scatter plot

neurodata · Jan 3, 2024 · ed9df83 · ed9df83
1 parent 8c98326
commit ed9df83
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Showing 14 changed files with 48 additions and 347 deletions.
diff --git a/brainlit/BrainLine/analyze_results.py b/brainlit/BrainLine/analyze_results.py
@@ -459,17 +459,14 @@ def region_barchart(
             "y": "Region",
             "hue": "Subtype",
             "data": df,
-            # "jitter": False,
-            "dodge": True,
         }
 
         sns.set(font_scale=2)
-        bplot = sns.stripplot(ax=axes[0, 0], orient="h", legend=False, **fig_args)
+        bplot = sns.scatterplot(ax=axes[0, 0], **fig_args)
         fig_args["boxprops"] = {"facecolor": "none"}
         bplot = sns.boxplot(ax=axes[0, 0], orient="h", **fig_args)
         bplot.set_xscale("log")
 
-        fig_args.pop("dodge")
         fig_args.pop("boxprops")
         fig_args["style"] = "Brain ID"
         sns.scatterplot(ax=axes[1, 0], **fig_args)
@@ -483,14 +480,12 @@ def region_barchart(
 
         # second panel
         fig_args["x"] = "Percent of Total Somas (%)"
-        fig_args["dodge"] = True
 
-        bplot = sns.stripplot(ax=axes[0, 1], orient="h", legend=False, **fig_args)
+        bplot = sns.scatterplot(ax=axes[0, 1], **fig_args)
         fig_args["boxprops"] = {"facecolor": "none"}
         bplot = sns.boxplot(ax=axes[0, 1], orient="h", **fig_args)
         bplot.set_xscale("log")
 
-        fig_args.pop("dodge")
         fig_args.pop("boxprops")
         fig_args["style"] = "Brain ID"
         sns.scatterplot(ax=axes[1, 1], **fig_args)
@@ -507,15 +502,13 @@ def region_barchart(
         # third panel
         if normalize_region >= 0:
             fig_args["x"] = "Normalized Somas"
-            fig_args["dodge"] = True
 
             sns.set(font_scale=2)
-            bplot = sns.stripplot(ax=axes[0, 2], orient="h", legend=False, **fig_args)
+            bplot = sns.scatterplot(ax=axes[0, 2], **fig_args)
             fig_args["boxprops"] = {"facecolor": "none"}
             bplot = sns.boxplot(ax=axes[0, 2], orient="h", **fig_args)
             bplot.set_xscale("log")
 
-            fig_args.pop("dodge")
             fig_args.pop("boxprops")
             fig_args["style"] = "Brain ID"
             sns.scatterplot(ax=axes[1, 2], **fig_args)
@@ -1199,12 +1192,10 @@ def region_barchart(
             "y": "Region",
             "hue": "Subtype",
             "data": df,
-            # "jitter": False,
-            "dodge": True,
         }
 
         sns.set(font_scale=2)
-        bplot = sns.stripplot(ax=axes[0], orient="h", legend=False, **fig_args)
+        bplot = sns.scatterplot(ax=axes[0], **fig_args)
         fig_args["boxprops"] = {"facecolor": "none"}
         bplot = sns.boxplot(ax=axes[0], orient="h", **fig_args)
         bplot.set_xscale("log")
@@ -1220,11 +1211,9 @@ def region_barchart(
             "y": "Region",
             "hue": "Subtype",
             "data": df,
-            # "jitter": False,
-            "dodge": True,
         }
 
-        bplot = sns.stripplot(ax=axes[1], orient="h", legend=False, **fig_args)
+        bplot = sns.scatterplot(ax=axes[1], **fig_args)
         fig_args["boxprops"] = {"facecolor": "none"}
         bplot = sns.boxplot(ax=axes[1], orient="h", **fig_args)
         bplot.set_xscale("log")
@@ -1243,12 +1232,10 @@ def region_barchart(
                 "y": "Region",
                 "hue": "Subtype",
                 "data": df,
-                # "jitter": False,
-                "dodge": True,
             }
 
             sns.set(font_scale=2)
-            bplot = sns.stripplot(ax=axes[2], orient="h", legend=False, **fig_args)
+            bplot = sns.scatterplot(ax=axes[2], **fig_args)
             fig_args["boxprops"] = {"facecolor": "none"}
             bplot = sns.boxplot(ax=axes[2], orient="h", **fig_args)
             bplot.set_xscale("log")

diff --git a/docs/notebooks/pipelines/BrainLine/axon_analysis.ipynb b/docs/notebooks/pipelines/BrainLine/axon_analysis.ipynb
@@ -117,7 +117,8 @@
     "with open(data_file, \"r\") as f:\n",
     "    data = json.load(f)\n",
     "\n",
-    "data[\"brain2paths\"][\"test\"][\"base\"] = (\n",
+    "\n",
+    "base = (\n",
     "    \"precomputed://file://\"\n",
     "    + str(\n",
     "        brainlit_path\n",
@@ -129,6 +130,8 @@
     "    )\n",
     "    + \"/\"\n",
     ")\n",
+    "data[\"brain2paths\"][\"test\"][\"base_s3\"] = base\n",
+    "data[\"brain2paths\"][\"test\"][\"base_local\"] = base\n",
     "\n",
     "brain2paths = data[\"brain2paths\"]\n",
     "\n",

diff --git a/docs/notebooks/pipelines/BrainLine/axon_data.json b/docs/notebooks/pipelines/BrainLine/axon_data.json
@@ -15,8 +15,7 @@
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=Ap9ZkdUyOAZqMg",
                 "layer": "val"
             },
-            "subtype": "test_type",
-            "base": "precomputed://file:///Users/thomasathey/Documents/mimlab/mouselight/brainlit_parent/brainlit/docs/notebooks/pipelines/BrainLine/example-data/"
+            "subtype": "test_type"
         },
         "pytest": {
             "base_s3": "precomputed://https://open-neurodata.s3.amazonaws.com/ara_2016/sagittal_10um/",

diff --git a/docs/notebooks/pipelines/BrainLine/soma_analysis.ipynb b/docs/notebooks/pipelines/BrainLine/soma_analysis.ipynb
@@ -118,7 +118,7 @@
     "with open(data_file, \"r\") as f:\n",
     "    data = json.load(f)\n",
     "\n",
-    "data[\"brain2paths\"][\"test\"][\"base\"] = (\n",
+    "base = (\n",
     "    \"precomputed://file://\"\n",
     "    + str(\n",
     "        brainlit_path\n",
@@ -130,6 +130,8 @@
     "    )\n",
     "    + \"/\"\n",
     ")\n",
+    "data[\"brain2paths\"][\"test\"][\"base_s3\"] = base\n",
+    "data[\"brain2paths\"][\"test\"][\"base_local\"] = base\n",
     "\n",
     "brain2paths = data[\"brain2paths\"]\n",
     "\n",

diff --git a/docs/notebooks/pipelines/BrainLine/soma_data.json b/docs/notebooks/pipelines/BrainLine/soma_data.json
@@ -16,8 +16,7 @@
                 "nonsomas_layer": "nonsoma_val"
             },
             "somas_atlas_url": "https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=iRoE0KP6J0ULDg",
-            "subtype": "test_type",
-            "base": "precomputed://file:///Users/thomasathey/Documents/mimlab/mouselight/brainlit_parent/brainlit/docs/notebooks/pipelines/BrainLine/example-data/"
+            "subtype": "test_type"
         },
         "biccn": {
             "somas_atlas_url": "https://ara.viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=8VHD-seixZg9pg",

diff --git a/docs/notebooks/pipelines/BrainLine/validation-data/axon/192_192_1536.pickle b/docs/notebooks/pipelines/BrainLine/validation-data/axon/192_192_1536.pickle
diff --git a/docs/notebooks/pipelines/BrainLine/validation-data/axon/256_192_1536.pickle b/docs/notebooks/pipelines/BrainLine/validation-data/axon/256_192_1536.pickle
diff --git a/docs/notebooks/pipelines/BrainLine/validation-data/axon/archive/250_237_1800.pickle b/docs/notebooks/pipelines/BrainLine/validation-data/axon/archive/250_237_1800.pickle
diff --git a/...inLine/validation-data/axon/archive/braintest/val/2054_1951_1825-image_3channel_Labels.h5 b/...inLine/validation-data/axon/archive/braintest/val/2054_1951_1825-image_3channel_Labels.h5
diff --git a/...otebooks/pipelines/BrainLine/validation-data/axon/archive/braintest/val/2054_1951_1825.h5 b/...otebooks/pipelines/BrainLine/validation-data/axon/archive/braintest/val/2054_1951_1825.h5
diff --git a/...ines/BrainLine/validation-data/axon/archive/braintest/val/2054_1951_1825_Probabilities.h5 b/...ines/BrainLine/validation-data/axon/archive/braintest/val/2054_1951_1825_Probabilities.h5
diff --git a/docs/notebooks/pipelines/BrainLine/validation-data/axon/archive/wholebrain_test.pkl b/docs/notebooks/pipelines/BrainLine/validation-data/axon/archive/wholebrain_test.pkl
diff --git a/experiments/BrainLine/data/axon_data.json b/experiments/BrainLine/data/axon_data.json
@@ -6,7 +6,8 @@
             "filepath": "/Users/thomasathey/Documents/mimlab/mouselight/ailey/ara/ara_10um.tif"
         },
         "test": {
-            "base": "precomputed://file:///Users/thomasathey/Documents/mimlab/mouselight/brainlit_parent/brainlit/brainlit/BrainLine/data/example/",
+            "base_s3": "precomputed://file:///Users/thomasathey/Documents/mimlab/mouselight/brainlit_parent/brainlit/brainlit/BrainLine/data/example/",
+            "base_local": "precomputed://file:///Users/thomasathey/Documents/mimlab/mouselight/brainlit_parent/brainlit/brainlit/BrainLine/data/example/",
             "transformed_mask": "precomputed://file:///Users/thomasathey/Documents/mimlab/mouselight/brainlit_parent/brainlit/brainlit/BrainLine/data/example/axon_mask_transformed/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=rywXvJ3kVOV71w",
@@ -38,7 +39,7 @@
             "subtype": "sert cre"
         },
         "8613": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2022_01_14/8613/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2022_01_14/8613/",
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_01_14/8613/axon_mask_transformed",
             "subtype": "tph2 vglut3"
         },
@@ -54,7 +55,7 @@
             "subtype": "tbd"
         },
         "8650": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2022_01_21/8650/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2022_01_21/8650/",
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_01_21/8650/axon_mask_transformed",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=tnXt-hF7Uyuq-w",
@@ -63,7 +64,7 @@
             "subtype": "tph2 gad2"
         },
         "8589": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2022_11_03/8589/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2022_11_03/8589/",
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_11_03/8589/axon_mask_transformed",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=sCrJq3bVmN5N4Q",
@@ -72,7 +73,7 @@
             "subtype": "tph2 vglut3"
         },
         "8590": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2022_03_04/8590/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2022_03_04/8590/",
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_03_04/8590/axon_mask_transformed",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=gq91htCi35XdPw",
@@ -81,7 +82,7 @@
             "subtype": "tph2 vglut3"
         },
         "8649": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2022_03_28/8649/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2022_03_28/8649/",
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_03_28/8649/axon_mask_transformed",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=b0unpdsrz-bO6A",
@@ -139,7 +140,7 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_10_26/11537/axon_mask_transformed"
         },
         "8786": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2022_11_02/8786/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2022_11_02/8786/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=YRB3G4Hn19TjIA",
                 "layer": "val"
@@ -148,7 +149,7 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_11_02/8786/axon_mask_transformed"
         },
         "8790": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2022_11_01/8790/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2022_11_01/8790/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=hhlEcKDIfqrY-w",
                 "layer": "val"
@@ -157,7 +158,6 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2022_11_01/8790/axon_mask_transformed"
         },
         "MS32": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2023_04_03/MS32/",
             "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_04_03/MS32/",
             "val_info": {
                 "url": "/Users/thomasathey/Documents/mimlab/mouselight/ailey/detection_axon/brainMS32/val.json",
@@ -172,7 +172,6 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2023_04_03/MS32/axon_mask_transformed"
         },
         "MS15": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2023_04_03/MS15/",
             "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_04_03/MS15/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=uN171hvFEvDw-Q",
@@ -182,7 +181,6 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2023_04_03/MS15/axon_mask_transformed"
         },
         "MS29": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2023_04_07/MS29/",
             "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_04_07/MS29/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=gf8YOhsEvdGXgQ",
@@ -196,7 +194,6 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2023_04_07/MS29/axon_mask_transformed"
         },
         "MS11": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2023_04_10/MS11/",
             "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_04_10/MS11/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=kcPAtNm-SdK2IQ",
@@ -216,15 +213,14 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2023_04_10/MS12/axon_mask_transformed"
         },
         "MS10": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2023_04_28/MS10/",
+            "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_04_28/MS10/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=43c44vvUgelrsw",
                 "layer": "val"
             },
             "subtype": "gad2 vgat"
         },
         "MS9": {
-            "base": "precomputed://file:///mnt/data/Neuroglancer_Data/2023_05_24/MS9/",
             "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_05_24/MS9/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=30O_uxkW67rv2Q",
@@ -234,7 +230,6 @@
             "transformed_mask": "precomputed://s3://smartspim-precomputed-volumes/2023_05_24/MS9/axon_mask_transformed"
         },
         "MS33": {
-            "base": "precomputed://s3://smartspim-precomputed-volumes/2023_09_18/MS33/",
             "base_s3": "precomputed://s3://smartspim-precomputed-volumes/2023_09_18/MS33/",
             "val_info": {
                 "url": "https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=H3idZ1oxxfEWdg",