How do I select only the area inside contours?
I'm implementing a Foreground Extraction algorithm in Python which creates a mask and contours of the foreground of the image.
However, I'm working with SVS files (tif files with less properties) and after extracting the foreground and I still need to tile it because my image has gigapixel resolution. I'm using openCV to handle these images.
This is my getContours function:
def getContours(oslIm, level=2):
"""
Loads the requested level from oslIm and returns identified contours in the slide.
:param oslIm: openslide image
:param level: level from which to load the data (usually 2)
:return: contours
"""
image_array = np.asarray(oslIm.read_region((1, 1), level, oslIm.level_dimensions[level]), dtype=np.uint8)
image = image_array[:, :, 0:3]
mask = segment(image)
_, contours, _ = cv2.findContours(mask, mode=cv2.RETR_EXTERNAL, method=cv2.CHAIN_APPROX_SIMPLE)
return contours
I read my image at the desired level, I extract the mask of the foreground and then the contours.
This is the process:
Input Image:
Mask:
Final Image:
Everything is good, I have the contours and the final image.
But as I said before I want to crop my image so I can apply my
sample_and_store_patches_by_row(
file_name,
pixel_overlap,
patch_size=512,
level=17,
)
and tile my image in 512x512 images. For that I need to get inside the contours and tile the whats inside of it.
I'm struggling with this for days, any help would be highly appreciated.
Thank you
python opencv
asked Nov 13 at 5:33
Luís Costa
283217
add a comment |
I'm implementing a Foreground Extraction algorithm in Python which creates a mask and contours of the foreground of the image.
However, I'm working with SVS files (tif files with less properties) and after extracting the foreground and I still need to tile it because my image has gigapixel resolution. I'm using openCV to handle these images.
This is my getContours function:
def getContours(oslIm, level=2):
"""
Loads the requested level from oslIm and returns identified contours in the slide.
:param oslIm: openslide image
:param level: level from which to load the data (usually 2)
:return: contours
"""
image_array = np.asarray(oslIm.read_region((1, 1), level, oslIm.level_dimensions[level]), dtype=np.uint8)
image = image_array[:, :, 0:3]
mask = segment(image)
_, contours, _ = cv2.findContours(mask, mode=cv2.RETR_EXTERNAL, method=cv2.CHAIN_APPROX_SIMPLE)
return contours
I read my image at the desired level, I extract the mask of the foreground and then the contours.
This is the process:
Input Image:
Mask:
Final Image:
Everything is good, I have the contours and the final image.
But as I said before I want to crop my image so I can apply my
sample_and_store_patches_by_row(
file_name,
pixel_overlap,
patch_size=512,
level=17,
)
and tile my image in 512x512 images. For that I need to get inside the contours and tile the whats inside of it.
I'm struggling with this for days, any help would be highly appreciated.
Thank you
python opencv
asked Nov 13 at 5:33
Luís Costa
283217
So you want to iterate inside the contour row by row ?
– ZdaR
Nov 13 at 5:38
I want to do something like this: original_image > generate mask > get contours oritinal_image * contours = image_to_tile generate_patches(image_to_tile)
– Luís Costa
Nov 13 at 5:41
Please explain thisimage_to_tilefunctionality? What is the expected output ?
– ZdaR
Nov 13 at 6:20
image_to_tile is the original image without the background. I want to tile the foreground of the original svs image
– Luís Costa
Nov 13 at 19:33
Can you please provide sample output? I am really unable to get your expected output here. Do you want the background to be white instead of black as in current output ?
– ZdaR
Nov 14 at 4:09
add a comment |
I'm implementing a Foreground Extraction algorithm in Python which creates a mask and contours of the foreground of the image.
However, I'm working with SVS files (tif files with less properties) and after extracting the foreground and I still need to tile it because my image has gigapixel resolution. I'm using openCV to handle these images.
This is my getContours function:
def getContours(oslIm, level=2):
"""
Loads the requested level from oslIm and returns identified contours in the slide.
:param oslIm: openslide image
:param level: level from which to load the data (usually 2)
:return: contours
"""
image_array = np.asarray(oslIm.read_region((1, 1), level, oslIm.level_dimensions[level]), dtype=np.uint8)
image = image_array[:, :, 0:3]
mask = segment(image)
_, contours, _ = cv2.findContours(mask, mode=cv2.RETR_EXTERNAL, method=cv2.CHAIN_APPROX_SIMPLE)
return contours
I read my image at the desired level, I extract the mask of the foreground and then the contours.
This is the process:
Input Image:
Mask:
Final Image:
Everything is good, I have the contours and the final image.
But as I said before I want to crop my image so I can apply my
sample_and_store_patches_by_row(
file_name,
pixel_overlap,
patch_size=512,
level=17,
)
and tile my image in 512x512 images. For that I need to get inside the contours and tile the whats inside of it.
I'm struggling with this for days, any help would be highly appreciated.
Thank you
python opencv
asked Nov 13 at 5:33
Luís Costa
283217
I'm implementing a Foreground Extraction algorithm in Python which creates a mask and contours of the foreground of the image.
However, I'm working with SVS files (tif files with less properties) and after extracting the foreground and I still need to tile it because my image has gigapixel resolution. I'm using openCV to handle these images.
This is my getContours function:
def getContours(oslIm, level=2):
"""
Loads the requested level from oslIm and returns identified contours in the slide.
:param oslIm: openslide image
:param level: level from which to load the data (usually 2)
:return: contours
"""
image_array = np.asarray(oslIm.read_region((1, 1), level, oslIm.level_dimensions[level]), dtype=np.uint8)
image = image_array[:, :, 0:3]
mask = segment(image)
_, contours, _ = cv2.findContours(mask, mode=cv2.RETR_EXTERNAL, method=cv2.CHAIN_APPROX_SIMPLE)
return contours
I read my image at the desired level, I extract the mask of the foreground and then the contours.
This is the process:
Input Image:
Mask:
Final Image:
Everything is good, I have the contours and the final image.
But as I said before I want to crop my image so I can apply my
sample_and_store_patches_by_row(
file_name,
pixel_overlap,
patch_size=512,
level=17,
)
and tile my image in 512x512 images. For that I need to get inside the contours and tile the whats inside of it.
I'm struggling with this for days, any help would be highly appreciated.
Thank you
python opencv
python opencv
asked Nov 13 at 5:33
Luís Costa
283217
asked Nov 13 at 5:33
Luís Costa
283217
asked Nov 13 at 5:33
Luís Costa
283217
asked Nov 13 at 5:33
Luís Costa
283217
asked Nov 13 at 5:33
Luís Costa
283217
283217
So you want to iterate inside the contour row by row ?
– ZdaR
Nov 13 at 5:38
I want to do something like this: original_image > generate mask > get contours oritinal_image * contours = image_to_tile generate_patches(image_to_tile)
– Luís Costa
Nov 13 at 5:41
Please explain thisimage_to_tilefunctionality? What is the expected output ?
– ZdaR
Nov 13 at 6:20
image_to_tile is the original image without the background. I want to tile the foreground of the original svs image
– Luís Costa
Nov 13 at 19:33
Can you please provide sample output? I am really unable to get your expected output here. Do you want the background to be white instead of black as in current output ?
– ZdaR
Nov 14 at 4:09
add a comment |
So you want to iterate inside the contour row by row ?
– ZdaR
Nov 13 at 5:38
I want to do something like this: original_image > generate mask > get contours oritinal_image * contours = image_to_tile generate_patches(image_to_tile)
– Luís Costa
Nov 13 at 5:41
Please explain thisimage_to_tilefunctionality? What is the expected output ?
– ZdaR
Nov 13 at 6:20
image_to_tile is the original image without the background. I want to tile the foreground of the original svs image
– Luís Costa
Nov 13 at 19:33
Can you please provide sample output? I am really unable to get your expected output here. Do you want the background to be white instead of black as in current output ?
– ZdaR
Nov 14 at 4:09
So you want to iterate inside the contour row by row ?
– ZdaR
Nov 13 at 5:38
So you want to iterate inside the contour row by row ?
– ZdaR
Nov 13 at 5:38
I want to do something like this: original_image > generate mask > get contours oritinal_image * contours = image_to_tile generate_patches(image_to_tile)
– Luís Costa
Nov 13 at 5:41
I want to do something like this: original_image > generate mask > get contours oritinal_image * contours = image_to_tile generate_patches(image_to_tile)
– Luís Costa
Nov 13 at 5:41
Please explain this
image_to_tile functionality? What is the expected output ?– ZdaR
Nov 13 at 6:20
Please explain this
image_to_tile functionality? What is the expected output ?– ZdaR
Nov 13 at 6:20
image_to_tile is the original image without the background. I want to tile the foreground of the original svs image
– Luís Costa
Nov 13 at 19:33
image_to_tile is the original image without the background. I want to tile the foreground of the original svs image
– Luís Costa
Nov 13 at 19:33
Can you please provide sample output? I am really unable to get your expected output here. Do you want the background to be white instead of black as in current output ?
– ZdaR
Nov 14 at 4:09
Can you please provide sample output? I am really unable to get your expected output here. Do you want the background to be white instead of black as in current output ?
– ZdaR
Nov 14 at 4:09
add a comment |
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So you want to iterate inside the contour row by row ?
– ZdaR
Nov 13 at 5:38
I want to do something like this: original_image > generate mask > get contours oritinal_image * contours = image_to_tile generate_patches(image_to_tile)
– Luís Costa
Nov 13 at 5:41
Please explain this
image_to_tilefunctionality? What is the expected output ?– ZdaR
Nov 13 at 6:20
image_to_tile is the original image without the background. I want to tile the foreground of the original svs image
– Luís Costa
Nov 13 at 19:33
Can you please provide sample output? I am really unable to get your expected output here. Do you want the background to be white instead of black as in current output ?
– ZdaR
Nov 14 at 4:09