Merge pull request #690 from dirac-institute/runner/masking

Obsolete the old masking

src/kbmod/configuration.py

@@ -18,27 +18,6 @@ class SearchConfiguration:
     def __init__(self):
         self._required_params = set()
 
-        default_mask_bits_dict = {
-            "BAD": 0,
-            "CLIPPED": 9,
-            "CR": 3,
-            "CROSSTALK": 10,
-            "DETECTED": 5,
-            "DETECTED_NEGATIVE": 6,
-            "EDGE": 4,
-            "INEXACT_PSF": 11,
-            "INTRP": 2,
-            "NOT_DEBLENDED": 12,
-            "NO_DATA": 8,
-            "REJECTED": 13,
-            "SAT": 1,
-            "SENSOR_EDGE": 14,
-            "SUSPECT": 7,
-            "UNMASKEDNAN": 15,
-        }
-        default_flag_keys = ["BAD", "EDGE", "NO_DATA", "SUSPECT", "UNMASKEDNAN"]
-        default_repeated_flag_keys = []
-
         self._params = {
             "ang_arr": [math.pi / 15, math.pi / 15, 128],
             "average_angle": None,
@@ -53,7 +32,6 @@ def __init__(self):
             "do_stamp_filter": True,
             "eps": 0.03,
             "encode_num_bytes": -1,
-            "flag_keys": default_flag_keys,
             "generator_config": None,
             "gpu_filter": False,
             "ind_output_files": True,
@@ -62,11 +40,6 @@ def __init__(self):
             "known_obj_thresh": None,
             "known_obj_jpl": False,
             "lh_level": 10.0,
-            "mask_bits_dict": default_mask_bits_dict,
-            "mask_bit_vector": None,
-            "mask_grow": 10,
-            "mask_num_images": 2,
-            "mask_threshold": None,
             "max_lh": 1000.0,
             "mjd_lims": None,
             "mom_lims": [35.5, 35.5, 2.0, 0.3, 0.3],
@@ -75,7 +48,6 @@ def __init__(self):
             "peak_offset": [2.0, 2.0],
             "psf_val": 1.4,
             "psf_file": None,
-            "repeated_flag_keys": default_repeated_flag_keys,
             "res_filepath": None,
             "result_filename": None,
             "results_per_pixel": 8,

src/kbmod/run_search.py

@@ -11,7 +11,7 @@
 from .filters.clustering_filters import apply_clustering
 from .filters.sigma_g_filter import apply_clipped_sigma_g, SigmaGClipping
 from .filters.stamp_filters import append_all_stamps, append_coadds, get_coadds_and_filter_results
-from .masking import apply_mask_operations
+
 from .results import Results
 from .trajectory_generator import create_trajectory_generator, KBMODV1SearchConfig
 from .wcs_utils import calc_ecliptic_angle
@@ -233,7 +233,8 @@ def run_search(self, config, stack, trj_generator=None):
 
         # Apply the mask to the images.
         if config["do_mask"]:
-            stack = apply_mask_operations(config, stack)
+            for i in range(stack.img_count()):
+                stack.get_single_image(i).apply_mask(0xFFFFFF)
 
         # Perform the actual search.
         if trj_generator is None:

src/kbmod/trajectory_explorer.py

@@ -2,7 +2,6 @@
 
 from kbmod.configuration import SearchConfiguration
 from kbmod.filters.sigma_g_filter import apply_clipped_sigma_g, SigmaGClipping
-from kbmod.masking import apply_mask_operations
 from kbmod.results import Results
 from kbmod.search import StackSearch, StampCreator, Logging
 from kbmod.filters.stamp_filters import append_all_stamps, append_coadds
@@ -48,10 +47,6 @@ def initialize_data(self):
         if self._data_initalized:
             return
 
-        # Check if we need to apply legacy masking.
-        if self.config["do_mask"]:
-            self.im_stack = apply_mask_operations(self.config, self.im_stack)
-
         # If we are using an encoded image representation on GPU, enable it and
         # set the parameters.
         if self.config["encode_num_bytes"] > 0:

tests/test_configuration.py

@@ -71,7 +71,6 @@ def test_to_hdu(self):
             "im_filepath": "Here2",
             "num_obs": 5,
             "cluster_type": None,
-            "mask_bits_dict": {"bit1": 1, "bit2": 2},
             "do_clustering": False,
             "res_filepath": "There",
             "ang_arr": [1.0, 2.0, 3.0],
@@ -82,7 +81,6 @@ def test_to_hdu(self):
         self.assertEqual(hdu.data["im_filepath"][0], "Here2\n...")
         self.assertEqual(hdu.data["num_obs"][0], "5\n...")
         self.assertEqual(hdu.data["cluster_type"][0], "null\n...")
-        self.assertEqual(hdu.data["mask_bits_dict"][0], "{bit1: 1, bit2: 2}")
         self.assertEqual(hdu.data["res_filepath"][0], "There\n...")
         self.assertEqual(hdu.data["ang_arr"][0], "[1.0, 2.0, 3.0]")
 
@@ -91,7 +89,6 @@ def test_to_yaml(self):
             "im_filepath": "Here2",
             "num_obs": 5,
             "cluster_type": None,
-            "mask_bits_dict": {"bit1": 1, "bit2": 2},
             "do_clustering": False,
             "res_filepath": "There",
             "ang_arr": [1.0, 2.0, 3.0],
@@ -103,8 +100,6 @@ def test_to_yaml(self):
         self.assertEqual(yaml_dict["im_filepath"], "Here2")
         self.assertEqual(yaml_dict["num_obs"], 5)
         self.assertEqual(yaml_dict["cluster_type"], None)
-        self.assertEqual(yaml_dict["mask_bits_dict"]["bit1"], 1)
-        self.assertEqual(yaml_dict["mask_bits_dict"]["bit2"], 2)
         self.assertEqual(yaml_dict["res_filepath"], "There")
         self.assertEqual(yaml_dict["ang_arr"][0], 1.0)
         self.assertEqual(yaml_dict["ang_arr"][1], 2.0)
@@ -117,7 +112,6 @@ def test_save_and_load_yaml(self):
         # Overwrite some defaults.
         config.set("im_filepath", "Here")
         config.set("output_suffix", "txt")
-        config.set("mask_grow", 5)
 
         with tempfile.TemporaryDirectory() as dir_name:
             file_path = os.path.join(dir_name, "tmp_config_data.yaml")
@@ -139,7 +133,6 @@ def test_save_and_load_yaml(self):
             self.assertEqual(len(config2._params), num_defaults)
             self.assertEqual(config2["im_filepath"], "Here")
             self.assertEqual(config2["res_filepath"], None)
-            self.assertEqual(config2["mask_grow"], 5)
             self.assertEqual(config2["output_suffix"], "txt")
 
     def test_save_and_load_fits(self):
@@ -149,8 +142,6 @@ def test_save_and_load_fits(self):
         # Overwrite some defaults.
         config.set("im_filepath", "Here2")
         config.set("output_suffix", "csv")
-        config.set("mask_grow", 7)
-        config.set("mask_bits_dict", {"bit1": 1, "bit2": 2})
 
         with tempfile.TemporaryDirectory() as dir_name:
             file_path = os.path.join(dir_name, "test.fits")
@@ -172,11 +163,9 @@ def test_save_and_load_fits(self):
 
             self.assertEqual(len(config2._params), num_defaults)
             self.assertEqual(config2["im_filepath"], "Here2")
-            self.assertEqual(config2["mask_grow"], 7)
             self.assertEqual(config2["output_suffix"], "csv")
 
             # Check that we correctly parse dictionaries and Nones.
-            self.assertEqual(len(config2["mask_bits_dict"]), 2)
             self.assertIsNone(config2["res_filepath"])