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Updating documentation file for Read EDAX H5 file filter.
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Source/Plugins/OrientationAnalysis/Documentation/OrientationAnalysisFilters/ReadEdaxH5Data.md

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@@ -5,15 +5,21 @@ Read EDAX EBSD Data (.h5) {#readedaxh5data}
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## Description ##
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This **Filter** will read a single .h5 file into a new **Data Container** with a corresponding **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and **Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**. The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be undefined or simply **wrong**. In order to bring the [crystal reference frame](@ref rotateeulerrefframe) and [sample reference frame](@ref rotatesamplerefframe) into coincidence, rotations will need to be applied to the data.
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This **Filter** will read a single .h5 file into a new **Data Container** with a corresponding **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and **Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**.
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### Default TSL Transformations ###
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If the data has come from a TSL acquisition system and the settings of the acquisition software were in the default modes, he following reference frame transformations may need to be performed based on the version of the OIM Analysis software being used to collect the data:
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## Notes About Reference Frames ##
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The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be undefined or simply **wrong**. In order to bring the [crystal reference frame](@ref rotateeulerrefframe) and [sample reference frame](@ref rotatesamplerefframe) into coincidence, rotations will need to be applied to the data. The recommended filters are:
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+ [Rotate Euler Reference Frame](rotateeulerrefframe.html)
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+ [Rotate Sample Reference Frame](rotatesamplerefframe.html)
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If the data has come from a TSL acquisition system and the settings of the acquisition software were in the default modes, the following reference frame transformations may need to be performed based on the version of the OIM Analysis software being used to collect the data:
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+ Sample Reference Frame: 180<sup>o</sup> about the <010> Axis
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+ Crystal Reference Frame: 90<sup>o</sup> about the <001> Axis
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The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The [Threshold Objects](@ref multithresholdobjects) **Filter** can be used to define this _mask_ by thresholding on values such as _Confidence Index_ > 0.1 or _Image Quality_ > desired quality.
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The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The [Threshold Objects](@ref multithresholdobjects) **Filter** can be used to define this _mask_ by thresholding on values such as _Confidence Index_ > xx or _Image Quality_ > desired quality.
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## Parameters ##
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| Name | Type | Description |

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