Initial commit (38f25a5) - plClump4p · Pawel Netzel

Initial commit

netzel commited on 2024-02-21 22:59:53
Showing 8 changed files, with 1524 additions and 0 deletions.

Makefile 0000000..a6d09ee
Makefile.win 0000000..137920c
clump.c 0000000..e5e3dec
data.c 0000000..7f171e8
data.h 0000000..535408a
gpl-3.0.txt 0000000..94a9ed0
main.c 0000000..e665b88
main.h 0000000..ae3d031

Makefile

...	...	@@ -0,0 +1,28 @@
	1	+
	2	+PROG = plclump4p
	3	+
	4	+CC = gcc
	5	+
	6	+CFLAGS=-Wall -O3 -fopenmp -msse2 -mfpmath=sse -Wl,-rpath,'$$ORIGIN/' -I/usr/include/gdal -lgdal -lezgdal -largtable3 -lm
	7	+
	8	+COMMON_C = $(shell ls *.c)
	9	+COMMON_C_O = $(COMMON_C:%.c=%.o)
	10	+
	11	+ifndef PREFIX
	12	+ PREFIX = /usr/local
	13	+endif
	14	+
	15	+
	16	+default: $(PROG)
	17	+
	18	+$(PROG): $(COMMON_C_O) $(HEADERS)
	19	+ $(CC) $(CFLAGS) -o $(PROG) $(COMMON_O) $(COMMON_C_O)
	20	+
	21	+$(COMMON_C_O): $(COMMON_C) $(HEADERS_C)
	22	+ $(CC) $(CFLAGS) -c $(COMMON_C)
	23	+
	24	+install:
	25	+ cp -f $(PROG) $(PREFIX)/bin
	26	+
	27	+clean:
	28	+ rm -f *.o $(PROG)

Makefile.win

View file @ 38f25a5

...	...	@@ -0,0 +1,20 @@
	1	+PROG = plclump4p.exe
	2	+
	3	+CC = x86_64-w64-mingw32-gcc
	4	+
	5	+CFLAGS= -I../../Win64_cross/gdal/include -I../../Win64_cross/ezgdal -I../../Win64_cross/argtable3 -L../../Win64_cross/argtable3 -L../../Win64_cross/gdal/bin -L../../Win64_cross/ezgdal -Wall -O3 -fopenmp -msse2 -mfpmath=sse -lgdal -llibezgdal -llibargtable3 -lm
	6	+
	7	+COMMON_C = $(shell ls *.c)
	8	+COMMON_C_O = $(COMMON_C:%.c=%.o)
	9	+HEADERS = $(shell ls *.h)
	10	+
	11	+default: $(PROG)
	12	+
	13	+$(PROG): $(COMMON_C_O) $(HEADERS)
	14	+ $(CC) $(CFLAGS) -o $(PROG) $(COMMON_C_O)
	15	+
	16	+$(COMMON_C_O): $(COMMON_C) $(HEADERS)
	17	+ $(CC) $(CFLAGS) -c $(COMMON_C)
	18	+
	19	+clean:
	20	+ rm -f *.o $(PROG)

clump.c

View file @ 38f25a5

...	...	@@ -0,0 +1,380 @@
	1	+/****************************************************************************
	2	+ *
	3	+ * PROGRAM: clump4p
	4	+ *
	5	+ * AUTHOR(S): Pawel Netzel - SIL UC
	6	+ * Jarek Jasiewicz - SIL UC
	7	+ * (the clumping algorithm for a region)
	8	+ *
	9	+ * PURPOSE: Recategorizes data in a raster map layer by grouping cells
	10	+ * that form physically discrete areas into unique categories.
	11	+ *
	12	+ * COPYRIGHT: (C) 2012 by Pawel Netzel
	13	+ *
	14	+ * This program is a free software under the GNU General Public
	15	+ * License (>=v2).
	16	+ *
	17	+ ***************************************************************************/
	18	+
	19	+#include <stdio.h>
	20	+#include <string.h>
	21	+#include <time.h>
	22	+#include <gdal.h>
	23	+#include <ezgdal.h>
	24	+#include <omp.h>
	25	+#include "main.h"
	26	+#include "data.h"
	27	+
	28	+static int nextr[] = {-1, 0, 1, 0 ,-1, 1,-1, 1};
	29	+static int nextc[] = { 0,-1, 0, 1 ,-1, 1, 1,-1};
	30	+
	31	+#define NR(x) 1 + r + nextr[(x)]
	32	+#define NC(x) 1 + c + nextc[(x)]
	33	+#define INDEX(r,c) ((r)-1)*ncols+(c)-1
	34	+
	35	+
	36	+void clumpRegion(int regionNum, int nDirections) {
	37	+
	38	+ int** map;
	39	+ int** map_clump;
	40	+ int nrows;
	41	+ int ncols;
	42	+ int colMax,colMin;
	43	+
	44	+ unsigned current_clump, index, i;
	45	+ unsigned row, col, r, c;
	46	+ int last, first, next_r, next_c;
	47	+ //double sum=0;
	48	+ unsigned* queue;
	49	+
	50	+ /* The size of the region */
	51	+ colMin=regions[regionNum].colMin;
	52	+ colMax=regions[regionNum].colMax;
	53	+ ncols=colMax-colMin+1;
	54	+ nrows=regions[regionNum].rowMax-regions[regionNum].rowMin+1;
	55	+
	56	+ /* Allocating memory and copying input data */
	57	+ queue=(unsigned)malloc((nrows+2)(ncols+2)*sizeof(unsigned));
	58	+ map=malloc((nrows+2)sizeof(int));
	59	+ map_clump=malloc((nrows+2)sizeof(int));
	60	+ map_clump[0]=calloc(ncols+2,sizeof(int));
	61	+ map_clump[nrows+1]=calloc(ncols+2,sizeof(int));
	62	+ map[0]=calloc(ncols+2,sizeof(int));
	63	+ map[nrows+1]=calloc(ncols+2,sizeof(int));
	64	+ for(r=1; r<=nrows; r++) {
	65	+ map_clump[r]=calloc(ncols+2,sizeof(int));
	66	+ map[r]=calloc(ncols+2,sizeof(int));
	67	+ // Data copying
	68	+ memcpy(map[r]+1,dataBuffer[r-1]+colMin,ncols*sizeof(int));
	69	+ }
	70	+
	71	+ /* start clumping */
	72	+ current_clump=0;
	73	+ for(row=1;row<=nrows;row++)
	74	+ for(col=1;col<=ncols;col++) {
	75	+ if(map_clump[row][col] \|\| !map[row][col]) /* NULL == 0 */
	76	+ continue;
	77	+ current_clump++;
	78	+ map_clump[row][col]=current_clump;
	79	+ last=1;
	80	+ first=0;
	81	+ queue[first]=INDEX(row,col);
	82	+ do {
	83	+ index=queue[first++];
	84	+ r=index/ncols;
	85	+ c=index%ncols;
	86	+ for(i=0; i<nDirections; i++) {
	87	+ next_r=NR(i);
	88	+ next_c=NC(i);
	89	+ if(map[r+1][c+1]==map[next_r][next_c]) {
	90	+ if(!map_clump[next_r][next_c]) {
	91	+ map_clump[next_r][next_c]=current_clump;
	92	+ queue[last++]=INDEX(next_r,next_c);
	93	+ }
	94	+ }
	95	+ }
	96	+ } while(first!=last);
	97	+ }
	98	+
	99	+ /* Creating labels list */
	100	+ if(current_clump>INCR) {
	101	+ free(regions[regionNum].labels);
	102	+ regions[regionNum].labels=(int )malloc((current_clump+2)sizeof(int));
	103	+ }
	104	+ for(i=1; i<=current_clump; i++)
	105	+ regions[regionNum].labels[i]=i+1;
	106	+ regions[regionNum].nLabels=current_clump;
	107	+
	108	+ /* Copying resultant map of clumps */
	109	+ for(r=1;r<=nrows;r++)
	110	+ memcpy(resultBuffer[r-1]+colMin,map_clump[r]+1,ncols*sizeof(int));
	111	+
	112	+ /* Releasing memmory */
	113	+ for(r=0;r<=nrows+1;r++) {
	114	+ free(map[r]);
	115	+ free(map_clump[r]);
	116	+ }
	117	+ free(map);
	118	+ free(map_clump);
	119	+ free(queue);
	120	+}
	121	+
	122	+void shiftLablesForRegion(int regionNum) {
	123	+
	124	+ int i,nLabels;
	125	+ int lbl,maxLbl, *labels;
	126	+
	127	+ labels=regions[regionNum].labels;
	128	+ nLabels=regions[regionNum].nLabels;
	129	+ maxLbl=0;
	130	+ for(i=1; i<=nLabels; i++) {
	131	+ lbl=labels[i];
	132	+ labels[i]+=totalIndex;
	133	+ if(lbl>maxLbl)
	134	+ maxLbl=lbl;
	135	+ }
	136	+ totalIndex+=maxLbl;
	137	+}
	138	+
	139	+void resolveEquivalence(int labelP, int regionP, int labelQ, int regionQ) {
	140	+ int idxP,idxQ,maxLab, minLab,n;//,*kLabels;
	141	+ int j,k;
	142	+ Region* reg;
	143	+ int* lab;
	144	+
	145	+ idxP=regions[regionP].labels[labelP];
	146	+ idxQ=regions[regionQ].labels[labelQ];
	147	+ if(idxP!=idxQ) {
	148	+ maxLab=(idxP>idxQ)?idxP:idxQ;
	149	+ minLab=(idxP>idxQ)?idxQ:idxP;
	150	+
	151	+#pragma omp parallel for private(k,j,n,lab,reg) shared(maxLab,minLab,regions,regionP)
	152	+ for(k=0; k<=regionP; k++) {
	153	+ reg=regions+k;
	154	+ n=(*reg).nLabels;
	155	+ lab=(*reg).labels+1;
	156	+ if(k<regionP) reg++;
	157	+ for(j=1; j<=n; j++) {
	158	+ if(*lab>maxLab)
	159	+ (*lab)--;
	160	+ else if(*lab==maxLab)
	161	+ *lab=minLab;
	162	+ lab++;
	163	+ }
	164	+ }
	165	+ totalIndex--;
	166	+ }
	167	+}
	168	+
	169	+void merge4(int regionNum) {
	170	+ int colMin,colMax,i,j,n;
	171	+
	172	+ colMin=regions[regionNum].colMin;
	173	+ colMax=regions[regionNum].colMax;
	174	+ /* Left vertical border */
	175	+ if(colMin>0) {
	176	+ n=regions[regionNum].rowMax-regions[regionNum].rowMin+1;
	177	+ j=colMin-1;
	178	+ for(i=0; i<n; i++)
	179	+ if(resultBuffer[i][colMin]>0)
	180	+ if(resultBuffer[i][j]>0 && dataBuffer[i][j]==dataBuffer[i][colMin])
	181	+ resolveEquivalence(resultBuffer[i][colMin],regionNum,
	182	+ resultBuffer[i][j],regionNum-1);
	183	+ }
	184	+ /* Top horizontal border */
	185	+ if(regions[regionNum].rowMin>0)
	186	+ for(i=colMin; i<=colMax; i++) {
	187	+ if(resultBuffer[0][i]>0)
	188	+ if(borderResultBuffer[i]>0 && dataBuffer[0][i]==borderDataBuffer[i])
	189	+ resolveEquivalence(resultBuffer[0][i],regionNum,
	190	+ borderResultBuffer[i],
	191	+ regions[regionNum].regionUp);
	192	+ }
	193	+}
	194	+
	195	+void merge8(int regionNum) {
	196	+ int colMin,colMax,i,j,n;
	197	+
	198	+ colMin=regions[regionNum].colMin;
	199	+ colMax=regions[regionNum].colMax;
	200	+ /* Left vertical border */
	201	+ if(colMin>0) {
	202	+ n=regions[regionNum].rowMax-regions[regionNum].rowMin;
	203	+ j=colMin-1;
	204	+ for(i=1; i<n; i++)
	205	+ if(resultBuffer[i][colMin]>0) {
	206	+ if(resultBuffer[i-1][j]>0 && dataBuffer[i-1][j]==dataBuffer[i][colMin])
	207	+ resolveEquivalence(resultBuffer[i][colMin],regionNum,
	208	+ resultBuffer[i-1][j],regionNum-1);
	209	+ if(resultBuffer[i][j]>0 && dataBuffer[i][j]==dataBuffer[i][colMin])
	210	+ resolveEquivalence(resultBuffer[i][colMin],regionNum,
	211	+ resultBuffer[i][j],regionNum-1);
	212	+ if(resultBuffer[i+1][j]>0 && dataBuffer[i+1][j]==dataBuffer[i][colMin])
	213	+ resolveEquivalence(resultBuffer[i][colMin],regionNum,
	214	+ resultBuffer[i+1][j],regionNum-1);
	215	+ }
	216	+ if(resultBuffer[n][colMin]>0) {
	217	+ if(resultBuffer[n-1][j]>0 && dataBuffer[n-1][j]==dataBuffer[n][colMin])
	218	+ resolveEquivalence(resultBuffer[n][colMin],regionNum,
	219	+ resultBuffer[n-1][j],regionNum-1);
	220	+ if(resultBuffer[n][j]>0 && dataBuffer[n][j]==dataBuffer[n][colMin])
	221	+ resolveEquivalence(resultBuffer[n][colMin],regionNum,
	222	+ resultBuffer[n][j],regionNum-1);
	223	+ }
	224	+ }
	225	+
	226	+ /* Left, top corner */
	227	+ if(resultBuffer[0][colMin]>0) {
	228	+ /* Left region*/
	229	+ if(colMin>0) {
	230	+ if(resultBuffer[0][colMin-1]>0 && dataBuffer[0][colMin]==dataBuffer[0][colMin-1])
	231	+ resolveEquivalence(resultBuffer[0][colMin],regionNum,
	232	+ resultBuffer[0][colMin-1],regionNum-1);
	233	+ if(resultBuffer[1][colMin-1]>0 && dataBuffer[0][colMin]==dataBuffer[1][colMin-1])
	234	+ resolveEquivalence(resultBuffer[0][colMin],regionNum,
	235	+ resultBuffer[1][colMin-1],regionNum-1);
	236	+ }
	237	+ /* Left-Top region*/
	238	+ if((regions[regionNum].rowMin>0)&&(colMin>0))
	239	+ if(borderResultBuffer[colMin-1]>0 && dataBuffer[0][colMin]==borderDataBuffer[colMin-1])
	240	+ resolveEquivalence(resultBuffer[0][colMin],regionNum,
	241	+ borderResultBuffer[colMin-1],
	242	+ regions[regionNum].regionUp-1);
	243	+ /* Top region */
	244	+ if(regions[regionNum].rowMin>0) {
	245	+ if(borderResultBuffer[colMin]>0 && dataBuffer[0][colMin]==borderDataBuffer[colMin])
	246	+ resolveEquivalence(resultBuffer[0][colMin],regionNum,
	247	+ borderResultBuffer[colMin],
	248	+ regions[regionNum].regionUp);
	249	+ if(borderResultBuffer[colMin+1]>0 && dataBuffer[0][colMin]==borderDataBuffer[colMin+1])
	250	+ resolveEquivalence(resultBuffer[0][colMin],regionNum,
	251	+ borderResultBuffer[colMin+1],
	252	+ regions[regionNum].regionUp);
	253	+ }
	254	+ }
	255	+ /* Top horizontal border */
	256	+ if(regions[regionNum].rowMin>0) {
	257	+ for(i=colMin+1; i<colMax; i++) {
	258	+ if(resultBuffer[0][i]>0) {
	259	+ if(borderResultBuffer[i-1]>0 && dataBuffer[0][i]==borderDataBuffer[i-1])
	260	+ resolveEquivalence(resultBuffer[0][i],regionNum,
	261	+ borderResultBuffer[i-1],
	262	+ regions[regionNum].regionUp);\
	263	+ if(borderResultBuffer[i]>0 && dataBuffer[0][i]==borderDataBuffer[i])
	264	+ resolveEquivalence(resultBuffer[0][i],regionNum,
	265	+ borderResultBuffer[i],
	266	+ regions[regionNum].regionUp);\
	267	+ if(borderResultBuffer[i+1]>0 && dataBuffer[0][i]==borderDataBuffer[i+1])
	268	+ resolveEquivalence(resultBuffer[0][i],regionNum,
	269	+ borderResultBuffer[i+1],
	270	+ regions[regionNum].regionUp);\
	271	+ }
	272	+ }
	273	+ if(resultBuffer[0][i]>0) {
	274	+ if(borderResultBuffer[colMax-1]>0 && dataBuffer[0][colMax]==borderDataBuffer[colMax-1])
	275	+ resolveEquivalence(resultBuffer[0][colMax],regionNum,
	276	+ borderResultBuffer[colMax-1],
	277	+ regions[regionNum].regionUp);
	278	+ if(borderResultBuffer[colMax]>0 && dataBuffer[0][colMax]==borderDataBuffer[colMax])
	279	+ resolveEquivalence(resultBuffer[0][colMax],regionNum,
	280	+ borderResultBuffer[colMax-1],
	281	+ regions[regionNum].regionUp);
	282	+ }
	283	+ }
	284	+}
	285	+
	286	+void merge(int n, int nDirections) {
	287	+ if(nDirections==4)
	288	+ merge4(n);
	289	+ else
	290	+ merge8(n);
	291	+}
	292	+
	293	+void clump(EZGDAL_LAYER in_fd, EZGDAL_LAYER out_fd, int nDirections) {
	294	+ int rowMin,rowMax,i,j,n,reg;
	295	+
	296	+ totalIndex=0;
	297	+ for(i=0; i<nRegionRows; i++) {
	298	+ reg=i*nRegionCols;
	299	+ ezgdal_show_progress(stdout,reg,nRegions);
	300	+ n=nDataCols*sizeof(int);
	301	+ if(i==0) {
	302	+ memset(borderDataBuffer,0,n);
	303	+ memset(borderResultBuffer,0,n);
	304	+ } else {
	305	+ memcpy(borderDataBuffer,dataBuffer[rowMax-rowMin],n);
	306	+ memcpy(borderResultBuffer,resultBuffer[rowMax-rowMin],n);
	307	+ }
	308	+ rowMin=regions[reg].rowMin;
	309	+ rowMax=regions[reg].rowMax;
	310	+ loadDataBuffer(in_fd,rowMin,rowMax);
	311	+
	312	+#pragma omp parallel for private(j) shared(reg,nRegionCols,regions, dataBuffer, resultBuffer, borderDataBuffer,borderResultBuffer)
	313	+ for(j=0; j<nRegionCols; j++)
	314	+ clumpRegion(reg+j, nDirections);
	315	+
	316	+ for(j=0; j<nRegionCols; j++) {
	317	+ n=reg+j;
	318	+ shiftLablesForRegion(n);
	319	+ merge(n,nDirections);
	320	+ }
	321	+ saveResultBuffer(out_fd,rowMin,rowMax);
	322	+ }
	323	+ ezgdal_show_progress(stdout,nRegions,nRegions);
	324	+}
	325	+
	326	+void labelsOrdering() {
	327	+ int *index,lbl;
	328	+ int i,j,x;
	329	+ index=(int *)calloc(totalIndex+1,sizeof(int));
	330	+ x=1;
	331	+ for(i=0; i<nRegions; i++)
	332	+ for(j=1; j<=regions[i].nLabels; j++) {
	333	+ lbl=regions[i].labels[j];
	334	+ if(index[lbl]==0)
	335	+ index[lbl]=x++;
	336	+ }
	337	+#pragma omp parallel for private(i,j)
	338	+ for(i=0; i<nRegions; i++)
	339	+ for(j=1; j<=regions[i].nLabels; j++)
	340	+ regions[i].labels[j]=index[regions[i].labels[j]];
	341	+ free(index);
	342	+}
	343	+
	344	+void replaceLabels(EZGDAL_LAYER in_fd, EZGDAL_LAYER out_fd) {
	345	+ int rowMin,rowMax,i,colMin,colMax;
	346	+ int row,rows,col,cols,colAbs;
	347	+
	348	+ ezgdal_show_progress(stdout,0,nRegions);
	349	+ labelsOrdering();
	350	+
	351	+ rowMin=regions[0].rowMin;
	352	+ rowMax=regions[0].rowMax;
	353	+
	354	+ loadDataBuffer(in_fd,rowMin,rowMax);
	355	+ for(i=0; i<nRegions; i++) {
	356	+ ezgdal_show_progress(stdout,i,nRegions);
	357	+ if(rowMin<regions[i].rowMin) {
	358	+ saveResultBuffer(out_fd,rowMin,rowMax);
	359	+ rowMin=regions[i].rowMin;
	360	+ rowMax=regions[i].rowMax;
	361	+ loadDataBuffer(in_fd,rowMin,rowMax);
	362	+ }
	363	+ colMin=regions[i].colMin;
	364	+ colMax=regions[i].colMax;
	365	+ cols=colMax-colMin+1;
	366	+ rows=rowMax-rowMin+1;
	367	+#pragma omp parallel for private(row,col,colAbs) shared(rows,cols,dataBuffer,resultBuffer,regions)
	368	+ for(row=0; row<rows; row++)
	369	+ for(col=0; col<cols; col++) {
	370	+ colAbs=col+colMin;
	371	+ if(!ezgdal_is_null(in_fd,(double)dataBuffer[row][colAbs]))
	372	+ resultBuffer[row][colAbs]=regions[i].labels[dataBuffer[row][colAbs]];
	373	+ else
	374	+ resultBuffer[row][colAbs]=0;
	375	+ }
	376	+ }
	377	+ saveResultBuffer(out_fd,rowMin,rowMax);
	378	+
	379	+ ezgdal_show_progress(stdout,i,nRegions);
	380	+}

data.c

View file @ 38f25a5

...	...	@@ -0,0 +1,164 @@
	1	+/****************************************************************************
	2	+ *
	3	+ * PROGRAM: clump4p
	4	+ *
	5	+ * AUTHOR(S): Pawel Netzel - SIL UC
	6	+ * Jarek Jasiewicz - SIL UC
	7	+ * (clumping algorithm for region)
	8	+ *
	9	+ * PURPOSE: Recategorizes data in a raster map layer by grouping cells
	10	+ * that form physically discrete areas into unique categories.
	11	+ *
	12	+ * COPYRIGHT: (C) 2012 by Pawel Netzel
	13	+ *
	14	+ * This program is free software under the GNU General Public
	15	+ * License (>=v2).
	16	+ *
	17	+ ***************************************************************************/
	18	+
	19	+#include <stdio.h>
	20	+#include <ezgdal.h>
	21	+#include "data.h"
	22	+
	23	+int totalIndex=0;
	24	+
	25	+int nRegions=0;
	26	+int nRegionCols=0;
	27	+int nRegionRows=0;
	28	+Region *regions;
	29	+
	30	+int nDataCols=0;
	31	+int nDataRows=0;
	32	+
	33	+int borderDataBuffer, borderResultBuffer;
	34	+int **dataBuffer;
	35	+int **resultBuffer;
	36	+int **calcBuffer;
	37	+
	38	+
	39	+void createRegions() {
	40	+ int i,j,rMin,rMax,c,nr;
	41	+
	42	+ nRegionRows=(nDataRows-1)/REGION_SIZE+1;
	43	+ nRegionCols=(nDataCols-1)/REGION_SIZE+1;
	44	+ nRegions=nRegionRows*nRegionCols;
	45	+ regions=(Region )malloc(nRegionssizeof(Region));
	46	+
	47	+ rMin=0;
	48	+ nr=0;
	49	+ c=0;
	50	+ for(i=0; i<nRegionRows; i++) {
	51	+ rMax=rMin+REGION_SIZE-1;
	52	+ if(rMax>=nDataRows) rMax=nDataRows-1;
	53	+ for(j=0; j<nRegionCols; j++) {
	54	+ regions[nr].rowMin=rMin;
	55	+ regions[nr].rowMax=rMax;
	56	+ regions[nr].colMin=c;
	57	+ c+=REGION_SIZE-1;
	58	+ if(c>=nDataCols) c=nDataCols-1;
	59	+ regions[nr].colMax=c;
	60	+ regions[nr].nLabels=0;
	61	+ regions[nr].labels=(int )malloc(INCRsizeof(int));
	62	+ regions[nr].labels[0]=0;
	63	+ if(i==0)
	64	+ regions[nr].regionUp=-1;
	65	+ else
	66	+ regions[nr].regionUp=(i-1)*nRegionCols+j;
	67	+ nr++;
	68	+ c+=1;
	69	+ }
	70	+ c=0;
	71	+ rMin=rMax+1;
	72	+ }
	73	+}
	74	+
	75	+void dumpArray(int *arr, int num) {
	76	+ int i;
	77	+ for(i=0; i<num; i++) {
	78	+ if(i>0) printf(", ");
	79	+ printf("[%d]=%d",i,arr[i]);
	80	+ }
	81	+}
	82	+
	83	+void dumpRegions(char *Comment) {
	84	+ int i;
	85	+ printf("%s\n",Comment);
	86	+ for(i=0; i<nRegions; i++) {
	87	+ printf("%d: c(%d,%d), r(%d,%d) nLab: %d, Labs: ",
	88	+ i, regions[i].colMin,regions[i].colMax,
	89	+ regions[i].rowMin,regions[i].rowMax,
	90	+ regions[i].nLabels);
	91	+ dumpArray(regions[i].labels,regions[i].nLabels+1);
	92	+ printf("\n");
	93	+ }
	94	+}
	95	+
	96	+void destroyRegions() {
	97	+ int i;
	98	+ for(i=0; i<nRegions; i++)
	99	+ free(regions[i].labels);
	100	+ free(regions);
	101	+}
	102	+
	103	+void createBuffers() {
	104	+ dataBuffer=(int *)malloc(REGION_SIZEsizeof(int*));
	105	+ resultBuffer=(int *)malloc(REGION_SIZEsizeof(int*));
	106	+ int i,n;
	107	+ n=nDataCols*sizeof(int);
	108	+ for(i=0; i<REGION_SIZE; i++) {
	109	+ dataBuffer[i]=(int *)malloc(n);
	110	+ resultBuffer[i]=(int *)malloc(n);
	111	+ }
	112	+ borderDataBuffer=(int *)calloc(n,1);
	113	+ borderResultBuffer=(int *)calloc(n,1);
	114	+}
	115	+
	116	+void destroyBuffers() {
	117	+ int i;
	118	+ free(borderDataBuffer);
	119	+ free(borderResultBuffer);
	120	+ for(i=0; i<REGION_SIZE; i++) {
	121	+ free(dataBuffer[i]);
	122	+ free(resultBuffer[i]);
	123	+ }
	124	+ free(dataBuffer);
	125	+ free(resultBuffer);
	126	+}
	127	+
	128	+void loadDataBuffer(EZGDAL_LAYER *layer, int minRow, int maxRow) {
	129	+ int i,n,j;
	130	+ n=maxRow-minRow+1;
	131	+ for(i=0; i<n; i++) {
	132	+ ezgdal_read_buffer(layer,i+minRow);
	133	+ for(j=0; j<nDataCols; j++)
	134	+ dataBuffer[i][j]=(int)layer->buffer[j];
	135	+ }
	136	+}
	137	+
	138	+void saveResultBuffer(EZGDAL_LAYER *layer, int minRow, int maxRow) {
	139	+ int i,j,n;
	140	+ n=maxRow-minRow+1;
	141	+ for(i=0; i<n; i++) {
	142	+ for(j=0; j<nDataCols; j++)
	143	+ if(resultBuffer[i][j] == 0)
	144	+ ezgdal_set_null(layer, &(layer->buffer[j]));
	145	+ else
	146	+ layer->buffer[j] = (double)resultBuffer[i][j];
	147	+ ezgdal_write_buffer(layer, i+minRow);
	148	+ }
	149	+}
	150	+
	151	+void initVariables(EZGDAL_LAYER *layer) {
	152	+ nDataRows = layer->rows;
	153	+ nDataCols = layer->cols;
	154	+ totalIndex=0;
	155	+ createRegions();
	156	+ createBuffers();
	157	+}
	158	+
	159	+void freeVariables() {
	160	+ destroyRegions();
	161	+ destroyBuffers();
	162	+}
	163	+
	164	+

data.h

View file @ 38f25a5

...	...	@@ -0,0 +1,61 @@
	1	+/****************************************************************************
	2	+ *
	3	+ * PROGRAM: clump4p
	4	+ *
	5	+ * AUTHOR(S): Pawel Netzel - SIL UC
	6	+ * Jarek Jasiewicz - SIL UC
	7	+ * (the clumping algorithm for a region)
	8	+ *
	9	+ * PURPOSE: Recategorizes data in a raster map layer by grouping cells
	10	+ * that form physically discrete areas into unique categories.
	11	+ *
	12	+ * COPYRIGHT: (C) 2012 by Pawel Netzel
	13	+ *
	14	+ * This program is a free software under the GNU General Public
	15	+ * License (>=v2).
	16	+ *
	17	+ ***************************************************************************/
	18	+
	19	+#ifndef _DATA_H_
	20	+#define _DATA_H_
	21	+
	22	+#include <ezgdal.h>
	23	+#include "main.h"
	24	+
	25	+#define REGION_SIZE 500
	26	+#define INCR 4096
	27	+
	28	+typedef struct {
	29	+ int rowMin,rowMax;
	30	+ int colMin,colMax;
	31	+ int nLabels; // max labal number
	32	+ int *labels; // array from 1
	33	+ int regionUp;
	34	+} Region;
	35	+
	36	+extern int totalIndex;
	37	+
	38	+extern int nRegions;
	39	+extern int nRegionCols;
	40	+extern int nRegionRows;
	41	+extern Region *regions;
	42	+
	43	+extern int nDataCols;
	44	+extern int nDataRows;
	45	+
	46	+extern int borderDataBuffer, borderResultBuffer;
	47	+extern int **dataBuffer;
	48	+extern int **resultBuffer;
	49	+extern int **calcBuffer;
	50	+
	51	+void initVariables(EZGDAL_LAYER *);
	52	+void freeVariables();
	53	+
	54	+void loadDataBuffer(EZGDAL_LAYER *, int, int);
	55	+void saveResultBuffer(EZGDAL_LAYER *, int, int);
	56	+
	57	+void dumpArray(int *, int);
	58	+void dumpRegions(char *);
	59	+
	60	+#endif
	61	+

gpl-3.0.txt

View file @ 38f25a5

...	...	@@ -0,0 +1,674 @@
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	535	+
	536	+ Nothing in this License shall be construed as excluding or limiting
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	538	+otherwise be available to you under applicable patent law.
	539	+
	540	+ 12. No Surrender of Others' Freedom.
	541	+
	542	+ If conditions are imposed on you (whether by court order, agreement or
	543	+otherwise) that contradict the conditions of this License, they do not
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	619	+copy of the Program in return for a fee.
	620	+
	621	+ END OF TERMS AND CONDITIONS
	622	+
	623	+ How to Apply These Terms to Your New Programs
	624	+
	625	+ If you develop a new program, and you want it to be of the greatest
	626	+possible use to the public, the best way to achieve this is to make it
	627	+free software which everyone can redistribute and change under these terms.
	628	+
	629	+ To do so, attach the following notices to the program. It is safest
	630	+to attach them to the start of each source file to most effectively
	631	+state the exclusion of warranty; and each file should have at least
	632	+the "copyright" line and a pointer to where the full notice is found.
	633	+
	634	+ <one line to give the program's name and a brief idea of what it does.>
	635	+ Copyright (C) <year> <name of author>
	636	+
	637	+ This program is free software: you can redistribute it and/or modify
	638	+ it under the terms of the GNU General Public License as published by
	639	+ the Free Software Foundation, either version 3 of the License, or
	640	+ (at your option) any later version.
	641	+
	642	+ This program is distributed in the hope that it will be useful,
	643	+ but WITHOUT ANY WARRANTY; without even the implied warranty of
	644	+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	645	+ GNU General Public License for more details.
	646	+
	647	+ You should have received a copy of the GNU General Public License
	648	+ along with this program. If not, see <http://www.gnu.org/licenses/>.
	649	+
	650	+Also add information on how to contact you by electronic and paper mail.
	651	+
	652	+ If the program does terminal interaction, make it output a short
	653	+notice like this when it starts in an interactive mode:
	654	+
	655	+ <program> Copyright (C) <year> <name of author>
	656	+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
	657	+ This is free software, and you are welcome to redistribute it
	658	+ under certain conditions; type `show c' for details.
	659	+
	660	+The hypothetical commands `show w' and `show c' should show the appropriate
	661	+parts of the General Public License. Of course, your program's commands
	662	+might be different; for a GUI interface, you would use an "about box".
	663	+
	664	+ You should also get your employer (if you work as a programmer) or school,
	665	+if any, to sign a "copyright disclaimer" for the program, if necessary.
	666	+For more information on this, and how to apply and follow the GNU GPL, see
	667	+<http://www.gnu.org/licenses/>.
	668	+
	669	+ The GNU General Public License does not permit incorporating your program
	670	+into proprietary programs. If your program is a subroutine library, you
	671	+may consider it more useful to permit linking proprietary applications with
	672	+the library. If this is what you want to do, use the GNU Lesser General
	673	+Public License instead of this License. But first, please read
	674	+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

main.c

View file @ 38f25a5

...	...	@@ -0,0 +1,166 @@
	1	+/****************************************************************************
	2	+ *
	3	+ * PROGRAM: clump4p
	4	+ *
	5	+ * AUTHOR(S): Pawel Netzel - SIL UC
	6	+ * Jarek Jasiewicz - SIL UC
	7	+ * (the clumping algorithm for a region)
	8	+ *
	9	+ * PURPOSE: Recategorizes data in a raster map layer by grouping cells
	10	+ * that form physically discrete areas into unique categories.
	11	+ *
	12	+ * COPYRIGHT: (C) 2012 by Pawel Netzel
	13	+ *
	14	+ * This program is a free software under the GNU General Public
	15	+ * License (>=v2).
	16	+ *
	17	+ ***************************************************************************/
	18	+
	19	+#include <stdlib.h>
	20	+#include <string.h>
	21	+#include <unistd.h>
	22	+#include <omp.h>
	23	+#include <gdal.h>
	24	+#include <ezgdal.h>
	25	+#include <argtable3.h>
	26	+#include "data.h"
	27	+#include "main.h"
	28	+
	29	+void usage(char progname, void argtable) {
	30	+
	31	+ printf("\nclump4p recategorizes data in a raster map by grouping cells \n");
	32	+ printf("that form physically discrete areas into unique categories.\n");
	33	+
	34	+ printf("\nclump4p uses \"divide and conquer\" algorithm to speed up \n");
	35	+ printf("the clumping process. By default, clumps are generated by the four \n");
	36	+ printf("directions clumping algorithm. One can change this to the eight directions\n");
	37	+ printf("clumping algorithm (flag -8).\n");
	38	+
	39	+ printf("\nUsage:\n\t%s", progname);
	40	+ arg_print_syntax(stdout,argtable,"\n");
	41	+ printf("\n");
	42	+ arg_print_glossary_gnu(stdout,argtable);
	43	+ printf("\n");
	44	+ exit(0);
	45	+}
	46	+
	47	+
	48	+int main(int argc, char *argv[])
	49	+{
	50	+ EZGDAL_LAYER in_fd, tmp_fd, *out_fd;
	51	+ char *OUTPUT;
	52	+ char *INPUT;
	53	+ char TEMPLAYER[1024];
	54	+ int DIRECTIONS=4;
	55	+
	56	+ struct arg_str *inp = arg_str1("i","input","<file_name>","name of input files (GeoTIFF)");
	57	+ struct arg_str *out = arg_str1("o","output","<file_name>","name of output file with clumps (GeoTIFF)");
	58	+ struct arg_int *th = arg_int0("t",NULL,"<n>","number of threads (default: 1)");
	59	+ struct arg_lit *dirs = arg_lit0("8",NULL,"8 direction connecting");
	60	+ struct arg_lit *local = arg_lit0("l",NULL,"temporary files in local directory (default: /tmp)");
	61	+ struct arg_str *path = arg_str0(NULL,"path","<existing_path>","location for temporary files (default: /tmp)");
	62	+ struct arg_lit *help = arg_lit0("h","help","print help and exit");
	63	+ struct arg_end *end = arg_end(20);
	64	+
	65	+ void* argtable[] = {inp,out,th,dirs,local,path,help,end};
	66	+
	67	+ int nerrors = arg_parse(argc,argv,argtable);
	68	+
	69	+ if (help->count > 0)
	70	+ usage(argv[0],argtable);
	71	+
	72	+ if (nerrors > 0) {
	73	+ arg_print_errors(stdout,end,argv[0]);
	74	+ usage(argv[0],argtable);
	75	+ }
	76	+
	77	+ if(th->count > 0)
	78	+ omp_set_num_threads(th->ival[0]);
	79	+ else
	80	+ omp_set_num_threads(1);
	81	+
	82	+
	83	+ INPUT = (char *)inp->sval[0];
	84	+ OUTPUT = (char *)out->sval[0];
	85	+
	86	+ if(dirs->count>0)
	87	+ DIRECTIONS=8;
	88	+
	89	+ int pid = getpid();
	90	+ memset(TEMPLAYER,0,1024);
	91	+ if(local->count>0)
	92	+ sprintf(TEMPLAYER,"tmp_clump_%06d.tif",pid);
	93	+ else if(path->count>0)
	94	+ sprintf(TEMPLAYER,"%s/tmp_clump_%06d.tif",path->sval[0],pid);
	95	+ else
	96	+ sprintf(TEMPLAYER,"/tmp/tmp_clump_%06d.tif",pid);
	97	+
	98	+ if(!ezgdal_file_exists(INPUT)) {
	99	+ printf("\nThe file '%s' does not exist!\n\n",INPUT);
	100	+ exit(0);
	101	+ }
	102	+
	103	+ printf("Opening input file...");
	104	+ in_fd = ezgdal_open_layer(INPUT);
	105	+
	106	+
	107	+ if(in_fd==NULL) {
	108	+ printf("\nThe file '%s' can't be opened!\n\n",INPUT);
	109	+ exit(0);
	110	+ } else
	111	+ printf(" OK\n");
	112	+
	113	+ initVariables(in_fd);
	114	+
	115	+ int nodata = -9999;
	116	+ printf("Creating temporary file...");
	117	+ tmp_fd = ezgdal_create_layer(TEMPLAYER,
	118	+ ezgdal_layer_get_wkt(in_fd),
	119	+ "Int32",
	120	+ ezgdal_layer_get_at(in_fd),
	121	+ in_fd->rows,
	122	+ in_fd->cols,
	123	+ &nodata, EZGDAL_COMPRESS_NONE
	124	+ );
	125	+
	126	+ if(tmp_fd==NULL) {
	127	+ printf("\nThe file '%s' can't be created!\n\n",TEMPLAYER);
	128	+ exit(0);
	129	+ } else
	130	+ printf("OK\n");
	131	+
	132	+ printf("Clumping... ");
	133	+ clump(in_fd, tmp_fd, DIRECTIONS);
	134	+ printf(" OK\n");
	135	+
	136	+ ezgdal_close_layer(in_fd);
	137	+ ezgdal_close_layer(tmp_fd);
	138	+
	139	+ printf("Creating output file...");
	140	+ tmp_fd = ezgdal_open_layer(TEMPLAYER);
	141	+ out_fd = ezgdal_create_layer(OUTPUT,
	142	+ ezgdal_layer_get_wkt(tmp_fd),
	143	+ "Int32",
	144	+ ezgdal_layer_get_at(tmp_fd),
	145	+ tmp_fd->rows,
	146	+ tmp_fd->cols,
	147	+ &nodata, EZGDAL_COMPRESS_NONE
	148	+ );
	149	+ if(out_fd==NULL) {
	150	+ printf("\nThe file '%s' can't be created!\n\n",OUTPUT);
	151	+ exit(0);
	152	+ } else
	153	+ printf(" OK\n");
	154	+
	155	+
	156	+ replaceLabels(tmp_fd,out_fd);
	157	+
	158	+ ezgdal_close_layer(out_fd);
	159	+ ezgdal_close_layer(tmp_fd);
	160	+
	161	+ freeVariables();
	162	+
	163	+ unlink(TEMPLAYER);
	164	+
	165	+ exit(EXIT_SUCCESS);
	166	+}

main.h

View file @ 38f25a5

...	...	@@ -0,0 +1,31 @@
	1	+/****************************************************************************
	2	+ *
	3	+ * PROGRAM: clump4p
	4	+ *
	5	+ * AUTHOR(S): Pawel Netzel - SIL UC
	6	+ * Jarek Jasiewicz - SIL UC
	7	+ * (clumping algorithm for region)
	8	+ *
	9	+ * PURPOSE: Recategorizes data in a raster map layer by grouping cells
	10	+ * that form physically discrete areas into unique categories.
	11	+ *
	12	+ * COPYRIGHT: (C) 2012 by Pawel Netzel
	13	+ *
	14	+ * This program is free software under the GNU General Public
	15	+ * License (>=v2).
	16	+ *
	17	+ ***************************************************************************/
	18	+
	19	+#ifndef __MAIN_H__
	20	+#define __MAIN_H__
	21	+
	22	+typedef int CELL;
	23	+
	24	+/* clump.c */
	25	+void clump(EZGDAL_LAYER , EZGDAL_LAYER , int);
	26	+void replaceLabels(EZGDAL_LAYER , EZGDAL_LAYER );
	27	+
	28	+/* main.c */
	29	+int main(int, char *[]);
	30	+
	31	+#endif /* __MAIN_H__ */
0	32