paradigma 0.1.2__py3-none-any.whl → 0.2.0__py3-none-any.whl

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Files changed (112) hide show
  1. paradigma/__init__.py +1 -3
  2. paradigma/constants.py +35 -0
  3. paradigma/feature_extraction.py +678 -0
  4. paradigma/gait_analysis.py +413 -0
  5. paradigma/gait_analysis_config.py +244 -0
  6. paradigma/heart_rate_analysis.py +127 -0
  7. paradigma/heart_rate_analysis_config.py +9 -0
  8. paradigma/heart_rate_util.py +173 -0
  9. paradigma/imu_preprocessing.py +229 -0
  10. paradigma/ppg/classifier/LR_PPG_quality.pkl +0 -0
  11. paradigma/ppg/classifier/LR_model.mat +0 -0
  12. paradigma/ppg/feat_extraction/acc_feature.m +20 -0
  13. paradigma/ppg/feat_extraction/peakdet.m +64 -0
  14. paradigma/ppg/feat_extraction/ppg_features.m +53 -0
  15. paradigma/ppg/glob_functions/extract_hr_segments.m +37 -0
  16. paradigma/ppg/glob_functions/extract_overlapping_segments.m +23 -0
  17. paradigma/ppg/glob_functions/jsonlab/AUTHORS.txt +41 -0
  18. paradigma/ppg/glob_functions/jsonlab/ChangeLog.txt +74 -0
  19. paradigma/ppg/glob_functions/jsonlab/LICENSE_BSD.txt +25 -0
  20. paradigma/ppg/glob_functions/jsonlab/LICENSE_GPLv3.txt +699 -0
  21. paradigma/ppg/glob_functions/jsonlab/README.txt +394 -0
  22. paradigma/ppg/glob_functions/jsonlab/examples/.svn/entries +368 -0
  23. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/demo_jsonlab_basic.m.svn-base +180 -0
  24. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/demo_ubjson_basic.m.svn-base +180 -0
  25. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/example1.json.svn-base +23 -0
  26. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/example2.json.svn-base +22 -0
  27. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/example3.json.svn-base +11 -0
  28. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/example4.json.svn-base +34 -0
  29. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/jsonlab_basictest.matlab.svn-base +662 -0
  30. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/jsonlab_selftest.m.svn-base +27 -0
  31. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/jsonlab_selftest.matlab.svn-base +144 -0
  32. paradigma/ppg/glob_functions/jsonlab/examples/.svn/text-base/jsonlab_speedtest.m.svn-base +21 -0
  33. paradigma/ppg/glob_functions/jsonlab/examples/demo_jsonlab_basic.m +180 -0
  34. paradigma/ppg/glob_functions/jsonlab/examples/demo_ubjson_basic.m +180 -0
  35. paradigma/ppg/glob_functions/jsonlab/examples/example1.json +23 -0
  36. paradigma/ppg/glob_functions/jsonlab/examples/example2.json +22 -0
  37. paradigma/ppg/glob_functions/jsonlab/examples/example3.json +11 -0
  38. paradigma/ppg/glob_functions/jsonlab/examples/example4.json +34 -0
  39. paradigma/ppg/glob_functions/jsonlab/examples/jsonlab_basictest.matlab +662 -0
  40. paradigma/ppg/glob_functions/jsonlab/examples/jsonlab_selftest.m +27 -0
  41. paradigma/ppg/glob_functions/jsonlab/examples/jsonlab_selftest.matlab +144 -0
  42. paradigma/ppg/glob_functions/jsonlab/examples/jsonlab_speedtest.m +21 -0
  43. paradigma/ppg/glob_functions/jsonlab/jsonopt.m +32 -0
  44. paradigma/ppg/glob_functions/jsonlab/loadjson.m +566 -0
  45. paradigma/ppg/glob_functions/jsonlab/loadubjson.m +528 -0
  46. paradigma/ppg/glob_functions/jsonlab/mergestruct.m +33 -0
  47. paradigma/ppg/glob_functions/jsonlab/savejson.m +475 -0
  48. paradigma/ppg/glob_functions/jsonlab/saveubjson.m +504 -0
  49. paradigma/ppg/glob_functions/jsonlab/varargin2struct.m +40 -0
  50. paradigma/ppg/glob_functions/sample_prob_final.m +49 -0
  51. paradigma/ppg/glob_functions/synchronization.m +76 -0
  52. paradigma/ppg/glob_functions/tsdf_scan_meta.m +22 -0
  53. paradigma/ppg/hr_functions/Long_TFD_JOT.m +37 -0
  54. paradigma/ppg/hr_functions/PPG_TFD_HR.m +59 -0
  55. paradigma/ppg/hr_functions/TFD toolbox JOT/.gitignore +4 -0
  56. paradigma/ppg/hr_functions/TFD toolbox JOT/CHANGELOG.md +23 -0
  57. paradigma/ppg/hr_functions/TFD toolbox JOT/LICENCE.md +27 -0
  58. paradigma/ppg/hr_functions/TFD toolbox JOT/README.md +251 -0
  59. paradigma/ppg/hr_functions/TFD toolbox JOT/README.pdf +0 -0
  60. paradigma/ppg/hr_functions/TFD toolbox JOT/common/gen_Doppler_kern.m +142 -0
  61. paradigma/ppg/hr_functions/TFD toolbox JOT/common/gen_Doppler_lag_kern.m +314 -0
  62. paradigma/ppg/hr_functions/TFD toolbox JOT/common/gen_lag_kern.m +123 -0
  63. paradigma/ppg/hr_functions/TFD toolbox JOT/dec_tfd.m +154 -0
  64. paradigma/ppg/hr_functions/TFD toolbox JOT/decimated_TFDs/dec_di_gdtfd.m +194 -0
  65. paradigma/ppg/hr_functions/TFD toolbox JOT/decimated_TFDs/dec_li_gdtfd.m +200 -0
  66. paradigma/ppg/hr_functions/TFD toolbox JOT/decimated_TFDs/dec_nonsep_gdtfd.m +229 -0
  67. paradigma/ppg/hr_functions/TFD toolbox JOT/decimated_TFDs/dec_sep_gdtfd.m +241 -0
  68. paradigma/ppg/hr_functions/TFD toolbox JOT/full_TFDs/di_gdtfd.m +157 -0
  69. paradigma/ppg/hr_functions/TFD toolbox JOT/full_TFDs/li_gdtfd.m +190 -0
  70. paradigma/ppg/hr_functions/TFD toolbox JOT/full_TFDs/nonsep_gdtfd.m +196 -0
  71. paradigma/ppg/hr_functions/TFD toolbox JOT/full_TFDs/sep_gdtfd.m +199 -0
  72. paradigma/ppg/hr_functions/TFD toolbox JOT/full_tfd.m +144 -0
  73. paradigma/ppg/hr_functions/TFD toolbox JOT/load_curdir.m +13 -0
  74. paradigma/ppg/hr_functions/TFD toolbox JOT/pics/decimated_TFDs_examples.png +0 -0
  75. paradigma/ppg/hr_functions/TFD toolbox JOT/pics/full_TFDs_examples.png +0 -0
  76. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/check_dec_params_seq.m +79 -0
  77. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/dispEE.m +9 -0
  78. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/dispVars.m +26 -0
  79. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/disp_bytes.m +25 -0
  80. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/fold_vector_full.m +40 -0
  81. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/fold_vector_half.m +34 -0
  82. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/gen_LFM.m +29 -0
  83. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/get_analytic_signal.m +76 -0
  84. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/get_window.m +176 -0
  85. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/isreal_fn.m +11 -0
  86. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/padWin.m +97 -0
  87. paradigma/ppg/hr_functions/TFD toolbox JOT/utils/vtfd.m +149 -0
  88. paradigma/ppg/preprocessing/preprocessing_imu.m +15 -0
  89. paradigma/ppg/preprocessing/preprocessing_ppg.m +13 -0
  90. paradigma/ppg_preprocessing.py +313 -0
  91. paradigma/preprocessing_config.py +64 -0
  92. paradigma/quantification.py +58 -0
  93. paradigma/tremor/TremorFeaturesAndClassification.m +345 -0
  94. paradigma/tremor/feat_extraction/DerivativesExtract.m +22 -0
  95. paradigma/tremor/feat_extraction/ExtractBandSignalsRMS.m +72 -0
  96. paradigma/tremor/feat_extraction/MFCCExtract.m +100 -0
  97. paradigma/tremor/feat_extraction/PSDBandPower.m +52 -0
  98. paradigma/tremor/feat_extraction/PSDEst.m +63 -0
  99. paradigma/tremor/feat_extraction/PSDExtrAxis.m +88 -0
  100. paradigma/tremor/feat_extraction/PSDExtrOpt.m +95 -0
  101. paradigma/tremor/preprocessing/InterpData.m +32 -0
  102. paradigma/tremor/weekly_aggregates/WeeklyAggregates.m +295 -0
  103. paradigma/util.py +50 -0
  104. paradigma/windowing.py +217 -0
  105. paradigma-0.2.0.dist-info/LICENSE +192 -0
  106. paradigma-0.2.0.dist-info/METADATA +58 -0
  107. paradigma-0.2.0.dist-info/RECORD +108 -0
  108. paradigma/dummy.py +0 -3
  109. paradigma-0.1.2.dist-info/LICENSE +0 -201
  110. paradigma-0.1.2.dist-info/METADATA +0 -18
  111. paradigma-0.1.2.dist-info/RECORD +0 -6
  112. {paradigma-0.1.2.dist-info → paradigma-0.2.0.dist-info}/WHEEL +0 -0
@@ -0,0 +1,144 @@
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+
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+ < M A T L A B >
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+ Copyright 1984-2007 The MathWorks, Inc.
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+ Version 7.4.0.287 (R2007a)
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+ January 29, 2007
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+
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+
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+ To get started, type one of these: helpwin, helpdesk, or demo.
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+ For product information, visit www.mathworks.com.
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+
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+ >> >> >> >> >> ===============================================
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+ >> example1.json
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+ {
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+ "data": {
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+ "firstName": "John",
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+ "lastName": "Smith",
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+ "age": 25,
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+ "address": {
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+ "streetAddress": "21 2nd Street",
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+ "city": "New York",
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+ "state": "NY",
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+ "postalCode": "10021"
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+ },
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+ "phoneNumber": [
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+ {
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+ "type": "home",
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+ "number": "212 555-1234"
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+ },
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+ {
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+ "type": "fax",
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+ "number": "646 555-4567"
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+ }
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+ ]
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+ }
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+ }
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+
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+ {"data": {"firstName": "John","lastName": "Smith","age": 25,"address": {"streetAddress": "21 2nd Street","city": "New York","state": "NY","postalCode": "10021"},"phoneNumber": [{"type": "home","number": "212 555-1234"},{"type": "fax","number": "646 555-4567"}]}}
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+
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+ ===============================================
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+ >> example2.json
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+ {
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+ "data": {
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+ "glossary": {
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+ "title": "example glossary",
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+ "GlossDiv": {
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+ "title": "S",
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+ "GlossList": {
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+ "GlossEntry": {
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+ "ID": "SGML",
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+ "SortAs": "SGML",
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+ "GlossTerm": "Standard Generalized Markup Language",
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+ "Acronym": "SGML",
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+ "Abbrev": "ISO 8879:1986",
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+ "GlossDef": {
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+ "para": "A meta-markup language, used to create markup languages such as DocBook.",
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+ "GlossSeeAlso": [
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+ "GML",
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+ "XML"
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+ ]
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+ },
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+ "GlossSee": "markup"
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+ }
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+ }
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+ }
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+ }
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+ }
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+ }
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+
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+ {"data": {"glossary": {"title": "example glossary","GlossDiv": {"title": "S","GlossList": {"GlossEntry": {"ID": "SGML","SortAs": "SGML","GlossTerm": "Standard Generalized Markup Language","Acronym": "SGML","Abbrev": "ISO 8879:1986","GlossDef": {"para": "A meta-markup language, used to create markup languages such as DocBook.","GlossSeeAlso": ["GML","XML"]},"GlossSee": "markup"}}}}}}
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+
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+ ===============================================
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+ >> example3.json
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+ {
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+ "data": {
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+ "menu": {
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+ "id": "file",
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+ "value": "_&File",
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+ "popup": {
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+ "menuitem": [
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+ {
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+ "value": "_&New",
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+ "onclick": "CreateNewDoc(\"\"\")"
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+ },
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+ {
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+ "value": "_&Open",
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+ "onclick": "OpenDoc()"
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+ },
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+ {
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+ "value": "_&Close",
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+ "onclick": "CloseDoc()"
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+ }
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+ ]
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+ }
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+ }
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+ }
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+ }
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+
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+ {"data": {"menu": {"id": "file","value": "_&File","popup": {"menuitem": [{"value": "_&New","onclick": "CreateNewDoc(\"\"\")"},{"value": "_&Open","onclick": "OpenDoc()"},{"value": "_&Close","onclick": "CloseDoc()"}]}}}}
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+
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+ ===============================================
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+ >> example4.json
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+ {
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+ "data": [
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+ {
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+ "sample": {
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+ "rho": 1
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+ }
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+ },
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+ {
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+ "sample": {
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+ "rho": 2
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+ }
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+ },
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+ [
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+ [1,0],
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+ [1,1],
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+ [1,2]
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+ ],
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+ [
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+ "Paper",
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+ "Scissors",
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+ "Stone"
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+ ]
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+ ]
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+ }
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+
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+ {"data": [{"sample": {"rho": 1}},{"sample": {"rho": 2}},[[1,0],[1,1],[1,2]],["Paper","Scissors","Stone"]]}
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+
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+ >> >> ===============================================
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+ >> example1.json
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+ {SUdata{SU firstNameSUJohnSUlastNameSUSmithSUageiSUaddress{SU
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+ postalCodeSU10021}SU phoneNumber[{SUtypeSUhomeSUnumberSU 212 555-1234}{SUtypeSUfaxSUnumberSU 646 555-4567}]}}
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+ ===============================================
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+ >> example2.json
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+ {SUdata{SUglossary{SUtitleSUexample glossarySUGlossDiv{SUtitleCSSU GlossList{SU
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+ GlossEntry{SUIDSUSGMLSUSortAsSUSGMLSU GlossTermSU$Standard Generalized Markup LanguageSUAcronymSUSGMLSUAbbrevSU
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+ ===============================================
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+ >> example3.json
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+ {SUdata{SUmenu{SUidSUfileSUvalueSU_&FileSUpopup{SUmenuitem[{SUvalueSU_&NewSUonclickSUCreateNewDoc(""")}{SUvalueSU_&OpenSUonclickSU OpenDoc()}{SUvalueSU_&CloseSUonclickSU
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+ CloseDoc()}]}}}}
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+ ===============================================
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+ >> example4.json
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+ {SUdata[{SUsample{SUrhoi}}{SUsample{SUrhoi}}[[$i#U
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+ >>
@@ -0,0 +1,21 @@
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+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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+ % Benchmarking processing speed of savejson and loadjson
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+ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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+
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+ datalen=[1e3 1e4 1e5 1e6];
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+ len=length(datalen);
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+ tsave=zeros(len,1);
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+ tload=zeros(len,1);
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+ for i=1:len
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+ tic;
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+ json=savejson('data',struct('d1',rand(datalen(i),3),'d2',rand(datalen(i),3)>0.5));
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+ tsave(i)=toc;
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+ data=loadjson(json);
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+ tload(i)=toc-tsave(i);
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+ fprintf(1,'matrix size: %d\n',datalen(i));
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+ end
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+
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+ loglog(datalen,tsave,'o-',datalen,tload,'r*-');
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+ legend('savejson runtime (s)','loadjson runtime (s)');
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+ xlabel('array size');
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+ ylabel('running time (s)');
@@ -0,0 +1,32 @@
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+ function val=jsonopt(key,default,varargin)
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+ %
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+ % val=jsonopt(key,default,optstruct)
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+ %
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+ % setting options based on a struct. The struct can be produced
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+ % by varargin2struct from a list of 'param','value' pairs
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+ %
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+ % authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
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+ %
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+ % $Id: loadjson.m 371 2012-06-20 12:43:06Z fangq $
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+ %
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+ % input:
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+ % key: a string with which one look up a value from a struct
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+ % default: if the key does not exist, return default
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+ % optstruct: a struct where each sub-field is a key
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+ %
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+ % output:
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+ % val: if key exists, val=optstruct.key; otherwise val=default
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+ %
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+ % license:
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+ % BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
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+ %
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+ % -- this function is part of jsonlab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
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+ %
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+
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+ val=default;
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+ if(nargin<=2) return; end
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+ opt=varargin{1};
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+ if(isstruct(opt) && isfield(opt,key))
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+ val=getfield(opt,key);
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+ end
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+