Changes DIPimage 3.0 beta 1

Here we list the changes to DIPimage as compared to version 2.9. DIPimage is built on DIPlib, which was completely rewritten for this release. Consequently, there are many changes to DIPimage as well. It is possible that we missed some changes here, but hopefully this list will help in porting your old code that used DIPimage to the new version.

• It is no longer necessary to call dip_initialise (which doesn’t exist any more). The DIPlib library no longer requires initialization.

• The dip_image object has changed completely internally. Pixel data is stored differently: tensor images have all samples in the same MATLAB array. Complex images are stored as a single real matrix, with real and complex samples next to each other (this translates much more nicely to DIPlib, where complex data is stored in that same way).

  Consequently, the dip_image_array pseudo-class no longer exists. Both scalar and tensor images report to be of class dip_image. If you need to store multiple images in one object, create a cell array instead.

  Additionally, the tensor no longer can hold arbitrary number of dimensions, it is limited to vectors and matrices, as it is in DIPlib. I don’t expect this to impact any user’s code, and I’d be happy to hear if you actually used tensors with more than two dimensions.

  We tried keeping how the dip_image object is used as similar as possible to how it was in DIPimage 2, so that users need not change their code. Nonetheless, some changes must occur:

  • The size method was discouraged, we asked users to use imsize and imarsize instead. Those two functions work as before, except that they don’t return 1 for dimensions that don’t exist. size now always works like imsize, except that it always returns at least two values, and will return 1 for non-existing dimensions. This makes it similar to the default size, and plays nice with the whos command. tensorsize is like imarsize, but with a more sensical name, since image arrays no longer exist.

  • end was discouraged as well, as the meaning changed from dip_image to dip_image_array. Now end will always work for spatial dimensions, and cannot be used with tensor indexing. That is, end will work in () indexing, but not in {} indexing.

  • Methods that changed behavior for scalar and tensor images (i.e. sum, max, etc.) now always operate only along spatial dimensions. To sum over the tensor dimension, convert it to a spatial dimension using tensortospatial.

  • Likewise, methods such as cat used to concatenate images in an dip_image_array, and consequently concatenated the various tensor elements as separate images. These functions now all work along spatial dimensions only, leaving the tensor dimension unaffected.

  • The reshape method now takes pixels column-wise instead of row-wise from the input. This is the natural way of doing it, as it doesn’t require data copy. I don’t remember why it was row-wise in DIPimage 2, and I presume there are few (if any) programs that depend on the old behavior.

  • Related to the previous point, squeeze now might reorder dimensions. But it’s cheaper this way!

  • There are slight changes to how array data types are handled when converting to a dip_image object and when using an array as input to a DIPimage function. Most importantly, the DIPlib interface translates double-precision scalar arrays to 0D images of a single-precision type as long as that does not cause overflow or underflow. This typically yields the expected results. To avoid this behavior, explicitly cast to dip_image. For example: img + 1 vs img + dip_image(1).

  • The inner and outer methods no longer exist, use cross and dot.

  • New methods: clone, cosh, cumsum, erfc, flip, gammaln, iscomplex, issigned, isunsigned, numArgumentsFromSubscript, numberchannels, numpixels, numtensorel, sinh, slice_ex, slice_in, slice_op, spatialtotensor, swapdim, tanh, tensorfun, tensorsize, tensortospatial.

  • eig_largest has been moved to the toolbox directory.

  • besselj, length and unique are no longer methods of dip_image.

• Related to the tensor image changes above, newimar and imarfun are now in the alias subdirectory, and are identical to the new functions newtensorim and tensorfun.

• The dip_measurement object has changed completely internally. The interface is identical except:

  • It is not (yet?) possible to add a feature.

  • It is no longer possible to convert to/from a struct. However, it is possible to convert to a table.

  • Fixed a bug: msr.featureID now returns an array that is transposed w.r.t. previous versions. This was a bug that we never fixed because of backwards compatibility, we took this opportunity to fix it. Now we have total consistency: no matter how the measurement data are extracted or converted, objects are always rows, and features are always columns.

  • For consistency, msr.ID now returns object IDs as a column vector (objects are rows).

  • A new method, remap, implements what used to be the independent function msr_remap. msr_remap is in the alias subdirectory.

• The interactive image display window from dipshow has had some internal changes. User-visible changes are:

  • Three new options in the “Mappings” menu for 3D and 4D images, labeled “Slice”, “Max projection” and “Mean projection”. These allow to display max or mean projection instead of the default thin slice.

  • Removal of the “Orientation testing” (2D), and “Max projection” and “Sum projection” (3D) options in the “Actions” menu. The two functions that implemented this functionality, diporien and dipprojection, have also been removed.

  • A new function viewslice can be used to display any image (including tensor images and higher-dimensional images) in DIPviewer. This is an alternative way to examine images, but none of the tools to programmatically interact with images displayed through dipshow will work with this viewer.

• Configuration settings accessed through dipsetpref and dipgetpref have been changed since DIPimage 2:

  • Added settings:

    • 'DisplayFunction' can be set to either 'dipshow' (the default), or 'viewslice', and determines which of these functions is invoked by default when the dip_image/display method is invoked (see the DIPimage User Manual for more details).

  • Changed settings:

    • 'KeepDataType', which changes how the output data type for arithmetic operations is chosen, has the same intent but does not always make the same choice. For example the result is different when mixing signed and unsigned integers. (see the DIPimage User Manual for details on the current logic).

  • Removed settings:

    • 'BoundaryCondition', 'Truncation', and 'DerivativeFlavour', because relevant functions take these parameters as optional input arguments.

    • 'MorphologicalFlavour', as it didn’t seem useful (the associated function dip_morph_flavour has also been removed).

    • 'ComputationLimit', because image arithmetic is now always performed by DIPlib.

    • 'ConflictingPixelSize' and 'InconsistentPixelSize', because the DIPlib library keeps track of pixel sizes and handles these situations in a fixed manner.

    • 'CommandFilePath', because the DIPimage GUI no longer probes functions to put them in the menus.

    • 'DebugMode', as DIPlib stack traces are shown or not depending on a compile-time flag.

    • 'FFTtype', because DIPlib can optionally be compiled to use FFTW for the FFT.

    • 'FastSubscriptedAssignment', introduced recently in DIPimage 2.9, because the related functionality has not been ported over (yet?).

• Many filters now have a boundary condition parameter. In DIPimage 2, one would change the boundary condition through a global parameter, which no longer exists. If you never touched the global parameter, nothing should change for you. If you did change this global parameter in a program, you now need to pass the value to the relevant functions instead. See help boundary_condition.

• Many functions have been added to match new functionality in DIPlib, as well as previous functionality that was not accessible from MATLAB. Some old functions have gained additional parameters to expose more functionality; we tried to do so without breaking backwards compatibility.

• Some functions have changed in a way that is not backwards compatible, either by having a different interface or different behavior:

  • dilation_se, erosion_se, etc. are now folded into dilation, erosion, etc. For functions with an _se appended to the name, remove the _se. Alternatively, the alias sub-directory contains these names and forwards the calls to the correct functions.

  • rankmax_opening and rankmin_closing now have rank as the second parameter, instead of percentile. This should make them match the literature better, and make them more usable.

  • smooth is no longer relevant, moved to the alias directory. Use gaussf instead.

  • derivative has the 2^nd and 3^rd arguments switched, it makes more sense having the order first.

  • mdhistogram has fewer options, but should still be able to produce the same results as previously. In hist2image, the coords input is transposed w.r.t. previous versions, for consistency: each row is interpreted as a vertex.

  • ft now does normalization in the more common way (forward transform not normalized, inverse transform normalized by 1/N), but an option ('symmetric') allows to change the normalization to be consistent with DIPimage 2, which used a symmetric normalization scheme (both forward and backward transforms use 1/N^1/2).

  • resample and shift shift the image in the opposite direction from what it did in DIPimage 2, where the shift was unintuitive.

  • affine_trans rotates in the opposite direction it did before, to match the interpretation of angles in the rest of the toolbox. The function now also accepts an affine transformation matrix to direct the transformation. The function transform provided duplicate functionality and no longer exists. find_affine_trans no longer exists, as fmmatch provides a much better algorithm to do the same.

  • readim and writeim work differently now, in part because DIPlib natively supports fewer file types now. The file_info struct output for readim has changed somewhat. The last two input parameters to the old writeim are no longer supported (compression and physDim): to change the compression method, call writeics or writetiff directly; the pixel size is always given by the image, use dip_image/pixelsize to set it. readics and readtiff are the interfaces to the corresponding DIPlib file reading functions.

  • The AVI reading and writing functions readavi, writeavi and writedisplayavi depended on outdated MATLAB functionality and have been removed. You can use MATLAB’s video reading and writing capabilities, converting between standard MATLAB arrays and a dip_image is trivial.

  • countneighbours has been renamed to countneighbors for consistency in spelling.

  • mse, mae and several similar functions have been collected in a new function errormeasure. The old functions are still available in the alias sub-directory.

  • slice_in and slice_ex specify dimensions starting at 1 (not at 0 as previously). This change is for consistency with the rest of the toolbox. These functions now reorder dimensions in a way consistent with dip_image/squeeze (removing dimension 1 causes dimension 3 to become dimension 1), which is more efficient. slice_in, slice_ex and slice_op have been made into dip_image methods, for efficiency.

  • get_subpixel no longer supports the spline interpolation method, this string is still accepted, but selects the cubic method.

  • structuretensor3d has been moved to the alias directory, structuretensor now works for any number of dimensions (with special support for 2D and 3D images).

  • curvature_thirion and isophote_curvature have been moved to the alias directory. The function curvature now takes 'thirion' and 'isophote' as options. orientation4d has been moved to the alias directory. A new function orientation generalizes it to arbitrary dimensionality.

  • granulometry has changed, but it is still possible to call it the old way. However, the parameters in this old syntax are interpreted to match the new capabilities of this function. 'usegrey' and 'verbose' options no longer have an effect. Default values have changed a bit.

  • ht no longer exists. Use riesz instead. The Riesz transform is the multi-dimensional generalization of the 1D Hilbert transform. See also the new function monogenicsignal.

  • nconv no longer exists, the new function normconv will compute the normalized convolution with a Gaussian, as well as estimate first derivatives using a Gaussian normalized convolution.

  • dt has a new algorithm, which is used by default. It gives exact results and works for any number of dimensions, and it should be faster than the previous default algorithm. The old default algorithm can be executed with dt(...,'fast').

  • gdt has a new algorithm, which is used by default. It approximates Euclidean distances better. The old default algorithm can be executed with gdt(...,3). The second output image is no longer produced. A new, optional argument specifies a mask image to further constrain paths.

  • testobject has a changed interface, the input argument order has changed and most arguments are now name-value pairs. Its functionality has been greatly extended.

  • radoncircle and orientationspace have a different implementation with different capabilities and a different interface.

  • measurehelp is no longer a separate function. You can now do measure help or measure('help').

  • jacobi moved to the alias directory, the eig method has improved to make jacobi irrelevant.

• New functions not mentioned above: abssqr, areaclosing, areaopening, asf, cell2im, cluster, compactwaterseed, coordinates, cornerdetector, curlvector, distancedistribution, divergencevector, drawshape, extendregion, getmaximumandminimum, getsamplestatistics, im2cell, integral_image, lee, linedetector, loggabor, nonmaximumsuppression, pathclosing, pathopening, perobjecthist, psf, quantize, randomseeds, select, semivariogram, setborder, skew, smallobjectsremove, stochasticwatershed, superpixels, thetatheta, traceobjects, warp_subpixel, window, wrap. Use help <functionname> in MATLAB to learn what these functions provide.

• Old functions not (yet) ported: afm_flatten, arcf, backgroundoffset, cal_readnoise, change_chroma, change_gamma, change_xyz, color_rotation, correctshift, cpf, deblock, distancebetweenpointsets, dpr, find_lambda, findlocalshift, findlocmax, findospeaks, frc, gamut_destretch, gamut_mapping, gamut_stretch, huecorr, hybridf, iso_luminance_lines, jpeg_quality_score, lfmse, localshift, luminance_steered_dilation, luminance_steered_erosion, make_gamut, mappg, mcd, morphscales, nufft_type1, nufft_type2, opticflow, orientationplot, out_of_gamut, percf_adap, percf_adap_banana, plot_gamut, pst, quadraturetensor, rgb_to_border, rotation3d, scale2rgb, scalespace, splitandmerge, structf, tikhonovmiller, view5d, write_add. These functions will be ported as they are needed.

• Old functions that will not be ported: acquireim, dipmaxaspect, edir, fixlsmfile, fast_str2double, msr2ds, measure_gamma_monitor, mon_rgb2xyz, mon_xyz2rgb, monitor_icc, print_cmy2xyz, print_xyz2cmy, printer_icc, read_icc_profile, scan_rgb2xyz, scan_xyz2rgb, scanner_calibration, scanner_icc, spectra2xyz, write_icc_profile.

• Old functions that used to be in the alias directory are no longer. We recommend that you correct affected code, but if you want, you can always create those aliases again (copy the files from an older version of DIPimage).

• If you customized the menus in the DIPimage GUI, you will have to update your localdipmenus.m file. If you wrote your own functions that integrated in the GUI, you’ll have to do so through your localdipmenus.m now. Preference setting 'CommandFilePath' no longer exists, nor the associated function dipaddpath, only functions mentioned in dipmenus and localdipmenus are added to the menu system. Functions are no longer probed with 'DIP_GetParamList', their parameter descriptions are given by dipmenus and localdipmenus.

• getparams no longer exists. It was a nifty idea but incurred a large overhead. Each function now must do its own input parameter checking, for example through inputParser and/or validateattributes.