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remove max_val param from threshold.texture() #1219

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merged 2 commits into from
Jul 6, 2023
Merged

remove max_val param from threshold.texture() #1219

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48ed9ba
remove max_val param from threshold.texture()
afinit Jul 6, 2023
ca0e3a5
Merge branch 'release-4.0' into release-4.0-texture-max-val
nfahlgren Jul 6, 2023
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6 changes: 2 additions & 4 deletions docs/texture_threshold.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ Creates a binary image from a grayscale image using [skimage](http://scikit-imag
texture calculation for thresholding.


**plantcv.threshold.texture**(*gray_img, ksize, threshold, offset=3, texture_method='dissimilarity', borders='nearest', max_value=255*)
**plantcv.threshold.texture**(*gray_img, ksize, threshold, offset=3, texture_method='dissimilarity', borders='nearest'*)

**returns** thresholded/binary image

Expand All @@ -17,7 +17,6 @@ texture calculation for thresholding.
‘contrast’, ‘dissimilarity’ (default), ‘homogeneity’, ‘ASM’, ‘energy’,
or ‘correlation’. For equations of different features see [this link](http://scikit-image.org/docs/dev/api/skimage.feature.html#greycoprops)
- borders - How the array borders are handled, either ‘reflect’, ‘constant’, ‘nearest’ (default), ‘mirror’, or ‘wrap’
- max_value - Value to apply above threshold (usually 255 = white)
- **Context:**
- Used to threshold based on texture
- **Note:**
Expand All @@ -40,8 +39,7 @@ pcv.params.debug = "plot"

# Create binary image from a gray image based on texture values.
texture_img = pcv.threshold.texture(gray_img, ksize=6, threshold=7, offset=3,
texture_method='dissimilarity', borders='nearest',
max_value=255)
texture_method='dissimilarity', borders='nearest')

```

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7 changes: 4 additions & 3 deletions docs/updating.md
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Expand Up @@ -1057,12 +1057,13 @@ pages for more details on the input and output variable types.
#### plantcv.threshold.saturation

* pre v3.8: NA
* post v3.8: bin_img = **plantcv.threshold.saturation**(*rgb_img, threshold=255, channel="any")
* post v3.8: bin_img = **plantcv.threshold.saturation**(*rgb_img, threshold=255, channel="any"*)
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noticed this missing *


#### plantcv.threshold.texture_filter
#### plantcv.threshold.texture
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the texture function name was mismatched here. I took a look at the git history and it looks like it's always been mismatched, so i changed it here. happy to adjust if needed


* pre v3.0: NA
* post v3.0: bin_img = **plantcv.threshold.texture_filter**(*gray_img, ksize, threshold, offset=3, texture_method='dissimilarity', borders='nearest', max_value=255*)
* post v3.0: bin_img = **plantcv.threshold.texture**(*gray_img, ksize, threshold, offset=3, texture_method='dissimilarity', borders='nearest', max_value=255*)
* post v4.0: bin_img = **plantcv.threshold.texture**(*gray_img, ksize, threshold, offset=3, texture_method='dissimilarity', borders='nearest'*)

#### plantcv.threshold.triangle

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5 changes: 1 addition & 4 deletions plantcv/plantcv/threshold/threshold_methods.py
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Expand Up @@ -286,8 +286,7 @@ def triangle(gray_img, object_type="light", xstep=1):
return bin_img


def texture(gray_img, ksize, threshold, offset=3, texture_method='dissimilarity', borders='nearest',
max_value=255):
def texture(gray_img, ksize, threshold, offset=3, texture_method='dissimilarity', borders='nearest'):
"""Creates a binary image from a grayscale image using skimage texture calculation for thresholding.
This function is quite slow.

Expand All @@ -302,7 +301,6 @@ def texture(gray_img, ksize, threshold, offset=3, texture_method='dissimilarity'
scikit-image.
borders = How the array borders are handled, either 'reflect',
'constant', 'nearest', 'mirror', or 'wrap'
max_value = Value to apply above threshold (usually 255 = white)

Returns:
bin_img = Thresholded, binary image
Expand All @@ -313,7 +311,6 @@ def texture(gray_img, ksize, threshold, offset=3, texture_method='dissimilarity'
:param offset: int
:param texture_method: str
:param borders: str
:param max_value: int
:return bin_img: numpy.ndarray
"""
# Function that calculates the texture of a kernel
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3 changes: 1 addition & 2 deletions tests/plantcv/threshold/test_threshold_methods.py
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Expand Up @@ -176,8 +176,7 @@ def test_texture(threshold_test_data):
gray_img = cv2.imread(threshold_test_data.small_gray_img, -1)
# Subset input data
gray_img = gray_img[150:200, 200:250]
binary_img = texture(gray_img, ksize=6, threshold=7, offset=3, texture_method='dissimilarity', borders='nearest',
max_value=255)
binary_img = texture(gray_img, ksize=6, threshold=7, offset=3, texture_method='dissimilarity', borders='nearest')
# Assert that the output image has the dimensions of the input image and is binary
assert gray_img.shape == binary_img.shape and np.array_equal(np.unique(binary_img), np.array([0, 255]))

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