You can download the corresponding toy dataset using this link: https://bigmail.cbs.mpg.de/i/b06cfdd4e67af51a4a75f404861ebe8b.hdf5
----- Original Message ----- From: "kuhl" <[email protected]> To: "pkg-exppsy-pymvpa" <[email protected]> Sent: Thursday, 26 November, 2015 09:30:01 Subject: Re: [pymvpa] Dataset with multidimensional feature vector per voxel (The mail with the dataset attached is still waiting for moderator approval since it extends the limit of 240 KB.) The code producing the error: ############################## # set up DS as we worked out before: DS_noisy = setup_ds ( sub_list, param_list, data_path ) # define a partitioner npart = ChainNode([ NFoldPartitioner(len(DS_noisy.sa['targets'].unique), attr='chunks'), Sifter([('partitions', 2), ('targets', { 'uvalues': DS_noisy.sa['targets'].unique, 'balanced': True}) ]), Balancer(attr='targets',count=10,limit='partitions',apply_selection=False) ], space='partitions') clf_noisy = LinearCSVMC() cvte_noisy = CrossValidation(clf_noisy, npart,errorfx=lambda p, t: np.mean(p == t),enable_ca=['stats'],postproc=mean_sample()) sl = Searchlight( cvte_noisy, IndexQueryEngine( # so we look for neighbors in both space and across modality_index voxel_indices=Sphere(3), # that is pretty much what sphere_searchlight(radius=3) does modality_index=Sphere(len(param_list))), # 1cover all parameter values! postproc=mean_sample(), enable_ca=['stats'], roi_ids=np.where(DS_noisy.fa.modality_index == 0)[0] # restrict it to search for "modality_index" neighbors only when we are looking at modality_index==0 ) res_noisy = sl(DS_noisy) ############################## The last line returns the IndexError. DS_noisy.summary() returns: Dataset: 7x3472@float32, <sa: chunks,subject,targets>, <fa: modality,modality_index,voxel_indices>, <a: imghdr,mapper> stats: mean=0.516962 std=0.298723 var=0.0892352 min=9.75631e-06 max=1.78471 Counts of targets in each chunk: chunks\targets 0 1 --- --- 0 1 0 1 1 0 2 1 0 3 1 0 4 0 1 5 0 1 6 0 1 Summary for targets across chunks targets mean std min max #chunks 0 0.571 0.495 0 1 4 1 0.429 0.495 0 1 3 Summary for chunks across targets chunks mean std min max #targets 0 0.5 0.5 0 1 1 1 0.5 0.5 0 1 1 2 0.5 0.5 0 1 1 3 0.5 0.5 0 1 1 4 0.5 0.5 0 1 1 5 0.5 0.5 0 1 1 6 0.5 0.5 0 1 1 Sequence statistics for 7 entries from set [0, 1] Counter-balance table for orders up to 2: Targets/Order O1 | O2 | 0: 3 1 | 2 2 | 1: 0 2 | 0 1 | Correlations: min=-0.75 max=0.42 mean=-0.17 sum(abs)=2.7 ----- Original Message ----- From: "Yaroslav Halchenko" <[email protected]> To: "pkg-exppsy-pymvpa" <[email protected]> Sent: Tuesday, 24 November, 2015 21:10:52 Subject: Re: [pymvpa] Dataset with multidimensional feature vector per voxel On Tue, 24 Nov 2015, Ulrike Kuhl wrote: > I was able to reproduce the error when using a mask (1736 voxels) on my toy > data: could you share the code snippet and this toy dataset (h5save it)? > Traceback (most recent call last): > File "DummyMvpa_noisy.py", line 322, in <module> > res_noisy = sl(DS_noisy) > File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 259, in > __call__ > return super(Learner, self).__call__(ds) > File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 121, in > __call__ > result = self._call(ds) > File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line > 143, in _call > results = self._sl_call(dataset, roi_ids, nproc) > File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line > 371, in _sl_call > results=self.__handle_all_results(p_results)) > File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line > 207, in _concat_results > results = sum(results, []) > File "/usr/lib/python2.7/dist-packages/mvpa2/measures/searchlight.py", line > 527, in __handle_all_results > for r in results: > File "/usr/lib/pymodules/python2.7/pprocess.py", line 764, in next > self.store() > File "/usr/lib/pymodules/python2.7/pprocess.py", line 400, in store > self.store_data(channel) > File "/usr/lib/pymodules/python2.7/pprocess.py", line 747, in store_data > data = channel.receive() > File "/usr/lib/pymodules/python2.7/pprocess.py", line 135, in receive > obj = self._receive() > File "/usr/lib/pymodules/python2.7/pprocess.py", line 121, in _receive > raise obj > IndexError: index 1736 out of bounds 0<=index<1736 > Why does the searchlight run out of the mask? not sure yet -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa -- Max Planck Institute for Human Cognitive and Brain Sciences Department of Neuropsychology (A219) Stephanstraße 1a 04103 Leipzig Phone: +49 (0) 341 9940 2625 Mail: [email protected] Internet: http://www.cbs.mpg.de/staff/kuhl-12160 _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa -- Max Planck Institute for Human Cognitive and Brain Sciences Department of Neuropsychology (A219) Stephanstraße 1a 04103 Leipzig Phone: +49 (0) 341 9940 2625 Mail: [email protected] Internet: http://www.cbs.mpg.de/staff/kuhl-12160 _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
