Merge branch 'rm-splits' into simpler-make

Author: davidfrantz

Dockerfile

@@ -43,7 +43,6 @@ COPY --chown=docker:docker . .
 
 # Build, install, check FORCE
 RUN echo "building FORCE" && \
-  ./splits.sh enable && \
   ./debug.sh $debug && \
   sed -i "/^INSTALLDIR=/INSTALLDIR=$INSTALL_DIR/" Makefile && \
   make -j && \

Makefile

@@ -243,7 +243,7 @@ misc:
 ### dummy code for testing stuff  
 
 #dummy: temp cross aux higher src/dummy.c
-#	$(G11) $(CFLAGS) $(GDAL) $(GSL) $(CURL) $(SPLITS) $(OPENCV) $(PYTHON) $(PYTHON2) $(RSTATS) -o $(TB)/dummy src/dummy.c $(TC)/*.o $(TA)/*.o $(TH)/*.o $(LDGDAL) $(LDGSL) $(LDCURL) $(LDSPLITS) $(LDOPENCV) $(LDPYTHON) $(LDRSTATS)
+#	$(G11) $(CFLAGS) $(GDAL) $(GSL) $(CURL) $(OPENCV) $(PYTHON) $(PYTHON2) $(RSTATS) -o $(TB)/dummy src/dummy.c $(TC)/*.o $(TA)/*.o $(TH)/*.o $(LDGDAL) $(LDGSL) $(LDCURL) $(LDOPENCV) $(LDPYTHON) $(LDRSTATS)
 
 
 ##########################################################################

docs.sh

@@ -1,11 +1,11 @@
 #!/bin/bash
 
-make -j force-parameter
+make -j aux
 
-MOD=$(temp-bin/force-parameter -m | grep -v 'available modules' | sed 's/^ *//' | cut -d ':' -f 1)
+MOD=$(bin/force-parameter -m | grep -v 'available modules' | sed 's/^ *//' | cut -d ':' -f 1)
 
 for m in $MOD; do
-  temp-bin/force-parameter docs/source/_static/parameter-files/parameter_$m.prm $m
+  bin/force-parameter docs/source/_static/parameter-files/parameter_$m.prm $m
 done
 
 make clean

docs/source/_static/parameter-files/parameter_TSA.prm

@@ -406,75 +406,6 @@ OUTPUT_CAM = FALSE
 OUTPUT_CAW = FALSE
 OUTPUT_CAD = FALSE
 
-# LAND SURFACE PHENOLOGY PARAMETERS - SPLITS-BASED
-# ------------------------------------------------------------------------
-# The Land Surface Phenology (LSP) options are only available if FORCE was
-# compiled with SPLITS (see installation section in the FORCE user guide).
-# ------------------------------------------------------------------------
-# For estimating LSP for one year, some data from the previous/next year
-# need to be considered to find the seasonal minima, which define a season.
-# The parameters are given in DOY, i.e. LSP_DOY_PREV_YEAR = 273, and 
-# LSP_DOY_NEXT_YEAR = 91 will use all observations from October (Year-1)
-# to March (Year+1)
-# Type: Integer. Valid range: [1,365]
-LSP_DOY_PREV_YEAR = 273
-LSP_DOY_NEXT_YEAR = 91
-# Seasonality is of Northern-, Southern-hemispheric or of mixed type? If
-# mixed, the code will attempt to estimate the type on a per-pixel basis.
-# Type: Character. Valid values: {NORTH,SOUTH,MIXED}
-LSP_HEMISPHERE = NORTH
-# How many segments per year should be used for the spline fitting? More
-# segments follow the seasonality more closely, less segments smooth the
-# time series stronger.
-# Type: Integer. Valid range: [1,...
-LSP_N_SEGMENT = 4
-# Amplitude threshold for detecing Start, and End of Season, i.e. the date,
-# at which xx% of the amplitude is observed
-# Type: Float. Valid range: ]0,1[
-LSP_AMP_THRESHOLD = 0.2
-# LSP won't be derived if the seasonal index values do not exceed following
-# value. This is useful to remove unvegetated surfaces.
-# Type: Integer. Valid range: [-10000,10000]
-LSP_MIN_VALUE = 500
-# LSP won't be derived if the seasonal amplitude is below following value
-# This is useful to remove surfaces that do not have a seasonality.
-# Type: Integer. Valid range: [0,10000]
-LSP_MIN_AMPLITUDE = 500
-# Which Phenometrics should be computed? There will be a LSP output file for
-# each metric (with years as bands).
-# Currently available are the dates of the early minimum, start of season,
-# rising inflection, peak of season, falling inflection, end of season, late
-# minimum; lengths of the total season, green season; values of the early
-# minimum, start of season, rising inflection, peak of season, falling 
-# inflection, end of season, late minimum, base level, seasonal amplitude;
-# integrals of the total season, base level, base+total, green season; rates
-# of average rising, average falling, maximum rising, maximum falling.
-# Type: Character list. Valid values: {DEM,DSS,DRI,DPS,DFI,DES,DLM,LTS,LGS,
-#   VEM,VSS,VRI,VPS,VFI,VES,VLM,VBL,VSA,IST,IBL,IBT,IGS,RAR,RAF,RMR,RMF}
-LSP = VSS VPS VES VSA RMR IGS
-# Standardize the LSP time series with pixel mean and/or standard deviation?
-# Type: Logical. Valid values: {NONE,NORMALIZE,CENTER}
-STANDARDIZE_LSP = NONE
-# Output the Spline fit? This is a layer stack of fitted index values for
-# interpolated date.
-# Type: Logical. Valid values: {TRUE,FALSE}
-OUTPUT_SPL = FALSE
-# Output the Phenometrics? These are layer stacks per phenometric with as many
-# bands as years (excluding one year at the beginning/end of the time series).
-# Type: Logical. Valid values: {TRUE,FALSE}
-OUTPUT_LSP = FALSE
-# Compute and output a linear trend analysis on the requested Phenometric time
-# series? Note that the OUTPUT_LSP parameters don't need to be TRUE to do this.
-# See also the TREND PARAMETERS block below.
-# Type: Logical. Valid values: {TRUE,FALSE}
-OUTPUT_TRP = FALSE
-# Compute and output an extended Change, Aftereffect, Trend (CAT) analysis on
-# the requested Phenometric time series?
-# Note that the OUTPUT_LSP parameters don't need to be TRUE to do this.
-# See also the TREND PARAMETERS block below.
-# Type: Logical. Valid values: {TRUE,FALSE}
-OUTPUT_CAP = FALSE
-
 # LAND SURFACE PHENOLOGY PARAMETERS - POLAR-BASED
 # ------------------------------------------------------------------------
 # Please note that these only work well with non-negative indices.--------

docs/source/components/higher-level/tsa/format.rst

@@ -148,8 +148,6 @@ Example filename: 1984-2020_182-274_HL_TSA_LNDLG_TCG_STM.tif
 +                + TRX     + Trend Analysis on Folds (replace X with Table 2)        +
 +                +---------+---------------------------------------------------------+
 +                + CAX     + Extended CAT Analysis on Folds (replace X with Table 2) +
-+                +---------+---------------------------------------------------------+
-+                + SPL     + Spline fitted Time Series                               +
 +----------------+---------+---------------------------------------------------------+
 + 36-42          + Product Type: Phenometrics (replace XXX with Table 3)             +
 +                +---------+---------------------------------------------------------+
@@ -204,95 +202,87 @@ Phenology
 
 **Table 3:** Phenology name tags
 
-+-----+---------------------------------------------------+-------+--------+
-+ Tag + Description                                       + Polar + SPLITS +
-+=====+===================================================+=======+========+
-+ DEM + Date of Early Minimum                             + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ DSS + Date of Start of Season                           + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ DRI + Date of Rising Inflection                         +       + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ DPS + Date of Peak of Season                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ DMS + Date of Mid of Season                             + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ DFI + Date of Falling Inflection                        +       + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ DES + Date of End of Season                             + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ DLM + Date of Late Minimum                              + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ DEV + Date of Early Average Vector                      + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ DAV + Date of Average Vector                            + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ DLV + Date of Late Average Vector                       + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ DPY + Date of Start of Phenological Year                + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ DPV + delta Date of adaptive Start of Phenological Year + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ LTS + Length of Total Season                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ LGS + Length of Green Season                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ LGV + Length of between early/late vectors              + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VEM + Value of Early Minimum                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VSS + Value of Start of Season                          + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VRI + Value of Rising Inflection                        +       + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VPS + Value of Peak of Season                           + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VMS + Value of Mid of Season                            + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VFI + Value of Falling Inflection                       +       + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VES + Value of End of Season                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VLM + Value of Late Minimum                             + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VEV + Value of Early Average Vector                     + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VAV + Value of Average Vector                           + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VLV + Value of Late Average Vector                      + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VBL + Value of Base Level                               + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VSA + Value of Seasonal Amplitude                       + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ VGA + Value of Green Amplitude                          + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VPA + Value of Peak Amplitude                           + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VGM + Value of Green Mean                               + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ VGV + Value of Green Variability                        + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ IST + Integral of Total Season                          + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ IBL + Integral of Base Level                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ IBT + Integral of Base+Total                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ IGS + Integral of Green Season                          + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ IRR + Integral of Rising Rate                           + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ IFR + Integral of Falling Rate                          + X     +        +
-+-----+---------------------------------------------------+-------+--------+
-+ RAR + Rate of Average Rising                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ RAF + Rate of Average Falling                           + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ RMR + Rate of Maximum Rising                            + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
-+ RMF + Rate of Maximum Falling                           + X     + X      +
-+-----+---------------------------------------------------+-------+--------+
++-----+---------------------------------------------------+
++ Tag + Description                                       +
++=====+===================================================+
++ DEM + Date of Early Minimum                             +
++-----+---------------------------------------------------+
++ DSS + Date of Start of Season                           +
++-----+---------------------------------------------------+
++ DPS + Date of Peak of Season                            +
++-----+---------------------------------------------------+
++ DMS + Date of Mid of Season                             +
++-----+---------------------------------------------------+
++ DES + Date of End of Season                             +
++-----+---------------------------------------------------+
++ DLM + Date of Late Minimum                              +
++-----+---------------------------------------------------+
++ DEV + Date of Early Average Vector                      +
++-----+---------------------------------------------------+
++ DAV + Date of Average Vector                            +
++-----+---------------------------------------------------+
++ DLV + Date of Late Average Vector                       +
++-----+---------------------------------------------------+
++ DPY + Date of Start of Phenological Year                +
++-----+---------------------------------------------------+
++ DPV + delta Date of adaptive Start of Phenological Year +
++-----+---------------------------------------------------+
++ LTS + Length of Total Season                            +
++-----+---------------------------------------------------+
++ LGS + Length of Green Season                            +
++-----+---------------------------------------------------+
++ LGV + Length of between early/late vectors              +
++-----+---------------------------------------------------+
++ VEM + Value of Early Minimum                            +
++-----+---------------------------------------------------+
++ VSS + Value of Start of Season                          +
++-----+---------------------------------------------------+
++ VPS + Value of Peak of Season                           +
++-----+---------------------------------------------------+
++ VMS + Value of Mid of Season                            +
++-----+---------------------------------------------------+
++ VES + Value of End of Season                            +
++-----+---------------------------------------------------+
++ VLM + Value of Late Minimum                             +
++-----+---------------------------------------------------+
++ VEV + Value of Early Average Vector                     +
++-----+---------------------------------------------------+
++ VAV + Value of Average Vector                           +
++-----+---------------------------------------------------+
++ VLV + Value of Late Average Vector                      +
++-----+---------------------------------------------------+
++ VBL + Value of Base Level                               +
++-----+---------------------------------------------------+
++ VSA + Value of Seasonal Amplitude                       +
++-----+---------------------------------------------------+
++ VGA + Value of Green Amplitude                          +
++-----+---------------------------------------------------+
++ VPA + Value of Peak Amplitude                           +
++-----+---------------------------------------------------+
++ VGM + Value of Green Mean                               +
++-----+---------------------------------------------------+
++ VGV + Value of Green Variability                        +
++-----+---------------------------------------------------+
++ IST + Integral of Total Season                          +
++-----+---------------------------------------------------+
++ IBL + Integral of Base Level                            +
++-----+---------------------------------------------------+
++ IBT + Integral of Base+Total                            +
++-----+---------------------------------------------------+
++ IGS + Integral of Green Season                          +
++-----+---------------------------------------------------+
++ IRR + Integral of Rising Rate                           +
++-----+---------------------------------------------------+
++ IFR + Integral of Falling Rate                          +
++-----+---------------------------------------------------+
++ RAR + Rate of Average Rising                            +
++-----+---------------------------------------------------+
++ RAF + Rate of Average Falling                           +
++-----+---------------------------------------------------+
++ RMR + Rate of Maximum Rising                            +
++-----+---------------------------------------------------+
++ RMF + Rate of Maximum Falling                           +
++-----+---------------------------------------------------+
 
 
 File format

docs/source/components/higher-level/tsa/index.rst

@@ -66,13 +66,11 @@ hARD+ products can be directly used to fuel your research questions without any
   * If folded by day, the observations are grouped by DOY, which gives up to 365 values per pixel.
 
 * Annual Land Surface Phenology (LSP) metrics a.k.a. phenometrics can be extracted.
-  This option is only available if FORCE was compiled with SPLITS (see :ref:`depend-opt`).
-  The SPLITS code fits a spline to the time series in a first step (can be output).
-  The number of segments for fitting the splines need to be specified (in segments per year); more segments give a more detailed fit; the detail vs. smoothing capability of the spline needs to be considered with respect to application, land cover of interest and data density.
   Deriving LSP will only work nicely if data availability throughout the year is high; do not expect good results for sparse data.
   To derive LSP metrics for a given year, some data from the previous and next year need to be included, as the early/late minima may not be found in the year of interest (the data range can be specified by the user).
-  The same can be true for the peak.
-  The user can select if a Northern hemisphere (peak assumed in the middle of the year), Southern hemisphere (peak is assumed around the turn of the year) or mixed phenology (both can happen, let the program decide) should be assumed.
+  The same can be true for the peak. 
+  The code will autodetect whether we have a Northern hemisphere (peak assumed in the middle of the year) or Southern hemisphere (peak is assumed around the turn of the year) type of phenology.
+  This decision is taken on the pixel-level.
   In total, 26 LSP metrics can be derived for each year (see :ref:`tsa-format`).
 
 * Trend analysis and/or an change/trend analyses can be performed on any of the folded and/or LSP time series.