitionTime = '075649.057496'
+    ds.ContentTime = ''
+    ds.AccessionNumber = '2819497684894126'
+    ds.Modality = 'MR'
+    ds.Manufacturer = 'SIEMENS'
+    ds.ReferringPhysicianName = ''
+    ds.StationName = ''
+    ds.StudyDescription = 'BRAIN^RESEARCH'
+    ds.SeriesDescription = 'sag 3d gre +c'
+    ds.ManufacturerModelName = ''
+    ds.ReferencedSOPClassUID = '1.3.6.1.4.1.9328.50.16.295504506656781074046411123909869020125'
+    ds.ReferencedSOPInstanceUID = '1.3.6.1.4.1.9328.50.16.303143938897288157958328401346374476407'
+    ds.PatientName = '281949'
+    ds.PatientID = pydicom.uid.generate_uid()
+    ds.PatientBirthDate = ''
+    ds.PatientSex = ''
+    ds.PatientIdentityRemoved = 'YES'
+    ds.DeidentificationMethod = 'CTP:NBIA Default w/ extra date removal:20100323:172722'
+    ds.ContrastBolusAgent = 'Magnevist'
+    ds.BodyPartExamined = 'FAKE'
+    ds.ScanningSequence = 'GR'
+    ds.SequenceVariant = 'SP'
+    ds.ScanOptions = ''
+    ds.MRAcquisitionType = '3D'
+    ds.SequenceName = '*fl3d1'
+    ds.AngioFlag = 'N'
+    ds.SliceThickness = '1.0'
+    ds.RepetitionTime = '8.6'
+    ds.EchoTime = '4.11'
+    ds.NumberOfAverages = '1.0'
+    ds.ImagingFrequency = '63.676701'
+    ds.ImagedNucleus = '1H'
+    ds.EchoNumbers = '0'
+    ds.MagneticFieldStrength = '1.4939999580383'
+    ds.NumberOfPhaseEncodingSteps = '224'
+    ds.EchoTrainLength = '1'
+    ds.PercentSampling = '100.0'
+    ds.PercentPhaseFieldOfView = '100.0'
+    ds.PixelBandwidth = '150.0'
+    ds.DeviceSerialNumber = '25445'
+    ds.SoftwareVersions = 'syngo MR 2004V 4VB11D'
+    ds.ProtocolName = 'sag 3d gre +c'
+    ds.ContrastBolusVolume = '20.0'
+    ds.DateOfLastCalibration = '19031229'
+    ds.TimeOfLastCalibration = '155156.000000'
+    ds.TransmitCoilName = 'Body'
+    ds.InPlanePhaseEncodingDirection = 'ROW'
+    ds.FlipAngle = '20.0'
+    ds.VariableFlipAngleFlag = 'N'
+    ds.SAR = '0.09494107961655'
+    ds.dBdt = '0.0'
+    ds.PatientPosition = 'HFS'
+    ds.StudyInstanceUID = pydicom.uid.generate_uid()
+    ds.SeriesInstanceUID = pydicom.uid.generate_uid()
+    ds.StudyID = ''
+    ds.SeriesNumber = '14'
+    ds.AcquisitionNumber = '1'
+    ds.InstanceNumber = '1'
+    ds.ImagePositionPatient = [0, 0, 0]
+    ds.ImageOrientationPatient = [1, 0, 0, 0, 1, 0]
+    ds.FrameOfReferenceUID = '1.3.6.1.4.1.9328.50.16.22344679587635360510174487884943834158'
+    ds.PositionReferenceIndicator = ''
+    ds.SliceLocation = '0.0'
+    ds.SamplesPerPixel = 1
+    ds.PhotometricInterpretation = 'MONOCHROME2'
+    ds.Rows = 64
+    ds.Columns = 64
+    ds.PixelSpacing = [1, 1]
+    ds.BitsAllocated = 16
+    ds.BitsStored = 16
+    ds.HighBit = 15
+    ds.PixelRepresentation = 0
+    ds.SmallestImagePixelValue = 0
+    ds.LargestImagePixelValue = 913
+    ds.WindowCenter = '136.0'
+    ds.WindowWidth = '380.0'
+    ds.RescaleIntercept = '0.0'
+    ds.RescaleSlope = '1.0'
+    ds.RescaleType = 'PIXELVALUE'
+    ds.WindowCenterWidthExplanation = 'Algo1'
+    ds.RequestedProcedureDescription = 'MRI BRAIN W/WO ENHANCEMENT'
+    ds.ScheduledProcedureStepDescription = 'MRI BRAIN W/WO ENHANCEMENT'
+    ds.ScheduledProcedureStepID = '5133240'
+    ds.PerformedProcedureStepStartDate = '19040611'
+    ds.PerformedProcedureStepDescription = 'MRI BRAIN W/WO ENHANCEMENT'
+    ds.RequestAttributesSequence = Sequence()
+    ds.RequestedProcedureID = '5133240'
+    ds.StorageMediaFileSetUID = '1.3.6.1.4.1.9328.50.16.162890465625511526068665093825399871205'
+    pixel_values = np.arange(ds.Rows*ds.Columns)*ds.LargestImagePixelValue/(ds.Rows*ds.Columns)
+    ds.PixelData = pixel_values.astype(np.uint16).tobytes()
+
+    return ds
+
+
+def chat_gpt_3d(num_frames=10, rows=256, columns=256):
+
+    # File meta info
+    file_meta = FileMetaDataset()
+    file_meta.MediaStorageSOPClassUID = MRImageStorage
+    file_meta.MediaStorageSOPInstanceUID = generate_uid()
+    file_meta.ImplementationClassUID = generate_uid()
+    file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
+
+    # Create FileDataset in memory
+    ds = FileDataset(
+        filename_or_obj=None,
+        dataset=Dataset(),
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+    )
+
+    # Transfer syntax
+    ds.is_little_endian = True
+    ds.is_implicit_VR = False
+
+    now = datetime.now()
+
+    # Required fields
+    ds.SOPClassUID = MRImageStorage
+    ds.SOPInstanceUID = file_meta.MediaStorageSOPInstanceUID
+    ds.PatientName = "Multi^Frame"
+    ds.PatientID = "999999"
+    ds.StudyInstanceUID = generate_uid()
+    ds.SeriesInstanceUID = generate_uid()
+    ds.StudyDate = now.strftime("%Y%m%d")
+    ds.StudyTime = now.strftime("%H%M%S")
+    ds.Modality = "MR"
+    ds.Manufacturer = "PythonPACS"
+    ds.StudyID = "1"
+    ds.SeriesNumber = "1"
+    ds.InstanceNumber = "1"
+
+    # Image geometry
+    ds.Rows = rows
+    ds.Columns = columns
+    ds.PixelSpacing = [1.0, 1.0]
+    ds.ImagePositionPatient = [0.0, 0.0, 0.0]
+    ds.ImageOrientationPatient = [1.0, 0.0, 0.0, 0.0, 1.0, 0.0]
+    ds.FrameOfReferenceUID = generate_uid()
+    ds.PositionReferenceIndicator = ""
+
+    # Multi-frame specific
+    ds.NumberOfFrames = str(num_frames)
+    ds.InstanceNumber = "1"
+
+    # Pixel data requirements
+    ds.SamplesPerPixel = 1
+    ds.PhotometricInterpretation = "MONOCHROME2"
+    ds.BitsAllocated = 16
+    ds.BitsStored = 12
+    ds.HighBit = 11
+    ds.PixelRepresentation = 0  # unsigned
+
+    # Create dummy image data (e.g., black frames)
+    pixel_array = np.zeros((num_frames, rows, columns), dtype=np.uint16)
+    ds.PixelData = pixel_array.tobytes()
+
+    return ds
+
+
+
+def chat_gpt_2d():
+    # Basic identifiers
+    file_meta = FileMetaDataset()
+    file_meta.MediaStorageSOPClassUID = MRImageStorage
+    file_meta.MediaStorageSOPInstanceUID = generate_uid()
+    file_meta.ImplementationClassUID = generate_uid()
+
+    # Create the main dataset
+    ds = FileDataset(
+        filename_or_obj=None,
+        dataset=Dataset(),
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+    )
+
+    # Set transfer syntax
+    ds.is_little_endian = True
+    ds.is_implicit_VR = False
+
+    # Required DICOM tags for MR Image Storage
+    now = datetime.now()
+    ds.SOPClassUID = MRImageStorage
+    ds.SOPInstanceUID = file_meta.MediaStorageSOPInstanceUID
+    ds.PatientName = "Anonymous^Patient"
+    ds.PatientID = "123456"
+    ds.StudyInstanceUID = generate_uid()
+    ds.SeriesInstanceUID = generate_uid()
+    ds.StudyDate = now.strftime("%Y%m%d")
+    ds.StudyTime = now.strftime("%H%M%S")
+    ds.Modality = "MR"
+    ds.Manufacturer = "PythonPACS"
+    ds.StudyID = "1"
+    ds.SeriesNumber = "1"
+    ds.InstanceNumber = "1"
+    ds.ImagePositionPatient = [0.0, 0.0, 0.0]
+    ds.ImageOrientationPatient = [1.0, 0.0, 0.0, 0.0, 1.0, 0.0]
+    ds.FrameOfReferenceUID = generate_uid()
+    ds.PositionReferenceIndicator = ""
+    ds.Rows = 256
+    ds.Columns = 256
+    ds.PixelSpacing = [1.0, 1.0]
+    ds.BitsAllocated = 16
+    ds.BitsStored = 12
+    ds.HighBit = 11
+    ds.PixelRepresentation = 0  # unsigned
+    ds.SamplesPerPixel = 1
+    ds.PhotometricInterpretation = "MONOCHROME2"
+    ds.PixelData = (b"\0" * (ds.Rows * ds.Columns * 2))  # Dummy black image
+
+    return ds
+
+
+
+
+
+
+
+if __name__ == '__main__':
+    file = os.path.join(os.getcwd(), 'chat_gpt_mri.dcm')
+    chat_gpt_3d().save_as(file)
+    file = os.path.join(os.getcwd(), 'default_mri.dcm')
+    default().save_as(file)
+    print(file)
+
+
+