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I am trying to implement convolution by hand in Julia. I'm not too familiar with image processing or Julia, so maybe I'm biting more than I can chew.
Anyway, when I apply this method with a 3*3 edge filter edge = [0 -1 0; -1 4 -1; 0 -1 0] as convolve(img, edge), I am getting an error saying that my values are exceeding the allowed values for the RGBA type.
Code
function convolve(img::Matrix{<:Any}, kernel)
(half_kernel_w, half_kernel_h) = size(kernel) .÷ 2
(width, height) = size(img)
cpy_im = copy(img)
for row ∈ 1+half_kernel_h:height-half_kernel_h
for col ∈ 1+half_kernel_w:width-half_kernel_w
from_row, to_row = row .+ (-half_kernel_h, half_kernel_h)
from_col, to_col = col .+ (-half_kernel_h, half_kernel_h)
cpy_im[row, col] = sum((kernel .* RGB.(img[from_row:to_row, from_col:to_col])))
end
end
cpy_im
end
Error (original)
ArgumentError: element type FixedPointNumbers.N0f8 is an 8-bit type representing 256 values from 0.0 to 1.0, but the values (-0.0039215684f0, -0.007843137f0, -0.007843137f0, 1.0f0) do not lie within this range.
See the READMEs for FixedPointNumbers and ColorTypes for more information.
I am able to identify a simple case where such error may occur (a white pixel surrounded by all black pixels or vice-versa). I tried "fixing" this by attempting to follow the advice here from another stackoverflow question, but I get more errors to the effect of Math on colors is deliberately undefined in ColorTypes, but see the ColorVectorSpace package..
Code attempting to apply solution from the other SO question
function convolve(img::Matrix{<:Any}, kernel)
(half_kernel_w, half_kernel_h) = size(kernel) .÷ 2
(width, height) = size(img)
cpy_im = copy(img)
for row ∈ 1+half_kernel_h:height-half_kernel_h
for col ∈ 1+half_kernel_w:width-half_kernel_w
from_row, to_row = row .+ [-half_kernel_h, half_kernel_h]
from_col, to_col = col .+ [-half_kernel_h, half_kernel_h]
cpy_im[row, col] = sum((kernel .* RGB.(img[from_row:to_row, from_col:to_col] ./ 2 .+ 128)))
end
end
cpy_im
end
Corresponding error
MethodError: no method matching +(::ColorTypes.RGBA{Float32}, ::Int64)
Math on colors is deliberately undefined in ColorTypes, but see the ColorVectorSpace package.
Closest candidates are:
+(::Any, ::Any, !Matched::Any, !Matched::Any...) at operators.jl:591
+(!Matched::T, ::T) where T<:Union{Int128, Int16, Int32, Int64, Int8, UInt128, UInt16, UInt32, UInt64, UInt8} at int.jl:87
+(!Matched::ChainRulesCore.AbstractThunk, ::Any) at ~/.julia/packages/ChainRulesCore/a4mIA/src/tangent_arithmetic.jl:122
Now, I can try using convert etc., but when I look at the big picture, I start to wonder what the idiomatic way of solving this problem in Julia is. And that is my question. If you had to implement convolution by hand from scratch, what would be a good way to do so?
EDIT:
Here is an implementation that works, though it may not be idiomatic
function convolve(img::Matrix{<:Any}, kernel)
(half_kernel_h, half_kernel_w) = size(kernel) .÷ 2
(height, width) = size(img)
cpy_im = copy(img)
# println(Dict("width" => width, "height" => height, "half_kernel_w" => half_kernel_w, "half_kernel_h" => half_kernel_h, "row range" => 1+half_kernel_h:(height-half_kernel_h), "col range" => 1+half_kernel_w:(width-half_kernel_w)))
for row ∈ 1+half_kernel_h:(height-half_kernel_h)
for col ∈ 1+half_kernel_w:(width-half_kernel_w)
from_row, to_row = row .+ (-half_kernel_h, half_kernel_h)
from_col, to_col = col .+ (-half_kernel_w, half_kernel_w)
vals = Dict()
for method ∈ [red, green, blue, alpha]
x = sum((kernel .* method.(img[from_row:to_row, from_col:to_col])))
if x > 1
x = 1
elseif x < 0
x = 0
end
vals[method] = x
end
cpy_im[row, col] = RGBA(vals[red], vals[green], vals[blue], vals[alpha])
end
end
cpy_im
end
First of all, the error
Math on colors is deliberately undefined in ColorTypes, but see the ColorVectorSpace package.
should direct you to read the docs of the ColorVectorSpace package, where you will learn that using ColorVectorSpace will now enable math on RGB types. (The absence of default support it deliberate, because the way the image-processing community treats RGB is colorimetrically wrong. But everyone has agreed not to care, hence the ColorVectorSpace package.)
Second,
ArgumentError: element type FixedPointNumbers.N0f8 is an 8-bit type representing 256 values from 0.0 to 1.0, but the values (-0.0039215684f0, -0.007843137f0, -0.007843137f0, 1.0f0) do not lie within this range.
indicates that you're trying to write negative entries with an element type, N0f8, that can't support such values. Instead of cpy_im = copy(img), consider something like cpy_im = [float(c) for c in img] which will guarantee a floating-point representation that can support negative values.
Third, I would recommend avoiding steps like RGB.(img...) when nothing about your function otherwise addresses whether images are numeric, grayscale, or color. Fundamentally the only operations you need are scalar multiplication and addition, and it's better to write your algorithm generically leveraging only those two properties.
Tim Holy's answer above is correct - keep things simple and avoid relying on third-party packages when you don't need to.
I might point out that another option you may not have considered is to use a different algorithm. What you are implementing is the naive method, whereas many convolution routines using different algorithms for different sizes, such as im2col and Winograd (you can look these two up, I have a website that covers the idea behind both here).
The im2col routine might be worth doing as essentially you can break the routine in several pieces:
Unroll all 'regions' of the image to do a dot-product with the filter/kernel on, and stack them together into a single matrix.
Do a matrix-multiply with the unrolled input and filter/kernel.
Roll the output back into the correct shape.
It might be more complicated overall, but each part is simpler, so you may find this easier to do. A matrix multiply routine is definitely quite easy to implement. For 1x1 (single-pixel) convolutions where the image and filter have the same ordering (i.e. NCHW images and FCHW filter) the first and last steps are trivial as essentially no rolling/unrolling is necessary.
A final word of advice - start simpler and add in the code to handle edge-cases, convolutions are definitely fiddly to work with.
Hope this helps!
Given input signal x (e.g. a voltage, sampled thousand times per second couple of minutes long), I'd like to calculate e.g.
/ this is not q
y[3] = -3*x[0] - x[1] + x[2] + 3*x[3]
y[4] = -3*x[1] - x[2] + x[3] + 3*x[4]
. . .
I'm aiming for variable window length and weight coefficients. How can I do it in q? I'm aware of mavg and signal processing in q and moving sum qidiom
In the DSP world it's called applying filter kernel by doing convolution. Weight coefficients define the kernel, which makes a high- or low-pass filter. The example above calculates the slope from last four points, placing the straight line via least squares method.
Something like this would work for parameterisable coefficients:
q)x:10+sums -1+1000?2f
q)f:{sum x*til[count x]xprev\:y}
q)f[3 1 -1 -3] x
0n 0n 0n -2.385585 1.423811 2.771659 2.065391 -0.951051 -1.323334 -0.8614857 ..
Specific cases can be made a bit faster (running 0 xprev is not the best thing)
q)g:{prev[deltas x]+3*x-3 xprev x}
q)g[x]~f[3 1 -1 -3]x
1b
q)\t:100000 f[3 1 1 -3] x
4612
q)\t:100000 g x
1791
There's a kx white paper of signal processing in q if this area interests you: https://code.kx.com/q/wp/signal-processing/
This may be a bit old but I thought I'd weigh in. There is a paper I wrote last year on signal processing that may be of some value. Working purely within KDB, dependent on the signal sizes you are using, you will see much better performance with a FFT based convolution between the kernel/window and the signal.
However, I've only written up a simple radix-2 FFT, although in my github repo I do have the untested work for a more flexible Bluestein algorithm which will allow for more variable signal length. https://github.com/callumjbiggs/q-signals/blob/master/signal.q
If you wish to go down the path of performing a full manual convolution by a moving sum, then the best method would be to break it up into blocks equal to the kernel/window size (which was based on some work Arthur W did many years ago)
q)vec:10000?100.0
q)weights:30?1.0
q)wsize:count weights
q)(weights$(((wsize-1)#0.0),vec)til[wsize]+) each til count v
32.5931 75.54583 100.4159 124.0514 105.3138 117.532 179.2236 200.5387 232.168.
If your input list not big then you could use the technique mentioned here:
https://code.kx.com/q/cookbook/programming-idioms/#how-do-i-apply-a-function-to-a-sequence-sliding-window
That uses 'scan' adverb. As that process creates multiple lists which might be inefficient for big lists.
Other solution using scan is:
q)f:{sum y*next\[z;x]} / x-input list, y-weights, z-window size-1
q)f[x;-3 -1 1 3;3]
This function also creates multiple lists so again might not be very efficient for big lists.
Other option is to use indices to fetch target items from the input list and perform the calculation. This will operate only on input list.
q) f:{[l;w;i]sum w*l i+til 4} / w- weight, l- input list, i-current index
q) f[x;-3 -1 1 3]#'til count x
This is a very basic function. You can add more variables to it as per your requirements.
I am working with a data-set of patient information and trying to calculate the Propensity Score from the data using MATLAB. After removing features with many missing values, I am still left with several missing (NaN) values.
I get errors due to these missing values, as the values of my cost-function and gradient vector become NaN, when I try to perform logistic regression using the following Matlab code (from Andrew Ng's Coursera Machine Learning class) :
[m, n] = size(X);
X = [ones(m, 1) X];
initial_theta = ones(n+1, 1);
[cost, grad] = costFunction(initial_theta, X, y);
options = optimset('GradObj', 'on', 'MaxIter', 400);
[theta, cost] = ...
fminunc(#(t)(costFunction(t, X, y)), initial_theta, options);
Note: sigmoid and costfunction are working functions I created for overall ease of use.
The calculations can be performed smoothly if I replace all NaN values with 1 or 0. However I am not sure if that is the best way to deal with this issue, and I was also wondering what replacement value I should pick (in general) to get the best results for performing logistic regression with missing data. Are there any benefits/drawbacks to using a particular number (0 or 1 or something else) for replacing the said missing values in my data?
Note: I have also normalized all feature values to be in the range of 0-1.
Any insight on this issue will be highly appreciated. Thank you
As pointed out earlier, this is a generic problem people deal with regardless of the programming platform. It is called "missing data imputation".
Enforcing all missing values to a particular number certainly has drawbacks. Depending on the distribution of your data it can be drastic, for example, setting all missing values to 1 in a binary sparse data having more zeroes than ones.
Fortunately, MATLAB has a function called knnimpute that estimates a missing data point by its closest neighbor.
From my experience, I often found knnimpute useful. However, it may fall short when there are too many missing sites as in your data; the neighbors of a missing site may be incomplete as well, thereby leading to inaccurate estimation. Below, I figured out a walk-around solution to that; it begins with imputing the least incomplete columns, (optionally) imposing a safe predefined distance for the neighbors. I hope this helps.
function data = dnnimpute(data,distCutoff,option,distMetric)
% data = dnnimpute(data,distCutoff,option,distMetric)
%
% Distance-based nearest neighbor imputation that impose a distance
% cutoff to determine nearest neighbors, i.e., avoids those samples
% that are more distant than the distCutoff argument.
%
% Imputes missing data coded by "NaN" starting from the covarites
% (columns) with the least number of missing data. Then it continues by
% including more (complete) covariates in the calculation of pair-wise
% distances.
%
% option,
% 'median' - Median of the nearest neighboring values
% 'weighted' - Weighted average of the nearest neighboring values
% 'default' - Unweighted average of the nearest neighboring values
%
% distMetric,
% 'euclidean' - Euclidean distance (default)
% 'seuclidean' - Standardized Euclidean distance. Each coordinate
% difference between rows in X is scaled by dividing
% by the corresponding element of the standard
% deviation S=NANSTD(X). To specify another value for
% S, use D=pdist(X,'seuclidean',S).
% 'cityblock' - City Block distance
% 'minkowski' - Minkowski distance. The default exponent is 2. To
% specify a different exponent, use
% D = pdist(X,'minkowski',P), where the exponent P is
% a scalar positive value.
% 'chebychev' - Chebychev distance (maximum coordinate difference)
% 'mahalanobis' - Mahalanobis distance, using the sample covariance
% of X as computed by NANCOV. To compute the distance
% with a different covariance, use
% D = pdist(X,'mahalanobis',C), where the matrix C
% is symmetric and positive definite.
% 'cosine' - One minus the cosine of the included angle
% between observations (treated as vectors)
% 'correlation' - One minus the sample linear correlation between
% observations (treated as sequences of values).
% 'spearman' - One minus the sample Spearman's rank correlation
% between observations (treated as sequences of values).
% 'hamming' - Hamming distance, percentage of coordinates
% that differ
% 'jaccard' - One minus the Jaccard coefficient, the
% percentage of nonzero coordinates that differ
% function - A distance function specified using #, for
% example #DISTFUN.
%
if nargin < 3
option = 'mean';
end
if nargin < 4
distMetric = 'euclidean';
end
nanVals = isnan(data);
nanValsPerCov = sum(nanVals,1);
noNansCov = nanValsPerCov == 0;
if isempty(find(noNansCov, 1))
[~,leastNans] = min(nanValsPerCov);
noNansCov(leastNans) = true;
first = data(nanVals(:,noNansCov),:);
nanRows = find(nanVals(:,noNansCov)==true); i = 1;
for row = first'
data(nanRows(i),noNansCov) = mean(row(~isnan(row)));
i = i+1;
end
end
nSamples = size(data,1);
if nargin < 2
dataNoNans = data(:,noNansCov);
distances = pdist(dataNoNans);
distCutoff = min(distances);
end
[stdCovMissDat,idxCovMissDat] = sort(nanValsPerCov,'ascend');
imputeCols = idxCovMissDat(stdCovMissDat>0);
% Impute starting from the cols (covariates) with the least number of
% missing data.
for c = reshape(imputeCols,1,length(imputeCols))
imputeRows = 1:nSamples;
imputeRows = imputeRows(nanVals(:,c));
for r = reshape(imputeRows,1,length(imputeRows))
% Calculate distances
distR = inf(nSamples,1);
%
noNansCov_r = find(isnan(data(r,:))==0);
noNansCov_r = noNansCov_r(sum(isnan(data(nanVals(:,c)'==false,~isnan(data(r,:)))),1)==0);
%
for i = find(nanVals(:,c)'==false)
distR(i) = pdist([data(r,noNansCov_r); data(i,noNansCov_r)],distMetric);
end
tmp = min(distR(distR>0));
% Impute the missing data at sample r of covariate c
switch option
case 'weighted'
data(r,c) = (1./distR(distR<=max(distCutoff,tmp)))' * data(distR<=max(distCutoff,tmp),c) / sum(1./distR(distR<=max(distCutoff,tmp)));
case 'median'
data(r,c) = median(data(distR<=max(distCutoff,tmp),c),1);
case 'mean'
data(r,c) = mean(data(distR<=max(distCutoff,tmp),c),1);
end
% The missing data in sample r is imputed. Update the sample
% indices of c which are imputed.
nanVals(r,c) = false;
end
fprintf('%u/%u of the covariates are imputed.\n',find(c==imputeCols),length(imputeCols));
end
To deal with missing data you can use one of the following three options:
If there are not many instances with missing values, you can just delete the ones with missing values.
If you have many features and it is affordable to lose some information, delete the entire feature with missing values.
The best method is to fill some value (mean, median) in place of missing value. You can calculate the mean of the rest of the training examples for that feature and fill all the missing values with the mean. This works out pretty well as the mean value stays in the distribution of your data.
Note: When you replace the missing values with the mean, calculate the mean only using training set. Also, store that value and use it to change the missing values in the test set also.
If you use 0 or 1 to replace all the missing values then the data may get skewed so it is better to replace the missing values by an average of all the other values.
Let's suppose I have database with thousands of images with different forms and sizes (smaller than 100 x 100px) and it's guaranted that every of images shows only one object - symbol, logo, road sign, etc. I would like to be able to take any image ("my_image.jpg") from the Internet and answer the question "Do my_image contains any object (object can be resized, but without deformations) from my database?" - let's say with 95% reliability. To simplify my_images will have white background.
I was trying use imagehash (https://github.com/JohannesBuchner/imagehash), which would be very helpful, but to get rewarding results I think I have to calculate (almost) every possible hash of my_image - the reason is I don't know object size and location on my_image:
hash_list = []
MyImage = Image.open('my_image.jpg')
for x_start in range(image_width):
for y_start in range(image_height):
for x_end in range(x_start, image_width):
for y_end in range(y_start, image_height):
hash_list.append(imagehash.phash(MyImage.\
crop(x_start, y_start, x_end, y_end)))
...and then try to find similar hash in database, but when for example image_width = image_height = 500 this loops and searching will take ages. Of course I can optymalize it a little bit but it still looks like seppuku for bigger images:
MIN_WIDTH = 30
MIN_HEIGHT = 30
STEP = 2
hash_list = []
MyImage = Image.open('my_image.jpg')
for x_start in range(0, image_width - MIN_WIDTH, STEP):
for y_start in range(0, image_height - MIN_HEIGHT, STEP):
for x_end in range(x_start + MIN_WIDTH, image_width, STEP):
for y_end in range(y_start + MIN_HEIGHT, image_height, STEP):
hash_list.append(...)
I wonder if there is some nice way to define which parts of my_image are profitable to calculate hashes - for example cutting edges looks like bad idea. And maybe there is an easier solve? It will be great if the program could give the answer in max 20 minutes. I would be gratefull for any advice.
PS: sorry for my English :)
This looks like an image retrieval problem to me. However, in your case, you are more interested in a binary YES / NO answer which tells if the input image (my_image.jpg) is of an object which is present in your database.
The first thing which I can suggest is that you can resize all the images (including input) to a fixed size, say 100 x 100. But if an object in some image is very small or is present in a specific region of image (for e.g., top left) then resizing can make things worse. However, it was not clear from your question that how likely this is in you case.
About your second question for finding out the location of object, I think you were considering this because your input images are of large size, such as 500 x 500? If so, then resizing is better idea. However, if you asked this question because objects a localized to particular regions in images, then I think you can compute a gradient image which will help you to identify background regions as follows: since background has no variation (complete white) gradient values will be zero for pixels belonging to background regions.
Rather than calculating and using image hash, I suggest you to read about bag-of-visual-words (for e.g., here) based approaches for object categorization. Although your aim is not to categorize objects, but it will help you come up with a different approach to solve your problem.
After all I found solution that looks really nice for me and maybe it will be useful for someone else:
I'm using SIFT to detect "best candidates" from my_image:
def multiscale_template_matching(template, image):
results = []
for scale in np.linspace(0.2, 1.4, 121)[::-1]:
res = imutils.resize(image, width=int(image.shape[1] * scale))
r = image.shape[1] / float(res.shape[1])
if res.shape[0] < template.shape[0] or res.shape[1] < template.shape[1];
break
## bigger correlation <==> better matching
## template_mathing uses SIFT to return best correlation and coordinates
correlation, (x, y) = template_matching(template, res)
coordinates = (x * r, y * r)
results.appent((correlation, coordinates, r))
results.sort(key=itemgetter(0), reverse=True)
return results[:10]
Then for results I'm calculating hashes:
ACCEPTABLE = 10
def find_best(image, template, candidates):
template_hash = imagehash.phash(template)
best_result = 50 ## initial value must be greater than ACCEPTABLE
best_cand = None
for cand in candidates:
cand_hash = get_hash(...)
hash_diff = template_hash - cand_hash
if hash_diff < best_result:
best_result = hash_diff
best_cand = cand
if best_result <= ACCEPTABLE:
return best_cand, best_result
else:
return None, None
If result < ACCEPTABLE, I'm almost sure the answer is "GOT YOU!" :) This solve allows me to compare my_image with 1000 of objects in 7 minutes.
I'm trying to develop an application using SOM in analyzing data. However, after finishing training, I cannot find a way to visualize the result. I know that U-Matrix is one of the method but I cannot understand it properly. Hence, I'm asking for a specific and detail example how to construct U-Matrix.
I also read an answer at U-matrix and self organizing maps but it only refers to 1 row map, how about 3x3 map? I know that for 3x3 map:
m(1) m(2) m(3)
m(4) m(5) m(6)
m(7) m(8) m(9)
a 5x5 matrix must me created:
u(1) u(1,2) u(2) u(2,3) u(3)
u(1,4) u(1,2,4,5) u(2,5) u(2,3,5,6) u(3,6)
u(4) u(4,5) u(5) u(5,6) u(6)
u(4,7) u(4,5,7,8) u(5,8) u(5,6,8,9) u(6,9)
u(7) u(7,8) u(8) u(8,9) u(9)
but I don't know how to calculate u-weight u(1,2,4,5), u(2,3,5,6), u(4,5,7,8) and u(5,6,8,9).
Finally, after constructing U-Matrix, is there any way to visualize it using color, e.g. heat map?
Thank you very much for your time.
Cheers
I don't know if you are still interested in this but I found this link
http://www.uni-marburg.de/fb12/datenbionik/pdf/pubs/1990/UltschSiemon90
which explains very speciffically how to calculate the U-matrix.
Hope it helps.
By the way, the site were I found the link has several resources referring to SOMs I leave it here in case anyone is interested:
http://www.ifs.tuwien.ac.at/dm/somtoolbox/visualisations.html
The essential idea of a Kohonen map is that the data points are mapped to a
lattice, which is often a 2D rectangular grid.
In the simplest implementations, the lattice is initialized by creating a 3D
array with these dimensions:
width * height * number_features
This is the U-matrix.
Width and height are chosen by the user; number_features is just the number
of features (columns or fields) in your data.
Intuitively this is just creating a 2D grid of dimensions w * h
(e.g., if w = 10 and h = 10 then your lattice has 100 cells), then
into each cell, placing a random 1D array (sometimes called "reference tuples")
whose size and values are constrained by your data.
The reference tuples are also referred to as weights.
How is the U-matrix rendered?
In my example below, the data is comprised of rgb tuples, so the reference tuples
have length of three and each of the three values must lie between 0 and 255).
It's with this 3D array ("lattice") that you begin the main iterative loop
The algorithm iteratively positions each data point so that it is closest to others similar to it.
If you plot it over time (iteration number) then you can visualize cluster
formation.
The plotting tool i use for this is the brilliant Python library, Matplotlib,
which plots the lattice directly, just by passing it into the imshow function.
Below are eight snapshots of the progress of a SOM algorithm, from initialization to 700 iterations. The newly initialized (iteration_count = 0) lattice is rendered in the top left panel; the result from the final iteration, in the bottom right panel.
Alternatively, you can use a lower-level imaging library (in Python, e.g., PIL) and transfer the reference tuples onto the 2D grid, one at a time:
for y in range(h):
for x in range(w):
img.putpixel( (x, y), (
SOM.Umatrix[y, x, 0],
SOM.Umatrix[y, x, 1],
SOM.Umatrix[y, x, 2])
)
Here img is an instance of PIL's Image class. Here the image is created by iterating over the grid one pixel at a time; for each pixel, putpixel is called on img three times, the three calls of course corresponding to the three values in an rgb tuple.
From the matrix that you create:
u(1) u(1,2) u(2) u(2,3) u(3)
u(1,4) u(1,2,4,5) u(2,5) u(2,3,5,6) u(3,6)
u(4) u(4,5) u(5) u(5,6) u(6)
u(4,7) u(4,5,7,8) u(5,8) u(5,6,8,9) u(6,9)
u(7) u(7,8) u(8) u(8,9) u(9)
The elements with single numbers like u(1), u(2), ..., u(9) as just the elements with more than two numbers like u(1,2,4,5), u(2,3,5,6), ... , u(5,6,8,9) are calculated using something like the mean, median, min or max of the values in the neighborhood.
It's a nice idea calculate the elements with two numbers first, one possible code for that is:
for i in range(self.h_u_matrix):
for j in range(self.w_u_matrix):
nb = (0,0)
if not (i % 2) and (j % 2):
nb = (0,1)
elif (i % 2) and not (j % 2):
nb = (1,0)
self.u_matrix[(i,j)] = np.linalg.norm(
self.weights[i //2, j //2] - self.weights[i //2 +nb[0], j // 2 + nb[1]],
axis = 0
)
In the code above the self.h_u_matrix = self.weights.shape[0]*2 - 1 and self.w_u_matrix = self.weights.shape[1]*2 - 1 are the dimensions of the U-Matrix. With that said, for calculate the others elements it's necessary obtain a list with they neighboors and apply a mean for example. The following code implements that's idea:
for i in range(self.h_u_matrix):
for j in range(self.w_u_matrix):
if not (i % 2) and not (j % 2):
nodelist = []
if i > 0:
nodelist.append((i-1,j))
if i < 4:
nodelist.append((i+1, j))
if j > 0:
nodelist.append((i,j -1))
if j < 4:
nodelist.append((i,j+1))
meanlist = [self.u_matrix[u_node] for u_node in nodelist]
self.u_matrix[(i,j)] = np.mean(meanlist)
elif (i % 2) and (j % 2):
meanlist = [
(i - 1, j),
(i + 1, j),
(i, j - 1),
(i, j + 1)]
self.u_matrix[(i,j)] = np.mean(meanlist)