Problem in skimage rgb2hed when applied to part of a matrix-CodePudding

I am trying to convert an image from RBG to HED using the rgb2hed function from skimage. My image is very big and if I just try and put the whole thing into the rgb2hed function then I run out of memory. To get around this I have written some code to split the image into sections and apply rgb2hed to each section, but I get very different results when doing so. Getting a matrix of almost all 0's when splitting up the function. Minimal reprex given below.

import numpy as np
from skimage.color import rgb2hed

np.random.seed(42)
sample = np.random.randint(0, 255, size=(100, 100, 3))

n_splits = 10
x_split_inds = np.linspace(0, sample.shape[0], n_splits   1, dtype=int)
        
for x in range(len(x_split_inds) - 1):
    x_start = x_split_inds[x]
    x_end = x_split_inds[x   1]
    sample[x_start:x_end, :, :] = rgb2hed(sample[x_start:x_end, :, :])
        
print(rgb2hed(sample))

print()

print(sample)

This is the first matrix I get

[[[1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  ...
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]]

 [[1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  ...
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]]

 [[1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  ...
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]]

 ...

 [[1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  ...
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]]

 [[1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  ...
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]]

 [[1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  ...
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]
  [1.21016731 0.         0.88195046]]]

and this is the second

[[[1 0 0]
  [1 0 0]
  [1 0 0]
  ...
  [1 0 0]
  [1 0 0]
  [1 0 0]]

 [[1 0 0]
  [1 0 0]
  [1 0 0]
  ...
  [1 0 0]
  [1 0 0]
  [1 0 0]]

 [[1 0 0]
  [1 0 0]
  [1 0 0]
  ...
  [1 0 0]
  [1 0 0]
  [1 0 0]]

 ...

 [[1 0 0]
  [1 0 0]
  [1 0 0]
  ...
  [1 0 0]
  [1 0 0]
  [1 0 0]]

 [[1 0 0]
  [1 0 0]
  [1 0 0]
  ...
  [1 0 0]
  [1 0 0]
  [1 0 0]]

 [[1 0 0]
  [1 0 0]
  [1 0 0]
  ...
  [1 0 0]
  [1 0 0]
  [1 0 0]]]

CodePudding user response：

The issue is related to dtype mismatching:

The dtype of sample = np.random.randint(...) is 'int32'
The dtype of rgb2hed(...) is float64

When updating a slice of NumPy array, the data is converted to the type of that updated NumPy array.
The expression sample[x_start:x_end, :, :] = rgb2hed(...) automatically converts from float64 to 'int32' type.
The cast from float64 to 'int32' converts 1.21016731 to 1 and 0.88195046 to 0...

We may solve it by avoiding "in place" processing:

output_sample = np.zeros((100, 100, 3), np.float64)  # Allocate output_sample
...
output_sample[x_start:x_end, :, :] = rgb2hed(sample[x_start:x_end, :, :])

Does it require too much RAM?

We may also solve it by converting type of sample to np.float64:

import numpy as np
from skimage.color import rgb2hed

np.random.seed(42)
sample = np.random.randint(0, 255, size=(4, 4, 3)).astype(np.uint8)
sample_copy = sample.copy()
sample = sample.astype(np.float64) / 255.0  # Divide by 255, because rgb2hed expects range [0, 1] for float64 type

n_splits = 4 #10
x_split_inds = np.linspace(0, sample.shape[0], n_splits   1, dtype=int)

for x in range(len(x_split_inds) - 1):
    x_start = x_split_inds[x]
    x_end = x_split_inds[x   1]
    sample[x_start:x_end, :, :] = rgb2hed(sample[x_start:x_end, :, :])

print(rgb2hed(sample_copy))

print()

print(sample)

Output of print(rgb2hed(sample_copy)):

[[[-0.46103368  0.07251299 -0.31709355]
  [-0.34690713  0.05235859 -0.33691324]
  [-0.57147719  0.26278779 -0.31203784]
  [-0.43647159  0.10270586 -0.43322983]]

...

Output of print(sample)):

[[[-0.46103368  0.07251299 -0.31709355]
  [-0.34690713  0.05235859 -0.33691324]
  [-0.57147719  0.26278779 -0.31203784]
  [-0.43647159  0.10270586 -0.43322983]]

Saving memory:

Each float64 elements is 8 bytes in RAM.
For saving memory space, we may use float32 type that is only 4 bytes in RAM.
Example: sample = np.random.randint(0, 255, size=(4, 4, 3)).astype(np.float32) / 255.0...

For saving more RAM in expense of accuracy, we may use int16 type with scaling and rounding.

Example:

import numpy as np
from skimage.color import rgb2hed
    
np.random.seed(42)
sample = np.random.randint(0, 255, size=(4, 4, 3)).astype(np.uint8)
sample_copy = sample.copy()
sample = sample.astype(np.int16)  # Convert to int16 (used for "in place" processing).
    
n_splits = 4 #10
x_split_inds = np.linspace(0, sample.shape[0], n_splits   1, dtype=int)
            
for x in range(len(x_split_inds) - 1):
    x_start = x_split_inds[x]
    x_end = x_split_inds[x   1]
    
    # Scale by 10000 and convert to int16 with rounding and clipping:
    sample[x_start:x_end, :, :] = np.round(rgb2hed(sample[x_start:x_end, :, :].astype(np.uint8))*10000).clip(-32768, 32767).astype(np.int16)
            
print(rgb2hed(sample_copy))
    
print()
    
print(sample*1e-4)  # Divide by 10000

Output of print(sample*1e-4):

[[[-0.461   0.0725 -0.3171]
  [-0.3469  0.0524 -0.3369]
  [-0.5715  0.2628 -0.312 ]
  [-0.4365  0.1027 -0.4332]]

As you can see, the accuracy is reduced to 4 decimal digits.