forked from TIO-IKIM/CellViT
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathpatch_extraction.yaml
71 lines (66 loc) · 6.62 KB
/
patch_extraction.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
# dataset paths
wsi_paths: # Path to the folder where all WSI are stored or path to a single WSI-file [str]
wsi_filelist: # Path to a csv-filelist with WSI files (separator: `,`), if provided just these files are
# used.Must include full paths to WSIs, including suffixes.Can be used as an replacement for
# the wsi_paths option.If both are provided, yields an error. [str] [Optional, defaults to None]
output_path: # Path to the folder where the resulting dataset should be stored [str]
wsi_extensions: # The extension of the WSI-files [str] [Optional, defaults to "svs"]
# basic setups
patch_size: # The size of the patches in pixel that will be retrieved from the WSI, e.g. 256 for 256px. [][Optional, defaults to 256]
patch_overlap: # The percentage amount pixels that should overlap between two different patches.
# Please Provide as integer between 0 and 100, indicating overlap in percentage.
# [int][Optional, defaults to 0]
downsample: # Each WSI level is downsampled by a factor of 2, downsample
# expresses which kind of downsampling should be used with
# respect to the highest possible resolution. [int][Optional, defaults to 0]
target_mpp: # If this parameter is provided, the output level of the WSI
# corresponds to the level that is at the target microns per pixel of the WSI.
# Alternative to target_mag, downsaple and level. Highest priority, overwrites all other setups for magnifcation, downsample, or level.
# [int][Optional, defaults to None]
target_mag: # If this parameter is provided, the output level of the WSI
# corresponds to the level that is at the target magnification of the WSI.
# Alternative to target_mpp, downsaple and level. High priority, just target_mpp has a higher priority, overwrites downsample and level if provided.
# [int][Optional, defaults to None]
level: # The tile level for sampling, alternative to downsample. [int][Optional, defaults to None]
context_scales: # Define context scales for context patches. Context patches are centered around a central patch.
# The context-patch size is equal to the patch-size, but downsampling is different.
# [List[int]][Optional, defaults to None]
check_resolution: # If a float value is supplies, the program checks whether
# the resolution of all images corresponds to the given value.
# [float][Optional, defaults to None]
processes: # The number of processes to use. [int][Optional, defaults to 24]
overwrite: # Overwrite the patches that have already been created in
# case they already exist. Removes dataset. Handle with care! If false, skips already processed files from "processed.json".
# [bool][Optional, defaults to False]
# annotation specific settings
annotation_paths: # Path to the subfolder where the annotations are
# stored or path to a file. [str][Optional, defaults to None]
annotation_extension: # The extension types used for the annotation files. [str][Optional, defaults to None]
incomplete_annotations: # Set to allow WSI without annotation file. [bool][Optional, defaults to False]
label_map_file: # The path to a json file that contains the mapping between
# he annotation labels and some integers; an example can be found in examples. [str][Optional, defaults to None]
save_only_annotated_patches: # If true only patches containing annotations will be stored. [bool][Optional, defaults to False]
exclude_classes: # Can be used to exclude annotation classes. [List[str]][Optional, defaults to []].
store_masks: # Set to store masks per patch. [bool][Optional, defaults to False]
overlapping_labels: # Per default, labels (annotations) are mutually exclusive.
# If labels overlap, they are overwritten according to the label_map.json ordering (highest number = highest priority).
# True means that the mask array is 3D with shape [patch_size, patch_size, len(label_map)], otherwise just [patch_size, patch_size].
# [bool][Optional, defaults to False]
# macenko stain normalization
normalize_stains: # Uses Macenko normalization on a portion of the whole slide images. [bool][Optional, defaults to False]
normalization_vector_json: # The path to a JSON file where the normalization vectors are stored. [str][Optional, defaults to None]
# finding patches
min_intersection_ratio: # The minimum intersection between the tissue mask and the patch.
# Must be between 0 and 1. 0 means that all patches are extracted. [float][Optional, defaults to 0.01]
tissue_annotation: # Can be used to name a polygon annotation to determine the tissue area
# If a tissue annotation is provided, no Otsu-thresholding is performed. [str][Optional, defaults to None]
masked_otsu: # Use annotation to mask the thumbnail before otsu-thresholding is used. [bool][Optional, defaults to False]
otsu_annotation: # Can be used to name a polygon annotation to determine the area
# for masked otsu thresholding. [List][Optional, defaults to None]
filter_patches: # Post-extraction patch filtering to sort out artefacts, marker and other non-tissue patches with a DL model. Time consuming.
# [bool] [Optional, defaults to False]
# logging
log_path: # Path where log files should be stored. Otherwise, log files are stored in the output folder. [str][Optional, defaults to None]
log_level: # Set the logging level. [str][Optional, defaults to info]
hardware_selection: # Select hardware device (just if available, otherwise always cucim). [str] [Optional, defaults to cucim]
wsi_properties: # Dictionary with manual WSI metadata. Required keys are: ... TODO: add keys [dict] [Optional, default selection from files]