Hi，
A couple days ago, I ran the following code and it was working, but now it's reporting an error，and I don't know how to fix this:
import nibabel as nib atlas = nib.load('E:\BN_Atlas_246_2mm.nii') import pandas as pd atlas_info = pd.read_csv('E:\BN246_info.csv') expression3 = abagen.get_expression_data(atlas, atlas_info, probe_selection='rnaseq', norm_structures = True, sim_threshold = 0.2) print(expression3)
KeyError Traceback (most recent call last)
Cell In[5], line 5
3 import pandas as pd
4 atlas_info = pd.read_csv('E:\BN246_info.csv')
----> 5 expression3 = abagen.get_expression_data(atlas, atlas_info, probe_selection='rnaseq', norm_structures = True, sim_threshold = 0.2)
6 print(expression3)
File ~.conda\envs\abagen_test\Lib\site-packages\abagen\allen.py:430, in get_expression_data(atlas, atlas_info, ibf_threshold, probe_selection, donor_probes, sim_threshold, lr_mirror, exact, missing, tolerance, sample_norm, gene_norm, norm_matched, norm_structures, region_agg, agg_metric, corrected_mni, reannotated, return_counts, return_donors, return_report, donors, data_dir, verbose, n_proc)
428 annot = samples_.drop_mismatch_samples(annot, ontol)
429 if sim_threshold is not None:
--> 430 annot = samples_.similarity_threshold(data['microarray'],
431 annot, probe_info,
432 threshold=sim_threshold)
433 data['annotation'] = annot
434 annotation = flatten_dict(files, 'annotation')
File ~.conda\envs\abagen_test\Lib\site-packages\abagen\samples_.py:365, in similarity_threshold(microarray, annotation, probes, threshold)
362 probes = io.read_probes(probes)
363 microarray = io.read_microarray(microarray, copy=False)
--> 365 corrs = np.corrcoef(microarray.loc[probes.index, annotation.index].T)
366 sim = np.sum(corrs, axis=1)
367 thresh = np.mean(sim) - (threshold * np.std(sim, ddof=1))
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1184, in _LocationIndexer.getitem(self, key)
1182 if self._is_scalar_access(key):
1183 return self.obj._get_value(*key, takeable=self._takeable)
-> 1184 return self._getitem_tuple(key)
1185 else:
1186 # we by definition only have the 0th axis
1187 axis = self.axis or 0
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1375, in _LocIndexer._getitem_tuple(self, tup)
1373 # ugly hack for GH #836
1374 if self._multi_take_opportunity(tup):
-> 1375 return self._multi_take(tup)
1377 return self._getitem_tuple_same_dim(tup)
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1326, in _LocIndexer._multi_take(self, tup)
1310 """
1311 Create the indexers for the passed tuple of keys, and
1312 executes the take operation. This allows the take operation to be
(...)
1323 values: same type as the object being indexed
1324 """
1325 # GH 836
-> 1326 d = {
1327 axis: self._get_listlike_indexer(key, axis)
1328 for (key, axis) in zip(tup, self.obj._AXIS_ORDERS)
1329 }
1330 return self.obj._reindex_with_indexers(d, copy=True, allow_dups=True)
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1327, in (.0)
1310 """
1311 Create the indexers for the passed tuple of keys, and
1312 executes the take operation. This allows the take operation to be
(...)
1323 values: same type as the object being indexed
1324 """
1325 # GH 836
1326 d = {
-> 1327 axis: self._get_listlike_indexer(key, axis)
1328 for (key, axis) in zip(tup, self.obj._AXIS_ORDERS)
1329 }
1330 return self.obj._reindex_with_indexers(d, copy=True, allow_dups=True)
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1558, in _LocIndexer._get_listlike_indexer(self, key, axis)
1555 ax = self.obj._get_axis(axis)
1556 axis_name = self.obj._get_axis_name(axis)
-> 1558 keyarr, indexer = ax._get_indexer_strict(key, axis_name)
1560 return keyarr, indexer
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexes\base.py:6200, in Index._get_indexer_strict(self, key, axis_name)
6197 else:
6198 keyarr, indexer, new_indexer = self._reindex_non_unique(keyarr)
-> 6200 self._raise_if_missing(keyarr, indexer, axis_name)
6202 keyarr = self.take(indexer)
6203 if isinstance(key, Index):
6204 # GH 42790 - Preserve name from an Index
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexes\base.py:6252, in Index._raise_if_missing(self, key, indexer, axis_name)
6249 raise KeyError(f"None of [{key}] are in the [{axis_name}]")
6251 not_found = list(ensure_index(key)[missing_mask.nonzero()[0]].unique())
-> 6252 raise KeyError(f"{not_found} not in index")
KeyError: '[1071165, 1071173, 1071193, 1071199, 1071210] not in index'
Hi，
A couple days ago, I ran the following code and it was working, but now it's reporting an error，and I don't know how to fix this:
import nibabel as nib atlas = nib.load('E:\BN_Atlas_246_2mm.nii') import pandas as pd atlas_info = pd.read_csv('E:\BN246_info.csv') expression3 = abagen.get_expression_data(atlas, atlas_info, probe_selection='rnaseq', norm_structures = True, sim_threshold = 0.2) print(expression3)KeyError Traceback (most recent call last)
Cell In[5], line 5
3 import pandas as pd
4 atlas_info = pd.read_csv('E:\BN246_info.csv')
----> 5 expression3 = abagen.get_expression_data(atlas, atlas_info, probe_selection='rnaseq', norm_structures = True, sim_threshold = 0.2)
6 print(expression3)
File ~.conda\envs\abagen_test\Lib\site-packages\abagen\allen.py:430, in get_expression_data(atlas, atlas_info, ibf_threshold, probe_selection, donor_probes, sim_threshold, lr_mirror, exact, missing, tolerance, sample_norm, gene_norm, norm_matched, norm_structures, region_agg, agg_metric, corrected_mni, reannotated, return_counts, return_donors, return_report, donors, data_dir, verbose, n_proc)
428 annot = samples_.drop_mismatch_samples(annot, ontol)
429 if sim_threshold is not None:
--> 430 annot = samples_.similarity_threshold(data['microarray'],
431 annot, probe_info,
432 threshold=sim_threshold)
433 data['annotation'] = annot
434 annotation = flatten_dict(files, 'annotation')
File ~.conda\envs\abagen_test\Lib\site-packages\abagen\samples_.py:365, in similarity_threshold(microarray, annotation, probes, threshold)
362 probes = io.read_probes(probes)
363 microarray = io.read_microarray(microarray, copy=False)
--> 365 corrs = np.corrcoef(microarray.loc[probes.index, annotation.index].T)
366 sim = np.sum(corrs, axis=1)
367 thresh = np.mean(sim) - (threshold * np.std(sim, ddof=1))
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1184, in _LocationIndexer.getitem(self, key)
1182 if self._is_scalar_access(key):
1183 return self.obj._get_value(*key, takeable=self._takeable)
-> 1184 return self._getitem_tuple(key)
1185 else:
1186 # we by definition only have the 0th axis
1187 axis = self.axis or 0
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1375, in _LocIndexer._getitem_tuple(self, tup)
1373 # ugly hack for GH #836
1374 if self._multi_take_opportunity(tup):
-> 1375 return self._multi_take(tup)
1377 return self._getitem_tuple_same_dim(tup)
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1326, in _LocIndexer._multi_take(self, tup)
1310 """
1311 Create the indexers for the passed tuple of keys, and
1312 executes the take operation. This allows the take operation to be
(...)
1323 values: same type as the object being indexed
1324 """
1325 # GH 836
-> 1326 d = {
1327 axis: self._get_listlike_indexer(key, axis)
1328 for (key, axis) in zip(tup, self.obj._AXIS_ORDERS)
1329 }
1330 return self.obj._reindex_with_indexers(d, copy=True, allow_dups=True)
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1327, in (.0)
1310 """
1311 Create the indexers for the passed tuple of keys, and
1312 executes the take operation. This allows the take operation to be
(...)
1323 values: same type as the object being indexed
1324 """
1325 # GH 836
1326 d = {
-> 1327 axis: self._get_listlike_indexer(key, axis)
1328 for (key, axis) in zip(tup, self.obj._AXIS_ORDERS)
1329 }
1330 return self.obj._reindex_with_indexers(d, copy=True, allow_dups=True)
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexing.py:1558, in _LocIndexer._get_listlike_indexer(self, key, axis)
1555 ax = self.obj._get_axis(axis)
1556 axis_name = self.obj._get_axis_name(axis)
-> 1558 keyarr, indexer = ax._get_indexer_strict(key, axis_name)
1560 return keyarr, indexer
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexes\base.py:6200, in Index._get_indexer_strict(self, key, axis_name)
6197 else:
6198 keyarr, indexer, new_indexer = self._reindex_non_unique(keyarr)
-> 6200 self._raise_if_missing(keyarr, indexer, axis_name)
6202 keyarr = self.take(indexer)
6203 if isinstance(key, Index):
6204 # GH 42790 - Preserve name from an Index
File ~.conda\envs\abagen_test\Lib\site-packages\pandas\core\indexes\base.py:6252, in Index._raise_if_missing(self, key, indexer, axis_name)
6249 raise KeyError(f"None of [{key}] are in the [{axis_name}]")
6251 not_found = list(ensure_index(key)[missing_mask.nonzero()[0]].unique())
-> 6252 raise KeyError(f"{not_found} not in index")
KeyError: '[1071165, 1071173, 1071193, 1071199, 1071210] not in index'