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Improve the auto_size logic during coordinates generation #11
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -98,6 +98,7 @@ def seg_and_patch( | |
| stitch=False, | ||
| patch=False, | ||
| auto_skip=True, | ||
| auto_size=False, | ||
| process_list=None, | ||
| wsi_format="svs", | ||
| ): | ||
|
|
@@ -152,20 +153,26 @@ def seg_and_patch( | |
| full_path = os.path.join(source, slide) | ||
| try: | ||
| WSI_object = wsi_slide_image(full_path) | ||
| mpp = WSI_object.mpp | ||
| if mpp is None: | ||
| # Fallback: assume 40x magnification (mpp=0.25) for files without MPP metadata | ||
| print(f"WARNING: MPP information not available for {slide}. Assuming 40x magnification (mpp=0.25).") | ||
| mpp = 0.25 | ||
| object_power = 40 | ||
| if auto_size: | ||
| mpp = WSI_object.mpp | ||
| if mpp is None: | ||
| # Fallback: assume 40x magnification (mpp=0.25) for files without MPP metadata | ||
| print(f"WARNING: MPP information not available for {slide}. Assuming 40x magnification (mpp=0.25).") | ||
| mpp = 0.25 | ||
| object_power = 40 | ||
| else: | ||
| # Convert mpp to magnification | ||
| object_power = int(round(10.0 / mpp)) | ||
| patch_size, step_size = adjust_size(object_power) | ||
| print("#" * 100) | ||
| print("levels:", WSI_object.wsi.level_dimensions) | ||
| print("mpp: {:.3f}, object_power: {}x, patch_size: {}, step_size: {} (auto-adjusted)".format(mpp, object_power, patch_size, step_size)) | ||
| print("#" * 100) | ||
| else: | ||
| # Convert mpp to magnification | ||
| object_power = int(round(10.0 / mpp)) | ||
| patch_size, step_size = adjust_size(object_power) | ||
| print("#" * 100) | ||
| print("levels:", WSI_object.wsi.level_dimensions) | ||
| print("mpp: {:.3f}, object_power: {}x, patch_size: {}, step_size: {}".format(mpp, object_power, patch_size, step_size)) | ||
| print("#" * 100) | ||
| print("#" * 100) | ||
| print("levels:", WSI_object.wsi.level_dimensions) | ||
| print("Using fixed patch_size: {}, step_size: {}".format(patch_size, step_size)) | ||
| print("#" * 100) | ||
| except Exception as e: | ||
| print("Failed to reading:", full_path) | ||
| print('Exception:', e) | ||
|
|
@@ -321,6 +328,7 @@ def mp_seg_and_patch( | |
| stitch=False, | ||
| patch=False, | ||
| auto_skip=True, | ||
| auto_size=False, | ||
| process_list=None, | ||
| wsi_format="svs", | ||
| ): | ||
|
|
@@ -373,6 +381,29 @@ def func(i): | |
| full_path = os.path.join(source, slide) | ||
| try: | ||
| WSI_object = wsi_slide_image(full_path) | ||
| # Auto-adjust patch_size and step_size based on mpp if auto_size is enabled | ||
| current_patch_size = patch_size | ||
| current_step_size = step_size | ||
| if auto_size: | ||
| mpp = WSI_object.mpp | ||
| if mpp is None: | ||
| # Fallback: assume 40x magnification (mpp=0.25) for files without MPP metadata | ||
| print(f"WARNING: MPP information not available for {slide}. Assuming 40x magnification (mpp=0.25).") | ||
| mpp = 0.25 | ||
| object_power = 40 | ||
| else: | ||
| # Convert mpp to magnification | ||
| object_power = int(round(10.0 / mpp)) | ||
| current_patch_size, current_step_size = adjust_size(object_power) | ||
| print("#" * 100) | ||
| print("levels:", WSI_object.wsi.level_dimensions) | ||
| print("mpp: {:.3f}, object_power: {}x, patch_size: {}, step_size: {} (auto-adjusted)".format(mpp, object_power, current_patch_size, current_step_size)) | ||
| print("#" * 100) | ||
| else: | ||
| print("#" * 100) | ||
| print("levels:", WSI_object.wsi.level_dimensions) | ||
| print("Using fixed patch_size: {}, step_size: {}".format(current_patch_size, current_step_size)) | ||
| print("#" * 100) | ||
| except: | ||
| print("Failed to reading:", full_path) | ||
| return | ||
|
|
@@ -472,7 +503,7 @@ def func(i): | |
|
|
||
| patch_time_elapsed = -1 # Default time | ||
| if patch: | ||
| current_patch_params.update({"patch_level": patch_level, "patch_size": patch_size, "step_size": step_size, "save_path": patch_save_dir}) | ||
| current_patch_params.update({"patch_level": patch_level, "patch_size": current_patch_size, "step_size": current_step_size, "save_path": patch_save_dir}) | ||
| file_path, patch_time_elapsed = patching( | ||
| WSI_object=WSI_object, | ||
| **current_patch_params, | ||
|
|
@@ -510,6 +541,7 @@ def func(i): | |
| parser.add_argument("--patch_level", type=int, default=0, help="downsample level at which to patch") | ||
| parser.add_argument("--process_list", type=str, default=None, help="name of list of images to process with parameters (.csv)") | ||
| parser.add_argument("--wsi_format", type=str, default="svs") | ||
| parser.add_argument("--auto_size", default=False, action="store_true", help="automatically adjust patch_size and step_size based on WSI magnification (mpp)") | ||
| parser.add_argument("--use_mp", default=False, action="store_true") | ||
|
|
||
|
|
||
|
|
@@ -566,4 +598,4 @@ def func(i): | |
| fn = mp_seg_and_patch | ||
| else: | ||
| fn = seg_and_patch | ||
| seg_times, patch_times = fn(**directories, **parameters, patch_size=args.patch_size, step_size=args.step_size, seg=args.seg, use_default_params=False, save_mask=True, stitch=args.stitch, patch_level=args.patch_level, patch=args.patch, process_list=process_list, auto_skip=args.no_auto_skip, wsi_format=wsi_format) | ||
| seg_times, patch_times = fn(**directories, **parameters, patch_size=args.patch_size, step_size=args.step_size, seg=args.seg, use_default_params=False, save_mask=True, stitch=args.stitch, patch_level=args.patch_level, patch=args.patch, process_list=process_list, auto_skip=args.no_auto_skip, auto_size=args.auto_size, wsi_format=wsi_format) | ||
|
||
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The table separator has inconsistent formatting. The row contains only dashes with no pipe characters, which breaks the markdown table structure. It should be removed or properly formatted as a standard table row with pipe delimiters.