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@ -296,11 +296,13 @@ class ImageAnalyser(): |
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if fringeRemoval: |
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if fringeRemoval: |
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dataSetAtoms = dataSet[self._image_name['atoms']] - dataSet[self._image_name['dark']] |
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scanAxis = list(get_scanAxis(dataSet)) |
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scanAxis = list(get_scanAxis(dataSet)) |
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if not scanAxis[1] is None: |
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if not scanAxis[1] is None: |
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OptimumRef = self._fringeRemoval.fringe_removal(dataSet[self._image_name['atoms']].stack(_imgIdx=scanAxis)) |
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OptimumRef = self._fringeRemoval.fringe_removal(dataSetAtoms.stack(_imgIdx=scanAxis)) |
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else: |
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else: |
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OptimumRef = self._fringeRemoval.fringe_removal(dataSet[self._image_name['atoms']]) |
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OptimumRef = self._fringeRemoval.fringe_removal(dataSetAtoms) |
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dataSet = dataSet.assign( |
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dataSet = dataSet.assign( |
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{ |
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{ |
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@ -310,7 +312,7 @@ class ImageAnalyser(): |
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dataSet = dataSet.assign( |
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dataSet = dataSet.assign( |
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{ |
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{ |
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self._image_name['OD']: xr.apply_ufunc(self.get_OD_no_dark, dataSet[self._image_name['atoms']], dataSet[self._image_name['optimumBackground']], **kwargs) |
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self._image_name['OD']: xr.apply_ufunc(self.get_OD_no_dark, dataSetAtoms, dataSet[self._image_name['optimumBackground']], **kwargs) |
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} |
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} |
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) |
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) |
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else: |
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else: |
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@ -395,7 +397,7 @@ class ImageAnalyser(): |
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dataSet = read_hdf5_file(filePath, group, **kwargs) |
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dataSet = read_hdf5_file(filePath, group, **kwargs) |
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scanAxis = dataSet.scanAxis |
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scanAxis = dataSet.scanAxis |
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dataSet = dataSet[self._image_name['background']] |
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dataSet = dataSet[self._image_name['background']] - dataSet[self._image_name['dark']] |
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dataSet.attrs['scanAxis'] = scanAxis |
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dataSet.attrs['scanAxis'] = scanAxis |
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if crop: |
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if crop: |
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