pool settings

meteor/diffmaps.py

@@ -6,12 +6,10 @@
 import reciprocalspaceship as rs
 
 from .rsmap import Map, _assert_is_map
-from .settings import MAP_SAMPLING
+from .settings import DEFAULT_KPARAMS_TO_SCAN, MAP_SAMPLING
 from .utils import filter_common_indices
 from .validate import ScalarMaximizer, negentropy
 
-DEFAULT_KPARAMS_TO_SCAN = np.linspace(0.0, 1.0, 101)
-
 
 def set_common_crystallographic_metadata(map1: Map, map2: Map, *, output: Map) -> None:
     if hasattr(map1, "cell"):

meteor/io.py

@@ -5,30 +5,14 @@
 from __future__ import annotations
 
 import re
-from typing import Final
-
-OBSERVED_INTENSITY_COLUMNS: Final[list[str]] = [
-    "I",  # generic
-    "IMEAN",  # CCP4
-    "I-obs",  # phenix
-]
-
-OBSERVED_AMPLITUDE_COLUMNS: Final[list[str]] = [
-    "F",  # generic
-    "FP",  # CCP4 & GLPh native
-    r"FPH\d",  # CCP4 derivative
-    "F-obs",  # phenix
-]
-
-OBSERVED_UNCERTAINTY_COLUMNS: Final[list[str]] = [
-    "SIGF",  # generic
-    "SIGFP",  # CCP4 & GLPh native
-    r"SIGFPH\d",  # CCP4
-]
-
-COMPUTED_AMPLITUDE_COLUMNS: Final[list[str]] = ["FC"]
-
-COMPUTED_PHASE_COLUMNS: Final[list[str]] = ["PHIC"]
+
+from .settings import (
+    COMPUTED_AMPLITUDE_COLUMNS,
+    COMPUTED_PHASE_COLUMNS,
+    OBSERVED_AMPLITUDE_COLUMNS,
+    OBSERVED_INTENSITY_COLUMNS,
+    OBSERVED_UNCERTAINTY_COLUMNS,
+)
 
 
 class AmbiguousMtzColumnError(ValueError): ...

meteor/iterative.py

@@ -6,14 +6,13 @@
 import pandas as pd
 
 from .rsmap import Map
+from .settings import DEFAULT_TV_WEIGHTS_TO_SCAN_AT_EACH_ITERATION
 from .tv import TvDenoiseResult, tv_denoise_difference_map
 from .utils import (
     average_phase_diff_in_degrees,
     complex_array_to_rs_dataseries,
 )
 
-DEFAULT_TV_WEIGHTS_TO_SCAN = [0.001, 0.01, 0.1, 1.0]
-
 
 def _project_derivative_on_experimental_set(
     *,
@@ -140,7 +139,7 @@ def iterative_tv_phase_retrieval(
     *,
     convergence_tolerance: float = 1e-4,
     max_iterations: int = 1000,
-    tv_weights_to_scan: list[float] = DEFAULT_TV_WEIGHTS_TO_SCAN,
+    tv_weights_to_scan: list[float] = DEFAULT_TV_WEIGHTS_TO_SCAN_AT_EACH_ITERATION,
 ) -> tuple[Map, pd.DataFrame]:
     """
     Here is a brief pseudocode sketch of the alogrithm. Structure factors F below are complex unless

meteor/settings.py

@@ -1,12 +1,44 @@
 from __future__ import annotations
 
+import numpy as np
+
+# map computation
+COMPUTED_MAP_RESOLUTION_LIMIT: float = 1.0
+GEMMI_HIGH_RESOLUTION_BUFFER: float = 1e-6
+
+
+# known map labels
+OBSERVED_INTENSITY_COLUMNS: list[str] = [
+    "I",  # generic
+    "IMEAN",  # CCP4
+    "I-obs",  # phenix
+]
+OBSERVED_AMPLITUDE_COLUMNS: list[str] = [
+    "F",  # generic
+    "FP",  # CCP4 & GLPh native
+    r"FPH\d",  # CCP4 derivative
+    "F-obs",  # phenix
+]
+OBSERVED_UNCERTAINTY_COLUMNS: list[str] = [
+    "SIGF",  # generic
+    "SIGFP",  # CCP4 & GLPh native
+    r"SIGFPH\d",  # CCP4
+]
+COMPUTED_AMPLITUDE_COLUMNS: list[str] = ["FC"]
+COMPUTED_PHASE_COLUMNS: list[str] = ["PHIC"]
+
+
+# k-weighting
+KWEIGHT_PARAMETER_DEFAULT: float = 0.05
+DEFAULT_KPARAMS_TO_SCAN = np.linspace(0.0, 1.0, 101)
+
+
+# tv denoising
+TV_WEIGHT_DEFAULT: float = 0.01
 BRACKET_FOR_GOLDEN_OPTIMIZATION: tuple[float, float] = (0.0, 0.05)
 TV_STOP_TOLERANCE: float = 0.00000005
 TV_MAX_NUM_ITER: int = 50
 MAP_SAMPLING: int = 3
 
-KWEIGHT_PARAMETER_DEFAULT: float = 0.05
-TV_WEIGHT_DEFAULT: float = 0.01
-
-COMPUTED_MAP_RESOLUTION_LIMIT: float = 1.0
-GEMMI_HIGH_RESOLUTION_BUFFER: float = 1e-6
+# iterative tv
+DEFAULT_TV_WEIGHTS_TO_SCAN_AT_EACH_ITERATION = [0.001, 0.01, 0.1, 1.0]

test/unit/scripts/test_common.py

@@ -51,7 +51,9 @@ def test_diffmap_set_scale(diffmap_set: DiffMapSet, use_uncertainties: bool) ->
     assert np.all(derivative_amps_before * 2 == diffmap_set.derivative["F"].to_numpy())
 
 
-def test_diffmap_argparser_parse_args(base_cli_arguments: list[str]) -> None:
+def test_diffmap_argparser_parse_args(
+    base_cli_arguments: list[str], fixed_kparameter: float
+) -> None:
     parser = DiffmapArgParser()
     args = parser.parse_args(base_cli_arguments)
 
@@ -65,7 +67,7 @@ def test_diffmap_argparser_parse_args(base_cli_arguments: list[str]) -> None:
     assert args.mtzout == Path("fake-output.mtz")
     assert args.metadataout == Path("fake-output-metadata.csv")
     assert args.kweight_mode == WeightMode.fixed
-    assert args.kweight_parameter == 0.75
+    assert args.kweight_parameter == fixed_kparameter
 
 
 def test_diffmap_argparser_check_output_filepaths(