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Merge pull request #89 from KamitaniLab/origin/myaokai/fix_preproc
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テストケースの修正(preproc)
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@ShuntaroAoki
ShuntaroAoki committed Apr 4, 2024
2 parents 70b6825 + 4bf563c commit cdd1084
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions bdpy/preproc/select_top.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,17 +41,17 @@ def select_top(data, value, num, axis=0, verbose=True):
value = np.array([-np.inf if np.isnan(a) else a for a in value])
sorted_index = np.argsort(value)[::-1]

rank = np.zeros(num_elem, dtype=np.int)
rank = np.zeros(num_elem, dtype=np.uint8)
rank[sorted_index] = np.array(range(0, num_elem))

selected_index_bool = rank < num

if axis == 0:
selected_data = data[selected_index_bool, :]
selected_index = np.array(range(0, num_elem), dtype=np.int)[selected_index_bool]
selected_index = np.array(range(0, num_elem), dtype=np.uint8)[selected_index_bool]
elif axis == 1:
selected_data = data[:, selected_index_bool]
selected_index = np.array(range(0, num_elem), dtype=np.int)[selected_index_bool]
selected_index = np.array(range(0, num_elem), dtype=np.uint8)[selected_index_bool]
else:
raise ValueError('Invalid axis')

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Coverage

Coverage Report
FileStmtsMissCoverMissing
bdpy/bdata
   bdata.py39919551%79, 104, 109, 113, 118, 122, 132–134, 190, 233–239, 252–262, 276–277, 310, 314, 318–356, 405–411, 419–420, 425–426, 443–450, 468–469, 475, 508, 539, 548, 560, 589–598, 610, 625, 661, 683–691, 696–729, 738, 750–757, 761–767, 771–799, 803–824, 828–862, 866–868, 872–874, 878–887
   featureselector.py641281%62–67, 69–74
   metadata.py67199%84
   utils.py1133767%71, 82, 85–86, 95, 127–173, 201, 246, 258, 263
bdpy/dataform
   datastore.py1078521%59–75, 90–93, 97–98, 102–113, 116–119, 122–127, 131–132, 137–158, 190–197, 222–259, 262–265
   features.py29816545%31–32, 43–46, 90–92, 101–103, 107, 111, 115, 119, 152–153, 157–161, 168–197, 214–215, 224–225, 232–236, 274, 288, 305–319, 323, 327, 331, 335, 339, 343, 347, 351, 355, 359, 364–394, 398–418, 422–462, 465, 470–477, 491–493, 496–499, 502–505, 508–512, 515–516, 536–549
   pd.py9544%25–27, 43–44
   sparse.py67790%29, 52–58, 74, 109, 123
   utils.py12120%3–18
bdpy/dataset
   utils.py45450%3–98
bdpy/distcomp
   distcomp.py921880%33, 35, 49, 53, 55, 66–70, 74, 76, 81–82, 89–93, 97
bdpy/dl
   caffe.py60600%4–129
bdpy/dl/torch
   base.py432444%31–41, 48, 54, 60, 63, 73–83, 90, 96, 102, 105
   models.py33422632%149–170, 298–317, 328–332, 346–351, 443–495, 516–518, 529–588, 612–615, 626–685, 709–712, 723–772, 791–794, 805–854, 873–876
   torch.py1096045%49, 60, 81, 100, 107, 110, 172–202, 205, 208–220, 223–258
bdpy/evals
   metrics.py956729%49–53, 59–61, 82–112, 118–159, 172–179
bdpy/feature
   feature.py30293%69–70
bdpy/fig
   __init__.py440%6–9
   draw_group_image_set.py90900%3–182
   fig.py88880%16–164
   makeplots.py3363360%1–729
   tile_images.py59590%1–193
bdpy/ml
   crossvalidation.py592754%47–48, 113–114, 117–118, 138, 164–196
   learning.py3089669%43–44, 48, 52, 59, 91–104, 109–125, 128, 158–170, 184–209, 293, 309, 313–315, 318–319, 329, 339–340, 345–346, 356–364, 367–368, 376, 411–418, 439, 452, 460, 469, 501–503, 542, 554, 557, 565, 573, 578, 599
   model.py14012014%29–39, 54–70, 86–144, 156–169, 184–222, 225, 230–250, 254–258, 271–285
   searchlight.py161319%32–51
bdpy/mri
   fmriprep.py4974519%25–34, 38, 44–62, 65–75, 78–89, 92–160, 163–194, 230–360, 367–380, 384, 388–390, 394, 398–400, 410–434, 437–454, 457–464, 471–472, 475–491, 494, 498, 502–815, 819–831, 842–862
   glm.py403610%46–95
   image.py241921%29–54
   load_epi.py281836%36–50, 56–63, 82–88
   load_mri.py191616%16–36
   roi.py2482346%37–100, 122–148, 165–235, 241–314, 320–387, 399–466, 473–499
   spm.py15813912%26–155, 162–166, 170, 174–179, 183–300
bdpy/opendata
   __init__.py110%1
   openneuro.py2102100%1–329
bdpy/pipeline
   config.py36294%37–38
bdpy/preproc
   interface.py521669%111–123, 148–157
   preprocessor.py1296947%35, 44, 112–114, 121–128, 138–189, 196–227
   select_top.py22195%56
bdpy/recon
   utils.py55550%4–146
bdpy/recon/torch
   __init__.py110%1
   icnn.py1611610%15–478
bdpy/stats
   corr.py43393%57, 68, 102
bdpy/util
   info.py473623%19–79
   utils.py36878%60, 116–121, 140–142
TOTAL4928333032% 

Tests Skipped Failures Errors Time
115 0 💤 6 ❌ 0 🔥 10.436s ⏱️

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Coverage

Coverage Report
FileStmtsMissCoverMissing
bdpy/bdata
   bdata.py40019651%79, 104, 109, 113, 118, 122, 132–134, 190, 233–239, 252–262, 276–277, 310, 314, 318–356, 405–411, 419–420, 425–426, 443–450, 468–469, 475, 508, 539, 548, 560, 589–598, 610, 625, 661, 683–691, 696–729, 738, 750–757, 761–767, 771–799, 803–824, 828–862, 866–868, 872–874, 878–887
   featureselector.py641281%62–67, 69–74
   metadata.py67199%84
   utils.py1133767%71, 82, 85–86, 95, 127–173, 201, 246, 258, 263
bdpy/dataform
   datastore.py1078521%59–75, 90–93, 97–98, 102–113, 116–119, 122–127, 131–132, 137–158, 190–197, 222–259, 262–265
   features.py29816545%31–32, 43–46, 90–92, 101–103, 107, 111, 115, 119, 152–153, 157–161, 168–197, 214–215, 224–225, 232–236, 274, 288, 305–319, 323, 327, 331, 335, 339, 343, 347, 351, 355, 359, 364–394, 398–418, 422–462, 465, 470–477, 491–493, 496–499, 502–505, 508–512, 515–516, 536–549
   pd.py9544%25–27, 43–44
   sparse.py67790%29, 52–58, 74, 109, 123
   utils.py12120%3–18
bdpy/dataset
   utils.py45450%3–98
bdpy/distcomp
   distcomp.py921880%33, 35, 49, 53, 55, 66–70, 74, 76, 81–82, 89–93, 97
bdpy/dl
   caffe.py60600%4–129
bdpy/dl/torch
   base.py432444%31–41, 48, 54, 60, 63, 73–83, 90, 96, 102, 105
   models.py33422632%149–170, 298–317, 328–332, 346–351, 443–495, 516–518, 529–588, 612–615, 626–685, 709–712, 723–772, 791–794, 805–854, 873–876
   torch.py1096045%49, 60, 81, 100, 107, 110, 172–202, 205, 208–220, 223–258
bdpy/evals
   metrics.py956729%49–53, 59–61, 82–112, 118–159, 172–179
bdpy/feature
   feature.py30293%69–70
bdpy/fig
   __init__.py440%6–9
   draw_group_image_set.py88880%3–182
   fig.py88880%16–164
   makeplots.py3363360%1–729
   tile_images.py59590%1–193
bdpy/ml
   crossvalidation.py592754%47–48, 113–114, 117–118, 138, 164–196
   learning.py3099769%43–44, 48, 52, 59, 91–104, 109–125, 128, 158–170, 184–209, 293, 309, 313–315, 318–319, 329, 339–340, 345–346, 356–364, 367–368, 376, 410–418, 439, 452, 460, 469, 501–503, 542, 554, 557, 565, 573, 578, 599
   model.py14012014%29–39, 54–70, 86–144, 156–169, 184–222, 225, 230–250, 254–258, 271–285
   searchlight.py161319%32–51
bdpy/mri
   fmriprep.py4974529%25–34, 38, 44–62, 65–75, 78–89, 92–160, 163–194, 230–360, 367–380, 384, 388–390, 394, 398–400, 410–434, 437–454, 457–464, 471–472, 475–491, 494, 498, 502–815, 819–831, 842–862, 866
   glm.py403610%46–95
   image.py241921%29–54
   load_epi.py281836%36–50, 56–63, 82–88
   load_mri.py191616%16–36
   roi.py2482346%37–100, 122–148, 165–235, 241–314, 320–387, 399–466, 473–499
   spm.py15813912%26–155, 162–166, 170, 174–179, 183–300
bdpy/opendata
   __init__.py110%1
   openneuro.py2102100%1–329
bdpy/pipeline
   config.py36294%37–38
bdpy/preproc
   interface.py521669%111–123, 148–157
   preprocessor.py1296947%35, 44, 112–114, 121–128, 138–189, 196–227
   select_top.py22195%56
bdpy/recon
   utils.py55550%4–146
bdpy/recon/torch
   __init__.py110%1
   icnn.py1611610%15–478
bdpy/stats
   corr.py43393%57, 68, 102
bdpy/util
   info.py473623%19–79
   utils.py36878%60, 116–121, 140–142
TOTAL4928333132% 

Tests Skipped Failures Errors Time
115 0 💤 6 ❌ 0 🔥 10.538s ⏱️

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Coverage

Coverage Report
FileStmtsMissCoverMissing
bdpy/bdata
   bdata.py40019651%79, 104, 109, 113, 118, 122, 132–134, 190, 233–239, 252–262, 276–277, 310, 314, 318–356, 405–411, 419–420, 425–426, 443–450, 468–469, 475, 508, 539, 548, 560, 589–598, 610, 625, 661, 683–691, 696–729, 738, 750–757, 761–767, 771–799, 803–824, 828–862, 866–868, 872–874, 878–887
   featureselector.py641281%62–67, 69–74
   metadata.py67199%84
   utils.py1133767%71, 82, 85–86, 95, 127–173, 201, 246, 258, 263
bdpy/dataform
   datastore.py1078521%59–75, 90–93, 97–98, 102–113, 116–119, 122–127, 131–132, 137–158, 190–197, 222–259, 262–265
   features.py29816545%31–32, 43–46, 90–92, 101–103, 107, 111, 115, 119, 152–153, 157–161, 168–197, 214–215, 224–225, 232–236, 274, 288, 305–319, 323, 327, 331, 335, 339, 343, 347, 351, 355, 359, 364–394, 398–418, 422–462, 465, 470–477, 491–493, 496–499, 502–505, 508–512, 515–516, 536–549
   pd.py9544%25–27, 43–44
   sparse.py67790%29, 52–58, 74, 109, 123
   utils.py12120%3–18
bdpy/dataset
   utils.py45450%3–98
bdpy/distcomp
   distcomp.py921880%33, 35, 49, 53, 55, 66–70, 74, 76, 81–82, 89–93, 97
bdpy/dl
   caffe.py60600%4–129
bdpy/dl/torch
   base.py432444%31–41, 48, 54, 60, 63, 73–83, 90, 96, 102, 105
   models.py33422632%149–170, 298–317, 328–332, 346–351, 443–495, 516–518, 529–588, 612–615, 626–685, 709–712, 723–772, 791–794, 805–854, 873–876
   torch.py1096045%49, 60, 81, 100, 107, 110, 172–202, 205, 208–220, 223–258
bdpy/evals
   metrics.py956729%49–53, 59–61, 82–112, 118–159, 172–179
bdpy/feature
   feature.py30293%69–70
bdpy/fig
   __init__.py440%6–9
   draw_group_image_set.py88880%3–182
   fig.py88880%16–164
   makeplots.py3363360%1–729
   tile_images.py59590%1–193
bdpy/ml
   crossvalidation.py592754%47–48, 113–114, 117–118, 138, 164–196
   learning.py3099769%43–44, 48, 52, 59, 91–104, 109–125, 128, 158–170, 184–209, 293, 309, 313–315, 318–319, 329, 339–340, 345–346, 356–364, 367–368, 376, 410–418, 439, 452, 460, 469, 501–503, 542, 554, 557, 565, 573, 578, 599
   model.py14012014%29–39, 54–70, 86–144, 156–169, 184–222, 225, 230–250, 254–258, 271–285
   searchlight.py161319%32–51
bdpy/mri
   fmriprep.py4974529%25–34, 38, 44–62, 65–75, 78–89, 92–160, 163–194, 230–360, 367–380, 384, 388–390, 394, 398–400, 410–434, 437–454, 457–464, 471–472, 475–491, 494, 498, 502–815, 819–831, 842–862, 866
   glm.py403610%46–95
   image.py241921%29–54
   load_epi.py281836%36–50, 56–63, 82–88
   load_mri.py191616%16–36
   roi.py2482346%37–100, 122–148, 165–235, 241–314, 320–387, 399–466, 473–499
   spm.py15813912%26–155, 162–166, 170, 174–179, 183–300
bdpy/opendata
   __init__.py110%1
   openneuro.py2102100%1–329
bdpy/pipeline
   config.py36294%37–38
bdpy/preproc
   interface.py521669%111–123, 148–157
   preprocessor.py1296947%35, 44, 112–114, 121–128, 138–189, 196–227
   select_top.py22195%56
bdpy/recon
   utils.py55550%4–146
bdpy/recon/torch
   __init__.py110%1
   icnn.py1611610%15–478
bdpy/stats
   corr.py43393%57, 68, 102
bdpy/util
   info.py473623%19–79
   utils.py36878%60, 116–121, 140–142
TOTAL4928333132% 

Tests Skipped Failures Errors Time
115 0 💤 6 ❌ 0 🔥 10.414s ⏱️

@github-actions
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Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Coverage

Coverage Report
FileStmtsMissCoverMissing
bdpy/bdata
   bdata.py39919551%79, 104, 109, 113, 118, 122, 132–134, 190, 233–239, 252–262, 276–277, 310, 314, 318–356, 405–411, 419–420, 425–426, 443–450, 468–469, 475, 508, 539, 548, 560, 589–598, 610, 625, 661, 683–691, 696–729, 738, 750–757, 761–767, 771–799, 803–824, 828–862, 866–868, 872–874, 878–887
   featureselector.py641281%62–67, 69–74
   metadata.py67199%84
   utils.py1133767%71, 82, 85–86, 95, 127–173, 201, 246, 258, 263
bdpy/dataform
   datastore.py1078521%59–75, 90–93, 97–98, 102–113, 116–119, 122–127, 131–132, 137–158, 190–197, 222–259, 262–265
   features.py29816545%31–32, 43–46, 90–92, 101–103, 107, 111, 115, 119, 152–153, 157–161, 168–197, 214–215, 224–225, 232–236, 274, 288, 305–319, 323, 327, 331, 335, 339, 343, 347, 351, 355, 359, 364–394, 398–418, 422–462, 465, 470–477, 491–493, 496–499, 502–505, 508–512, 515–516, 536–549
   pd.py9544%25–27, 43–44
   sparse.py67790%29, 52–58, 74, 109, 123
   utils.py12120%3–18
bdpy/dataset
   utils.py45450%3–98
bdpy/distcomp
   distcomp.py921880%33, 35, 49, 53, 55, 66–70, 74, 76, 81–82, 89–93, 97
bdpy/dl
   caffe.py60600%4–129
bdpy/dl/torch
   base.py432444%31–41, 48, 54, 60, 63, 73–83, 90, 96, 102, 105
   models.py33422632%149–170, 298–317, 328–332, 346–351, 443–495, 516–518, 529–588, 612–615, 626–685, 709–712, 723–772, 791–794, 805–854, 873–876
   torch.py1096045%49, 60, 81, 100, 107, 110, 172–202, 205, 208–220, 223–258
bdpy/evals
   metrics.py956729%49–53, 59–61, 82–112, 118–159, 172–179
bdpy/feature
   feature.py30293%69–70
bdpy/fig
   __init__.py440%6–9
   draw_group_image_set.py90900%3–182
   fig.py88880%16–164
   makeplots.py3363360%1–729
   tile_images.py59590%1–193
bdpy/ml
   crossvalidation.py592754%47–48, 113–114, 117–118, 138, 164–196
   learning.py3089669%43–44, 48, 52, 59, 91–104, 109–125, 128, 158–170, 184–209, 293, 309, 313–315, 318–319, 329, 339–340, 345–346, 356–364, 367–368, 376, 411–418, 439, 452, 460, 469, 501–503, 542, 554, 557, 565, 573, 578, 599
   model.py14012014%29–39, 54–70, 86–144, 156–169, 184–222, 225, 230–250, 254–258, 271–285
   searchlight.py161319%32–51
bdpy/mri
   fmriprep.py4974519%25–34, 38, 44–62, 65–75, 78–89, 92–160, 163–194, 230–360, 367–380, 384, 388–390, 394, 398–400, 410–434, 437–454, 457–464, 471–472, 475–491, 494, 498, 502–815, 819–831, 842–862
   glm.py403610%46–95
   image.py241921%29–54
   load_epi.py281836%36–50, 56–63, 82–88
   load_mri.py191616%16–36
   roi.py2482346%37–100, 122–148, 165–235, 241–314, 320–387, 399–466, 473–499
   spm.py15813912%26–155, 162–166, 170, 174–179, 183–300
bdpy/opendata
   __init__.py110%1
   openneuro.py2102100%1–329
bdpy/pipeline
   config.py36294%37–38
bdpy/preproc
   interface.py521669%111–123, 148–157
   preprocessor.py1296947%35, 44, 112–114, 121–128, 138–189, 196–227
   select_top.py22195%56
bdpy/recon
   utils.py55550%4–146
bdpy/recon/torch
   __init__.py110%1
   icnn.py1611610%15–478
bdpy/stats
   corr.py43393%57, 68, 102
bdpy/util
   info.py473623%19–79
   utils.py36878%60, 116–121, 140–142
TOTAL4928333032% 

Tests Skipped Failures Errors Time
115 0 💤 6 ❌ 0 🔥 9.185s ⏱️

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