From 407fd80f9543775d8a6b94e5daee79b1aa0566dc Mon Sep 17 00:00:00 2001 From: Rémi Lacroix Date: Wed, 14 Jun 2023 21:29:41 +0200 Subject: ctffind: Add a patch to fix incorrect return types. (#38085) Prevent the code from crashing (cf. https://grigoriefflab.umassmed.edu/comment/1696#comment-1696). --- .../packages/ctffind/fix_return_types.patch | 34 ++++++++++++++++++++++ .../repos/builtin/packages/ctffind/package.py | 1 + 2 files changed, 35 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ctffind/fix_return_types.patch diff --git a/var/spack/repos/builtin/packages/ctffind/fix_return_types.patch b/var/spack/repos/builtin/packages/ctffind/fix_return_types.patch new file mode 100644 index 0000000000..6ec4b2f6cf --- /dev/null +++ b/var/spack/repos/builtin/packages/ctffind/fix_return_types.patch @@ -0,0 +1,34 @@ +--- a/src/programs/ctffind/ctffind.cpp 2023-06-02 16:47:21.975662000 +0200 ++++ b/src/programs/ctffind/ctffind.cpp 2023-06-02 16:48:06.565418037 +0200 +@@ -267,11 +267,11 @@ + float FindRotationalAlignmentBetweenTwoStacksOfImages(Image *self, Image *other_image, int number_of_images, float search_half_range, float search_step_size, float minimum_radius, float maximum_radius); + void ComputeImagesWithNumberOfExtremaAndCTFValues(CTF *ctf, Image *number_of_extrema, Image *ctf_values); + int ReturnSpectrumBinNumber(int number_of_bins, float number_of_extrema_profile[], Image *number_of_extrema, long address, Image *ctf_values, float ctf_values_profile[]); +-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]); ++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]); + void ComputeEquiPhaseAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Curve *epa_pre_max, Curve *epa_post_max); + void OverlayCTF( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins_in_1d_spectra, double spatial_frequency[], double rotational_average_astig[], float number_of_extrema_profile[], float ctf_values_profile[], Curve *equiphase_average_pre_max, Curve *equiphase_average_post_max); + void ComputeFRCBetween1DSpectrumAndFit( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[], double frc[], double frc_sigma[], int first_fit_bin); +-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ); ++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ); + void Renormalize1DSpectrumForFRC( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[]); + float ReturnAzimuthToUseFor1DPlots(CTF *ctf); + +@@ -2419,7 +2419,7 @@ + + // Rescale the spectrum and its 1D rotational avereage so that the peaks and troughs are at 0.0 and 1.0. The location of peaks and troughs are worked out + // by parsing the suppilied 1D average_fit array +-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ) ++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ) + { + MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); + MyDebugAssertTrue(number_of_bins > 1,"Bad number of bins: %i\n",number_of_bins); +@@ -2762,7 +2762,7 @@ + } + + // +-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[]) ++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[]) + { + MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); + MyDebugAssertTrue(number_of_extrema->is_in_memory,"Number of extrema image not allocated"); diff --git a/var/spack/repos/builtin/packages/ctffind/package.py b/var/spack/repos/builtin/packages/ctffind/package.py index 342ab8d194..a57833be16 100644 --- a/var/spack/repos/builtin/packages/ctffind/package.py +++ b/var/spack/repos/builtin/packages/ctffind/package.py @@ -34,6 +34,7 @@ class Ctffind(AutotoolsPackage): patch("configure.patch", when="@4.1.8") patch("power9.patch", when="@4.1.14 target=power9le") + patch("fix_return_types.patch", when="@4.1.13:4.1.14") def configure_args(self): config_args = [] -- cgit v1.2.3-70-g09d2