def show_thumb_when_selected(self, event):
idx = self.selected_files.curselection()[0]
filepath = self.selected_files_list[idx]
slide = wp.slide(filepath)
slide.export_thumbnail(save_to=".", size=256)
self.thumb = ImageTk.PhotoImage(file="thumb.png")
x = (256 - self.thumb.width()) / 2
y = (256 - self.thumb.height()) / 2
self.thumb_canvas.create_image(x, y, image=self.thumb, anchor=tk.NW)
def main(command=None):
args = Args(command)
slide = wp.slide(args.wsi)
rule = wp.rule(args.rule) if hasattr(args, "rule") and args.rule else False
annotation = process_annotation(args, slide, rule)
if hasattr(args, "export_thumbs") and args.export_thumbs:
thumbs_dir = args.save_to/slide.filestem/"thumbs"
if not thumbs_dir.exists():
thumbs_dir.mkdir(parents=True)
annotation.export_thumb_masks(thumbs_dir)
if args.method == "evaluation":
on_annotation = False
else:
on_annotation = args.on_annotation
crop_bbox = args.crop_bbox if hasattr(args, "crop_bbox") else False
patcher = wp.patcher(
slide, args.method,
annotation=annotation,
save_to=args.save_to,
patch_width=args.patch_width,
patch_height=args.patch_height,
overlap_width=args.overlap_width,
overlap_height=args.overlap_height,
on_foreground=args.on_foreground,
on_annotation=on_annotation,
offset_x=args.offset_x,
offset_y=args.offset_y,
start_sample=args.start_sample,
finished_sample=args.finished_sample,
no_patches=args.no_patches,
crop_bbox=crop_bbox,
verbose=args.verbose)
patcher.get_patch_parallel(annotation.classes)
if args.method == "detection":
converter = wp.converter(
args.save_to/slide.filestem,
args.save_to/slide.filestem,
args.ratio)
if args.voc_style:
converter.to_voc()
if args.coco_style:
converter.to_coco()
if args.yolo_style:
converter.to_yolo()
if args.crop_bbox:
patcher.get_mini_patch_parallel(annotation.classes)
def run_process(self):
wsiidx = self.selected_files.curselection()[0]
self.params["wsi"] = self.selected_files_list[wsiidx]
slide = wp.slide(self.params["wsi"])
if self.params["rule file"].get():
rule = wp.rule(self.params["rule file"].get())
else:
rule = False
if self.params["annotation file"].get():
annotation = wp.annotation(self.params["annotation file"].get())
annotation.make_masks(slide, rule, foreground=True)
annotation.classes.remove("foreground")
classes = annotation.classes
else:
annotation = wp.annotation("")
annotation.make_masks(slide, foreground=True)
classes = annotation.classes
patcher = wp.patcher(
slide,
self.params["method"].get(),
annotation=annotation,
save_to=self.params["where to save"].get(),
patch_width=self.params["patch width"].get(),
patch_height=self.params["patch height"].get(),
overlap_width=self.params["overlap width"].get(),
overlap_height=self.params["overlap height"].get(),
on_foreground=self.params["ratio of foreground"].get(),
on_annotation=self.params["ratio of annotation"].get(),
start_sample=False,
finished_sample=False,
extract_patches=True)
patcher.get_patch_parallel(classes)
if self.params["convert to voc"].get(
) or self.params["convert to coco"].get():
converter = wp.converter(
self.params["where to save"].get() + "/" + slide.filestem,
self.params["where to save"].get(), "8:1:1")
if self.params["convert to voc"].get():
converter.to_voc()
if self.params["convert to coco"].get():
converter.to_coco()
def cli(params):
slide = wp.slide(params.wsi)
if params.rule:
rule = wp.rule(params.rule)
else:
rule = False
if params.annotation:
annotation = wp.annotation(params.annotation)
annotation.make_masks(slide, rule, foreground=True)
annotation.classes.remove("foreground")
else:
annotation = wp.annotation("")
if params.on_annotation:
annotation.make_masks(slide, foreground=True)
patcher = wp.patcher(slide,
params.method,
annotation=annotation,
save_to=params.save_to,
patch_width=params.patch_width,
patch_height=params.patch_height,
overlap_width=params.overlap_width,
overlap_height=params.overlap_height,
offset_x=params.offset_x,
offset_y=params.offset_y,
on_foreground=params.on_foreground,
on_annotation=params.on_annotation,
no_patches=params.no_patches)
patcher.get_patch_parallel(annotation.classes)
if params.voc_style or params.coco_style or params.yolo_style:
converter = wp.converter(params.save_to / slide.filestem,
params.save_to, params.ratio)
if params.voc_style:
converter.to_voc()
if params.coco_style:
converter.to_coco()
if params.yolo_style:
converter.to_yolo()
import wsiprocess as wp
import cv2
slide = wp.slide("CMU-1.ndpi")
annotation = wp.annotation("", is_image=True)
target_classes = ["benign", "malignant"]
annotation.add_class(target_classes)
benign_mask = cv2.imread("benign_mask.png", 0) * 255
malignant_mask = cv2.imread("malignant_mask.png", 0) * 255
# Make sure your mask data includes only 0 as background or 255 as foreground
annotation.from_image(benign_mask, "benign")
annotation.from_image(malignant_mask, "malignant")
patcher = wp.patcher(slide, "classification", annotation=annotation)
patcher.get_patch_parallel(target_classes)