alc and gex header fix

libaarhusxyz/alc.py

@@ -17,6 +17,8 @@ def parse(nameorfile, xyz_columns=None):
 
 supported_fields = ["DateTime","Date","Time","Flight","Line","GdSpeed","Alt","DEM",
                     "Magnetic","PowerLineMonitor",
+                    "Misc1","Misc2","Misc3","Misc4",
+                    "Current_Ch01","Current_Ch02",
                     "RxPitch","RxRoll","Topography","TxAltitude",
                     "TxOffTime","TxOnTime","TxPeakTime",
                     "TxPitch","TxRoll","TxRxHoriSep","TxRxVertSep","UTMX","UTMY",
@@ -35,10 +37,19 @@ def is_supported_field(fieldname):
 def _dump(xyz, f, columns=None):
     if columns is None:
         columns = xyz["file_meta"]["columns"]
+    else:
+        columns_=[]
+        for column_name in columns:
+            words=re.split('\[|\]', column_name)
+            if len(words)==1:
+                columns_.append(words[0])
+            else:
+                newname="{0}_{1:02d}".format(words[0],int(words[1])+1)
+                columns_.append(newname)
+        columns=columns_
     rows = [{"canonical_name": col, "position": idx + 1}
              for idx, col in enumerate(columns)
              if is_supported_field(col)]
-
     channels = set([row["canonical_name"][len("Gate_Ch"):].split("_")[0]
                     for row in rows
                     if row["canonical_name"].startswith("Gate_Ch")])

libaarhusxyz/gex.py

@@ -28,7 +28,7 @@ def split_sections(text):
     sectionlineidx.append(len(text)+1)
     sections={"header":text[0]}
     for k in range(len(sectionheaders)):
-        sections[sectionheaders[k]]=text[sectionlineidx[k]+1:sectionlineidx[k+1]-1]
+        sections[sectionheaders[k]]=text[sectionlineidx[k]+1:sectionlineidx[k+1]]
     return sections, sectionheaders
 
 def parse_parameters(textlines):
@@ -64,7 +64,7 @@ def _parse(inputfile):
     gex={"header":sections["header"]}
     for header in sectionheaders:
         gex[header.strip("[").strip("]")]=parse_parameters(sections[header])
-        print("header {} parsed".format(header))
+        # print("header {} parsed".format(header))
     return gex
 
 def parse(nameorfile, **kw):

libaarhusxyz/xyz.py

@@ -24,14 +24,15 @@
 # with the naming convention used in Aaarhus Workbench / ALC files.
 _RE_LAYER_COL = re.compile(r"^(.*?)[(_\[]([0-9]+)[)\]]?$")
 
-_NA_VALUES = ["", "#N/A", "#N/A N/A", "#NA", "-1.#IND", "-1.#QNAN", "-NaN", "-nan", "1.#IND", "1.#QNAN", "<NA>",
+
+_NA_VALUES = [9999, 9999.9, "9999", "9999.9", "", "#N/A", "#N/A N/A", "#NA", "-1.#IND", "-1.#QNAN", "-NaN", "-nan", "1.#IND", "1.#QNAN", "<NA>",
              "N/A", "NA", "NULL", "NaN", "n/a", "nan", "null", "*"]
 
 
 def _split_layer_columns(df):
     per_layer_cols = [col for col in df.columns if re.match(_RE_LAYER_COL, col)]
     per_sounding_cols = [col for col in df.columns if not col in per_layer_cols]
-
+    
     colgroups = {}
     for col in per_layer_cols:
         group = re.match(_RE_LAYER_COL, col).groups()[0]
@@ -115,7 +116,7 @@ def _parse(inputfile, source=None, alcfile=None, **kw):
     res = {"flightlines": df,
             "layer_data": layer_dfs,
             "model_info": headers,
-            "file_meta": {"columns": full_df.columns}}
+            "file_meta": {"columns": list(full_df.columns)}}
 
     if alcdata is not None:
         res["alc_info"] = alcdata["meta"]
@@ -142,13 +143,14 @@ def _un_split_layer_columns(data):
 
 def _dump(data, file, alcfile=None):
     df = _un_split_layer_columns(data)
-    for key, value in data['model_info'].items():
-        if key != 'source':
-            file.write("/" + str(key) + "\n")
-            if isinstance(value, list):
-                file.write("/" + ' '.join(str(item) for item in value) + "\n")
-            else:
-                file.write("/" + str(value) + "\n")
+    if alcfile==None:
+        for key, value in data['model_info'].items():
+            if key != 'source':
+                file.write("/" + str(key) + "\n")
+                if isinstance(value, list):
+                    file.write("/" + ' '.join(str(item) for item in value) + "\n")
+                else:
+                    file.write("/" + str(value) + "\n")
     file.write('/ ')
     df.to_csv(file, index=False, sep=' ', na_rep="*", encoding='utf-8')