Add -morphooptiini ori and id

It is now possible to assign orientations and ids to the initial seeds,
using -morphooptiini.  To retain the orientations, `-ori initial` must
also be used.

Author: rquey

VERSIONS

@@ -1,6 +1,6 @@
-New in 4.8.2-8 (25 Mar 2024):
-- module -T: added -transform "cut(cube)", improved -transform "cut(cubei)",
-  made minor fixes and improvements.
+New in 4.8.2-9 (25 Mar 2024):
+- module -T: added -transform "cut(cube)", added -morphooptiini ori and id,
+  improved -transform "cut(cubei)", made minor fixes and improvements.
 - module -M: made minor improvements.
 
 New in 4.8.1 (02 Feb 2024):

doc/conf.py

@@ -11,8 +11,8 @@
 import sphinx_rtd_theme
 
 project = u'Neper'
-version = u'4.8.2-8'
-release = u'4.8.2-8'
+version = u'4.8.2-9'
+release = u'4.8.2-9'
 author = u'Romain Quey'
 copyright = u'Romain Quey'
 language = 'en'

doc/neper_t.rst

@@ -257,9 +257,9 @@ These options can be used to set the cell morphology.
 
 .. option:: -morphooptiini <seed_attributes>
 
-  Specify the initial positions and/or weights of the seeds.
+  Specify the initial positions, weights, orientations and/or ids of the seeds.
 
-  The general form of the argument is :data:`coo:\<coo_definition\>,weight:\<weight_definition\>`.  Different values of :data:`<coo_definition>` and :data:`<weight_definition>` are available, depending on the value of option :option:`-morpho`:
+  The general form of the argument is :data:`coo:\<coo_definition\>,weight:\<weight_definition\>,...`.  Different values of :data:`<coo_definition>` and :data:`<weight_definition>` are available, depending on the value of option :option:`-morpho`:
 
   - :data:`<coo_definition>` can be:
 
@@ -278,6 +278,16 @@ These options can be used to set the cell morphology.
 
     The default depends on the value of option :data:`-morpho`: for :data:`voronoi`, it is :data:`0`, for a cell-size statistical distribution, it is :data:`avradeq`, and for cell-based size values (including :data:`-morpho tesr`) , it is :data:`radeq`.
 
+  It is also possible to load orientations or ids using :data:`ori:\<ori_definition\>` and :data:`id:\<id_definition\>`:
+
+  - :data:`<ori_definition>` can be:
+
+    - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
+
+  - :data:`<id_definition>` can be:
+
+    - :data:`file(<file_name>)`: values from a :ref:`data_file`.
+
   Alternatively, :data:`file(<file_name>)` can be used to load the seed coordinates and weights from a unique :ref:`tess_file` (thereby replicating the tessellation).
 
   **Default value**: :data:`default`.
@@ -483,6 +493,8 @@ Crystal Orientation Options
 
   - :data:`file(<file_name>[,des=<descriptor>])`: discrete orientations to be read from a :ref:`data_file` written using a specific descriptor (see :ref:`rotations_and_orientations`, default :data:`rodrigues`).
 
+  - :data:`from_morpho`: discrete orientations read from :option:`-morphooptiini`:data:`ori`.
+
   For :option:`-ori`:data:`<orientation>` and :option:`-ori`:data:`parent`, the optional distributions are:
 
     - :data:`normal(<var>=<val>)`: a 3-variate normal distribution, where :data:`<var>` can be:

src/CMakeLists.txt

@@ -7,7 +7,7 @@ if(POLICY CMP0077)
   cmake_policy(SET CMP0077 NEW)
 endif()
 
-set(NEPER_VERSION \"4.8.2-8\")
+set(NEPER_VERSION \"4.8.2-9\")
 project(neper)
 
 if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8.1)

src/neper_t/CMakeLists.txt

@@ -183,6 +183,7 @@ add_library(neper_t
 ./net_stat/net_stat2.c
 ./net_res/net_res_ori/net_res_ori1.c
 ./net_tess/net_tess_opt/net_tess_opt_init/net_tess_opt_init_sset/net_tess_opt_init_sset_ori/net_tess_opt_init_sset_ori1.c
+./net_tess/net_tess_opt/net_tess_opt_init/net_tess_opt_init_sset/net_tess_opt_init_sset_id/net_tess_opt_init_sset_id1.c
 ./net_ori/net_ori1.c
 ./net_ori/net_ori2.c
 ./net_ori/net_ori3.c

src/neper_t/net_ori/net_ori.h

@@ -26,6 +26,7 @@ extern "C"
   extern void net_ori_random (long random, struct OL_SET *pOSet);
 
   extern void net_ori_file (char *label, struct OL_SET *pOSet);
+  extern void net_ori_memcpy (struct OL_SET OSet, struct SEEDSET *pSSet);
 
   extern void net_ori_post (struct TESR *pTesr);
 

src/neper_t/net_ori/net_ori1.c

@@ -38,104 +38,116 @@ net_ori (struct IN_T In, int level, struct MTESS MTess, struct TESS *Tess,
 
   net_ori_mtess_params (In, level, MTess, Tess, dtess, dcell, &ori, &orisampling, &orispread, &oricrysym);
 
-  OSet = ol_set_alloc ((*pSSet).N, oricrysym);
+  if (!strcmp (ori, "from_morpho"))
+  {
+    // oris already in *pSSet
+  }
+  else
+  {
+    OSet = ol_set_alloc ((*pSSet).N, oricrysym);
 
-  ut_list_break (ori, "+", &parts, &partqty);
+    ut_list_break (ori, "+", &parts, &partqty);
 
-  net_ori_qty (pSSet, parts, partqty, &qty);
+    net_ori_qty (pSSet, parts, partqty, &qty);
 
-  OSets = malloc (partqty * sizeof (struct OL_SET));
-  size = ut_alloc_1d_int (partqty);
-  for (i = 0; i < partqty; i++)
-    OSets[i] = ol_set_alloc (qty[i], oricrysym);
+    OSets = malloc (partqty * sizeof (struct OL_SET));
+    size = ut_alloc_1d_int (partqty);
+    for (i = 0; i < partqty; i++)
+      OSets[i] = ol_set_alloc (qty[i], oricrysym);
 
-  for (i = 0; i < partqty; i++)
-  {
-    if (!strcmp (parts[i], "random") || strstr (In.orioptiini[level], "ori=random"))
+    for (i = 0; i < partqty; i++)
     {
-      if (!strcmp (In.orisampling[level], "random"))
-        net_ori_random ((*pSSet).Random, OSets + i);
-
-      else if (!strcmp (In.orisampling[level], "uniform"))
-        net_ori_uniform (In, level, MTess, Tess, dtess, dcell, (*pSSet).Random,
-                         OSets + i, verbositylevel);
+      if (!strcmp (parts[i], "from_morpho"))
+      {
+
+      }
+
+      else if (!strcmp (parts[i], "random") || strstr (In.orioptiini[level], "ori=random"))
+      {
+        if (!strcmp (In.orisampling[level], "random"))
+          net_ori_random ((*pSSet).Random, OSets + i);
+
+        else if (!strcmp (In.orisampling[level], "uniform"))
+          net_ori_uniform (In, level, MTess, Tess, dtess, dcell, (*pSSet).Random,
+                           OSets + i, verbositylevel);
+
+        else
+          ut_print_message (2, 3, "Failed to process `%s'.\n", In.orisampling[level]);
+      }
+
+      else if (!strncmp (parts[i], "fiber", 5))
+        net_ori_fiber (SSet, dtess, dcell, (*pSSet).Random, parts[i], OSets + i);
+
+      else if (!strncmp (ori, "file(", 5))
+      {
+        net_ori_file (ori, OSets + i);
+        ut_string_string (oricrysym, &(OSets[i].crysym));
+      }
+
+      else if (strstr (In.orioptiini[level], "ori="))
+      {
+        int qty, *qty1 = NULL;
+        char ***parts = NULL;
+        ut_list_break2 (In.orioptiini[level], ",", "=", &parts, &qty1, &qty);
+        for (j = 0; j < qty; j++)
+          if (!strcmp (parts[j][0], "ori"))
+            net_ori_file (parts[j][1], OSets + i);
+        ut_string_string (oricrysym, &(OSets[i].crysym));
+
+        ut_free_3d_char (&parts, qty, 2);
+        ut_free_1d_int (&qty1);
+      }
+
+      else if (!strncmp (parts[i], "odf", 3))
+        net_ori_odf ((*pSSet).Random, parts[i], OSets + i);
 
       else
-        ut_print_message (2, 3, "Failed to process `%s'.\n", In.orisampling[level]);
+        net_ori_label (parts[i], SSet, dtess, dcell, OSets + i);
+
+      if (strstr (In.orioptiini[level], "weight="))
+      {
+        int qty, *qty1 = NULL;
+        char ***parts = NULL;
+        ut_list_break2 (In.orioptiini[level], ",", "=", &parts, &qty1, &qty);
+
+        OSets[i].weight = ut_alloc_1d (OSets[i].size);
+        for (j = 0; j < qty; j++)
+          if (!strcmp (parts[j][0], "weight"))
+            ut_array_1d_fnscanf_wcard (parts[j][1], OSets[i].weight, OSets[i].size, "numeral", "r");
+      }
+
+      if (strstr (In.orioptiini[level], "theta="))
+      {
+        int qty, *qty1 = NULL;
+        char ***parts = NULL;
+        ut_list_break2 (In.orioptiini[level], ",", "=", &parts, &qty1, &qty);
+
+        OSets[i].theta = ut_alloc_1d (OSets[i].size);
+        for (j = 0; j < qty; j++)
+          if (!strcmp (parts[j][0], "theta"))
+          {
+            ut_array_1d_fnscanf_wcard (parts[j][1], OSets[i].theta, OSets[i].size, "numeral", "r");
+            ut_array_1d_scale (OSets[i].theta, OSets[i].size, M_PI / 180);
+          }
+      }
     }
 
-    else if (!strncmp (parts[i], "fiber", 5))
-      net_ori_fiber (SSet, dtess, dcell, (*pSSet).Random, parts[i], OSets + i);
-
-    else if (!strncmp (ori, "file(", 5))
-    {
-      net_ori_file (ori, OSets + i);
-      ut_string_string (oricrysym, &(OSets[i].crysym));
-    }
-
-    else if (strstr (In.orioptiini[level], "ori="))
-    {
-      int qty, *qty1 = NULL;
-      char ***parts = NULL;
-      ut_list_break2 (In.orioptiini[level], ",", "=", &parts, &qty1, &qty);
-      for (j = 0; j < qty; j++)
-        if (!strcmp (parts[j][0], "ori"))
-          net_ori_file (parts[j][1], OSets + i);
-      ut_string_string (oricrysym, &(OSets[i].crysym));
-
-      ut_free_3d_char (&parts, qty, 2);
-      ut_free_1d_int (&qty1);
-    }
+    ol_set_cat (OSets, partqty, &OSet);
+    for (i = 0; i < partqty; i++)
+      size[i] = OSets[i].size;
 
-    else if (!strncmp (parts[i], "odf", 3))
-      net_ori_odf ((*pSSet).Random, parts[i], OSets + i);
+    if (ut_array_1d_int_sum (size, partqty) > ut_array_1d_int_max (size, partqty))
+      ol_set_shuf (&OSet, (*pSSet).Random);
 
-    else
-      net_ori_label (parts[i], SSet, dtess, dcell, OSets + i);
+    for (i = 0; i < partqty; i++)
+      ol_set_free (OSets + i);
+    free (OSets);
 
-    if (strstr (In.orioptiini[level], "weight="))
-    {
-      int qty, *qty1 = NULL;
-      char ***parts = NULL;
-      ut_list_break2 (In.orioptiini[level], ",", "=", &parts, &qty1, &qty);
-
-      OSets[i].weight = ut_alloc_1d (OSets[i].size);
-      for (j = 0; j < qty; j++)
-        if (!strcmp (parts[j][0], "weight"))
-          ut_array_1d_fnscanf_wcard (parts[j][1], OSets[i].weight, OSets[i].size, "numeral", "r");
-    }
+    net_ori_oricrysym (&OSet);
 
-    if (strstr (In.orioptiini[level], "theta="))
-    {
-      int qty, *qty1 = NULL;
-      char ***parts = NULL;
-      ut_list_break2 (In.orioptiini[level], ",", "=", &parts, &qty1, &qty);
-
-      OSets[i].theta = ut_alloc_1d (OSets[i].size);
-      for (j = 0; j < qty; j++)
-        if (!strcmp (parts[j][0], "theta"))
-        {
-          ut_array_1d_fnscanf_wcard (parts[j][1], OSets[i].theta, OSets[i].size, "numeral", "r");
-          ut_array_1d_scale (OSets[i].theta, OSets[i].size, M_PI / 180);
-        }
-    }
+    net_ori_memcpy (OSet, pSSet);
   }
 
-  ol_set_cat (OSets, partqty, &OSet);
-  for (i = 0; i < partqty; i++)
-    size[i] = OSets[i].size;
-
-  if (ut_array_1d_int_sum (size, partqty) > ut_array_1d_int_max (size, partqty))
-    ol_set_shuf (&OSet, (*pSSet).Random);
-
-  for (i = 0; i < partqty; i++)
-    ol_set_free (OSets + i);
-  free (OSets);
-
-  net_ori_oricrysym (&OSet);
-
-  net_ori_memcpy (OSet, pSSet);
-
   // processing -orispread
   net_ori_orispread (orispread, pSSet);
 

src/neper_t/net_ori/net_ori_.h

@@ -39,8 +39,6 @@ extern void net_ori_mtess_params (struct IN_T In, int level, struct MTESS MTess,
 
 extern int net_ori_mtess_randseed_rand (int *N, int *id, int *poly, int levelqty);
 
-extern void net_ori_memcpy (struct OL_SET OSet, struct SEEDSET *pSSet);
-
 extern void net_ori_orispread (char *orispread, struct SEEDSET *pSSet);
 
 extern void net_orispread_file (char *orispread, struct SEEDSET *pSSet);

src/neper_t/net_tess/net_tess_opt/net_tess_opt_init/net_tess_opt_init_sset/net_tess_opt_init_sset1.c

@@ -12,28 +12,36 @@ net_tess_opt_init_sset (struct IN_T In, int level, struct MTESS MTess,
   int pos;
   int *qty = ut_alloc_1d_int ((*pTOpt).CellQty + 1);
   double *rad = ut_alloc_1d ((*pTOpt).CellQty + 1);
-  char *var = NULL, *cooexpr = NULL, *weightexpr = NULL;
+  char *var = NULL, *cooexpr = NULL, *weightexpr = NULL, *idexpr = NULL, *oriexpr = NULL;
 
   if (!strcmp ((*pTOpt).optitype, "morpho"))
     ut_print_message (0, 2, "Setting seeds... ");
 
   net_tess_opt_init_sset_pre (In, level, MTess, Tess, dtess, dcell, SSet, &var,
-                              &pos, &weightexpr, &cooexpr, pTOpt);
+                              &pos, &weightexpr, &cooexpr, &idexpr, &oriexpr, pTOpt);
 
   if (!strcmp ((*pTOpt).optitype, "morpho"))
+  {
     net_tess_opt_init_sset_weight (MTess, Tess, dtess, dcell, *pTOpt, var, pos,
                                    weightexpr, rad);
-  else
-    ut_array_1d_set (rad + 1, (*pTOpt).CellQty, 1);
 
-  net_tess_opt_init_sset_multiseed (In, level, *pTOpt, var, rad, qty);
+    net_tess_opt_init_sset_multiseed (In, level, *pTOpt, var, rad, qty);
 
-  if (!strcmp ((*pTOpt).optitype, "morpho"))
     net_tess_opt_init_sset_coo (MTess, Tess, dtess, dcell, pTOpt, var, pos,
                                 cooexpr, rad, qty);
 
-  if (!strcmp ((*pTOpt).optitype, "ori"))
-    net_tess_opt_init_sset_ori (TessId, SSet, pTOpt);
+    if (oriexpr)
+      net_tess_opt_init_sset_ori (TessId, SSet, oriexpr, pTOpt);
+
+    if (idexpr)
+      net_tess_opt_init_sset_id (TessId, SSet, idexpr, pTOpt);
+  }
+
+  else if (!strcmp ((*pTOpt).optitype, "ori"))
+  {
+    ut_array_1d_set (rad + 1, (*pTOpt).CellQty, 1);
+    net_tess_opt_init_sset_ori (TessId, SSet, oriexpr, pTOpt);
+  }
 
   net_tess_opt_init_sset_post (In, level, Tess[dtess], dcell, pTOpt);
 
@@ -42,6 +50,8 @@ net_tess_opt_init_sset (struct IN_T In, int level, struct MTESS MTess,
   ut_free_1d_char (&var);
   ut_free_1d_char (&cooexpr);
   ut_free_1d_char (&weightexpr);
+  ut_free_1d_char (&idexpr);
+  ut_free_1d_char (&oriexpr);
 
   return;
 }

src/neper_t/net_tess/net_tess_opt/net_tess_opt_init/net_tess_opt_init_sset/net_tess_opt_init_sset_.h

@@ -23,5 +23,6 @@
 #include "net_tess_opt_init_sset_coo/net_tess_opt_init_sset_coo.h"
 #include "net_tess_opt_init_sset_multiseed/net_tess_opt_init_sset_multiseed.h"
 #include "net_tess_opt_init_sset_ori/net_tess_opt_init_sset_ori.h"
+#include "net_tess_opt_init_sset_id/net_tess_opt_init_sset_id.h"
 #include "net_tess_opt_init_sset_post/net_tess_opt_init_sset_post.h"
 #include "net_tess_opt_init_sset_pre/net_tess_opt_init_sset_pre.h"