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

dbdicom/dataset.py

@@ -0,0 +1,721 @@
+# Test data
+# https://www.aliza-dicom-viewer.com/download/datasets
+
+import os
+from datetime import datetime
+import struct
+from tqdm import tqdm
+
+import numpy as np
+import pandas as pd
+import pydicom
+from pydicom.util.codify import code_file
+import pydicom.config
+from pydicom.dataset import Dataset
+import vreg
+
+import dbdicom.utils.image as image
+import dbdicom.utils.variables as variables
+from dbdicom.sop_classes import (
+    xray_angiographic_image,
+    ct_image,
+    mr_image,
+    enhanced_mr_image,
+    ultrasound_multiframe_image,
+    parametric_map,
+    segmentation,
+)
+
+
+# This ensures that dates and times are read as TM, DT and DA classes
+pydicom.config.datetime_conversion = True
+
+
+SOPCLASS = {
+    '1.2.840.10008.5.1.4.1.1.4': 'MRImage',
+    '1.2.840.10008.5.1.4.1.1.4.1': 'EnhancedMRImage',
+    '1.2.840.10008.5.1.4.1.1.2': 'CTImage',
+    '1.2.840.10008.5.1.4.1.1.12.2': 'XrayAngiographicImage',
+    '1.2.840.10008.5.1.4.1.1.3.1': 'UltrasoundMultiFrameImage',
+    '1.2.840.10008.5.1.4.1.1.30': 'ParametricMap',
+    '1.2.840.10008.5.1.4.1.1.66.4': 'Segmentation',
+}
+SOPCLASSMODULE = {
+    '1.2.840.10008.5.1.4.1.1.4': mr_image,
+    '1.2.840.10008.5.1.4.1.1.4.1': enhanced_mr_image,
+    '1.2.840.10008.5.1.4.1.1.2': ct_image,
+    '1.2.840.10008.5.1.4.1.1.12.2': xray_angiographic_image,
+    '1.2.840.10008.5.1.4.1.1.3.1': ultrasound_multiframe_image,
+    '1.2.840.10008.5.1.4.1.1.30': parametric_map,
+    '1.2.840.10008.5.1.4.1.1.66.4': segmentation,
+}
+
+
+def read_dataset(file):
+
+    try:
+        ds = pydicom.dcmread(file)
+        # ds = pydicom.dcmread(file, force=True) # more robust but hides corrupted data
+    except Exception:
+        raise FileNotFoundError('File not found')
+    
+    return ds
+
+
+def new_dataset(sop_class):
+
+    if sop_class == 'MRImage':
+        return mr_image.default()
+    if sop_class == 'EnhancedMRImage':
+        return enhanced_mr_image.default()
+    if sop_class == 'CTImage':
+        return ct_image.default()
+    if sop_class == 'XrayAngiographicImage':
+        return xray_angiographic_image.default()
+    if sop_class == 'UltrasoundMultiFrameImage':
+        return ultrasound_multiframe_image.default()
+    else:
+        raise ValueError(
+            f"DICOM class {sop_class} is not currently supported"
+        )
+
+
+
+def get_values(ds, tags):
+    """Return a list of values for a dataset"""
+
+    # https://pydicom.github.io/pydicom/stable/guides/element_value_types.html
+    if np.isscalar(tags): 
+        return get_values(ds, [tags])[0]
+            
+    row = []  
+    for tag in tags:
+        value = None
+
+        # If the tag is provided as string
+        if isinstance(tag, str):
+            if hasattr(ds, tag):
+                pydcm_value = ds[tag].value
+                try:
+                    VR = pydicom.datadict.dictionary_VR(tag)
+                except:
+                    VR = None
+                value = to_set_type(pydcm_value, VR) # ELIMINATE THIS STEP - return pydicom datatypes
+
+        # If the tag is a tuple of hexadecimal values
+        else: 
+            if tag in ds:
+                try:
+                    VR = pydicom.datadict.dictionary_VR(tag)
+                except:
+                    VR = None
+                value = to_set_type(ds[tag].value, VR)
+
+        # If a tag is not present in the dataset, check if it can be derived
+        if value is None:
+            value = derive_data_element(ds, tag)
+
+        row.append(value)
+    return row
+
+
+def set_values(ds, tags, values, VR=None, coords=None):
+
+    if np.isscalar(tags): 
+        tags = [tags]
+        values = [values]
+        VR = [VR]
+    elif VR is None:
+        VR = [None] * len(tags)
+
+    if coords is not None:
+        tags += list(coords.keys())
+        values += list(coords.values())
+
+    for i, tag in enumerate(tags):
+                
+        if values[i] is None:
+            if isinstance(tag, str):
+                if hasattr(ds, tag):
+                    del ds[tag]
+            else: # hexadecimal tuple
+                if tag in ds:
+                    del ds[tag]
+
+        elif isinstance(tag, str):
+            if hasattr(ds, tag):
+                ds[tag].value = format_value(values[i], tag=tag)
+            else:
+                _add_new(ds, tag, values[i], VR=VR[i])
+
+        else: # hexadecimal tuple
+            if tag in ds:
+                ds[tag].value = format_value(values[i], tag=tag)
+            else:
+                _add_new(ds, tag, values[i], VR=VR[i])
+
+        #_set_derived_data_element(ds, tag, values[i])
+                
+    return ds
+
+
+
+def value(ds, tags):
+    # Same as get_values but without VR lookup
+
+    # https://pydicom.github.io/pydicom/stable/guides/element_value_types.html
+    if np.isscalar(tags): 
+        return get_values(ds, [tags])[0]
+            
+    row = []  
+    for tag in tags:
+        value = None
+
+        # If the tag is provided as string
+        if isinstance(tag, str):
+
+            if hasattr(ds, tag):
+                value = to_set_type(ds[tag].value)
+
+        # If the tag is a tuple of hexadecimal values
+        else: 
+            if tag in ds:
+                value = to_set_type(ds[tag].value)
+
+        # If a tag is not present in the dataset, check if it can be derived
+        if value is None:
+            value = derive_data_element(ds, tag)
+
+        row.append(value)
+    return row
+
+
+def set_value(ds, tags, values):
+    # Same as set_values but without VR lookup
+    # This excludes new private tags - set those using add_private()
+    if np.isscalar(tags): 
+        tags = [tags]
+        values = [values]
+
+    for i, tag in enumerate(tags):
+                
+        if values[i] is None:
+            if isinstance(tag, str):
+                if hasattr(ds, tag):
+                    del ds[tag]
+            else: # hexadecimal tuple
+                if tag in ds:
+                    del ds[tag]
+
+        elif isinstance(tag, str):
+            if hasattr(ds, tag):
+                ds[tag].value = check_value(values[i], tag)
+            else:
+                add_new(ds, tag, values[i])
+
+        else: # hexadecimal tuple
+            if tag in ds:
+                ds[tag].value = check_value(values[i], tag)
+            else:
+                add_new(ds, tag, values[i])
+                
+    return ds
+
+
+
+def write(ds, file, status=None):
+    # check if directory exists and create it if not
+    dir = os.path.dirname(file)
+    if not os.path.exists(dir):
+        os.makedirs(dir)
+    ds.save_as(file, write_like_original=False)
+
+
+def codify(source_file, save_file, **kwargs):
+    str = code_file(source_file, **kwargs)
+    file = open(save_file, "w")
+    file.write(str)
+    file.close()
+
+
+def read_data(files, tags, path=None, images_only=False):
+
+    if np.isscalar(files):
+        files = [files]
+    if np.isscalar(tags):
+        tags = [tags]
+    dict = {}
+    for i, file in tqdm(enumerate(files), 'reading files..'):
+        try:
+            ds = pydicom.dcmread(file, force=True, specific_tags=tags+['Rows'])
+        except:
+            pass
+        else:
+            if isinstance(ds, pydicom.dataset.FileDataset):
+                if 'TransferSyntaxUID' in ds.file_meta:
+                    if images_only:
+                        if not 'Rows' in ds:
+                            continue
+                    row = get_values(ds, tags)
+                    if path is None:
+                        index = file
+                    else:
+                        index = os.path.relpath(file, path)
+                    dict[index] = row 
+    return dict
+
+
+
+def read_dataframe(files, tags, path=None, images_only=False):
+    if np.isscalar(files):
+        files = [files]
+    if np.isscalar(tags):
+        tags = [tags]
+    array = []
+    dicom_files = []
+    for i, file in tqdm(enumerate(files), desc='Reading DICOM folder'):
+        try:
+            ds = pydicom.dcmread(file, force=True, specific_tags=tags+['Rows'])
+        except:
+            pass
+        else:
+            if isinstance(ds, pydicom.dataset.FileDataset):
+                if 'TransferSyntaxUID' in ds.file_meta:
+                    if images_only:
+                        if not 'Rows' in ds:
+                            continue
+                    row = get_values(ds, tags)
+                    array.append(row)
+                    if path is None:
+                        index = file
+                    else:
+                        index = os.path.relpath(file, path)
+                    dicom_files.append(index) 
+    df = pd.DataFrame(array, index = dicom_files, columns = tags)
+    return df
+
+
+def _add_new(ds, tag, value, VR='OW'):
+    if not isinstance(tag, pydicom.tag.BaseTag):
+        tag = pydicom.tag.Tag(tag)
+    if not tag.is_private: # Add a new data element
+        value_repr = pydicom.datadict.dictionary_VR(tag)
+        if value_repr == 'US or SS':
+            if value >= 0:
+                value_repr = 'US'
+            else:
+                value_repr = 'SS'
+        elif value_repr == 'OB or OW':
+            value_repr = 'OW'
+        ds.add_new(tag, value_repr, format_value(value, value_repr))
+    else:
+        if (tag.group, 0x0010) not in ds:
+            ds.private_block(tag.group, 'dbdicom ' + str(tag.group), create=True)
+        ds.add_new(tag, VR, format_value(value, VR))
+
+
+def add_new(ds, tag, value):
+    if not isinstance(tag, pydicom.tag.BaseTag):
+        tag = pydicom.tag.Tag(tag)
+    if tag.is_private:
+        raise ValueError("if you want to add a private data element, use "
+                         "dataset.add_private()")
+   # Add a new data element
+    value_repr = pydicom.datadict.dictionary_VR(tag)
+    if value_repr == 'US or SS':
+        if value >= 0:
+            value_repr = 'US'
+        else:
+            value_repr = 'SS'
+    elif value_repr == 'OB or OW':
+        value_repr = 'OW'
+    ds.add_new(tag, value_repr, format_value(value, value_repr))
+
+
+
+def add_private(ds, tag, value, VR):
+    if not isinstance(tag, pydicom.tag.BaseTag):
+        tag = pydicom.tag.Tag(tag)
+    if (tag.group, 0x0010) not in ds:
+        ds.private_block(tag.group, 'dbdicom ' + str(tag.group), create=True)
+    ds.add_new(tag, VR, format_value(value, VR))
+
+
+def derive_data_element(ds, tag):
+    """Tags that are not required but can be derived from other required tags"""
+
+    if tag == 'SliceLocation' or tag == (0x0020, 0x1041):
+        if 'ImageOrientationPatient' in ds and 'ImagePositionPatient' in ds:
+            return image.slice_location(
+                ds['ImageOrientationPatient'].value, 
+                ds['ImagePositionPatient'].value,
+            )
+    # To be extended ad hoc with other tags that can be derived
+
+
+
+def format_value(value, VR=None, tag=None):
+
+    # If the change below is made (TM, DA, DT) then this needs to 
+    # convert those to string before setting
+
+    # Slow - dictionary lookup for every value write
+
+    if VR is None:
+        VR = pydicom.datadict.dictionary_VR(tag)
+
+    if VR == 'LO':
+        if len(value) > 64:
+            return value[-64:]
+            #return value[:64]
+    if VR == 'TM':
+        return variables.seconds_to_str(value)
+    
+    return value
+
+
+def check_value(value, tag):
+
+    # If the change below is made (TM, DA, DT) then this needs to 
+    # convert those to string before setting
+
+    LO = [
+        'SeriesDescription',
+        'StudyDescription',
+    ]
+    TM = [
+        'AcquisitionTime',
+    ]
+
+    if tag in LO:
+        if len(value) > 64:
+            return value[-64:]
+    if tag in TM:
+        return variables.seconds_to_str(value)
+    
+    return value
+
+
+def to_set_type(value, VR=None):
+    """
+    Convert pydicom datatypes to the python datatypes used to set the parameter.
+    """
+    # Not a good idea to modify pydicom set/get values. confusing and requires extra VR lookups
+
+    if VR == 'TM':
+        # pydicom sometimes returns string values for TM data types
+        if isinstance(value, str):
+            return variables.str_to_seconds(value)
+
+    if value.__class__.__name__ == 'MultiValue':
+        return [to_set_type(v, VR) for v in value]
+    if value.__class__.__name__ == 'PersonName':
+        return str(value)
+    if value.__class__.__name__ == 'Sequence':
+        return [ds for ds in value]
+    if value.__class__.__name__ == 'TM': 
+        return variables.time_to_seconds(value) # return datetime.time
+    if value.__class__.__name__ == 'UID': 
+        return str(value) 
+    if value.__class__.__name__ == 'IS': 
+        return int(value)
+    if value.__class__.__name__ == 'DT': 
+        return variables.datetime_to_str(value) # return datetime.datetime
+    if value.__class__.__name__ == 'DA':  # return datetime.date
+        return variables.date_to_str(value)
+    if value.__class__.__name__ == 'DSfloat': 
+        return float(value)
+    if value.__class__.__name__ == 'DSdecimal': 
+        return int(value)
+    
+    return value
+
+
+def new_uid(n=None):
+    
+    if n is None:
+        return pydicom.uid.generate_uid()
+    else:
+        return [pydicom.uid.generate_uid() for _ in range(n)]
+
+
+
+
+def window(ds):
+    """Centre and width of the pixel data after applying rescale slope and intercept"""
+
+    if 'WindowCenter' in ds: 
+        centre = ds.WindowCenter
+    if 'WindowWidth' in ds: 
+        width = ds.WindowWidth
+    if centre is None or width is None:
+        array = pixel_data(ds)
+        #p = np.percentile(array, [25, 50, 75])
+        min = np.min(array)
+        max = np.max(array)
+    if centre is None: 
+        centre = (max+min)/2
+        #centre = p[1]
+    if width is None: 
+        width = 0.9*(max-min)
+        #width = p[2] - p[0]
+    return centre, width
+
+def set_window(ds, center, width):
+    ds.WindowCenter = center
+    ds.WindowWidth = width
+
+# List of all supported (matplotlib) colormaps
+
+COLORMAPS =  ['cividis',  'magma', 'plasma', 'viridis', 
+    'Greys', 'Purples', 'Blues', 'Greens', 'Oranges', 'Reds',
+    'YlOrBr', 'YlOrRd', 'OrRd', 'PuRd', 'RdPu', 'BuPu',
+    'GnBu', 'PuBu', 'YlGnBu', 'PuBuGn', 'BuGn', 'YlGn',
+    'binary', 'gist_yarg', 'gist_gray', 'bone', 'pink',
+    'spring', 'summer', 'autumn', 'winter', 'cool', 'Wistia',
+    'hot', 'afmhot', 'gist_heat', 'copper',
+    'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu',
+    'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic',
+    'twilight', 'twilight_shifted', 'hsv',
+    'flag', 'prism', 'ocean', 'gist_earth', 'terrain', 'gist_stern',
+    'gnuplot', 'gnuplot2', 'CMRmap', 'cubehelix', 'brg', 'turbo',
+    'gist_rainbow', 'rainbow', 'jet', 'nipy_spectral', 'gist_ncar']
+
+# Include support for DICOM natiove colormaps (see pydicom guide on working with pixel data)
+
+
+def lut(ds):
+    """Return RGB as float with values in [0,1]"""
+
+    if 'PhotometricInterpretation' not in ds:
+        return None
+    if ds.PhotometricInterpretation != 'PALETTE COLOR':
+        return None
+
+    if ds.BitsAllocated == 8:
+        dtype = np.ubyte
+    elif ds.BitsAllocated == 16:
+        dtype = np.uint16
+    
+    R = ds.RedPaletteColorLookupTableData
+    G = ds.GreenPaletteColorLookupTableData
+    B = ds.BluePaletteColorLookupTableData
+
+    R = np.frombuffer(R, dtype=dtype)
+    G = np.frombuffer(G, dtype=dtype)
+    B = np.frombuffer(B, dtype=dtype)
+
+    R = R.astype(np.float32)
+    G = G.astype(np.float32)
+    B = B.astype(np.float32)
+
+    R *= 1.0/(np.power(2, ds.RedPaletteColorLookupTableDescriptor[2]) - 1)
+    G *= 1.0/(np.power(2, ds.GreenPaletteColorLookupTableDescriptor[2]) - 1)
+    B *= 1.0/(np.power(2, ds.BluePaletteColorLookupTableDescriptor[2]) - 1)
+    
+    return np.transpose([R, G, B])
+
+
+def set_lut(ds, RGB):
+    """Set RGB as float with values in range [0,1]"""
+
+    ds.PhotometricInterpretation = 'PALETTE COLOR'
+
+    RGB *= (np.power(2, ds.BitsAllocated) - 1)
+
+    if ds.BitsAllocated == 8:
+        RGB = RGB.astype(np.ubyte)
+    elif ds.BitsAllocated == 16:
+        RGB = RGB.astype(np.uint16)
+
+    # Define the properties of the LUT
+    ds.add_new('0x00281101', 'US', [255, 0, ds.BitsAllocated])
+    ds.add_new('0x00281102', 'US', [255, 0, ds.BitsAllocated])
+    ds.add_new('0x00281103', 'US', [255, 0, ds.BitsAllocated])
+
+    # Scale the colorsList to the available range
+    ds.RedPaletteColorLookupTableData = bytes(RGB[:,0])
+    ds.GreenPaletteColorLookupTableData = bytes(RGB[:,1])
+    ds.BluePaletteColorLookupTableData = bytes(RGB[:,2])
+
+
+
+def affine(ds, multislice=False):
+    if multislice:
+        return image.affine_matrix(
+            get_values(ds, 'ImageOrientationPatient'), 
+            get_values(ds, 'ImagePositionPatient'), 
+            get_values(ds, 'PixelSpacing'), 
+            get_values(ds, 'SpacingBetweenSlices'),
+        )
+    else:
+        return image.affine_matrix(
+            get_values(ds, 'ImageOrientationPatient'), 
+            get_values(ds, 'ImagePositionPatient'), 
+            get_values(ds, 'PixelSpacing'), 
+            get_values(ds, 'SliceThickness'),
+        )
+
+
+def set_affine(ds, affine, multislice=False):
+    if affine is None:
+        raise ValueError('The affine cannot be set to an empty value')
+    v = image.dismantle_affine_matrix(affine)
+    set_values(ds, 'PixelSpacing', v['PixelSpacing'])
+    if multislice:
+        set_values(ds, 'SpacingBetweenSlices', v['SliceThickness'])
+    else:
+        set_values(ds, 'SliceThickness', v['SliceThickness'])
+    set_values(ds, 'ImageOrientationPatient', v['ImageOrientationPatient'])
+    set_values(ds, 'ImagePositionPatient', v['ImagePositionPatient'])
+    set_values(ds, 'SliceLocation', np.dot(v['ImagePositionPatient'], v['slice_cosine']))
+
+
+
+def pixel_data(ds):
+
+    try:
+        mod = SOPCLASSMODULE[ds.SOPClassUID]
+    except KeyError:
+        raise ValueError(
+            f"DICOM class {ds.SOPClassUID} is not currently supported."
+        )
+    if hasattr(mod, 'pixel_data'):
+        return getattr(mod, 'pixel_data')(ds)
+    
+    try:
+        array = ds.pixel_array
+    except:
+        return None
+    array = array.astype(np.float32)
+    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, value_range=None):
+    if array is None:
+        raise ValueError('The pixel array cannot be set to an empty value.')
+    
+    try:
+        mod = SOPCLASSMODULE[ds.SOPClassUID]
+    except KeyError:
+        raise ValueError(
+            f"DICOM class {ds.SOPClassUID} is not currently supported."
+        )
+    if hasattr(mod, 'set_pixel_data'):
+        return getattr(mod, 'set_pixel_data')(ds, array)
+    
+    # if array.ndim >= 3: # remove spurious dimensions of 1
+    #     array = np.squeeze(array) 
+
+    array = image.clip(array.astype(np.float32), value_range=value_range)
+    array, slope, intercept = image.scale_to_range(array, ds.BitsAllocated)
+    array = np.transpose(array)
+
+    ds.PixelRepresentation = 0
+    #ds.SmallestImagePixelValue = int(0)
+    #ds.LargestImagePixelValue = int(2**ds.BitsAllocated - 1)
+    #ds.set_values('SmallestImagePixelValue', int(0))
+    #ds.set_values('LargestImagePixelValue', int(2**ds.BitsAllocated - 1))
+    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 volume(ds, multislice=False):
+    return vreg.volume(pixel_data(ds), affine(ds, multislice))
+
+def set_volume(ds, volume:vreg.Volume3D, multislice=False):
+    if volume is None:
+        raise ValueError('The volume cannot be set to an empty value.')
+    image = np.squeeze(volume.values)
+    if image.ndim != 2:
+        raise ValueError("Can only write 2D images to a dataset.")
+    set_pixel_data(ds, image)
+    set_affine(ds, volume.affine, multislice)
+    if volume.coords is not None:
+        # All other dimensions should have size 1
+        coords = volume.coords.reshape((volume.coords.shape[0], -1))
+        for i, d in enumerate(volume.dims):
+            try:
+                set_values(ds, d, coords[i,0])
+            except KeyError:
+                raise ValueError(
+                    "Cannot write volume to DICOM. "
+                    f"Volume dimension {d} is not a recognized DICOM data-element. "
+                    f"Use Volume3D.set_dims() with proper DICOM keywords "
+                    "or (group, element) tags to change the dimensions."
+                )
+
+
+def 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_image_type(ds, value):
+    ds.ImageType = value
+
+
+def 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_signal_type(ds, value):
+    ds.ImageType = value
+
+
+
+if __name__=='__main__':
+
+    pass
+    #codify('C:\\Users\\md1spsx\\Documents\\f32bit.dcm', 'C:\\Users\\md1spsx\\Documents\\f32bit.py')