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Merge pull request #226 from dzenanz/testsAndDocs
ENH: Enable unit tests which are no longer failing
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@@ -35,6 +35,13 @@ namespace itk | |
| * | ||
| * Determines registrations which can be used to resample a mosaic into a single image. | ||
| * | ||
| * This deals with n-dimensional rectangular arrays of image tiles. | ||
| * Arbitrarily shaped tile arrays (e.g. circular) are not directly supported. | ||
| * A possible (untested) workaround is adding all-zero (black) tiles around the shape | ||
| * to make a regular rectangular tile array (2D, 3D, or nD). | ||
| * | ||
| * Take a look a documentation of parameters, most influential of which is PositionTolerance. | ||
| * | ||
| * \author Dženan Zukić, [email protected] | ||
| * | ||
| * \ingroup Montage | ||
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@@ -111,6 +118,7 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject | |
| /** Set/Get absolute registration threshold. | ||
| * The maximum allowed residual error for a registration pair during | ||
| * global optimization. Expressed in number of pixels. Default: 1.0. | ||
| * Reasonable values are from around 0.8 to around 1.5. | ||
| * When a registration pair exceeds the threshold, it is replaced by | ||
| * the next best candidate for that pair. If all canidates are | ||
| * exhausted, the registration pair is assumed to have no translation. | ||
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@@ -121,6 +129,7 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject | |
| /** Set/Get relative registration threshold. | ||
| * The maximum allowed deviation for a registration pair during global | ||
| * optimization. Expressed in multiples of standard deviation. Default: 3.0. | ||
| * Reasonable values are from around 2 to around 5. | ||
| * The deviation is calculated by taking the translations of all the | ||
| * registration pairs, while assuming zero mean. This implies expectation | ||
| * that deviations from expected positions for all registration pairs | ||
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@@ -131,7 +140,10 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject | |
| /** Set/Get tile positioning precision. | ||
| * Get/Set expected maximum linear translation needed, in pixels. | ||
| * Zero (the default) means unknown, and allows translations | ||
| * up to about half the image size.*/ | ||
| * up to about half the image size. | ||
| * This is an important parameter for reliability of pair-wise registrations, | ||
| * but it is microscope-dependent so we cannot have a restrictive default. | ||
| */ | ||
| itkSetMacro(PositionTolerance, SizeValueType); | ||
| itkGetConstMacro(PositionTolerance, SizeValueType); | ||
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@@ -145,7 +157,7 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject | |
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| /** Set/Get obligatory padding. | ||
| * If set, padding of this many pixels is added on both beginning and end | ||
| * sides of each dimension of the image. */ | ||
| * sides of each dimension of the image. Default value of 8 is usually fine. */ | ||
| virtual void | ||
| SetObligatoryPadding(const SizeType pad) | ||
| { | ||
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@@ -157,11 +169,13 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject | |
| } | ||
| itkGetConstMacro(ObligatoryPadding, SizeType); | ||
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| /** Set/Get the padding method. */ | ||
| /** Set/Get the padding method. | ||
| * The default (MirrorWithExponentialDecay) is usually the best. */ | ||
| itkSetEnumMacro(PaddingMethod, typename PCMType::PaddingMethodEnum); | ||
| itkGetConstMacro(PaddingMethod, typename PCMType::PaddingMethodEnum); | ||
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| /** Set/Get the peak interpolation method. */ | ||
| /** Set/Get the peak interpolation method. | ||
| * The default (Parabolic) is usually the best. */ | ||
| itkSetEnumMacro(PeakInterpolationMethod, typename PCMOptimizerType::PeakInterpolationMethodEnum); | ||
| itkGetConstMacro(PeakInterpolationMethod, typename PCMOptimizerType::PeakInterpolationMethodEnum); | ||
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@@ -203,11 +217,12 @@ class ITK_TEMPLATE_EXPORT TileMontage : public ProcessObject | |
| return static_cast<TransformOutputType *>(this->GetOutput(this->nDIndexToLinearIndex(position)))->Get(); | ||
| } | ||
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| /** Reliability of each tile, highest normalized to 1.0. */ | ||
| /** Reliability of each tile, highest normalized to 1.0.*/ | ||
| using TileReliabilities = std::vector<float>; | ||
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| /** Tile reliability, from 0.0 (lowest) to 1.0 (highest). | ||
| * This can be used to judge successfulness of registration to adjacent tiles. */ | ||
| * This can be used to judge successfulness of registration to adjacent tiles. | ||
| * The lowest reliability is usually around 0.01 to 0.1. */ | ||
| itkGetConstReferenceMacro(TileReliabilities, TileReliabilities); | ||
| float | ||
| GetTileReliability(DataObjectPointerArraySizeType linearIndex) const | ||
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