tomwer 1.3.0.dev2__py3-none-any.whl → 1.3.0rc10__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 (156) hide show
  1. orangecontrib/tomwer/widgets/__init__.py +11 -12
  2. orangecontrib/tomwer/widgets/control/DataListenerOW.py +6 -6
  3. orangecontrib/tomwer/widgets/control/DataValidatorOW.py +6 -6
  4. orangecontrib/tomwer/widgets/control/NXTomomillMixIn.py +3 -3
  5. orangecontrib/tomwer/widgets/control/NXTomomillOW.py +10 -8
  6. orangecontrib/tomwer/widgets/control/SingleTomoObjOW.py +6 -6
  7. orangecontrib/tomwer/widgets/debugtools/DatasetGeneratorOW.py +1 -1
  8. orangecontrib/tomwer/widgets/icat/RawDataScreenshotCreatorOW.py +98 -98
  9. orangecontrib/tomwer/widgets/icat/SaveToGalleryAndPublishOW.py +129 -129
  10. orangecontrib/tomwer/widgets/reconstruction/AxisOW.py +13 -12
  11. orangecontrib/tomwer/widgets/reconstruction/SAAxisOW.py +11 -9
  12. orangecontrib/tomwer/widgets/reconstruction/SADeltaBetaOW.py +11 -9
  13. orangecontrib/tomwer/widgets/reconstruction/SinoNormOW.py +12 -15
  14. orangecontrib/tomwer/widgets/visualization/DataViewerOW.py +9 -9
  15. orangecontrib/tomwer/widgets/visualization/DiffViewerOW.py +1 -1
  16. orangecontrib/tomwer/widgets/visualization/SinogramViewerOW.py +0 -1
  17. tomwer/__main__.py +0 -10
  18. tomwer/app/canvas_launcher/config.py +3 -3
  19. tomwer/app/canvas_launcher/environ.py +1 -0
  20. tomwer/app/intensitynormalization.py +12 -11
  21. tomwer/app/nabuapp.py +0 -11
  22. tomwer/app/zstitching.py +11 -1
  23. tomwer/core/process/control/datalistener/datalistener.py +15 -10
  24. tomwer/core/process/control/nxtomomill.py +1 -1
  25. tomwer/core/process/control/scantransfer.py +8 -32
  26. tomwer/core/process/edit/darkflatpatch.py +8 -9
  27. tomwer/core/process/edit/imagekeyeditor.py +20 -22
  28. tomwer/core/process/icat/screenshots.py +1 -0
  29. tomwer/core/process/reconstruction/axis/axis.py +263 -59
  30. tomwer/core/process/reconstruction/axis/mode.py +161 -50
  31. tomwer/core/process/reconstruction/axis/params.py +23 -20
  32. tomwer/core/process/reconstruction/darkref/darkrefs.py +12 -13
  33. tomwer/core/process/reconstruction/nabu/castvolume.py +3 -3
  34. tomwer/core/process/reconstruction/nabu/nabucommon.py +43 -19
  35. tomwer/core/process/reconstruction/nabu/nabuscores.py +34 -7
  36. tomwer/core/process/reconstruction/nabu/nabuslices.py +81 -26
  37. tomwer/core/process/reconstruction/nabu/nabuvolume.py +31 -26
  38. tomwer/core/process/reconstruction/nabu/plane.py +9 -0
  39. tomwer/core/process/reconstruction/nabu/utils.py +32 -9
  40. tomwer/core/process/reconstruction/saaxis/saaxis.py +4 -1
  41. tomwer/core/process/reconstruction/sadeltabeta/sadeltabeta.py +9 -1
  42. tomwer/core/process/reconstruction/scores/params.py +3 -3
  43. tomwer/core/process/reconstruction/test/test_darkref_copy.py +4 -4
  44. tomwer/core/process/stitching/nabustitcher.py +11 -10
  45. tomwer/core/process/task.py +33 -27
  46. tomwer/core/process/test/test_axis.py +7 -6
  47. tomwer/core/process/test/test_data_transfer.py +3 -3
  48. tomwer/core/process/test/test_nabu.py +10 -2
  49. tomwer/core/process/test/test_normalization.py +2 -2
  50. tomwer/core/scan/blissscan.py +3 -3
  51. tomwer/core/scan/edfscan.py +9 -9
  52. tomwer/core/scan/nxtomoscan.py +11 -11
  53. tomwer/core/scan/scanbase.py +31 -24
  54. tomwer/core/scan/test/test_future_scan.py +1 -1
  55. tomwer/core/scan/test/test_h5.py +4 -4
  56. tomwer/core/scan/test/test_process_registration.py +2 -2
  57. tomwer/core/scan/test/test_scan.py +1 -75
  58. tomwer/core/settings.py +3 -3
  59. tomwer/core/test/test_utils.py +2 -2
  60. tomwer/core/volume/edfvolume.py +6 -6
  61. tomwer/core/volume/hdf5volume.py +6 -6
  62. tomwer/core/volume/jp2kvolume.py +6 -6
  63. tomwer/core/volume/rawvolume.py +6 -6
  64. tomwer/core/volume/tiffvolume.py +12 -12
  65. tomwer/gui/cluster/slurm.py +14 -9
  66. tomwer/gui/cluster/supervisor.py +12 -0
  67. tomwer/gui/cluster/test/test_cluster.py +1 -2
  68. tomwer/gui/cluster/test/test_supervisor.py +1 -1
  69. tomwer/gui/control/datalist.py +5 -0
  70. tomwer/gui/control/datawatcher/controlwidget.py +2 -4
  71. tomwer/gui/control/reducedarkflatselector.py +8 -8
  72. tomwer/gui/control/test/test_single_tomo_obj.py +1 -1
  73. tomwer/gui/edit/dkrfpatch.py +4 -4
  74. tomwer/gui/edit/nxtomowarmer.py +2 -2
  75. tomwer/gui/edit/test/test_dkrf_patch.py +6 -6
  76. tomwer/gui/imagefromfile.py +2 -2
  77. tomwer/gui/qfolderdialog.py +5 -0
  78. tomwer/gui/reconstruction/axis/CompareImages.py +94 -168
  79. tomwer/gui/reconstruction/axis/radioaxis.py +58 -182
  80. tomwer/gui/reconstruction/darkref/darkrefwidget.py +2 -1
  81. tomwer/gui/reconstruction/nabu/castvolume.py +8 -1
  82. tomwer/gui/reconstruction/nabu/nabuconfig/reconstruction.py +54 -21
  83. tomwer/gui/reconstruction/normalization/intensity.py +3 -25
  84. tomwer/gui/reconstruction/saaxis/corrangeselector.py +1 -1
  85. tomwer/gui/reconstruction/saaxis/saaxis.py +1 -11
  86. tomwer/gui/reconstruction/sadeltabeta/saadeltabeta.py +0 -10
  87. tomwer/gui/reconstruction/scores/scoreplot.py +1 -6
  88. tomwer/gui/reconstruction/test/test_axis.py +18 -4
  89. tomwer/gui/reconstruction/test/test_nabu.py +3 -0
  90. tomwer/gui/stitching/stitching.py +2 -2
  91. tomwer/gui/stitching/stitching_preview.py +7 -53
  92. tomwer/gui/stitching/stitching_raw.py +3 -3
  93. tomwer/gui/utils/inputwidget.py +12 -2
  94. tomwer/gui/utils/lineselector/lineselector.py +1 -1
  95. tomwer/gui/visualization/dataviewer.py +47 -17
  96. tomwer/gui/visualization/sinogramviewer.py +19 -26
  97. tomwer/gui/visualization/test/test_volumeviewer.py +64 -66
  98. tomwer/gui/visualization/volumeviewer.py +105 -105
  99. tomwer/io/utils/h5pyutils.py +7 -3
  100. tomwer/io/utils/utils.py +3 -3
  101. tomwer/resources/gui/icons/parameters.svg +1 -1
  102. tomwer/resources/gui/illustrations/no_rot.svg +1 -1
  103. tomwer/synctools/stacks/edit/darkflatpatch.py +17 -12
  104. tomwer/tests/test_scripts.py +0 -3
  105. tomwer/third_part/WaitingOverlay.py +110 -0
  106. tomwer/third_part/__init__.py +0 -0
  107. tomwer/version.py +2 -2
  108. {tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/METADATA +32 -31
  109. {tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/RECORD +115 -153
  110. {tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/WHEEL +1 -1
  111. orangecontrib/tomwer/widgets/reconstruction/TofuOW.py +0 -197
  112. orangecontrib/tomwer/widgets/reconstruction/icons/XY_lamino.svg +0 -168
  113. orangecontrib/tomwer/widgets/reconstruction/icons/XZ_lamino.svg +0 -275
  114. orangecontrib/tomwer/widgets/reconstruction/icons/YZ_lamino.svg +0 -182
  115. tomwer/app/lamino.py +0 -143
  116. tomwer/core/process/reconstruction/lamino/__init__.py +0 -1
  117. tomwer/core/process/reconstruction/lamino/tofu.py +0 -1000
  118. tomwer/core/process/test/test_lamino.py +0 -76
  119. tomwer/core/test/test_lamino.py +0 -92
  120. tomwer/gui/reconstruction/lamino/__init__.py +0 -31
  121. tomwer/gui/reconstruction/lamino/tofu/TofuOptionLoader.py +0 -107
  122. tomwer/gui/reconstruction/lamino/tofu/__init__.py +0 -1
  123. tomwer/gui/reconstruction/lamino/tofu/misc.py +0 -148
  124. tomwer/gui/reconstruction/lamino/tofu/projections.py +0 -896
  125. tomwer/gui/reconstruction/lamino/tofu/settings.py +0 -75
  126. tomwer/gui/reconstruction/lamino/tofu/tofu.py +0 -432
  127. tomwer/gui/reconstruction/lamino/tofu/tofuexpert.py +0 -567
  128. tomwer/gui/reconstruction/lamino/tofu/tofuoutput.py +0 -757
  129. tomwer/gui/reconstruction/test/test_lamino.py +0 -194
  130. tomwer/resources/gui/icons/lamino_parameters.svg +0 -70
  131. tomwer/resources/gui/illustrations/lamino_angle.png +0 -0
  132. tomwer/resources/gui/illustrations/lamino_angle.svg +0 -509
  133. tomwer/resources/gui/illustrations/lamino_beta_angle.png +0 -0
  134. tomwer/resources/gui/illustrations/lamino_beta_angle.svg +0 -97
  135. tomwer/resources/gui/illustrations/lamino_theta_angle.png +0 -0
  136. tomwer/resources/gui/illustrations/lamino_theta_angle.svg +0 -368
  137. tomwer/resources/gui/illustrations/manual_slice.png +0 -0
  138. tomwer/resources/gui/illustrations/manual_slice.svg +0 -221
  139. tomwer/resources/gui/illustrations/psi_angle.png +0 -0
  140. tomwer/resources/gui/illustrations/psi_angle.svg +0 -479
  141. tomwer/resources/gui/illustrations/rotation_center.png +0 -0
  142. tomwer/resources/gui/illustrations/rotation_center.svg +0 -276
  143. tomwer/resources/gui/illustrations/slice_stack.png +0 -0
  144. tomwer/resources/gui/illustrations/slice_stack.svg +0 -266
  145. tomwer/resources/gui/illustrations/xy_slice.png +0 -0
  146. tomwer/resources/gui/illustrations/xy_slice.svg +0 -269
  147. tomwer/resources/gui/illustrations/xz_slice.png +0 -0
  148. tomwer/resources/gui/illustrations/xz_slice.svg +0 -270
  149. tomwer/resources/gui/illustrations/yz_slice.png +0 -0
  150. tomwer/resources/gui/illustrations/yz_slice.svg +0 -270
  151. tomwer/synctools/stacks/reconstruction/lamino.py +0 -233
  152. /tomwer-1.3.0.dev2-py3.11-nspkg.pth → /tomwer-1.3.0rc10-py3.11-nspkg.pth +0 -0
  153. {tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/LICENSE +0 -0
  154. {tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/entry_points.txt +0 -0
  155. {tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/namespace_packages.txt +0 -0
  156. {tomwer-1.3.0.dev2.dist-info → tomwer-1.3.0rc10.dist-info}/top_level.txt +0 -0
@@ -1,194 +0,0 @@
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- # coding: utf-8
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- # /*##########################################################################
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- #
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- # Copyright (c) 2017 European Synchrotron Radiation Facility
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- #
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- # Permission is hereby granted, free of charge, to any person obtaining a copy
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- # of this software and associated documentation files (the "Software"), to deal
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- # in the Software without restriction, including without limitation the rights
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- # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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- # copies of the Software, and to permit persons to whom the Software is
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- # furnished to do so, subject to the following conditions:
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- #
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- # The above copyright notice and this permission notice shall be included in
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- # all copies or substantial portions of the Software.
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- #
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- # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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- # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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- # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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- # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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- # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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- # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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- # THE SOFTWARE.
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- #
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- # ###########################################################################*/
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- __authors__ = ["H. Payno"]
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- __license__ = "MIT"
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- __date__ = "16/06/2021"
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-
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-
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- import os
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- import shutil
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- import tempfile
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- import unittest
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-
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- import pytest
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- from silx.gui import qt
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-
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- from tomwer.core import settings
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- from tomwer.gui.reconstruction.lamino.tofu import TofuWindow
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- from tomwer.tests.datasets import TomwerCIDatasets
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- from tomwer.tests.utils import skip_gui_test
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-
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-
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- @pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
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- class TestLamino(unittest.TestCase):
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- """Test the TofuWidget"""
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-
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- def setUp(self):
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- super().setUp()
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- self._window = TofuWindow(parent=None)
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- self._widget = self._window._mainWidget
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- # add a dark.edf file and a darkHSTFile
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- self._folder = tempfile.mkdtemp()
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-
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- def tearDown(self):
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- super().tearDown()
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- self._window.setAttribute(qt.Qt.WA_DeleteOnClose)
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- self._window.close()
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- shutil.rmtree(self._folder)
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-
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- def testSetup(self):
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- """Make sure the widget is correctly setting parameters from a scan"""
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- dataset = TomwerCIDatasets.get_dataset(
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- "edf_datasets/test01",
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- )
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- self._window.loadFromScan(dataset)
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- reconsParams = self._widget.getParameters()
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- # check general information
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- # note : the .info file is incorrect
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- self.assertTrue(self._widget._tabs._inputWidget.getNumber() == 1)
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- self.assertTrue(reconsParams["number"] == 1)
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- # check flat field correction is set
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- ffcWidget = self._widget._tabs._inputWidget.widget._ffcWidget
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- thFlats = os.path.join(dataset, "refHST0000.edf")
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- self.assertTrue(ffcWidget.getFlats() == thFlats)
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- self.assertTrue(reconsParams["flats"] == thFlats)
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- thSecondFlats = os.path.join(dataset, "refHST0010.edf")
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- self.assertTrue(ffcWidget.getSecondFlats() == thSecondFlats)
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- self.assertTrue(reconsParams["flats2"] == thSecondFlats)
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- thDarks = os.path.join(dataset, "darkend0000.edf")
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- self.assertTrue(ffcWidget.getDarks() == thDarks)
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- self.assertTrue(reconsParams["darks"] == thDarks)
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-
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- inputWidget = self._widget._tabs._inputWidget.widget
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- self.assertTrue(inputWidget.rotationAngle._overallAngle.getAngle() == 180.0)
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- self.assertTrue(inputWidget.rotationAngle._axisAngleY.getAngle() == 0.0)
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- self.assertTrue(inputWidget.rotationAngle._axisAngleZ.getAngle() == 0.0)
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-
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- def testSetupWithLockedParams(self):
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- """Make sure lockers are corrcetly taking into account"""
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- # check flat field correction is set
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-
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- inputWidget = self._widget._tabs._inputWidget.widget
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- inputWidget.rotationAngle._overallAngle.setAngle(12.0)
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- inputWidget.rotationAngle._overallAngle.lock()
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-
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- inputWidget.rotationAngle._axisAngleY.setAngle(-26.0)
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- inputWidget.rotationAngle._axisAngleY.lock()
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-
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- inputWidget.rotationAngle._axisAngleZ.setAngle(63.5)
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- inputWidget.rotationAngle._axisAngleZ.lock()
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-
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- outputWidget = self._widget._tabs._outputWidget
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- outputWidget.setOutput("toto")
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- outputWidget.lockOutput()
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-
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- dataset = TomwerCIDatasets.get_dataset(
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- "edf_datasets/test01",
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- )
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- self._window.loadFromScan(dataset)
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-
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- self.assertTrue(inputWidget.rotationAngle._overallAngle.getAngle() == 12.0)
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- self.assertTrue(inputWidget.rotationAngle._axisAngleY.getAngle() == -26.0)
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- self.assertTrue(inputWidget.rotationAngle._axisAngleZ.getAngle() == 63.5)
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-
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- self.assertTrue(outputWidget.getOutput() == "toto")
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-
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- def testEditionDisplay(self):
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- """
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- Test that edition of parameters by the user are taking into account
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- """
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- displayWidget = self._widget._tabs._inputWidget.widget.rotationAngle
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- # angles
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- displayWidget._laminoAngle.setAngle(12.0)
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- self.assertTrue(self._widget.getParameters()["axis-angle-x"] == 12.0)
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- displayWidget._axisAngleY.setAngle(10.0)
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- self.assertTrue(self._widget.getParameters()["axis-angle-y"] == 10.0)
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-
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- # regions
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- regionWidget = self._widget._tabs._outputWidget._region
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- regionWidget._xRegion._regionLE.setText("0")
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- self.assertTrue(self._widget.getParameters()["x-region"] == (0, -1, 1))
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- regionWidget.setYRegion(10, 12, 25)
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- self.assertTrue(self._widget.getParameters()["y-region"] == (10, 12, 25))
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-
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- # make sure saving and loading is correct
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- savingFile = os.path.join(self._folder, "savingFile.ini")
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- self._widget.saveTo(savingFile)
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- self.assertTrue(os.path.exists(savingFile))
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- regionWidget.setYRegion(10, 12, 22)
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- self.assertTrue(self._widget.getParameters()["y-region"] == (10, 12, 22))
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- self._widget.loadFile(savingFile)
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- self.assertTrue(self._widget.getParameters()["y-region"] == (10, 12, 25))
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-
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- def testOutputWidget(self):
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- """test behavior of the output widget and link with get and set
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- parameters"""
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- outputWidget = self._widget._tabs._outputWidget
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- # volume angles
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- outputWidget._volumeAngleGrp.setAngles(0, 20, -36.0)
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- reconsParams = self._widget.getParameters()
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- self.assertTrue(reconsParams["volume-angle-x"] == 0)
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- self.assertTrue(reconsParams["volume-angle-y"] == 20.0)
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- self.assertTrue(reconsParams["volume-angle-z"] == -36.0)
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-
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- def testCenteringWidget(self):
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- """test behavior of the centering widget and link with get and set
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- parameters"""
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- centeringWidget = self._widget._tabs._inputWidget.widget.centeringWidget
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- centeringWidget._xCenterLE.setText("12")
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- centeringWidget._yCenterLE.setText("2")
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- self.assertTrue(self._widget.getParameters()["center-position-x"] == 12.0)
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- self.assertTrue(self._widget.getParameters()["center-position-z"] == 2.0)
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-
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- def testForceLbsRam(self):
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- """Test the behavior of the forcelbsram option"""
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- scan1 = tempfile.mkdtemp(suffix="1")
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- self._window.loadFromScan(scan1)
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- _end = os.path.join("1", "xySlice")
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- self.assertTrue(self._window.getParameters()["output"].endswith(_end))
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-
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- self._window._mainWidget._tabs._outputWidget.lockOutput()
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- scan2 = tempfile.mkdtemp(suffix="2")
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- self._window.loadFromScan(scan2)
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- _end = os.path.join("1", "xySlice")
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- self.assertTrue(self._window.getParameters()["output"].endswith(_end))
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-
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- self._window._mainWidget._tabs._outputWidget.lockOutput(False)
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- self._window.loadFromScan(scan2)
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- _end = os.path.join("2", "xySlice")
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- self.assertTrue(self._window.getParameters()["output"].endswith(_end))
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-
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- self._window._mainWidget._tabs._outputWidget.setForceLbsram(True)
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- self.assertTrue(
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- self._window.getParameters()["output"].startswith(
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- settings.get_lbsram_path()
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- )
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- )
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- self._window.loadFromScan(scan1)
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- self.assertTrue(
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- self._window.getParameters()["output"].startswith(
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- settings.get_lbsram_path()
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- )
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- )
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