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| pyhrf-0.2$ sudo pyhrf_maketests | |
| [sudo] password for vahid: | |
| _test_single_sampler bold_mixt_params ... | |
| ._test_single_sampler brf ... | |
| ._test_single_sampler brf_var ... | |
| ._test_single_sampler brl ... | |
| .E_test_single_sampler drift_coeff ... | |
| .._test_single_sampler label ... | |
| ._test_specific_samplers ['perf_baseline', 'noise_var'] ... | |
| out_dir: /tmp/pyhrf_jaSwEP | |
| ._test_single_sampler noise_var ... | |
| ._test_single_sampler perf_baseline ... | |
| ._test_single_sampler perf_baseline_var ... | |
| ._test_single_sampler perf_mixt_params ... | |
| ._test_single_sampler prf ... | |
| ._test_single_sampler prf_var ... | |
| ._test_single_sampler prl ... | |
| ...../usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/jde/beta.py:3527: RuntimeWarning: invalid value encountered in double_scalars | |
| P_beta=(VecBetaVal[-1]-VecBetaVal[i])/(VecBetaVal[-1]-thresh) | |
| ..........Traceback (most recent call last): | |
| File "/usr/local/bin/pyhrf_parcellate_spatial", line 5, in <module> | |
| pkg_resources.run_script('pyhrf==0.2', 'pyhrf_parcellate_spatial') | |
| File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 505, in run_script | |
| self.require(requires)[0].run_script(script_name, ns) | |
| File "/usr/local/lib/python2.7/dist-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py", line 1245, in run_script | |
| execfile(script_filename, namespace, namespace) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/pyhrf_parcellate_spatial", line 114, in <module> | |
| from nipy.algorithms.clustering.clustering import voronoi | |
| ImportError: No module named clustering | |
| E.........................................................................sshape: (5,) | |
| ....root_node: | |
| |------dummy | type:Initable init_obj:<class 'pyhrf.test.test_sandbox.Dummy3'> | |
| |------d | type:dict | |
| |------subdummy | type:Initable init_obj:<class 'pyhrf.test.test_sandbox.Dummy'> | |
| |------string_p | type:<type 'str'> | |
| |------a | |
| |------float_p | type:<type 'float'> | |
| |------1.3 | |
| |------int_p | type:<type 'int'> | |
| |------5 | |
| |------array_p | dtype:int64 shape:(5,) type:ndarray | |
| |------0 1 2 3 4 | |
| |------obj_p | type:Initable init_obj:<class 'pyhrf.test.test_sandbox.Dummy2'> | |
| |------p | type:<type 'str'> | |
| |------rr | |
| .QDomDocument: | |
| <treatment pickled_init_obj="cpyhrf.test.test_sandbox
Treatment
p0
." pickled_type="S'Initable'
p0
."> | |
| <data pickled_init_obj="cpyhrf.test.test_sandbox
FmriData
p0
." pickled_type="S'Initable'
p0
."> | |
| <paradigm dtype="int64" shape="(5,)" pickled_type="S'ndarray'
p0
.">0 1 2 3 4</paradigm> | |
| <func_file pickled_type="c__builtin__
str
p0
.">blah.nii</func_file> | |
| </data> | |
| <analyser pickled_init_obj="cpyhrf.test.test_sandbox
Analyser
p0
." pickled_type="S'Initable'
p0
."> | |
| <nb_iterations pickled_type="c__builtin__
int
p0
.">345</nb_iterations> | |
| <make_outputs pickled_type="c__builtin__
bool
p0
.">True</make_outputs> | |
| </analyser> | |
| <info pickled_type="c__builtin__
dict
p0
.">{'test': 53}</info> | |
| <l pickled_type="c__builtin__
list
p0
.">[5, 6]</l> | |
| </treatment> | |
| .Warning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| .Warning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| .........output: | |
| /tmp/pyhrf_testsan2V1G: | |
| /tmp/pyhrf_testsan2V1G/subject1: | |
| /tmp/pyhrf_testsan2V1G/subject1/fmri: | |
| paradigm.csv | |
| /tmp/pyhrf_testsan2V1G/subject1/fmri/analysis: | |
| analysis_result_1.nii | |
| analysis_result_2.csv | |
| analysis_summary.txt | |
| /tmp/pyhrf_testsan2V1G/subject1/fmri/run1: | |
| bold_scan_[1...3].nii | |
| /tmp/pyhrf_testsan2V1G/subject1/fmri/run2: | |
| bold_scan_[1...3].nii | |
| /tmp/pyhrf_testsan2V1G/subject1/t1mri: | |
| anatomy.{hdr,img} | |
| ....._test_specific_samplers ['mixtureParameters_for_responseLevels_by_session'] ... | |
| out_dir: /tmp/pyhrf_aeO3QF | |
| . | |
| Warning ppm_empiricall_vt put to 0 | |
| ._test_specific_samplers ['drift', 'driftVar'] ... | |
| out_dir: /tmp/pyhrf_O9HQni | |
| ._test_specific_samplers ['drift'] ... | |
| out_dir: /tmp/pyhrf_YK8x89 | |
| ._test_specific_samplers ['driftVar'] ... | |
| out_dir: /tmp/pyhrf_PmmWB9 | |
| .._test_specific_samplers ['HRF'] ... | |
| out_dir: /tmp/pyhrf_IM8nrB | |
| ._test_specific_samplers ['HRFVariance'] ... | |
| out_dir: /tmp/pyhrf_hcGN1q | |
| ._test_specific_samplers ['MeanresponseLevels'] ... | |
| out_dir: /tmp/pyhrf_oEJ21w | |
| ._test_specific_samplers ['noiseVariance'] ... | |
| out_dir: /tmp/pyhrf_Q_U8bG | |
| ._test_specific_samplers ['MeanresponseLevels'] ... | |
| out_dir: /tmp/pyhrf_Bwm0v1 | |
| ._test_specific_samplers ['MeanresponseLevels'] ... | |
| out_dir: /tmp/pyhrf_BC51hV | |
| ._test_specific_samplers ['responseLevels_by_session', 'HRF'] ... | |
| out_dir: /tmp/pyhrf_Ogqqs7 | |
| ._test_specific_samplers ['responseLevels_by_session'] ... | |
| out_dir: /tmp/pyhrf_H0pFLF | |
| ._test_specific_samplers ['responseLevels_by_sessionVariance'] ... | |
| out_dir: /tmp/pyhrf_CqXPXc | |
| ..EE...........................sh: 1: convert: not found | |
| .sh: 1: convert: not found | |
| sh: 1: convert: not found | |
| sh: 1: convert: not found | |
| .sh: 1: convert: not found | |
| .rebin func onto anat | |
| sh: 1: convert: not found | |
| .rebin func onto anat | |
| sh: 1: convert: not found | |
| rebin func onto anat | |
| sh: 1: convert: not found | |
| rebin func onto anat | |
| sh: 1: convert: not found | |
| ................Warning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| ..Warning ppm_empiricall_vt put to 0 | |
| ......sh: 1: pyhrf_generate: not found | |
| EWarning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| .Warning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| .Warning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| .Warning ppm_empiricall_vt put to 0 | |
| .Warning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| ..Warning ppm_empiricall_vt put to 0 | |
| Warning ppm_empiricall_vt put to 0 | |
| .n: | |
| |------n | dtype:int64 shape:(5,) type:ndarray | |
| |------0 1 2 3 4 | |
| sshape: (5,) | |
| .n: | |
| |------n | dtype:int64 shape:(2, 3, 4, 5) type:ndarray | |
| |------0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 | |
| sshape: (2, 3, 4, 5) | |
| .n: | |
| |------a | type:<type 'numpy.float128'> | |
| |------1.2 | |
| .n: | |
| |------dummy | type:Initable init_obj:<class 'pyhrf.test.test_sandbox.Dummy2'> | |
| |------p | type:<type 'int'> | |
| |------56 | |
| xml: | |
| <dummy pickled_init_obj="cpyhrf.test.test_sandbox
Dummy2
p0
." pickled_type="S'Initable'
p0
."> | |
| <p pickled_type="c__builtin__
int
p0
.">56</p> | |
| </dummy> | |
| QDomDocument: | |
| <dummy pickled_init_obj="cpyhrf.test.test_sandbox
Dummy2
p0
." pickled_type="S'Initable'
p0
."> | |
| <p pickled_type="c__builtin__
int
p0
.">56</p> | |
| </dummy> | |
| n2: | |
| |------dummy | type:Initable init_obj:<class 'pyhrf.test.test_sandbox.Dummy2'> | |
| |------p | |
| |------56 | |
| ..xml: | |
| <dummy pickled_init_obj="cpyhrf.test.test_sandbox
Dummy2
p0
." pickled_type="S'Initable'
p0
."> | |
| <p pickled_type="c__builtin__
int
p0
.">3</p> | |
| </dummy> | |
| ....________________________________________________________________________________ | |
| [Memory] Calling pyhrf.test.toolsTest.slow_func... | |
| slow_func(a=5, b=6) | |
| ________________________________________________________slow_func - 1.0s, 0.0min | |
| ....................... | |
| ====================================================================== | |
| ERROR: test_default_jde_small_simulation (pyhrf.test.jdetest.ASLTest) | |
| Test ASL sampler on small simulation with small nb of iterations. | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/test/jdetest.py", line 345, in test_default_jde_small_simulation | |
| treatment.run() | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/ui/treatment.py", line 409, in run | |
| self.make_outputs) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/ui/treatment.py", line 455, in output | |
| r = self.analyser.outputResults(result, self.output_dir) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/ui/analyser_ui.py", line 356, in outputResults | |
| all_outputs = stack_trees([r[1].getOutputs() for r in results]) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/jde/samplerbase.py", line 375, in getOutputs | |
| outputs.update(self.getGlobalOutputs()) | |
| TypeError: 'NoneType' object is not iterable | |
| ====================================================================== | |
| ERROR: test_voronoi_with_seeds (pyhrf.test.test_parcellation.CmdParcellationTest) | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/test/test_parcellation.py", line 295, in test_voronoi_with_seeds | |
| raise Exception('"' + cmd + '" did not execute correctly') | |
| Exception: "pyhrf_parcellate_spatial /usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/datafiles/audio-video_nalocalizer__roimask.nii.gz -m voronoi -c /tmp/pyhrf_IP11Zw/voronoi_seeds.nii -o /tmp/pyhrf_IP11Zw/voronoi_parcellation.nii -v 0" did not execute correctly | |
| ====================================================================== | |
| ERROR: test_default_jde_small_simulation (pyhrf.test.jdetest.MultiSubjTest) | |
| Test JDE multi-subject sampler on small | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/test/jdetest.py", line 915, in setUp | |
| hrf_group=genBezierHRF(pic=[10,1],ushoot=[20,-.1], normalize=True)[1], nbSubj=4) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/jde/jde_multi_sujets.py", line 3807, in simulate_subjects | |
| drift_amplitude, hrf_group, dt=0.6, dsf=4) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/jde/jde_multi_sujets.py", line 3725, in simulate_single_subject | |
| simu_graph = UpdateGraph(simulation_steps) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/tools/misc.py", line 636, in __init__ | |
| self.init_dependencies(quantities) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/tools/misc.py", line 680, in init_dependencies | |
| %(arg, val.__name__)) | |
| Exception: arg "alpha" of function "create_gaussian_hrf_subject" undefined (no quantity found or no default value) | |
| ====================================================================== | |
| ERROR: test_simulation (pyhrf.test.jdetest.MultiSubjTest) | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/test/jdetest.py", line 915, in setUp | |
| hrf_group=genBezierHRF(pic=[10,1],ushoot=[20,-.1], normalize=True)[1], nbSubj=4) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/jde/jde_multi_sujets.py", line 3807, in simulate_subjects | |
| drift_amplitude, hrf_group, dt=0.6, dsf=4) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/jde/jde_multi_sujets.py", line 3725, in simulate_single_subject | |
| simu_graph = UpdateGraph(simulation_steps) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/tools/misc.py", line 636, in __init__ | |
| self.init_dependencies(quantities) | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/tools/misc.py", line 680, in init_dependencies | |
| %(arg, val.__name__)) | |
| Exception: arg "alpha" of function "create_gaussian_hrf_subject" undefined (no quantity found or no default value) | |
| ====================================================================== | |
| ERROR: test_jde_from_simu_default (pyhrf.test.commandTest.TreatmentCommandTest) | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/usr/local/lib/python2.7/dist-packages/pyhrf-0.2-py2.7-linux-x86_64.egg/pyhrf/test/commandTest.py", line 235, in test_jde_from_simu_default | |
| raise Exception('"' + cmd + '" did not execute correctly') | |
| Exception: "pyhrf_generate /tmp/pyhrf_tests1cEe42/simu.pck" did not execute correctly | |
| ---------------------------------------------------------------------- | |
| Ran 238 tests in 1345.230s | |
| FAILED (errors=5) |
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