Merge pull request #616 from int-brain-lab/swanson_split

Swanson split

Author: mayofaulkner

ibllib/atlas/flatmaps.py

@@ -137,13 +137,16 @@ def swanson(filename="swanson2allen.npz"):
 
 def swanson_json(filename="swansonpaths.json"):
 
-    OLD_MD5 = ['f848783954883c606ca390ceda9e37d2']
+    OLD_MD5 = ['97ccca2b675b28ba9b15ca8af5ba4111',  # errored map with FOTU and CUL4, 5 mixed up
+               '56daa7022b5e03080d8623814cda6f38',  # old md5 of swanson json without CENT and PTLp
+               # and CUL4 split (on s3 called swansonpaths_56daa.json)
+               'f848783954883c606ca390ceda9e37d2']
 
     json_file = AllenAtlas._get_cache_dir().joinpath(filename)
     if not json_file.exists() or md5(json_file) in OLD_MD5:
         json_file.parent.mkdir(exist_ok=True, parents=True)
         _logger.info(f'downloading swanson paths from {aws.S3_BUCKET_IBL} s3 bucket...')
-        aws.s3_download_file(f'atlas/{json_file.name}', json_file)
+        aws.s3_download_file(f'atlas/{json_file.name}', json_file, overwrite=True)
 
     with open(json_file) as f:
         sw_json = json.load(f)
@@ -198,44 +201,45 @@ def plot_swanson_vector(acronyms=None, values=None, ax=None, hemisphere=None, br
                     color = empty_color
 
         coords = reg['coordsReg']
+        reg_id = reg['thisID']
 
         if reg['hole']:
             vertices, codes = coords_for_poly_hole(coords)
             if orientation == 'portrait':
                 vertices[:, [0, 1]] = vertices[:, [1, 0]]
-                plot_polygon_with_hole(ax, vertices, codes, color, **kwargs)
+                plot_polygon_with_hole(ax, vertices, codes, color, reg_id, **kwargs)
                 if hemisphere is not None:
                     color_inv = color if hemisphere == 'mirror' else empty_color
                     vertices_inv = np.copy(vertices)
                     vertices_inv[:, 0] = -1 * vertices_inv[:, 0] + (sw.shape[0] * 2)
-                    plot_polygon_with_hole(ax, vertices_inv, codes, color_inv, **kwargs)
+                    plot_polygon_with_hole(ax, vertices_inv, codes, color_inv, reg_id, **kwargs)
             else:
-                plot_polygon_with_hole(ax, vertices, codes, color, **kwargs)
+                plot_polygon_with_hole(ax, vertices, codes, color, reg_id, **kwargs)
                 if hemisphere is not None:
                     color_inv = color if hemisphere == 'mirror' else empty_color
                     vertices_inv = np.copy(vertices)
                     vertices_inv[:, 1] = -1 * vertices_inv[:, 1] + (sw.shape[0] * 2)
-                    plot_polygon_with_hole(ax, vertices_inv, codes, color_inv, **kwargs)
+                    plot_polygon_with_hole(ax, vertices_inv, codes, color_inv, reg_id, **kwargs)
         else:
             coords = [coords] if type(coords) == dict else coords
             for c in coords:
 
                 if orientation == 'portrait':
                     xy = np.c_[c['y'], c['x']]
-                    plot_polygon(ax, xy, color, **kwargs)
+                    plot_polygon(ax, xy, color, reg_id, **kwargs)
                     if hemisphere is not None:
                         color_inv = color if hemisphere == 'mirror' else empty_color
                         xy_inv = np.copy(xy)
                         xy_inv[:, 0] = -1 * xy_inv[:, 0] + (sw.shape[0] * 2)
-                        plot_polygon(ax, xy_inv, color_inv, **kwargs)
+                        plot_polygon(ax, xy_inv, color_inv, reg_id, **kwargs)
                 else:
                     xy = np.c_[c['x'], c['y']]
-                    plot_polygon(ax, xy, color, **kwargs)
+                    plot_polygon(ax, xy, color, reg_id, **kwargs)
                     if hemisphere is not None:
                         color_inv = color if hemisphere == 'mirror' else empty_color
                         xy_inv = np.copy(xy)
                         xy_inv[:, 1] = -1 * xy_inv[:, 1] + (sw.shape[0] * 2)
-                        plot_polygon(ax, xy_inv, color_inv, **kwargs)
+                        plot_polygon(ax, xy_inv, color_inv, reg_id, **kwargs)
 
     if orientation == 'portrait':
         ax.set_ylim(0, sw.shape[1])

ibllib/atlas/plots.py

@@ -39,14 +39,14 @@ def get_bc_10():
     return bc
 
 
-def plot_polygon(ax, xy, color, edgecolor='k', linewidth=0.3, alpha=1):
-    p = Polygon(xy, facecolor=color, edgecolor=edgecolor, linewidth=linewidth, alpha=alpha)
+def plot_polygon(ax, xy, color, reg_id, edgecolor='k', linewidth=0.3, alpha=1):
+    p = Polygon(xy, facecolor=color, edgecolor=edgecolor, linewidth=linewidth, alpha=alpha, gid=f'region_{reg_id}')
     ax.add_patch(p)
 
 
-def plot_polygon_with_hole(ax, vertices, codes, color, edgecolor='k', linewidth=0.3, alpha=1):
+def plot_polygon_with_hole(ax, vertices, codes, color, reg_id, edgecolor='k', linewidth=0.3, alpha=1):
     path = mpath.Path(vertices, codes)
-    patch = PathPatch(path, facecolor=color, edgecolor=edgecolor, linewidth=linewidth, alpha=alpha)
+    patch = PathPatch(path, facecolor=color, edgecolor=edgecolor, linewidth=linewidth, alpha=alpha, gid=f'region_{reg_id}')
     ax.add_patch(patch)
 
 

ibllib/oneibl/data_handlers.py

@@ -1,6 +1,5 @@
 import logging
 import pandas as pd
-import numpy as np
 from pathlib import Path
 import shutil
 import os
@@ -11,7 +10,6 @@
 from one.webclient import AlyxClient
 from one.util import filter_datasets
 from one.alf.files import add_uuid_string, session_path_parts
-from iblutil.io.parquet import np2str
 from ibllib.oneibl.registration import register_dataset, get_lab, get_local_data_repository
 from ibllib.oneibl.patcher import FTPPatcher, SDSCPatcher, SDSC_ROOT_PATH, SDSC_PATCH_PATH
 
@@ -168,12 +166,7 @@ def setUp(self):
             sess_path = Path(rel_sess_path).joinpath(d['rel_path'])
             full_local_path = Path(self.globus.endpoints['local']['root_path']).joinpath(sess_path)
             if not full_local_path.exists():
-
-                if one._index_type() is int:
-                    uuid = np2str(np.r_[i[0], i[1]])
-                elif one._index_type() is str:
-                    uuid = i
-
+                uuid = i
                 self.local_paths.append(full_local_path)
                 target_paths.append(sess_path)
                 source_paths.append(add_uuid_string(sess_path, uuid))
@@ -382,12 +375,7 @@ def setUp(self):
         SDSC_TMP = Path(SDSC_PATCH_PATH.joinpath(self.task.__class__.__name__))
         for i, d in df.iterrows():
             file_path = Path(d['session_path']).joinpath(d['rel_path'])
-
-            if self.one._index_type() is int:
-                uuid = np2str(np.r_[i[0], i[1]])
-            elif self.one._index_type() is str:
-                uuid = i
-
+            uuid = i
             file_uuid = add_uuid_string(file_path, uuid)
             file_link = SDSC_TMP.joinpath(file_path)
             file_link.parent.mkdir(exist_ok=True, parents=True)

ibllib/pipes/training_status.py

@@ -19,7 +19,9 @@
 import seaborn as sns
 
 
-TRAINING_STATUS = {'not_computed': (-2, (0, 0, 0, 0)),
+TRAINING_STATUS = {'untrainable': (-4, (0, 0, 0, 0)),
+                   'unbiasable': (-3, (0, 0, 0, 0)),
+                   'not_computed': (-2, (0, 0, 0, 0)),
                    'habituation': (-1, (0, 0, 0, 0)),
                    'in training': (0, (0, 0, 0, 0)),
                    'trained 1a': (1, (195, 90, 80, 255)),