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ctffind: Add a patch to fix incorrect return types. (#38085)

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Prevent the code from crashing (cf. https://grigoriefflab.umassmed.edu/comment/1696#comment-1696).
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Rémi Lacroix 2023-06-14 21:29:41 +02:00 committed by GitHub
parent 62525d9076
commit 407fd80f95
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GPG Key ID: 4AEE18F83AFDEB23
2 changed files with 35 additions and 0 deletions
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34
var/spack/repos/builtin/packages/ctffind/fix_return_types.patch Normal file
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@ -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");

1
var/spack/repos/builtin/packages/ctffind/package.py
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@ -34,6 +34,7 @@ def url_for_version(self, version):
patch("configure.patch", when="@4.1.8") patch("configure.patch", when="@4.1.8")
patch("power9.patch", when="@4.1.14 target=power9le") 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): def configure_args(self):
config_args = [] config_args = []