clean and refactor spot detection

fish-quant · May 5, 2020 · 7e4d47d · 7e4d47d
1 parent 3091a1c
commit 7e4d47d
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Showing 5 changed files with 300 additions and 313 deletions.
diff --git a/bigfish/detection/__init__.py b/bigfish/detection/__init__.py
@@ -7,17 +7,14 @@
 3-d.
 """
 
-from .spot_detection import log_lm
+from .utils import get_sigma
+from .utils import get_radius
+from .utils import compute_snr
+from .utils import from_threshold_to_snr
+
+from .spot_detection import spot_detector
 from .spot_detection import local_maximum_detection
 from .spot_detection import spots_thresholding
-from .spot_detection import compute_snr
-from .spot_detection import from_threshold_to_snr
-from .spot_detection import get_sigma
-from .spot_detection import log_cc
-from .spot_detection import get_cc
-from .spot_detection import log_lm
-from .spot_detection import log_lm
-from .spot_detection import log_lm
 
 from .cluster_decomposition import gaussian_3d
 from .cluster_decomposition import precompute_erf
@@ -36,16 +33,16 @@
 from .foci_detection import extract_foci
 
 
+_utils = [
+    "get_sigma",
+    "get_radius",
+    "compute_snr",
+    "from_threshold_to_snr"]
+
 _spots = [
-    "log_lm",
+    "spot_detector",
     "local_maximum_detection",
-    "spots_thresholding",
-    "compute_snr",
-    "from_threshold_to_snr",
-    "get_sigma",
-    "log_cc",
-    "get_cc",
-    "filter_cc"]
+    "spots_thresholding"]
 
 _clusters = [
     "gaussian_3d",
@@ -65,4 +62,4 @@
     "cluster_spots",
     "extract_foci"]
 
-__all__ = _spots + _clusters + _foci
+__all__ = _utils + _spots + _clusters + _foci