Re-ordering post-processing functions

schilling40 · schilling40 · commit f6e2183c10a1 · 2025-11-24T15:20:49.000+01:00
diff --git a/flamingo_tools/measurements.py b/flamingo_tools/measurements.py
@@ -22,7 +22,7 @@
 from tqdm import tqdm
 
 from .file_utils import read_image_data
-from .segmentation.postprocessing import compute_table_on_the_fly
+from .postprocessing.label_components import compute_table_on_the_fly
 import flamingo_tools.s3_utils as s3_utils
 
 
diff --git a/flamingo_tools/postprocessing/chreef_utils.py b/flamingo_tools/postprocessing/chreef_utils.py
diff --git a/flamingo_tools/postprocessing/cochlea_mapping.py b/flamingo_tools/postprocessing/cochlea_mapping.py
@@ -7,7 +7,7 @@
 from scipy.ndimage import distance_transform_edt, binary_dilation, binary_closing
 from scipy.interpolate import interp1d
 
-from flamingo_tools.segmentation.postprocessing import downscaled_centroids
+from flamingo_tools.postprocessing.label_components import downscaled_centroids
 
 
 def find_most_distant_nodes(G: nx.classes.graph.Graph, weight: str = 'weight') -> Tuple[float, float]:
diff --git a/flamingo_tools/postprocessing/label_components.py b/flamingo_tools/postprocessing/label_components.py
diff --git a/flamingo_tools/postprocessing/sgn_subtype_utils.py b/flamingo_tools/postprocessing/sgn_subtype_utils.py
diff --git a/flamingo_tools/postprocessing/synapse_per_ihc_utils.py b/flamingo_tools/postprocessing/synapse_per_ihc_utils.py
@@ -0,0 +1,50 @@
+SYNAPSE_DICT = {
+    "M_LR_000226_L": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
+    "M_LR_000226_R": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
+    "M_LR_000227_L": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
+    "M_LR_000227_R": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
+    "G_EK_000233_L": {"synapse_table_name": "synapse_v3_ihc_v6", "ihc_table_name": "IHC_v6"},
+    "G_LR_000233_R": {"synapse_table_name": "synapse_v3_ihc_v6", "ihc_table_name": "IHC_v6"},
+
+    # fHC
+    "M_AMD_N139_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                     "component_list": [1, 4]},
+    "M_AMD_N139_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                     "component_list": [2, 5, 3]},
+    "M_AMD_N153_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b"},
+    "M_AMD_N153_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                     "component_list": [7, 1, 4]},
+
+    # PELCOfHC1
+    "M_AMD_N140_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                     "component_list": [1, 5]},
+    "M_AMD_N140_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b"},
+    "M_AMD_N142_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b"},
+    "M_AMD_N142_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                     "component_list": [2, 4, 3]},
+
+    # PELCOfHC2
+    "M_AMD_N75_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                    "component_list": [1, 3]},
+    "M_AMD_N75_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                    "component_list": [1, 5, 12, 4, 2, 13, 7]},
+    "M_AMD_N129_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                     "component_list": [2, 5, 3, 6]},
+    "M_AMD_N129_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                     "component_list": [4, 2, 6]},
+
+    # PELCODISCO2
+    "M_AMD_N88_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b"},
+    "M_AMD_N89_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                    "component_list": [1, 2]},
+
+    # PELCODISCO2
+    "M_AMD_N95_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                    "component_list": [1, 4, 3, 9, 17, 2]},
+    "M_AMD_N95_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                    "component_list": [8, 4, 2, 29, 6, 9, 3]},
+    "M_AMD_N97_L": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                    "component_list": [2, 1, 3]},
+    "M_AMD_N97_R": {"synapse_table_name": "synapse_v3_ihc_v4b", "ihc_table_name": "IHC_v4b",
+                    "component_list": [2, 5]},
+}
diff --git a/flamingo_tools/test_data.py b/flamingo_tools/test_data.py
@@ -10,7 +10,7 @@
 from skimage.measure import label
 
 from .file_utils import get_cache_dir
-from .segmentation.postprocessing import compute_table_on_the_fly
+from .postprocessing.label_components import compute_table_on_the_fly
 
 SEGMENTATION_URL = "https://owncloud.gwdg.de/index.php/s/kwoGRYiJRRrswgw/download"
 
diff --git a/reproducibility/block_extraction/repro_equidistant_centers.py b/reproducibility/block_extraction/repro_equidistant_centers.py
@@ -5,7 +5,7 @@
 
 import pandas as pd
 from flamingo_tools.s3_utils import get_s3_path
-from flamingo_tools.segmentation.cochlea_mapping import equidistant_centers
+from flamingo_tools.postprocessing.cochlea_mapping import equidistant_centers
 
 
 def repro_equidistant_centers(
diff --git a/reproducibility/label_components/repro_label_components.py b/reproducibility/label_components/repro_label_components.py
@@ -5,7 +5,7 @@
 
 import pandas as pd
 from flamingo_tools.s3_utils import get_s3_path
-from flamingo_tools.segmentation.postprocessing import label_components_sgn, label_components_ihc
+from flamingo_tools.postprocessing.label_components import label_components_sgn, label_components_ihc
 
 
 def label_custom_components(tsv_table, custom_dict):
diff --git a/reproducibility/tonotopic_mapping/repro_tonotopic_mapping.py b/reproducibility/tonotopic_mapping/repro_tonotopic_mapping.py
@@ -5,7 +5,7 @@
 
 import pandas as pd
 from flamingo_tools.s3_utils import get_s3_path
-from flamingo_tools.segmentation.cochlea_mapping import tonotopic_mapping
+from flamingo_tools.postprocessing.cochlea_mapping import tonotopic_mapping
 
 
 def repro_tonotopic_mapping(
diff --git a/scripts/assign_subtypes.py b/scripts/assign_subtypes.py
@@ -4,7 +4,7 @@
 import pandas as pd
 
 from flamingo_tools.s3_utils import get_s3_path, BUCKET_NAME, SERVICE_ENDPOINT
-from flamingo_tools.segmentation.sgn_subtype_utils import STAIN_TO_TYPE, COCHLEAE
+from flamingo_tools.postprocessing.sgn_subtype_utils import STAIN_TO_TYPE, COCHLEAE
 # from skimage.segmentation import relabel_sequential
 
 
diff --git a/scripts/export_lower_resolution.py b/scripts/export_lower_resolution.py
@@ -10,7 +10,7 @@
 from elf.parallel import isin
 
 from flamingo_tools.s3_utils import get_s3_path, BUCKET_NAME, SERVICE_ENDPOINT
-from flamingo_tools.segmentation.postprocessing import filter_cochlea_volume, filter_cochlea_volume_single
+from flamingo_tools.postprocessing.label_components import filter_cochlea_volume, filter_cochlea_volume_single
 # from skimage.segmentation import relabel_sequential
 
 
diff --git a/scripts/export_lower_resolution_subtypes.py b/scripts/export_lower_resolution_subtypes.py
@@ -7,7 +7,7 @@
 import zarr
 
 from flamingo_tools.s3_utils import get_s3_path, BUCKET_NAME, SERVICE_ENDPOINT
-from flamingo_tools.segmentation.sgn_subtype_utils import STAIN_TO_TYPE, COCHLEAE
+from flamingo_tools.postprocessing.sgn_subtype_utils import STAIN_TO_TYPE, COCHLEAE
 # from skimage.segmentation import relabel_sequential
 
 
diff --git a/scripts/figures/plot_SGNsub_thresholds.py b/scripts/figures/plot_SGNsub_thresholds.py
@@ -8,7 +8,7 @@
 import pandas as pd
 
 from flamingo_tools.s3_utils import get_s3_path
-from flamingo_tools.segmentation.sgn_subtype_utils import CUSTOM_THRESHOLDS, COCHLEAE, ALIAS
+from flamingo_tools.postprocessing.sgn_subtype_utils import CUSTOM_THRESHOLDS, COCHLEAE, ALIAS
 
 png_dpi = 300
 
diff --git a/scripts/figures/plot_fig3.py b/scripts/figures/plot_fig3.py
@@ -18,7 +18,7 @@
 from flamingo_tools.s3_utils import BUCKET_NAME, create_s3_target, get_s3_path
 from util import frequency_mapping, SYNAPSE_DIR_ROOT, custom_formatter_1, average_by_fraction
 from util import prism_style, prism_cleanup_axes, export_legend, get_marker_handle, get_flatline_handle
-from flamingo_tools.segmentation.sgn_subtype_utils import stain_to_type, COCHLEAE, ALIAS
+from flamingo_tools.postprocessing.sgn_subtype_utils import stain_to_type, COCHLEAE, ALIAS
 
 INPUT_ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/frequency_mapping/M_LR_000227_R/scale3"
 SYNAPSE_DIR = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/predictions/synapses"
diff --git a/scripts/figures/plot_supp_fig3.py b/scripts/figures/plot_supp_fig3.py
@@ -10,9 +10,8 @@
 
 from flamingo_tools.s3_utils import get_s3_path
 from sklearn.metrics import confusion_matrix, ConfusionMatrixDisplay
-from flamingo_tools.segmentation.sgn_subtype_utils import COCHLEAE, CUSTOM_THRESHOLDS
+from flamingo_tools.postprocessing.sgn_subtype_utils import ALIAS, COCHLEAE, CUSTOM_THRESHOLDS
 from util import prism_style, prism_cleanup_axes, export_legend, get_flatline_handle
-from flamingo_tools.segmentation.sgn_subtype_utils import ALIAS
 
 png_dpi = 300
 FILE_EXTENSION = "png"
diff --git a/scripts/la-vision/segment_sgns.py b/scripts/la-vision/segment_sgns.py
@@ -3,7 +3,7 @@
 
 import pandas as pd
 from flamingo_tools.segmentation import run_unet_prediction
-from flamingo_tools.segmentation.postprocessing import label_components_sgn
+from flamingo_tools.postprocessing.label_components import label_components_sgn
 from mobie import add_segmentation
 from mobie.metadata import add_remote_project_metadata
 
diff --git a/scripts/measurements/evaluate_marker_annotations_subtype.py b/scripts/measurements/evaluate_marker_annotations_subtype.py
@@ -7,8 +7,8 @@
 
 from flamingo_tools.s3_utils import get_s3_path
 from flamingo_tools.file_utils import read_image_data
-from flamingo_tools.segmentation.chreef_utils import localize_median_intensities, find_annotations
-from flamingo_tools.segmentation.sgn_subtype_utils import CUSTOM_THRESHOLDS, COCHLEAE
+from flamingo_tools.postprocessing.chreef_utils import localize_median_intensities, find_annotations
+from flamingo_tools.postprocessing.sgn_subtype_utils import CUSTOM_THRESHOLDS, COCHLEAE
 
 MARKER_DIR_SUBTYPE = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/SGN_subtypes"
 
diff --git a/scripts/measurements/measure_synapses.py b/scripts/measurements/measure_synapses.py
@@ -6,28 +6,10 @@
 import pandas as pd
 
 from flamingo_tools.s3_utils import BUCKET_NAME, create_s3_target
-
-OUTPUT_FOLDER = "./ihc_counts"
-
-COCHLEAE = [
-    "M_LR_000226_L",
-    "M_LR_000226_R",
-    "M_LR_000227_L",
-    "M_LR_000227_R",
-    "G_EK_000233_L",
-    "G_LR_000233_R",
-
-]
+from flamingo_tools.postprocessing.synapse_per_ihc_utils import SYNAPSE_DICT
 
 
-SYNAPSE_DICT = {
-    "M_LR_000226_L": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
-    "M_LR_000226_R": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
-    "M_LR_000227_L": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
-    "M_LR_000227_R": {"synapse_table_name": "synapse_v3_ihc_v4c", "ihc_table_name": "IHC_v4c"},
-    "G_EK_000233_L": {"synapse_table_name": "synapse_v3_ihc_v6", "ihc_table_name": "IHC_v6"},
-    "G_LR_000233_R": {"synapse_table_name": "synapse_v3_ihc_v6", "ihc_table_name": "IHC_v6"},
-}
+OUTPUT_FOLDER = "./ihc_counts"
 
 
 def check_project(cochleae, output_folder, plot=False, save_ihc_table=False, max_dist=None):
@@ -37,12 +19,12 @@ def check_project(cochleae, output_folder, plot=False, save_ihc_table=False, max
         if cochlea in SYNAPSE_DICT.keys():
             synapse_table_name = SYNAPSE_DICT[cochlea]["synapse_table_name"]
             ihc_table_name = SYNAPSE_DICT[cochlea]["ihc_table_name"]
+            component_id = SYNAPSE_DICT[cochlea].get("component_list", [1])
 
         else:
-            synapse_table_name = "synapse_v3_ihc_v4c"
-            ihc_table_name = "IHC_v4c"
-
-        component_id = [1]
+            synapse_table_name = "synapse_v3_ihc_v4b"
+            ihc_table_name = "IHC_v4b"
+            component_id = [1]
 
         if cochlea == "M_AMD_OTOF1_L":
             synapse_table_name = "synapse_v3_ihc_v4b"
@@ -132,7 +114,8 @@ def main():
         description="Assign each segmentation instance a marker based on annotation thresholds."
     )
 
-    parser.add_argument("-c", "--cochlea", type=str, nargs="+", default=COCHLEAE, help="Cochlea(e) to process.")
+    parser.add_argument("-c", "--cochlea", type=str, nargs="+", default=list(SYNAPSE_DICT.keys()),
+                        help="Cochlea(e) to process.")
     parser.add_argument("-o", "--output", type=str, default=OUTPUT_FOLDER, help="Output directory.")
 
     args = parser.parse_args()
diff --git a/scripts/measurements/sgn_subtypes.py b/scripts/measurements/sgn_subtypes.py
@@ -9,7 +9,7 @@
 
 from flamingo_tools.s3_utils import BUCKET_NAME, create_s3_target
 from flamingo_tools.measurements import compute_object_measures
-from flamingo_tools.segmentation.sgn_subtype_utils import COCHLEAE, stain_to_type
+from flamingo_tools.postprocessing.sgn_subtype_utils import COCHLEAE, stain_to_type
 
 
 # Define the animal specific octave bands.
diff --git a/scripts/measurements/subtype_overview.py b/scripts/measurements/subtype_overview.py
@@ -4,7 +4,7 @@
 import numpy as np
 import pandas as pd
 from flamingo_tools.s3_utils import BUCKET_NAME, create_s3_target
-from sgn_subtypes import COCHLEAE
+from flamingo_tools.postprocessing.sgn_subtype_utils import COCHLEAE
 
 
 def get_overview(cochlea, seg_name, component_ids):
diff --git a/scripts/prediction/expand_seg_table.py b/scripts/prediction/expand_seg_table.py
@@ -4,7 +4,7 @@
 
 import pandas as pd
 
-import flamingo_tools.segmentation.postprocessing as postprocessing
+import flamingo_tools.postprocessing.label_components as postprocessing
 import flamingo_tools.s3_utils as s3_utils
 
 
diff --git a/scripts/prediction/postprocess_seg.py b/scripts/prediction/postprocess_seg.py
@@ -6,8 +6,8 @@
 
 import flamingo_tools.s3_utils as s3_utils
 from flamingo_tools.segmentation import filter_segmentation
-from flamingo_tools.segmentation.postprocessing import nearest_neighbor_distance, local_ripleys_k, neighbors_in_radius
-from flamingo_tools.segmentation.postprocessing import label_components_sgn
+from flamingo_tools.postprocessing.label_components import nearest_neighbor_distance, local_ripleys_k, neighbors_in_radius
+from flamingo_tools.postprocessing.label_components import label_components_sgn
 
 
 # TODO needs updates
diff --git a/scripts/prediction/tonotopic_mapping.py b/scripts/prediction/tonotopic_mapping.py
@@ -3,7 +3,7 @@
 import pandas as pd
 
 import flamingo_tools.s3_utils as s3_utils
-from flamingo_tools.segmentation.cochlea_mapping import tonotopic_mapping
+from flamingo_tools.postprocessing.cochlea_mapping import tonotopic_mapping
 
 
 def main():
diff --git a/scripts/synapse_marker_detection/add_synapse_per_ihc.py b/scripts/synapse_marker_detection/add_synapse_per_ihc.py
@@ -5,14 +5,7 @@
 import pandas as pd
 
 from flamingo_tools.s3_utils import get_s3_path, BUCKET_NAME, SERVICE_ENDPOINT
-
-COCHLEAE = {
-    "M_LR_000226_L": {"seg_name": "IHC_v4c", "component_list": [1]},
-    "M_LR_000226_R": {"seg_name": "IHC_v4c", "component_list": [1]},
-    "M_LR_000227_L": {"seg_name": "IHC_v4c", "component_list": [1]},
-    "M_LR_000227_R": {"seg_name": "IHC_v4c", "component_list": [1]},
-    "M_AMD_OTOF1_L": {"seg_name": "IHC_v4b", "component_list": [3, 11]},
-}
+from flamingo_tools.postprocessing.synapse_per_ihc_utils import SYNAPSE_DICT
 
 COCHLEA_DIR = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet"
 OUT_DIR = f"{COCHLEA_DIR}/mobie_project/cochlea-lightsheet/tables/syn_per_ihc"
@@ -28,19 +21,19 @@ def add_syn_per_ihc(args):
 
     for cochlea in args.cochlea:
         if args.seg_version is None:
-            seg_version = COCHLEAE[cochlea]["seg_name"]
+            seg_version = SYNAPSE_DICT[cochlea]["ihc_table_name"]
         else:
-            seg_version = args.seg_version
+            seg_version = "IHC_v4b"
 
         print(f"Evaluating cochlea {cochlea}.")
 
         ihc_version = seg_version.split("_")[1]
         syn_per_ihc_dir = f"{COCHLEA_DIR}/predictions/synapses/ihc_counts_{ihc_version}"
 
         if args.component_list is None:
-            component_list = COCHLEAE[cochlea]["component_list"]
+            component_list = SYNAPSE_DICT[cochlea].get("component_list", [1])
         else:
-            component_list = args.component_list
+            component_list = [1]
 
         s3_path = os.path.join(f"{cochlea}", "tables", seg_version, "default.tsv")
         tsv_path, fs = get_s3_path(s3_path, bucket_name=BUCKET_NAME,
@@ -50,6 +43,10 @@ def add_syn_per_ihc(args):
 
         # synapse_table
         syn_path = os.path.join(syn_per_ihc_dir, f"ihc_count_{cochlea}.tsv")
+        if not os.path.isfile(syn_path):
+            print(f"Skipping cochlea {cochlea}. Synapse table {syn_path} does not exist.")
+            continue
+
         with open(syn_path, 'r') as f:
             syn_table = pd.read_csv(f, sep="\t")
 
@@ -81,7 +78,8 @@ def add_syn_per_ihc(args):
 def main():
 
     parser = argparse.ArgumentParser()
-    parser.add_argument("-c", "--cochlea", type=str, nargs="+", default=COCHLEAE, help="Cochlea(e) to process.")
+    parser.add_argument("-c", "--cochlea", type=str, nargs="+", default=list(SYNAPSE_DICT.keys()),
+                        help="Cochlea(e) to process.")
     parser.add_argument("-o", "--output_folder", type=str, default=None, help="Path to output folder.")
     parser.add_argument("-s", "--seg_version", type=str, default=None, help="Path to output folder.")
     parser.add_argument("--ihc_syn", action="store_true", help="Consider only IHC with synapses.")
diff --git a/test/test_segmentation/test_postprocessing.py b/test/test_segmentation/test_postprocessing.py
@@ -17,7 +17,7 @@ def _create_example_seg(self, tmp_dir):
         return seg
 
     def _test_postprocessing(self, spatial_statistics, threshold, **spatial_statistics_kwargs):
-        from flamingo_tools.segmentation.postprocessing import filter_segmentation
+        from flamingo_tools.postprocessing.label_components import filter_segmentation
 
         with tempfile.TemporaryDirectory() as tmp_dir:
             example_seg = self._create_example_seg(tmp_dir)
@@ -33,22 +33,22 @@ def _test_postprocessing(self, spatial_statistics, threshold, **spatial_statisti
             self.assertEqual(filtered_seg.shape, example_seg.shape)
 
     def test_nearest_neighbor_distance(self):
-        from flamingo_tools.segmentation.postprocessing import nearest_neighbor_distance
+        from flamingo_tools.postprocessing.label_components import nearest_neighbor_distance
 
         self._test_postprocessing(nearest_neighbor_distance, threshold=5)
 
     def test_local_ripleys_k(self):
-        from flamingo_tools.segmentation.postprocessing import local_ripleys_k
+        from flamingo_tools.postprocessing.label_components import local_ripleys_k
 
         self._test_postprocessing(local_ripleys_k, threshold=0.5)
 
     def test_neighbors_in_radius(self):
-        from flamingo_tools.segmentation.postprocessing import neighbors_in_radius
+        from flamingo_tools.postprocessing.label_components import neighbors_in_radius
 
         self._test_postprocessing(neighbors_in_radius, threshold=5)
 
     def test_compute_table_on_the_fly(self):
-        from flamingo_tools.segmentation.postprocessing import compute_table_on_the_fly
+        from flamingo_tools.postprocessing.label_components import compute_table_on_the_fly
         from flamingo_tools.test_data import get_test_volume_and_segmentation
 
         with tempfile.TemporaryDirectory() as tmp_dir:
