Questions tagged [scipy.ndimage]
23 questions
4
votes
1 answer
2D local maxima and minima in Python
I have a data frame, df, representing a correlation matrix, with this heatmap with example extrema. Every point has, obviously, (x,y,value):
I am looking into getting the local extrema. I looked into argrelextrema, I tried it on individual rows and…
Adam
- 3,407
- 2
- 29
- 52
2
votes
2 answers
Using regionprops in Python
I am trying to analyze greyscale TIFF stacks, in which a given frame will look like this. I filter it (using Gaussian blur), and then binarize it (using Otsu's method for threshold).
MATLAB code, which works great:
image_conncomp =…
oofin
- 120
- 1
- 2
- 11
1
vote
1 answer
Using shift() on MNIST data. Getting strange results
I am trying to use the shift() function on MNIST images.
Somehow, though, when I look at the original data and the shifted data, it looks like the shifted values that were exactly zero are becoming really small nonzero values instead of zero. An…
THill3
- 79
- 4
1
vote
1 answer
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
- 8,418
- 10
- 72
- 132
1
vote
0 answers
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
- 181
- 1
- 11
0
votes
0 answers
Resampling/Interpolation of 3D Multi-class Mask without changing label values/scipy.ndimage.interpolation or RegularGridInterpolator
I have a 3D mask volume L with the following:
print(L.shape)
(170, 256, 256)
print("L: ", np.unique(L))
L: [0 1 2 3 4 5 6 7 8]
I want to downsample and then upsample the mask to its original size keeping the label values the same.
Failed…
banikr
- 11
- 4
0
votes
1 answer
How does maximum_filter1d work in scipy? How does cval, origin, mode parameter affect it?
Documentation link:
https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.maximum_filter1d.html#r4df4f294a847-2
The example given in the documentation is,
>>> maximum_filter1d([2, 8, 0, 4, 1, 9, 9, 0,1], size=3)
array([8, 8, 8, 4, 9, 9,…
Sanjay S
- 13
- 3
0
votes
0 answers
to use scipy.ndimage.gaussian_filter for 2d array of prmsl data and plot without breaking near 0 meridian
Good Day! I have a problem with ploting prmsl data after scipy.ndimage.gaussian_filter (sigma=2) near the 0 meridian. I have my longitude data like a np.arange(0,359.5,0.5) - after addcyclic np.arange(0,360,0.5), and when i try plot isobars i get…
0
votes
0 answers
How to perform labelling with ndimage without running out of memory?
For Geospatial analysis I created a clump function that will identify patches of deforestation in a .tif file. The deforestation events are labelled as 1 the rest is background (0)
I created the following function :
import rasterio as rio
from…
Pierrick Rambaud
- 870
- 9
- 31
0
votes
0 answers
Reshape changes the range of scipy.ndimage.rotate
import scipy.ndimage as snd
np.max(snd.rotate(roi_old, Rotangle))
Out[166]: 1.642610287502076
np.max(snd.rotate(roi_old, Rotangle,reshape=False))
Out[167]: 1.6771061860083012
Note that the smaller image yields greater max value, meaning that it is…
Leon
- 3
- 3
0
votes
1 answer
Librosa ModuleNotFoundError: No module named 'scipy.ndimage'
I am trying to use librosa library but whatever I do I take the following massage (Using Python 3.8 and PyCharm on Anaconda)
What I am trying:
import librosa
import IPython.display as ipd
sr = 22050 # sample rate
T = 5.0 # seconds
t =…
UIAT
- 1
0
votes
2 answers
Use a custom kernel / image filter to find a specific pattern in a 2d array
Given an image im,
>>> np.random.seed(0)
>>> im = np.random.randint(0, 100, (10,5))
>>> im
array([[44, 47, 64, 67, 67],
[ 9, 83, 21, 36, 87],
[70, 88, 88, 12, 58],
[65, 39, 87, 46, 88],
[81, 37, 25, 77, 72],
[ 9,…
Markus Dutschke
- 5,003
- 2
- 34
- 38
0
votes
0 answers
scipy.ndimage RuntimeError: coordinate array data type not supported
I was using the method scipy.ndimage.map_coordinates, and it seemed to work fine in my code. However, when I called it from another method, it gave me a RuntimeError: coordinate array data type not supported.
Here is the traceback:
Traceback (most…
Eboyer
- 23
- 5
0
votes
1 answer
How to set different stride with uniform filter in scipy?
I am using the following code to run uniform filter on my data:
from scipy.ndimage.filters import uniform_filter
a = np.arange(1000)
b = uniform_filter(a, size=10)
The filter right now semms to work as if a stride was set to size // 2.
How to…
JAV
- 259
- 2
- 8
0
votes
1 answer
How to get the list of values of scipy.ndimage gaussian_filter?
I'm trying to get a list of values when I use a gaussian_filter.
I read a file with a column and float values. Example:
0.8457
0.0
0.505
etc...
My script is this:
#!/usr/bin/env python
import numpy as np
from scipy.ndimage.filters import…
Hdez
- 129
- 6