dbdicom 0.2.6__py3-none-any.whl → 0.3.0__py3-none-any.whl

dbdicom/extensions/numpy.py

@@ -1,271 +0,0 @@
-"""
-``dbdicom`` extensions calling numpy functions. These do not require additional packages to be installed.
-"""
-
-import numpy as np
-import dbdicom as dbd
-
-
-def mean_intensity_projection(series:dbd.Series, dims=('SliceLocation','InstanceNumber'), axis=-1) -> dbd.Series:
-    """Create a mean intensity projection along a specified dimension.
-
-    Args:
-        series (dbdicom.Series): Original series.
-        dims (tuple, optional): Dimensions of the array. Defaults to ('SliceLocation','InstanceNumber').
-        axis (int, optional): axis along which the maximum is to be taken. Defaults to -1.
-        
-    Returns:
-        dbicom.Series: mean intensity projection. 
-
-    Example:
-
-        Get the MIP function from the numpy extension to dbdicom:
-
-        >>> from db.extensions.numpy import mean_intensity_projection
-
-        Create a zero-filled array, describing 8 MRI images each measured at 3 flip angles and 2 repetition times:
-
-        >>> coords = {
-        ...    'SliceLocation': np.arange(8),
-        ...    'FlipAngle': [2, 15, 30],
-        ...    'RepetitionTime': [2.5, 5.0],
-        ... }
-        >>> series = db.zeros((128,128,8,3,2), coords)
-
-        Create a mean intensity projection on the slice locations and check the dimensions:
-
-        >>> mip = mean_intensity_projection(series)
-        >>> array = mip.pixel_values(dims=('SliceLocation', 'ImageNumber'))
-        >>> print(array.shape)
-        (128, 128, 8, 1)
-
-        Create a mean intensity projection along the Slice Location axis:
-
-        >>> mip = mean_intensity_projection(series, dims=tuple(coords), axis=0)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 1, 3, 2)
-
-        Create a mean intensity projection along the Flip Angle axis:
-
-        >>> mip = mean_intensity_projection(series, dims=tuple(coords), axis=1)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 8, 1, 2)
-
-        Create a mean intensity projection along the Repetition Time axis:
-
-        >>> mip = mean_intensity_projection(series, dims=tuple(coords), axis=2)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 8, 3, 1)
-    """
-    array = series.pixel_values(dims=dims)
-    array = np.mean(array, axis=axis)
-
-    # Save as DICOM
-    proj = series.new_sibling(SeriesDescription = series.SeriesDescription + '[mean axis ' + str(axis) + ']')
-    frames = series.frames(dims)
-    frames = np.take(frames, 0, axis=axis)
-    frames = frames.ravel()
-    array = array.reshape((array.shape[0], array.shape[1], -1))
-    for z in range(frames.size):
-        series.progress(z+1, frames.size, 'Saving results.. ')
-        frames_z = frames[z].copy_to(proj)
-        frames_z.set_pixel_values(array[:,:,z])
-
-    return proj
-
-
-def maximum_intensity_projection(series:dbd.Series, dims=('SliceLocation','InstanceNumber'), axis=-1) -> dbd.Series:
-    """Create a maximum intensity projection along a specified dimension.
-
-    Args:
-        series (dbdicom.Series): Original series.
-        dims (tuple, optional): Dimensions of the array. Defaults to ('SliceLocation','InstanceNumber').
-        axis (int, optional): axis along which the maximum is to be taken. Defaults to -1.
-        
-    Returns:
-        dbicom.Series: maximum intensity projection. 
-
-    Example:
-
-        Get the MIP function from the numpy extension to dbdicom:
-
-        >>> from db.extensions.numpy import maximum_intensity_projection
-
-        Create a zero-filled array, describing 8 MRI images each measured at 3 flip angles and 2 repetition times:
-
-        >>> coords = {
-        ...    'SliceLocation': np.arange(8),
-        ...    'FlipAngle': [2, 15, 30],
-        ...    'RepetitionTime': [2.5, 5.0],
-        ... }
-        >>> series = db.zeros((128,128,8,3,2), coords)
-
-        Create a maximum intensity projection on the slice locations and check the dimensions:
-
-        >>> mip = maximum_intensity_projection(series)
-        >>> array = mip.pixel_values(dims=('SliceLocation', 'ImageNumber'))
-        >>> print(array.shape)
-        (128, 128, 8, 1)
-
-        Create a maximum intensity projection along the Slice Location axis:
-
-        >>> mip = maximum_intensity_projection(series, dims=tuple(coords), axis=0)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 1, 3, 2)
-
-        Create a maximum intensity projection along the Flip Angle axis:
-
-        >>> mip = maximum_intensity_projection(series, dims=tuple(coords), axis=1)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 8, 1, 2)
-
-        Create a maximum intensity projection along the Repetition Time axis:
-
-        >>> mip = maximum_intensity_projection(series, dims=tuple(coords), axis=2)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 8, 3, 1)
-    """
-
-    array = series.pixel_values(dims=dims)
-    array = np.amax(array, axis=axis)
-
-    # Save as DICOM
-    proj = series.new_sibling(SeriesDescription = series.SeriesDescription + '[max axis ' + str(axis) + ']')
-    frames = series.frames(dims)
-    frames = np.take(frames, 0, axis=axis)
-    frames = frames.ravel()
-    array = array.reshape((array.shape[0], array.shape[1], -1))
-    for z in range(frames.size):
-        series.progress(z+1, frames.size, 'Saving results.. ')
-        frames_z = frames[z].copy_to(proj)
-        frames_z.set_pixel_values(array[:,:,z])
-
-    return proj
-
-
-def norm_projection(series:dbd.Series, dims=('SliceLocation','InstanceNumber'), axis=-1, ord=None) -> dbd.Series:
-    """Projection along a specified dimension using the vector norm.
-
-    This functions uses numpy.linalg.norm to calculate the projection, see: https://numpy.org/doc/stable/reference/generated/numpy.linalg.norm.html
-
-    Args:
-        series (dbdicom.Series): Original series.
-        dims (tuple, optional): Dimensions of the array. Defaults to ('SliceLocation','InstanceNumber').
-        axis (int, optional): axis along which the maximum is to be taken. Defaults to -1.
-        ord (int, optional): order of the norm - see documentation of numpy.linalg.norm for details
-        
-    Returns:
-        dbicom.Series: maximum intensity projection. 
-
-    Example:
-
-        Get the function from the numpy extension to dbdicom:
-
-        >>> from db.extensions.numpy import norm_projection
-
-        Create a zero-filled array, describing 8 MRI images each measured at 3 flip angles and 2 repetition times:
-
-        >>> coords = {
-        ...    'SliceLocation': np.arange(8),
-        ...    'FlipAngle': [2, 15, 30],
-        ...    'RepetitionTime': [2.5, 5.0],
-        ... }
-        >>> series = db.zeros((128,128,8,3,2), coords)
-
-        Create a norm projection on the slice locations and check the dimensions:
-
-        >>> mip = norm_projection(series)
-        >>> array = mip.pixel_values(dims=('SliceLocation', 'ImageNumber'))
-        >>> print(array.shape)
-        (128, 128, 8, 1)
-
-        Create a norm projection along the Slice Location axis:
-
-        >>> mip = norm_projection(series, dims=tuple(coords), axis=0)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 1, 3, 2)
-
-        Create a norm projection along the Flip Angle axis:
-
-        >>> mip = norm_projection(series, dims=tuple(coords), axis=1)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 8, 1, 2)
-
-        Create a norm projection along the Repetition Time axis:
-
-        >>> mip = norm_projection(series, dims=tuple(coords), axis=2)
-        >>> array = mip.pixel_values(dims=tuple(coords))
-        >>> print(array.shape)
-        (128, 128, 8, 3, 1)
-    """
-    array = series.pixel_values(dims=dims)
-    array = np.linalg.norm(array, ord=ord, axis=axis)
-
-    # Save as DICOM
-    proj = series.new_sibling(SeriesDescription = series.SeriesDescription + '[norm axis ' + str(axis) + ']')
-    frames = series.frames(dims)
-    frames = np.take(frames, 0, axis=axis)
-    frames = frames.ravel()
-    array = array.reshape((array.shape[0], array.shape[1], -1))
-    for z in range(frames.size):
-        series.progress(z+1, frames.size, 'Saving results.. ')
-        frames_z = frames[z].copy_to(proj)
-        frames_z.set_pixel_values(array[:,:,z])
-
-    return proj
-    
-
-
-def threshold(input:dbd.Series, low_threshold=0, high_threshold=1, method='absolute')-> dbd.Series:
-    """Create a mask series by thresholding.
-
-    Args:
-        input (dbd.Series): original data to be masked
-        low_threshold (int, optional): Lower threshold for masking. Defaults to 0.
-        high_threshold (int, optional): Upper threshold for masking. Defaults to 1.
-        method (str, optional): Type of thresholding, either 'absolute' (thresholds are absolute signal values), 'quantiles' (thresholds are quantiles), or 'range' (thresholds are between 0 and 1). Defaults to 'absolute'.
-
-    Returns:
-        dbd.Series: mask series with values = 1 inside and 0 outside.
-    """
-    suffix = ' [Threshold segmentation]'
-    desc = input.instance().SeriesDescription
-    filtered = input.copy(SeriesDescription = desc+suffix)
-    #images = filtered.instances()
-    images = filtered.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Filtering ' + desc)
-        image.read()
-        array = image.array()
-        if method == 'quantiles':
-            range = np.quantile(array, [low_threshold, high_threshold])
-        elif method == 'range':
-            min, max = np.amin(array), np.amax(array)
-            range = [min+low_threshold*(max-min), min+high_threshold*(max-min)]
-        else:
-            range = [low_threshold, high_threshold]
-        array = np.logical_and(array > range[0],  array < range[1])
-        image.set_array(array)
-        array = array.astype(np.ubyte)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-
-# Helper functions
-
-def _reset_window(image, array):
-    min = np.amin(array)
-    max = np.amax(array)
-    image.WindowCenter= (max+min)/2
-    image.WindowWidth = 0.9*(max-min)