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

dbdicom/ds/dataset.py

@@ -1,841 +0,0 @@
-"""A colections of tools to extend functionality of pydicom datasets."""
-
-import os
-from datetime import datetime
-
-import numpy as np
-import pandas as pd
-from matplotlib import cm
-import nibabel as nib
-import pydicom
-from pydicom.dataset import Dataset
-from pydicom.sequence import Sequence
-from pydicom.util.codify import code_file
-import pydicom.config
-
-import dbdicom.utils.image as image
-import dbdicom.utils.variables as variables
-
-# This ensures that dates and times are read as TM, DT and DA classes
-pydicom.config.datetime_conversion= True
-
-
-class DbDataset(Dataset):
-
-    def __init__(self, dataset=None):
-        super().__init__()
-
-        if dataset is not None:
-            self.__dict__ = dataset.__dict__
-
-    def write(self, file, status=None):
-        write(self, file, status=status)
-
-    def get_values(self, tags):
-        return get_values(self, tags)
-
-    def set_values(self, tags, values):
-        return set_values(self, tags, values)
-
-    def get_lut(self): 
-        return get_lut(self)
-
-    def set_lut(*args, **kwargs): 
-        set_lut(*args, **kwargs)
-
-    def get_colormap(self):
-        return get_colormap(self)
-
-    def set_colormap(*args, **kwargs):
-        set_colormap(*args, **kwargs)
-
-    # Should be just pixel_array to fit in with logic 
-    # of custom attributes but conflicts with pydicom definition
-    # go back to just array?
-    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 map_mask_to(self, ds_target):
-        return map_mask_to(self, ds_target)
-
-    ##
-    ## CUSTOM ATTRIBUTES
-    ## 
-
-    def get_attribute_affine_matrix(self):
-        return get_affine_matrix(self)
-
-    def set_attribute_affine_matrix(*args, **kwargs):
-        set_affine_matrix(*args, **kwargs)
-
-    def get_attribute_window(self):
-        return get_window(self)
-
-    def set_attribute_window(self):
-        set_window(self)
-
-    def get_attribute_lut(self): # use _get_attribute to encode these
-        return get_lut(self)
-
-    def set_attribute_lut(*args, **kwargs): # use _set_attribute to encode these
-        set_lut(*args, **kwargs)
-
-    def get_attribute_colormap(self):
-        return get_colormap(self)
-
-    def set_attribute_colormap(*args, **kwargs):
-        set_colormap(*args, **kwargs)
-
-
-
-def get_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 = ds.get_pixel_array()
-        #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
-
-
-def read(file, dialog=None, nifti=False):
-    try:
-        if nifti:
-            nim = nib.load(file)
-            ds = nim.header.extensions[0].get_content()
-            array = nim.get_fdata()
-            set_pixel_array(ds, array)
-        else:
-            ds = pydicom.dcmread(file)
-        return DbDataset(ds)
-    except:
-        message = "Failed to read " + file
-        if dialog is not None:
-            dialog.information(message)  
-        raise FileNotFoundError(message)
-
-
-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)
-    # try:
-    #     # 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)
-    # except:
-    #     msg = 'Cannot write to file \n' + file
-    #     if status is not None:
-    #         status.message(msg)
-    #     else:
-    #         print(msg)
-    #     raise RuntimeError
-
-
-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, status=None, path=None, message='Reading DICOM folder..', images_only=False):
-    """Reads a list of tags in a list of files.
-
-    Arguments
-    ---------
-    files : str or list
-        A filepath or a list of filepaths
-    tags : str or list 
-        A DICOM tag or a list of DICOM tags
-    status : StatusBar
-
-    Creates
-    -------
-    dataframe : pandas.DataFrame
-        A Pandas dataframe with one row per file
-        The index is the file path 
-        Each column corresponds to a Tag in the list of Tags
-        The returned dataframe is sorted by the given tags.
-    """
-    if not isinstance(files, list):
-        files = [files]
-    if not isinstance(tags, list):
-        tags = [tags]
-    dict = {}
-    for i, file in enumerate(files):
-        if status is not None: 
-            status.progress(i+1, len(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, status=None, path=None, message='Reading DICOM folder..', images_only=False):
-    """Reads a list of tags in a list of files.
-
-    Arguments
-    ---------
-    files : str or list
-        A filepath or a list of filepaths
-    tags : str or list 
-        A DICOM tag or a list of DICOM tags
-    status : StatusBar
-
-    Creates
-    -------
-    dataframe : pandas.DataFrame
-        A Pandas dataframe with one row per file
-        The index is the file path 
-        Each column corresponds to a Tag in the list of Tags
-        The returned dataframe is sorted by the given tags.
-    """
-    if not isinstance(files, list):
-        files = [files]
-    if not isinstance(tags, list):
-        tags = [tags]
-    array = []
-    dicom_files = []
-    for i, file in enumerate(files):
-        if status is not None: 
-            status.progress(i+1, len(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)
-                    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 set_values(ds, tags, values, VR=None):
-    """
-    Sets DICOM tags in the pydicom dataset in memory
-    
-    Private and standard tags can both be set.
-    tags, values and VR must either be lists of equal lengths,
-    or single values.
-    VR is required for private tags. 
-    If private and standard tags are set in the same function call, 
-    VR can be set to any value for the standard tags: e.g. 
-        set_values(ds, ['Rows', (0x0019, 0x0100)], [128, 'Hello'], [None, 'LO'])
-    """
-
-    if not isinstance(tags, list): 
-        tags = [tags]
-        values = [values]
-        VR = [VR]
-    elif VR is None:
-        VR = [None] * len(tags)
-    for i, tag in enumerate(tags):
-                
-        if values[i] is None:
-            if isinstance(tag, str):
-                if hasattr(ds, tag):
-                    # Setting standard DICOM attribute to None
-                    del ds[tag]
-                else:
-                    # Setting custom attribute to None
-                    if hasattr(ds, 'set_attribute_' + tag):
-                        getattr(ds, 'set_attribute_' + tag)(values[i])  
-            else: # hexadecimal tuple
-                if tag in ds:
-                    del ds[tag]
-        else:
-            if isinstance(tag, str):
-                if hasattr(ds, tag):
-                    ds[tag].value = format_value(values[i], tag=tag)
-                else:
-                    if hasattr(ds, 'set_attribute_' + tag):
-                        getattr(ds, 'set_attribute_' + tag)(values[i])
-                        continue
-                    _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])
-    return ds
-
-
-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, 'Wezel ' + str(tag.group), create=True)
-        ds.add_new(tag, VR, format_value(value, VR))
-
-
-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 not isinstance(tags, list): 
-        return get_values(ds, [tags])[0]
-            
-    row = []  
-    for tag in tags:
-        value = None
-
-        # If the tag is provided as string
-        # check first if it is a custom attribute
-        if isinstance(tag, str):
-            if not hasattr(ds, tag):
-                if hasattr(ds, 'get_attribute_' + tag):
-                    value = getattr(ds, 'get_attribute_' + tag)()
-            else:
-                pydcm_value = ds[tag].value
-                value = to_set_type(pydcm_value, pydicom.datadict.dictionary_VR(tag)) # ELIMINATE THIS STEP - return pydicom datatypes
-
-        # If the tag is a tuple of hexadecimal values
-        else: 
-            if tag in ds:
-                value = to_set_type(ds[tag].value, pydicom.datadict.dictionary_VR(tag))
-
-        # 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 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 to_set_type(value, VR):
-    """
-    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 get_affine_matrix(ds):
-    """Affine transformation matrix for a DICOM image"""
-
-    # slice_spacing = get_values(ds, 'SpacingBetweenSlices')
-    # if slice_spacing is None:
-    #     slice_spacing = get_values(ds, 'SliceThickness')
-    slice_spacing = get_values(ds, 'SliceThickness')
-
-    return image.affine_matrix(
-        get_values(ds, 'ImageOrientationPatient'), 
-        get_values(ds, 'ImagePositionPatient'), 
-        get_values(ds, 'PixelSpacing'), 
-        slice_spacing)
-
-
-def set_affine_matrix(ds, affine):
-    v = image.dismantle_affine_matrix(affine)
-    set_values(ds, 'PixelSpacing', v['PixelSpacing'])
-    #set_values(ds, 'SpacingBetweenSlices', v['SpacingBetweenSlices'])
-    set_values(ds, 'SliceThickness', v['SpacingBetweenSlices'])
-    set_values(ds, 'ImageOrientationPatient', v['ImageOrientationPatient'])
-    set_values(ds, 'ImagePositionPatient', v['ImagePositionPatient'])
-
-
-def map_mask_to(ds_source, ds_target):
-    """Map non-zero image pixels onto a target image.
-    
-    Overwrite pixel values in the target"""
-
-    # Create a coordinate array of non-zero pixels
-    coords = np.transpose(np.where(ds_source.get_pixel_array() != 0)) 
-    coords = [[coord[0], coord[1], 0] for coord in coords] 
-    coords = np.array(coords)
-
-    # Determine coordinate transformation matrix
-    affine_source = ds_source.get_values('affine_matrix')
-    affine_target = ds_target.get_values('affine_matrix')
-    source_to_target = np.linalg.inv(affine_target).dot(affine_source)
-
-    # Apply coordinate transformation and interpolate (nearest neighbour)
-    coords = nib.affines.apply_affine(source_to_target, coords)
-    coords = np.round(coords).astype(int)
-    # x = y = []
-    # for r in coords:
-    #     if r[2] == 0:
-    #         if (0 <= r[0]) & (r[0] < ds_target.Columns):
-    #             if (0 <= r[1]) & (r[1] < ds_target.Rows):
-    #                 x.append(r[0])
-    #                 y.append(r[1])
-    # x = tuple(x)
-    # y = tuple(y)
-    x = tuple([c[0] for c in coords if (c[2] == 0) & (0 <= c[0]) & (c[0] < ds_target.Columns) & (0 <= c[1]) & (c[1] < ds_target.Rows)])
-    y = tuple([c[1] for c in coords if (c[2] == 0) & (0 <= c[0]) & (c[0] < ds_target.Columns) & (0 <= c[1]) & (c[1] < ds_target.Rows)])
-    # x = tuple([c[0] for c in coords if c[2] == 0])
-    # y = tuple([c[1] for c in coords if c[2] == 0])
-
-    # Set values in the target image
-    # array = np.zeros((record.Rows, record.Columns))
-    array = np.zeros((ds_target.Columns, ds_target.Rows))
-    array[(x, y)] = 1.0
-
-    return array
-
-# 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 get_colormap(ds):
-    """Returns the colormap if there is any."""
-
-    # Hijacking this free text field to store the colormap
-    # This should use ContentDescription instead (0070, 0081)
-    # 
-    if 'WindowCenterWidthExplanation' in ds:
-        if ds.WindowCenterWidthExplanation in COLORMAPS:
-            return ds.WindowCenterWidthExplanation
-
-
-def set_colormap(ds, colormap=None):
-
-    if colormap is None:
-        ds.PhotometricInterpretation = 'MONOCHROME2'
-        if hasattr(ds, 'WindowCenterWidthExplanation'):
-            del ds.WindowCenterWidthExplanation
-        if hasattr(ds, 'RGBLUTTransferFunction'):
-            del ds.RGBLUTTransferFunction
-        if hasattr(ds, 'GreenPaletteColorLookupTableData'):
-            del ds.GreenPaletteColorLookupTableData
-        if hasattr(ds, 'RedPaletteColorLookupTableData'):
-            del ds.RedPaletteColorLookupTableData
-        if hasattr(ds, 'BluePaletteColorLookupTableData'):
-            del ds.BluePaletteColorLookupTableData
-        if hasattr(ds, 'RedPaletteColorLookupTableDescriptor'):
-            del ds.RedPaletteColorLookupTableDescriptor
-        if hasattr(ds, 'GreenPaletteColorLookupTableDescriptor'):
-            del ds.GreenPaletteColorLookupTableDescriptor
-        if hasattr(ds, 'BluePaletteColorLookupTableDescriptor'):
-            del ds.BluePaletteColorLookupTableDescriptor
-    else:
-        ds.WindowCenterWidthExplanation = colormap
-        # Get a LUT as float numpy array with values in the range [0,1]
-        RGBA = cm.ScalarMappable(cmap=colormap).to_rgba(np.arange(256))
-        set_lut(ds, RGBA[:,:3])
-
-
-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 get_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 get_pixel_array(ds):
-    """Read the pixel array from an image"""
-
-    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_array(ds, array, value_range=None):
-    
-    # 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)
-
-    #maximum = np.amax(array)
-    #minimum = np.amin(array)
-    shape = np.shape(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 = shape[0]
-    ds.Columns = shape[1]
-    ds.PixelData = array.tobytes()
-
-
-def module_patient():
-
-    return [
-        'ReferencedPatientSequence',
-        'PatientName',
-        'PatientID',
-        'IssuerOfPatientID',
-        'TypeOfPatientID',
-        'IssuerOfPatientIDQualifiersSequence',
-        'SourcePatientGroupIdentificationSequence',
-        'GroupOfPatientsIdentificationSequence',
-        'PatientBirthDate',
-        'PatientBirthTime',
-        'PatientBirthDateInAlternativeCalendar',
-        'PatientDeathDateInAlternativeCalendar',
-        'PatientAlternativeCalendar',
-        'PatientSex',
-        'QualityControlSubject',
-        'StrainDescription',
-        'StrainNomenclature',
-        'StrainStockSequence',
-        'StrainAdditionalInformation',
-        'StrainCodeSequence',
-        'GeneticModificationsSequence',
-        'OtherPatientNames',
-        'OtherPatientIDsSequence',
-        'ReferencedPatientPhotoSequence',
-        'EthnicGroup',
-        'PatientSpeciesDescription',
-        'PatientSpeciesCodeSequence',
-        'PatientBreedDescription',
-        'PatientBreedCodeSequence',
-        'BreedRegistrationSequence',
-        'ResponsiblePerson',
-        'ResponsiblePersonRole',
-        'ResponsibleOrganization',
-        'PatientComments',
-        'PatientIdentityRemoved',
-        'DeidentificationMethod',
-        'DeidentificationMethodCodeSequence',
-        'ClinicalTrialSponsorName',
-        'ClinicalTrialProtocolID',
-        'ClinicalTrialProtocolName',
-        'ClinicalTrialSiteID',
-        'ClinicalTrialSiteName',
-        'ClinicalTrialSubjectID',
-        'ClinicalTrialSubjectReadingID',
-        'ClinicalTrialProtocolEthicsCommitteeName',
-        'ClinicalTrialProtocolEthicsCommitteeApprovalNumber',
-    ]
-
-
-def module_study():
-
-    return [
-        'StudyDate',
-        'StudyTime',
-        'AccessionNumber',
-        'IssuerOfAccessionNumberSequence',
-        'ReferringPhysicianName',
-        'ReferringPhysicianIdentificationSequence',
-        'ConsultingPhysicianName',
-        'ConsultingPhysicianIdentificationSequence',
-        'StudyDescription',
-        'ProcedureCodeSequence',
-        'PhysiciansOfRecord',
-        'PhysiciansOfRecordIdentificationSequence',
-        'NameOfPhysiciansReadingStudy',
-        'PhysiciansReadingStudyIdentificationSequence',
-        'ReferencedStudySequence',
-        'StudyInstanceUID',
-        'StudyID',
-        'RequestingService',
-        'RequestingServiceCodeSequence',
-        'ReasonForPerformedProcedureCodeSequence',
-        'AdmittingDiagnosesDescription',
-        'AdmittingDiagnosesCodeSequence',
-        'PatientAge',
-        'PatientSize',
-        'PatientSizeCodeSequence',
-        'PatientBodyMassIndex',
-        'MeasuredAPDimension',
-        'MeasuredLateralDimension',
-        'PatientWeight',
-        'MedicalAlerts',
-        'Allergies',
-        'Occupation',
-        'SmokingStatus',
-        'AdditionalPatientHistory',
-        'PregnancyStatus',
-        'LastMenstrualDate',
-        'PatientSexNeutered',
-        'ReasonForVisit',
-        'ReasonForVisitCodeSequence',
-        'AdmissionID',
-        'IssuerOfAdmissionIDSequence',
-        'ServiceEpisodeID',
-        'ServiceEpisodeDescription',
-        'IssuerOfServiceEpisodeIDSequence',
-        'PatientState',
-        'ClinicalTrialTimePointID',
-        'ClinicalTrialTimePointDescription',
-        'LongitudinalTemporalOffsetFromEvent',
-        'LongitudinalTemporalEventType',
-        'ConsentForClinicalTrialUseSequence',
-    ]   
-
-
-def module_series():
-
-    return [
-        'SeriesDate',
-        'SeriesTime',
-        'Modality',
-        'SeriesDescription',
-        'SeriesDescriptionCodeSequence',
-        'PerformingPhysicianName',
-        'PerformingPhysicianIdentificationSequence',
-        'OperatorsName',
-        'OperatorIdentificationSequence',
-        'ReferencedPerformedProcedureStepSequence',
-        'RelatedSeriesSequence',
-        'AnatomicalOrientationType',
-        'BodyPartExamined',
-        'ProtocolName',
-        'PatientPosition',
-        'ReferencedDefinedProtocolSequence',
-        'ReferencedPerformedProtocolSequence',
-        'SeriesInstanceUID',
-        'SeriesNumber',
-        'Laterality',
-        'SmallestPixelValueInSeries',
-        'LargestPixelValueInSeries',
-        'PerformedProcedureStepStartDate',
-        'PerformedProcedureStepStartTime',
-        'PerformedProcedureStepEndDate',
-        'PerformedProcedureStepEndTime',
-        'PerformedProcedureStepID',
-        'PerformedProcedureStepDescription',
-        'PerformedProtocolCodeSequence',
-        'RequestAttributesSequence',
-        'CommentsOnThePerformedProcedureStep',
-        'ClinicalTrialCoordinatingCenterName',
-        'ClinicalTrialSeriesID',
-        'ClinicalTrialSeriesDescription',
-    ]
-
-
-# def _initialize(ds, UID=None, ref=None): # ds is pydicom dataset
-
-#     # Date and Time of Creation
-#     dt = datetime.now()
-#     timeStr = dt.strftime('%H%M%S')  # long format with micro seconds
-
-#     ds.ContentDate = dt.strftime('%Y%m%d')
-#     ds.ContentTime = timeStr
-#     ds.AcquisitionDate = dt.strftime('%Y%m%d')
-#     ds.AcquisitionTime = timeStr
-#     ds.SeriesDate = dt.strftime('%Y%m%d')
-#     ds.SeriesTime = timeStr
-#     ds.InstanceCreationDate = dt.strftime('%Y%m%d')
-#     ds.InstanceCreationTime = timeStr
-
-#     if UID is not None:
-
-#         # overwrite UIDs
-#         ds.PatientID = UID[0]
-#         ds.StudyInstanceUID = UID[1]
-#         ds.SeriesInstanceUID = UID[2]
-#         ds.SOPInstanceUID = UID[3]
-
-#     if ref is not None: 
-
-#         # Series, Instance and Class for Reference
-#         refd_instance = Dataset()
-#         refd_instance.ReferencedSOPClassUID = ref.SOPClassUID
-#         refd_instance.ReferencedSOPInstanceUID = ref.SOPInstanceUID
-
-#         refd_series = Dataset()
-#         refd_series.ReferencedInstanceSequence = Sequence([refd_instance])
-#         refd_series.SeriesInstanceUID = ds.SeriesInstanceUID
-
-#         ds.ReferencedSeriesSequence = Sequence([refd_series])
-
-#     return ds