Merge branch 'develop'

Author: davidfrantz

README.md

@@ -2,7 +2,7 @@
 
 **Framework for Operational Radiometric Correction for Environmental monitoring**
 
-**Version 3.7.4**
+**Version 3.7.5-develop**
 
 ![FORCE Logo](/images/force.png)
 

docs/source/history/v3.rst

@@ -1,5 +1,43 @@
 .. _v3:
 
+FORCE v. 3.7.5
+--------------
+
+Release: 04.01.2022
+
+* **FORCE HLPS**
+
+  * in force-higher-level, TSA sub-module:
+    Added a fix to prevent truncation of the Chlorophyll Index red-edge (Clre) index.
+    Thanks to Dirk Pflugmacher for the notification.
+
+  * in force-higher-level, ML sub-module:
+    Fixed a bug that resulted in a segfault when using RF classification, but
+    not with RF probability output.
+
+
+FORCE v. 3.7.4
+--------------
+
+Release: 12.11.2021
+
+* **FORCE L1AS**
+
+  * Stefan Ernst fixed some issues in force-level1-csd regarding checks for coorindate ranges and quotes.
+
+* **FORCE HLPS**
+
+  * in force-higher-level, all sub-modules:
+    Implemented a fix to prevent a segfault when we have many good cluster in the
+    spectral adjustment.
+
+* **FORCE AUX**
+
+  * fixed an error in ``force-tile-extent``, which still used the *old* syntax of
+    ``force-cube`` in its call.
+    Thanks to Fabian Thiel for the notification.
+
+
 FORCE v. 3.7.3
 --------------
 

docs/source/howto/udf.rst

@@ -11,7 +11,7 @@ This tutorial introduces User-Defined Functions in the FORCE Higher Level Proces
 
 .. admonition:: Info
 
-  *This tutorial uses FORCE v. 3.7.3*.
+  *This tutorial uses FORCE v. 3.7.4*.
 
   We assume that you already have an existing Level 2 ARD data pool, which contains preprocessed data for multiple years (see Level 2 ARD tutorial). 
   We also assume that you have a basic understanding of the higher-level processing system (see interpolation tutorial).

docs/source/index.rst

@@ -5,7 +5,7 @@ FORCE documentation
 
 **FORCE: Framework for Operational Radiometric Correction for Environmental monitoring**
 
-**Version 3.7.4**
+**Version 3.7.5-develop**
 
 `Download from Github <https://github.com/davidfrantz/force>`_.
 

docs/source/refs-applied.rst

@@ -3,14 +3,28 @@
 Applied Publications
 ====================
 
-This list summarizes all scientific publications that have used FORCE. If you have used FORCE, or are aware of unlisted papers, I would be happy if you you could send me your published papers with DOI, and I will include them here in this list (:ref:`contact`).
+This list summarizes all scientific publications that have used FORCE. 
+If you have used FORCE, or are aware of unlisted papers, 
+I would be happy if you you could send me your published papers with DOI, 
+and I will include them here in this list (:ref:`contact`).
 
 
+* **in press**
+
+  | M. Schwieder, M. Wesemeyer, D. Frantz, K. Pfoch, S. Erasmi, J. Pickert, C. Nendel, and P. Hostert (in press): Mapping grassland mowing events across Germany based on combined Sentinel-2 and Landsat 8 time series. Remote Sensing of Environment, 112795.
+  | https://doi.org/10.1016/j.rse.2021.112795
+
 * **2022**
 
+  | L. Blickensdörfer, M. Schwieder, D. Pflugmacher, C. Nendel, S. Erasmi, and P. Hostert (2022): Mapping of crop types and crop sequences with combined time series of Sentinel-1, Sentinel-2 and Landsat 8 data for Germany. Remote Sensing of Environment 269, 112831.
+  | https://doi.org/10.1016/j.rse.2021.112831
+
   | K. Kowalski, A. Okujeni, M. Brell, and P. Hostert (2022): Quantifying drought effects in Central European grasslands through regression-based unmixing of intra-annual Sentinel-2 time series. Remote Sensing of Environment 268, 112781.
   | https://doi.org/10.1016/j.rse.2021.112781
 
+  | M. Ziliani, M. Altaf, B. Aragon, R. Houburg, T. Franz, Y. Lu, J. Sheffield, I. Hoteit, and M. McCabe (2022): Early season prediction of within-field crop yield variability by assimilating CubeSat data into a crop model. Agricultural and Forest Meteorology 313, 108736.
+  | https://doi.org/10.1016/j.agrformet.2021.108736
+  
 * **2021**
 
   | J. Ardö (2021). A Sentinel-2 Dataset for Uganda. Data, 6. 
@@ -37,9 +51,11 @@ This list summarizes all scientific publications that have used FORCE. If you ha
   | F. Schug, D. Frantz, S. van der Linden, and P. Hostert (2021): Gridded population mapping for Germany based on building density, height and type from Earth Observation data using census disaggregation and bottom-up estimates. PLOS ONE 16, e0249044. 
   | https://doi.org/10.1371/journal.pone.0249044
 
-  | G. Tetteh, A. Gocht, S. Erasmi, M. Schwieder, and C. Conrad (): Evaluation of Sentinel-1 and Sentinel-2 Feature Sets for Delineating Agricultural Fields in Heterogeneous Landscapes. IEEE Access, 9, 116702 - 116719
+  | G. Tetteh, A. Gocht, S. Erasmi, M. Schwieder, and C. Conrad (2021): Evaluation of Sentinel-1 and Sentinel-2 Feature Sets for Delineating Agricultural Fields in Heterogeneous Landscapes. IEEE Access, 9, 116702 - 116719
   | https://doi.org/10.1109/ACCESS.2021.3105903
 
+  | F. Weiser, A. Sauer, D. Gettueva, R. Field, S. Irl, O. Vetaas, A. Chiarucci, S. Hoffmann, J. Fernández-Palacios, R. Otto, A. Jentsch, A. Provenzale, and C. Beierkuhnlein (2021): Impacts of Forest Fire on Understory Species Diversity in Canary Pine Ecosystems on the Island of La Palma. Forests 12, 1638.
+  | https://doi.org/10.3390/f12121638
 
 * **2020**
 
@@ -125,4 +141,3 @@ This list summarizes all scientific publications that have used FORCE. If you ha
 
   | A. Schneibel, M. Stellmes, A. Röder, M. Finckh, R. Revermann, D. Frantz and J. Hill (2016): Evaluating the trade-off between food and timber resulting from the conversion of Miombo forests to agricultural land in Angola using multi-temporal Landsat data. Science of The Total Environment, 548–549: 390-401. 
   | https://doi.org/10.1016/j.scitotenv.2015.12.137
-

src/cross-level/_version-cl.h

@@ -32,7 +32,7 @@ Version number
 extern "C" {
 #endif
 
-#define _VERSION_ "3.7.4"
+#define _VERSION_ "3.7.5-develop"
 
 #ifdef __cplusplus
 }

src/higher-level/index-hl.c

@@ -169,7 +169,7 @@ float ind, scale = 10000.0;
         if (!ard[t].msk[p]){
           ts->tss_[t][p] = nodata;
         } else {
-          ind = (ard[t].dat[b1][p]/ard[t].dat[b2][p])-1;
+          ind = (ard[t].dat[b1][p] / (float)ard[t].dat[b2][p]) - 1.0;
           if (ard[t].dat[b2][p] == 0 || ind*scale > SHRT_MAX || ind*scale < SHRT_MIN){
             ts->tss_[t][p] = nodata;
           } else {

src/higher-level/ml-hl.c

@@ -284,7 +284,7 @@ bool valid;
 
         mean = mean_old = var = 0;
         ntree = 0;
-        memset(mean_prob, 0, phl->mcl.nclass_all_sets*sizeof(double));
+        if (rfprob) memset(mean_prob, 0, phl->mcl.nclass_all_sets*sizeof(double));
 
         for (m=0; m<phl->mcl.nmodel[s]; m++, k++){
 

src/higher-level/read-ard-hl.c

@@ -332,10 +332,18 @@ int nchar;
   if (nchar < 0 || nchar >= NPOW_10){ 
     printf("Buffer Overflow in assembling dirname\n"); return FAILURE;}
 
+  #ifdef FORCE_DEBUG
+  printf("scanning %s for files\n", d.name);
+  #endif
+
   // directory listing
   if ((d.N = scandir(d.name, &d.LIST, 0, alphasort)) < 0){
     return FAILURE;}
 
+  #ifdef FORCE_DEBUG
+  printf("found %d files, filtering now\n");
+  #endif
+
   // reflectance products
   alloc_2D((void***)&d.list, d.N, NPOW_10, sizeof(char));
 
@@ -356,7 +364,11 @@ int nchar;
       // check against sensor list
       for (s=0, vs=false; s<sen->n; s++){
         if (strstr(d.LIST[t]->d_name, sen->sensor[s]) != NULL){
-          vs = true; break;
+          #ifdef FORCE_DEBUG
+          printf("sensor is: %s\n", sen->sensor[s]);
+          #endif
+          vs = true; 
+          break;
         }
       }
 
@@ -477,7 +489,7 @@ int n = 0;
   // get mask file listing, skip if tile is empty
   if (list_mask(tx, ty, phl, &dir) == FAILURE){
     #ifdef FORCE_DEBUG
-    printf("No data in here. Skip.\n");
+    printf("No data in here (no mask). Skip.\n");
     #endif
     *success = CANCEL;
     return NULL;
@@ -772,7 +784,7 @@ bool level3 = false;
   // get ARD file listing, skip if tile is empty
   if (list_ard(tx, ty, sen, phl, &dir) == FAILURE){
     #ifdef FORCE_DEBUG
-    printf("No data in here. Skip.\n");
+    printf("No data in here (datasets). Skip.\n");
     #endif
     *nt = 0;
     return NULL;