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

dbdicom/extensions/skimage.py

@@ -1,1030 +0,0 @@
-import numpy as np
-import pandas as pd
-import scipy.ndimage as ndi
-import skimage
-
-from dbdicom.extensions import scipy
-from dbdicom.utils.image import interpolate3d_isotropic
-
-
-def volume_features(series):
-
-    if isinstance(series, list):
-        df = None
-        for sery in series:
-            df_sery = volume_features(sery)
-            if df is None:
-                df = df_sery
-            else:
-                df = pd.concat([df, df_sery], ignore_index=True)
-        return df
-
-    n_steps = 8
-    step = 0
-
-    step+=1
-    series.status.progress(step, n_steps, 'Reading affine matrix..')
-
-    affine = series.affine_matrix()
-    if isinstance(affine, list):
-        series.dialog.information('This series contains multiple orientations')
-        return
-    else:
-        affine = affine[0]
-
-    step+=1
-    series.status.progress(step, n_steps, 'Reading array..')
-
-    # Get array sorted by slice location
-    arr, _ = series.array('SliceLocation', pixels_first=True)
-
-    # If there are multiple volumes, show only the first one
-    arr = arr[...,0]
-
-    series_props = _volume_features(arr, affine=affine, show_progress=series.status.progress)
-
-    instance = series.instance()
-    columns = ['PatientID', 'StudyDescription', 'SeriesDescription', 'Parameter', 'Value', 'Unit']
-    ids = [instance.PatientID, instance.StudyDescription, instance.SeriesDescription] 
-    data = []
-    for par, val in series_props.items():
-        row = ids + [par, val[0], val[1]]
-        data.append(row)
-    return pd.DataFrame(data, columns = columns)
-
-
-def _volume_features(arr, spacing=[1,1,1], affine=None, show_progress=print):
-    """Calculate shape features from a mask array
-    
-    This function calculates various shape features from a given mask array.
-    
-    Arguments:
-    - arr (numpy.ndarray): The input mask array - 3D but does not have to be binary
-    - spacing (list, optional): The voxel dimensions in mm. Default is [1, 1, 1].
-    - affine (numpy.ndarray, optional): The affine transformation matrix. Default is None. If the affine is 
-    provided then the spacing argument is ignored and spacing is derived from the affine.
-    - show_progress (function, optional): A function to display progress messages. Default is print.
-    
-    Returns:
-    - dict: A dictionary containing the calculated shape features with their corresponding units.
-    """
-
-    show_progress(1, 6, 'Preprocessing mask...')
-
-    # Scale array in the range [0,1] so it can be treated as mask
-    # Motivation: the function is intended for mask arrays but this will make
-    # sure the results are meaningful even if non-binary arrays are provided.
-    max = np.amax(arr)
-    min = np.amin(arr)
-    arr -= min
-    arr /= max-min
-    # Add zeropadding at the boundary slices for masks that extend to the edge
-    # Motivation: this could have some effect if surfaces are extracted - could create issues
-    # if the values extend right up to the boundary of the slab.
-    shape = list(arr.shape)
-    shape[-1] = shape[-1] + 2*4
-    array = np.zeros(shape)
-    array[:,:,4:-4] = arr
-
-    show_progress(2, 6, 'Extracting surface...')
-
-    # Get voxel dimensions from the affine
-    # We are assuming here the voxel dimensions are in mm.
-    # If not the units provided with the return values are incorrect.
-    if affine is not None:
-        column_spacing = np.linalg.norm(affine[:3, 0])
-        row_spacing = np.linalg.norm(affine[:3, 1])
-        slice_spacing = np.linalg.norm(affine[:3, 2])
-        spacing = (column_spacing, row_spacing, slice_spacing) 
-    voxel_volume = spacing[0]*spacing[1]*spacing[2]
-    nr_of_voxels = np.count_nonzero(array > 0.5)
-    volume = nr_of_voxels * voxel_volume
-    # Surface properties - for now only extracting surface area
-    # Note: this is smoothing the surface first - not tested in depth whether this is necessary or helpful.
-    # It does appear to make a big difference on surface area so should be looked at more carefully.
-    smooth_array = ndi.gaussian_filter(array, 1.0)
-    verts, faces, _, _ = skimage.measure.marching_cubes(smooth_array, spacing=spacing, level=0.5, step_size=1.0)
-    surface_area = skimage.measure.mesh_surface_area(verts, faces)
-
-    show_progress(3, 6, 'Interpolating to isotropic...')
-
-    # Interpolate to isotropic for non-isotropic voxels
-    # Motivation: this is required by the region_props function
-    spacing = np.array(spacing)
-    if np.amin(spacing) != np.amax(spacing):
-        array, isotropic_spacing = interpolate3d_isotropic(array, spacing)
-        isotropic_voxel_volume = isotropic_spacing**3
-    else:
-        isotropic_spacing = np.mean(spacing)
-        isotropic_voxel_volume = voxel_volume
-
-    show_progress(4, 6, 'Extracting volume properties...')
-
-    # Get volume properties - mostly from region_props, except for compactness and depth
-    array = np.round(array).astype(np.int16)
-    region_props_3D = skimage.measure.regionprops(array)[0]
-    # Calculate 'compactness' (our definition) - define as volume to surface ratio
-    # expressed as a percentage of the volume-to-surface ration of an equivalent sphere.
-    # The sphere is the most compact of all shapes, i.e. it has the largest volume to surface area ratio,
-    # so this is guaranteed to be between 0 and 100%
-    radius = region_props_3D['equivalent_diameter_area']*isotropic_spacing/2 # mm
-    v2s = volume/surface_area # mm
-    v2s_equivalent_sphere = radius/3 # mm
-    compactness = 100 * v2s/v2s_equivalent_sphere # %
-    # Fractional anisotropy - in analogy with FA in diffusion 
-    m0 = region_props_3D['inertia_tensor_eigvals'][0]
-    m1 = region_props_3D['inertia_tensor_eigvals'][1]
-    m2 = region_props_3D['inertia_tensor_eigvals'][2]
-    m = (m0 + m1 + m2)/3 # average moment of inertia (trace of the inertia tensor)
-    FA = np.sqrt(3/2) * np.sqrt((m0-m)**2 + (m1-m)**2 + (m2-m)**2) / np.sqrt(m0**2 + m1**2 + m2**2)
-
-    show_progress(5, 6, 'Calculating depth...')
-
-    # Measure maximum depth (our definition)
-    distance = ndi.distance_transform_edt(array)
-    max_depth = np.amax(distance)
-
-    show_progress(6, 6, 'Creating output...')
-
-    # Summarise all values with human-readable names and proper units in a dictionary with values and units.
-    # Some of the definitions are rephrased or tweaked for more intuitive interpretation.
-    # The volume can be calculated independently from regionprops - included as sanity check.
-    series_props = {
-        'Surface area': (surface_area/100, 'cm^2'),
-        'Volume': (volume/1000, 'mL'),
-        'Bounding box volume': (region_props_3D['area_bbox']*isotropic_voxel_volume/1000, 'mL'),
-        'Convex hull volume': (region_props_3D['area_convex']*isotropic_voxel_volume/1000, 'mL'),
-        'Volume of holes': ((region_props_3D['area_filled']-region_props_3D['area'])*isotropic_voxel_volume/1000, 'mL'),
-        'Extent': (region_props_3D['extent']*100, '%'),    # Percentage of bounding box filled
-        'Solidity': (region_props_3D['solidity']*100, '%'),    # Percentage of convex hull filled
-        'Compactness': (compactness, '%'),
-        'Long axis length': (region_props_3D['axis_major_length']*isotropic_spacing/10, 'cm'),
-        'Short axis length': (region_props_3D['axis_minor_length']*isotropic_spacing/10, 'cm'),
-        'Equivalent diameter': (region_props_3D['equivalent_diameter_area']*isotropic_spacing/10, 'cm'),
-        'Longest caliper diameter': (region_props_3D['feret_diameter_max']*isotropic_spacing/10, 'cm'),
-        'Maximum depth': (max_depth*isotropic_spacing/10, 'cm'),
-        'Primary moment of inertia': (region_props_3D['inertia_tensor_eigvals'][0]*isotropic_spacing**2/100, 'cm^2'),
-        'Second moment of inertia': (region_props_3D['inertia_tensor_eigvals'][1]*isotropic_spacing**2/100, 'cm^2'),
-        'Third moment of inertia': (region_props_3D['inertia_tensor_eigvals'][2]*isotropic_spacing**2/100, 'cm^2'),
-        'Mean moment of inertia': (m*isotropic_spacing**2/100, 'cm^2'),
-        'Fractional anisotropy of inertia': (100*FA, '%'),
-        'QC - Volume check': (region_props_3D['area']*isotropic_voxel_volume/1000, 'mL'),
-        # From eigenvectors of inertia tensor: 
-        # Include orientation info with respect to LPH coordinate system (tilt, roll)
-    }
-
-    return series_props
-
-
-
-def area_opening_2d(input, **kwargs):
-    """
-    Return grayscale area opening of an image.
-    
-    Wrapper for skimage.morphology.area_opening. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [area opening 2D]'
-    result = input.copy(SeriesDescription = desc)
-    images = result.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Calculating ' + desc)
-        image.read()
-        array = image.array()
-        array = skimage.morphology.area_opening(array, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return result
-
-
-def area_opening_3d(input, **kwargs):
-    """
-    Return grayscale area opening of an image.
-    
-    Wrapper for skimage.morphology.area_opening. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    desc = input.instance().SeriesDescription + ' [area opening 3D]'
-    result = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        array[...,t] = skimage.morphology.area_opening(array[...,t], **kwargs)
-        result.set_array(array[...,t], headers[:,t], pixels_first=True)
-    _reset_window(result, array)
-    input.status.hide()
-    return result
-
-
-def area_closing_2d(input, **kwargs):
-    """
-    Return grayscale area closing of an image.
-    
-    Wrapper for skimage.morphology.area_closing. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [area closing 2D]'
-    result = input.copy(SeriesDescription = desc)
-    images = result.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Calculating ' + desc)
-        image.read()
-        array = image.array()
-        array = skimage.morphology.area_closing(array, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return result
-
-
-def area_closing_3d(input, **kwargs):
-    """
-    Return grayscale area closing of an image.
-    
-    Wrapper for skimage.morphology.area_closing. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    desc = input.instance().SeriesDescription + ' [area closing 3D]'
-    result = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        array[...,t] = skimage.morphology.area_closing(array[...,t], **kwargs)
-        result.set_array(array[...,t], headers[:,t], pixels_first=True)
-    _reset_window(result, array)
-    input.status.hide()
-    return result
-
-
-def opening_2d(input, **kwargs):
-    """
-    Return grayscale morphological opening of an image.
-    
-    Wrapper for skimage.morphology.opening. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [opening 2D]'
-    result = input.copy(SeriesDescription = desc)
-    images = result.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Calculating ' + desc)
-        image.read()
-        array = image.array()
-        array = skimage.morphology.opening(array, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return result
-
-
-def opening_3d(input, **kwargs):
-    """
-    Return grayscale morphological opening of an image.
-    
-    Wrapper for skimage.morphology.opening. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    desc = input.instance().SeriesDescription + ' [opening 3D]'
-    result = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        array[...,t] = skimage.morphology.opening(array[...,t], **kwargs)
-        result.set_array(array[...,t], headers[:,t], pixels_first=True)
-    _reset_window(result, array)
-    input.status.hide()
-    return result
-
-
-def closing_2d(input, **kwargs):
-    """
-    Return grayscale morphological closing of an image.
-    
-    Wrapper for skimage.morphology.closing. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [closing 2D]'
-    result = input.copy(SeriesDescription = desc)
-    images = result.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Calculating ' + desc)
-        image.read()
-        array = image.array()
-        array = skimage.morphology.closing(array, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return result
-
-
-def closing_3d(input, **kwargs):
-    """
-    Return grayscale morphological closing of an image.
-    
-    Wrapper for skimage.morphology.closing. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    desc = input.instance().SeriesDescription + ' [closing 3D]'
-    result = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        array[...,t] = skimage.morphology.closing(array[...,t], **kwargs)
-        result.set_array(array[...,t], headers[:,t], pixels_first=True)
-    _reset_window(result, array)
-    input.status.hide()
-    return result
-
-
-def remove_small_holes_2d(input, **kwargs):
-    """
-    Remove contiguous holes smaller than the specified size.
-    
-    Wrapper for skimage.morphology.remove_small_holes. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [remove small holes 2D]'
-    result = input.copy(SeriesDescription = desc)
-    images = result.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Calculating ' + desc)
-        image.read()
-        array = image.array().astype(np.int16)
-        array = skimage.morphology.remove_small_holes(array, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return result
-
-
-def remove_small_holes_3d(input, **kwargs):
-    """
-    Remove contiguous holes smaller than the specified size.
-    
-    Wrapper for skimage.morphology.remove_small_holes. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    output : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    else:
-        array = array.astype(np.int16)
-    desc = input.instance().SeriesDescription + ' [remove holes 3D]'
-    result = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        array[...,t] = skimage.morphology.remove_small_holes(array[...,t], **kwargs)
-        result.set_array(array[...,t], headers[:,t], pixels_first=True)
-    _reset_window(result, array)
-    input.status.hide()
-    return result
-
-
-def watershed_2d(input, markers=None, mask=None, **kwargs):
-    """
-    Labels structures in an image
-    
-    Wrapper for skimage.segmentation.watershed function. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-    markers: dbdicom series of the same dimensions as series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [watershed 2D]'
-    result = input.copy(SeriesDescription = desc)
-    sortby = ['SliceLocation', 'AcquisitionTime']
-    images = result.images(sortby=sortby)
-    if markers is not None:
-        markers = scipy.map_to(markers, input, label=True)
-        markers = markers.images(sortby=sortby)
-    if mask is not None:
-        mask = scipy.map_to(mask, input, mask=True)
-        mask = mask.images(sortby=sortby)
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Calculating ' + desc)
-        image.read()
-        array = image.array()
-        if markers is None:
-            mrk = None
-        else:
-            mrk = markers[i].array().astype(np.uint)
-        if mask is None:
-            msk = None
-        else:
-            msk = mask[i].array().astype(np.bool8)
-        array = skimage.segmentation.watershed(array, markers=mrk, mask=msk, **kwargs)
-        array.astype(np.float32) # unnecessary - test
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return result
-
-
-def watershed_3d(input, markers=None, mask=None, **kwargs):
-    """
-    Determine watershed in 3D
-    
-    Wrapper for skimage.segmentation.watershed function.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    if markers is not None:
-        markers = scipy.map_to(markers, input)
-        markers, _ = markers.array('SliceLocation', pixels_first=True)
-        markers = markers.astype(np.uint)
-    if mask is not None:
-        mask = scipy.map_to(mask, input)
-        mask, _ = mask.array('SliceLocation', pixels_first=True)
-        mask = mask.astype(np.bool8)
-    desc = input.instance().SeriesDescription + ' [watershed 3D]'
-    result = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        array[...,t] = skimage.segmentation.watershed(
-            array[...,t], 
-            markers = None if markers is None else markers[...,t], 
-            mask = None if mask is None else mask[...,t], 
-            **kwargs)
-        result.set_array(array[...,t], headers[:,t], pixels_first=True)
-    _reset_window(result, array)
-    input.status.hide()
-    return result
-
-
-def skeletonize(input, **kwargs):
-    """
-    Labels structures in an image
-    
-    Wrapper for skimage.segmentation.watershed function. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-    markers: dbdicom series of the same dimensions as series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [2d skeleton]'
-    filtered = input.copy(SeriesDescription = desc)
-    #images = filtered.instances() #sort=False should be faster - check
-    images = filtered.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Calculating ' + desc)
-        image.read()
-        array = image.array()
-        array = skimage.morphology.skeletonize(array, **kwargs)
-        #array.astype(np.float32)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-def skeletonize_3d(input, **kwargs):
-    """
-    Labels structures in an image
-    
-    Wrapper for skimage.segmentation.watershed function. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-    markers: dbdicom series of the same dimensions as series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [skeleton 3D]'
-    filtered = input.copy(SeriesDescription = desc)
-    array, headers = filtered.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return filtered
-    for t in range(array.shape[3]):
-        if array.shape[3] > 1:
-            input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        else:
-            input.status.message('Calculating ' + desc + '. Please bear with me..')
-        array[:,:,:,t] = skimage.morphology.skeletonize_3d(array[:,:,:,t], **kwargs)
-        filtered.set_array(array, headers[:,t], pixels_first=True)
-    _reset_window(filtered, array)
-    input.status.hide()
-    return filtered
-
-
-def peak_local_max_3d(input, labels=None, **kwargs):
-    """
-    Determine local maxima
-    
-    Wrapper for skimage.feature.peak_local_max function. 
-    # https://scikit-image.org/docs/stable/api/skimage.feature.html#skimage.feature.peak_local_max
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    if labels is not None:
-        labels = scipy.map_to(labels, input)
-        labels_array, _ = labels.array('SliceLocation', pixels_first=True)
-    desc = input.instance().SeriesDescription + ' [peak local max 3D]'
-    filtered = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        if labels is None:
-            labels_t = None
-        else:
-            labels_t = labels_array[:,:,:,t].astype(np.int16)
-        coords = skimage.feature.peak_local_max(array[:,:,:,t], labels=labels_t, **kwargs)
-        mask = np.zeros(array.shape[:3], dtype=bool)
-        mask[tuple(coords.T)] = True
-        filtered.set_array(mask, headers[:,t], pixels_first=True)
-    _reset_window(filtered, array)
-    input.status.hide()
-    return filtered
-
-
-def canny(input, sigma=1.0, **kwargs):
-    """
-    wrapper for skimage.feature.canny
-    # https://scikit-image.org/docs/dev/api/skimage.feature.html#skimage.feature.canny
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Canny filter x ' + str(sigma) + ' ]'
-    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()
-        array = skimage.feature.canny(array, sigma=sigma, **kwargs)
-        image.set_array(array)
-        array = array.astype(np.ubyte)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-def convex_hull_image(series, **kwargs):
-    """
-    wrapper for skimage.morphology.convex_hull_image
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Convex hull 2D]'
-    desc = series.instance().SeriesDescription 
-    chull = series.copy(SeriesDescription = desc+suffix)
-    images = chull.images()
-    for i, image in enumerate(images):
-        series.status.progress(i+1, len(images), 'Calculating convex hull for ' + desc)
-        image.read()
-        array = np.around(image.array())
-        array = skimage.morphology.convex_hull_image(array, **kwargs)
-        image.set_array(array)
-        array = array.astype(np.ubyte)
-        _reset_window(image, array)
-        image.clear()
-    series.status.hide()
-    return chull
-
-
-def convex_hull_image_3d(input, **kwargs):
-    """
-    wrapper for skimage.morphology.convex_hull_image
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return input
-    desc = input.instance().SeriesDescription + ' [Convex hull 3D]'
-    result = input.new_sibling(SeriesDescription = desc)
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        volume = np.around(array[:,:,:,t])
-        hull = skimage.morphology.convex_hull_image(volume,  **kwargs)
-        result.set_array(hull, headers[:,t], pixels_first=True)
-    _reset_window(result, hull)
-    input.status.hide()
-    return result
-
-
-def coregister_2d_to_2d(moving, fixed, return_array=False, attachment=1):
-    # https://scikit-image.org/docs/stable/api/skimage.registration.html#skimage.registration.optical_flow_tvl1
-
-    #fixed = fixed.map_to(moving)
-    fixed = scipy.map_to(fixed, moving)
-
-    # Get arrays for fixed and moving series
-    array_fixed, _ = fixed.array('SliceLocation', pixels_first=True)
-    array_moving, headers = moving.array('SliceLocation', pixels_first=True)
-    if array_fixed is None or array_moving is None:
-        return fixed
-    array_moving, headers, array_fixed = array_moving[...,0], headers[...,0], array_fixed[...,0]
-
-    # Coregister fixed and moving slice-by-slice
-    row_coords, col_coords = np.meshgrid( 
-        np.arange(array_moving.shape[0]), 
-        np.arange(array_moving.shape[1]),
-        indexing='ij')
-    deformation = np.empty(array_moving.shape + (2,))
-    for z in range(array_moving.shape[2]):
-        moving.status.progress(z+1, array_moving.shape[2], 'Performing coregistration..')
-        image0 = array_fixed[:,:,z]
-        image1 = array_moving[:,:,z]
-        v, u = skimage.registration.optical_flow_tvl1(image0, image1, attachment=attachment)
-        new_coords = np.array([row_coords + v, col_coords + u])
-        array_moving[:,:,z] = skimage.transform.warp(image1, new_coords, mode='edge')
-        deformation[:,:,z,:] = np.stack([v, u], axis=-1)
-
-    # Return array or new series
-    if return_array:
-        moving.status.message('Finished coregistration..')
-        return array_moving, deformation, headers
-    else:
-        moving.status.message('Writing coregistered series to database..')
-        # Create new dicom series
-        desc = moving.instance().SeriesDescription 
-        coreg = moving.new_sibling(SeriesDescription = desc + ' [coregistered]')
-        deform = moving.new_sibling(SeriesDescription = desc + ' [deformation field]')
-        # Set arrays of new series
-        coreg.set_array(array_moving, headers, pixels_first=True)
-        for dim in range(deformation.shape[-1]):
-            deform.set_array(deformation[...,dim], headers, pixels_first=True)
-        moving.status.message('Finished coregistration..')
-        return coreg, deform
-    
-
-def coregister_3d_to_3d(moving, fixed, return_array=False, attachment=1):
-    # https://scikit-image.org/docs/stable/api/skimage.registration.html#skimage.registration.optical_flow_tvl1
-
-    fixed = scipy.map_to(fixed, moving)
-
-    # Get arrays for fixed and moving series
-    array_fixed, _ = fixed.array('SliceLocation', pixels_first=True)
-    array_moving, headers = moving.array('SliceLocation', pixels_first=True)
-    if array_fixed is None or array_moving is None:
-        return fixed
-    array_moving, headers, array_fixed = array_moving[...,0], headers[...,0], array_fixed[...,0]
-
-    moving.status.message('Performing coregistration. Please be patient. Its hard work and I need to concentrate..')
-    # Coregister fixed and moving slice-by-slice
-    row_coords, col_coords, slice_coords = np.meshgrid( 
-        np.arange(array_moving.shape[0]), 
-        np.arange(array_moving.shape[1]),
-        np.arange(array_moving.shape[2]),
-        indexing='ij')
-    v, u, w = skimage.registration.optical_flow_tvl1(array_fixed,  array_moving, attachment=attachment)
-    new_coords = np.array([row_coords + v, col_coords + u, slice_coords + w])
-    array_moving = skimage.transform.warp(array_moving, new_coords, mode='edge')
-    deformation = np.stack([v, u, w], axis=-1)
-
-    # Return array or new series
-    if return_array:
-        moving.status.message('Finished coregistration..')
-        return array_moving, deformation, headers
-    else:
-        moving.status.message('Writing coregistered series to database..')
-        # Create new dicom series
-        desc = moving.instance().SeriesDescription
-        coreg = moving.new_sibling(SeriesDescription = desc + ' [coregistered]')
-        deform = moving.new_sibling(SeriesDescription = desc + ' [deformation field]')
-        # Set arrays of new series
-        coreg.set_array(array_moving, headers, pixels_first=True)
-        for dim in range(deformation.shape[-1]):
-            deform.set_array(deformation[...,dim], headers, pixels_first=True)
-        moving.status.message('Finished coregistration..')
-        return coreg, deform
-    
-
-def warp(image, deformation_field):
-
-    # Get arrays for fixed and moving series
-    array, headers = image.array('SliceLocation', pixels_first=True, first_volume=True)
-    array_deform, _ = deformation_field.array('SliceLocation', pixels_first=True, first_volume=True)
-
-    # For the deformation field the last dimension is the components
-    # For the image use only the first time point
-    # array, headers = array[...,0], headers[...,0]
-
-    # For this function, image and deformation field must be aligned
-    if array.shape != array_deform.shape[:-1]:
-        msg = 'The dimensions of image and deformation field are not matching up. \n'
-        msg += 'Please select two series with matching dimensions.'
-        raise ValueError(msg)
-
-    # Warp the arrays
-    if array_deform.shape[-1] == 3:
-        x, y, z = np.meshgrid( 
-            np.arange(array.shape[0]), 
-            np.arange(array.shape[1]),
-            np.arange(array.shape[2]),
-            indexing='ij')
-        v, u, w = array_deform[...,0], array_deform[...,1], array_deform[...,2]
-        new_coords = np.array([x+v, y+u, z+w])
-        array = skimage.transform.warp(array, new_coords, mode='edge')
-    elif array_deform.shape[-1] == 2:
-        x, y = np.meshgrid( 
-            np.arange(array.shape[0]), 
-            np.arange(array.shape[1]),
-            indexing='ij')
-        for z in range(array.shape[2]):
-            image.status.progress(z+1, array.shape[2], 'Deforming slices..')
-            v, u = array_deform[...,z,0], array_deform[...,z,1]
-            new_coords = np.array([x+v, y+u])
-            array[...,z] = skimage.transform.warp(array[...,z], new_coords, mode='edge')
-    else:
-        msg = 'The deformation field does not have the correct dimensions. \n'
-        msg += 'This needs to have the either 2 or 3 images for each slice location.'
-        raise ValueError(msg)
-    
-    # Create new dicom series
-    warped = image.new_sibling(suffix='warped')
-    warped.set_array(array, headers, pixels_first=True)
-    
-    return warped
-
-    
-
-def mdreg_constant_3d(series, attachment=1, max_improvement=1, max_iter=5):
-
-    # Get arrays for fixed and moving series
-    array, headers = series.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-    if array is None:
-        return
-    array, headers = array[...,0], headers[...,0]
-    
-    # Coregister fixed and moving slice-by-slice
-    row_coords, col_coords, slice_coords = np.meshgrid(
-        np.arange(array.shape[0]),
-        np.arange(array.shape[1]),
-        np.arange(array.shape[2]),
-        indexing='ij')
-    v, u, w = np.zeros(array.shape), np.zeros(array.shape), np.zeros(array.shape)
-    coreg = array.copy()
-    for it in range(max_iter):
-        target = np.mean(coreg, axis=3) # constant model
-        cnt=0
-        improvement = 0 # pixel sizes
-        for t in range(array.shape[3]):
-            cnt+=1
-            msg = 'Performing iteration ' + str(it) + ' < ' + str(max_iter)
-            msg += ' (best improvement so far = ' + str(round(improvement,2)) + ' pixels)'
-            series.status.progress(cnt, array.shape[3], msg)
-            v_t, u_t, w_t = skimage.registration.optical_flow_tvl1(
-                target, 
-                array[:,:,:,t], 
-                attachment=attachment)
-            coreg[:,:,:,t] = skimage.transform.warp(
-                array[:,:,:,t], 
-                np.array([row_coords + v_t, col_coords + u_t, slice_coords + w_t]),
-                mode='edge')
-            improvement_t = np.amax(np.sqrt(np.square(v_t-v[:,:,:,t]) + np.square(u_t-u[:,:,:,t]) + np.square(w_t-w[:,:,:,t])))
-            if improvement_t > improvement:
-                improvement = improvement_t
-            v[:,:,:,t], u[:,:,:,t], w[:,:,:,t] = v_t, u_t, w_t
-        if improvement < max_improvement:
-            break
-    
-    series.status.message('Writing coregistered series to database..')
-    desc = series.instance().SeriesDescription + ' [coregistered]'
-    registered_series = series.new_sibling(SeriesDescription=desc)
-    registered_series.set_array(coreg, headers, pixels_first=True)
-    series.status.message('Finished coregistration..')
-    return registered_series
-
-    
-
-def coregister_series_2d_to_2d(series, attachment=1):
-
-    # Get arrays for fixed and moving series
-    array, headers = series.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-    if array is None:
-        return
-    array, headers = array[:,:,:,:,0], headers[:,:,0]
-
-    
-    # Coregister fixed and moving slice-by-slice
-    row_coords, col_coords = np.meshgrid(
-        np.arange(array.shape[0]), 
-        np.arange(array.shape[1]),
-        indexing='ij')
-    target = np.mean(array, axis=3)
-    cnt=0
-    for t in range(array.shape[3]):
-        for z in range(array.shape[2]):
-            cnt+=1
-            series.status.progress(cnt, array.shape[2]*array.shape[3], 'Performing coregistration..')
-            fixed = target[:,:,z]
-            moving = array[:,:,z,t]
-            v, u = skimage.registration.optical_flow_tvl1(fixed, moving, attachment=attachment)
-            array[:,:,z,t] = skimage.transform.warp(
-                moving, 
-                np.array([row_coords + v, col_coords + u]),
-                mode='edge')
-
-    # Return array or new series
-    series.status.message('Writing coregistered series to database..')
-    desc = series.instance().SeriesDescription + ' [coregistered]'
-    registered_series = series.new_sibling(SeriesDescription=desc)
-    registered_series.set_array(array, headers, pixels_first=True)
-    series.status.message('Finished coregistration..')
-    return registered_series
-
-
-def mdreg_constant_2d(series, attachment=1, max_improvement=1, max_iter=5):
-
-    # Get arrays for fixed and moving series
-    array, headers = series.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-    if array is None:
-        return
-    array, headers = array[:,:,:,:,0], headers[:,:,0]
-
-    
-    # Coregister fixed and moving slice-by-slice
-    row_coords, col_coords = np.meshgrid(
-        np.arange(array.shape[0]), 
-        np.arange(array.shape[1]),
-        indexing='ij')
-    v, u = np.zeros(array.shape), np.zeros(array.shape)
-    coreg = array.copy()
-    for it in range(max_iter):
-        target = np.mean(coreg, axis=3) # constant model
-        cnt=0
-        improvement = 0 # pixel sizes
-        for t in range(array.shape[3]):
-            for z in range(array.shape[2]):
-                cnt+=1
-                msg = 'Performing iteration ' + str(it) + ' < ' + str(max_iter)
-                msg += ' (best improvement so far = ' + str(round(improvement,2)) + ' pixels)'
-                series.status.progress(cnt, array.shape[2]*array.shape[3], msg)
-                v_zt, u_zt = skimage.registration.optical_flow_tvl1(
-                    target[:,:,z], 
-                    array[:,:,z,t], 
-                    attachment=attachment)
-                coreg[:,:,z,t] = skimage.transform.warp(
-                    array[:,:,z,t], 
-                    np.array([row_coords + v_zt, col_coords + u_zt]),
-                    mode='edge')
-                improvement_zt = np.amax(np.sqrt(np.square(v_zt-v[:,:,z,t]) + np.square(u_zt-u[:,:,z,t])))
-                if improvement_zt > improvement:
-                    improvement = improvement_zt
-                v[:,:,z,t], u[:,:,z,t] = v_zt, u_zt
-        if improvement < max_improvement:
-            break
-    
-    series.status.message('Writing coregistered series to database..')
-    desc = series.instance().SeriesDescription + ' [coregistered]'
-    registered_series = series.new_sibling(SeriesDescription=desc)
-    registered_series.set_array(coreg, headers, pixels_first=True)
-    series.status.message('Finished coregistration..')
-    return registered_series
-
-
-
-    
-
-# Helper functions
-
-def _reset_window(image, array):
-    arr = array.astype(np.float32)
-    min = np.amin(arr)
-    max = np.amax(arr)
-    image.WindowCenter= (max+min)/2
-    if min==max:
-        if min == 0:
-            image.WindowWidth = 1
-        else:
-            image.WindowWidth = min
-    else:
-        image.WindowWidth = 0.9*(max-min)