Image_Analysis.Image_Processing¶
- class Image_Analysis.Image_Processing(image, skeleton, spacing, viewer)¶
Bases:
object
A class that will perform image processing operations.
…
- image: ndarray
an image to be processed
- skeleton: ndarray
the skeleton of the image to be processed
- spacing: float
the z spacing of the image
- viewer: napari.viewer
the viewer to be used to view the image layers in 3D
- skeleton_dilation(dilation=10)
Dilates the skeleton of the image as many times as you indicate. Crops the image to only the region of interest
- get_cropped()
returns the cropped image
- median_filter(image, cube_width)
Performs the median filter operation from skimage on the image passed. Uses the cube width provided.
- background_subtract(image, gauss_sigma)
Subtracts the background from the passed in image. Uses the gaussian filter from skimage on the image passed in.
- sobel(image)
Performs the sobel transformation on the passed in image using the sobel filter from skimage
- ahe_contrast(image)
Performs the adaptive histogram equalization on the passed in image using the equalize_adapthist from skimage. Multiplies the image to the image passed in to improve the contrast
- rescaled_intensity(image, vmin, vmax)
Performs the rescale intensity operation on the passed in image using the operation from skimage
- multiotsu_mask(image, classes)
Performs the multiotsu mask operation using threshold_multiots from skimage using the number of classes specified
- otsu_mask(image)
Performs the otsu mask operation using threshold_otsu from skimage
- li_mask(image)
Performs the li mask operation using threshold_li from skimage
- yen_mask(image)
Performs the yen mask operation using threshold_yen from skimage
- default_morphology(image)
Uses a default morphology operation consisting of closing and dilation morphological operations.
- closing(image)
Performs the closing operation on the provided mask
- opening(image)
Performs the opening operation on the provided mask
- dilation(image)
Performs the dilation operation on the provided mask
- erosion(image)
Performs the erosion operation on the provided mask
- labels(image)
Generates labels based on the mask created
- region_props(labels, intensity_image, properties)
Generates the region properties from the labels depending on the properties selected
- __init__(image, skeleton, spacing, viewer)¶
- imagendarray
The image to use for analysis
- skeletonndarray
The binary image used to identify the area of interest of the image
- spacingfloat
The z spacing of the images being passed
- viewernapari viewer
The viewer to use for visualization of the images
Methods
__init__
(image, skeleton, spacing, viewer)Parameters image ndarray The image to use for analysis skeleton ndarray The binary image used to identify the area of interest of the image spacing float The z spacing of the images being passed viewer napari viewer The viewer to use for visualization of the images
ahe_contrast
([image])Performs the adaptive histogram equalization operation and multiplies the provided image and the AHE image
background_subtract
([image, gauss_sigma])Subtracts the background from the image provided
closing
([mask])Performs the closing morphology operation from skimage
Performs the default morphology operations: Binary Dilation and Binary Closing from skimage
dilation
([mask])Performs the dilation morphology operation from skimage
erosion
([mask])Performs the erosion morphology operation from skimage
Returns the cropped image used in the analysis.
labels
([mask])Generates labels based on the provided mask
li_mask
([image])Performs the li mask operation from skimage
median_filter
([image, cube_width])Performs the median filter operation from skimage on the image passed.
multiotsu_mask
([image, classes])Performs the multiotsu mask operation from skimage
opening
([mask])Performs the opening morphology operation from skimage
otsu_mask
([image])Performs the otsu mask operation from skimage
region_props
(labels, intensity_image, properties)Generates a dictionary of properties requested for the labels provided
rescaled_intensity
([image, vmin, vmax])Rescales the intensity of the image using the intensities provided
skeleton_dilation
([dilation])Dilates the skeleton provide.
sobel
([image, mask])Performs the sobel transformation on a given image
yen_mask
([image])Performs the yen mask operation
- ahe_contrast(image=None)¶
Performs the adaptive histogram equalization operation and multiplies the provided image and the AHE image
- imagendarray
The image to apply the operation to
- final_contrast
An ndarray of of the same size as the input after the AHE and multiplication operations have been applied
- background_subtract(image=None, gauss_sigma=7)¶
Subtracts the background from the image provided
If the argument gauss_sigma isn’t provided, the default value of 7 is passed.
- imagendarray
The image to apply the operation to
- gauss_sigmaint, optional
The sigma used for the gaussian operation (default is 7)
- subtract
The image with the same shape as the input image after the subtraction has been applied
- closing(mask=None)¶
Performs the closing morphology operation from skimage
- maskndarray
The mask to perform the morph operation on
- mask_morph
The final mask of type ndarray after the morphology operation is performed
- default_morphology()¶
Performs the default morphology operations: Binary Dilation and Binary Closing from skimage
- mask_closing
an array of the same shape as the input image. The final mask after the morphology operations are performed
- final_mask
an array of the same shape as the input image. The final mask isolated only to the area within the skeleton
- dilation(mask=None)¶
Performs the dilation morphology operation from skimage
- maskndarray
The mask to perform the morph operation on
- mask_morph
The final mask of type ndarray after the morphology operation is performed
- erosion(mask=None)¶
Performs the erosion morphology operation from skimage
- maskndarray
The mask to perform the morph operation on
- mask_morph
The final mask of type ndarray after the morphology operation is performed
- get_cropped()¶
Returns the cropped image used in the analysis.
- labels(mask=None)¶
Generates labels based on the provided mask
- maskndarray
The mask to perform the morph operation on
- boundaries
an array of the same shape as the input
- label_image
an array with labels of the same shape as the input. All connected areas are under one label
- li_mask(image=None)¶
Performs the li mask operation from skimage
- imagendarray
The image to apply the operation to
- mask_morph
an array with the same shaqpe as the input after the mask has been applied
- median_filter(image=None, cube_width=3)¶
Performs the median filter operation from skimage on the image passed.
If the argument cube_width isn’t provided, the default value of 3 is passed.
- imagendarray
The image to apply the operation to
- cube_widthint, optional
The width of the cube used as the footprint for the filter (default is 3)
- median
The image after the median filter has been applied
- multiotsu_mask(image=None, classes=2)¶
Performs the multiotsu mask operation from skimage
If the argument classes isn’t provided, the default value of 2 is passed.
- imagendarray
The image to apply the operation to
- classesint, optional
The number of classes in the image (default is 2)
- mask_morph
an array with the same shaqpe as the input after the mask has been applied
- opening(mask=None)¶
Performs the opening morphology operation from skimage
- maskndarray
The mask to perform the morph operation on
- mask_morph
The final mask of type ndarray after the morphology operation is performed
- otsu_mask(image=None)¶
Performs the otsu mask operation from skimage
- imagendarray
The image to apply the operation to
- mask_morph
an array with the same shaqpe as the input after the mask has been applied
- region_props(labels, intensity_image, properties)¶
Generates a dictionary of properties requested for the labels provided
- labelsndarray
The labeled image to generate the properties for
- intensity_imagendarray
The image to reference intensity values for
- propertieslist
A list of strings with the properties desired
- props
a dictionary with the properties generated for each label
- rescaled_intensity(image=None, vmin=0.5, vmax=99.5)¶
Rescales the intensity of the image using the intensities provided
If the arguments vmin and vmax aren’t provided, the default values of 0 and 255 are passed.
- imagendarray
The image to apply the operation to
- vminint, optional
The minimum intensity value allowed for the image (default is 0)
- vmaxint, optional
The maximum intensity value allowed for the image (default is 255)
- final_contrast
An ndarray of of the same size as the input after the rescaled intensity operation has been applied
- skeleton_dilation(dilation=10)¶
Dilates the skeleton provide.
If the argument dilation isn’t passed in, the default dilation value is used. Crops the image to be analyzed to keep the image size small.
- dilationint, optional
The amount of dilation applied to the skeleton (default is 10)
- ROI
An array for the cropped image with the dimensions of the skeleton
- cropped_skeleton
An array for the cropped skeleton with the size of the skeleton
- sobel(image=None, mask=None)¶
Performs the sobel transformation on a given image
If the argument mask isn’t provided, the mask will not be used.
- imagendarray
The image to apply the operation to
- maskndarray, optional
mask to isolate the sobel filter to (default is None)
- sobel
The image of same shape as the input after the sobel filter has been applied
- yen_mask(image=None)¶
Performs the yen mask operation
- imagendarray
The image to apply the operation to
- mask_morph
an array with the same shaqpe as the input after the mask has been applied