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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,194 @@ | ||
| --- | ||
| layout: post | ||
| title: "Changes DIPlib 3.5.2" | ||
| date: 2024-12-27 | ||
| --- | ||
|
|
||
| ## Changes to *DIPlib* | ||
|
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| ### New functionality | ||
|
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||
| - `dip::ImageWriteTiff()` now can write 3D images to a TIFF file as a series of slices. | ||
| See [PR #182](https://github.com/DIPlib/diplib/pull/182). | ||
|
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| - Additions to the `dip::Graph` class: | ||
|
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| - Added `dip::Graph::EdgeVertex()` for convenience. `graph.EdgeVertex( edge, which )` is the same as what | ||
| previously was written `graph.Edges()[ edge ].vertices[ which ].` | ||
|
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||
| - Added `dip::Graph::IsValidEdge()`. | ||
|
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| - Added `dip::Graph::UpdateEdgeWeights<>()`, an overload that takes a function as input; this function | ||
| is applied to the two vertex weights for each edge, and should return an edge weight. | ||
|
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| - `dip::MinimumSpanningForest()` is now a free function. The `dip::Graph::MinimumSpanningForest()` class | ||
| function still exists for backwards-compatibility, it calls the free function. | ||
|
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| - Added `dip::DirectedGraph`, a directed version of `dip::Graph`. | ||
|
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| - Added `dip::GraphCut()`, a function that computes the minimum cut of a `dip::DirectedGraph`. | ||
| This is a segmentation algorithm that splits the graph into two sections based on two marker vertices (nodes). | ||
|
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| - Added `dip::GraphCut()`, a function that computes the grap-cut segmentation of an image. | ||
|
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| - Added `dip::Label()` with a `dip::Graph` and a `dip::DirectedGraph` as input. | ||
| It finds connected components in the graph. | ||
|
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| - Added `dip::Histogram::Configuration::Mode::IS_COMPLETE`, which prevents a configuration from being | ||
| modified when computing a histogram. It is set by `dip::Histogram::Configuration::Complete()`. | ||
| This option is dangerous to set manually! It is intended for re-using the same configuration across | ||
| multiple histogram computations. | ||
|
|
||
| - Added `dip::Image::ReinterpretCastBinToUint8()` and `dip::Image::ReinterpretCastUint8ToBin()` for the specific case | ||
| of casting bin to uint8 and back. They don't provide any functionality that `dip::Image::ReinterpretCast()` | ||
| didn't already provide, but they are much safer to use. | ||
|
|
||
| ### Changed functionality | ||
|
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||
| - `dip::AlignedAllocInterface` now aligns each of the scanlines (rows of the image), not just the first one. | ||
| This means it can be used to create images that are compatible with some image display widgets (Windows | ||
| bitmap, Qt image, etc.). | ||
|
|
||
| - `dip::LowestCommonAncestorSolver` is no longer in the public API. This class contained code used in the | ||
| Exact Stochastic Watershed (`dip::StochasticWatershed` with `seeds` set to `"exact"` or `nIterations` set to 0). | ||
|
|
||
| ### Bug fixes | ||
|
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||
| - `dip::Log2` computed the natural logarithm instead of the base-2 logarithm. | ||
| See [PR #168](https://github.com/DIPlib/diplib/pull/168). | ||
|
|
||
| - `dip::StructureTensorAnalysis3D()` would try to read a non-existing tensor element when requesting the 'l3' output | ||
| (producing an obscure error message). | ||
|
|
||
| - `dip::GaussFT()` could, under some circumstances, try to reforge the output image to an intermediate, extended size. | ||
| This would throw an exception if the image was protected, but was always a bad thing to do. | ||
| See [issue #170](https://github.com/DIPlib/diplib/issues/170). | ||
|
|
||
| - The Fourier Transform, when using the default PocketFFT, used a plan cache that was not thread safe. When calling | ||
| any function using a Fourier Transform from multiple threads, a race condition could occur. We've added a mutex | ||
| to the function that maintains the cache to avoid this. | ||
|
|
||
| - In 3.5.0, the original version of `dip::GetImageChainCodes()` was deprecated in favor of a new one that takes | ||
| a `std::vector< dip::LabelType >` as input, as opposed to a `dip::UnsignedArray`. This caused code that called | ||
| the function with an initializer array (`dip::GetImageChainCodes( image, { 1 } )`) to become ambiguous. A new | ||
| overload that takes an initializer list as input fixes this ambiguity. | ||
|
|
||
| - `operator+()` for `dip::Image` (i.e. the function called for `+img`) created a new data segment and copied | ||
| the data over when the input was binary. In that case it now creates a new uint8 image that points to the | ||
| same data segment of the binary image, as intended. | ||
|
|
||
| - `dip::EdgeObjectsRemove()` produced an empty output image when the input and output images were the same object. | ||
|
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||
| ### Build changes | ||
|
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||
| - The documentation building target was renamed to "doc" (as "apidoc"). This target builds much more documentation | ||
| than just the DIPlib API documentation (the DIPimage and PyDIP user manuals, build instructions, etc.). | ||
|
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||
|
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||
|
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||
|
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| ## Changes to *DIPimage* | ||
|
|
||
| ### New functionality | ||
|
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||
| - The function documentation now has links to the online DIPlib documentation. Instead of only | ||
| naming the DIPlib functions used, the function names are now hyperlinks. | ||
|
|
||
| ### Changed functionality | ||
|
|
||
| - The `'FileWriteWarning'` setting now also applies to the warning regarding conversion to `uint8` when | ||
| `imwrite` delegates to MATLAB's built-in image writing capability. A warning is no longer produced if | ||
| the image already was `uint8`. | ||
|
|
||
| (See also changes to *DIPlib*.) | ||
|
|
||
| ### Bug fixes | ||
|
|
||
| - The `dip_image` constructor (and consequently some functions such as `newim`) again accept | ||
| some data type aliases that existed in DIPimage 2.x (`'bin8'`, `'int'`, `'uint'`, `'float'`, `'complex'`). | ||
| These are not terribly useful, but there's no reason not to accept them. | ||
|
|
||
| - When `imread` delegated to MATLAB's built-in image file reading capability, it failed to tag | ||
| CMYK images as such. | ||
|
|
||
| (See also bugfixes to *DIPlib*.) | ||
|
|
||
| ### Build and installation changes | ||
|
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||
| - Ported and improved the old *DIPimage* test suite, which is not (yet?) run automatically with `make test` | ||
| because it requires *DIPimage* to be installed. | ||
|
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|
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|
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||
|
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||
| ## Changes to *PyDIP* | ||
|
|
||
| ### New functionality | ||
|
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||
| - Added the function `dip.Doc()`, which will open the documentation for the given function or class in the | ||
| default web browser. | ||
|
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| - Automatically copying the brief section of the documentation to each function as the Python doc string. | ||
| We finally have some documentation in Python! | ||
|
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||
| - Overloaded `len()` for `dip.Measurement`. It's equal to `NumberOfObjects()` (the number of rows), | ||
| and thus produces the same value it does when casting the measurement objects to a NumPy array | ||
| (`len(measurement)` is the same as `len(np.asarray(measurement))`). | ||
|
|
||
| - Overloaded `len()` and `iter()` for `dip.Measurement.IteratorFeature` and `dip.Measurement.IteratorObject`, | ||
| and added `keys()`, `values()` and `items()` class methods. Now both behave more like Python dicts. | ||
| But note that all three of these methods will output a list with a copy of the values, it's not a view | ||
| as with dicts. | ||
|
|
||
| ### Changed functionality | ||
|
|
||
| - Converted several tuple output arguments to `namedtuple`. Note of these changes should affect existing code: | ||
|
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||
| - The function `dip.MaximumAndMinimum()` now returns a `namedtuple` of type `MinMaxValues`. | ||
| The two values can now (and preferably) be accessed using the dot notation: `mm.maximum` instead of `mm[1]`. | ||
| See [issue #184](https://github.com/DIPlib/diplib/issues/184). | ||
|
|
||
| - The functions `dip.MandersColocalizationCoefficients()` and `dip.CostesColocalizationCoefficients()` | ||
| now return a `namedtuple` of type `ColocalizationCoefficients`. | ||
|
|
||
| - The functions `dip.ChainCode.BoundingBox()` and `dip.Polygon.BoundingBox()` now return a `namedtuple` | ||
| of type `BoundingBoxInteger` and `BoundingBoxFloat` respectively, which contain two `namedtuple`s of type | ||
| `VertexInteger` or `VertexFloat`. | ||
|
|
||
| - Other `dip.Polygon` functions such as `dip.Polygon.Centroid()` now return a `namedtuple` of type `VertexFloat`. | ||
|
|
||
| - `dip.ChainCode.start` is now a `namedtuple` of type `VertexInteger`. | ||
|
|
||
| - The types `SubpixelLocationResult`, `RadonCircleParameters`, `RegressionParameters`, `GaussianParameters`, | ||
| `FeatureInformation`, `ValueInformation`, `EllipseParameters`, `FeretValues`, `RadiusValues`, `QuartilesResult`, | ||
| `StatisticsValues`, `CovarianceValues`, `MomentValues` and `SpatialOverlapMetrics`, all used only as outputs to | ||
| functions, and all simply emulating a C++ `struct`, are no longer special types in the `diplib.PyDIP_bin` namespace, | ||
| but `namedtuple`s. They new types behave identically, but can additionally be unpacked, for example: | ||
| `_, q1, _, q3, _ = dip.Quartiles(img)`. | ||
|
|
||
| - `dip::Measurement::IteratorFeature` was bound in Python as `dip.Measurement.MeasurementFeature`, and | ||
| `dip::Measurement::IteratorObject` as `dip.Measurement.MeasurementObject`. The names of these classes now | ||
| match the C++ name, to make `dip.Doc()` useful with these classes. But the names don't make much sense in | ||
| Python because these objects don't work as iterators like they do in C++. | ||
|
|
||
| (See also changes to *DIPlib*.) | ||
|
|
||
| ### Bug fixes | ||
|
|
||
| None, but see bugfixes to *DIPlib*. | ||
|
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||
|
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|
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|
|
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| ## Changes to *DIPviewer* | ||
|
|
||
| ### Bug fixes | ||
|
|
||
| - The Java interface used `Native.loadLibrary()`, which was deprecated. It now uses `Native.load()` instead. | ||
|
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|
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||
|
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|
|
||
| ## Changes to *DIPjavaio* | ||
|
|
||
| None. |
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