void nibbParseImageDir(char *sourceDir, char *goodTab, char *badTab)
/* nibbParseImageDir - Look through nibb image directory and allowing for
* typos and the like create a table that maps a file name to clone name,
* developmental stage, and view of body part. */
{
struct fileInfo *l1List, *l1, *l2List, *l2, *l3List, *l3;
struct hash *stageHash = hashNew(0);
struct hash *viewHash = hashNew(0);
struct hash *otherHash = hashNew(0);
struct hash *probeHash = hashNew(0);
struct hash *fixHash = hashFixers();
struct imageInfo *imageList = NULL, *image;
FILE *good = mustOpen(goodTab, "w");
FILE *bad = mustOpen(badTab, "w");
int goodCount = 0, badCount = 0;
int jpgCount = 0, jpgDir = 0;
l1List = listDirX(sourceDir, "XL*", FALSE);
for (l1 = l1List; l1 != NULL; l1 = l1->next)
{
char l1Path[PATH_LEN];
safef(l1Path, sizeof(l1Path), "%s/%s", sourceDir, l1->name);
l2List = listDirX(l1Path, "XL*", FALSE);
for (l2 = l2List; l2 != NULL; l2 = l2->next)
{
char l2Path[PATH_LEN];
char cloneName[64], *permanentCloneName;
char *cloneDir = l2->name;
char *cloneEnd;
int cloneNameSize = 0;
if (stringIx(cloneDir, skipDir) >= 0)
continue;
/* Figure out clone name, whish is directory component up to
* first underbar. */
cloneEnd = strchr(cloneDir, '_');
if (cloneEnd != NULL)
cloneNameSize = cloneEnd - cloneDir;
else
errAbort("Strangely formatted image dir %s, no underbar", cloneDir);
if (cloneNameSize >= sizeof(cloneName))
errAbort("Clone name too long in dir %s", cloneDir);
if (cloneNameSize < 8 || cloneNameSize > 12)
errAbort("Clone name wrong size %s", cloneDir);
memcpy(cloneName, cloneDir, cloneNameSize);
cloneName[cloneNameSize] = 0;
/* Check format is XL###L##. We already checked the XL. */
if (!isdigit(cloneName[2]) || !isdigit(cloneName[3])
|| !isdigit(cloneName[4]) || isdigit(cloneName[5])
|| !isdigit(cloneName[6]) || !isdigit(cloneName[7]))
errAbort("Strangely formatted clone name %s", cloneDir);
permanentCloneName = hashStoreName(probeHash, cloneName);
/* Get all files in dir. */
safef(l2Path, sizeof(l2Path),
"%s/%s/%s", sourceDir, l1->name, l2->name);
l3List = listDirX(l2Path, "*.jpg", FALSE);
for (l3 = l3List; l3 != NULL; l3 = l3->next)
{
char *fileName = l3->name;
if (stringIx(l3->name, skipFile) >= 0)
continue;
image = getImageInfo(fixHash, permanentCloneName,
l1->name, cloneDir, fileName,
stageHash, viewHash, otherHash, probeHash);
slAddHead(&imageList, image);
++jpgCount;
}
++jpgDir;
}
}
slReverse(&imageList);
verbose(1, "%d jpg images in %d directories\n", jpgCount, jpgDir);
#ifdef OLD
verbose(1, "%d probes, %d stages, %d views, %d other\n",
probeHash->elCount, stageHash->elCount,
viewHash->elCount, otherHash->elCount);
printHash("stages", stageHash);
printHash("views", viewHash);
printHash("other", otherHash);
#endif /* OLD */
for (image = imageList; image != NULL; image = image->next)
{
if (image->clone != NULL && image->stage != NULL && image->view != NULL)
{
imageInfoOut(image, good);
++goodCount;
}
else
{
imageInfoOut(image, bad);
++badCount;
}
}
verbose(1, "%d (%4.1f%%) parsed ok, %d (%4.2f%%) didn't\n",
goodCount, 100.0 * goodCount/(goodCount + badCount),
badCount, 100.0 * badCount/(goodCount + badCount));
carefulClose(&good);
carefulClose(&bad);
}
int wormChromIx(char *name)
/* Return index of worm chromosome. */
{
return stringIx(name, chromIds);
}
