remove old powerspectrum normalization

flatironinstitute · Aug 15, 2024 · ddb19f9 · ddb19f9
1 parent 072c1ae
commit ddb19f9
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Showing 3 changed files with 0 additions and 43 deletions.
diff --git a/src/cryo_challenge/_preprocessing/__init__.py b/src/cryo_challenge/_preprocessing/__init__.py
@@ -3,7 +3,3 @@
     downsample_volume as downsample_volume,
     downsample_submission as downsample_submission,
 )
-from .normalize import (
-    compute_power_spectrum as compute_power_spectrum,
-    normalize_power_spectrum as normalize_power_spectrum,
-)
diff --git a/src/cryo_challenge/_svd/svd_pipeline.py b/src/cryo_challenge/_svd/svd_pipeline.py
@@ -8,10 +8,8 @@
     load_volumes,
     load_ref_vols,
     remove_mean_volumes,
-    normalize_power_spectrum_sub,
 )
 from ..data._validation.config_validators import validate_config_svd
-from .._preprocessing.normalize import compute_power_spectrum, normalize_power_spectrum
 
 
 def run_svd_with_ref(
@@ -127,13 +125,6 @@ def run_all_vs_all_pipeline(config: dict):
         dtype=dtype,
     )
 
-    volumes = normalize_power_spectrum_sub(
-        volumes,
-        metadata,
-        config["power_spectrum_normalization"]["ref_vol_key"],
-        config["power_spectrum_normalization"]["ref_vol_index"],
-    )
-
     volumes, mean_volumes = remove_mean_volumes(volumes, metadata)
 
     U, S, V, coeffs = run_svd_all_vs_all(volumes=volumes)
@@ -203,21 +194,6 @@ def run_all_vs_ref_pipeline(config: dict):
         dtype=dtype,
     )
 
-    # Normalize Power spectrums
-    idx_ref_vol = (
-        metadata[config["power_spectrum_normalization"]["ref_vol_key"]]["indices"][0]
-        + config["power_spectrum_normalization"]["ref_vol_index"]
-    )
-    ref_power_spectrum = compute_power_spectrum(volumes[idx_ref_vol])
-    ref_volumes = normalize_power_spectrum(ref_volumes, ref_power_spectrum)
-
-    volumes = normalize_power_spectrum_sub(
-        volumes,
-        metadata,
-        config["power_spectrum_normalization"]["ref_vol_key"],
-        config["power_spectrum_normalization"]["ref_vol_index"],
-    )
-
     # Remove mean volumes
     volumes, mean_volumes = remove_mean_volumes(volumes, metadata)
     ref_volumes, mean_volume = remove_mean_volumes(ref_volumes)

diff --git a/src/cryo_challenge/data/_io/svd_io_utils.py b/src/cryo_challenge/data/_io/svd_io_utils.py
@@ -2,7 +2,6 @@
 from typing import Tuple
 
 from ..._preprocessing.fourier_utils import downsample_volume
-from ..._preprocessing.normalize import compute_power_spectrum, normalize_power_spectrum
 
 
 def _remove_mean_volumes_sub(volumes, metadata):
@@ -33,20 +32,6 @@ def remove_mean_volumes(volumes, metadata=None):
     return volumes, mean_volumes
 
 
-def normalize_power_spectrum_sub(volumes, metadata, ref_vol_key, ref_vol_index):
-    volumes = volumes.clone()
-    idx_ref_vol = metadata[ref_vol_key]["indices"][0] + ref_vol_index
-    ref_power_spectrum = compute_power_spectrum(volumes[idx_ref_vol])
-
-    for key in metadata.keys():
-        indices = metadata[key]["indices"]
-        volumes[indices[0] : indices[1]] = normalize_power_spectrum(
-            volumes[indices[0] : indices[1]], ref_power_spectrum
-        )
-
-    return volumes
-
-
 def load_volumes(
     box_size_ds: float,
     submission_list: list,