Added SOL2json.py to convert DSSAST SOL file to json

Author: jchryssanthacopoulos

data/tapps/SOL2json.py

@@ -0,0 +1,112 @@
+#!/usr/bin/env python
+
+# import modules
+import json
+from optparse import OptionParser
+
+# helper functions
+def findVarIdx(var_dic, line_list):
+    idx_dic = {}
+    for i in range(len(var_dic)): 
+        key = var_dic.keys()[i]
+        if key in line_list: idx_dic[key] = line_list.index(key) - 1
+        # if not key in line_list:
+        #     print 'SOLtojson.findVarIdx: Variable', key, 'missing . . . Filling value . . .'
+        #     idx_dic[key] = -1 # variable not found
+        # else:
+        #     idx_dic[key] = line_list.index(key) - 1
+    return idx_dic
+def makeJSONDic(var_dic, idx_dic, line_list, fill_value):
+    # if len(var_dic) != len(idx_dic):
+    #     raise Exception('SOLtojson.makeJSONDic: Variable and index dictionaries must be same size')
+    out_dic = {}
+    for i in range(len(idx_dic)):
+        in_var = idx_dic.keys()[i]
+        out_var = var_dic[in_var]
+        idx = idx_dic[in_var]
+        if line_list[idx] != fill_value: out_dic[out_var] = line_list[idx] # variable exists
+        # if idx != -1:
+        #     out_dic[out_var] = line_list[idx] # variable exists
+        # else:
+        #     out_dic[out_var] = fill_value # fill value
+    return out_dic
+
+# parse inputs
+parser = OptionParser()
+parser.add_option("-i", "--input", dest = "inputfile", default = "Generic.SOL", type = "string",
+                  help = "SOL file to parse", metavar = "FILE")
+parser.add_option("-o", "--output", dest = "outputfile", default = "Generic.json", type = "string",
+                  help = "JSON file to create", metavar = "FILE")
+(options, args) = parser.parse_args()
+
+# mapping between DSSAT variables and json variables
+header_var_map = {'SCOM': 'sscol', 'SALB': 'salb', 'SLU1': 'slu1', 'SLDR': 'sldr', \
+    'SLRO': 'slro', 'SLNF': 'slnf', 'SLPF': 'slpf', 'SMHB': 'smhb', 'SMPX': 'smpx', \
+    'SMKE': 'smke'}    
+row1_var_map = {'SLB': 'sllb', 'SLMH': 'slmh', 'SLLL': 'slll', 'SDUL': 'sldul', \
+    'SSAT': 'slsat', 'SRGF': 'slrgf', 'SSKS': 'sksat', 'SBDM': 'slbdm', 'SLOC': 'sloc', \
+    'SLCL': 'slcly', 'SLSI': 'slsil', 'SLCF': 'slcf', 'SLNI': 'slni', 'SLHW': 'slphw', \
+    'SLHB': 'slphb', 'SCEC': 'slcec', 'SADC': 'sladc'}
+row2_var_map = {'SLPX': 'slpx', 'SLPT': 'slpt', 'SLPO': 'slpo', 'CACO3': 'caco3', \
+    'SLAL': 'slal', 'SLFE': 'slfe', 'SLMN': 'slmn', 'SLBS': 'slbs', 'SLPA': 'slpa', \
+    'SLPB': 'slpb', 'SLKE': 'slke', 'SLMG': 'slmg', 'SLNA': 'slna', 'SLSU': 'slsu', \
+    'SLEC': 'slec', 'SLCA': 'slca'}
+
+# value to fill with if datum is missing
+fill_value = '-99.0'
+
+# open SOL file
+lines = [l.split() for l in tuple(open(options.inputfile, 'r'))]
+
+header_var_idx = findVarIdx(header_var_map, lines[3]) # hardcoded for 4th line
+row1_var_idx = findVarIdx(row1_var_map, lines[5]) # hardcoded for 6th line
+        
+# calculuate number of layers and if data are stacked
+num_layers = 0
+stacked = False
+for i in range(len(lines[6 :])):
+    l = lines[6 + i]
+    if not l[0] == '@': # key off first column
+        num_layers += 1
+    else:
+        stacked = True
+        row2_var_idx = findVarIdx(row2_var_map, l)
+        break
+
+# make dictionary to store data
+
+# write preliminary
+data_dic = {}
+# read 1st line
+data_dic['soil_id'] = lines[0][0].replace('*', '') # remove asterisk from soil id
+data_dic['sl_source'] = lines[0][1]
+data_dic['sltx'] = lines[0][2]
+data_dic['sldp'] = lines[0][3]
+# read 3rd line
+data_dic['soil_name'] = ' '.join(lines[0][4 :])
+data_dic['sl_loc_3'] = lines[2][0]
+data_dic['sl_loc_1'] = lines[2][1]
+data_dic['soil_lat'] = lines[2][2]
+data_dic['soil_long'] = lines[2][3]
+data_dic['classification'] = ' '.join(lines[2][4 :])
+
+# write header variables
+header_dic = makeJSONDic(header_var_map, header_var_idx, lines[4], fill_value)
+data_dic.update(header_dic)
+
+# write specific soil parameters for each layer
+data_dic['soilLayer'] = [0] * num_layers
+for i in range(num_layers):
+    line = lines[6 + i]
+    data_dic['soilLayer'][i] = makeJSONDic(row1_var_map, row1_var_idx, line, fill_value)
+    if stacked:
+        line2 = lines[7 + num_layers + i]
+        print line2
+        stacked_dic = makeJSONDic(row2_var_map, row2_var_idx, line2, fill_value)
+        data_dic['soilLayer'][i].update(stacked_dic)
+
+# save into bigger dictionary
+all_data = {'soils': [data_dic]}
+
+# save json file
+json.dump(all_data, open(options.outputfile, 'w'), indent = 2, separators=(',', ': '))