Bumped version number to 3.3.0. [skip ci]

CMakeLists.txt

@@ -8,7 +8,7 @@ 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 "2")
+set(PROJECT_VERSION_MINOR "3")
 set(PROJECT_VERSION_PATCH "0")
 set(PROJECT_VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}")
 set(DIP_COPYRIGHT_YEAR "2022")
@@ -39,7 +39,7 @@ set(DIP_DESTINATIONS
     ARCHIVE DESTINATION ${ARCHIVE_DESTINATION})
 
 # Compiler flags
-if(CMAKE_CXX_COMPILER_ID MATCHES "Clang") # also matchs "AppleClang"
+if(CMAKE_CXX_COMPILER_ID MATCHES "Clang") # also matches "AppleClang"
    # Compiler flags for Clang C++
    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wconversion -Wsign-conversion -pedantic -Wno-c++17-extensions")
    #set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native") # This is optimal for local usage.

changelogs/diplib_3.3.0.md

@@ -0,0 +1,202 @@
+---
+layout: post
+title: "Changes DIPlib 3.3.0"
+---
+
+## Changes to *DIPlib*
+
+### New functionality
+
+- Added `dip::MakeRegionsConvex2D()`, which works for both labelled and binary images.
+
+- Added `Perimeter()` (as an alias for `Length()`), `Reverse()`, `Rotate()`, `Scale()`, and `Translate()`
+  as member functions to `dip::Polygon`.
+
+- `dip::MomentAccumulator` has a new method `PlainSecondOrder()`, which returns the plain old second
+  order central moments, compared to the moment of inertia tensor returned by `SecondOrder()`.
+
+- Added `dip::Image::Mask()`, to apply a mask to an image.
+
+- Added `dip::DimensionArray<>::reverse()` and `dip::PixelSize::Reverse()` to reverse the elements of an array.
+
+- Added `dip::Image::ReverseDimensions()`, which permutes dimensions to reverse their order.
+
+- `dip::Label` has a new string argument, `mode`, which can be set to `"largest"` to return a labeled
+  image that only contains the largest connected component in the input image.
+
+- Added `dip::PixelSize::UnitLength()`, `dip::PixelSize::UnitSize()`, `dip::PixelSize::ForcePhysical()`,
+  and `dip::PixelSize::SameUnits()` to simplify finding the right units for measurement results.
+
+- Added operators to multiply and divide two `dip::Vertex` objects. They apply an element-wise product.
+
+- `dip::ChainCode::Length` has an optional parameter to include the image boundary pixels in the measurement.
+
+- The `"Perimeter"` feature can be configured: setting the `"include boundary pixels"` parameter to a non-zero
+  value causes the perimeter measurement to include pixels at the image boundary.
+
+- `dip::TriangleThreshold()` and `dip::BackgroundThreshold()` have a new parameter `sigma`, which defaults to
+  4 to preserve the old behavior.
+
+### Changed functionality
+
+- The deterministic initialization for `dip::GaussianMixtureModel()` is more robust, making the
+  initial Gaussians overlap instead of setting their sigma to 1.
+
+- `dip::ConvexHull` no longer holds a `dip::Polygon` as a private member, instead it uses `dip::Polygon`
+  as a base class. This makes all of the `dip::Polygon` functionality directly available on the convex
+  hull. `dip::ConvexHull::Polygon()` now just returns a base class reference.
+
+- `dip::Units` (and by extension `dip::PhysicalQuantity` and `dip::PixelSize`) now uses the Greek letter
+  μ (U+03BC), instead of the legacy symbol µ (U+00B5) for micron (when *DIPlib* is built with Unicode
+  enabled). Both symbols are recognized when parsing a string, but the strings generated are now different.
+
+- `dip::BackgroundThreshold()` now determines the half width at half height with sub-sample precision,
+  and takes the smoothing of the histogram into account, such that the amount of smoothing should have
+  little influence in the computed threshold.
+
+- The "Mu" and "GreyMu" features no longer use the pixel sizes if the units for different image
+  dimensions differ. No uses of the tensor make sense if the units for the various dimensions
+  don't match, in this case it is more useful to report the tensor in pixel units.
+
+### Bug fixes
+
+- `dip::DrawPolygon2D()`, when drawing filled polygons, would skip the bottom row in the polygon. The
+  algorithm is a bit more sophisticated now to properly handle these bottom rows. This also takes care
+  of some rounding errors that could be seen for polygons with very short edges.
+
+- `dip::ResampleAt` with a `map` input argument and using `"cubic"` interpolation could overflow,
+  yielding unsightly artifacts. See [issue #107](https://github.com/DIPlib/diplib/issues/107).
+
+- Better error messages for some forms of `dip::Image::View::At()`
+
+- `dip::ImageDisplay()` didn't pay attention to the `dim1` and `dim2` parameters if the image was 2D.
+
+- `dip::DefineROI()` was incorrect if the input and output images were the same object.
+
+- `dip::GaussianMixtureModel()` could produce NaN for amplitude, those components now have a zero amplitude.
+
+- The "SolidArea" feature didn't take the pixel size into account. This also caused the "Roundness" feature
+  to report wrong values. The "SurfaceArea" feature didn't properly scale the result by the pixel size.
+  Several composed features (computed from other features) didn't produce correct values for anisotropic
+  pixels ("P2A", "Roundness", and "PodczeckShapes").
+
+- `dip::div_round()` was incorrect, which caused `dip::DirectedPathOpening()` to not use certain
+  directions.
+
+- `dip::DirectionalStatisticsAccumulator::StandardDeviation()` returned NaN if the mean was identical to zero.
+
+
+
+
+## Changes to *DIPimage*
+
+### Changed functionality
+
+- `threshold(.., 'triangle')` now accepts a parameter to control how much smoothing to apply.
+
+(See also changes to *DIPlib*.)
+
+### Bug fixes
+
+None, but see bugfixes to *DIPlib*.
+
+
+
+
+## Changes to *PyDIP*
+
+### New functionality
+
+- Added `dip.MakeRegionsConvex2D()`.
+
+- Added `Perimeter()` (as an alias for `Length()`), `Reverse()`, `Rotate()`, `Scale()`, and `Translate()`
+  as methods to `dip.Polygon`.
+
+- `dip.Polygon` and `dip.ChainCode` now both have `__len__`, `__getitem__` and `__iter__` methods,
+  meaning that they can be treated like lists or other iterables. Previously, the values of `dip.Polygon`
+  had to be extracted by conversion to a NumPy array, and the values of `dip.ChainCode` by copying to
+  a list when accessing its `codes` property.
+
+- The structure returned by `dip.Moments()` has a new component `plainSecondOrder`, which contains
+  the plain old second order central moments, compared to the moment of inertia tensor contained
+  in `secondOrder`.
+
+- Added `Mask()` and `ReverseDimensions()` as methods to `dip.Image`.
+
+- Added `dip.ReverseDimensions()`, which reverses the indexing order for images for the remainder of the
+  session. Has repercussion on how the `dip.Image` buffer is exposed, buffer protocol objects are
+  converted to a `dip.Image`, files are read and written, and how *DIPviewer* displays images.
+  It is intended to make indexing into a `dip.Image` match the indexing into the corresponding
+  *NumPy* array, which should make it easier to mix calls to *DIPlib* and *scikit-image* in the same
+  program. Note that this also causes positive angles to be counter-clockwise instead of clockwise.
+
+- Added the `@` and `@=` operators for `dip.Image` objects. These apply matrix multiplication if both
+  operands are non-scalar images. That is, the vector or matrix at each pixel is multiplied by the
+  vector or matrix at the corresponding pixel in the other operand. The two image's tensor dimensions
+  must be compatible. If one of the operands is a scalar image, the normal element-wise multiplication
+  is applied. One of the operands can be a single pixel (a list of numbers).
+
+- Added `dip.MeasurementTool.Configure` to allow measurement features to be configured.
+
+- Added `AspectRatio()`, `SameUnits()`, `UnitLength()`, `UnitSize()`, `ForcePhysical()`,
+  and `ApproximatelyEquals()` as methods to `dip.PixelSize`.
+
+### Changed functionality
+
+- Operators overloaded for `dip.Image` objects can use lists of numbers as a second argument, which
+  is interpreted as a 0D tensor image (column vector). This makes `img / img[0]` possible.
+
+- When *PyDIPjavaio* fails to load, the error is no longer displayed immediately. Instead, it is
+  shown when `dip.ImageRead()` fails. The error message is also a bit more helpful.
+  See [issue #106](https://github.com/DIPlib/diplib/issues/106).
+
+- The `__repr__` string for many classes has changed to be more consistent and informative.
+
+- The `*` and `*=` operators have changed meaning, they now always apply element-wise multiplication,
+  their previous behavior is now obtained with the new `@` and `@=` operators.
+  **NOTE! This breaks backwards compatibility.** To keep old code working that depends on image matrix
+  multiplications, you can do
+  ```python
+  import diplib as dip
+  dip.Image.__mul__ = dip.Image.__matmul__
+  dip.Image.__rmul__ = dip.Image.__rmatmul__
+  dip.Image.__imul__ = dip.Image.__imatmul__
+  ```
+  But we recommend instead that you update the code to use the right operators.
+
+(See also changes to *DIPlib*.)
+
+### Bug fixes
+
+- `__len__()` now properly returns 0 for an empty (raw) image. This makes `if img` fail for a raw image.
+
+- Fixed a few issues with indexing into image, allowing using a list of coordinates, and allowing assigning
+  a scalar value into a multi-channel image.
+
+- `dip.SubpixelMaxima()` and `dip.SubpixelMinima()`, when a mask image was given, didn't work correctly.
+
+- The `**=` operator did the computations correctly, but then assigned `None` to the variable instead of the
+  result of the operation. The `**` operator didn't work with a single pixel (a number or a list) on the
+  left-hand side.
+
+(See also bugfixes to *DIPlib*.)
+
+
+
+
+## Changes to *DIPviewer*
+
+### New functionality
+
+- Added option to change axis labels.
+
+### Bug fixes
+
+- Automatically close all *PyDIPviewer* windows at program exit to avoid segfault.
+
+
+
+
+## Changes to *DIPjavaio*
+
+None.