melage 0.0.68__py3-none-any.whl → 1.0.0__py3-none-any.whl

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 (1017) hide show
  1. assets/copyright.png +0 -0
  2. assets/resource/color/FreeSurferColorLUT.txt +2006 -0
  3. assets/resource/color/LUT_30.txt +31 -0
  4. assets/resource/color/SynthSeg.txt +34 -0
  5. resource/color/Simple.txt → assets/resource/color/lut_prostate.txt +20 -18
  6. assets/resource/horizontalview.png +0 -0
  7. assets/resource/theme/create_ticks.py +85 -0
  8. assets/resource/theme/rc/checkbox_checked.png +0 -0
  9. assets/resource/theme/rc/checkbox_checked@2x.png +0 -0
  10. assets/resource/theme/rc/checkbox_checked_disabled.png +0 -0
  11. assets/resource/theme/rc/checkbox_checked_disabled@2x.png +0 -0
  12. assets/resource/theme/rc/checkbox_checked_focus.png +0 -0
  13. assets/resource/theme/rc/checkbox_checked_focus@2x.png +0 -0
  14. assets/resource/theme/rc/checkbox_checked_pressed.png +0 -0
  15. assets/resource/theme/rc/checkbox_checked_pressed@2x.png +0 -0
  16. assets/resource/theme/rc/checkbox_indeterminate.png +0 -0
  17. assets/resource/theme/rc/checkbox_indeterminate@2x.png +0 -0
  18. assets/resource/theme/rc/checkbox_indeterminate_disabled.png +0 -0
  19. assets/resource/theme/rc/checkbox_indeterminate_disabled@2x.png +0 -0
  20. assets/resource/theme/rc/checkbox_indeterminate_focus.png +0 -0
  21. assets/resource/theme/rc/checkbox_indeterminate_focus@2x.png +0 -0
  22. assets/resource/theme/rc/checkbox_indeterminate_pressed.png +0 -0
  23. assets/resource/theme/rc/checkbox_indeterminate_pressed@2x.png +0 -0
  24. assets/resource/theme/rc/checkbox_unchecked.png +0 -0
  25. assets/resource/theme/rc/checkbox_unchecked@2x.png +0 -0
  26. assets/resource/theme/rc/checkbox_unchecked_disabled.png +0 -0
  27. assets/resource/theme/rc/checkbox_unchecked_disabled@2x.png +0 -0
  28. assets/resource/theme/rc/checkbox_unchecked_focus.png +0 -0
  29. assets/resource/theme/rc/checkbox_unchecked_focus@2x.png +0 -0
  30. assets/resource/theme/rc/checkbox_unchecked_pressed.png +0 -0
  31. assets/resource/theme/rc/checkbox_unchecked_pressed@2x.png +0 -0
  32. assets/resource/verticalview.png +0 -0
  33. assets/resource/zoom_in.png +0 -0
  34. assets/resource/zoom_neutral (copy).png +0 -0
  35. assets/resource/zoom_neutral.png +0 -0
  36. assets/resource/zoom_out.png +0 -0
  37. data/MNI/mni_icbm152_t1_tal_nlin_sym_09a.nii +0 -0
  38. data/MNI/mni_icbm152_t1_tal_nlin_sym_09a_masked.nii.gz +0 -0
  39. data/MNI/mni_icbm152_t1_tal_nlin_sym_09a_seg.nii.gz +0 -0
  40. melage/__init__.py +1 -1
  41. melage/config/__init__.py +100 -0
  42. melage/core/Registration/registration.py +54 -0
  43. melage/{utils/readData.py → core/io.py} +12 -4
  44. melage/{widgets/melageAbout.py → dialogs/AboutDialog.py} +1 -1
  45. melage/dialogs/MaskOperationsDialog.py +146 -0
  46. melage/dialogs/MaskingDialog.py +139 -0
  47. melage/dialogs/RegistrationDialog.py +311 -0
  48. melage/{widgets/ImageThresholding.py → dialogs/ThresholdingDialog.py} +2 -2
  49. melage/dialogs/TransformationDialog.py +275 -0
  50. melage/dialogs/__init__.py +9 -0
  51. melage/dialogs/dynamic_gui.py +327 -0
  52. melage/{widgets/fileDialog_widget.py → dialogs/helpers/FileDialog.py} +226 -1
  53. melage/dialogs/helpers/__init__.py +5 -0
  54. melage/main.py +13 -13
  55. melage/{widgets/mainwindow_widget.py → mainwindow_widget.py} +1434 -1408
  56. melage/plugins/N4_bias/N4.py +115 -0
  57. melage/plugins/N4_bias/N4_schema.py +40 -0
  58. melage/plugins/N4_bias/main/utils.py +46 -0
  59. melage/plugins/__init__.py +2 -0
  60. melage/plugins/bet/bet.py +176 -0
  61. melage/plugins/bet/bet_schema.py +73 -0
  62. melage/{widgets/brain_extraction.py → plugins/bet/main/BET.py} +51 -316
  63. melage/plugins/change_coord/change_coord.py +197 -0
  64. melage/plugins/change_coord/change_coord_schema.py +31 -0
  65. melage/plugins/change_coord/main/utils.py +15 -0
  66. melage/{widgets/Segmentation → plugins/esfcm/main}/FCM.py +3 -5
  67. melage/plugins/esfcm/main/test.py +57 -0
  68. melage/{widgets/Segmentation → plugins/esfcm/main}/utils.py +20 -0
  69. melage/plugins/esfcm/tissue_segmentation.py +124 -0
  70. melage/plugins/esfcm/tissue_segmentation_schema.py +33 -0
  71. melage/plugins/masking_operation/mo.py +115 -0
  72. melage/plugins/masking_operation/mo_schema.py +33 -0
  73. melage/plugins/mga_net/MGA_Net.py +145 -0
  74. melage/plugins/mga_net/MGA_Net_schema.py +29 -0
  75. melage/plugins/mga_net/main/figures/Network.txt +1 -0
  76. melage/{widgets/DeepLModels/new_unet.py → plugins/mga_net/main/model/mga_net.py} +3 -3
  77. melage/plugins/mga_net/main/model/utils.py +258 -0
  78. melage/plugins/mga_net/main/test_mgaNet.py +134 -0
  79. melage/plugins/resize/resize.py +136 -0
  80. melage/plugins/resize/resize_schema.py +41 -0
  81. melage/plugins/ui_helpers.py +144 -0
  82. melage/plugins/warpseg/WarpSeg.py +195 -0
  83. melage/plugins/warpseg/WarpSeg_schema.py +41 -0
  84. melage/plugins/warpseg/__init__.py +2 -0
  85. melage/plugins/warpseg/warpseg_main/data_reader/DDSet.py +303 -0
  86. melage/plugins/warpseg/warpseg_main/data_reader/DDSetSeg.py +279 -0
  87. melage/plugins/warpseg/warpseg_main/data_reader/__init__.py +60 -0
  88. melage/plugins/warpseg/warpseg_main/data_reader/baseData.py +18 -0
  89. melage/plugins/warpseg/warpseg_main/data_reader/utils.py +267 -0
  90. melage/plugins/warpseg/warpseg_main/dist_utils.py +18 -0
  91. melage/plugins/warpseg/warpseg_main/requirements.txt +10 -0
  92. melage/plugins/warpseg/warpseg_main/test.py +272 -0
  93. melage/plugins/warpseg/warpseg_main/train.py +432 -0
  94. melage/plugins/warpseg/warpseg_main/train_reg.py +373 -0
  95. melage/plugins/warpseg/warpseg_main/verify_post_process.py +73 -0
  96. melage/plugins/warpseg/warpseg_main/voxelmorph/__init__.py +45 -0
  97. melage/plugins/warpseg/warpseg_main/voxelmorph/py/__init__.py +1 -0
  98. melage/plugins/warpseg/warpseg_main/voxelmorph/py/utils.py +99 -0
  99. melage/{widgets/Synthstrip.py → plugins/warpseg/warpseg_main/voxelmorph/torch/Unet.py} +71 -51
  100. melage/plugins/warpseg/warpseg_main/voxelmorph/torch/__init__.py +4 -0
  101. melage/plugins/warpseg/warpseg_main/voxelmorph/torch/layers.py +97 -0
  102. melage/plugins/warpseg/warpseg_main/voxelmorph/torch/losses.py +462 -0
  103. melage/plugins/warpseg/warpseg_main/voxelmorph/torch/modelio.py +77 -0
  104. melage/{widgets/DeepLModels/InfantSegment/Unet.py → plugins/warpseg/warpseg_main/voxelmorph/torch/multi_stage_net.py} +76 -52
  105. melage/plugins/warpseg/warpseg_main/voxelmorph/torch/networks.py +308 -0
  106. melage/plugins/warpseg/warpseg_main/voxelmorph/torch/utils.py +470 -0
  107. melage/{utils/DispalyIm.py → rendering/DisplayIm.py} +67 -79
  108. melage/{utils → rendering}/glScientific.py +1 -1
  109. melage/utils/__init__.py +1 -0
  110. melage/utils/utils.py +343 -196
  111. melage/widgets/{dockWidgets.py → DockWidgets.py} +123 -55
  112. melage/widgets/SettingsWidget.py +98 -0
  113. melage/widgets/__init__.py +49 -0
  114. melage/widgets/openglWidgets.py +344 -156
  115. melage/widgets/openglWidgets_bu.py +645 -0
  116. melage/widgets/plugin_manager.py +62 -0
  117. melage-1.0.0.dist-info/METADATA +953 -0
  118. melage-1.0.0.dist-info/RECORD +571 -0
  119. melage-1.0.0.dist-info/entry_points.txt +2 -0
  120. melage-1.0.0.dist-info/top_level.txt +4 -0
  121. melage/requirements22.txt +0 -25
  122. melage/requirements_old.txt +0 -28
  123. melage/resource/theme/rc/checkbox_checked.png +0 -0
  124. melage/resource/theme/rc/checkbox_checked@2x.png +0 -0
  125. melage/resource/theme/rc/checkbox_checked@2x0.png +0 -0
  126. melage/resource/theme/rc/checkbox_checked@2x000.png.png +0 -0
  127. melage/resource/theme/rc/checkbox_checked_disabled.png +0 -0
  128. melage/resource/theme/rc/checkbox_checked_disabled0.png +0 -0
  129. melage/resource/theme/rc/checkbox_checked_disabled@2x.png +0 -0
  130. melage/resource/theme/rc/checkbox_checked_disabled@2x0.png +0 -0
  131. melage/resource/theme/rc/checkbox_checked_focus.png +0 -0
  132. melage/resource/theme/rc/checkbox_checked_focus0.png +0 -0
  133. melage/resource/theme/rc/checkbox_checked_focus@2x.png +0 -0
  134. melage/resource/theme/rc/checkbox_checked_focus@2x0.png +0 -0
  135. melage/resource/theme/rc/checkbox_checked_pressed.png +0 -0
  136. melage/resource/theme/rc/checkbox_checked_pressed0.png +0 -0
  137. melage/resource/theme/rc/checkbox_checked_pressed@2x.png +0 -0
  138. melage/resource/theme/rc/checkbox_checked_pressed@2x0.png +0 -0
  139. melage/resource/theme/rc/checkbox_indeterminate.png +0 -0
  140. melage/resource/theme/rc/checkbox_indeterminate@2x.png +0 -0
  141. melage/resource/theme/rc/checkbox_indeterminate_disabled.png +0 -0
  142. melage/resource/theme/rc/checkbox_indeterminate_disabled@2x.png +0 -0
  143. melage/resource/theme/rc/checkbox_indeterminate_focus.png +0 -0
  144. melage/resource/theme/rc/checkbox_indeterminate_focus@2x.png +0 -0
  145. melage/resource/theme/rc/checkbox_indeterminate_pressed.png +0 -0
  146. melage/resource/theme/rc/checkbox_indeterminate_pressed@2x.png +0 -0
  147. melage/resource/theme/rc/checkbox_unchecked.png +0 -0
  148. melage/resource/theme/rc/checkbox_unchecked0.png +0 -0
  149. melage/resource/theme/rc/checkbox_unchecked00.png +0 -0
  150. melage/resource/theme/rc/checkbox_unchecked@2x.png +0 -0
  151. melage/resource/theme/rc/checkbox_unchecked@2x0.png +0 -0
  152. melage/resource/theme/rc/checkbox_unchecked@2x00.png +0 -0
  153. melage/resource/theme/rc/checkbox_unchecked_disabled.png +0 -0
  154. melage/resource/theme/rc/checkbox_unchecked_disabled0.png +0 -0
  155. melage/resource/theme/rc/checkbox_unchecked_disabled00.png +0 -0
  156. melage/resource/theme/rc/checkbox_unchecked_disabled@2x.png +0 -0
  157. melage/resource/theme/rc/checkbox_unchecked_disabled@2x0.png +0 -0
  158. melage/resource/theme/rc/checkbox_unchecked_disabled@2x00.png +0 -0
  159. melage/resource/theme/rc/checkbox_unchecked_focus.png +0 -0
  160. melage/resource/theme/rc/checkbox_unchecked_focus0.png +0 -0
  161. melage/resource/theme/rc/checkbox_unchecked_focus00.png +0 -0
  162. melage/resource/theme/rc/checkbox_unchecked_focus@2x.png +0 -0
  163. melage/resource/theme/rc/checkbox_unchecked_focus@2x0.png +0 -0
  164. melage/resource/theme/rc/checkbox_unchecked_focus@2x00.png +0 -0
  165. melage/resource/theme/rc/checkbox_unchecked_pressed.png +0 -0
  166. melage/resource/theme/rc/checkbox_unchecked_pressed0.png +0 -0
  167. melage/resource/theme/rc/checkbox_unchecked_pressed00.png +0 -0
  168. melage/resource/theme/rc/checkbox_unchecked_pressed@2x.png +0 -0
  169. melage/resource/theme/rc/checkbox_unchecked_pressed@2x0.png +0 -0
  170. melage/resource/theme/rc/checkbox_unchecked_pressed@2x00.png +0 -0
  171. melage/some_notes.txt +0 -3
  172. melage/utils/GMM.py +0 -720
  173. melage/utils/Shaders_bu.py +0 -314
  174. melage/utils/__init__0.py +0 -7
  175. melage/utils/glScientific_bc.py +0 -1585
  176. melage/utils/registration.py +0 -512
  177. melage/utils/source_folder.py +0 -18
  178. melage/version.txt +0 -1
  179. melage/widgets/ApplyMask.py +0 -212
  180. melage/widgets/ChangeSystem.py +0 -152
  181. melage/widgets/DeepLModels/NPP/dataset/mri_dataset_affine.py +0 -149
  182. melage/widgets/DeepLModels/NPP/models/checkpoints/npp_v1.pth.py +0 -0
  183. melage/widgets/DeepLModels/NPP/models/losses.py +0 -146
  184. melage/widgets/DeepLModels/NPP/models/model.py +0 -272
  185. melage/widgets/DeepLModels/NPP/models/utils.py +0 -303
  186. melage/widgets/DeepLModels/NPP/npp.py +0 -116
  187. melage/widgets/DeepLModels/NPP/requirements.txt +0 -8
  188. melage/widgets/DeepLModels/NPP/train/train.py +0 -116
  189. melage/widgets/DeepLModels/Unet3DAtt.py +0 -657
  190. melage/widgets/DeepLModels/Unet3D_basic.py +0 -648
  191. melage/widgets/DeepLModels/new_unet_old.py +0 -639
  192. melage/widgets/DeepLModels/new_unet_old2.py +0 -658
  193. melage/widgets/MaskOperations.py +0 -147
  194. melage/widgets/N4Dialog.py +0 -241
  195. melage/widgets/Segmentation/__init__.py +0 -588
  196. melage/widgets/SemiAutoSeg.py +0 -666
  197. melage/widgets/__init__0.py +0 -5
  198. melage/widgets/about.py +0 -246
  199. melage/widgets/activator.py +0 -147
  200. melage/widgets/be_dl.py +0 -409
  201. melage/widgets/be_dl_unet3d.py +0 -441
  202. melage/widgets/brain_extraction_dl.py +0 -887
  203. melage/widgets/brain_extraction_dl_bu.py +0 -869
  204. melage/widgets/registrationWidget.py +0 -342
  205. melage/widgets/settings_widget.py +0 -77
  206. melage/widgets/tranformationWidget.py +0 -275
  207. melage-0.0.68.dist-info/METADATA +0 -740
  208. melage-0.0.68.dist-info/RECORD +0 -916
  209. melage-0.0.68.dist-info/entry_points.txt +0 -2
  210. melage-0.0.68.dist-info/top_level.txt +0 -2
  211. resource/0circle.png +0 -0
  212. resource/0circle_faded.png +0 -0
  213. resource/3d.png +0 -0
  214. resource/3d.psd +0 -0
  215. resource/3dFaded.png +0 -0
  216. resource/Eraser.png +0 -0
  217. resource/EraserFaded.png +0 -0
  218. resource/EraserX.png +0 -0
  219. resource/EraserXFaded.png +0 -0
  220. resource/Eraser_icon.svg +0 -79
  221. resource/Hand.png +0 -0
  222. resource/HandIcons_0.png +0 -0
  223. resource/Hand_IX.png +0 -0
  224. resource/Hand_IXFaded.png +0 -0
  225. resource/Handsqueezed.png +0 -0
  226. resource/Handwriting (copy).png +0 -0
  227. resource/Handwriting.png +0 -0
  228. resource/HandwritingMinus.png +0 -0
  229. resource/HandwritingMinusX.png +0 -0
  230. resource/HandwritingPlus.png +0 -0
  231. resource/HandwritingPlusX.png +0 -0
  232. resource/Move_icon.svg +0 -8
  233. resource/PngItem_2422924.png +0 -0
  234. resource/about.png +0 -0
  235. resource/about_logo.png +0 -0
  236. resource/about_logo0.png +0 -0
  237. resource/action_check.png +0 -0
  238. resource/action_check_OFF.png +0 -0
  239. resource/arrow).png +0 -0
  240. resource/arrow.png +0 -0
  241. resource/arrowFaded.png +0 -0
  242. resource/arrow_org.png +0 -0
  243. resource/arrow_org.png.png +0 -0
  244. resource/arrows.png +0 -0
  245. resource/authors.mp4 +0 -0
  246. resource/box.png +0 -0
  247. resource/check-image-icon-0.jpg +0 -0
  248. resource/circle.png +0 -0
  249. resource/circle_faded.png +0 -0
  250. resource/circle_or.png +0 -0
  251. resource/close.png +0 -0
  252. resource/close_bg.png +0 -0
  253. resource/color/Tissue.txt +0 -24
  254. resource/color/Tissue12.txt +0 -27
  255. resource/color/albert_LUT.txt +0 -102
  256. resource/color/mcrib_LUT.txt +0 -102
  257. resource/color/pediatric1.txt +0 -29
  258. resource/color/pediatric1_old.txt +0 -27
  259. resource/color/pediatric2.txt +0 -87
  260. resource/color/pediatric3.txt +0 -29
  261. resource/color/pediatrics (copy).csv +0 -103
  262. resource/color/tissue_seg.txt +0 -4
  263. resource/contour.png +0 -0
  264. resource/contour.svg +0 -2
  265. resource/contourFaded.png +0 -0
  266. resource/contourX.png +0 -0
  267. resource/contourXFaded.png +0 -0
  268. resource/dti.png +0 -0
  269. resource/dti0.png +0 -0
  270. resource/dti222.png +0 -0
  271. resource/dti_or.png +0 -0
  272. resource/eco.png +0 -0
  273. resource/eco22.png +0 -0
  274. resource/eco_old.png +0 -0
  275. resource/eco_or.png +0 -0
  276. resource/eco_or2.png +0 -0
  277. resource/eco_seg.png +0 -0
  278. resource/eco_seg_old.png +0 -0
  279. resource/export.png +0 -0
  280. resource/hand-grab-icon-10.jpg +0 -0
  281. resource/hand-grab-icon-25.jpg +0 -0
  282. resource/info.png +0 -0
  283. resource/line.png +0 -0
  284. resource/linefaded.png +0 -0
  285. resource/load.png +0 -0
  286. resource/melage_top.ico +0 -0
  287. resource/melage_top.png +0 -0
  288. resource/melage_top0.png +0 -0
  289. resource/melage_top1.png +0 -0
  290. resource/melage_top4.png +0 -0
  291. resource/mri (copy).png +0 -0
  292. resource/mri.png +0 -0
  293. resource/mri0.png +0 -0
  294. resource/mri000.png +0 -0
  295. resource/mri22.png +0 -0
  296. resource/mri_big.png +0 -0
  297. resource/mri_old.png +0 -0
  298. resource/mri_seg.png +0 -0
  299. resource/mri_seg_old.png +0 -0
  300. resource/new.png +0 -0
  301. resource/open.png +0 -0
  302. resource/open2.png +0 -0
  303. resource/pan.png +0 -0
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  311. resource/s.png +0 -0
  312. resource/s.psd +0 -0
  313. resource/save.png +0 -0
  314. resource/saveas.png +0 -0
  315. resource/seg_mri.png +0 -0
  316. resource/seg_mri2.png +0 -0
  317. resource/settings.png +0 -0
  318. resource/synch.png +0 -0
  319. resource/synchFaded.png +0 -0
  320. resource/theme/rc/.keep +0 -1
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  353. resource/theme/rc/base_icon.png +0 -0
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  992. /melage/{widgets/activation.py → dialogs/ActivationDialog.py} +0 -0
  993. /melage/{widgets/HistImage.py → dialogs/HistogramDialog.py} +0 -0
  994. /melage/{widgets/iminfo.py → dialogs/ImInfoDialog.py} +0 -0
  995. /melage/{widgets/colorwidget.py → dialogs/helpers/ColorDialog.py} +0 -0
  996. /melage/{utils/custom_QScrollBar.py → dialogs/helpers/CustomScrollbar.py} +0 -0
  997. /melage/{widgets/repeat_widget.py → dialogs/helpers/RepeatDialog.py} +0 -0
  998. /melage/{widgets/screenshot_widget.py → dialogs/helpers/ScreenshotDialog.py} +0 -0
  999. /melage/{cli.py → melage.py} +0 -0
  1000. /melage/{utils/brain_extraction_helper.py → plugins/bet/main/utils.py} +0 -0
  1001. /melage/{graphics → rendering}/GLGraphicsItem.py +0 -0
  1002. /melage/{graphics → rendering}/GLViewWidget.py +0 -0
  1003. /melage/{graphics → rendering}/Transform3D.py +0 -0
  1004. /melage/{graphics → rendering}/__init__.py +0 -0
  1005. /melage/{graphics → rendering}/functions.py +0 -0
  1006. /melage/{utils → rendering/helpers}/Shaders_120.py +0 -0
  1007. /melage/{utils → rendering/helpers}/Shaders_330.py +0 -0
  1008. /melage/{graphics → rendering}/items/GLAxisItem.py +0 -0
  1009. /melage/{graphics → rendering}/items/GLGridItem.py +0 -0
  1010. /melage/{graphics → rendering}/items/GLPolygonItem.py +0 -0
  1011. /melage/{graphics → rendering}/items/GLScatterPlotItem.py +0 -0
  1012. /melage/{graphics → rendering}/items/GLVolumeItem.py +0 -0
  1013. /melage/{graphics → rendering}/items/GLVolumeItem_b.py +0 -0
  1014. /melage/{graphics → rendering}/items/__init__.py +0 -0
  1015. /melage/{graphics → rendering}/shaders.py +0 -0
  1016. /melage/widgets/{enhanceImWidget.py → EnhanceImageWidget.py} +0 -0
  1017. {melage-0.0.68.dist-info → melage-1.0.0.dist-info}/WHEEL +0 -0
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