included the r scripts

included the r scripts in github to have a better versioning control.

ArcGIS/##Arcpy on Python Console ArcMAP.py

@@ -0,0 +1,89 @@
+##Arcpy on Python Console ArcMAP
+#################### CHANGE SYMBOLOGY###############
+import arcpy, sys
+
+try:
+    symbologyLayer = arcpy.mapping.Layer(sys.argv[1])
+except:
+    arcpy.AddError("Input parameters could not be resolved")
+    sys.exit(-1)
+
+arcpy.AddMessage("Source Layer is %s" % symbologyLayer.symbologyType)
+
+# Exit if the source layer is broken
+if symbologyLayer.isBroken:
+    arcpy.AddError("Source layer is broken")
+    sys.exit(-2)
+
+# Exit if the source layer is not a raster layer
+if not symbologyLayer.isRasterLayer:
+    arcpy.AddError("Source layer is not a raster layer")
+    sys.exit(-3)    
+mxd = arcpy.mapping.MapDocument("Current") # This MXD
+
+#df = arcpy.mapping.ListDataFrames(mxd,"Georgia")[0] # the first data frame called Georgia
+df = arcpy.mapping.ListDataFrames(mxd)[0] # Just the first data frame in the MXD
+rasters = arcpy.mapping.ListLayers(mxd,"*",df) # all the layers
+
+for ThisLayer in rasters:
+    arcpy.AddMessage( "Working on " + ThisLayer.name)
+    if not ThisLayer.isBroken: # only try to work with layers that aren't broken
+        arcpy.AddMessage( "-not broken")
+        if not ThisLayer.name.upper() == symbologyLayer.name.upper():
+            arcpy.AddMessage( "-not the source layer")
+            # not the source layer
+            if ThisLayer.isRasterLayer:
+                arcpy.AddMessage( "-is a raster layer")
+                # only applies to raster layers
+                arcpy.CalculateStatistics_management(ThisLayer.dataSource)
+                arcpy.AddMessage( "--Statistics calculated")
+                arcpy.AddMessage( "--Raster symbology is %s" % ThisLayer.symbologyType)
+                arcpy.ApplySymbologyFromLayer_management(ThisLayer,symbologyLayer)
+                arcpy.AddMessage( "--Symbology Applied")
+
+#mxd.save() # I'm not saving, uncomment this to save
+del mxd
+
+
+############################ TURN ON AND OFF##########################
+
+l1 = arcpy.mapping.Layer(r'h160303\h160303bgsort.bsq') # Get layer by its name (belongs to group)
+#l1.longName # This will give the name including the group
+
+#A list of layer names that you want to be turned off.
+names = [x,y,z,etc]
+
+mxd = arcpy.mapping.MapDocument("current")
+df = arcpy.mapping.ListDataFrames(, mxd, "Layers")[0] #Get the 1st dataframe called "Layers"
+layers = arcpy.mapping.ListLayers(mxd, "*", df)
+
+for layer in layers:
+  if layer.name in names:
+    layer.visible = False
+
+arcpy.RefreshTOC()
+arcpy.RefreshActiveView()
+
+###################turn off layer in group layer h160303?
+#lyr.isGroupLayer == 1      
+mxd = arcpy.mapping.MapDocument("current")
+df = arcpy.mapping.ListDataFrames(mxd, "Layers")[0] #Get the 1st dataframe called "Layers"
+groupLayer = arcpy.mapping.Layer(r'h160303') # fixed the name of the group layer
+for i in arcpy.mapping.ListLayers(groupLayer): print (i) ## Print layers in group layer, INCLUDES THE layer group itself
+for i in arcpy.mapping.ListLayers(groupLayer): i.visible = True ## Turn Off layers in group layer
+>>> arcpy.RefreshTOC() # Refresh Layers Panel
+
+## Calsulate statistics and apply symbology from layer on all layer of group layer
+
+layerRef = arcpy.mapping.Layer("h160303bgsort.bsq") #Layer to use as symbology, hardcoded
+groupLayer = arcpy.mapping.Layer(r'h160303') # fixed the name of the group layer
+for i in arcpy.mapping.ListLayers(groupLayer):
+    if not i.isGroupLayer:
+        if not i.name.upper() == layerRef.name.upper(): #If its not the reference layer
+            if i.isRasterLayer: #apply only to rasters
+                arcpy.CalculateStatistics_management(i.dataSource,"1","1","0")
+                arcpy.ApplySymbologyFromLayer_management(i,layerRef)
+                i.visible = False    #Uncheck visibility
+arcpy.RefreshTOC() #Apply the layer state update: visibility
+arcpy.RefreshActiveView()
+

ArcGIS/Batch_zonal_stats.py

@@ -0,0 +1,193 @@
+# -*- coding: utf-8 -*-
+# ---------------------------------------------------------------------------
+# joinZonalStats_hyper_BW_pruebas.py
+# Created on: 2014-06-07 11:06:16.00000
+#   (generated by ArcGIS/ModelBuilder)
+# Usage: joinZonalStats_hyper_BW_pruebas <Buffer> <Stats_table> <Grid> <Zone_field_and_join_Field> <Field_Name_Calculate_field> <Expression_Calculate_field> <Expression> <band> <Raster_set> 
+# Description: 
+# ---------------------------------------------------------------------------
+
+# Import arcpy module
+import os
+import arcpy
+
+try:
+    # Check out any necessary licenses
+    arcpy.CheckOutExtension("spatial")
+
+    #workspace
+
+    bwPath = "D:\\AB2013-2014\\Bread_wheat"
+    bwVectoresPath = bwPath + "\\" + "vectores"
+    bwDataPath = bwPath + "\\" + "data"
+    bwGdbPath = bwPath + "\\" + "AB_BreadWheat.gdb"
+    tempGdb = "C:\\vuelos\\temp.gdb"
+    arcpy.env.workspace = bwPath
+
+    #List of band names
+    bandNames = ["392.03027","393.87228","395.71426","397.55627","399.39830","401.24026","403.08228","404.92430","406.76627","408.60828","410.45030","412.29227","414.13428","415.97630","417.81827","419.66028","421.50230","423.34427","425.18628","427.02830","428.87027","430.71228","432.55430","434.39627","436.23828","438.08030","439.92227","441.76428","443.60630","445.44827","447.29028","449.13230","450.97427","452.81628","454.65826","456.50027","458.34230","460.18427","462.02628","463.86830","465.71027","467.55228","469.39430","471.23627","473.07828","474.92030","476.76227","478.60428","480.44630","482.28827","484.13028","485.97230","487.81427","489.65628","491.49830","493.34027","495.18228","497.02430","498.86627","500.70828","502.55030","504.39227","506.23428","508.07626","509.91827","511.76028","513.60230","515.44430","517.28625","519.12830","520.97030","522.81226","524.65430","526.49630","528.33826","530.18030","532.02230","533.86426","535.70630","537.54830","539.39026","541.23230","543.07430","544.91626","546.75830","548.60030","550.44226","552.28430","554.12630","555.96826","557.81030","559.65230","561.49426","563.33630","565.17830","567.02026","568.86230","570.70430","572.54626","574.38830","576.23030","578.07227","579.91430","581.75630","583.59827","585.44030","587.28230","589.12427","590.96630","592.80830","594.65027","596.49225","598.33430","600.17630","602.01825","603.86030","605.70230","607.54425","609.38630","611.22830","613.07025","614.91230","616.75430","618.59625","620.43830","622.28030","624.12225","625.96430","627.80630","629.64825","631.49030","633.33230","635.17426","637.01630","638.85830","640.70026","642.54230","644.38430","646.22626","648.06830","649.91030","651.75226","653.59430","655.43630","657.27826","659.12030","660.96230","662.80426","664.64630","666.48830","668.33026","670.17230","672.01430","673.85626","675.69830","677.54030","679.38226","681.22430","683.06630","684.90826","686.75030","688.59230","690.43427","692.27630","694.11830","695.96027","697.80230","699.64430","701.48627","703.32830","705.17030","707.01227","708.85430","710.69630","712.53827","714.38025","716.22230","718.06430","719.90625","721.74830","723.59030","725.43225","727.27430","729.11630","730.95825","732.80030","734.64230","736.48425","738.32630","740.16830","742.01025","743.85230","745.69430","747.53625","749.37830","751.22030","753.06226","754.90430","756.74630","758.58826","760.43030","762.27230","764.11426","765.95630","767.79830","769.64026","771.48230","773.32430","775.16626","777.00830","778.85030","780.69226","782.53430","784.37630","786.21826","788.06030","789.90230","791.74426","793.58630","795.42830","797.27026","799.11230","800.95430","802.79626","804.63830","806.48030","808.32227","810.16430","812.00630","813.84827","815.69030","817.53230","819.37427","821.21630","823.05830","824.90027","826.74225","828.58430","830.42630","832.26825","834.11030","835.95230","837.79425","839.63630","841.47830","843.32025","845.16230","847.00430","848.84625","850.68830"]
+    #Short list of band names for test
+    #bandNames = ["392.03027","393.87228"] #Testing purpose
+
+
+    # Load required toolboxes
+    print "Start!"
+    #Type: Feature layer
+    bf_Lx_1 = arcpy.GetParameterAsText(0)
+    arcpy.AddMessage("read b1 " + bf_Lx_1)
+    print bf_Lx_1
+
+
+    #Type: Feature layer
+    # Script arguments
+    bf_Lx_2 = arcpy.GetParameterAsText(1)
+    #bf_Lx_2 = bwVectoresPath + "\\" + "EYTBWMEL\\H\\H140117_EYTBWMEL_bf_L3.shp" # provide a default value if unspecified
+    arcpy.AddMessage("read b2 " + bf_Lx_2)
+    print bf_Lx_2
+
+    #Type: Feature layer
+    # Script arguments
+    bf_Lx_3 = arcpy.GetParameterAsText(2)
+    arcpy.AddMessage("read b3 " + bf_Lx_2)
+    print bf_Lx_3
+
+    #type: Feature layer
+    Grid = arcpy.GetParameterAsText(3)
+    #gridName = "H140117_BW"
+    #Grid = bwGdbPath + "\\" + gridName 
+    arcpy.AddMessage("read " + Grid)
+    desc = arcpy.Describe(Grid)
+    gPath = desc.path
+    gridSource = str(gPath) + "\\" + Grid
+    arcpy.AddMessage("Grid source: " + gridSource)
+    gridName = desc.baseName
+    arcpy.AddMessage("Grid basename: " + gridName)
+
+    print Grid
+
+    #type: Raster layer
+    Raster = arcpy.GetParameterAsText(4)
+    #Raster = "E:\\140117\\140117H\\ortho\\140117_3_810.bsq" # provide a default value if unspecified
+    #Raster = "c:\\vuelos\\140117_3_810.bsq"
+    arcpy.AddMessage("read " + Raster)
+    desc = arcpy.Describe(Raster)
+    rPath = desc.path
+    Raster = str(rPath) + "\\" + desc.baseName+ "." +desc.extension
+    arcpy.AddMessage("Raster source: " + Raster)
+    print Raster
+
+    #Folder to store the tables with the bands  
+    #type: Geodatabase
+    #tablesPath = arcpy.GetParameterAsText(5) 
+    tablesPath = tempGdb
+    print tablesPath
+
+    # Local variables:
+    arcpy.AddMessage("Local variables")
+    print "Local variables"
+    Zone_field_and_join_Field = "Name"
+    gridLayer = "gridLayer"
+    #Line
+    line = bf_Lx_1[-2:]
+
+
+    ## Make a layer
+    print "Make layer"
+    arcpy.MakeFeatureLayer_management(Grid, "gridLayer")
+
+    #Where to store the merge feature
+    print "Where to store the merge feature"
+    L_merge = tempGdb + "\\l_merge"
+    arcpy.AddMessage("merge path: " + L_merge)
+    if arcpy.Exists(L_merge):
+        arcpy.Delete_management(L_merge)
+
+    #List of features to merge
+    mergeList =  ""
+
+    # Process: Merge
+    arcpy.AddMessage("Merging")
+    print "merging..."
+    if bf_Lx_1 != '#':
+        mergeList += bf_Lx_1
+    if bf_Lx_2 != '#':
+        mergeList += ";"+bf_Lx_2
+    if bf_Lx_3 != '#':
+        mergeList += ";"+bf_Lx_3
+    arcpy.AddMessage("merge List: " + str(mergeList))    
+    m = arcpy.Merge_management(mergeList, L_merge)
+    arcpy.AddMessage(m)
+
+    i=1
+    for b in bandNames:
+        band = Raster + "\\" + b
+        bandField = "B" + str(i)
+        print bandField
+        #Set table name
+        tableName = gridName + "_" + line + "_" + bandField #+ ".dbf"
+        L_Stats_table = tablesPath + "\\" + tableName
+        print L_Stats_table
+        Field_Name_Calculate_field = gridName + "." + bandField
+        print Field_Name_Calculate_field
+        Expression_Select_layer = tableName+".Mean IS NOT NULL"
+        # Use this if the stats were saved to a dbf file "\""+tableName+".Mean\" IS NOT NULL"
+        # Use this if the stats were saved to a table "\""+tableName+":Mean\" IS NOT NULL"
+        # Use this if the stats were saved to a database table tableName+".Mean IS NOT NULL"
+        print Expression_Select_layer
+        Expression_Calculate_field = "round(!"+tableName+".Mean!,0)"
+        #the "!"+tableName+":Mean!" notation (:)is used when the stats are saved to a table
+        #the "!"+tableName+".Mean!" notation (.)is used when the stats are saved to a dbf file
+        print Expression_Calculate_field
+
+
+
+        # Process: Zonal Statistics as Table
+        print "Zonal statistics..."
+        zs = arcpy.gp.ZonalStatisticsAsTable_sa(L_merge, Zone_field_and_join_Field, band, L_Stats_table, "DATA", "MEAN")
+        arcpy.AddMessage("stats table: " + str(zs))
+
+##        # Process: Join Field
+##        print "Joining Field..."
+##        arcpy.AddMessage("Joining Field...")
+##        arcpy.JoinField_management(gridLayer, Zone_field_and_join_Field, L_Stats_table, Zone_field_and_join_Field, "MEAN") 
+
+
+        # Process: Add Join
+        print "Joining..."
+        arcpy.AddMessage("grid..."+ gridLayer)
+        arcpy.AddMessage("field..."+Zone_field_and_join_Field)
+        arcpy.AddJoin_management(gridLayer, Zone_field_and_join_Field, zs, Zone_field_and_join_Field, "KEEP_ALL")    
+
+        # Process: Select Layer By Attribute
+        if i==1:
+            print "Selecting Layer..."
+            gridLayerSelection = arcpy.SelectLayerByAttribute_management(gridLayer, "NEW_SELECTION", Expression_Select_layer)
+
+        # Process: Calculate Field
+        print "Calculating field"
+        arcpy.AddMessage("Calculating field...")
+        arcpy.CalculateField_management(gridLayerSelection, Field_Name_Calculate_field, Expression_Calculate_field, "PYTHON")
+
+        # Process: Remove Join
+        arcpy.AddMessage("remove Join")
+        arcpy.RemoveJoin_management(gridLayer, "")
+        #Erase stats table
+        #arcpy.Delete_management(zs)        
+        i+=1
+
+    #Erase merge file
+    arcpy.AddMessage("delete merge temp")
+    arcpy.Delete_management(L_merge)
+    print "Finish"
+
+except Exception, e:
+    # If an error occurred, print line number and error message
+    import traceback, sys
+    tb = sys.exc_info()[2]
+    arcpy.AddMessage("Line:" + str(tb.tb_lineno))
+    print "Line %i" % tb.tb_lineno
+    arcpy.AddMessage("Error " + e.message)
+    print e.message
+    print "OMG!"
+
+

ArcGIS/CalculateNDVIandNiblackFromHyperIterate.py

@@ -0,0 +1,104 @@
+# -*- coding: utf-8 -*-
+# ---------------------------------------------------------------------------
+# CalculateNDVIandNiblackFromHyperIterate.py
+# Created on: 2015-08-31 23:45:21.00000
+#   (generated by ArcGIS/ModelBuilder)
+# Usage: CalculateNDVIandNiblackFromHyperIterate <raster> <ndvi> <NIR_wl> <RED_wl> <niblack> <Dark_background> <Neighborhood> <truncate_charsEnd> 
+# Description: 
+# ---------------------------------------------------------------------------
+
+# Import arcpy module
+import arcpy, os
+
+# Check out any necessary licenses
+arcpy.CheckOutExtension("spatial")
+
+#Method to truncate string
+def getBasename(inputName, fromChar, toChar):
+    subsetName = inputName[fromChar:int(toChar)]
+    arcpy.AddMessage("Truncated name: "+subsetName)
+    return subsetName
+
+def upLevel(locationpath):
+    #Up one level the path
+    folderUp = "\\".join(locationpath.split("\\")[0:-1])
+    folderUp.replace("\\", "\\\\")
+    return folderUp
+
+def checkFolder(folderPath):
+#Create folder if it doesnt exists
+    folderPath.replace("\\", "\\\\")
+    if not os.path.exists(folderPath):
+       os.makedirs(folderPath)
+
+# Script arguments
+raster = arcpy.GetParameterAsText(0)
+
+truncate_charsEnd = arcpy.GetParameterAsText(1)
+if truncate_charsEnd == '#' or not truncate_charsEnd:
+    truncate_charsEnd = "-3" # provide a default value if unspecified
+
+# Process: Parse Path
+desc = arcpy.Describe(raster)
+name = desc.name
+arcpy.AddMessage("name: "+name)
+path = desc.path
+arcpy.AddMessage("path: "+path)
+folderUp = upLevel(path)
+saveFolder = folderUp+"\\mask"
+checkFolder(saveFolder) #Check if exists
+
+# Process: truncateString to get basename
+basename = getBasename(name,0,truncate_charsEnd)
+
+ndvi = arcpy.GetParameterAsText(7)
+if ndvi == '#' or not ndvi:
+    ndvi = saveFolder+"\\"+basename+"nvi.tif" # provide the automatic value unless other is indicated
+
+NIR_wl = arcpy.GetParameterAsText(2)
+if NIR_wl == '#' or not NIR_wl:
+    NIR_wl = "802.79626" # provide a default value if unspecified
+
+RED_wl = arcpy.GetParameterAsText(3)
+if RED_wl == '#' or not RED_wl:
+    RED_wl = "670.17230" # provide a default value if unspecified
+
+niblack = arcpy.GetParameterAsText(4)
+if niblack == '#' or not niblack:
+    niblack = saveFolder+"\\"+basename+"msk.tif" # provide the automatic value unless other is indicated
+
+Dark_background = arcpy.GetParameterAsText(5)
+if Dark_background == '#' or not Dark_background:
+    Dark_background = "true" # provide a default value if unspecified
+
+Neighborhood = arcpy.GetParameterAsText(6)
+if Neighborhood == '#' or not Neighborhood:
+    Neighborhood = "Rectangle 3 3 CELL" # provide a default value if unspecified
+
+
+
+# Local variables:
+focalSTD = "C:\Users\usuario\Documents\ArcGIS\Default.gdb\std"
+focalMEAN = "C:\Users\usuario\Documents\ArcGIS\Default.gdb\mean"
+
+#Assign names
+
+NIR_path = raster+"\\"+NIR_wl
+RED_path = raster+"\\"+RED_wl
+
+
+# Process: Raster Calculator
+arcpy.gp.RasterCalculator_sa("Float((Float(\""+NIR_path+"\") - Float(\""+RED_path+"\"))/(Float(\""+NIR_path+"\") + Float(\""+RED_path+"\")))", ndvi)
+
+# Process: Focal MEAN 3x3
+arcpy.gp.FocalStatistics_sa(ndvi, focalMEAN, Neighborhood, "MEAN", "DATA")
+
+# Process: Focal STD 3x3
+arcpy.gp.FocalStatistics_sa(ndvi, focalSTD, Neighborhood, "STD", "DATA")
+
+# Process: calculate Nib
+#######REEEROOR
+arcpy.gp.RasterCalculator_sa("Con("+Dark_background+" == true,Con(\"Float("+ndvi+")\">(\"Float("+focalMEAN+")\" +(0.2 * \"Float("+focalSTD+")\")),1,0),Con(\"Float("+ndvi+")\">(\"Float("+focalMEAN+")\" +(Float(-0.2) * \"Float("+focalSTD+")\")),1,0))", niblack)
+#Delete temporals
+arcpy.Delete_management(FocalSTD)
+arcpy.Delete_management(FocalMEAN)

ArcGIS/ChooseFieldValue/Script/DynamicValueList.py

@@ -0,0 +1,9 @@
+# Import system modules
+import arcpy
+
+# Set the parameters
+InputFeatureClass = arcpy.GetParameterAsText(0)
+InputField = arcpy.GetParameterAsText(1)
+InputValue = arcpy.GetParameterAsText(2)
+
+arcpy.SetParameter(3, InputValue)