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

dbdicom/wrappers/numpy.py

@@ -1,119 +0,0 @@
-"""
-Functions for a new (sub)package dbimage inside dbdicom
-
-A set of dbdicom wrappers for numpy
-"""
-
-import numpy as np
-
-
-def mean_intensity_projection(series):
-    """
-    Segment by thresholding
-
-    Parameters
-    ----------
-    series: dbdicom series (4D: slice + time)
-
-    Returns
-    -------
-    mean : dbdicom series (3D)
-
-    Example:
-
-    mean_series = mean(series, axis=-1)
-    """
-    # Get numpy array with dimensions (slice, time, x, y)
-    # array = series.array('SliceLocation')
-
-    # Get numpy array with dimensions (x, y, slice, time)
-    array, headers = series.array('SliceLocation', pixels_first=True)
-    array = np.mean(array, axis=-1)
-    desc = series.instance().SeriesDescription + ' [Mean Intensity Projection]'
-    new_series = series.new_sibling(SeriesDescription=desc)
-    new_series.set_array(array, headers[:,0], pixels_first=True)
-    return new_series
-
-
-def maximum_intensity_projection(series):
-    """
-    Segment by thresholding
-
-    Parameters
-    ----------
-    series: dbdicom series (4D: slice + time)
-
-    Returns
-    -------
-    mean : dbdicom series (3D)
-
-    Example:
-
-    mean_series = mean(series, axis=-1)
-    """
-    # Get numpy array with dimensions (slice, time, x, y)
-    # array = series.array('SliceLocation')
-
-    # Get numpy array with dimensions (x, y, slice, time)
-    array, headers = series.array('SliceLocation', pixels_first=True)
-    array = np.amax(array, axis=-1)
-    desc = series.instance().SeriesDescription + ' [Maximum Intensity Projection]'
-    new_series = series.new_sibling(SeriesDescription=desc)
-    new_series.set_array(array, headers[:,0], pixels_first=True)
-    return new_series
-
-def norm_projection(series, ord=None):
-    array, headers = series.array('SliceLocation', pixels_first=True)
-    array = np.linalg.norm(array, ord=ord, axis=-1)
-    desc = series.instance().SeriesDescription + ' [Norm projection]'
-    new_series = series.new_sibling(SeriesDescription=desc)
-    new_series.set_array(array, headers[:,0], pixels_first=True)
-    return new_series
-    
-
-
-def threshold(input, low_threshold=0, high_threshold=1, method='absolute'):
-    """
-    Segment by thresholding
-
-    Parameters
-    ----------
-    input: dbdicom series
-
-    Returns
-    -------
-    filtered : dbdicom series
-    """
-    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)