rapidtide 3.0a12__py3-none-any.whl → 3.0a14__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 (70) hide show
  1. cloud/gmscalc-HCPYA +1 -1
  2. cloud/rapidtide-HCPYA +3 -3
  3. rapidtide/Colortables.py +10 -10
  4. rapidtide/DerivativeDelay.py +213 -0
  5. rapidtide/{Refiner.py → RegressorRefiner.py} +1 -1
  6. rapidtide/__init__.py +2 -1
  7. rapidtide/_version.py +1 -1
  8. rapidtide/data/examples/src/test_mlregressallt.py +32 -17
  9. rapidtide/data/examples/src/testalign +1 -1
  10. rapidtide/data/examples/src/testboth +1 -1
  11. rapidtide/data/examples/src/testcifti +11 -0
  12. rapidtide/data/examples/src/testdelayvar +14 -0
  13. rapidtide/data/examples/src/testfmri +1 -0
  14. rapidtide/data/examples/src/testglmfilt +8 -6
  15. rapidtide/data/examples/src/testhappy +1 -1
  16. rapidtide/data/examples/src/testnewrefine +11 -11
  17. rapidtide/data/examples/src/testnoiseamp +2 -2
  18. rapidtide/data/examples/src/testretro +16 -7
  19. rapidtide/data/examples/src/testretrolagtcs +1 -1
  20. rapidtide/dlfilter.py +0 -1
  21. rapidtide/fit.py +41 -9
  22. rapidtide/happy_supportfuncs.py +5 -0
  23. rapidtide/io.py +13 -2
  24. rapidtide/{glmpass.py → linfitfiltpass.py} +23 -19
  25. rapidtide/makelaggedtcs.py +8 -5
  26. rapidtide/multiproc.py +8 -11
  27. rapidtide/refinedelay.py +234 -109
  28. rapidtide/resample.py +3 -0
  29. rapidtide/scripts/{retroglm.py → delayvar.py} +2 -2
  30. rapidtide/scripts/{glmfilt.py → linfitfilt.py} +2 -2
  31. rapidtide/scripts/retroregress.py +28 -0
  32. rapidtide/scripts/stupidramtricks.py +9 -7
  33. rapidtide/simfuncfit.py +1 -1
  34. rapidtide/tests/cleanposttest +21 -0
  35. rapidtide/tests/test_delayestimation.py +3 -3
  36. rapidtide/tests/test_fastresampler.py +1 -2
  37. rapidtide/tests/test_fullrunhappy_v1.py +14 -6
  38. rapidtide/tests/test_fullrunhappy_v2.py +17 -9
  39. rapidtide/tests/test_fullrunhappy_v3.py +16 -8
  40. rapidtide/tests/test_fullrunhappy_v4.py +16 -8
  41. rapidtide/tests/test_fullrunhappy_v5.py +14 -6
  42. rapidtide/tests/test_fullrunrapidtide_v1.py +20 -12
  43. rapidtide/tests/test_fullrunrapidtide_v2.py +21 -13
  44. rapidtide/tests/test_fullrunrapidtide_v3.py +15 -7
  45. rapidtide/tests/test_fullrunrapidtide_v4.py +14 -7
  46. rapidtide/tests/test_fullrunrapidtide_v5.py +13 -5
  47. rapidtide/tests/test_fullrunrapidtide_v6.py +34 -26
  48. rapidtide/tests/{test_glmpass.py → test_linfitfiltpass.py} +9 -9
  49. rapidtide/tests/test_motionregress.py +3 -3
  50. rapidtide/tests/test_refinedelay.py +14 -12
  51. rapidtide/tidepoolTemplate_alt_qt6.py +172 -45
  52. rapidtide/tidepoolTemplate_big_qt6.py +196 -53
  53. rapidtide/tidepoolTemplate_qt6.py +150 -39
  54. rapidtide/workflows/atlasaverage.py +40 -12
  55. rapidtide/workflows/delayvar.py +1136 -0
  56. rapidtide/workflows/happy.py +37 -11
  57. rapidtide/workflows/happy_parser.py +4 -4
  58. rapidtide/workflows/{glmfilt.py → linfitfilt.py} +4 -4
  59. rapidtide/workflows/rapidtide.py +246 -178
  60. rapidtide/workflows/rapidtide_parser.py +116 -101
  61. rapidtide/workflows/{glmfrommaps.py → regressfrommaps.py} +30 -26
  62. rapidtide/workflows/retrolagtcs.py +13 -12
  63. rapidtide/workflows/{retroglm.py → retroregress.py} +182 -141
  64. {rapidtide-3.0a12.dist-info → rapidtide-3.0a14.dist-info}/METADATA +3 -2
  65. {rapidtide-3.0a12.dist-info → rapidtide-3.0a14.dist-info}/RECORD +69 -64
  66. {rapidtide-3.0a12.dist-info → rapidtide-3.0a14.dist-info}/WHEEL +1 -1
  67. {rapidtide-3.0a12.dist-info → rapidtide-3.0a14.dist-info}/entry_points.txt +3 -2
  68. rapidtide/data/examples/src/testoutputsize +0 -45
  69. {rapidtide-3.0a12.dist-info → rapidtide-3.0a14.dist-info/licenses}/LICENSE +0 -0
  70. {rapidtide-3.0a12.dist-info → rapidtide-3.0a14.dist-info}/top_level.txt +0 -0
rapidtide/tidepoolTemplate_qt6.py CHANGED
@@ -13,7 +13,10 @@ class Ui_MainWindow(object):
13
13
  def setupUi(self, MainWindow):
14
14
  MainWindow.setObjectName("MainWindow")
15
15
  MainWindow.resize(1129, 909)
16
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding)
16
+ sizePolicy = QtWidgets.QSizePolicy(
17
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
18
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
19
+ )
17
20
  sizePolicy.setHorizontalStretch(1)
18
21
  sizePolicy.setVerticalStretch(1)
19
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  sizePolicy.setHeightForWidth(MainWindow.sizePolicy().hasHeightForWidth())
@@ -25,7 +28,9 @@ class Ui_MainWindow(object):
25
28
  self.centralwidget.setObjectName("centralwidget")
26
29
  self.logOutput_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)
27
30
  self.logOutput_groupBox.setGeometry(QtCore.QRect(440, 520, 671, 171))
28
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.Expanding)
31
+ sizePolicy = QtWidgets.QSizePolicy(
32
+ QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.Expanding
33
+ )
29
34
  sizePolicy.setHorizontalStretch(0)
30
35
  sizePolicy.setVerticalStretch(0)
31
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  sizePolicy.setHeightForWidth(self.logOutput_groupBox.sizePolicy().hasHeightForWidth())
@@ -42,7 +47,9 @@ class Ui_MainWindow(object):
42
47
  self.logOutput.setObjectName("logOutput")
43
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  self.imageData_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)
44
49
  self.imageData_groupBox.setGeometry(QtCore.QRect(10, 0, 1100, 312))
45
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.Preferred)
50
+ sizePolicy = QtWidgets.QSizePolicy(
51
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.Preferred
52
+ )
46
53
  sizePolicy.setHorizontalStretch(0)
47
54
  sizePolicy.setVerticalStretch(0)
48
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  sizePolicy.setHeightForWidth(self.imageData_groupBox.sizePolicy().hasHeightForWidth())
@@ -58,11 +65,16 @@ class Ui_MainWindow(object):
58
65
  self.layoutWidget.setGeometry(QtCore.QRect(10, 20, 1074, 286))
59
66
  self.layoutWidget.setObjectName("layoutWidget")
60
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  self.largeimage_horizontalLayout = QtWidgets.QHBoxLayout(self.layoutWidget)
61
- self.largeimage_horizontalLayout.setSizeConstraint(QtWidgets.QLayout.SizeConstraint.SetNoConstraint)
68
+ self.largeimage_horizontalLayout.setSizeConstraint(
69
+ QtWidgets.QLayout.SizeConstraint.SetNoConstraint
70
+ )
62
71
  self.largeimage_horizontalLayout.setContentsMargins(0, 0, 0, 0)
63
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  self.largeimage_horizontalLayout.setObjectName("largeimage_horizontalLayout")
64
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  self.main_graphicsView_ax = GraphicsLayoutWidget(parent=self.layoutWidget)
65
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding)
74
+ sizePolicy = QtWidgets.QSizePolicy(
75
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
76
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
77
+ )
66
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  sizePolicy.setHorizontalStretch(0)
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  sizePolicy.setVerticalStretch(0)
68
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  sizePolicy.setHeightForWidth(self.main_graphicsView_ax.sizePolicy().hasHeightForWidth())
@@ -75,7 +87,10 @@ class Ui_MainWindow(object):
75
87
  self.main_graphicsView_ax.setObjectName("main_graphicsView_ax")
76
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  self.largeimage_horizontalLayout.addWidget(self.main_graphicsView_ax)
77
89
  self.main_graphicsView_cor = GraphicsLayoutWidget(parent=self.layoutWidget)
78
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding)
90
+ sizePolicy = QtWidgets.QSizePolicy(
91
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
92
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
93
+ )
79
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  sizePolicy.setHorizontalStretch(0)
80
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  sizePolicy.setVerticalStretch(0)
81
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  sizePolicy.setHeightForWidth(self.main_graphicsView_cor.sizePolicy().hasHeightForWidth())
@@ -88,7 +103,10 @@ class Ui_MainWindow(object):
88
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  self.main_graphicsView_cor.setObjectName("main_graphicsView_cor")
89
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  self.largeimage_horizontalLayout.addWidget(self.main_graphicsView_cor)
90
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  self.main_graphicsView_sag = GraphicsLayoutWidget(parent=self.layoutWidget)
91
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding)
106
+ sizePolicy = QtWidgets.QSizePolicy(
107
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
108
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
109
+ )
92
110
  sizePolicy.setHorizontalStretch(0)
93
111
  sizePolicy.setVerticalStretch(0)
94
112
  sizePolicy.setHeightForWidth(self.main_graphicsView_sag.sizePolicy().hasHeightForWidth())
@@ -101,7 +119,10 @@ class Ui_MainWindow(object):
101
119
  self.main_graphicsView_sag.setObjectName("main_graphicsView_sag")
102
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  self.largeimage_horizontalLayout.addWidget(self.main_graphicsView_sag)
103
121
  self.graphicsView_colorbar = GraphicsView(parent=self.layoutWidget)
104
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding)
122
+ sizePolicy = QtWidgets.QSizePolicy(
123
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
124
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding,
125
+ )
105
126
  sizePolicy.setHorizontalStretch(0)
106
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  sizePolicy.setVerticalStretch(0)
107
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  sizePolicy.setHeightForWidth(self.graphicsView_colorbar.sizePolicy().hasHeightForWidth())
@@ -117,11 +138,17 @@ class Ui_MainWindow(object):
117
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  self.verticalLayout_3.setSpacing(0)
118
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  self.verticalLayout_3.setObjectName("verticalLayout_3")
119
140
  self.dispmax_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.layoutWidget)
120
- self.dispmax_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
141
+ self.dispmax_doubleSpinBox.setAlignment(
142
+ QtCore.Qt.AlignmentFlag.AlignRight
143
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
144
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
145
+ )
121
146
  self.dispmax_doubleSpinBox.setDecimals(3)
122
147
  self.dispmax_doubleSpinBox.setObjectName("dispmax_doubleSpinBox")
123
148
  self.verticalLayout_3.addWidget(self.dispmax_doubleSpinBox)
124
- spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Policy.Minimum, QtWidgets.QSizePolicy.Policy.Expanding)
149
+ spacerItem = QtWidgets.QSpacerItem(
150
+ 20, 40, QtWidgets.QSizePolicy.Policy.Minimum, QtWidgets.QSizePolicy.Policy.Expanding
151
+ )
125
152
  self.verticalLayout_3.addItem(spacerItem)
126
153
  self.resetDispLimits_Button = QtWidgets.QPushButton(parent=self.layoutWidget)
127
154
  self.resetDispLimits_Button.setObjectName("resetDispLimits_Button")
@@ -135,14 +162,20 @@ class Ui_MainWindow(object):
135
162
  self.setMask_Button = QtWidgets.QPushButton(parent=self.layoutWidget)
136
163
  self.setMask_Button.setObjectName("setMask_Button")
137
164
  self.verticalLayout_3.addWidget(self.setMask_Button)
138
- spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Policy.Minimum, QtWidgets.QSizePolicy.Policy.Expanding)
165
+ spacerItem1 = QtWidgets.QSpacerItem(
166
+ 20, 40, QtWidgets.QSizePolicy.Policy.Minimum, QtWidgets.QSizePolicy.Policy.Expanding
167
+ )
139
168
  self.verticalLayout_3.addItem(spacerItem1)
140
169
  self.transparency_checkBox = QtWidgets.QCheckBox(parent=self.layoutWidget)
141
170
  self.transparency_checkBox.setChecked(False)
142
171
  self.transparency_checkBox.setObjectName("transparency_checkBox")
143
172
  self.verticalLayout_3.addWidget(self.transparency_checkBox)
144
173
  self.dispmin_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.layoutWidget)
145
- self.dispmin_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
174
+ self.dispmin_doubleSpinBox.setAlignment(
175
+ QtCore.Qt.AlignmentFlag.AlignRight
176
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
177
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
178
+ )
146
179
  self.dispmin_doubleSpinBox.setDecimals(3)
147
180
  self.dispmin_doubleSpinBox.setObjectName("dispmin_doubleSpinBox")
148
181
  self.verticalLayout_3.addWidget(self.dispmin_doubleSpinBox)
@@ -258,7 +291,9 @@ class Ui_MainWindow(object):
258
291
  self.largeimage_horizontalLayout.addLayout(self.verticalLayout_2)
259
292
  self.overlays_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)
260
293
  self.overlays_groupBox.setGeometry(QtCore.QRect(10, 315, 421, 376))
261
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Minimum, QtWidgets.QSizePolicy.Policy.Preferred)
294
+ sizePolicy = QtWidgets.QSizePolicy(
295
+ QtWidgets.QSizePolicy.Policy.Minimum, QtWidgets.QSizePolicy.Policy.Preferred
296
+ )
262
297
  sizePolicy.setHorizontalStretch(0)
263
298
  sizePolicy.setVerticalStretch(0)
264
299
  sizePolicy.setHeightForWidth(self.overlays_groupBox.sizePolicy().hasHeightForWidth())
@@ -274,7 +309,9 @@ class Ui_MainWindow(object):
274
309
  self.overlay_radioButton_05.setObjectName("overlay_radioButton_05")
275
310
  self.overlay_graphicsView_01 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
276
311
  self.overlay_graphicsView_01.setGeometry(QtCore.QRect(10, 30, 198, 64))
277
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
312
+ sizePolicy = QtWidgets.QSizePolicy(
313
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
314
+ )
278
315
  sizePolicy.setHorizontalStretch(0)
279
316
  sizePolicy.setVerticalStretch(0)
280
317
  sizePolicy.setHeightForWidth(self.overlay_graphicsView_01.sizePolicy().hasHeightForWidth())
@@ -332,7 +369,9 @@ class Ui_MainWindow(object):
332
369
  self.overlay_radioButton_08.setObjectName("overlay_radioButton_08")
333
370
  self.overlay_graphicsView_04 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
334
371
  self.overlay_graphicsView_04.setGeometry(QtCore.QRect(10, 115, 192, 64))
335
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
372
+ sizePolicy = QtWidgets.QSizePolicy(
373
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
374
+ )
336
375
  sizePolicy.setHorizontalStretch(0)
337
376
  sizePolicy.setVerticalStretch(0)
338
377
  sizePolicy.setHeightForWidth(self.overlay_graphicsView_04.sizePolicy().hasHeightForWidth())
@@ -344,7 +383,9 @@ class Ui_MainWindow(object):
344
383
  self.overlay_graphicsView_04.setObjectName("overlay_graphicsView_04")
345
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  self.overlay_graphicsView_06 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
346
385
  self.overlay_graphicsView_06.setGeometry(QtCore.QRect(220, 200, 192, 64))
347
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
386
+ sizePolicy = QtWidgets.QSizePolicy(
387
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
388
+ )
348
389
  sizePolicy.setHorizontalStretch(0)
349
390
  sizePolicy.setVerticalStretch(0)
350
391
  sizePolicy.setHeightForWidth(self.overlay_graphicsView_06.sizePolicy().hasHeightForWidth())
@@ -356,7 +397,9 @@ class Ui_MainWindow(object):
356
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  self.overlay_graphicsView_06.setObjectName("overlay_graphicsView_06")
357
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  self.overlay_graphicsView_03 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
358
399
  self.overlay_graphicsView_03.setGeometry(QtCore.QRect(220, 115, 192, 64))
359
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
400
+ sizePolicy = QtWidgets.QSizePolicy(
401
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
402
+ )
360
403
  sizePolicy.setHorizontalStretch(0)
361
404
  sizePolicy.setVerticalStretch(0)
362
405
  sizePolicy.setHeightForWidth(self.overlay_graphicsView_03.sizePolicy().hasHeightForWidth())
@@ -368,7 +411,9 @@ class Ui_MainWindow(object):
368
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  self.overlay_graphicsView_03.setObjectName("overlay_graphicsView_03")
369
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  self.overlay_graphicsView_08 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
370
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  self.overlay_graphicsView_08.setGeometry(QtCore.QRect(220, 285, 192, 64))
371
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
414
+ sizePolicy = QtWidgets.QSizePolicy(
415
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
416
+ )
372
417
  sizePolicy.setHorizontalStretch(0)
373
418
  sizePolicy.setVerticalStretch(0)
374
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  sizePolicy.setHeightForWidth(self.overlay_graphicsView_08.sizePolicy().hasHeightForWidth())
@@ -380,7 +425,9 @@ class Ui_MainWindow(object):
380
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  self.overlay_graphicsView_08.setObjectName("overlay_graphicsView_08")
381
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  self.overlay_graphicsView_05 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
382
427
  self.overlay_graphicsView_05.setGeometry(QtCore.QRect(10, 200, 192, 64))
383
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
428
+ sizePolicy = QtWidgets.QSizePolicy(
429
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
430
+ )
384
431
  sizePolicy.setHorizontalStretch(0)
385
432
  sizePolicy.setVerticalStretch(0)
386
433
  sizePolicy.setHeightForWidth(self.overlay_graphicsView_05.sizePolicy().hasHeightForWidth())
@@ -392,7 +439,9 @@ class Ui_MainWindow(object):
392
439
  self.overlay_graphicsView_05.setObjectName("overlay_graphicsView_05")
393
440
  self.overlay_graphicsView_02 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
394
441
  self.overlay_graphicsView_02.setGeometry(QtCore.QRect(220, 30, 192, 64))
395
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
442
+ sizePolicy = QtWidgets.QSizePolicy(
443
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
444
+ )
396
445
  sizePolicy.setHorizontalStretch(0)
397
446
  sizePolicy.setVerticalStretch(0)
398
447
  sizePolicy.setHeightForWidth(self.overlay_graphicsView_02.sizePolicy().hasHeightForWidth())
@@ -404,7 +453,9 @@ class Ui_MainWindow(object):
404
453
  self.overlay_graphicsView_02.setObjectName("overlay_graphicsView_02")
405
454
  self.overlay_graphicsView_07 = GraphicsLayoutWidget(parent=self.overlays_groupBox)
406
455
  self.overlay_graphicsView_07.setGeometry(QtCore.QRect(10, 285, 192, 64))
407
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred)
456
+ sizePolicy = QtWidgets.QSizePolicy(
457
+ QtWidgets.QSizePolicy.Policy.Preferred, QtWidgets.QSizePolicy.Policy.Preferred
458
+ )
408
459
  sizePolicy.setHorizontalStretch(0)
409
460
  sizePolicy.setVerticalStretch(0)
410
461
  sizePolicy.setHeightForWidth(self.overlay_graphicsView_07.sizePolicy().hasHeightForWidth())
@@ -433,7 +484,9 @@ class Ui_MainWindow(object):
433
484
  self.overlay_graphicsView_07.raise_()
434
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  self.histogram_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)
435
486
  self.histogram_groupBox.setGeometry(QtCore.QRect(440, 315, 381, 201))
436
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.Expanding)
487
+ sizePolicy = QtWidgets.QSizePolicy(
488
+ QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.Expanding
489
+ )
437
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  sizePolicy.setHorizontalStretch(0)
438
491
  sizePolicy.setVerticalStretch(0)
439
492
  sizePolicy.setHeightForWidth(self.histogram_groupBox.sizePolicy().hasHeightForWidth())
@@ -443,7 +496,9 @@ class Ui_MainWindow(object):
443
496
  self.histogram_groupBox.setObjectName("histogram_groupBox")
444
497
  self.histogram_graphicsView = GraphicsLayoutWidget(parent=self.histogram_groupBox)
445
498
  self.histogram_graphicsView.setGeometry(QtCore.QRect(10, 30, 361, 161))
446
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding)
499
+ sizePolicy = QtWidgets.QSizePolicy(
500
+ QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.MinimumExpanding
501
+ )
447
502
  sizePolicy.setHorizontalStretch(0)
448
503
  sizePolicy.setVerticalStretch(0)
449
504
  sizePolicy.setHeightForWidth(self.histogram_graphicsView.sizePolicy().hasHeightForWidth())
@@ -459,7 +514,11 @@ class Ui_MainWindow(object):
459
514
  self.label_4.setObjectName("label_4")
460
515
  self.pixnumX_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
461
516
  self.pixnumX_doubleSpinBox.setGeometry(QtCore.QRect(30, 30, 67, 24))
462
- self.pixnumX_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
517
+ self.pixnumX_doubleSpinBox.setAlignment(
518
+ QtCore.Qt.AlignmentFlag.AlignRight
519
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
520
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
521
+ )
463
522
  self.pixnumX_doubleSpinBox.setDecimals(0)
464
523
  self.pixnumX_doubleSpinBox.setObjectName("pixnumX_doubleSpinBox")
465
524
  self.label_7 = QtWidgets.QLabel(parent=self.mainimagedata_groupBox)
@@ -470,7 +529,11 @@ class Ui_MainWindow(object):
470
529
  self.label_7.setObjectName("label_7")
471
530
  self.coordX_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
472
531
  self.coordX_doubleSpinBox.setGeometry(QtCore.QRect(100, 30, 67, 24))
473
- self.coordX_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
532
+ self.coordX_doubleSpinBox.setAlignment(
533
+ QtCore.Qt.AlignmentFlag.AlignRight
534
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
535
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
536
+ )
474
537
  self.coordX_doubleSpinBox.setDecimals(3)
475
538
  self.coordX_doubleSpinBox.setObjectName("coordX_doubleSpinBox")
476
539
  self.label_9 = QtWidgets.QLabel(parent=self.mainimagedata_groupBox)
@@ -481,22 +544,38 @@ class Ui_MainWindow(object):
481
544
  self.label_9.setObjectName("label_9")
482
545
  self.pixnumY_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
483
546
  self.pixnumY_doubleSpinBox.setGeometry(QtCore.QRect(30, 55, 67, 24))
484
- self.pixnumY_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
547
+ self.pixnumY_doubleSpinBox.setAlignment(
548
+ QtCore.Qt.AlignmentFlag.AlignRight
549
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
550
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
551
+ )
485
552
  self.pixnumY_doubleSpinBox.setDecimals(0)
486
553
  self.pixnumY_doubleSpinBox.setObjectName("pixnumY_doubleSpinBox")
487
554
  self.coordY_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
488
555
  self.coordY_doubleSpinBox.setGeometry(QtCore.QRect(100, 55, 67, 24))
489
- self.coordY_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
556
+ self.coordY_doubleSpinBox.setAlignment(
557
+ QtCore.Qt.AlignmentFlag.AlignRight
558
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
559
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
560
+ )
490
561
  self.coordY_doubleSpinBox.setDecimals(3)
491
562
  self.coordY_doubleSpinBox.setObjectName("coordY_doubleSpinBox")
492
563
  self.pixnumZ_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
493
564
  self.pixnumZ_doubleSpinBox.setGeometry(QtCore.QRect(30, 80, 67, 24))
494
- self.pixnumZ_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
565
+ self.pixnumZ_doubleSpinBox.setAlignment(
566
+ QtCore.Qt.AlignmentFlag.AlignRight
567
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
568
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
569
+ )
495
570
  self.pixnumZ_doubleSpinBox.setDecimals(0)
496
571
  self.pixnumZ_doubleSpinBox.setObjectName("pixnumZ_doubleSpinBox")
497
572
  self.coordZ_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
498
573
  self.coordZ_doubleSpinBox.setGeometry(QtCore.QRect(100, 80, 67, 24))
499
- self.coordZ_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
574
+ self.coordZ_doubleSpinBox.setAlignment(
575
+ QtCore.Qt.AlignmentFlag.AlignRight
576
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
577
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
578
+ )
500
579
  self.coordZ_doubleSpinBox.setDecimals(3)
501
580
  self.coordZ_doubleSpinBox.setObjectName("coordZ_doubleSpinBox")
502
581
  self.label_6 = QtWidgets.QLabel(parent=self.mainimagedata_groupBox)
@@ -507,12 +586,20 @@ class Ui_MainWindow(object):
507
586
  self.label_8.setObjectName("label_8")
508
587
  self.coordT_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
509
588
  self.coordT_doubleSpinBox.setGeometry(QtCore.QRect(100, 130, 67, 24))
510
- self.coordT_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
589
+ self.coordT_doubleSpinBox.setAlignment(
590
+ QtCore.Qt.AlignmentFlag.AlignRight
591
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
592
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
593
+ )
511
594
  self.coordT_doubleSpinBox.setDecimals(3)
512
595
  self.coordT_doubleSpinBox.setObjectName("coordT_doubleSpinBox")
513
596
  self.pixnumT_doubleSpinBox = QtWidgets.QDoubleSpinBox(parent=self.mainimagedata_groupBox)
514
597
  self.pixnumT_doubleSpinBox.setGeometry(QtCore.QRect(30, 130, 67, 24))
515
- self.pixnumT_doubleSpinBox.setAlignment(QtCore.Qt.AlignmentFlag.AlignRight|QtCore.Qt.AlignmentFlag.AlignTrailing|QtCore.Qt.AlignmentFlag.AlignVCenter)
598
+ self.pixnumT_doubleSpinBox.setAlignment(
599
+ QtCore.Qt.AlignmentFlag.AlignRight
600
+ | QtCore.Qt.AlignmentFlag.AlignTrailing
601
+ | QtCore.Qt.AlignmentFlag.AlignVCenter
602
+ )
516
603
  self.pixnumT_doubleSpinBox.setDecimals(0)
517
604
  self.pixnumT_doubleSpinBox.setObjectName("pixnumT_doubleSpinBox")
518
605
  self.label_3 = QtWidgets.QLabel(parent=self.mainimagedata_groupBox)
@@ -539,7 +626,9 @@ class Ui_MainWindow(object):
539
626
  self.runMovieButton.setObjectName("runMovieButton")
540
627
  self.regressor_groupBox = QtWidgets.QGroupBox(parent=self.centralwidget)
541
628
  self.regressor_groupBox.setGeometry(QtCore.QRect(10, 690, 1101, 181))
542
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.Expanding)
629
+ sizePolicy = QtWidgets.QSizePolicy(
630
+ QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.Expanding
631
+ )
543
632
  sizePolicy.setHorizontalStretch(0)
544
633
  sizePolicy.setVerticalStretch(0)
545
634
  sizePolicy.setHeightForWidth(self.regressor_groupBox.sizePolicy().hasHeightForWidth())
@@ -549,22 +638,32 @@ class Ui_MainWindow(object):
549
638
  self.regressor_groupBox.setObjectName("regressor_groupBox")
550
639
  self.regressorspectrum_graphicsView = GraphicsLayoutWidget(parent=self.regressor_groupBox)
551
640
  self.regressorspectrum_graphicsView.setGeometry(QtCore.QRect(490, 23, 472, 131))
552
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.Preferred)
641
+ sizePolicy = QtWidgets.QSizePolicy(
642
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.Preferred
643
+ )
553
644
  sizePolicy.setHorizontalStretch(0)
554
645
  sizePolicy.setVerticalStretch(0)
555
- sizePolicy.setHeightForWidth(self.regressorspectrum_graphicsView.sizePolicy().hasHeightForWidth())
646
+ sizePolicy.setHeightForWidth(
647
+ self.regressorspectrum_graphicsView.sizePolicy().hasHeightForWidth()
648
+ )
556
649
  self.regressorspectrum_graphicsView.setSizePolicy(sizePolicy)
557
650
  self.regressorspectrum_graphicsView.setMinimumSize(QtCore.QSize(100, 100))
558
651
  self.regressorspectrum_graphicsView.setMaximumSize(QtCore.QSize(1000, 1000))
559
652
  self.regressorspectrum_graphicsView.setSizeIncrement(QtCore.QSize(1, 1))
560
653
  self.regressorspectrum_graphicsView.setObjectName("regressorspectrum_graphicsView")
561
- self.regressortimecourse_graphicsView = GraphicsLayoutWidget(parent=self.regressor_groupBox)
654
+ self.regressortimecourse_graphicsView = GraphicsLayoutWidget(
655
+ parent=self.regressor_groupBox
656
+ )
562
657
  self.regressortimecourse_graphicsView.setEnabled(True)
563
658
  self.regressortimecourse_graphicsView.setGeometry(QtCore.QRect(10, 23, 472, 131))
564
- sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.Preferred)
659
+ sizePolicy = QtWidgets.QSizePolicy(
660
+ QtWidgets.QSizePolicy.Policy.MinimumExpanding, QtWidgets.QSizePolicy.Policy.Preferred
661
+ )
565
662
  sizePolicy.setHorizontalStretch(0)
566
663
  sizePolicy.setVerticalStretch(0)
567
- sizePolicy.setHeightForWidth(self.regressortimecourse_graphicsView.sizePolicy().hasHeightForWidth())
664
+ sizePolicy.setHeightForWidth(
665
+ self.regressortimecourse_graphicsView.sizePolicy().hasHeightForWidth()
666
+ )
568
667
  self.regressortimecourse_graphicsView.setSizePolicy(sizePolicy)
569
668
  self.regressortimecourse_graphicsView.setMinimumSize(QtCore.QSize(100, 100))
570
669
  self.regressortimecourse_graphicsView.setMaximumSize(QtCore.QSize(1000, 1000))
@@ -626,12 +725,22 @@ class Ui_MainWindow(object):
626
725
  MainWindow.setWindowTitle(_translate("MainWindow", "MainWindow"))
627
726
  self.logOutput_groupBox.setTitle(_translate("MainWindow", "Information"))
628
727
  self.imageData_groupBox.setTitle(_translate("MainWindow", "Image Data"))
629
- self.label.setText(_translate("MainWindow", "Click in image to position ROI. Drag right or left to increase or decrease the ROI size"))
728
+ self.label.setText(
729
+ _translate(
730
+ "MainWindow",
731
+ "Click in image to position ROI. Drag right or left to increase or decrease the ROI size",
732
+ )
733
+ )
630
734
  self.resetDispLimits_Button.setText(_translate("MainWindow", "Full Range"))
631
735
  self.resetDispSmart_Button.setText(_translate("MainWindow", "Smart"))
632
736
  self.saveDisp_Button.setText(_translate("MainWindow", "Save"))
633
737
  self.setMask_Button.setText(_translate("MainWindow", "No mask"))
634
- self.transparency_checkBox.setToolTip(_translate("MainWindow", "With transparency on, map values outside the range limits are not displayed."))
738
+ self.transparency_checkBox.setToolTip(
739
+ _translate(
740
+ "MainWindow",
741
+ "With transparency on, map values outside the range limits are not displayed.",
742
+ )
743
+ )
635
744
  self.transparency_checkBox.setText(_translate("MainWindow", "Transparency"))
636
745
  self.label_2.setText(_translate("MainWindow", "Colormap"))
637
746
  self.gray_radioButton.setText(_translate("MainWindow", "Gray"))
@@ -679,4 +788,6 @@ class Ui_MainWindow(object):
679
788
  self.label_5.setText(_translate("MainWindow", "Timecourse (seconds)"))
680
789
  self.label_12.setText(_translate("MainWindow", "Power spectrum (Hz)"))
681
790
  self.actionQuit.setText(_translate("MainWindow", "Quit"))
791
+
792
+
682
793
  from pyqtgraph import GraphicsLayoutWidget, GraphicsView
rapidtide/workflows/atlasaverage.py CHANGED
@@ -135,6 +135,15 @@ def _get_parser():
135
135
  ),
136
136
  default=None,
137
137
  )
138
+ parser.add_argument(
139
+ "--regionlabelfile",
140
+ type=lambda x: pf.is_valid_file(parser, x),
141
+ help=(
142
+ "The name of of a text file containing the labels of the regions, one per line. The first line is "
143
+ "the label integer value 1, etc."
144
+ ),
145
+ default=None,
146
+ )
138
147
  parser.add_argument(
139
148
  "--includemask",
140
149
  dest="includespec",
@@ -224,11 +233,9 @@ def atlasaverage(args):
224
233
  sys.exit()
225
234
 
226
235
  print("reshaping")
227
- xsize = thedims[1]
228
- ysize = thedims[2]
229
- numslices = thedims[3]
230
- numtimepoints = thedims[4]
231
- numvoxels = int(xsize) * int(ysize) * int(numslices)
236
+ xdim, ydim, numslices, numtimepoints = tide_io.parseniftidims(thedims)
237
+ xsize, ysize, slicethickness, tr = tide_io.parseniftisizes(thesizes)
238
+ numvoxels = int(xdim) * int(ydim) * int(numslices)
232
239
 
233
240
  templatevoxels = np.reshape(template_data, numvoxels).astype(int)
234
241
  inputvoxels = np.reshape(input_data, (numvoxels, numtimepoints))
@@ -273,7 +280,7 @@ def atlasaverage(args):
273
280
  themask = themask * includemask.reshape((numvoxels))
274
281
  if args.debug:
275
282
  tide_io.savetonifti(
276
- includemask.reshape((xsize, ysize, numslices)),
283
+ includemask.reshape((xdim, ydim, numslices)),
277
284
  template_hdr,
278
285
  f"{args.outputroot}_includemask",
279
286
  )
@@ -281,7 +288,7 @@ def atlasaverage(args):
281
288
  themask = themask * (1 - excludemask.reshape((numvoxels)))
282
289
  if args.debug:
283
290
  tide_io.savetonifti(
284
- excludemask.reshape((xsize, ysize, numslices)),
291
+ excludemask.reshape((xdim, ydim, numslices)),
285
292
  template_hdr,
286
293
  f"{args.outputroot}_excludemask",
287
294
  )
@@ -289,11 +296,21 @@ def atlasaverage(args):
289
296
  themask = themask * extramask.reshape((numvoxels))
290
297
  if args.debug:
291
298
  tide_io.savetonifti(
292
- extramask.reshape((xsize, ysize, numslices)),
299
+ extramask.reshape((xdim, ydim, numslices)),
293
300
  template_hdr,
294
301
  f"{args.outputroot}_extramask",
295
302
  )
296
303
 
304
+ # get the region names
305
+ if args.regionlabelfile is None:
306
+ regionlabels = []
307
+ numregions = np.max(templatevoxels)
308
+ numdigits = int(np.log10(numregions)) + 1
309
+ for regnum in range(1, numregions + 1):
310
+ regionlabels.append(f"region_{str(regnum).zfill(numdigits)}")
311
+ else:
312
+ regionlabels = tide_io.readlabels(args.regionlabelfile)
313
+
297
314
  # decide what regions we will summarize
298
315
  if args.regionlistfile is None:
299
316
  numregions = np.max(templatevoxels)
@@ -301,6 +318,11 @@ def atlasaverage(args):
301
318
  else:
302
319
  regionlist = tide_io.readvec(args.regionlistfile).astype(int)
303
320
  numregions = len(regionlist)
321
+ newlabels = []
322
+ for theregion in range(numregions):
323
+ newlabels.append(regionlabels[theregion])
324
+ regionlabels = newlabels
325
+
304
326
  timecourses = np.zeros((numregions, numtimepoints), dtype="float")
305
327
  print(f"{numregions=}, {regionlist=}")
306
328
 
@@ -348,7 +370,13 @@ def atlasaverage(args):
348
370
  )
349
371
  if args.debug:
350
372
  print("timecourses shape:", timecourses.shape)
351
- tide_io.writenpvecs(timecourses, args.outputroot)
373
+ tide_io.writebidstsv(
374
+ args.outputroot,
375
+ timecourses,
376
+ 1.0 / tr,
377
+ columns=regionlabels,
378
+ yaxislabel="delay offset",
379
+ )
352
380
  else:
353
381
  print("processing 3D input file")
354
382
  outputvoxels = inputvoxels * 0.0
@@ -416,19 +444,19 @@ def atlasaverage(args):
416
444
  segmentedatlasvoxels += scratchvoxels
417
445
  template_hdr["dim"][4] = 1
418
446
  tide_io.savetonifti(
419
- outputvoxels.reshape((xsize, ysize, numslices)),
447
+ outputvoxels.reshape((xdim, ydim, numslices)),
420
448
  template_hdr,
421
449
  args.outputroot,
422
450
  )
423
451
  tide_io.savetonifti(
424
- segmentedatlasvoxels.reshape((xsize, ysize, numslices)),
452
+ segmentedatlasvoxels.reshape((xdim, ydim, numslices)),
425
453
  template_hdr,
426
454
  args.outputroot + "_percentiles",
427
455
  )
428
456
 
429
457
  if args.includename is not None or args.excludename is not None:
430
458
  tide_io.savetonifti(
431
- (templatevoxels * themask).reshape((xsize, ysize, numslices)),
459
+ (templatevoxels * themask).reshape((xdim, ydim, numslices)),
432
460
  template_hdr,
433
461
  f"{args.outputroot}_maskedatlas",
434
462
  )