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Questions tagged [scipy.ndimage]

50 questions
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Why does find_objects give a bunch of Nones and then range of the whole image?

I am trying to find all objects detected in difference of frames, I thougt this would give a list of each area detected in the threshold, but find_objects is giving a bunch of "None"s and a range of the whole…
NoBugs
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Any recommendation to resize 3d image array which consists of only 0 and 1?

I want to resize(downscale) the ground truth 3d images of brain tumor segmentation. Here are some g.t. + brain images: G.t. images are 3d numpy array and consist of only 0 and 1 value(only green voxel and black voxel, brain is not included in g.t.…
Crispy13
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What are the values (coefficients) of a Gaussian Kernel?

A Gaussian filter can be applied to an image using the following commands: cv.GaussianBlur(src, ksize, sigmaX[, dst[, sigmaY[, borderType=BORDER_DEFAULT]]] ) For Example: import cv2 import numpy as np a = np.arange(50,…
Winter 2019
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Convolving a 1D array with Gaussian filtering returns array of all zeros Python

Im trying to take a 1D array of 1's and 0's (mostly zeroes) and convolve it with a gaussian to get a more probablistic representation. When I use scipy.ndimage.gaussian_filter1d I keep getting back arrays that are just full of zeroes. spike_bins, _…
Julia Gorman
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Affine transformation from 2D to 3D using SciPy leads to empty arrays

Using scipy.ndimage.affine_transform, I am trying to apply an affine transformation on a 3D array with one degenerate dimension, e.g. with shape (10, 1, 10), and get a non-degenerate 3D output shape, e.g. (10, 10, 10). The purpose of this operation…
Biblot
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correctly rotate a scipy.ndimage.rotate back

I rotate a image with scipy.ndimage in one direction and do a operation on it and than rotate it backwards. Is there a way/function/parameters to savegard that rotate a image by angle x rotate the rotated image by angle -x results in the same…
Sebastian H
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image labelling and anisotropy

I have a 3d image which I want to label. Typically I use from label from scipy.ndimage. I want to ask how do you handle anisotropy, the z-dimension is cut more coarsely than x and y. My structuring element is like a ball: from scipy.ndimage import…
Aenaon
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Can scipy.ndimage's binary_erosion function be used to erode an image from one side?

I have an elevation array from a .tif LiDAR surface. Example array below. Existing_example_arrayV0 = [[ 0, 0, 1, 0, 0, 0, 0], [ 0, 1, 1, 1, 0, 0, 0], [ 0, 1, 1, 1, 1, 0, 0], …
Patstro
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Can scipy ndimage affine_transform increase intensity range?

We were doing some experiment on scipy.ndimage.affine_transform From our understanding, it is a linear transformation through spline interpolation method. Thus, it could reduce the overall image intensity range if some parts of the image is cut off,…
jongsung park
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Difference between `scipy.ndimage.fourier_gaussian` and own implementation

I am trying to implement myself a 2D gaussian filter (to debug some C++ code, outside the scope of this question). I focus on the first step: multiplication of the image and the Gaussian kernel in the Fourier space. The input data and its TF: import…
dagnic
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Use scipy ndimage generic_filter to compute set intersection across pixel-neighborhoods

I have raster images reporting the start day and end day of some periods across the globe. For each pixel (read numpy array element) I'd like to get a measure of how much its day-unit period overlap/intersect with that of the neighboring pixels.…
Matteo
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Why does the scipy.ndimage.gaussian_filter changes the shape of my masked image?

I would like to apply a Gaussian filter to a masked array, however, this appears to alter the shape of my image. The higher I put sigma, the more of the image disappears. I don't really understand why this happens? I would expect both figures to…
Emma
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Why is ndimage.maximum_filter not working a expected

I have a problem where I need to detect the local maximum of an image. I used the ndimage.maximum_filter to detect local maximas. Here is a sample code: image = np.array([1,0,6,1,8,9,6,4]) neigh = [1,0,1] filtered_image =…
Boubaker
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C++ Implementation of Gaussian Filter (from scipy.ndimage import gaussian_filter)?

I am trying to replicate the scipy gaussian_filter in C++. from scipy.ndimage import gaussian_filter data = np.zeros([120]) gaussian_filter(data, sigma=0.5) Can any one guide/share similar raw implementation in python. I can implement the same in…
kskill
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How to apply convolution in-place on GPU (in Python)

I need to perform a convolution on an image in-place, and by in-place I mean such that as the structuring element gets applied to different pixels, I want the result of the previous steps to overwrite the image. To put it in context, this is useful…
Blademaster
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