ara fixes

brainlit/BrainLine/analyze_results.py

@@ -43,14 +43,21 @@ class BrainDistribution:
         brain_ids (list): List of brain IDs (keys of data json file).
     """
 
-    def __init__(self, brain_ids: list, data_file: str, ontology_file: str):
+    def __init__(self, brain_ids: list, data_file: str, ontology_file: str, fixes_file: str = None):
         self.brain_ids = brain_ids
         with open(data_file) as f:
             data = json.load(f)
         self.brain2paths = data["brain2paths"]
         self.subtype_counts = self._get_subtype_counts()
         self.ontology_file = ontology_file
 
+        if fixes_file == None:
+            self.ontology_fixes = None
+        else:
+            with open(fixes_file) as f:
+                data = json.load(f)
+            self.ontology_fixes = data
+
     def _slicetolabels(self, slice, fold_on: bool = False, atlas_level: int = 5):
         region_graph = _setup_atlas_graph(self.ontology_file)
         atlas_level_nodes = _get_atlas_level_nodes(atlas_level, region_graph)
@@ -121,11 +128,12 @@ def __init__(
         brain_ids: list,
         data_file: str,
         ontology_file: str,
+        fixes_file: str = None,
         show_plots: bool = True,
         bootstrap: int = 0,
         shuffle: bool = False,
     ):
-        super().__init__(brain_ids, data_file, ontology_file)
+        super().__init__(brain_ids, data_file, ontology_file, fixes_file)
         self.show_plots = show_plots
 
         atlas_points = self._retrieve_soma_coords(brain_ids)
@@ -209,6 +217,7 @@ def _retrieve_soma_coords(self, brain_ids: list):
 
     def _get_regions(self, points: dict, side: str = None):
         brain2paths = self.brain2paths
+        ontology_fixes = self.ontology_fixes
         if "filepath" in brain2paths["atlas"].keys():
             vol_atlas = io.imread(brain2paths["atlas"]["filepath"])
         else:
@@ -227,6 +236,9 @@ def _get_regions(self, points: dict, side: str = None):
                     continue
                 try:
                     region = int(vol_atlas[point_int[0], point_int[1], point_int[2]])
+
+                    if ontology_fixes != None and str(region) in ontology_fixes.keys():
+                        region = ontology_fixes[str(region)]["replacement"]
                 except IndexError:
                     continue
                 except OutOfBoundsError:
@@ -566,6 +578,7 @@ def _setup_regiongraph(self):
                         region_graph.nodes[region][brain_id]
                         + id_to_regioncounts[brain_id][region]
                     )
+
 
         # propagate counts up the hierarchy
         for brain_id in brain_ids:
@@ -989,9 +1002,10 @@ def __init__(
         data_file: str,
         regional_distribution_dir: str,
         ontology_file: str,
+        fixes_file: str = None,
         show_plots: bool = True,
     ):
-        super().__init__(brain_ids, data_file, ontology_file)
+        super().__init__(brain_ids, data_file, ontology_file, fixes_file)
         self.regional_distribution_dir = regional_distribution_dir
         region_graph, total_axon_vols = self._setup_regiongraph(
             regional_distribution_dir
@@ -1002,6 +1016,7 @@ def __init__(
     def _setup_regiongraph(self, regional_distribution_dir):
         regional_distribution_dir = self.regional_distribution_dir
         brain_ids = self.brain_ids
+        ontology_fixes = self.ontology_fixes
         region_graph = _setup_atlas_graph(self.ontology_file)
         max_level = 0
 
@@ -1023,14 +1038,19 @@ def _setup_regiongraph(self, regional_distribution_dir):
                 quantification_dict = pickle.load(f)
 
             for region in quantification_dict.keys():
-                if region in region_graph.nodes:
-                    region_graph.nodes[region][brain_id + " axon"] = region_graph.nodes[
-                        region
-                    ][brain_id + " axon"] + float(quantification_dict[region][1])
-                    region_graph.nodes[region][
+                if ontology_fixes != None and str(region) in ontology_fixes.keys():
+                    region_idx = ontology_fixes[str(region)]["replacement"]
+                else:
+                    region_idx = region
+
+                if region_idx in region_graph.nodes:
+                    region_graph.nodes[region_idx][brain_id + " axon"] = region_graph.nodes[
+                        region_idx
+                    ][brain_id + " axon"] + float(quantification_dict[region_idx][1])
+                    region_graph.nodes[region_idx][
                         brain_id + " total"
-                    ] = region_graph.nodes[region][brain_id + " total"] + float(
-                        quantification_dict[region][0]
+                    ] = region_graph.nodes[region_idx][brain_id + " total"] + float(
+                        quantification_dict[region_idx][0]
                     )
 
         total_axon_vols = {}

brainlit/BrainLine/data/open-nd-ara-fixes.json

@@ -0,0 +1,82 @@
+{
+    "182305696" : {
+        "point" : [473, 168, 252],
+        "replacement" : 182305689
+    },
+    "182305712" : {
+        "point" : [499, 216, 285],
+        "replacement" : 182305689
+    },
+    "312782560" : {
+        "point" : [666, 36, 441],
+        "replacement" : 312782546
+    },
+    "312782592" : {
+        "point" : [711, 71, 287],
+        "replacement" : 22
+    },
+    "312782656" : {
+        "point" : [896, 254, 197],
+        "replacement" : 312782628
+    },
+    "484682464" : {
+        "point" : [765, 203, 514],
+        "replacement" : 484682470
+    },
+    "526157184" : {
+        "point" : [211, 262, 474],
+        "replacement" : 526157192
+    },
+    "526322272" : {
+        "point" : [337, 320, 432],
+        "replacement" : 526322264
+    },
+    "527696992" : {
+        "point" : [337, 319, 457],
+        "replacement" : 527696977
+    },
+    "549009216" : {
+        "point" : [774, 335, 513],
+        "replacement" : 549009203
+    },
+    "560581568" : {
+        "point" : [592, 509, 566],
+        "replacement" : 560581559
+    },
+    "563807424" : {
+        "point" : [764, 348, 375],
+        "replacement" : 563807435
+    },
+    "576073728" : {
+        "point" : [521, 669, 540],
+        "replacement" : 576073699
+    },
+    "589508416" : {
+        "point" : [796, 611, 349],
+        "replacement" : 589508447
+    },
+    "589508480" : {
+        "point" : [1108, 405, 462],
+        "replacement" : 589508451
+    },
+    "599626944" : {
+        "point" : [752, 300, 563],
+        "replacement" : 599626923
+    },
+    "606826624" : {
+        "point" : [767, 608, 504],
+        "replacement" : 606826655
+    },
+    "606826688" : {
+        "point" : [787, 580, 541],
+        "replacement" : 606826659
+    },
+    "607344832" : {
+        "point" : [822, 532, 564],
+        "replacement" : 607344834
+    },
+    "614454272" : {
+        "point" : [903, 350, 541],
+        "replacement" : 614454277
+    }
+}

brainlit/BrainLine/data/open-nd-ara-fixes.txt

@@ -0,0 +1,25 @@
+https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=HxplM7aMw4lxeQ
+
+region 182305696 not found with vol: 685646 e.g.[473, 168, 252]: primary somatosensory area unassigned
+region 182305712 not found with vol: 576686 e.g.[499, 216, 285]: primary somatosensory area unassigned
+region 312782560 not found with vol: 1439164 e.g.[666, 36, 441]: anterior area
+region 312782592 not found with vol: 939216 e.g.[711, 71, 287]: anterior area and rostrolateral area and laterointermediate area
+region 312782656 not found with vol: 658788 e.g.[896, 254, 197]: postrhinal area
+region 484682464 not found with vol: 1328060 e.g.[765, 203, 514]: prosubiculum
+region 526157184 not found with vol: 483806 e.g.[211, 262, 474]: frontal pole layer 5
+region 526322272 not found with vol: 942 e.g.[337, 320, 432]: frontal pole, layer 6b
+region 527696992 not found with vol: 3708 e.g.[337, 319, 457]: orbital area, medial part, layer 6b
+region 549009216 not found with vol: 529062 e.g.[774, 335, 513]: retroparafasicular nucleus
+region 560581568 not found with vol: 499022 e.g.[592, 509, 566]: xiphoid thalamic nucleus
+region 563807424 not found with vol: 302102 e.g.[764, 348, 375]: posterior triangular thalamic nucleus
+region 576073728 not found with vol: 264382 e.g.[521, 669, 540]: ventromedial preoptic nucleus
+region 589508416 not found with vol: 421334 e.g.[796, 611, 349]: hippocampo-amygdalar transition area
+region 589508480 not found with vol: 187780 e.g.[1108, 405, 462]: paratrigeminal nucleus
+region 599626944 not found with vol: 62506 e.g.[752, 300, 563]: subcommissural organ
+region 606826624 not found with vol: 386320 e.g.[767, 608, 504]: medial mammillary nucleus, posterior part
+region 606826688 not found with vol: 93024 e.g.[787, 580, 541]: medial mammillary nucleus, dorsal part
+region 607344832 not found with vol: 365658 e.g.[822, 532, 564]: interpeduncular nucleus, rostral
+region 614454272 not found with vol: 42112 e.g.[903, 350, 541]: Supraoculomotor periaqueductal gray
+
+https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=_mB5Z7DqCWbDxA
+https://connectivity.brain-map.org/3d-viewer?v=1&types=IMAGEPLANE&IMAGEPLANE=imageplanes