Changeset 3144

Timestamp:

Oct 30, 2017 3:39:15 PM (5 years ago)

Author:

vondreele

Message:

fix MAR345 & CBF importers to work for python 3.6 as well as python 2.7; revised importers & new fortran decompression routines for py3.

Location:

trunk

Files:

• fsource/pack_f.for (modified) (4 diffs)
• fsource/unpack_cbf.for (modified) (1 diff)
• imports/G2img_CBF.py (modified) (3 diffs)
• imports/G2img_MAR.py (modified) (1 diff)

trunk/fsource/pack_f.for

@@ -15 +15 @@
       INTEGER*4 SPILL,ROW,COL,PIXNUM,MM1
       INTEGER*2 TMP
-      LOGICAL*1 CMPR(0:N-1)
+      CHARACTER*1 CMPR(0:N-1)
       DATA BITDECODE /0,4,5,6,7,8,16,32/
       DATA SETBITS /Z'0000',Z'0001',Z'0003',Z'0007',
@@ -40 +40 @@
             SPILLBITS = 0
           ELSE
-            SPILL = CMPR(IN)
-C            SPILL = ICHAR(CMPR(IN))
+            SPILL = ICHAR(CMPR(IN))
             IN = IN+1
             SPILLBITS = 8
@@ -65 +64 @@
                 END IF
               ELSE
-                SPILL = CMPR(IN)
-C                SPILL = ICHAR(CMPR(IN))
+                SPILL = ICHAR(CMPR(IN))
                 IN = IN+1
                 SPILLBITS = 8
@@ -119 +117 @@
 
       
+      SUBROUTINE PACK_F3(N,CMPR,MX,MY,IMG)
+
+Cf2py intent(in) N
+Cf2py intent(in) CMPR
+Cf2py depend(N) CMPR
+Cf2py intent(in) MX
+Cf2py intent(in) MY
+Cf2py intent(in,out) IMG
+Cf2py depend(MX,MY) IMG
+
+      IMPLICIT NONE
+      INTEGER*4 BITDECODE(0:7),SETBITS(0:16),IN,N,MX,MY,BITNUM
+      INTEGER*4 PIXEL,SPILLBITS,USEDBITS,VALIDS,WINDOW,TOTAL
+      INTEGER*4 IMG(0:MX-1,0:MY-1),NEXTINT
+      INTEGER*4 SPILL,ROW,COL,PIXNUM,MM1
+      INTEGER*2 TMP
+      INTEGER*1 CMPR(0:N-1)
+      DATA BITDECODE /0,4,5,6,7,8,16,32/
+      DATA SETBITS /Z'0000',Z'0001',Z'0003',Z'0007',
+     1  Z'000F',Z'001F',Z'003F',Z'007F',Z'00FF',
+     1  Z'01FF',Z'03FF',Z'07FF',Z'0FFF',Z'1FFF',
+     1  Z'3FFF',Z'7FFF',Z'FFFF'/
+
+      PIXEL = 0
+      SPILLBITS = 0
+      SPILL = 0
+      USEDBITS = 0
+      VALIDS = 0
+      WINDOW = 0
+      ROW = 0
+      COL = 0
+      TOTAL = MX*MY
+      MM1 = MX-1
+      IN = 0
+      DO WHILE (PIXEL .LT. TOTAL)
+        IF (VALIDS .LT. 6) THEN
+          IF (SPILLBITS .GT. 0) THEN
+            WINDOW = IOR(WINDOW,ISHFT(SPILL,VALIDS))
+            VALIDS = VALIDS + SPILLBITS
+            SPILLBITS = 0
+          ELSE
+            SPILL = ICHAR(CHAR(CMPR(IN)))
+            IN = IN+1
+            SPILLBITS = 8
+          END IF
+        ELSE
+          PIXNUM = ISHFT(1,IAND(WINDOW,SETBITS(3)))
+          WINDOW = ISHFT(WINDOW,-3)
+          BITNUM = BITDECODE(IAND(WINDOW,SETBITS(3)))
+          WINDOW = ISHFT(WINDOW,-3)
+          VALIDS = VALIDS-6
+          DO WHILE ( (PIXNUM .GT. 0) .AND. (PIXEL .LT. TOTAL) )
+            IF ( VALIDS .LT. BITNUM ) THEN
+              IF ( SPILLBITS .GT. 0 ) THEN
+                WINDOW = IOR(WINDOW,ISHFT(SPILL,VALIDS))
+                IF ( (32-VALIDS) .GT. SPILLBITS ) THEN
+                  VALIDS = VALIDS + SPILLBITS
+                  SPILLBITS = 0
+                ELSE
+                  USEDBITS = 32-VALIDS
+                  SPILL = ISHFT(SPILL,-USEDBITS)
+                  SPILLBITS = SPILLBITS-USEDBITS
+                  VALIDS = 32
+                END IF
+              ELSE
+                SPILL = ICHAR(CHAR(CMPR(IN)))
+                IN = IN+1
+                SPILLBITS = 8
+              END IF                
+            ELSE
+              PIXNUM = PIXNUM-1
+              IF ( BITNUM .EQ. 0 ) THEN
+                NEXTINT = 0
+              ELSE
+                NEXTINT = IAND(WINDOW,SETBITS(BITNUM))
+                VALIDS = VALIDS-BITNUM
+                WINDOW = ISHFT(WINDOW,-BITNUM)
+                IF ( BTEST(NEXTINT,BITNUM-1) ) 
+     1            NEXTINT = IOR(NEXTINT,NOT(SETBITS(BITNUM)))
+              END IF
+
+              ROW = PIXEL/MX
+              COL = MOD(PIXEL,MX)
+              IF ( PIXEL .GT. MX ) THEN
+                IF ( COL .EQ. 0 ) THEN
+                  TMP = NEXTINT +
+     1              (IMG(MM1,ROW-1)+IMG(COL+1,ROW-1)+
+     1              IMG(COL,ROW-1)+IMG(MM1,ROW-2) +2)/4
+                ELSE IF ( COL.EQ.MM1 ) THEN
+                  TMP = NEXTINT +
+     1              (IMG(COL-1,ROW)+IMG(0,ROW)+
+     1              IMG(MM1,ROW-1)+IMG(MM1-1,ROW-1) +2)/4
+                ELSE
+                  TMP = NEXTINT + 
+     1              (IMG(COL-1,ROW)+IMG(COL+1,ROW-1)+
+     1              IMG(COL,ROW-1)+IMG(COL-1,ROW-1) +2)/4
+                END IF
+              ELSE IF (PIXEL .NE. 0) THEN
+                TMP = IMG(COL-1,ROW)+NEXTINT
+              ELSE
+                TMP = NEXTINT
+              END IF
+              IMG(COL,ROW) = TMP
+              PIXEL = PIXEL+1
+            END IF
+          END DO
+        END IF      
+      END DO
+      DO ROW=0,MM1
+        DO COL=0,MM1
+            IF ( IMG(COL,ROW).LT.0 ) IMG(COL,ROW) = IMG(COL,ROW)+65536
+        END DO
+      END DO
+      
+      RETURN
+      END
+

trunk/fsource/unpack_cbf.for

@@ -68 +68 @@
       END
 
-      
+      SUBROUTINE UNPACK_CBF3(N,CMPR,MXY,IMG)
+
+Cf2py intent(in) N
+Cf2py intent(in) CMPR
+Cf2py depend(N) CMPR
+Cf2py intent(in) MXY
+Cf2py intent(in,out) IMG
+Cf2py depend(MXY) IMG
+
+      IMPLICIT NONE
+      INTEGER*4 N,MXY
+      INTEGER*1 CMPR(0:N-1)
+      INTEGER*4 IMG(0:MXY-1),BASEPIXEL
+      INTEGER*4 I,J,ISIZE
+      CHARACTER*1 C1,E1
+      CHARACTER*2 C2,E2
+      CHARACTER*4 C4,E4
+      INTEGER*1 IONEBYTE
+      INTEGER*2 ITWOBYTES
+      INTEGER*4 IFOURBYTES
+
+      E1 = CHAR(128)
+      E2 = CHAR(0)//CHAR(128)
+      E4 = CHAR(0)//CHAR(0)//CHAR(0)//CHAR(128)
+
+      I = 0
+      J = 0
+      BASEPIXEL = 0
+      DO WHILE ( I.LT.N )
+        C1 = CHAR(CMPR(I))
+        ISIZE = 1
+        IF ( C1.EQ.E1 ) THEN
+           ISIZE = 2
+           I = I+1
+           C2 = CHAR(CMPR(I))//CHAR(CMPR(I+1))
+           IF ( C2.EQ.E2 ) THEN
+              ISIZE = 4
+              I = I+2
+              C4 = CHAR(CMPR(I))//CHAR(CMPR(I+1))//
+     1            CHAR(CMPR(I+2))//CHAR(CMPR(I+3))
+              IF ( C4.EQ.E4 ) THEN
+                 ISIZE = 8
+                 I = I+4
+              END IF
+           END IF
+        END IF
+        IF ( ISIZE .EQ. 1 ) THEN
+           IONEBYTE = ICHAR(CHAR(CMPR(I)))
+           I = I+1
+           BASEPIXEL = BASEPIXEL+IONEBYTE
+        ELSE IF ( ISIZE .EQ. 2 ) THEN
+           ITWOBYTES = ICHAR(CHAR(CMPR(I)))
+           ITWOBYTES = ITWOBYTES+ISHFT(ICHAR(CHAR(CMPR(I+1))),8)
+           I = I+2
+           BASEPIXEL = BASEPIXEL+ITWOBYTES
+        ELSE IF ( ISIZE.EQ.4 ) THEN
+           IFOURBYTES = ICHAR(CHAR(CMPR(I)))
+           IFOURBYTES = IFOURBYTES+ISHFT(ICHAR(CHAR(CMPR(I+1))),8)
+           IFOURBYTES = IFOURBYTES+ISHFT(ICHAR(CHAR(CMPR(I+2))),16)
+           IFOURBYTES = IFOURBYTES+ISHFT(ICHAR(CHAR(CMPR(I+3))),24)
+           I = I+4
+           BASEPIXEL = BASEPIXEL+IFOURBYTES
+        END IF
+c        IF ( MOD(J,100000).EQ.0 ) PRINT *,I,J,BASEPIXEL
+        IMG(J) = BASEPIXEL
+        J = J+1
+      END DO
+      RETURN
+      END

trunk/imports/G2img_CBF.py

@@ -17 +17 @@
 import GSASIIobj as G2obj
 import GSASIIpath
+import struct as st
+import numpy as np
 import unpack_cbf as cbf
 GSASIIpath.SetVersionNumber("$Revision: 2133 $")
@@ -48 +50 @@
     'Read cif binarydetector data cbf file'
     
-    import numpy as np
     if GSASIIpath.GetConfigValue('debug'):
         print ('Read cif binary detector data cbf file: '+filename)
@@ -95 +96 @@
     img = File.read()[imageBeg:imageBeg+compImageSize]
     nimg = len(img)
-    if 'bytes' in str(type(img)):
-        img = np.array(img,dtype='a')
     image = np.zeros(nxy,dtype=np.int32)
     time0 = time.time()
-#    GSASIIpath.IPyBreak()
-    image = cbf.unpack_cbf(nimg,img,nxy,image)
+    if 'bytes' in str(type(img)):
+        img = np.frombuffer(img,dtype=np.uint8)
+        image = cbf.unpack_cbf3(nimg,img,nxy,image)
+    else:
+        image = cbf.unpack_cbf(nimg,img,nxy,image)
     image = np.reshape(image,(sizexy[1],sizexy[0]))
     print ('import time: %.3f'%(time.time()-time0))

trunk/imports/G2img_MAR.py

@@ -89 +89 @@
     pos += 37
     File.seek(pos)
+    image = np.zeros(shape=(sizex,sizey),dtype=np.int32)    
     if '2' in platform.python_version_tuple()[0]:
         raw = File.read()
+        image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T)  #transpose to get it right way around & flip
     else:
-        raw = File.read()
-        print (type(raw),sys.getsizeof(raw),raw[:10])
-    image = np.zeros(shape=(sizex,sizey),dtype=np.int32)    
-    image = np.flipud(pf.pack_f(len(raw),raw,sizex,sizey,image).T)  #transpose to get it right way around & flip
+        raw = np.frombuffer(File.read(),dtype=np.uint8)
+        image = np.flipud(pf.pack_f3(len(raw),raw,sizex,sizey,image).T)  #transpose to get it right way around & flip
     File.close()
     if imageOnly: