diff --git a/CMakeLists.txt b/CMakeLists.txt index 5b219a52..2a2086b2 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -20,8 +20,8 @@ project(DIPlib) # The version number and latest copyright year. Update these values here, they're used all throughout the project. set(PROJECT_VERSION_MAJOR "3") -set(PROJECT_VERSION_MINOR "4") -set(PROJECT_VERSION_PATCH "3") +set(PROJECT_VERSION_MINOR "5") +set(PROJECT_VERSION_PATCH "0") set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}") set(DIP_COPYRIGHT_YEAR "2024") diff --git a/changelogs/diplib_3.5.0.md b/changelogs/diplib_3.5.0.md new file mode 100644 index 00000000..3bab64f3 --- /dev/null +++ b/changelogs/diplib_3.5.0.md @@ -0,0 +1,292 @@ +--- +layout: post +title: "Changes DIPlib 3.5.0" +--- + +## Changes to *DIPlib* + +### New functionality + +- Added `dip::OutputBuffer` as a virtual base class, and `dip::SimpleOutputBuffer` and `dip::FixedOutputBuffer` + as specific instances. These are used to handle a buffer that a JPEG or PNG file can be written into by + `dip::ImageWriteJPEG()` and `dip::ImageWritePNG()`. + +- Added `dip::Framework::Projection()` as a public function. Previously it was a private library function for internal + use only. This framework function simplifies the creation of projection operations, and forms the basis of + functions such as `dip::Mean()` and `dip::Maximum()`. + +- Added macros `DIP_PARALLEL_ERROR_DECLARE`, `DIP_PARALLEL_ERROR_START` and `DIP_PARALLEL_ERROR_END` + to simplify writing parallel code with OpenMP that properly handles exceptions. + +- Added an operator to convert `dip::Units` to `bool`. The units object will test false if it's unitless. + +- Added `dip::Quartiles()`. + +- Added `dip::Measurement::IteratorFeature::AsImage()` and `AsScalarImage()`. + +- Added `dip::Histogram::OptimalConfiguration()` and `OptimalConfigurationWithFullRange()`, which make it possible + to configure the histogram to use the Freedman--Diaconis rule to choose the bin size. + +- Added `dip::LabelMap`, a class that holds labels (object IDs) and can map them to new values. The mapping can be + applied to a labeled image or to a `dip::Measurement` object. You can also index into a `dip::Measurement` + object with a `dip::LabelMap`. + +- Added comparison operators for `dip::Measurement::IteratorFeature`. They return a `dip::LabelMap`. + +- Added `dip::UnionFind::Size()`. + +- Added `dip::IsOnEdge()`. + +- Added an overload to `dip::GaussianMixtureModel()` that takes a 1D histogram as input. + +### Changed functionality + +- The `compressionLevel` argument to `dip::ImageWritePNG()` changed from `dip::uint` to `dip::sint`, allowing for + -1 to configure the deflate algorithm to use RLE instead of its default strategy. For some images this option + can lead to smaller files, and for some images to much faster compression. + +- The versions of `dip::ImageWriteJPEG()` and `dip::ImageWritePNG()` that write to a memory buffer now take + a version of a `dip::OutputBuffer` object to write to. Overloaded versions of these two functions maintain + the previous syntax where the buffer is created internally and returned to the caller. + +- `dip::Framework::Projection()` is now parallelized. All projection functions (for example `dip::Mean()` and + `dip::Maximum()`) now can use multithreading for faster computation if the output has at least one dimension. + For example, the mean value of each image row can be computed in parallel, but the mean value over the whole + image is still not computed in parallel. + +- `dip::PairCorrelation()`, `dip::ProbabilisticPairCorrelation()`, `dip::Semivariogram()`, and `dip::ChordLength()` + Have been parallelized for `"random"` sampling. + +- `dip::GrowRegionsWeighted()` with a `dip::Metric` parameter has been deprecated. The new version of the function + uses the fast marching algorithm in the grey-weighted distance transform. If both `grey` and `mask` are not + forged, `dip::EuclideanDistanceTransform()` is called instead of `dip::GreyWeightedDistanceTransform()`. + This makes the function efficient for when isotropic growing is required. And the function now has a new float + parameter, `distance` that determines how far the regions are grown. + +- `dip::ImageRead()` throws a `dip::RunTimeError` instead of a `dip::ParameterError` if the file doesn't exist + or is of an unrecognized type. + +- `dip::GetOptimalDFTSize()` has a new argument `maxFactor` that determines what the largest factor for the output + integer can be. Valid values are 5, 7 and 11. A new function `dip::MaxFactor()` will give the appropriate value + depending on whether a real or complex-valued transform is being computed, and what FFT implementation is being + used. When using *PocketFFT*, this function can now also return much larger values than before. + +- `dip::OptimalFourierTransformSize()`, which depends on `dip::GetOptimalDFTSize()` (see the bullet point above + this one) has a new argument `purpose` that can be either `"real"` or `"complex"`, and uses the new + `dip::MaxFactor()` to fill in the `maxFactor` argument. + +- `dip::GaussFT()` has a new parameter `boundaryCondition`, the default empty value gives the same behavior as + previously. `dip::Gauss()` now passes the boundary condition through to `dip::GaussFT()`. + See [issue #159](https://github.com/DIPlib/diplib/issues/159). + +- The versions of `dip::IsodataThreshold()`, `dip::OtsuThreshold()`, `dip::MinimumErrorThreshold()`, + `dip::GaussianMixtureModelThreshold()`, `dip::TriangleThreshold()` and `dip::BackgroundThreshold()` that take an + image as input, now compute the histogram using the new `dip::Histogram::OptimalConfiguration()` configuration. + This generally makes them more precise. In some cases, the previous behavior was not correct. + See [issue #161](https://github.com/DIPlib/diplib/issues/161). + To reproduce the previous behavior, compute a histogram with default configuration (`dip::Histogram(image)`), + and pass this histogram to the equivalent threshold estimation function. This function will return a threshold + value that can be applied to the image using the comparison operator (`image > threshold`). + +- `dip::EstimateNoiseVariance()` uses a potentially more precise threshold internally to exclude edges. + +- Made more consistent use of `dip::LabelType`, and we're no longer accepting any label (or object ID) with a value + that doesn't fit in that type. *DIPlib* has always produced labeled images of this type, but it accepts any + unsigned integer image as a label image. Both internally and in the API, sometimes we used `dip::LabelType` + (32-bit unsigned integer), and sometimes we used `dip::uint` (system-dependent size integer, usually 64-bit). + We now consistently use `dip::LabelType` everywhere: + + - If the input labeled image is of type `uint64`, any pixel value outside the `dip::LabelType` range will cause + an exception to the thrown. This is true for the measurement functionality and the functions in `regions.h`. + + - Added a version of `dip::Measurement::SetObjectIDs()` that takes a `std::vector< dip::LabelType >` as input. + + - `dip::ListObjectLabels()` is identical to `dip::GetObjectLabels()` (which is now deprecated), but it returns a + `std::vector< dip::LabelType >` instead of a `dip::UnsignedArray`. `dip::GetObjectLabels()` is deprecated. + + - Added `dip::CastLabelType()`, which can be called with any unsigned integer as input, and the same value + as a `dip::LabelType`. If the value is too large to fit in that type, an exception is thrown. + + - `dip::GetLabelBoundingBox()` with a `dip::uint` for the `objectID` parameter is deprecated, + it now needs to be a `dip::LabelType`. + + - `dip::GetImageChainCodes()` with a `dip::UnsignedArray` for the `objectIDs` parameter is deprecated, + it now needs to be a `std::vector< dip::LabelType >`. + + - `dip::ChainCode::objectID` is now of type `dip::LabelType`, was `dip::uint`. + + - The measurement functions and data structures still use `dip::uint` for object IDs. + +- `dip::ListObjectLabels()` adds an option to list only labels touching the image edge. + +- `dip::EdgeObjectsRemove()` also works for labeled images. + +- `dip::Image::View::Copy()` with an image as input now allows a 1-pixel input to be used. This behaves like + `dip::Image::View::Fill()` with a `dip::Image::Pixel` as input. + +### Bug fixes + +- `dip::PairCorrelation`, `dip::ProbabilisticPairCorrelation`, `dip::Semivariogram`, and `dip::ChordLength` + did not properly compute step sizes for `"grid"` sampling, effectively ignoring the value of `probes` + and using all pixels (as if `probes` were set to 0). + +- Tensor indexing did not remove color space information as expected (bug introduced with the fix to the move + constructor in 3.4.3). + +- `dip::Image::CheckIsMask()` didn't properly check for singleton-expandable masks, accepting masks of any size. + +- `dip::FourierTransform()` threw an exception when the real-to-complex dimension had a size of 2. + See [issue #158](https://github.com/DIPlib/diplib/issues/158). + +- A wrong assertion in internal code for `dip::FourierTransform()` made it impossible to inverse transform + a real-valued image under certain conditions, when *DIPlib* was built with assertions enabled (bug introduced + with the refactoring of the Fourier code in 3.4.0). + +- The 2D parabola fitting function used in `dip::SubpixelLocation()`, `dip::SubpixelMaxima()` and + `dip::SubpixelMinima()`, with the `"parabolic"` and `"gaussian"` methods, was using wrong weights, + making the result not precise. The 3D case was not affected. The faster `"parabolic separable"` and + `"gaussian separable"` methods were also not affected. + +### Updated dependencies + +- Updated included header-only library *robin-map* to version 1.3.0. Assorted minor improvements. + +- Updated included header-only library *pcg-cpp* to the current master branch (last updated 2022-04-08). + Assorted minor improvements. + +- Updated bundled *pybind11* to version 2.12.0. + +- Updated bundled library *PocketFFT* to the current master branch (last updated 2024-03-22). + This fixes a potential compilation problem on macOS. + +### Build changes + +- Minimum required version of *CMake* is now 3.12. + + + + +## Changes to *DIPimage* + +### Changed functionality + +- Added `'optimal'` to `diphist`, `diphist2` and `mdhistogram` as an option to choose an optimal bin size. + +(See also changes to *DIPlib*.) + +### Bug fixes + +None, but see bugfixes to *DIPlib*. + +### Build and installation changes + +- Added the *CMake* option `DIP_JAVA_VERSION`, which can be important when building *DIPimage* for older versions + of MATLAB. The Java version must be equal or older than the version used by MATLAB. Running `version -java` + in MATLAB will tell you what version of Java it is using. + +- Added the function `download_bioformats`, which does the same thing as `python -m diplib download_bioformats` in + *PyDIP*. This significantly simplifies the installation instructions for *Bio-Formats*. + + + + +## Changes to *PyDIP* + +### New functionality + +- Added bindings to `dip::GaussFIR()`, to complement `GaussIIR()` and `GaussFT()`. Though it is expected users will + keep using `dip.Gauss()` to access these various algorithms. + +- Added bindings for `dip.Units.HasSameDimensions`, `dip.Units.IsDimensionless`, `dip.Units.IsPhysical`, + `dip.Units.AdjustThousands`, `dip.Units.Thousands`. + +- Added `dip.Measurement.ToDataFrame()`, which converts the measurement results into a Pandas DataFrame. + This function will import NumPy and Pandas when used, these packages need to be installed. + +- Added `dip.Measurement.MeasurementFeature.Subset()` (binding for `dip::Measurement::IteratorFeature::Subset()`) + and `dip.Measurement.FeatureValuesView()`. + +- Added bindings for `dip.ColorSpaceManager.SetWhitePoint()`, as well as `dip.ColorSpaceManager.IlluminantA`, + `IlluminantD50`, `IlluminantD55`, `IlluminantD65` and `IlluminantE`. + +- Added bindings for `dip.SeparableConvolution()`, `dip.SeparateFilter()` and the `dip.OneDimensionalFilter` + struct. + +### Changed functionality + +- The *DIPlib* exception classes are now properly bound. This changes the type of the exceptions raised by + the library in Python: `dip.Error` is the new base class, raised exceptions are either `dip.ParameterError`, + `dip.RunTimeError` or `dip.AssertionError`. `dip.Error` is derived from `Exception`. + +- Made `diplib.PyDIPjavaio` more easily available as `diplib.javaio`. The new name matches the C++ library + namespace, and when imported properly loads the JVM before importing *PyDIPjavaio*. One can now: + ```python + import diplib as dip + import diplib.javaio + image = dip.javaio.ImageReadJavaIO("foo") + ``` + `dip.ImageRead()` still automatically loads *PyDIPjavaio* on first use. + +- `diplib.viewer` is no longer an alias, but a true submodule, like we did for `diplib.javaio`. This should + not change anything for the user, other than some IDEs having less trouble identifying the name. + +- `dip.ImageRead()` and `dip.javaio.ImageReadJavaIO()` now also have a version that takes the output image + as a keyword-only argument `out`. + +- All the functions named `dip.ImageRead...()` that have a keyword-only argument `out` now return the + `dip::FileInformation` structure (as a dict, just like `dip.ImageRead...Info()` does). + +- Unitless `dip.Units` now test false. + +- Moved `dip.MeasurementTool.MeasurementFeature` to `dip.Measurement.MeasurementFeature` and + `dip.MeasurementTool.MeasurementObject` to `dip.Measurement.MeasurementObject`. + They are the bindings to `dip::Measurement::IteratorFeature` and `dip::Measurement::IteratorObject` respectively. + +(See also changes to *DIPlib*.) + +### Bug fixes + +- `dip.viewer.Show()` would cause Python to crash if given a raw image. + +(See also bugfixes to *DIPlib*.) + +### Updated dependencies + +- Updated bundled *pybind11* to version 2.12.0. + +### Build and installation changes + +- The *CMake* option `PYTHON_EXECUTABLE` is no longer used, set `Python_EXECUTABLE` instead. The build script + will, for the time being, copy the value of the former to the latter if the former is set but the latter isn't. + +- The *CMake* option `PYBIND11_PYTHON_VERSION` is no longer used. It was mentioned in the documentation, but + probably never really worked. + +- Significantly improved the command to download *Bio-Formats*: `python -m diplib download_bioformats` now + has an optional argument `-u` to force an update of the existing library, and another one to specify + which verison to download. By default, it downloads whatever the latest version is, we no longer hard-code + a specific version number. + + + + +## Changes to *DIPviewer* + +### Bug fixes + +- Trying to display an image with wrong color space information would throw an exception. The image is now seen + as a generic tensor image. + +- Continuous scrolling devices were way too sensitive when using GLFW, it was really hard to zoom in and out + of an image. (The fix works at least on macOS, let us know if this produces issues on other platforms.) + + + + +## Changes to *DIPjavaio* + +### Changed functionality + +- `dip::javaio::ImageReadJavaIO()` has an additional parameter `imageNumber` to select which image in a multi-image + file to read. The `dip::FileInformation` structure returned now correctly indicates how many images are in the file + in the `numberOfImages` element. diff --git a/changelogs/diplib_next.md b/changelogs/diplib_next.md index 0166225a..3d8c238e 100644 --- a/changelogs/diplib_next.md +++ b/changelogs/diplib_next.md @@ -7,162 +7,14 @@ title: "Changes DIPlib 3.x.x" ### New functionality -- Added `dip::OutputBuffer` as a virtual base class, and `dip::SimpleOutputBuffer` and `dip::FixedOutputBuffer` - as specific instances. These are used to handle a buffer that a JPEG or PNG file can be written into by - `dip::ImageWriteJPEG()` and `dip::ImageWritePNG()`. - -- Added `dip::Framework::Projection()` as a public function. Previously it was a private library function for internal - use only. This framework function simplifies the creation of projection operations, and forms the basis of - functions such as `dip::Mean()` and `dip::Maximum()`. - -- Added macros `DIP_PARALLEL_ERROR_DECLARE`, `DIP_PARALLEL_ERROR_START` and `DIP_PARALLEL_ERROR_END` - to simplify writing parallel code with OpenMP that properly handles exceptions. - -- Added an operator to convert `dip::Units` to `bool`. The units object will test false if it's unitless. - -- Added `dip::Quartiles()`. - -- Added `dip::Measurement::IteratorFeature::AsImage()` and `AsScalarImage()`. - -- Added `dip::Histogram::OptimalConfiguration()` and `OptimalConfigurationWithFullRange()`, which make it possible - to configure the histogram to use the Freedman--Diaconis rule to choose the bin size. - -- Added `dip::LabelMap`, a class that holds labels (object IDs) and can map them to new values. The mapping can be - applied to a labeled image or to a `dip::Measurement` object. You can also index into a `dip::Measurement` - object with a `dip::LabelMap`. - -- Added comparison operators for `dip::Measurement::IteratorFeature`. They return a `dip::LabelMap`. - -- Added `dip::UnionFind::Size()`. - -- Added `dip::IsOnEdge()`. - -- Added an overload to `dip::GaussianMixtureModel()` that takes a 1D histogram as input. - ### Changed functionality -- The `compressionLevel` argument to `dip::ImageWritePNG()` changed from `dip::uint` to `dip::sint`, allowing for - -1 to configure the deflate algorithm to use RLE instead of its default strategy. For some images this option - can lead to smaller files, and for some images to much faster compression. - -- The versions of `dip::ImageWriteJPEG()` and `dip::ImageWritePNG()` that write to a memory buffer now take - a version of a `dip::OutputBuffer` object to write to. Overloaded versions of these two functions maintain - the previous syntax where the buffer is created internally and returned to the caller. - -- `dip::Framework::Projection()` is now parallelized. All projection functions (for example `dip::Mean()` and - `dip::Maximum()`) now can use multithreading for faster computation if the output has at least one dimension. - For example, the mean value of each image row can be computed in parallel, but the mean value over the whole - image is still not computed in parallel. - -- `dip::PairCorrelation()`, `dip::ProbabilisticPairCorrelation()`, `dip::Semivariogram()`, and `dip::ChordLength()` - Have been parallelized for `"random"` sampling. - -- `dip::GrowRegionsWeighted()` with a `dip::Metric` parameter has been deprecated. The new version of the function - uses the fast marching algorithm in the grey-weighted distance transform. If both `grey` and `mask` are not - forged, `dip::EuclideanDistanceTransform()` is called instead of `dip::GreyWeightedDistanceTransform()`. - This makes the function efficient for when isotropic growing is required. And the function now has a new float - parameter, `distance` that determines how far the regions are grown. - -- `dip::ImageRead()` throws a `dip::RunTimeError` instead of a `dip::ParameterError` if the file doesn't exist - or is of an unrecognized type. - -- `dip::GetOptimalDFTSize()` has a new argument `maxFactor` that determines what the largest factor for the output - integer can be. Valid values are 5, 7 and 11. A new function `dip::MaxFactor()` will give the appropriate value - depending on whether a real or complex-valued transform is being computed, and what FFT implementation is being - used. When using *PocketFFT*, this function can now also return much larger values than before. - -- `dip::OptimalFourierTransformSize()`, which depends on `dip::GetOptimalDFTSize()` (see the bullet point above - this one) has a new argument `purpose` that can be either `"real"` or `"complex"`, and uses the new - `dip::MaxFactor()` to fill in the `maxFactor` argument. - -- `dip::GaussFT()` has a new parameter `boundaryCondition`, the default empty value gives the same behavior as - previously. `dip::Gauss()` now passes the boundary condition through to `dip::GaussFT()`. - See [issue #159](https://github.com/DIPlib/diplib/issues/159). - -- The versions of `dip::IsodataThreshold()`, `dip::OtsuThreshold()`, `dip::MinimumErrorThreshold()`, - `dip::GaussianMixtureModelThreshold()`, `dip::TriangleThreshold()` and `dip::BackgroundThreshold()` that take an - image as input, now compute the histogram using the new `dip::Histogram::OptimalConfiguration()` configuration. - This generally makes them more precise. In some cases, the previous behavior was not correct. - See [issue #161](https://github.com/DIPlib/diplib/issues/161). - To reproduce the previous behavior, compute a histogram with default configuration (`dip::Histogram(image)`), - and pass this histogram to the equivalent threshold estimation function. This function will return a threshold - value that can be applied to the image using the comparison operator (`image > threshold`). - -- `dip::EstimateNoiseVariance()` uses a potentially more precise threshold internally to exclude edges. - -- Made more consistent use of `dip::LabelType`, and we're no longer accepting any label (or object ID) with a value - that doesn't fit in that type. *DIPlib* has always produced labeled images of this type, but it accepts any - unsigned integer image as a label image. Both internally and in the API, sometimes we used `dip::LabelType` - (32-bit unsigned integer), and sometimes we used `dip::uint` (system-dependent size integer, usually 64-bit). - We now consistently use `dip::LabelType` everywhere: - - - If the input labeled image is of type `uint64`, any pixel value outside the `dip::LabelType` range will cause - an exception to the thrown. This is true for the measurement functionality and the functions in `regions.h`. - - - Added a version of `dip::Measurement::SetObjectIDs()` that takes a `std::vector< dip::LabelType >` as input. - - - `dip::ListObjectLabels()` is identical to `dip::GetObjectLabels()` (which is now deprecated), but it returns a - `std::vector< dip::LabelType >` instead of a `dip::UnsignedArray`. `dip::GetObjectLabels()` is deprecated. - - - Added `dip::CastLabelType()`, which can be called with any unsigned integer as input, and the same value - as a `dip::LabelType`. If the value is too large to fit in that type, an exception is thrown. - - - `dip::GetLabelBoundingBox()` with a `dip::uint` for the `objectID` parameter is deprecated, - it now needs to be a `dip::LabelType`. - - - `dip::GetImageChainCodes()` with a `dip::UnsignedArray` for the `objectIDs` parameter is deprecated, - it now needs to be a `std::vector< dip::LabelType >`. - - - `dip::ChainCode::objectID` is now of type `dip::LabelType`, was `dip::uint`. - - - The measurement functions and data structures still use `dip::uint` for object IDs. - -- `dip::ListObjectLabels()` adds an option to list only labels touching the image edge. - -- `dip::EdgeObjectsRemove()` also works for labeled images. - -- `dip::Image::View::Copy()` with an image as input now allows a 1-pixel input to be used. This behaves like - `dip::Image::View::Fill()` with a `dip::Image::Pixel` as input. - ### Bug fixes -- `dip::PairCorrelation`, `dip::ProbabilisticPairCorrelation`, `dip::Semivariogram`, and `dip::ChordLength` - did not properly compute step sizes for `"grid"` sampling, effectively ignoring the value of `probes` - and using all pixels (as if `probes` were set to 0). - -- Tensor indexing did not remove color space information as expected (bug introduced with the fix to the move - constructor in 3.4.3). - -- `dip::Image::CheckIsMask()` didn't properly check for singleton-expandable masks, accepting masks of any size. - -- `dip::FourierTransform()` threw an exception when the real-to-complex dimension had a size of 2. - See [issue #158](https://github.com/DIPlib/diplib/issues/158). - -- A wrong assertion in internal code for `dip::FourierTransform()` made it impossible to inverse transform - a real-valued image under certain conditions, when *DIPlib* was built with assertions enabled (bug introduced - with the refactoring of the Fourier code in 3.4.0). - -- The 2D parabola fitting function used in `dip::SubpixelLocation()`, `dip::SubpixelMaxima()` and - `dip::SubpixelMinima()`, with the `"parabolic"` and `"gaussian"` methods, was using wrong weights, - making the result not precise. The 3D case was not affected. The faster `"parabolic separable"` and - `"gaussian separable"` methods were also not affected. - ### Updated dependencies -- Updated included header-only library *robin-map* to version 1.3.0. Assorted minor improvements. - -- Updated included header-only library *pcg-cpp* to the current master branch (last updated 2022-04-08). - Assorted minor improvements. - -- Updated bundled *pybind11* to version 2.12.0. - -- Updated bundled library *PocketFFT* to the current master branch (last updated 2024-03-22). - This fixes a potential compilation problem on macOS. - ### Build changes -- Minimum required version of *CMake* is now 3.12. - @@ -172,8 +24,6 @@ title: "Changes DIPlib 3.x.x" ### Changed functionality -- Added `'optimal'` to `diphist`, `diphist2` and `mdhistogram` as an option to choose an optimal bin size. - (See also changes to *DIPlib*.) ### Bug fixes @@ -183,13 +33,6 @@ None, but see bugfixes to *DIPlib*. ### Build and installation changes -- Added the *CMake* option `DIP_JAVA_VERSION`, which can be important when building *DIPimage* for older versions - of MATLAB. The Java version must be equal or older than the version used by MATLAB. Running `version -java` - in MATLAB will tell you what version of Java it is using. - -- Added the function `download_bioformats`, which does the same thing as `python -m diplib download_bioformats` in - *PyDIP*. This significantly simplifies the installation instructions for *Bio-Formats*. - @@ -197,79 +40,17 @@ None, but see bugfixes to *DIPlib*. ### New functionality -- Added bindings to `dip::GaussFIR()`, to complement `GaussIIR()` and `GaussFT()`. Though it is expected users will - keep using `dip.Gauss()` to access these various algorithms. - -- Added bindings for `dip.Units.HasSameDimensions`, `dip.Units.IsDimensionless`, `dip.Units.IsPhysical`, - `dip.Units.AdjustThousands`, `dip.Units.Thousands`. - -- Added `dip.Measurement.ToDataFrame()`, which converts the measurement results into a Pandas DataFrame. - This function will import NumPy and Pandas when used, these packages need to be installed. - -- Added `dip.Measurement.MeasurementFeature.Subset()` (binding for `dip::Measurement::IteratorFeature::Subset()`) - and `dip.Measurement.FeatureValuesView()`. - -- Added bindings for `dip.ColorSpaceManager.SetWhitePoint()`, as well as `dip.ColorSpaceManager.IlluminantA`, - `IlluminantD50`, `IlluminantD55`, `IlluminantD65` and `IlluminantE`. - -- Added bindings for `dip.SeparableConvolution()`, `dip.SeparateFilter()` and the `dip.OneDimensionalFilter` - struct. - ### Changed functionality -- The *DIPlib* exception classes are now properly bound. This changes the type of the exceptions raised by - the library in Python: `dip.Error` is the new base class, raised exceptions are either `dip.ParameterError`, - `dip.RunTimeError` or `dip.AssertionError`. `dip.Error` is derived from `Exception`. - -- Made `diplib.PyDIPjavaio` more easily available as `diplib.javaio`. The new name matches the C++ library - namespace, and when imported properly loads the JVM before importing *PyDIPjavaio*. One can now: - ```python - import diplib as dip - import diplib.javaio - image = dip.javaio.ImageReadJavaIO("foo") - ``` - `dip.ImageRead()` still automatically loads *PyDIPjavaio* on first use. - -- `diplib.viewer` is no longer an alias, but a true submodule, like we did for `diplib.javaio`. This should - not change anything for the user, other than some IDEs having less trouble identifying the name. - -- `dip.ImageRead()` and `dip.javaio.ImageReadJavaIO()` now also have a version that takes the output image - as a keyword-only argument `out`. - -- All the functions named `dip.ImageRead...()` that have a keyword-only argument `out` now return the - `dip::FileInformation` structure (as a dict, just like `dip.ImageRead...Info()` does). - -- Unitless `dip.Units` now test false. - -- Moved `dip.MeasurementTool.MeasurementFeature` to `dip.Measurement.MeasurementFeature` and - `dip.MeasurementTool.MeasurementObject` to `dip.Measurement.MeasurementObject`. - They are the bindings to `dip::Measurement::IteratorFeature` and `dip::Measurement::IteratorObject` respectively. - (See also changes to *DIPlib*.) ### Bug fixes -- `dip.viewer.Show()` would cause Python to crash if given a raw image. - +None, but see bugfixes to *DIPlib*. (See also bugfixes to *DIPlib*.) -### Updated dependencies - -- Updated bundled *pybind11* to version 2.12.0. - ### Build and installation changes -- The *CMake* option `PYTHON_EXECUTABLE` is no longer used, set `Python_EXECUTABLE` instead. The build script - will, for the time being, copy the value of the former to the latter if the former is set but the latter isn't. - -- The *CMake* option `PYBIND11_PYTHON_VERSION` is no longer used. It was mentioned in the documentation, but - probably never really worked. - -- Significantly improved the command to download *Bio-Formats*: `python -m diplib download_bioformats` now - has an optional argument `-u` to force an update of the existing library, and another one to specify - which verison to download. By default, it downloads whatever the latest version is, we no longer hard-code - a specific version number. - @@ -281,11 +62,7 @@ None, but see bugfixes to *DIPlib*. ### Bug fixes -- Trying to display an image with wrong color space information would throw an exception. The image is now seen - as a generic tensor image. - -- Continuous scrolling devices were way too sensitive when using GLFW, it was really hard to zoom in and out - of an image. (The fix works at least on macOS, let us know if this produces issues on other platforms.) +### Build changes @@ -296,8 +73,6 @@ None, but see bugfixes to *DIPlib*. ### Changed functionality -- `dip::javaio::ImageReadJavaIO()` has an additional parameter `imageNumber` to select which image in a multi-image - file to read. The `dip::FileInformation` structure returned now correctly indicates how many images are in the file - in the `numberOfImages` element. - ### Bug fixes + +### Build changes diff --git a/changelogs/template.md b/changelogs/template.md index 7821586f..3d8c238e 100644 --- a/changelogs/template.md +++ b/changelogs/template.md @@ -13,6 +13,8 @@ title: "Changes DIPlib 3.x.x" ### Updated dependencies +### Build changes + @@ -29,6 +31,8 @@ title: "Changes DIPlib 3.x.x" None, but see bugfixes to *DIPlib*. (See also bugfixes to *DIPlib*.) +### Build and installation changes + @@ -45,6 +49,8 @@ None, but see bugfixes to *DIPlib*. None, but see bugfixes to *DIPlib*. (See also bugfixes to *DIPlib*.) +### Build and installation changes + @@ -56,6 +62,8 @@ None, but see bugfixes to *DIPlib*. ### Bug fixes +### Build changes + @@ -66,3 +74,5 @@ None, but see bugfixes to *DIPlib*. ### Changed functionality ### Bug fixes + +### Build changes