From a7d4db84e8283ceb08e5d80b178cb98e106e91b0 Mon Sep 17 00:00:00 2001
From: Takuo Yasunaga <yasuanga@phys.kyutech.ac.jp>
Date: Mon, 11 Apr 2022 12:16:07 +0900
Subject: [PATCH]  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:   lib/ARM64MAC64/libEosObjects.a
	modified:   lib/ARM64MAC64/shared/pdbTrans.sharedo
	modified:   src/Objects/DataManip/pdbFile/src/pdbTrans.c
	modified:   src/Tools/filter/mrc2hdf/src/mrc2hdf.c
	modified:   src/Tools/filter/mrc2hdf/src/test/Makefile
	modified:   src/Tools/pdbUtil/pdbMove/src/pdbMove.html

 Changes not staged for commit:
	modified:   hostdepend/ARM64MAC64 (modified content)
	modified:   include/eosMATH.h
---
 hostdepend/ARM64MAC64                        |   2 +-
 lib/ARM64MAC64/libEosObjects.a               | Bin 1852312 -> 1852440 bytes
 lib/ARM64MAC64/shared/pdbTrans.sharedo       | Bin 1840 -> 1944 bytes
 src/Objects/DataManip/pdbFile/src/pdbTrans.c |   4 ++
 src/Tools/filter/mrc2hdf/src/mrc2hdf.c       |  54 +++++++++++++++++++--------
 src/Tools/filter/mrc2hdf/src/test/Makefile   |  21 ++++++++---
 src/Tools/pdbUtil/pdbMove/src/pdbMove.html   |  29 +++++++++++++-
 7 files changed, 87 insertions(+), 23 deletions(-)

diff --git a/hostdepend/ARM64MAC64 b/hostdepend/ARM64MAC64
index d7d0a0af3d..7c875f6f9d 160000
--- a/hostdepend/ARM64MAC64
+++ b/hostdepend/ARM64MAC64
@@ -1 +1 @@
-Subproject commit d7d0a0af3d76f7d933680dadefa4dcea06eadb83
+Subproject commit 7c875f6f9d1e61278a3839fbb3e1af4753cfb36a
diff --git a/lib/ARM64MAC64/libEosObjects.a b/lib/ARM64MAC64/libEosObjects.a
index c4f05a2fc3bd980be5ac79323429d977e2561266..b4d1717e3898d1764d21c497036712bd7db616cf 100644
GIT binary patch
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diff --git a/lib/ARM64MAC64/shared/pdbTrans.sharedo b/lib/ARM64MAC64/shared/pdbTrans.sharedo
index 7de70c32650f45e4608c284d8747e911ce75fa55..9f95db390ddf3e9c4df85df0aa046df2c19b784c 100644
GIT binary patch
delta 627
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YO7M+1B@09>axiuyBgVEw+*rfWA8=nkQvd(}

delta 553
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diff --git a/src/Objects/DataManip/pdbFile/src/pdbTrans.c b/src/Objects/DataManip/pdbFile/src/pdbTrans.c
index 26dd67a359..5223212ac9 100755
--- a/src/Objects/DataManip/pdbFile/src/pdbTrans.c
+++ b/src/Objects/DataManip/pdbFile/src/pdbTrans.c
@@ -42,6 +42,10 @@ pdbMatrixFileWrite(FILE* fpt, Matrix3D Matrix)
 	matrix3DFileWrite(fpt, Matrix);
 }
 
+#ifndef CUDA
+int __eosCuda__ = 0;
+#endif
+
 void
 pdbTrans(pdbFile* pdb, Matrix3D Matrix)
 {
diff --git a/src/Tools/filter/mrc2hdf/src/mrc2hdf.c b/src/Tools/filter/mrc2hdf/src/mrc2hdf.c
index 439748a8be..5617839d9b 100755
--- a/src/Tools/filter/mrc2hdf/src/mrc2hdf.c
+++ b/src/Tools/filter/mrc2hdf/src/mrc2hdf.c
@@ -481,37 +481,61 @@ lmrc2hdfimaris(hid_t* out, mrcImage* in, lmrc2hdfInfo* linfo, int mode)
         char* dsiGroupName[] = {"Channel 0", "Image", "Imaris", "ImarisDataSet", "Log", "TImeInfo"};
         int dsiNGroup = 6;
         hid_t dsiGroupID[dsiNGroup];
+        hid_t tmpdsiGroupID;
 
         for(i=0; i<dsiNGroup; i++) {
             sprintf(stmp, "%s/%s", groupName[1], dsiGroupName[i]);
             dsiGroupID[i] = H5Gcreate2(*out, stmp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
         }
         // Channel 0
-        lhdfAttributeString(dsiGroupID[0], "Name", "No");
-        lhdfAttributeString(dsiGroupID[0], "Color", "1.000 0.000 0.000");
-        lhdfAttributeString(dsiGroupID[0], "ColorMode", "BaseColor");
-        lhdfAttributeReal2String(dsiGroupID[0], "ColorOpacity", 1.000);
-        lhdfAttributeReal2String(dsiGroupID[0], "Min", in[0].HeaderAMax);
-        lhdfAttributeReal2String(dsiGroupID[0], "Max", in[0].HeaderAMin);
+        if(linfo->flagIn) {
+            lhdfAttributeString(dsiGroupID[0], "Name", "No");
+            sprintf(stmp, "%f %f %f", linfo->inColor[0], linfo->inColor[1], linfo->inColor[2]);
+            lhdfAttributeString(dsiGroupID[0], "Color", stmp);
+            lhdfAttributeString(dsiGroupID[0], "ColorMode", "BaseColor");
+            lhdfAttributeReal2String(dsiGroupID[0], "ColorOpacity", linfo->inColor[3]);
+            lhdfAttributeReal2String(dsiGroupID[0], "Min", in[0].HeaderAMin);
+            lhdfAttributeReal2String(dsiGroupID[0], "Max", in[0].HeaderAMax);
+        }
+        if(linfo->flagIn2) {
+            sprintf(stmp, "%s/%s", groupName[1], "Channel 1");
+            tmpdsiGroupID = H5Gcreate2(*out, stmp, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+            lhdfAttributeString(tmpdsiGroupID, "Name", "No");
+            sprintf(stmp, "%f %f %f", linfo->in2Color[0], linfo->in2Color[1], linfo->in2Color[2]);
+            lhdfAttributeString(tmpdsiGroupID, "Color", stmp);
+            lhdfAttributeString(tmpdsiGroupID, "ColorMode", "BaseColor");
+            lhdfAttributeReal2String(tmpdsiGroupID, "ColorOpacity", linfo->in2Color[3]);
+            lhdfAttributeReal2String(tmpdsiGroupID, "Min", linfo->in2[0].HeaderAMin);
+            lhdfAttributeReal2String(tmpdsiGroupID, "Max", linfo->in2[0].HeaderAMax);
+            status = H5Gclose(tmpdsiGroupID);
+        }
         // Image
         lhdfAttributeString(dsiGroupID[1], "Description", "No");
         lhdfAttributeString(dsiGroupID[1], "Name", "No");
         lhdfAttributeInt2String(dsiGroupID[1], "Noc", 1);
-        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin0", in[0].HeaderStartN.x*in[0].HeaderLength.x);
-        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin1", in[0].HeaderStartN.y*in[0].HeaderLength.y);
-        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin2", in[0].HeaderStartN.z*in[0].HeaderLength.z);
-        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax0", (in[0].HeaderStartN.x+dims[2]-1)*in[0].HeaderLength.x);
-        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax1", (in[0].HeaderStartN.y+dims[1]-1)*in[0].HeaderLength.y);
-        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax2", (in[0].HeaderStartN.z+dims[0]-1)*in[0].HeaderLength.z);
+        /*
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin0", linfo->in[0].HeaderStartN.x*linfo->in[0].HeaderLength.x);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin1", linfo->in[0].HeaderStartN.y*linfo->in[0].HeaderLength.y);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin2", linfo->in[0].HeaderStartN.z*linfo->in[0].HeaderLength.z);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax0", (linfo->in[0].HeaderStartN.x+linfo->in[0].HeaderN.x-1)*linfo->in[0].HeaderLength.x);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax1", (linfo->in[0].HeaderStartN.y+linfo->in[0].HeaderN.y-1)*linfo->in[0].HeaderLength.y);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax2", (linfo->in[0].HeaderStartN.z+linfo->in[0].HeaderN.z-1)*linfo->in[0].HeaderLength.z);
+        */
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin0", 0*linfo->in[0].HeaderLength.x);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin1", 0*linfo->in[0].HeaderLength.y);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMin2", 0*linfo->in[0].HeaderLength.z);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax0", (0+linfo->in[0].HeaderN.x-1)*linfo->in[0].HeaderLength.x);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax1", (0+linfo->in[0].HeaderN.y-1)*linfo->in[0].HeaderLength.y);
+        lhdfAttributeReal2String(dsiGroupID[1], "ExtMax2", (0+linfo->in[0].HeaderN.z-1)*linfo->in[0].HeaderLength.z);
         if(1<nres) {
             lhdfAttributeString(dsiGroupID[1], "ResampleDimensionX", "true");
             lhdfAttributeString(dsiGroupID[1], "ResampleDimensionY", "true");
             lhdfAttributeString(dsiGroupID[1], "ResampleDimensionZ", "true");
         }
         lhdfAttributeString(dsiGroupID[1], "Unit", "um");
-        lhdfAttributeInt2String(dsiGroupID[1], "X", dims[2]);
-        lhdfAttributeInt2String(dsiGroupID[1], "Y", dims[1]);
-        lhdfAttributeInt2String(dsiGroupID[1], "Z", dims[0]);
+        lhdfAttributeInt2String(dsiGroupID[1], "X", linfo->in[0].HeaderN.x);
+        lhdfAttributeInt2String(dsiGroupID[1], "Y", linfo->in[0].HeaderN.y);
+        lhdfAttributeInt2String(dsiGroupID[1], "Z", linfo->in[0].HeaderN.z);
         // Imaris 
         lhdfAttributeString(dsiGroupID[2], "Version", "5,5");
         // ImarisDataSet        
diff --git a/src/Tools/filter/mrc2hdf/src/test/Makefile b/src/Tools/filter/mrc2hdf/src/test/Makefile
index 548ef7f6bb..5754f97b50 100755
--- a/src/Tools/filter/mrc2hdf/src/test/Makefile
+++ b/src/Tools/filter/mrc2hdf/src/test/Makefile
@@ -9,27 +9,36 @@ help:
 	@echo "----- Help Message Check -----"
 	@../$(OSTYPE)/$(OBJECTNAME)	 -h
 
-exec: data/test.ims data/test2.ims data/test-5.ims data/test2-5.ims data/test4.ims
+init::
+	pdbMove -i data/4xvr.pdb -o data/test.pdb -GCtoOrigin
+	pdb2mrc -i data/test.pdb -o data/test.mrc -nx 64 -ny 64 -nz 64 -Sx -32 -Sy -32 -Sz -32 -dx 1 -dy 1 -dz 1 -sig 1.8
+
+exec: data/test.ims data/test2.ims data/test-5.ims data/test2-5.ims data/test4.ims data/test2-2.ims
 	@echo "----- Execution End -----"
+	ls -l data/*.ims
 
 
-data/test.ims:data/test.mrc
+data/test.ims:data/test.mrc ../$(OSTYPE)/$(OBJECTNAME)
 	rm -rf data/test.ims 
 	../$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc -o data/test.ims
 
-data/test-5.ims:data/test.mrc
+data/test-5.ims:data/test.mrc ../$(OSTYPE)/$(OBJECTNAME)
 	rm -rf data/test-5.ims 
 	../$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc -o data/test-5.ims -nres 5
 
-data/test2.ims:data/test.mrc
+data/test2.ims:data/test.mrc ../$(OSTYPE)/$(OBJECTNAME)
 	rm -rf data/test2.ims 
 	../$(OSTYPE)/$(OBJECTNAME) -I data/test.lst -o data/test2.ims
 
-data/test4.ims:data/test.mrc
+data/test2-2.ims:data/test.mrc ../$(OSTYPE)/$(OBJECTNAME)
+	rm -rf data/test2-2.ims 
+	../$(OSTYPE)/$(OBJECTNAME) -I data/test.lst -I2 data/test.lst -o data/test2-2.ims
+
+data/test4.ims:data/test.mrc ../$(OSTYPE)/$(OBJECTNAME)
 	rm -rf data/test4.ims 
 	../$(OSTYPE)/$(OBJECTNAME) -I data/test4.lst -o data/test4.ims
 
-data/test2-5.ims:data/test.mrc
+data/test2-5.ims:data/test.mrc ../$(OSTYPE)/$(OBJECTNAME)
 	rm -rf data/test2-5.ims 
 	../$(OSTYPE)/$(OBJECTNAME) -I data/test.lst -o data/test2-5.ims -nres 4
 
diff --git a/src/Tools/pdbUtil/pdbMove/src/pdbMove.html b/src/Tools/pdbUtil/pdbMove/src/pdbMove.html
index 9a2b54e921..4b6f1f19a8 100755
--- a/src/Tools/pdbUtil/pdbMove/src/pdbMove.html
+++ b/src/Tools/pdbUtil/pdbMove/src/pdbMove.html
@@ -1 +1,28 @@
-/bin/bash: pdbMove: No such file or directory
+<HTML>
+<HEAD>
+<TITLE>pdbMove</TITLE>
+</HEAD>
+<BODY>
+<H1>pdbMove</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: pdbMove
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
+    [-x                  X                   (0.0       ).as(Real                ) ] :Optional  :Move X[A]
+    [-y                  Y                   (0.0       ).as(Real                ) ] :Optional  :Move Y[A]
+    [-z                  Z                   (0.0       ).as(Real                ) ] :Optional  :Move Z[A]
+    [-originTo           toX                 (0.0       ).as(Real                ) 
+                         toY                 (0.0       ).as(Real                ) 
+                         toZ                 (0.0       ).as(Real                ) ] :Optional  :move (0,0,0) to (X,Y,Z)
+    [-toOrigin           fromX               (0.0       ).as(Real                ) 
+                         fromY               (0.0       ).as(Real                ) 
+                         fromZ               (0.0       ).as(Real                ) ] :Optional  :move (X,Y,Z) to (0,0,0)
+    [-GCtoOrigin                                                                   ] :Optional  :GC(Gravity Centre) to origin
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>
-- 
2.11.0