dbdicom 0.2.6__py3-none-any.whl → 0.3.1__py3-none-any.whl

dbdicom/{ds/types → sop_classes}/enhanced_mr_image.py

@@ -1,46 +1,173 @@
 # Coded version of DICOM file 'C:\Users\steve\Dropbox\Software\QIB-Sheffield\dbdicom\tests\data\MULTIFRAME\IM_0010'
 # Produced by pydicom codify utility script
-import numpy as np
+from datetime import datetime
+from datetime import timedelta
 
-from pydicom.dataset import Dataset, FileMetaDataset
+import numpy as np
+import pydicom
+from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
 from pydicom.sequence import Sequence
+from pydicom.uid import (
+    generate_uid,
+    MRImageStorage,
+    EnhancedMRImageStorage,
+    ExplicitVRLittleEndian
+)
 
-from dbdicom.ds.dataset import DbDataset
-import dbdicom.utils.image as image
 
-class EnhancedMRImage(DbDataset):
+from dbdicom.utils import image
 
-    def __init__(self, dataset=None, template=None):
-        super().__init__()
 
-        if (dataset is None) and (template is None):
-            template = 'UKRIN'
+import numpy as np
+import pydicom
+from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
+from pydicom.sequence import Sequence
+from pydicom.uid import ExplicitVRLittleEndian, EnhancedMRImageStorage, generate_uid
+from datetime import datetime, timedelta
+
+
+def create_5d_enhanced_mr_dataset(
+    time_points=20, flip_angles=10, slices=4, rows=128, cols=192
+):
+    total_frames = time_points * flip_angles * slices
+    now = datetime.now()
+
+    # File Meta Info
+    file_meta = FileMetaDataset()
+    file_meta.MediaStorageSOPClassUID = EnhancedMRImageStorage
+    file_meta.MediaStorageSOPInstanceUID = generate_uid()
+    file_meta.ImplementationClassUID = generate_uid()
+    file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
+
+    # Create FileDataset
+    ds = FileDataset(
+        filename_or_obj=None,
+        dataset=Dataset(),
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+    )
 
-        if dataset is not None:
-            self.__dict__ = dataset.__dict__
+    ds.is_little_endian = True
+    ds.is_implicit_VR = False
 
-        if template == 'UKRIN':
-            ukrin_maps(self)
+    # Identification
+    ds.SOPClassUID = EnhancedMRImageStorage
+    ds.SOPInstanceUID = file_meta.MediaStorageSOPInstanceUID
+    ds.PatientName = "FiveD^Phantom"
+    ds.PatientID = "555555"
+    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 Dimensions
+    ds.Rows = rows
+    ds.Columns = cols
+    ds.NumberOfFrames = str(total_frames)
+    ds.SamplesPerPixel = 1
+    ds.PhotometricInterpretation = "MONOCHROME2"
+    ds.BitsAllocated = 16
+    ds.BitsStored = 12
+    ds.HighBit = 11
+    ds.PixelRepresentation = 0
+    ds.PixelSpacing = [1.0, 1.0]
+    ds.SliceThickness = 1.0
+    ds.FrameOfReferenceUID = generate_uid()
+
+    # Dummy pixel data
+    pixel_array = np.zeros((total_frames, rows, cols), dtype=np.uint16)
+    ds.PixelData = pixel_array.tobytes()
+
+    # Shared Functional Groups
+    shared_fg = Dataset()
+    pix_meas = Dataset()
+    pix_meas.PixelSpacing = ds.PixelSpacing
+    pix_meas.SliceThickness = ds.SliceThickness
+    shared_fg.PixelMeasuresSequence = [pix_meas]
+    ds.SharedFunctionalGroupsSequence = [shared_fg]
+
+    # Dimension Organization
+    dim_org_uid = generate_uid()
+    ds.DimensionOrganizationSequence = Sequence([
+        Dataset()
+    ])
+    ds.DimensionOrganizationSequence[0].DimensionOrganizationUID = dim_org_uid
+
+    ds.DimensionIndexSequence = Sequence()
+
+    # Time dimension
+    temporal = Dataset()
+    temporal.DimensionOrganizationUID = dim_org_uid
+    temporal.DimensionIndexPointer = 0x00209164  # TemporalPositionIndex
+    temporal.FunctionalGroupPointer = 0x00209113  # TemporalPositionSequence
+    ds.DimensionIndexSequence.append(temporal)
+
+    # Flip angle dimension
+    flip = Dataset()
+    flip.DimensionOrganizationUID = dim_org_uid
+    flip.DimensionIndexPointer = 0x00181314  # FlipAngle
+    flip.FunctionalGroupPointer = 0x00189105  # MRImagingModifierSequence
+    ds.DimensionIndexSequence.append(flip)
+
+    # Slice position
+    slice_dim = Dataset()
+    slice_dim.DimensionOrganizationUID = dim_org_uid
+    slice_dim.DimensionIndexPointer = 0x00200032  # ImagePositionPatient
+    slice_dim.FunctionalGroupPointer = 0x00209113  # PlanePositionSequence
+    ds.DimensionIndexSequence.append(slice_dim)
+
+    # Per-Frame Functional Groups
+    per_frame_seq = []
+
+    base_time = now
+    flip_angle_values = np.linspace(5, 50, flip_angles)  # Example flip angles
+
+    for t in range(time_points):
+        for f in range(flip_angles):
+            for z in range(slices):
+                frame = Dataset()
+
+                # Frame content
+                fc = Dataset()
+                fc.FrameAcquisitionNumber = len(per_frame_seq)
+                fc.AcquisitionTime = (base_time + timedelta(seconds=t)).strftime("%H%M%S.%f")[:13]
+                frame.FrameContentSequence = [fc]
+
+                # Temporal position
+                tp = Dataset()
+                tp.TemporalPositionIndex = t + 1
+                frame.TemporalPositionSequence = [tp]
+
+                # Flip angle
+                fa = Dataset()
+                fa.FlipAngle = float(flip_angle_values[f])
+                frame.MRImagingModifierSequence = [fa]
+
+                # Slice position
+                pos = Dataset()
+                pos.ImagePositionPatient = [0.0, 0.0, float(z)]
+                frame.PlanePositionSequence = [pos]
+
+                per_frame_seq.append(frame)
+
+    ds.PerFrameFunctionalGroupsSequence = Sequence(per_frame_seq)
 
-    @property
-    def pixel_array(self):
-        """Reimplements pydicom property pixel_array"""
-        return get_pixel_array(self)
+    return ds
 
-    def get_pixel_array(self):
-        return get_pixel_array(self)
 
-    def set_pixel_array(self, array, value_range=None):
-        set_pixel_array(self, array, value_range=value_range)
 
-    def image_type(self):
-        return image_type(self)
 
-    def signal_type(self):
-        return signal_type(self)
 
 
-def ukrin_maps(ds):
+def default(): # UKRIN-MAPS
+
+
+    ds = Dataset()
 
     # File meta info data elements
     ds.file_meta = FileMetaDataset()

dbdicom/{ds/types → sop_classes}/mr_image.py

@@ -1,61 +1,208 @@
 # Coded version of DICOM file 
 # 'RIDER Neuro MRI-3369019796\03-21-1904-BRAINRESEARCH-00598\14.000000-sag 3d gre c-04769\1-010.dcm'
 # Produced by pydicom codify utility script
+import os
 import struct
 import numpy as np
 import pydicom
-from pydicom.dataset import Dataset, FileMetaDataset
+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 tempfile
 
-from dbdicom.ds.dataset import DbDataset
 import dbdicom.utils.image as image
 
 
-class MRImage(DbDataset):
+def pixel_data(ds):
+    """Read the pixel array from an MR image"""
+
+    #array = ds.pixel_array.astype(np.float64)
+    #array = ds.pixel_array
+    #array = np.frombuffer(ds.PixelData, dtype=np.uint16).reshape(ds.Rows, ds.Columns)
+    #array = array.astype(np.float32)
+
+    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
+        array -= intercept
+        array /= slope
+    else:
+        slope = float(getattr(ds, 'RescaleSlope', 1)) 
+        intercept = float(getattr(ds, 'RescaleIntercept', 0)) 
+        array *= slope
+        array += intercept
+    return np.transpose(array)
+
+
+def set_pixel_data(ds, array):
 
-    def __init__(self, dataset=None, template=None):
-        super().__init__()
+    if (0x2005, 0x100E) in ds: 
+        del ds[0x2005, 0x100E]  # Delete 'Philips Rescale Slope'
+    if (0x2005, 0x100D) in ds: 
+        del ds[0x2005, 0x100D]
 
-        if (dataset is None) and (template is None):
-            template = 'RIDER'
+    # clipping may slow down a lot
+    array = image.clip(array.astype(np.float32))
+    array, slope, intercept = image.scale_to_range(array, ds.BitsAllocated)
+    array = np.transpose(array)
 
-        if dataset is not None:
-            self.__dict__ = dataset.__dict__
+    ds.PixelRepresentation = 0
+    ds.RescaleSlope = 1 / slope
+    ds.RescaleIntercept = - intercept / slope
+#        ds.WindowCenter = (maximum + minimum) / 2
+#        ds.WindowWidth = maximum - minimum
+    ds.Rows = array.shape[0]
+    ds.Columns = array.shape[1]
+    ds.PixelData = array.tobytes()
+
+
+
+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
 
-        if template == 'RIDER': 
-            rider(self)
+    # Create dummy image data (e.g., black frames)
+    pixel_array = np.zeros((num_frames, rows, columns), dtype=np.uint16)
+    ds.PixelData = pixel_array.tobytes()
 
-    def get_pixel_array(self):
-        return get_pixel_array(self)
+    return ds
 
-    def set_pixel_array(self, array):
-        set_pixel_array(self, array)
 
-    def get_attribute_image_type(self):
-        return get_attribute_image_type(self)
 
-    def set_attribute_image_type(self, value):
-        set_attribute_image_type(self, value)
+def chat_gpt_2d():
+    # Basic identifiers
+    file_meta = FileMetaDataset()
+    file_meta.MediaStorageSOPClassUID = MRImageStorage
+    file_meta.MediaStorageSOPInstanceUID = generate_uid()
+    file_meta.ImplementationClassUID = generate_uid()
 
-    def get_attribute_signal_type(self):
-        return get_attribute_signal_type(self)
+    # Create the main dataset
+    ds = FileDataset(
+        filename_or_obj=None,
+        dataset=Dataset(),
+        file_meta=file_meta,
+        preamble=b"\0" * 128,
+    )
 
-    def set_attribute_signal_type(self, value):
-        set_attribute_signal_type(self, value)
+    # 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
 
 
-def rider(ds): # required only - check
+def default(): # from the RIDER dataset
 
     # File meta info data elements
-    ds.file_meta = FileMetaDataset()
-    ds.file_meta.FileMetaInformationGroupLength = 190
-    ds.file_meta.FileMetaInformationVersion = b'\x00\x01'
-    ds.file_meta.MediaStorageSOPClassUID = '1.2.840.10008.5.1.4.1.1.4'
-    ds.file_meta.MediaStorageSOPInstanceUID = '1.3.6.1.4.1.9328.50.16.175333593952805976694548436931998383940'
-    ds.file_meta.TransferSyntaxUID = '1.2.840.10008.1.2'
-    ds.file_meta.ImplementationClassUID = '1.2.40.0.13.1.1'
-    ds.file_meta.ImplementationVersionName = 'dcm4che-1.4.27'
+    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
@@ -162,117 +309,15 @@ def rider(ds): # required only - check
     return ds
 
 
-def get_pixel_array(ds):
-    """Read the pixel array from an MR image"""
-
-    #array = ds.pixel_array.astype(np.float64)
-    #array = ds.pixel_array
-    #array = np.frombuffer(ds.PixelData, dtype=np.uint16).reshape(ds.Rows, ds.Columns)
-    #array = array.astype(np.float32)
-
-    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
-        array -= intercept
-        array /= slope
-    else:
-        slope = float(getattr(ds, 'RescaleSlope', 1)) 
-        intercept = float(getattr(ds, 'RescaleIntercept', 0)) 
-        array *= slope
-        array += intercept
-    return np.transpose(array)
-
-
-def set_pixel_array(ds, array):
 
-    if (0x2005, 0x100E) in ds: 
-        del ds[0x2005, 0x100E]  # Delete 'Philips Rescale Slope'
-    if (0x2005, 0x100D) in ds: 
-        del ds[0x2005, 0x100D]
 
-    # clipping may slow down a lot
-    array = image.clip(array.astype(np.float32))
-    array, slope, intercept = image.scale_to_range(array, ds.BitsAllocated)
-    array = np.transpose(array)
-
-    ds.PixelRepresentation = 0
 
-    # Does this need setting? Optional and should not be used like this anyway.
-    # Prob
-    # 11 june 2016: commented this out it produced busg in some cases due to US vs SS confusion
-    # vr = ds.data_element('SmallestImagePixelValue').VR 
-    # if vr =='US':
-    #     ds.set_values('SmallestImagePixelValue', int(0))
-    #     ds.set_values('LargestImagePixelValue', int(2**ds.BitsAllocated - 1))
-    # else:
-    #     ds.set_values('SmallestImagePixelValue', int(-2**(ds.BitsAllocated - 1)))
-    #     ds.set_values('LargestImagePixelValue', int(2**(ds.BitsAllocated - 1)-1))
+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)
 
-    ds.RescaleSlope = 1 / slope
-    ds.RescaleIntercept = - intercept / slope
-#        ds.WindowCenter = (maximum + minimum) / 2
-#        ds.WindowWidth = maximum - minimum
-    ds.Rows = array.shape[0]
-    ds.Columns = array.shape[1]
-    ds.PixelData = array.tobytes()
 
 
-def get_attribute_image_type(ds):
-    """Determine if an image is Magnitude, Phase, Real or Imaginary image or None"""
-
-    if (0x0043, 0x102f) in ds:
-        private_ge = ds[0x0043, 0x102f]
-        try: 
-            value = struct.unpack('h', private_ge.value)[0]
-        except: 
-            value = private_ge.value
-        if value == 0: 
-            return 'MAGNITUDE'
-        if value == 1: 
-            return 'PHASE'
-        if value == 2: 
-            return 'REAL'
-        if value == 3: 
-            return 'IMAGINARY'
-
-    if 'ImageType' in ds:
-        type = set(ds.ImageType)
-        if set(['M', 'MAGNITUDE']).intersection(type):
-            return 'MAGNITUDE'
-        if set(['P', 'PHASE']).intersection(type):
-            return 'PHASE'
-        if set(['R', 'REAL']).intersection(type):
-            return 'REAL'
-        if set(['I', 'IMAGINARY']).intersection(type):
-            return 'IMAGINARY'
-
-    if 'ComplexImageComponent' in ds:
-        return ds.ComplexImageComponent
-
-    return 'UNKNOWN'
-
-
-def set_attribute_image_type(ds, value):
-    ds.ImageType = value
-
-
-def get_attribute_signal_type(ds):
-    """Determine if an image is Water, Fat, In-Phase, Out-phase image or None"""
-
-    if hasattr(ds, 'ImageType'):
-        type = set(ds.ImageType)
-        if set(['W', 'WATER']).intersection(type):
-            return 'WATER'
-        elif set(['F', 'FAT']).intersection(type):
-            return 'FAT'
-        elif set(['IP', 'IN_PHASE']).intersection(type):
-            return 'IN_PHASE'
-        elif set(['OP', 'OUT_PHASE']).intersection(type):
-            return 'OP_PHASE'
-    return 'UNKNOWN'
-
-
-def set_attribute_signal_type(ds, value):
-    ds.ImageType = value