Formally rename to sources

mirar/pipelines/summer/blocks.py

@@ -37,8 +37,6 @@
 from mirar.processors import BiasCalibrator, FlatCalibrator
 from mirar.processors.astromatic import PSFex, Scamp, Sextractor, Swarp
 from mirar.processors.astrometry.autoastrometry import AutoAstrometry
-from mirar.processors.candidates import DataframeWriter, DetectCandidates
-from mirar.processors.candidates.utils import RegionsWriter
 from mirar.processors.cosmic_rays import LACosmicCleaner
 from mirar.processors.csvlog import CSVLog
 from mirar.processors.database.database_exporter import (
@@ -50,6 +48,9 @@
 from mirar.processors.photometry.aperture_photometry import CandidateAperturePhotometry
 from mirar.processors.photometry.psf_photometry import CandidatePSFPhotometry
 from mirar.processors.reference import ProcessReference
+from mirar.processors.sources import DataframeWriter
+from mirar.processors.sources.source_detector import SourceDetector
+from mirar.processors.sources.utils import RegionsWriter
 from mirar.processors.sqldatabase.database_exporter import DatabaseImageExporter
 from mirar.processors.utils import ImageBatcher, ImageLoader, ImageSaver, ImageSelector
 from mirar.processors.utils.cal_hunter import CalHunter
@@ -244,7 +245,7 @@
 ]
 
 extract_candidates = [
-    DetectCandidates(output_sub_dir="subtract", **sextractor_candidates_config),
+    SourceDetector(output_sub_dir="subtract", **sextractor_candidates_config),
     RegionsWriter(output_dir_name="candidates"),
     CandidatePSFPhotometry(),
     CandidateAperturePhotometry(

mirar/pipelines/winter/blocks.py

@@ -53,7 +53,6 @@
 from mirar.processors.astromatic.swarp.swarp import Swarp
 from mirar.processors.astrometry.anet.anet_processor import AstrometryNet
 from mirar.processors.astrometry.validate import AstrometryStatsWriter
-from mirar.processors.candidates import DataframeWriter, DetectCandidates
 from mirar.processors.csvlog import CSVLog
 from mirar.processors.dark import DarkCalibrator
 from mirar.processors.database.database_modifier import ModifyImageDatabaseSeqList
@@ -68,6 +67,7 @@
 from mirar.processors.photometry.psf_photometry import CandidatePSFPhotometry
 from mirar.processors.reference import GetReferenceImage, ProcessReference
 from mirar.processors.sky import NightSkyMedianCalibrator, SkyFlatCalibrator
+from mirar.processors.sources import DataframeWriter, SourceDetector
 from mirar.processors.split import SUB_ID_KEY, SplitImage
 from mirar.processors.sqldatabase.database_exporter import (
     DatabaseImageBatchExporter,
@@ -501,7 +501,7 @@
 
 detect_candidates = [
     HeaderAnnotator(input_keys=["ZP_AUTO"], output_key="ZP"),
-    DetectCandidates(output_sub_dir="subtract", **sextractor_candidate_config),
+    SourceDetector(output_sub_dir="subtract", **sextractor_candidate_config),
 ]
 
 process_candidates = [

mirar/pipelines/wirc/blocks.py

@@ -33,15 +33,6 @@
 from mirar.processors.astromatic.swarp import ReloadSwarpComponentImages
 from mirar.processors.astrometry.autoastrometry import AutoAstrometry
 from mirar.processors.astrometry.utils import AstrometryFromFile
-from mirar.processors.candidates import (
-    CandidateNamer,
-    DataframeWriter,
-    DetectCandidates,
-)
-from mirar.processors.candidates.candidate_extractor import (
-    ForcedPhotometryCandidateTable,
-)
-from mirar.processors.candidates.utils import RegionsWriter
 from mirar.processors.csvlog import CSVLog
 from mirar.processors.dark import DarkCalibrator
 from mirar.processors.database.database_exporter import DatabaseDataframeExporter
@@ -65,6 +56,9 @@
 )
 from mirar.processors.reference import ProcessReference
 from mirar.processors.sky import NightSkyMedianCalibrator
+from mirar.processors.sources import CandidateNamer, DataframeWriter, SourceDetector
+from mirar.processors.sources.source_table_builder import ForcedPhotometryCandidateTable
+from mirar.processors.sources.utils import RegionsWriter
 from mirar.processors.utils import (
     HeaderAnnotator,
     ImageBatcher,
@@ -218,7 +212,7 @@
 ]
 
 detect_candidates = [
-    DetectCandidates(output_sub_dir="subtract", **sextractor_candidate_config),
+    SourceDetector(output_sub_dir="subtract", **sextractor_candidate_config),
 ]
 
 process_candidates = [

mirar/processors/alerts/avro_alert.py

@@ -18,12 +18,12 @@
 
 from mirar.data import SourceBatch
 from mirar.paths import get_output_dir
-from mirar.processors.base_processor import BaseDataframeProcessor
+from mirar.processors.base_processor import BaseSourceProcessor
 
 logger = logging.getLogger(__name__)
 
 
-class AvroPacketMaker(BaseDataframeProcessor):
+class AvroPacketMaker(BaseSourceProcessor):
     """Class to generate Avro Packets from a dataframe of candidates.
 
     Attributes:
@@ -48,7 +48,7 @@ def __init__(
         self.save_local = save_local
         self.broadcast = broadcast
 
-    def _apply_to_candidates(
+    def _apply_to_sources(
         self,
         batch: SourceBatch,
     ) -> SourceBatch:

mirar/processors/alerts/send_to_fritz.py

@@ -30,7 +30,7 @@
 
 from mirar.data import SourceBatch
 from mirar.paths import PACKAGE_NAME, __version__
-from mirar.processors.base_processor import BaseDataframeProcessor
+from mirar.processors.base_processor import BaseSourceProcessor
 
 matplotlib.use("agg")
 
@@ -69,7 +69,7 @@ def send(self, request, *args, **kwargs):
             kwargs["timeout"] = DEFAULT_TIMEOUT
 
 
-class SendToFritz(BaseDataframeProcessor):
+class SendToFritz(BaseSourceProcessor):
     """
     Processor for sending candidates to Fritz.
     """
@@ -154,7 +154,7 @@ def _get_fritz_token():
 
         return token_fritz
 
-    def _apply_to_candidates(
+    def _apply_to_sources(
         self,
         batch: SourceBatch,
     ) -> SourceBatch:

mirar/processors/base_processor.py

@@ -471,7 +471,7 @@ def get_cache_path(self, images: ImageBatch) -> Path:
         return self.master_image_path
 
 
-class BaseCandidateGenerator(BaseProcessor, ImageHandler, ABC):
+class BaseSourceGenerator(BaseProcessor, ImageHandler, ABC):
     """
     Base CandidateGenerator processor (image batch in, source batch out)
     """
@@ -495,7 +495,7 @@ def _apply_to_images(self, batch: ImageBatch) -> SourceBatch:
         raise NotImplementedError
 
 
-class BaseDataframeProcessor(BaseProcessor, ABC):
+class BaseSourceProcessor(BaseProcessor, ABC):
     """
     Base dataframe processor (Source batch in, source batch out)
     """
@@ -506,9 +506,9 @@ def __init_subclass__(cls, **kwargs):
         cls.subclasses[cls.base_key] = cls
 
     def _apply(self, batch: SourceBatch) -> SourceBatch:
-        return self._apply_to_candidates(batch)
+        return self._apply_to_sources(batch)
 
-    def _apply_to_candidates(
+    def _apply_to_sources(
         self,
         batch: SourceBatch,
     ) -> SourceBatch:

mirar/processors/database/database_exporter.py

@@ -5,7 +5,7 @@
 from abc import ABC
 
 from mirar.data import ImageBatch, SourceBatch
-from mirar.processors.base_processor import BaseDataframeProcessor, BaseImageProcessor
+from mirar.processors.base_processor import BaseImageProcessor, BaseSourceProcessor
 from mirar.processors.database.base_database_processor import BaseDatabaseProcessor
 
 logger = logging.getLogger(__name__)
@@ -45,12 +45,12 @@ def _apply_to_images(self, batch: ImageBatch) -> ImageBatch:
         return batch
 
 
-class DatabaseDataframeExporter(BaseDatabaseExporter, BaseDataframeProcessor):
+class DatabaseDataframeExporter(BaseDatabaseExporter, BaseSourceProcessor):
     """
     Processor for exporting sources to a database
     """
 
-    def _apply_to_candidates(self, batch: SourceBatch) -> SourceBatch:
+    def _apply_to_sources(self, batch: SourceBatch) -> SourceBatch:
         for source_list in batch:
             candidate_table = source_list.get_data()
 

mirar/processors/database/database_importer.py

@@ -9,7 +9,7 @@
 import pandas as pd
 
 from mirar.data import DataBlock, Image, ImageBatch, SourceBatch
-from mirar.processors.base_processor import BaseDataframeProcessor, BaseImageProcessor
+from mirar.processors.base_processor import BaseImageProcessor, BaseSourceProcessor
 from mirar.processors.database.base_database_processor import BaseDatabaseProcessor
 from mirar.processors.database.constraints import DBQueryConstraints
 
@@ -143,7 +143,7 @@ def get_constraints(self, data: DataBlock) -> DBQueryConstraints:
 #     return candidate_table
 
 
-class DatabaseDataframeImporter(BaseDatabaseImporter, BaseDataframeProcessor, ABC):
+class DatabaseDataframeImporter(BaseDatabaseImporter, BaseSourceProcessor, ABC):
     """
     Base Class for dataframe DB importers
     """
@@ -196,7 +196,7 @@ def __init__(
     #     raise NotImplementedError
 
 
-class DatabaseCrossmatchImporter(DatabaseDataframeImporter, BaseDataframeProcessor):
+class DatabaseCrossmatchImporter(DatabaseDataframeImporter, BaseSourceProcessor):
     """
     Processor to crossmatch to sources in a database
     """
@@ -253,7 +253,7 @@ def get_source_constraints(self, cand: pd.DataFrame) -> None | DBQueryConstraint
             return None
         return self.user_defined_constraints(cand)
 
-    def _apply_to_candidates(
+    def _apply_to_sources(
         self,
         batch: SourceBatch,
     ) -> SourceBatch:

mirar/processors/photometry/aperture_photometry.py

@@ -50,7 +50,7 @@ def __init__(
             self.col_suffix_list = self.aperture_photometer.aper_diameters
         self.zp_colname = zp_colname
 
-    def _apply_to_candidates(
+    def _apply_to_sources(
         self,
         batch: SourceBatch,
     ) -> SourceBatch:

mirar/processors/photometry/base_photometry.py

@@ -21,9 +21,9 @@
     get_output_dir,
 )
 from mirar.processors.base_processor import (
-    BaseDataframeProcessor,
     BaseImageProcessor,
     BaseProcessor,
+    BaseSourceProcessor,
     ImageHandler,
 )
 from mirar.processors.photometry.utils import (
@@ -224,7 +224,7 @@ def get_physical_coordinates(self, image: Image) -> (int, int):
         return int(np.round(x)), int(np.round(y))
 
 
-class BaseCandidatePhotometry(BasePhotometryProcessor, BaseDataframeProcessor):
+class BaseCandidatePhotometry(BasePhotometryProcessor, BaseSourceProcessor):
     """
     Processor to run photometry on a candidates table
     """

mirar/processors/photometry/psf_photometry.py

@@ -66,7 +66,7 @@ def get_psf_filename(self, row):
         psf_filename = row[self.psf_file_key]
         return psf_filename
 
-    def _apply_to_candidates(
+    def _apply_to_sources(
         self,
         batch: SourceBatch,
     ) -> SourceBatch:

mirar/processors/sources/__init__.py

@@ -0,0 +1,12 @@
+"""
+Central module for candidate detection and extraction.
+"""
+from mirar.processors.sources.candidate_filter import BaseSourceFilter
+from mirar.processors.sources.dataframe_writer import DataframeWriter
+from mirar.processors.sources.edge_mask import EdgeSourcesMask
+from mirar.processors.sources.namer import CandidateNamer
+from mirar.processors.sources.source_detector import SourceDetector
+from mirar.processors.sources.source_table_builder import (
+    SourceTablefromCoordinates,
+    SourceTablefromHeader,
+)

mirar/processors/sources/candidate_filter.py

@@ -0,0 +1,19 @@
+"""
+Base class for source filters
+"""
+import logging
+
+from mirar.data import SourceBatch
+from mirar.processors.base_processor import BaseSourceProcessor
+
+logger = logging.getLogger(__name__)
+
+
+class BaseSourceFilter(BaseSourceProcessor):
+    """
+    Base class for source filters
+    """
+    base_key = "filter"
+
+    def _apply_to_sources(self, batch: SourceBatch) -> SourceBatch:
+        raise NotImplementedError

mirar/processors/candidates/dataframe_writer.py → mirar/processors/sources/dataframe_writer.py

@@ -8,12 +8,12 @@
 
 from mirar.data import SourceBatch
 from mirar.paths import base_output_dir, get_output_dir, get_output_path
-from mirar.processors.base_processor import BaseDataframeProcessor
+from mirar.processors.base_processor import BaseSourceProcessor
 
 logger = logging.getLogger(__name__)
 
 
-class DataframeWriter(BaseDataframeProcessor):
+class DataframeWriter(BaseSourceProcessor):
     """
     Class to write a candidate table to a pandas dataframe
     """
@@ -35,7 +35,7 @@ def __str__(self) -> str:
             f"Processor to save candidates to {self.output_dir_name} as a json file. "
         )
 
-    def _apply_to_candidates(
+    def _apply_to_sources(
         self,
         batch: SourceBatch,
     ) -> SourceBatch: