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/pathaia/patches/object_api.py
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| a | b/pathaia/patches/object_api.py | ||
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| 1 | # coding: utf8 |
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| 2 | """ |
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| 3 | A module to extract patches in a slide. |
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| 4 | |||
| 5 | Enable filtering on tissue surface ratio. |
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| 6 | Draft for hierarchical patch extraction and representation is proposed. |
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| 7 | """ |
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| 8 | |||
| 9 | import os |
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| 10 | from typing import Optional, Sequence |
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| 11 | from ..util.basic import ifnone |
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| 12 | from ..util.types import PathLike, Filter, FilterList, Coord |
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| 13 | from .functional_api import patchify_slide |
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| 14 | from .functional_api import patchify_folder |
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| 15 | from .functional_api import patchify_slide_hierarchically |
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| 16 | from .functional_api import patchify_folder_hierarchically |
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| 17 | from .filters import standardize_filters |
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| 18 | from .errors import UnknownLevelError |
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| 19 | from .compat import convert_coords |
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| 20 | |||
| 21 | |||
| 22 | class Patchifier(object): |
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| 23 | """ |
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| 24 | A class to handle patchification tasks. |
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| 25 | |||
| 26 | Args: |
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| 27 | outdir: path to an output directory. |
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| 28 | level: pyramid level to extract. |
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| 29 | psize: size of the side of the patches (in pixels). |
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| 30 | interval: {"x", "y"} interval between 2 neighboring patches. |
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| 31 | offset: {"x", "y"} offset in px on x and y axis for patch start. |
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| 32 | filters: filters to accept patches. |
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| 33 | extensions: list of file extensions to consider. Defaults to '.mrxs'. |
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| 34 | verbose: 0 => nada, 1 => patchifying parameters, 2 => start-end of processes, |
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| 35 | thumbnail export. |
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| 36 | """ |
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| 37 | |||
| 38 | def __init__( |
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| 39 | self, |
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| 40 | outdir: PathLike, |
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| 41 | level: int, |
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| 42 | psize: int, |
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| 43 | interval: Coord, |
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| 44 | offset: Coord = (0, 0), |
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| 45 | filters: Optional[Sequence[Filter]] = None, |
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| 46 | extensions: Optional[Sequence[str]] = None, |
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| 47 | verbose: int = 2, |
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| 48 | ): |
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| 49 | self.outdir = outdir |
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| 50 | self.level = level |
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| 51 | self.psize = psize |
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| 52 | self.interval = convert_coords(interval) |
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| 53 | self.offset = convert_coords(offset) |
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| 54 | self.filters = ifnone(filters, []) |
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| 55 | self.verbose = verbose |
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| 56 | self.extensions = ifnone(extensions, (".mrxs",)) |
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| 57 | |||
| 58 | def patchify(self, path: PathLike): |
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| 59 | """ |
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| 60 | Patchify a slide or an entire folder of slides. |
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| 61 | |||
| 62 | Args: |
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| 63 | path: absolute path to a slide or a folder of slides. |
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| 64 | |||
| 65 | """ |
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| 66 | if os.path.isdir(path): |
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| 67 | patchify_folder( |
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| 68 | path, |
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| 69 | self.outdir, |
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| 70 | self.level, |
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| 71 | self.psize, |
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| 72 | self.interval, |
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| 73 | offset=self.offset, |
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| 74 | filters=self.filters, |
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| 75 | verbose=self.verbose, |
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| 76 | extensions=self.extensions, |
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| 77 | ) |
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| 78 | else: |
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| 79 | patchify_slide( |
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| 80 | path, |
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| 81 | self.outdir, |
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| 82 | self.level, |
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| 83 | self.psize, |
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| 84 | self.interval, |
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| 85 | offset=self.offset, |
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| 86 | filters=self.filters, |
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| 87 | verbose=self.verbose, |
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| 88 | ) |
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| 89 | |||
| 90 | def add_filter(self, filter_func: Filter): |
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| 91 | """ |
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| 92 | Add a filter function to this patch extractor. |
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| 93 | |||
| 94 | Args: |
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| 95 | filter_func: a function that take an image as argument and output a bool. |
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| 96 | |||
| 97 | """ |
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| 98 | self.filters.append(filter_func) |
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| 99 | |||
| 100 | |||
| 101 | class HierarchicalPatchifier(object): |
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| 102 | """ |
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| 103 | A class to handle hierachical patchification tasks. |
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| 104 | |||
| 105 | Args: |
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| 106 | outdir: path to an output directory. |
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| 107 | top_level: top pyramid level to consider. |
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| 108 | low_level: lowest pyramid level to consider. |
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| 109 | psize: size of the side of the patches (in pixels). |
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| 110 | interval: {"x", "y"} interval between 2 neighboring patches. |
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| 111 | offset: {"x", "y"} offset in px on x and y axis for patch start. |
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| 112 | filters: filters to accept patches. |
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| 113 | silent: pyramid level not to output. |
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| 114 | extensions: list of file extensions to consider. Defaults to '.mrxs'. |
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| 115 | verbose: 0 => nada, 1 => patchifying parameters, 2 => start-end of processes, thumbnail export. |
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| 116 | |||
| 117 | """ |
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| 118 | |||
| 119 | def __init__( |
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| 120 | self, |
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| 121 | outdir: PathLike, |
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| 122 | top_level: int, |
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| 123 | low_level: int, |
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| 124 | psize: int, |
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| 125 | interval: Coord, |
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| 126 | offset: Coord = (0, 0), |
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| 127 | filters: Optional[FilterList] = None, |
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| 128 | silent: Optional[Sequence[int]] = None, |
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| 129 | extensions: Optional[Sequence[str]] = None, |
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| 130 | verbose: int = 2, |
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| 131 | ): |
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| 132 | self.outdir = outdir |
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| 133 | self.top_level = top_level |
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| 134 | self.low_level = low_level |
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| 135 | self.psize = psize |
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| 136 | self.interval = convert_coords(interval) |
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| 137 | self.offset = convert_coords(offset) |
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| 138 | self.filters = standardize_filters(ifnone(filters, {}), top_level, low_level) |
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| 139 | self.verbose = verbose |
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| 140 | self.silent = ifnone(silent, []) |
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| 141 | self.extensions = ifnone(extensions, (".mrxs",)) |
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| 142 | |||
| 143 | def patchify(self, path: PathLike): |
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| 144 | """ |
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| 145 | Patchify hierarchically a slide or an entire folder of slides. |
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| 146 | |||
| 147 | Args: |
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| 148 | path: absolute path to a slide or a folder of slides. |
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| 149 | |||
| 150 | """ |
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| 151 | if os.path.isdir(path): |
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| 152 | patchify_folder_hierarchically( |
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| 153 | path, |
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| 154 | self.outdir, |
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| 155 | self.top_level, |
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| 156 | self.low_level, |
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| 157 | self.psize, |
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| 158 | self.interval, |
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| 159 | offset=self.offset, |
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| 160 | filters=self.filters, |
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| 161 | silent=self.silent, |
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| 162 | extensions=self.extensions, |
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| 163 | verbose=self.verbose, |
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| 164 | ) |
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| 165 | else: |
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| 166 | patchify_slide_hierarchically( |
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| 167 | path, |
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| 168 | self.outdir, |
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| 169 | self.top_level, |
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| 170 | self.low_level, |
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| 171 | self.psize, |
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| 172 | self.interval, |
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| 173 | offset=self.offset, |
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| 174 | filters=self.filters, |
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| 175 | silent=self.silent, |
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| 176 | verbose=self.verbose, |
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| 177 | ) |
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| 178 | |||
| 179 | def add_filter(self, filter_func: Filter, level: Optional[int] = None): |
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| 180 | """ |
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| 181 | Add a filter function to the hierarchical patch extractor. |
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| 182 | |||
| 183 | Args: |
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| 184 | filter_func: a function that take an image as argument and output a bool. |
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| 185 | |||
| 186 | """ |
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| 187 | # if level is None, append filter func to all levels |
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| 188 | if level is None: |
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| 189 | for lev in self.filters: |
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| 190 | self.filters[lev].append(filter_func) |
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| 191 | # if level is int, append filter func to this level |
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| 192 | elif type(level) == int: |
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| 193 | if level not in self.filters: |
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| 194 | raise UnknownLevelError( |
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| 195 | "Level {} is not in {} !!!".format(level, list(self.filters.keys())) |
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| 196 | ) |
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| 197 | self.filters[level].append(filter_func) |
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| 198 | elif type(level) == list: |
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| 199 | for lev in level: |
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| 200 | self.add_filter(filter_func, lev) |
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| 201 | else: |
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| 202 | raise UnknownLevelError("{} is not a valid type of level !!!".format(level)) |