--- trunk/src/dnorm/dnorm.c	2010/06/29 15:13:36	125
+++ branches/vis12/src/dnorm/dnorm.c	2012/03/20 19:19:37	1739
@@ -33,8 +33,9 @@
                    "a consistent form, and nixes various other fields. ");
 
 int
-main(int argc, char **argv) {
-  char *me, *outS;
+main(int argc, const char **argv) {
+  const char *me;
+  char *outS;
   hestOpt *hopt;
   hestParm *hparm;
   airArray *mop;
@@ -42,7 +43,7 @@
   char *err;
   Nrrd *nin, *nout;
   NrrdIoState *nio;
-  int kindIn, kindOut, headerOnly;
+  int kindIn, kindOut, headerOnly, haveMM, trivialOrient;
   unsigned int kindAxis, axi, si, sj;
   
   me = argv[0];
@@ -52,6 +53,11 @@
   airMopAdd(mop, hparm, (airMopper)hestParmFree, airMopAlways);
   hestOptAdd(&hopt, "h,header", NULL, airTypeInt, 0, 0, &headerOnly, NULL,
              "output header of nrrd file only, not the data itself");
+  hestOptAdd(&hopt, "to", NULL, airTypeInt, 0, 0, &trivialOrient, NULL,
+             "(*t*rivial *o*rientation) "
+             "even if the input nrrd comes with full orientation or "
+             "per-axis min-max info, ignore it and instead assert the "
+             "most trivial mapping between index and world space");
   hestOptAdd(&hopt, "i", "nin", airTypeOther, 1, 1, &nin, NULL,
              "input image", NULL, NULL, nrrdHestNrrd);
   hestOptAdd(&hopt, "o", "nout", airTypeString, 1, 1, &outS, "-",
@@ -71,22 +77,26 @@
 
   /* make sure all kinds are set to something */
   /* see if there's a range kind, verify that there's only one */
+  /* set haveMM */
+  haveMM = AIR_TRUE;
   kindIn = nrrdKindUnknown;
   kindAxis = 0;
   for (axi=0; axi<nin->dim; axi++) {
     if (nrrdKindUnknown == nin->axis[axi].kind
         || nrrdKindIsDomain(nin->axis[axi].kind)) {
-      continue;
-    }
-    if (nrrdKindUnknown != kindIn) {
-      fprintf(stderr, "%s: got non-domain kind %s on axis %u, but already "
-              "have %s from axis %u\n", me, 
-              airEnumStr(nrrdKind, nin->axis[axi].kind), axi,
-              airEnumStr(nrrdKind, kindIn), kindAxis);
-      airMopError(mop); exit(1);
+      haveMM &= AIR_EXISTS(nin->axis[axi].min);
+      haveMM &= AIR_EXISTS(nin->axis[axi].max);
+    } else {
+      if (nrrdKindUnknown != kindIn) {
+        fprintf(stderr, "%s: got non-domain kind %s on axis %u, but already "
+                "have %s from axis %u\n", me, 
+                airEnumStr(nrrdKind, nin->axis[axi].kind), axi,
+                airEnumStr(nrrdKind, kindIn), kindAxis);
+        airMopError(mop); exit(1);
+      }
+      kindIn = nin->axis[axi].kind;
+      kindAxis = axi;
     }
-    kindIn = nin->axis[axi].kind;
-    kindAxis = axi;
   }
   /* see if the non-domain kind is something we can interpret as a tensor */
   if (nrrdKindUnknown != kindIn) {
@@ -120,14 +130,13 @@
     kindOut = nrrdKindUnknown;
   }
 
-  /* prepare output (this may eventually be cropping or something else) */
+  /* initialize output by copying */
   nout = nrrdNew();
   airMopAdd(mop, nout, (airMopper)nrrdNuke, airMopAlways);
   if (nrrdCopy(nout, nin)) {
     airMopAdd(mop, err = biffGet(NRRD), airFree, airMopAlways);
     fprintf(stderr, "%s: trouble copying:\n%s", me, err);
     airMopError(mop); exit(1);
-    
   }
 
   /* no comments, either advertising the format URL or anything else */
@@ -183,8 +192,10 @@
      but we have to accept a greater variety of kinds and dimensions
      than gage ever has to process.
   */
-  if (nout->spaceDim) {
+  if (nout->spaceDim && !trivialOrient) {
     int saxi = 0;
+    /* we use only the space dimension, not any named space */
+    nout->space = nrrdSpaceUnknown;
     if (!nrrdSpaceVecExists(nout->spaceDim, nout->spaceOrigin)) {
       nrrdSpaceVecSetZero(nout->spaceOrigin);
     }
@@ -200,6 +211,20 @@
         nrrdSpaceVecSetNaN(nout->axis[axi].spaceDirection);
       }
     }
+  } else if (haveMM && !trivialOrient) {
+    int saxi = 0;
+    for (axi=0; axi<nout->dim; axi++) {
+      if (nrrdKindUnknown == kindOut || kindAxis != axi) {
+        nrrdSpaceVecSetZero(nout->axis[axi].spaceDirection);
+        nout->axis[axi].spaceDirection[saxi] 
+          = (nin->axis[axi].max - nin->axis[axi].min)/(nin->axis[axi].size-1);
+        nout->spaceOrigin[saxi] = nin->axis[axi].min;
+        saxi++;
+      } else {
+        nrrdSpaceVecSetNaN(nout->axis[axi].spaceDirection);
+      }
+    }
+    nout->spaceDim = saxi;
   } else {
     int saxi = 0;
     nrrdSpaceVecSetZero(nout->spaceOrigin);
@@ -217,7 +242,8 @@
     }
     nout->spaceDim = saxi;
   }
-  /* probably should be asserted earlier */
+
+  /* space dimension has to match the number of domain axes */
   if (nout->dim != nout->spaceDim + !!kindOut) {
     fprintf(stderr, "%s: output dim %d != spaceDim %d + %d %s%s%s\n",
             me, nout->dim, nout->spaceDim, !!kindOut,

<script type="text/javascript">//<![CDATA[
		function toggle_ffErrors() {
			var errorsblock = document.getElementById("ffErrorsBlock");
			var errorsgroup = document.getElementById("ffErrors");
			if (errorsblock.style.display == "none") {
				errorsblock.style.display = "block";
				errorsgroup.style.right = "10px";
			} else {
				errorsblock.style.display = "none";
				errorsgroup.style.right = "300px";
			}
		}
//]]></script>
<div id="ffErrors">
<a href="javascript:toggle_ffErrors();">Click to toggle</a>
<div id="ffErrorsBlock">
	<div class="error">does not end with &lt;/html&gt; tag</div>
	<div class="error">does not end with &lt;/body&gt; tag</div>
	<div class="info">The output has ended thus:  output dim %d != spaceDim %d + %d %s%s%s\n&quot;,
             me, nout-&gt;dim, nout-&gt;spaceDim, !!kindOut,</div>
</div></div>
</body></html>