From: Takuo Yasunaga Date: Tue, 20 Dec 2022 18:09:56 +0000 (+0900) Subject: Please enter the commit message for your changes. Lines starting X-Git-Tag: v2.4.22p0372 X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=82d71f6decbe7d008c9a7354b41f5fedef6bd2dd;p=eos%2Fbase.git Please enter the commit message for your changes. Lines starting with '#' will be ignored, and an empty message aborts the commit. On branch master Your branch is up to date with 'origin/master'. Changes to be committed: modified: hostdepend/ARM64MAC64 modified: include/eosStarFile.h deleted: src/Objects/.DS_Store deleted: src/Objects/.Source.org deleted: src/Objects/DataExpress/.Source.org deleted: src/Objects/DataExpress/Makefile.org deleted: src/Objects/DataManip/.Source.org deleted: src/Objects/DataManip/Makefile.org modified: src/Objects/DataManip/eosStarFile/doc/eosStarFile.html modified: src/Objects/DataManip/eosStarFile/inc/eosStarFile.h deleted: src/Objects/General/Makefile.org modified: src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c modified: src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c modified: util/src/DataFormat/Makefile Changes not staged for commit: modified: hostdepend/ARM64MAC64 (new commits) modified: include/eosMATH.h --- diff --git a/hostdepend/ARM64MAC64 b/hostdepend/ARM64MAC64 index b8745dfd26..3f7dd8c2cc 160000 --- a/hostdepend/ARM64MAC64 +++ b/hostdepend/ARM64MAC64 @@ -1 +1 @@ -Subproject commit b8745dfd26b78656350495ca523e2608ddcb3bfb +Subproject commit 3f7dd8c2ccc4056ad9956e03de20fa4605de3ad4 diff --git a/include/eosStarFile.h b/include/eosStarFile.h index 2bce2dbff9..fb268bef0a 100644 --- a/include/eosStarFile.h +++ b/include/eosStarFile.h @@ -83,15 +83,17 @@ extern int* eosStarFileDataGetIntegerP(eosStarFile* star, char* block, char* key extern int eosStarFilDataGetInterger (eosStarFile* star, char* block, char* key, int* value, int mode); // Loop -char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode); +extern char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode); -double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode); +extern double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode); -int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode); +extern int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode); +// Write +extern void eosStarFileWrite(FILE* fpt, eosStarFile* star, int mode); /* prototype end */ #ifdef __cplusplus diff --git a/src/Objects/.DS_Store b/src/Objects/.DS_Store deleted file mode 100644 index e401ed964f..0000000000 Binary files a/src/Objects/.DS_Store and /dev/null differ diff --git a/src/Objects/.Source.org b/src/Objects/.Source.org deleted file mode 100644 index f1269bae9e..0000000000 --- a/src/Objects/.Source.org +++ /dev/null @@ -1,6 +0,0 @@ -SOURCE=\ -DataExpress \ -DataManip \ -General \ -MachineManip \ -#LastSource diff --git a/src/Objects/DataExpress/.Source.org b/src/Objects/DataExpress/.Source.org deleted file mode 100644 index c941e3d608..0000000000 --- a/src/Objects/DataExpress/.Source.org +++ /dev/null @@ -1,11 +0,0 @@ -SOURCE=\ -Contour \ -TclTk \ -avsFile \ -eosAlsa \ -eosOpenGL \ -eosRuby \ -gifFile \ -pngFile \ -psFile \ -#LastSource diff --git a/src/Objects/DataExpress/Makefile.org b/src/Objects/DataExpress/Makefile.org deleted file mode 100755 index b69f906c53..0000000000 --- a/src/Objects/DataExpress/Makefile.org +++ /dev/null @@ -1,6 +0,0 @@ -include ../../Config/Define.inc -include ../Config/Define.inc -include Config/Define.inc -include .Source - -include Config/Target.inc diff --git a/src/Objects/DataManip/.Source.org b/src/Objects/DataManip/.Source.org deleted file mode 100644 index 8c4a3e7f64..0000000000 --- a/src/Objects/DataManip/.Source.org +++ /dev/null @@ -1,25 +0,0 @@ -SOURCE=\ -DCDFile \ -IMAGIC \ -bildFile \ -bmpFile \ -ctfInfo \ -ctfforBayes \ -dmFile \ -dsn6File \ -emData \ -eosMATH \ -eosStarFile \ -khorosData \ -largeIP \ -llData \ -ltlgData \ -mapFile \ -mrcImage \ -mrcImageShape \ -pdbFile \ -rigakuImage \ -simulation \ -tgaFile \ -transform \ -#LastSource diff --git a/src/Objects/DataManip/Makefile.org b/src/Objects/DataManip/Makefile.org deleted file mode 100755 index b69f906c53..0000000000 --- a/src/Objects/DataManip/Makefile.org +++ /dev/null @@ -1,6 +0,0 @@ -include ../../Config/Define.inc -include ../Config/Define.inc -include Config/Define.inc -include .Source - -include Config/Target.inc diff --git a/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html b/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html index db46102eda..ffd575c2ae 100644 --- a/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html +++ b/src/Objects/DataManip/eosStarFile/doc/eosStarFile.html @@ -3,13 +3,6 @@

Information from source codes

-../src/eosStarFileDataGet.c:
-
-../src/eosStarFileLoopDataGet.c:
-
-../src/eosStarFileRead.c:
-
-../src/eosStarFileWrite.c:
@@ -101,15 +94,17 @@ extern int* eosStarFileDataGetIntegerP(eosStarFile* star, char* block, char* key extern int eosStarFilDataGetInterger (eosStarFile* star, char* block, char* key, int* value, int mode); // Loop -char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode); +extern char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode); -double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode); +extern double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode); -int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode); +extern int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode); +// Write +extern void eosStarFileWrite(FILE* fpt, eosStarFile* star, int mode); /* prototype end */ #ifdef __cplusplus diff --git a/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h b/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h index 2bce2dbff9..fb268bef0a 100644 --- a/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h +++ b/src/Objects/DataManip/eosStarFile/inc/eosStarFile.h @@ -83,15 +83,17 @@ extern int* eosStarFileDataGetIntegerP(eosStarFile* star, char* block, char* key extern int eosStarFilDataGetInterger (eosStarFile* star, char* block, char* key, int* value, int mode); // Loop -char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode); +extern char** eosStarFileLoopDataGetStringP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetString(eosStarFile* star, char* key, char*** value, int mode); -double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode); +extern double* eosStarFileLoopDataGetRealP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetReal(eosStarFile* star, char* key, double** value, int mode); -int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode); -void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode); +extern int* eosStarFileLoopDataGetIntergerP(eosStarFile* star, char* key, int mode); +extern void eosStarFileLoopDataGetInterger(eosStarFile* star, char* key, int** value, int mode); +// Write +extern void eosStarFileWrite(FILE* fpt, eosStarFile* star, int mode); /* prototype end */ #ifdef __cplusplus diff --git a/src/Objects/General/Makefile.org b/src/Objects/General/Makefile.org deleted file mode 100755 index b69f906c53..0000000000 --- a/src/Objects/General/Makefile.org +++ /dev/null @@ -1,6 +0,0 @@ -include ../../Config/Define.inc -include ../Config/Define.inc -include Config/Define.inc -include .Source - -include Config/Target.inc diff --git a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c index 5d4c587982..16a0ae25c2 100755 --- a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c +++ b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.c @@ -223,7 +223,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -282,7 +285,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -329,7 +335,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -395,7 +404,10 @@ lmrcImageAbnormalValueRemoveAllArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -443,7 +455,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -483,7 +498,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -548,7 +566,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -604,7 +625,10 @@ lmrcImageAbnormalValueRemoveHighValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -652,7 +676,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -693,7 +720,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -759,7 +789,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -815,7 +848,10 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out, } } fprintf(linfo->paramOut,"AbnormalValue: %f -> %f at %f %f %f\n", data, dst, x, y, z); - } + } else { + dst = data; + } + mrcPixelDataSet(out, x, y, z, dst, mrcPixelRePart); } } } @@ -827,7 +863,6 @@ lmrcImageAbnormalValueRemoveLowValueArea(mrcImage* out, break; } } - mrcPixelDataSet(out, x, y, z, data, mrcPixelRePart); return; } diff --git a/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c b/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c index c973322303..40be221f1a 100755 --- a/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c +++ b/src/Tools/mrcImage/mrcImageBlurByTemperatureFactor/src/mrcImageBlurByTemperatureFactor.c @@ -19,9 +19,14 @@ #include "genUtil.h" #include "mrcImage.h" +typedef struct atomInfo { + int nAtom; + mrcImageParaTypeRealCoord* coord; + mrcImageParaTypeReal* Temparature; +} atomInfo; + typedef struct lmrcImageBlurByTemperatureFactorInfo { - float a; - int b; + atomInfo } lmrcImageBlurByTemperatureFactorInfo; typedef enum lmrcImageBlurByTemperatureFactorMode { diff --git a/util/src/DataFormat/Makefile b/util/src/DataFormat/Makefile index 4b6129bb53..ffa5e98e79 100644 --- a/util/src/DataFormat/Makefile +++ b/util/src/DataFormat/Makefile @@ -7,6 +7,7 @@ help:: @echo "make pkg-config" @echo "make icu" @echo "make cif_api" + @echo "make libcif" HDF5-VERSION=1.13.0 HDF5-VERSION2=1-13-0 @@ -14,12 +15,12 @@ HDF5-VERSION3=1.12.1 PKG-CONFIG-VERSION=0.29.2 - target:: make pkg-config make icu make hdf5 make cif_api + make libcif init:: init-hdf5 init-cif_api init-icu @@ -98,3 +99,12 @@ clean-hdf5:: cleanAll-hdf5:: rm -f hdf5-$(HDF5-VERSION3).tar.gz; rm -rf hdf5-$(HDF5-VERSION3) +libcif: + make init-libcif + make config-libcif + make all-libcif + make clean-libcif + make cleanAll-libcif + +init-libcif: + git clone https://github.com/ElectronicStructureLibrary/libcif.git