antspymm 1.1.7__tar.gz → 1.1.9__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (53) hide show
  1. {antspymm-1.1.7/antspymm.egg-info → antspymm-1.1.9}/PKG-INFO +3 -3
  2. {antspymm-1.1.7 → antspymm-1.1.9}/README.md +2 -2
  3. {antspymm-1.1.7 → antspymm-1.1.9}/antspymm/__init__.py +5 -0
  4. {antspymm-1.1.7 → antspymm-1.1.9}/antspymm/mm.py +418 -111
  5. {antspymm-1.1.7 → antspymm-1.1.9/antspymm.egg-info}/PKG-INFO +3 -3
  6. {antspymm-1.1.7 → antspymm-1.1.9}/antspymm.egg-info/SOURCES.txt +1 -2
  7. {antspymm-1.1.7 → antspymm-1.1.9}/setup.py +1 -1
  8. antspymm-1.1.9/tests/test_dwi_run.py +34 -0
  9. antspymm-1.1.9/tests/test_rsfmri_run_minimal.py +52 -0
  10. antspymm-1.1.7/docs/describe_mm_data.R +0 -144
  11. antspymm-1.1.7/docs/template_overlays.py +0 -17
  12. antspymm-1.1.7/tests/test_dwi_run.py +0 -66
  13. {antspymm-1.1.7 → antspymm-1.1.9}/LICENSE +0 -0
  14. {antspymm-1.1.7 → antspymm-1.1.9}/MANIFEST.in +0 -0
  15. {antspymm-1.1.7 → antspymm-1.1.9}/antspymm.egg-info/dependency_links.txt +0 -0
  16. {antspymm-1.1.7 → antspymm-1.1.9}/antspymm.egg-info/not-zip-safe +0 -0
  17. {antspymm-1.1.7 → antspymm-1.1.9}/antspymm.egg-info/requires.txt +0 -0
  18. {antspymm-1.1.7 → antspymm-1.1.9}/antspymm.egg-info/top_level.txt +0 -0
  19. {antspymm-1.1.7 → antspymm-1.1.9}/docs/antspymm_data_dictionary.csv +0 -0
  20. {antspymm-1.1.7 → antspymm-1.1.9}/docs/bids_cohort_example.py +0 -0
  21. {antspymm-1.1.7 → antspymm-1.1.9}/docs/blind_qc.Rmd +0 -0
  22. {antspymm-1.1.7 → antspymm-1.1.9}/docs/blind_qc.html +0 -0
  23. {antspymm-1.1.7 → antspymm-1.1.9}/docs/convert_adni_dti_to_nrg.R +0 -0
  24. {antspymm-1.1.7 → antspymm-1.1.9}/docs/example_run_from_directory.py +0 -0
  25. {antspymm-1.1.7 → antspymm-1.1.9}/docs/make_dict_table.Rmd +0 -0
  26. {antspymm-1.1.7 → antspymm-1.1.9}/docs/make_dict_table.html +0 -0
  27. {antspymm-1.1.7 → antspymm-1.1.9}/docs/nrg_cohort_example.py +0 -0
  28. {antspymm-1.1.7 → antspymm-1.1.9}/docs/outlierness.py +0 -0
  29. {antspymm-1.1.7 → antspymm-1.1.9}/docs/ptbp_nrg.py +0 -0
  30. {antspymm-1.1.7 → antspymm-1.1.9}/docs/roi_visualization.py +0 -0
  31. {antspymm-1.1.7 → antspymm-1.1.9}/docs/roi_visualization_ppmi.py +0 -0
  32. {antspymm-1.1.7 → antspymm-1.1.9}/docs/ukbb_to_nrg_processing.py +0 -0
  33. {antspymm-1.1.7 → antspymm-1.1.9}/docs/ukbb_to_nrg_processing2.py +0 -0
  34. {antspymm-1.1.7 → antspymm-1.1.9}/setup.cfg +0 -0
  35. {antspymm-1.1.7 → antspymm-1.1.9}/tests/blind_qc.py +0 -0
  36. {antspymm-1.1.7 → antspymm-1.1.9}/tests/mm.py +0 -0
  37. {antspymm-1.1.7 → antspymm-1.1.9}/tests/mm_nrg.py +0 -0
  38. {antspymm-1.1.7 → antspymm-1.1.9}/tests/outlierness.py +0 -0
  39. {antspymm-1.1.7 → antspymm-1.1.9}/tests/parallel_study_aggregation_example.py +0 -0
  40. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_bids_2_nrg.py +0 -0
  41. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_deformation_gradient_reo.py +0 -0
  42. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_dti_recon.py +0 -0
  43. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_dti_reg.py +0 -0
  44. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_dwi_rebasing.py +0 -0
  45. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_flair_run.py +0 -0
  46. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_joint_dti_recon.py +0 -0
  47. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_mm_csv.py +0 -0
  48. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_perfusion_ptbp.py +0 -0
  49. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_perfusion_run.py +0 -0
  50. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_rsfmri_run.py +0 -0
  51. {antspymm-1.1.7 → antspymm-1.1.9}/tests/test_ukbb_rsfmri.py +0 -0
  52. {antspymm-1.1.7 → antspymm-1.1.9}/tests/testsr.py +0 -0
  53. {antspymm-1.1.7 → antspymm-1.1.9}/tests/visualize_tractogram.py +0 -0
{antspymm-1.1.7/antspymm.egg-info → antspymm-1.1.9}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: antspymm
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- Version: 1.1.7
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+ Version: 1.1.9
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  Summary: multi-channel/time-series medical image processing with antspyx
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  Home-page: https://github.com/stnava/ANTsPyMM
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  Author: Avants, Gosselin, Tustison, Reardon
@@ -337,8 +337,8 @@ for each subject/timepoint, one would run:
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  studyfn="matched_mm_data2.csv"
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  df=pd.read_csv( studyfn )
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  index = 20 # 20th subject/timepoint
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- csvfns = df['fn']
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- csvrow = df[ df['fn'] == csvfns[index] ]
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+ csvfns = df['filename']
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+ csvrow = df[ df['filename'] == csvfns[index] ]
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  csvrow['projectID']='MyStudy'
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  ############################################################################################
{antspymm-1.1.7 → antspymm-1.1.9}/README.md RENAMED
@@ -315,8 +315,8 @@ for each subject/timepoint, one would run:
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  studyfn="matched_mm_data2.csv"
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  df=pd.read_csv( studyfn )
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  index = 20 # 20th subject/timepoint
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- csvfns = df['fn']
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- csvrow = df[ df['fn'] == csvfns[index] ]
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+ csvfns = df['filename']
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+ csvrow = df[ df['filename'] == csvfns[index] ]
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  csvrow['projectID']='MyStudy'
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  ############################################################################################
{antspymm-1.1.7 → antspymm-1.1.9}/antspymm/__init__.py RENAMED
@@ -103,9 +103,14 @@ from .mm import docsamson
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  from .mm import enantiomorphic_filling_without_mask
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  from .mm import loop_timeseries_censoring
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  from .mm import score_fmri_censoring
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+ from .mm import replace_elements_in_numpy_array
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  from .mm import remove_elements_from_numpy_array
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  from .mm import remove_volumes_from_timeseries
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  from .mm import impute_timeseries
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  from .mm import impute_dwi
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+ from .mm import scrub_dwi
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  from .mm import timeseries_n3
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  from .mm import calculate_CBF
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+ from .mm import estimate_optimal_pca_components
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+ from .mm import filter_df
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+