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

dbdicom/extensions/scipy.py

@@ -1,1512 +0,0 @@
-import numpy as np
-import pandas as pd
-import scipy
-from scipy.ndimage import affine_transform
-import dbdicom
-from dbdicom.utils.image import multislice_affine_transform
-
-
-
-# OBSOLETE - replaced by vreg._equal_geometry
-def _equal_geometry(affine1, affine2):
-    # Check if both are the same, 
-    # ignoring the order in the list
-    if not isinstance(affine2, list):
-        affine2 = [affine2]
-    if not isinstance(affine1, list):
-        affine1 = [affine1]
-    if len(affine1) != len(affine2):
-        return False
-    unmatched = list(range(len(affine2)))
-    for a1 in affine1:
-        imatch = None
-        for i in unmatched:
-            if np.array_equal(a1[0], affine2[i][0]):
-                # If a slice group with the same affine is found, 
-                # check if the image dimensions are the same too.
-                dim1 = a1[1][0].array().shape
-                dim2 = affine2[i][1][0].array().shape
-                if dim1 == dim2:
-                    imatch = i
-                    break
-        if imatch is not None:
-            unmatched.remove(imatch)
-    return unmatched == []
-
-
-# Better use set(tuple())
-# OBSOLETE - unused
-def _lists_have_equal_items(list1, list2):
-    # Convert the lists to sets
-    set1 = set([tuple(x) for x in list1])
-    set2 = set([tuple(x) for x in list2])
-
-    # Check if the sets are equal
-    return set1 == set2
-
-
-def mask_curve_3d(masks, images, **kwargs):
-    if not isinstance(masks, list):
-        masks = [masks]
-    if not isinstance(images, list):
-        images = [images]
-    df_all = []
-    for mask in masks:
-        for img in images:
-            df = _mask_curve_3d(mask, img, **kwargs)
-            df_all.append(df) 
-    return df_all
-
-
-def _mask_curve_3d(mask, series, dim='InstanceNumber'):
-
-    # Get 4D mask array overlaid on 4D series
-    msk_arr, img_hdrs = mask_array(mask, on=series, dim=dim)
-    
-    # Define variables
-    vars = ['PatientID', 'StudyDescription', 'SeriesDescription', 'Region of Interest']
-    vars += [str(dim), 'Mean', 'Stdev', 'Max', 'Min', 'Median', '2.5 perc', '97.5 perc']
-
-    # Read values
-    img = series.instance()
-    ids = [img.PatientID, img.StudyDescription, img.SeriesDescription, mask.instance().SeriesDescription]
-    if isinstance(msk_arr, list):
-        data = _mask_curve_3d_data(msk_arr, img_hdrs, ids, dim)
-    else:
-        data = _mask_curve_3d_data_slice_group(msk_arr, img_hdrs, ids, dim)
-
-    # Return as dataframe
-    return pd.DataFrame(data, columns=vars)
-
-
-def _mask_curve_3d_data_slice_group(msk_arr, img_hdrs, ids, dim):
-    data = []
-    nt = msk_arr.shape[-1]
-    for t in range(nt):
-        img_hdrs[0,0].status.progress(t+1, nt, 'Extracting mask time curves..')
-        arr = _mask_data(msk_arr[...,t], img_hdrs[...,t])
-        vals = [
-            img_hdrs[0,t][dim], # 3d-assuming all slice locations have the same time coordinate
-            np.mean(arr),
-            np.std(arr),
-            np.amax(arr),
-            np.amin(arr),
-            np.percentile(arr, 50),
-            np.percentile(arr, 2.5),
-            np.percentile(arr, 97.5),
-        ]
-        data.append(ids + vals)
-    return data
-
-
-def _mask_curve_3d_data(msk_arr, img_hdrs, ids, dim):
-    data = []
-    nt = msk_arr[0].shape[-1]
-    for t in range(nt):
-        img_hdrs[0][0,0].progress(t+1, nt, 'Extracting mask time curves..')
-        # Concatenate data at time t for each slice group
-        arr = [_mask_data(arr_i[...,t], img_hdrs[i][...,t]) for i, arr_i in enumerate(msk_arr)]
-        arr = [d for d in arr if d is not None]
-        arr = np.concatenate(arr)
-        # Get values
-        vals = [
-            img_hdrs[0][0,t][dim], # 3d-assuming all slice locations have the same time coordinate
-            np.mean(arr),
-            np.std(arr),
-            np.amax(arr),
-            np.amin(arr),
-            np.percentile(arr, 50),
-            np.percentile(arr, 2.5),
-            np.percentile(arr, 97.5),
-        ]
-        data.append(ids + vals)
-    return data
-
-# OBSOLETE to vreg
-def mask_statistics(masks, images):
-    if not isinstance(masks, list):
-        masks = [masks]
-    if not isinstance(images, list):
-        images = [images]
-    df_all_masks = None
-    for mask in masks:
-        df_mask = None
-        for img in images:
-            df_img = _mask_statistics(mask, img)
-            if df_mask is None:
-                df_mask = df_img
-            else:
-                df_mask = pd.concat([df_mask, df_img], ignore_index=True)
-        if df_all_masks is None:
-            df_all_masks = df_mask
-        else:
-            df_all_masks = pd.concat([df_all_masks, df_mask], ignore_index=True)
-    return df_all_masks
-
-# OBSOLETE to vreg
-def _mask_statistics(mask, image):
-
-    # Get mask array
-    msk_arr, img_hdrs = mask_array(mask, on=image)
-    data = _mask_data_slice_groups(msk_arr, img_hdrs)
-    props = _summary_stats(data)
-    instance = image.instance()
-    columns = ['PatientID', 'StudyDescription', 'SeriesDescription', 'Region of Interest', 'Parameter', 'Value', 'Unit']
-    ids = [instance.PatientID, instance.StudyDescription, instance.SeriesDescription, mask.instance().SeriesDescription]
-    data = []
-    for par, val in props.items():
-        row = ids + [par, val, '']
-        data.append(row)
-    return pd.DataFrame(data, columns=columns)
-
-# OBSOLETE to vreg
-def _mask_data_slice_groups(msk_arr, img_hdrs):
-    if isinstance(msk_arr, list): 
-        # Loop over slice groups
-        data = [_mask_data(arr, img_hdrs[m]) for m, arr in enumerate(msk_arr)]
-        data = [d for d in data if d is not None]
-        if data == []:
-            data = None
-        else:
-            data = np.concatenate(data)
-    else: 
-        # single slice group
-        data = _mask_data(msk_arr, img_hdrs)
-    return data
-
-# OBSOLETE to vreg
-def _mask_data(msk_arr, imgs):
-    data = []
-    for i, image in np.ndenumerate(imgs):
-        if image is not None:
-            if len(i) == 1:
-                mask = msk_arr[:,:,i[0]]
-            elif len(i) == 2:
-                mask = msk_arr[:,:,i[0],i[1]]
-            if np.count_nonzero(mask) > 0:
-                array = image.array()
-                array = array[mask > 0.5]  
-                data.append(array.ravel())
-    if data == []:
-        return None
-    else:
-        return np.concatenate(data)
-    
-# OBSOLETE to vreg
-def _summary_stats(data):
-    if data is None:
-        return {}
-    return {
-        'Mean': np.mean(data),
-        'Standard deviation': np.std(data),
-        'Maximum': np.amax(data),
-        'Minimum': np.amin(data),
-        '2.5% percentile': np.percentile(data, 2.5),
-        '5% percentile': np.percentile(data, 5),
-        '10% percentile': np.percentile(data, 10),
-        '25% percentile': np.percentile(data, 25),
-        'Median': np.percentile(data, 50),
-        '75% percentile': np.percentile(data, 75),
-        '90% percentile': np.percentile(data, 90),
-        '95% percentile': np.percentile(data, 95),
-        '97.5% percentile': np.percentile(data, 97.5),
-        'Range': np.amax(data) - np.amin(data),
-        'Interquartile range':np.percentile(data, 75) - np.percentile(data, 25),
-        '90 percent range': np.percentile(data, 95) - np.percentile(data, 5),
-        'Coefficient of variation': np.std(data)/np.mean(data),
-        'Heterogeneity': (np.percentile(data, 95) - np.percentile(data, 5))/np.percentile(data, 50),
-        'Kurtosis': scipy.stats.kurtosis(data),
-        'Skewness': scipy.stats.skew(data),
-    }
-        
-# Obsolete - moved to vreg
-def array(series, on=None, **kwargs):
-    """Return the array overlaid on another series"""
-
-    if on is None:
-        array, _ = series.array(**kwargs)
-    else:
-        series_map = map_to(series, on)
-        array, _ = series_map.array(**kwargs)
-        if series_map != series:
-            series_map.remove()
-    return array
-
-
-def overlay(features):
-    """ Ensure all the features are in the same geometry as the reference feature"""
-
-    msg = 'Mapping all features on the same geometry'
-    mapped_features = [features[0]]
-    for f, feature in enumerate(features[1:]):
-        feature.status.progress(f+1, len(features)-1, msg)
-        mapped = map_to(feature, features[0])
-        mapped_features.append(mapped)
-    return mapped_features
-    
-# OBSOLETE - see vreg
-def map_to(source, target, **kwargs):
-    """Map non-zero pixels onto another series"""
-
-    # Get transformation matrix
-    source.status.message('Loading transformation matrices..')
-    affine_source = source.affine_matrix()
-    affine_target = target.affine_matrix() 
-    if _equal_geometry(affine_source, affine_target): 
-        source.status.hide()
-        return source
-
-    if isinstance(affine_target, list):
-        mapped_series = []
-        for affine_slice_group in affine_target:
-            slice_group_target = target.new_sibling()
-            slice_group_target.adopt(affine_slice_group[1])
-            mapped = _map_series_to_slice_group(source, slice_group_target, affine_source, affine_slice_group[0], **kwargs)
-            mapped_series.append(mapped)
-            slice_group_target.remove()
-        desc = source.instance().SeriesDescription + ' [overlay]'
-        mapped_series = dbdicom.merge(mapped_series, inplace=True)
-        mapped_series.SeriesDescription = desc
-    else:
-        mapped_series = _map_series_to_slice_group(source, target, affine_source, affine_target[0], **kwargs)
-    return mapped_series
-
-
-def _map_series_to_slice_group(source, target, affine_source, affine_target, **kwargs):
-
-    if isinstance(affine_source, list):
-        array_target, headers_target = target.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-        array = None
-        for affine_slice_group in affine_source:
-            slice_group_source = source.new_sibling()
-            slice_group_source.adopt(affine_slice_group[1])
-            array_sg, weight_sg = _map_slice_group_to_slice_group_array(slice_group_source, affine_slice_group[0], target, affine_target, array_target.shape[:3], **kwargs)
-            slice_group_source.remove()
-            if array is None:
-                array = array_sg
-                weight = weight_sg
-            else:
-                array += weight_sg*array_sg
-                weight += weight_sg   
-        nozero = np.where(weight > 0)
-        array[nozero] = array[nozero]/weight[nozero]
-
-        # Create new series
-        mapped_series = source.new_sibling(suffix='overlay')
-        ns, nt, nk = array.shape[2], array.shape[3], array.shape[4]
-        cnt=0
-        for t in range(nt):
-            for k in range(nk):
-                for s in range(ns):
-                    cnt+=1
-                    source.progress(cnt, ns*nt*nk, 'Saving results..')
-                    image = headers_target[s,0,0].copy_to(mapped_series)
-                    image.AcquisitionTime = t
-                    image.set_array(array[:,:,s,t,k])
-        return mapped_series
-    else:
-        return _map_slice_group_to_slice_group(source, affine_source[0], target, affine_target, **kwargs)
-    
-
-def _map_slice_group_to_slice_group_array(source, affine_source, target, output_affine, target_shape, **kwargs):
-
-    # Get source arrays
-    array_source, headers_source = source.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-    
-    # Get message status updates
-    source_desc = source.instance().SeriesDescription
-    target_desc = target.instance().SeriesDescription
-    message = 'Mapping ' + source_desc + ' onto ' + target_desc
-    source.message(message)
-
-    array_mapped = multislice_affine_transform(
-        array_source, 
-        affine_source, 
-        output_affine, 
-        output_shape = target_shape, 
-        slice_thickness = headers_source[0,0,0].SliceThickness, 
-        **kwargs,
-    )
-    weights_mapped = multislice_affine_transform(
-        np.ones(array_source.shape), 
-        affine_source, 
-        output_affine, 
-        output_shape = target_shape, 
-        slice_thickness = headers_source[0,0,0].SliceThickness, 
-        **kwargs,
-    )
-    return array_mapped, weights_mapped
-
-
-def _map_slice_group_to_slice_group(source, affine_source, target, output_affine, **kwargs):
-
-    # Get source arrays
-    array_source, headers_source = source.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-    array_target, headers_target = target.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-
-    # Get message status updates
-    source_desc = source.instance().SeriesDescription
-    target_desc = target.instance().SeriesDescription
-    message = 'Mapping ' + source_desc + ' onto ' + target_desc
-    source.message(message)
-
-    array_mapped = multislice_affine_transform(
-        array_source, 
-        affine_source, 
-        output_affine, 
-        output_shape = array_target.shape[:3], 
-        slice_thickness = headers_source[0,0,0].SliceThickness, 
-        **kwargs,
-    )
-
-    # Create new series
-    # Retain source acquisition times
-    # Assign acquisition time of slice=0 to all slices
-    mapped_series = source.new_sibling(suffix='overlay')
-    nt, nk = array_source.shape[3], array_source.shape[4]
-    ns = headers_target.shape[0] 
-    acq_times = [headers_source[0,t,0].AcquisitionTime for t in range(nt)]
-    cnt=0
-    for t in range(nt):
-        for k in range(nk):
-            for s in range(ns):
-                cnt+=1
-                source.progress(cnt, ns*nt*nk, 'Saving results..')
-                image = headers_target[s,0,0].copy_to(mapped_series)
-                image.AcquisitionTime = acq_times[t]
-                image.set_array(array_mapped[:,:,s,t,k])
-    return mapped_series
-
-
-# OBSOLETE - see vreg
-def mask_array(mask, on=None, dim='InstanceNumber'):
-    """Map non-zero pixels onto another series"""
-
-    if on is None:
-        return dbdicom.array(mask, sortby=['SliceLocation', dim], mask=True, pixels_first=True, first_volume=True)
-
-    # Get transformation matrix
-    mask.status.message('Loading transformation matrices..')
-    affine_source = mask.affine_matrix()
-    affine_target = on.affine_matrix() 
-
-    if isinstance(affine_target, list):
-        mapped_arrays = []
-        mapped_headers = []
-        for affine_slice_group_target in affine_target:
-            mapped, headers = _map_mask_series_to_slice_group(
-                mask, 
-                affine_slice_group_target[1], 
-                affine_source, 
-                affine_slice_group_target[0],
-                dim=dim,
-            )
-            mapped_arrays.append(mapped)
-            mapped_headers.append(headers)
-    else:
-        mapped_arrays, mapped_headers = _map_mask_series_to_slice_group(
-            mask, on, affine_source, affine_target[0], dim=dim)
-    return mapped_arrays, mapped_headers
-
-
-def _map_mask_series_to_slice_group(source, target, affine_source, affine_target, **kwargs):
-
-    if isinstance(affine_source, list):
-        mapped_arrays = []
-        for affine_slice_group in affine_source:
-            mapped, headers = _map_mask_slice_group_to_slice_group(
-                affine_slice_group[1], 
-                target, 
-                affine_slice_group[0], 
-                affine_target,
-                **kwargs,
-            )
-            mapped_arrays.append(mapped)
-        array = np.logical_or(mapped_arrays[0], mapped_arrays[1])
-        for a in mapped_arrays[2:]:
-            array = np.logical_or(array, a)
-        return array, headers
-    else:
-        return _map_mask_slice_group_to_slice_group(source, target, affine_source[0], affine_target, **kwargs)
-
-
-def _map_mask_slice_group_to_slice_group(source, target, affine_source, affine_target, dim='InstanceNumber'):
-
-    if isinstance(source, list):
-        status = source[0].status
-    else:
-        status = source.status
-
-    # Get arrays
-    array_source, headers_source = dbdicom.array(source, sortby=['SliceLocation',dim], pixels_first=True, first_volume=True)
-    array_target, headers_target = dbdicom.array(target, sortby=['SliceLocation',dim], pixels_first=True, first_volume=True)
-
-    # For mapping mask onto series, the time dimensions must be the same.
-    # If they are not, the mask is extruded on to the series time dimensions.
-    nk = array_target.shape[3]
-    if array_source.shape[3] != nk:
-        status.message('Extruding ROI on time series..')
-        array_source = np.amax(array_source, axis=-1)
-        array_source = np.repeat(array_source[:,:,:,np.newaxis], nk, axis=3)
-    
-    # If the dimensions and affines are equal there is nothing to do
-    if np.array_equal(affine_source, affine_target):
-        if array_source.shape == array_target.shape:
-            # Make sure the result is a mask
-            array_source[array_source > 0.5] = 1
-            array_source[array_source <= 0.5] = 0
-            return array_source, headers_target
-
-    # Perform the affine transformation 
-    array_target = multislice_affine_transform(
-        array_source, 
-        affine_source, 
-        affine_target, 
-        output_shape = array_target.shape[:3], 
-        slice_thickness = headers_source[0,0].SliceThickness, 
-        mask = True,
-    )
-
-    return array_target, headers_target
-    
-    
-        
-
-
-
-# SEGMENTATION
-
-
-def label_2d(input, **kwargs):
-    """
-    Labels structures in an image
-    
-    Wrapper for scipy.ndimage.label function. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [label 2D]'
-    desc = input.instance().SeriesDescription
-    filtered = input.copy(SeriesDescription = desc+suffix)
-    #images = filtered.instances() # setting sort=False should be faster - TEST!!!!!!!
-    images = filtered.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Labelling ' + desc)
-        image.read()
-        array = image.array() 
-        array, _ = scipy.ndimage.label(array, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-def label_3d(input, **kwargs):
-    """
-    Labels structures in a 3D volume
-    
-    Wrapper for scipy.ndimage.label function. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [label 3D]'
-    transform = input.new_sibling(SeriesDescription = desc)
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return transform
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        array[:,:,:,t], _ = scipy.ndimage.label(array[:,:,:,t], **kwargs)
-        transform.set_array(array[:,:,:,t], headers[:,t], pixels_first=True)
-    _reset_window(transform, array)
-    input.status.hide()
-    return transform
-
-
-def extract_largest_cluster_3d(input, **kwargs):
-    """
-    Label structures in 3D and then extract the largest cluster, return as a mask. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [Largest cluster 3D]'
-    transform = input.new_sibling(SeriesDescription = desc)
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return transform
-    for t in range(array.shape[3]):
-        input.status.progress(t, array.shape[3], 'Calculating ' + desc)
-        label_img, cnt = scipy.ndimage.label(array[:,:,:,t], **kwargs)
-        # Find the label of the largest feature
-        labels = range(1,cnt+1)
-        size = [np.count_nonzero(label_img==l) for l in labels]
-        max_label = labels[size.index(np.amax(size))]
-        # Create a mask corresponding to the largest feature
-        label_img = label_img==max_label
-        #label_img = label_img[label_img==max_label]
-        #label_img /= max_label
-        transform.set_array(label_img, headers[:,t], pixels_first=True)
-    _reset_window(transform, array)
-    input.status.hide()
-    return transform
-
-
-def binary_fill_holes(input, **kwargs):
-    """
-    Fill holes in an existing segmentation.
-    
-    Wrapper for scipy.ndimage.binary_fill_holes function. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Fill holes]'
-    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), 'Filling holes ' + desc)
-        image.read()
-        array = image.array() 
-        array = scipy.ndimage.binary_fill_holes(array, **kwargs)
-        image.set_array(array)
-        #array = array.astype(np.ubyte)
-        #_reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-def distance_transform_edt_3d(input, **kwargs):
-    """
-    Euclidian distance transform in 3D
-    
-    Wrapper for scipy.ndimage.distance_transform_edt function. 
-
-    Parameters
-    ----------
-    input: dbdicom series
-    markers: dbdicom series of the same dimensions as series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    desc = input.instance().SeriesDescription + ' [distance transform 3D]'
-    #transform = input.copy(SeriesDescription = desc)
-    transform = input.new_sibling(SeriesDescription = desc)
-    array, headers = input.array('SliceLocation', pixels_first=True)
-    if array is None:
-        return transform
-    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] = scipy.ndimage.distance_transform_edt(array[:,:,:,t], **kwargs)
-        transform.set_array(array[:,:,:,t], headers[:,t], pixels_first=True)
-    _reset_window(transform, array)
-    input.status.hide()
-    return transform
-
-
-
-# FILTERS
-
-
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.fourier_uniform.html#scipy.ndimage.fourier_ellipsoid
-def fourier_ellipsoid(input, size, **kwargs):
-    """
-    wrapper for scipy.ndimage.fourier_ellipsoid
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Fourier Ellipsoid x ' + str(size) + ' ]'
-    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 = np.fft.fft2(array)
-        array = scipy.ndimage.fourier_ellipsoid(array, size, **kwargs)
-        array = np.fft.ifft2(array).real
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.fourier_uniform.html#scipy.ndimage.fourier_uniform
-def fourier_uniform(input, size, **kwargs):
-    """
-    wrapper for scipy.ndimage.fourier_uniform
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Fourier Uniform x ' + str(size) + ' ]'
-    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 = np.fft.fft2(array)
-        array = scipy.ndimage.fourier_uniform(array, size, **kwargs)
-        array = np.fft.ifft2(array).real
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.fourier_shift.html#scipy.ndimage.fourier_shift
-def fourier_gaussian(input, sigma, **kwargs):
-    """
-    wrapper for scipy.ndimage.fourier_gaussian.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Fourier Gaussian 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 = np.fft.fft2(array)
-        array = scipy.ndimage.fourier_gaussian(array, sigma, **kwargs)
-        array = np.fft.ifft2(array).real
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.gaussian_gradient_magnitude.html#scipy.ndimage.gaussian_gradient_magnitude
-def gaussian_gradient_magnitude(input, sigma, **kwargs):
-    """
-    wrapper for scipy.ndimage.gaussian_gradient_magnitude.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Gaussian Gradient Magnitude 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 = scipy.ndimage.gaussian_gradient_magnitude(array, sigma, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.gaussian_laplace.html#scipy.ndimage.gaussian_laplace
-def gaussian_laplace(input, sigma, **kwargs):
-    """
-    wrapper for scipy.ndimage.gaussian_laplace.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Gaussian Laplace 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 = scipy.ndimage.gaussian_laplace(array, sigma, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.laplace.html#scipy.ndimage.laplace
-def laplace(input, **kwargs):
-    """
-    wrapper for scipy.ndimage.sobel.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Laplace Filter]'
-    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 = scipy.ndimage.laplace(array, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.sobel.html#scipy.ndimage.sobel
-def sobel_filter(input, axis=-1, **kwargs):
-    """
-    wrapper for scipy.ndimage.sobel.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Sobel Filter along axis ' + str(axis) + ' ]'
-    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 = scipy.ndimage.sobel(array, axis=axis, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.prewitt.html#scipy.ndimage.prewitt
-def prewitt_filter(input, axis=-1, **kwargs):
-    """
-    wrapper for scipy.ndimage.prewitt.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Prewitt Filter along axis ' + str(axis) + ' ]'
-    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 = scipy.ndimage.prewitt(array, axis=axis, **kwargs)
-        image.set_array(array)
-        _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.median_filter.html#scipy.ndimage.median_filter
-def median_filter(input, size=3, **kwargs):
-    """
-    wrapper for scipy.ndimage.median_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Median Filter with size ' + str(size) + ' ]'
-    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 = scipy.ndimage.median_filter(array, size=size, **kwargs)
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.percentile_filter.html#scipy.ndimage.percentile_filter
-def percentile_filter(input, percentile, **kwargs):
-    """
-    wrapper for scipy.ndimage.percentile_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Percentile Filter x ' + str(percentile) + ' ]'
-    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 = scipy.ndimage.percentile_filter(array, percentile, **kwargs)
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.rank_filter.html#scipy.ndimage.rank_filter
-def rank_filter(input, rank, **kwargs):
-    """
-    wrapper for scipy.ndimage.rank_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Rank Filter x ' + str(rank) + ' ]'
-    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 = scipy.ndimage.rank_filter(array, rank, **kwargs)
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.minimum_filter.html#scipy.ndimage.maximum_filter
-def maximum_filter(input, size=3, **kwargs):
-    """
-    wrapper for scipy.ndimage.maximum_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Maximum Filter x ' + str(size) + ' ]'
-    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 = scipy.ndimage.maximum_filter(array, size=size, **kwargs)
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.minimum_filter.html#scipy.ndimage.minimum_filter
-def minimum_filter(input, size=3, **kwargs):
-    """
-    wrapper for scipy.ndimage.minimum_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Minimum Filter x ' + str(size) + ' ]'
-    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 = scipy.ndimage.minimum_filter(array, size=size, **kwargs)
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.uniform_filter.html#scipy.ndimage.uniform_filter
-def uniform_filter(input, size=3, **kwargs):
-    """
-    wrapper for scipy.ndimage.uniform_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Uniform Filter x ' + str(size) + ' ]'
-    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 = scipy.ndimage.uniform_filter(array, size=size, **kwargs)
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-#https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.uniform_filter.html#scipy.ndimage.uniform_filter
-# This has a bug it seems
-def uniform_filter_3d(input, size=3, **kwargs):
-    """
-    wrapper for scipy.ndimage.uniform_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    array, headers = input.array(sortby='SliceLocation', pixels_first=True, first_volume=True)
-    input.message('Computing uniform filter..')
-    array = scipy.ndimage.uniform_filter(array, size=size, **kwargs)
-    suffix = ' [Uniform Filter x ' + str(size) + ']'
-    output = input.new_sibling(suffix=suffix)
-    output.set_array(array, headers, pixels_first=True)
-    return output
-    
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.gaussian_filter.html#scipy.ndimage.gaussian_filter
-def gaussian_filter(input, sigma, **kwargs):
-    """
-    wrapper for scipy.ndimage.gaussian_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Gaussian 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 = scipy.ndimage.gaussian_filter(array, sigma, **kwargs)
-        image.set_array(array)
-        if 'order' in kwargs:
-            if kwargs['order'] > 0:
-                _reset_window(image, array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.gaussian_filter.html#scipy.ndimage.gaussian_filter
-def gaussian_filter_3d(input, sigma, **kwargs):
-    """
-    wrapper for scipy.ndimage.gaussian_filter.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Gaussian Filter x ' + str(sigma) + ' ]'
-    array, headers = input.array(sortby='SliceLocation', pixels_first=True, first_volume=True)
-    input.message('Computing Gaussian filter..')
-    array = scipy.ndimage.gaussian_filter(array, sigma, **kwargs)
-    output = input.new_sibling(suffix=suffix)
-    output.set_array(array, headers, pixels_first=True)
-    return output
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.fourier_shift.html#scipy.ndimage.fourier_shift
-def fourier_shift(input, shift, **kwargs):
-    """
-    wrapper for scipy.ndimage.fourier_shift.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    suffix = ' [Fourier Shift]'
-    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 = np.fft.fft2(array)
-        array = scipy.ndimage.fourier_shift(array, shift, **kwargs)
-        array = np.fft.ifft2(array).real
-        image.set_array(array)
-        image.clear()
-    input.status.hide()
-    return filtered
-
-
-
-
-# RESCALE AND RESLICE
-
-
-
-def series_calculator(series, operation='1 - series', param=None):
-
-    desc = series.instance().SeriesDescription
-    result = series.copy(SeriesDescription = desc + ' [' + operation + ']')
-    images = result.images()
-    for i, img in enumerate(images):
-        series.progress(i+1, len(images), 'Calculating..')
-        img.read()
-        array = img.array()
-        if operation == '1 - series':
-            array = 1 - array
-        elif operation == '- series':
-            array = -array
-        elif operation == '1 / series':
-            array = 1 / array
-        elif operation == 'exp(- series)':
-            array = np.exp(-array)
-        elif operation == 'exp(+ series)':
-            array = np.exp(array)
-        elif operation == 'integer(series)':
-            array = np.around(array)
-        elif operation == 'abs(series)':
-            array = np.abs(array)
-        elif operation == 'a * series':
-            array = array*param
-        array[~np.isfinite(array)] = 0
-        img.set_array(array)
-        _reset_window(img, array)
-        img.clear()
-    series.status.hide()
-    return result
-
-
-def image_calculator(series1, series2, operation='series 1 - series 2', integer=False, series_desc=None):
-
-    result = map_to(series2, series1)
-    if result == series2: # same geometry
-        result = series2.copy()
-    images1 = series1.images(sortby=['SliceLocation', 'AcquisitionTime'])
-    images2 = result.images(sortby=['SliceLocation', 'AcquisitionTime'])
-    for i, img1 in enumerate(images1):
-        series1.status.progress(i+1, len(images1), 'Calculating..')
-        if i > len(images2)-1:
-            break
-        img2 = images2[i]
-        img2.read()
-        array1 = img1.array()
-        array2 = img2.array()
-        if operation in ['series 1 + series 2', '+', 'sum']:
-            array = array1 + array2
-            desc = ' [add]'
-        elif operation in ['series 1 - series 2', '-', 'diff']:
-            array = array1 - array2
-            desc = ' [difference]'
-        elif operation in ['series 1 / series 2', '/', 'div']:
-            array = array1 / array2
-            desc = ' [divide]'
-        elif operation in ['series 1 * series 2', '*', 'mult']:
-            array = array1 * array2
-            desc = ' [multiply]'
-        elif operation in ['(series 1 - series 2)/series 2', 'rdiff']:
-            array = (array1 - array2)/array2
-            desc = ' [relative difference]'
-        elif operation in ['average(series 1, series 2)', 'avr', 'mean']:
-            array = (array1 + array2)/2
-            desc = ' [average]'
-        array[~np.isfinite(array)] = 0
-        if integer:
-            array = np.around(array)
-        img2.set_array(array)
-        _reset_window(img2, array.astype(np.ubyte))
-        img2.clear()
-    if series_desc is None:
-        result.SeriesDescription = result.instance().SeriesDescription + desc
-    else:
-        result.SeriesDescription = series_desc
-    return result
-
-
-def n_images_calculator(series, operation='mean'):
-
-    # Use the first series as geometrical reference
-    reference = series[0]
-
-    # Get arrays for all series and stack into one array
-    array_ref, headers_ref = reference.array(sortby='SliceLocation', pixels_first=True)
-    array_all = [array_ref]
-    for i, s in enumerate(series[1:]):
-        reference.progress(i+1, len(series[1:]), 'Loading arrays')
-        array_s = array(s, on=reference, sortby='SliceLocation', pixels_first=True)
-        array_all.append(array_s)
-    array_all = np.stack(array_all, axis=-1)
-
-    # Perform calculation
-    reference.message('Calculating ' + operation)
-    if operation == 'sum':
-        array_all = np.sum(array_all, axis=-1)
-    elif operation == 'mean':
-        array_all = np.mean(array_all, axis=-1)
-
-    # Save as new series and return
-    result = reference.new_sibling(suffix=operation)
-    result.set_array(array_all, headers_ref, pixels_first=True)
-    return result
-
-
-
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.zoom.html#scipy.ndimage.zoom
-def zoom(input, zoom, **kwargs):
-    """
-    wrapper for scipy.ndimage.zoom.
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    zoomed : dbdicom series
-    """
-    suffix = ' [Resize x ' + str(zoom) + ' ]'
-    desc = input.instance().SeriesDescription
-    zoomed = input.copy(SeriesDescription = desc + suffix)
-    #images = zoomed.instances()
-    images = zoomed.images()
-    for i, image in enumerate(images):
-        input.status.progress(i+1, len(images), 'Resizing ' + desc)
-        image.read()
-        array = image.array()
-        array = scipy.ndimage.zoom(array, zoom, **kwargs)
-        image.set_array(array)
-        pixel_spacing = image.PixelSpacing
-        if type(zoom) is tuple:
-            image.PixelSpacing = [pixel_spacing[i]/zoom[i] for i in range(2)]
-        else:
-            image.PixelSpacing = [p/zoom for p in pixel_spacing]
-        image.clear()
-    input.status.hide()
-    return zoomed
-
-
-def resample(series, voxel_size=[1.0, 1.0, 1.0]):
-    series.status.message('Reading transformations..')
-    affine_source = series.affine_matrix()
-    if affine_source is None:
-        return
-    if isinstance(affine_source, list):
-        mapped_series = []
-        for affine_slice_group in affine_source:
-            mapped = _resample_slice_group(series, affine_slice_group[0], affine_slice_group[0], voxel_size=voxel_size)
-            mapped_series.append(mapped)
-        desc = series.instance().SeriesDescription + '[resampled]'
-        mapped_series = dbdicom.merge(mapped_series, inplace=True)
-        mapped_series.SeriesDescription = desc
-    else:
-        mapped_series = _resample_slice_group(series, affine_source[0], affine_source[1], voxel_size=voxel_size)
-    return mapped_series
-
-
-
-
-
-def _resample_slice_group(series, affine_source, slice_group, voxel_size=[1.0, 1.0, 1.0]):
-
-    # Create new resliced series
-    desc = series.instance().SeriesDescription + '[resampled]'
-    resliced_series = series.new_sibling(SeriesDescription = desc)
-
-    # Work out the affine matrix of the new series
-    p = dbdicom.utils.image.dismantle_affine_matrix(affine_source)
-    affine_target = affine_source.copy()
-    affine_target[:3, 0] = voxel_size[0] * np.array(p['ImageOrientationPatient'][:3])
-    affine_target[:3, 1] = voxel_size[1] * np.array(p['ImageOrientationPatient'][3:]) 
-    affine_target[:3, 2] = voxel_size[2] * np.array(p['slice_cosine'])
-
-    # If the series already is in the right orientation, return a copy
-    if np.array_equal(affine_source, affine_target):
-        series.status.message('Series is already in the right orientation..')
-        resliced_series.adopt(slice_group)
-        return resliced_series
-
-    # Get arrays
-    array, headers = series.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-    if array is None:
-        return resliced_series
-
-    # Perform transformation on the arrays to determine the output shape
-    dim = [
-        array.shape[0] * p['PixelSpacing'][1],
-        array.shape[1] * p['PixelSpacing'][0],
-        array.shape[2] * p['SpacingBetweenSlices'],
-    ]
-    output_shape = [1 + round(dim[i]/voxel_size[i]) for i in range(3)]
-
-    # Determine the transformation matrix and offset
-    source_to_target = np.linalg.inv(affine_source).dot(affine_target)
-    #matrix, offset = nib.affines.to_matvec(source_to_target)
-    matrix, offset = source_to_target[:3,:3], source_to_target[:3,3]
-    
-    # Perform the affine transformation
-    cnt=0
-    ns, nt, nk = output_shape[2], array.shape[-2], array.shape[-1]
-    pos, loc = dbdicom.utils.image.image_position_patient(affine_target, ns)
-    for t in range(nt):
-        for k in range(nk):
-            cnt+=1
-            series.status.progress(cnt, nt*nk, 'Performing transformation..')
-            resliced = affine_transform(
-                array[:,:,:,t,k],
-                matrix = matrix,
-                offset = offset,
-                output_shape = output_shape,
-            )
-            resliced_series.set_array(resliced, 
-                source = headers[0,t,k],
-                pixels_first = True,
-                affine_matrix = affine_target,
-                ImagePositionPatient = pos,
-                SliceLocation = loc,
-            )
-    series.status.message('Finished mapping..')
-    return resliced_series
-
-
-def reslice(series, orientation='axial'):
-
-    # Define geometry of axial series (isotropic)
-    series.status.message('Reading transformations..')
-    affine_source = series.affine_matrix()
-    if isinstance(affine_source, list):
-        mapped_series = []
-        for affine_slice_group in affine_source:
-            mapped = _reslice_slice_group(series, affine_slice_group[0], affine_slice_group[0], orientation=orientation)
-            mapped_series.append(mapped)
-            #slice_group.remove()
-        desc = series.instance().SeriesDescription + '['+orientation+']'
-        mapped_series = dbdicom.merge(mapped_series, inplace=True)
-        mapped_series.SeriesDescription = desc
-    else:
-        mapped_series = _reslice_slice_group(series, affine_source[0], affine_source[1], orientation=orientation)
-    return mapped_series
-
-
-def _reslice_slice_group(series, affine_source, slice_group, orientation='axial'):
-
-    # Create new resliced series
-    desc = series.instance().SeriesDescription + '['+orientation+']'
-    resliced_series = series.new_sibling(SeriesDescription = desc)
-
-    # Work out the affine matrix of the new series
-    p = dbdicom.utils.image.dismantle_affine_matrix(affine_source)
-    image_positions = [s.ImagePositionPatient for s in slice_group]
-    rows = slice_group[0].Rows
-    columns = slice_group[0].Columns
-    box = dbdicom.utils.image.bounding_box(
-        p['ImageOrientationPatient'],  
-        image_positions,   
-        p['PixelSpacing'], 
-        rows,
-        columns)
-    spacing = np.mean([p['PixelSpacing'][0], p['PixelSpacing'][1], p['SpacingBetweenSlices']])
-    affine_target = dbdicom.utils.image.standard_affine_matrix(
-        box, 
-        [spacing, spacing],
-        spacing,
-        orientation=orientation)
-
-    # If the series already is in the right orientation, return a copy
-    if np.array_equal(affine_source, affine_target):
-        series.status.message('Series is already in the right orientation..')
-        resliced_series.adopt(slice_group)
-        return resliced_series
-
-    #Perform transformation on the arrays to determine the output shape
-    if orientation == 'axial':
-        dim = [
-            np.linalg.norm(np.array(box['RAF'])-np.array(box['LAF'])),
-            np.linalg.norm(np.array(box['RAF'])-np.array(box['RPF'])),
-            np.linalg.norm(np.array(box['RAF'])-np.array(box['RAH'])),
-        ]
-    elif orientation == 'coronal':
-        dim = [
-            np.linalg.norm(np.array(box['RAH'])-np.array(box['LAH'])),
-            np.linalg.norm(np.array(box['RAH'])-np.array(box['RAF'])),
-            np.linalg.norm(np.array(box['RAH'])-np.array(box['RPH'])),
-        ]
-    elif orientation == 'sagittal':
-        dim = [
-            np.linalg.norm(np.array(box['LAH'])-np.array(box['LPH'])),
-            np.linalg.norm(np.array(box['LAH'])-np.array(box['LAF'])),
-            np.linalg.norm(np.array(box['LAH'])-np.array(box['RAH'])),
-        ]
-    output_shape = [1 + round(d/spacing) for d in dim]
-
-    # Determine the transformation matrix and offset
-    source_to_target = np.linalg.inv(affine_source).dot(affine_target)
-    #matrix, offset = nib.affines.to_matvec(source_to_target)
-    matrix, offset = source_to_target[:3,:3], source_to_target[:3,3]
-    
-    # Get arrays
-    array, headers = series.array(['SliceLocation','AcquisitionTime'], pixels_first=True)
-
-    # Perform the affine transformation and save results
-    cnt=0
-    ns, nt, nk = output_shape[2], array.shape[-2], array.shape[-1] 
-    pos, loc = dbdicom.utils.image.image_position_patient(affine_target, ns)
-    for t in range(nt):
-        for k in range(nk):
-            cnt+=1
-            series.status.progress(cnt, nt*nk, 'Calculating..')
-            resliced = affine_transform(
-                array[:,:,:,t,k],
-                matrix = matrix,
-                offset = offset,
-                output_shape = output_shape,
-            )
-            # Saving results at each time to avoid memory problems.
-            # Assign acquisition time of slice=0 to all slices.
-            resliced_series.set_array(resliced, 
-                source = headers[0,t,k],
-                pixels_first = True,
-                affine_matrix = affine_target,
-                ImagePositionPatient = pos,
-                SliceLocation = loc,
-            )
-    series.status.message('Finished mapping..')
-    return resliced_series
-
-
-
-# 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)