Update to latest code from development version.

.gitignore

@@ -1,6 +1,7 @@
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
+*$py.class
 
 # C extensions
 *.so
@@ -22,7 +23,9 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
-
+src/*.egg-info*
+src/*.egg*
+src/*.egg-info/
 # PyInstaller
 # Usually these files are written by a python script from a template
 # before PyInstaller builds the exe, so as to inject date/other infos into it.
@@ -41,7 +44,9 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
-*,cover
+*.cover
+
+.hypothesis/
 
 # Translations
 *.mo
@@ -58,6 +63,16 @@ target/
 
 # Temporary files
 *.*~
+*~
+
+# Auxiliary image files
+*.tif.*
+Output/*.tif.*
+Input/*.tif.*
 
 # Jupyter Notebooks Checkpoints
 .ipynb_checkpoints/
+
+#Ipython Notebook
+.ipynb_checkpoints
+

CITATION.txt

@@ -48,6 +48,41 @@ In BibTeX format:
  Number = {7},
  Pages = {2809--2825},
  Volume = {17},
-
  Doi = {10.5194/hess-17-2809-2013}
 }
+
+If you use the Dual Angle inversion approach for obtaining canopy and soil temperature with 4SAIL you *must* cite the following paper
+
+Guzinski, R., Nieto, H., Stisen, S., & Fensholt, R. (2015) Inter-comparison of energy balance and hydrological models for land surface energy flux estimation over a whole river catchment, Hydrology and Earth System Sciences, 19, 2017-2036. 
+
+In BibTeX format:
+
+@Article{Guzinski2015,
+ Title = {Inter-comparison of energy balance and hydrological models for land surface energy flux estimation over a whole river catchment},
+ Author = {Guzinski, R. and Nieto, H. and Stisen, S. and Fensholt, R.},
+ Journal = {Hydrology and Earth System Sciences},
+ Year = {2015},
+ Number = {4},
+ Pages = {2017--2036},
+ Volume = {19},
+ Doi = {10.5194/hess-19-2017-2015},
+ Url = {http://www.hydrol-earth-syst-sci.net/19/2017/2015/}
+}
+
+If you use different coefficients for the Kustas and Norman resistances you *must* cite the following paper.
+
+William P. Kustas, Hector Nieto, Laura Morillas, Martha C. Anderson, Joseph G. Alfieri, Lawrence E. Hipps, Luis Villagarcía, Francisco Domingo, Monica Garcia: Revisiting the paper “Using radiometric surface temperature for surface energy flux estimation in Mediterranean drylands from a two-source perspective”, Remote Sensing of Environment, In Press. doi:10.1016/j.rse.2016.07.024.
+
+In BibTeX format:
+
+@Article{Kustas2016,
+ Title = {Revisiting the paper “Using radiometric surface temperature for surface energy flux estimation in Mediterranean drylands from a two-source perspective” },
+ Author = {William P. Kustas and Hector Nieto and Laura Morillas and Martha C. Anderson and Joseph G. Alfieri and Lawrence E. Hipps and Luis Villagarcía and Francisco Domingo and Monica Garcia},
+ Journal = {Remote Sensing of Environment },
+ Year = {2016},
+ Pages = { - },
+ Doi = {http://dx.doi.org/10.1016/j.rse.2016.07.024},
+ ISSN = {0034-4257},
+ Url = {http://www.sciencedirect.com/science/article/pii/S0034425716302814}
+}
+

Config_LocalImage.txt

@@ -1,103 +1,111 @@
 # TSEB model to run: [TSEB_PT: Kustas and Norman 1999 Priestley-Taylor TSEB, DTD: Norman et al. 2003 Dual Time Differenced TSEB, TSEB_2T: Component temperatures TSEB (To be implemented the patched/parallel very high resolution TSEB]
-TSEB_MODEL=TSEB_PT
+model=TSEB_PT
 
 #==============================================================================
 # Input Files with full path (any valid gdal raster file is accepcted (not HDF or NetCDF!!!)
 # Use forward slash '/' for path separators, even using Windows
 #==============================================================================
-# Input land surface temperature in Kelvin # mandatory file
-#If running DTD the input LST should contain at least 2 bands: [band 1: LST at time 1, band 2: LST at time 0 (sunrise)]
-#If running TSEB_2A the input LST should contain at least 2 bands: [band 1: Canopy temperature, band 2: soil temperature]
 
-Input_LST=./Input/ExampleImage_Trad_pm_am.tif
+# Input land surface temperature in Kelvin # mandatory file
+# If running DTD both T_R0 (sunrise) and T_R1 inputs are required
+# If running TSEB_2A the input T_R1 should contain at least 2 bands: [band 1: Canopy temperature, band 2: soil temperature]
+T_R1=./Input/ExampleImage_Trad_pm.tif
+T_R0=./Input/ExampleImage_Trad_am.tif
 
 # View Zenith Angle (degrees) # Optional, type either a full-path file or a single value for a constant value acroos the area
-Input_VZA=0.0 
+VZA=0.0 
 
 # Processing Mask (boolean) # Optional, type a full-path file for processing only on non-masked pixels (all pixels with values > 0 in the mask image will be processed)
-USE_MASK=0
+input_mask=0
 
 # Effective Leaf Area Index (m2/m2) # Optional, type either a full-path file or a single value for a constant value acroos the area
-Input_LAI=./Input/ExampleImage_LAI.tif
+LAI=./Input/ExampleImage_LAI.tif
 
 # Vegetation Fractional Cover # Optional, type either a full-path file or a single value for a constant value acroos the area
-Input_Fc=./Input/ExampleImage_Fc.tif
+f_c=./Input/ExampleImage_Fc.tif
 
 # Canopy height (m)# Optional, type either a full-path file or a single value for a constant value along the area
-Input_Hc=2.4 
+h_C=2.4 
 
 # Canopy height/with ratio (wc/hc) # Optional, type either a full-path file or a single value for a constant value along the area
-Input_Wc=1 
+w_C=1 
 
 # Green Fraction # Optional, type either a full-path file or a single value for a constant value along the area
-Input_Fg=1
+f_g=1
 
 #==============================================================================
 # Output File
 #==============================================================================
 # full path to output directory, The output GeoTIFF files will be stored in that folder with a standard name : Output_<TSEB_MODEL>.tif and Output_<TSEB_MODEL>_ancillary.tif
-OutputFile=./Output/test_image.tif
+output_file=./Output/test_image.tif
 
 #==============================================================================
 # Site Description
 #==============================================================================
 lat=38.289355 
 lon=-121.117794
-altitude=97
+alt=97
 stdlon=-105.0
-z_t=5
+z_T=5
 z_u=5
 
 
 #==============================================================================
 # Meteorology
 #==============================================================================
 DOY=221 
-Time=10.9992 
-Ta_0=291.11
-Ta_1=299.18
+time=10.9992 
+T_A0=291.11
+T_A1=./Input/ExampleImage_Ta.tif
 u=2.15
 p=1011
 ea=13.4
-Sdn=861.74
-Ldn=''
+S_dn=861.74
+L_dn=
 
 #==============================================================================
 # Canopy and Soil spectra
 #==============================================================================
-emisVeg=0.98 # leaf emissivity
-emisGrd=0.95 # soil emissivity
+emis_C=0.98 # leaf emissivity
+emis_S=0.95 # soil emissivity
 
-# Leaf spectral properties:{rho_leaf_vis: visible reflectance,tau_leaf_vis: visible transmittance, rho_leaf_nir: NIR reflectance, tau_leaf_nir: NIR transmittance}
-rhovis=0.07
-tauvis=0.08
-rhonir=0.32
-taunir=0.33 
+# Leaf spectral properties:{rho_vis_C: visible reflectance, tau_vis_C: visible transmittance, rho_nir_C: NIR reflectance, tau_nir_C: NIR transmittance}
+rho_vis_C=0.07
+tau_vis_C=0.08
+rho_nir_C=0.32
+tau_nir_C=0.33 
 
-# Leaf spectral properties:{rsoilv: visible reflectance, rsoiln: NIR reflectance}
-rsoilv=0.15
-rsoiln=0.25
+# Soil spectral properties:{rho_vis_S: visible reflectance, rho_nir_S: NIR reflectance}
+rho_vis_S=0.15
+rho_nir_S=0.25
 
 #==============================================================================
 # Canopy and soil parameters
 #==============================================================================
 # Initial value for Priestley Taylor canopy transpiration
-Max_alpha_PT=1.26 
+alpha_PT=1.26 
 
 # Cambpbell 1990 leaf inclination distribution parameter:[x_LAD=1 for spherical LIDF, x_LAD=0 for vertical LIDF, x_LAD=float(inf) for horzontal LIDF] 
 x_LAD=1 
 
 # Bare soil roughness lenght (m)
 z0_soil=0.01 
 
- # Primary land cover CROP=11, GRASS=2, SHRUB=5, CONIFER=4, BROADLEAVED=3
-LANDCOVER=3
+# Primary land cover IGBP Land Cover Type Classification: CROP=12, GRASS=10, SHRUB=6, CONIFER=1, BROADLEAVED=4
+landcover=4
 
 # leaf effective width (m)
 leaf_width=0.1 
 
-# Green fraction
-f_g=1
+
+#==============================================================================
+# Resistances
+#==============================================================================
+resistance_form=0 # Resistance formulations: 0 - Kustas & Norman 1999; 1 - Choudhury & Monteih 1998; 2 - McNaughton & Van der Hurk 1995
+KN_b=0.012 # Kustas & Norman formulation parameter
+KN_c=0.0025 # Kustas & Norman formulation parameter
+KN_C_dash=90 # Kustas & Norman formulation parameter
+
 
 #==============================================================================
 # Additional options
@@ -106,9 +114,9 @@ f_g=1
 #1: default, estimate G as a ratio of Rn_soil, default G_ratio=0.35
 #0: Use a constant G, usually use G_Constant=0 to ignore the computation of G
 #2: estimate G from Santanello and Friedl with GAmp the maximum ration amplitude, Gphase, the time shift between G and Rn (hours) and Gshape the typical diurnal shape (hours)
-CalcG=0
+G_form=1
 G_ratio=0.35
 G_constant=0
-GAmp=0.35
-Gphase=3
-Gshape=24
+G_amp=0.35
+G_phase=3
+G_shape=24

Config_PointTimeSeries.txt

@@ -1,6 +1,6 @@
-# TSEB model to run: 
+# TSEB model to run: 
 # TSEB_PT: Kustas and Norman 1999 Priestley-Taylor TSEB, DTD: Norman et al. 2003 Dual Time Differenced TSEB, TSEB_2T: Component temperatures TSEB (To be implemented the patched / parallel very high resolution TSEB
-TSEB_MODEL=TSEB_PT
+model=TSEB_PT
 
 #==============================================================================
 # Input ASCII File with full path
@@ -14,48 +14,59 @@ TSEB_MODEL=TSEB_PT
 # Additional input variables are: 'SAA': solar azimuth angle, 'SZA': solar zenith angle, 'Ldn': incoming longwave radiation, 'f_C': fractional cover, 'f_g': green fraction, 'wc': canopy width to height ratio, 'G': soil heat flux (see G_Calc flag below)
 # Other variables included (accidentaly or on purpose) in the text file are ignored
 
-InputFile=./Input/ExampleTableInput.txt# mandatory file
+input_file=./Input/ExampleTableInput.txt# mandatory file
 
 #==============================================================================
 # Output paramters
 #==============================================================================
 # full path to the output file table
-OutputFile=./Output/OutputTest.txt
+output_file=./Output/OutputTest.txt
 
 #==============================================================================
 # Site Parameters
 #==============================================================================
 lat=31.74 # Site latitude (degrees)
 lon= -110.05 # Site Longitue (degrees)
-altitude=1371 # Site altitude (m)
+alt=1371 # Site altitude (m)
 stdlon=-105 # Standard longitude of time zone (degrees)
-z_t=4.0 # Measurement height of air temperature (m)
+z_T=4.0 # Measurement height of air temperature (m)
 z_u=4.3 # Measurement height of wind speed (m)
 
 #==============================================================================
 # Canopy and Soil spectra
 #==============================================================================
-emisVeg=0.98 # leaf emissivity
-emisGrd=0.95 # soil emissivity
+emis_C=0.98 # leaf emissivity
+emis_S=0.95 # soil emissivity
 
-# Leaf spectral properties:{rho_leaf_vis: visible reflectance,tau_leaf_vis: visible transmittance, rho_leaf_nir: NIR reflectance, tau_leaf_nir: NIR transmittance}
-rhovis=0.094
-tauvis=0.021
-rhonir=0.345
-taunir=0.203 
+# Leaf spectral properties:{rho_vis_C: visible reflectance, tau_vis_C: visible transmittance, rho_nir_C: NIR reflectance, tau_nir_C: NIR transmittance}
+rho_vis_C=0.094
+tau_vis_C=0.021
+rho_nir_C=0.345
+tau_nir_C=0.203 
 
-# Leaf spectral properties:{rsoilv: visible reflectance, rsoiln: NIR reflectance}
-rsoilv=0.111
-rsoiln=0.410
+# Soil spectral properties:{rho_vis_S: visible reflectance, rho_nir_S: NIR reflectance}
+rho_vis_S=0.111
+rho_nir_S=0.410
 
 #==============================================================================
 # Canopy and soil parameters
 #==============================================================================
-Max_alpha_PT=1.26# Initial value for Priestley Taylor canopy transpiration
+alpha_PT=1.26 # Initial value for Priestley Taylor canopy transpiration
 x_LAD=1 # Cambpbell 1990 leaf inclination distribution parameter:[x_LAD=1 for spherical LIDF, x_LAD=0 for vertical LIDF, x_LAD=float(inf) for horzontal LIDF] 
 z0_soil=0.05 # Bare soil roughness lenght (m)
-LANDCOVER=5 # Primary land cover CROP=11, GRASS=2, SHRUB=5, CONIFER=4, BROADLEAVED=3
+landcover=6 # Primary land cover according to IGBP Land Cover Type Classification: CROP=12, GRASS=10, SHRUB=6, CONIFER=1, BROADLEAVED=4
 leaf_width=0.01 # leaf effective width (m)
+f_c=1 # Fractional cover
+f_g=1 # Green vegetation fraction
+w_C=1 # Canopy width to height ratio
+
+#==============================================================================
+# Resistances
+#==============================================================================
+resistance_form=0 # Resistance formulations: 0 - Kustas & Norman 1999; 1 - Choudhury & Monteih 1998; 2 - McNaughton & Van der Hurk 1995
+KN_b=0.012 # Kustas & Norman formulation parameter
+KN_c=0.0025 # Kustas & Norman formulation parameter
+KN_C_dash=90 # Kustas & Norman formulation parameter
 
 #==============================================================================
 # Additional options
@@ -64,9 +75,9 @@ leaf_width=0.01 # leaf effective width (m)
 #1: default, estimate G as a ratio of Rn_soil, default G_ratio=0.35
 #0: Use a constant G, usually use G_Constant=0 to ignore the computation of G
 #2: estimate G from Santanello and Friedl with GAmp the maximum ration amplitude, Gphase, the time shift between G and Rn (hours) and Gshape the typical diurnal shape (hours)
-CalcG=0
+G_form=0
 G_ratio=0.35
 G_constant=0
-GAmp=0.35
-Gphase=3
-Gshape=24
+G_amp=0.35
+G_phase=3
+G_shape=24

Input/ExampleTableInput.txt

@@ -1,4 +1,4 @@
-Site Year DOY Time Sdn Rn G H LE Ta u Ts Tc Trad RH ea LAI hc fc VZA Ta_0 Trad_0
+Site year DOY time S_dn Rn G H LE T_A1 u T_S T_C T_R1 RH ea LAI h_C f_c VZA T_A0 T_R0
 1 1990 209 0.5 0 -60 -87 12 -40 293.75 1.56 290.68 290.08 289.59 52 12.61139746 0.5 0.5 0.28 0 295.69 294.17
 1 1990 209 1.5 0 -57 -85 18 -45 292.67 2.11 290.1 289.74 289.12 58 13.15634245 0.5 0.5 0.28 0 295.69 294.17
 1 1990 209 2.5 0 -47 -77 17 -48 293.2 2 290.54 290.12 289.51 55 12.89308837 0.5 0.5 0.28 0 295.69 294.17

Input/ExampleTableInput_Headers.txt

@@ -2,24 +2,24 @@
 
 Year Year (YYYY)
 DOY Day of the Year (0-366)
-Time Decimal time (hrs), use the stdlong parameter to set the time zone
-Trad Radiometric composite temperature (Kelvin)
-Trad_0 Radiometric composite temperature near sunrise (Kelvin). OPTIONAL, only needed for DTD model.
-Tc Canopy component temperature (Kelvin). OPTIONAL only needed for the TSEB-2T model
-Ts Soil component temperature (Kelvin). OPTIONAL only needed for the TSEB-2T model
+time Decimal time (hrs), use the stdlong parameter to set the time zone
+T_R1 Radiometric composite temperature (Kelvin)
+T_R0 Radiometric composite temperature near sunrise (Kelvin). OPTIONAL, only needed for DTD model.
+T_C Canopy component temperature (Kelvin). OPTIONAL only needed for the TSEB-2T model
+T_S Soil component temperature (Kelvin). OPTIONAL only needed for the TSEB-2T model
 VZA View Zenith Angle (Degrees)
 SZA Solar Zenith Angle (Degrees). OPTIONAL, will be estimated otherwise
 SAA Solar Azimuth Angle (Degrees). OPTIONAL, will be estimated otherwise
-Ta Air temperature (Kelvin)
-Ta_0 Air temperature near sunrise (Kelvin). OPTIONAL only needed for DTD model
+T_A1 Air temperature (Kelvin)
+T_A0 Air temperature near sunrise (Kelvin). OPTIONAL only needed for DTD model
 u Wind speed (m/s)
 ea Vapor pressure (mb)
 p Atmospheric pressure (mb). OPTIONAL, will be estimated otherwise
-Sdn Incoming shortwave irradiance (W/m2)
-Ldn Incoming longwave irradiance (W/m2). OPTIONAL will be estimated otherwise
+S_dn Incoming shortwave irradiance (W/m2)
+L_dn Incoming longwave irradiance (W/m2). OPTIONAL will be estimated otherwise
 LAI Effective Leaf Area Index (m2/m2)
-hc Canopy height (m)
-fc Fractional cover (0-1). OPTIONAL, will be set to full cover (fc=1) otherwise
-fg Green fraction (0-1). OPTIONAL, will be set to full green vegetation (fg=1) otherwise
-wc Canopy with to height ratio (m/m). OPTIONAL, will be set to spherical/squared canopies (wc=1) otherwise
+h_C Canopy height (m)
+f_c Fractional cover (0-1). OPTIONAL, will be set to full cover (fc=1) otherwise
+f_g Green fraction (0-1). OPTIONAL, will be set to full green vegetation (fg=1) otherwise
+w_C Canopy with to height ratio (m/m). OPTIONAL, will be set to spherical/squared canopies (wc=1) otherwise
 G Soil heat flux (W/m2). OPTIONAL, will be estimated otherwise