(
self,
input_dir: str,
output_dir: str,
*,
wsi_dir: str = None,
region_extractor_kwargs: dict = None,
nuclei_extractor_kwargs: dict = None,
extras_extractor_kwargs: dict = None,
monitor: str = "",
logger: Any = None,
_debug: bool = False,
_reverse: bool = False,
)
| 2183 | Extracts features from MuTIsWSIRunner ouput. |
| 2184 | """ |
| 2185 | def __init__( |
| 2186 | self, |
| 2187 | input_dir: str, |
| 2188 | output_dir: str, |
| 2189 | *, |
| 2190 | wsi_dir: str = None, |
| 2191 | region_extractor_kwargs: dict = None, |
| 2192 | nuclei_extractor_kwargs: dict = None, |
| 2193 | extras_extractor_kwargs: dict = None, |
| 2194 | monitor: str = "", |
| 2195 | logger: Any = None, |
| 2196 | _debug: bool = False, |
| 2197 | _reverse: bool = False, |
| 2198 | ): |
| 2199 | """""" |
| 2200 | self.input_dir = input_dir |
| 2201 | self.output_dir = output_dir |
| 2202 | self.wsi_dir = wsi_dir |
| 2203 | self.region_extractor_kwargs = region_extractor_kwargs or {} |
| 2204 | self.nuclei_extractor_kwargs = nuclei_extractor_kwargs or {} |
| 2205 | self.collagen_extractor_kwargs = extras_extractor_kwargs or {} |
| 2206 | self.slide_names = os.listdir(input_dir) |
| 2207 | self.monitor = monitor |
| 2208 | self.logger = logger or logging.getLogger(__name__) |
| 2209 | self._debug = _debug |
| 2210 | self._reverse = _reverse |
| 2211 | self._slmonitor = self.monitor |
| 2212 | |
| 2213 | self.slide_names.sort(reverse=self._reverse) |
| 2214 | |
| 2215 | collect_errors.logger = self.logger |
| 2216 | collect_errors._debug = self._debug |
| 2217 | |
| 2218 | self._create_directory_structure() |
| 2219 | |
| 2220 | def run(self): |
| 2221 | """""" |
nothing calls this directly
no test coverage detected