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slideMacro.py
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slideMacro.py
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#!/usr/bin/env python
# script to extract a macro images (and display) whole-slide image files (*.TIF, *.NDPI, etc.)
#
# Ref: https://github.com/choosehappy/Snippets/blob/master/extract_macro_level_from_wsi_image_openslide_cli.py
#
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print(" slideMacro: extract macro images ")
print("")
print("* Version : v1.0.0")
print("")
print("* Last update : 2020-12-29")
print("* Written by : choosehappy | https://github.com/choosehappy")
print("* Edited by : Sander W. van der Laan | s.w.vanderlaan@gmail.com")
print("")
print("* Description : This script will get macro-images at a given level of magnification from ")
print(" (a list of given) images for quick inspection.")
print("")
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
# import required packages
import numpy as np
import glob
from pathlib import Path
# for argument parser
from sys import exit, argv
import argparse
import textwrap
# for openslide/openCV
import cv2
import os
import openslide
from openslide import *
parser = argparse.ArgumentParser(
prog='slideMacro',
description='This script will get macro-images at a given level of magnification from (a list of given) images for quick inspection.',
usage='slideMacro -i/--input -l/--level; optional: -d/--display -o/--outdir -s/--suffix -t/--type -f/--force -v/--verbose; for help: -h/--help',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=textwrap.dedent("Copyright (c) 1979-2020 Sander W. van der Laan | s.w.vanderlaan-2@umcutrecht.nl"))
parser.add_argument('-d', '--display', help="Also show macro on display, default simply writes macro.", action="store_true")
parser.add_argument('-o', '--outdir', help="Output dir, default is present working directory.", default="./", type=str)
parser.add_argument('-s', '--suffix', help="Suffix to append to end of file, default is 'macro'.", default="", type=str)
parser.add_argument('-t', '--type', help="Output file type, default is png (which is slower), other options are tif.", default="png", type=str)
parser.add_argument('-f', '--force', help="Force utput even if it exists.", default=False, action="store_true")
parser.add_argument('-v', '--verbose', help="While writing images also display image properties.", default=False, action="store_true")
requiredNamed = parser.add_argument_group('required named arguments')
requiredNamed.add_argument('-i','--input',help="Input (directory containing files). Try: *.TIF or /path_to/images/*.ndpi.", nargs="*")
requiredNamed.add_argument('-l','--level',help="Magnification level to extract, with '5' as level 5. Try: 5.")
args = parser.parse_args()
if not args.input:
print("\nOh, computer says no! You must supply correct arguments when running a *** slideMacro ***!")
print("Note that -i/--input is required. Try: *.TIF or /path_to/images/*.ndpi.\n")
parser.print_help()
exit()
if len(args.input) > 1: # bash has sent us a list of files
files = args.input
else: # user sent us a wildcard, need to use glob to find files
files = glob.glob(args.input[0])
# make the output directory if it does not exist
if not os.path.exists(args.outdir):
os.makedirs(args.outdir)
for fname in files:
fnameout=f"{Path(fname).stem}{args.suffix}.!!.{args.type if args.type[0] == '' else ''+args.type}"
fnameout=Path(args.outdir,fnameout)
if not args.force and os.path.exists(fnameout):
print(f"Skipping {fnameout} as output file exists and --force is not set")
continue
fimage=openslide.OpenSlide(fname)
level = int(args.level)
img = fimage.read_region((0, 0), level, fimage.level_dimensions[level]) # will get the given level of an image
img = np.asarray(img)[:,:, 0:3]
if args.display:
print("Displaying [",fname,"] at level [",level,"].")
# Let's print each dimension of the image
print('* image dimensions (height x width in pixels):', img.shape)
### FOR DEBUG
# print('Image data type:', img.dtype)
# print('Image type:', type(img))
img_size = img.size/1024 # to get kilobytes
print('* image size:', '{:,.2f}'.format(img_size), 'KB') # to get Kb
# To display our image variable, we use 'imshow'
# The first parameter will be title shown on image window
# The second parameter is the image variable
# rotate the image for easy reading (https://www.geeksforgeeks.org/python-opencv-cv2-rotate-method/)
img_r = cv2.rotate(img, cv2.cv2.ROTATE_90_CLOCKWISE)
cv2.imshow(print('Display image [',fname,'] at level [',level,']'), cv2.cvtColor(img_r, cv2.COLOR_RGB2BGR))
# 'waitKey' allows us to wait for a key stroke
# when a image window is open
# By leaving it blank it just waits for any key to be
# pressed before continuing.
# By placing numbers (except 0), we can specify a delay for
# how long you keep the window open (time is in millisecs here)
cv2.waitKey()
# This closes all open windows
# Failure to place this will cause your program to hang
cv2.destroyAllWindows()
elif args.verbose:
print("Processing [",fname,"] at level [",level,"].")
print('* image dimensions (height x width in pixels):', img.shape)
img_size = img.size/1024 # to get kilobytes
print('* image size:', '{:,.2f}'.format(img_size), 'KB') # to get Kb
cv2.imwrite(str(fnameout).replace("!!","macro"),cv2.cvtColor(img,cv2.COLOR_RGB2BGR))
else:
print("Writing macro for [",fname,"] at level [",level,"].")
cv2.imwrite(str(fnameout).replace("!!","macro"),cv2.cvtColor(img,cv2.COLOR_RGB2BGR))
print("+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print("+ The MIT License (MIT) +")
print("+ Copyright (c) 1979-2020 choosehappy, Sander W. van der Laan | UMC Utrecht, Utrecht, the Netherlands +")
print("+ +")
print("+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +")
print("+ associated documentation files (the \"Software\"), to deal in the Software without restriction, including +")
print("+ without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +")
print("+ copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the +")
print("+ following conditions: +")
print("+ +")
print("+ The above copyright notice and this permission notice shall be included in all copies or substantial +")
print("+ portions of the Software. +")
print("+ +")
print("+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT +")
print("+ LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO +")
print("+ EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +")
print("+ IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR +")
print("+ THE USE OR OTHER DEALINGS IN THE SOFTWARE. +")
print("+ +")
print("+ Reference: http://opensource.org. +")
print("+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")