Merge branch 'master' into fernando

matlab/generic_ATL09_Quickview/plot_ATL09_cab.m

@@ -1,4 +1,4 @@
-function plot_ATL09_cab(ATL09, inName, figVis, saveFigures, outDir)
+function plot_ATL09_cab(ATL09, inName, figVis, saveFigures, outDir, x_var)
 % Function to plot ATL09 calibrated attenuated backscatter.
 % Not as pretty as Steve Palm's plots, but it gets the message across.
 %
@@ -14,6 +14,15 @@ function plot_ATL09_cab(ATL09, inName, figVis, saveFigures, outDir)
     outDir = [];
 end
 
+%% 
+if ~exist('x_var','var')
+    x_var='delta_time';
+    xlabel_str='Delta Segment Time (seconds)';
+    subtract_min=true;
+else
+    xlabel_str=strrep(x_var,'_','\_');
+    subtract_min=false;
+end
 
 %% Find and loop through the profile groups
 
@@ -48,7 +57,15 @@ function plot_ATL09_cab(ATL09, inName, figVis, saveFigures, outDir)
     hold on
 
     cmap = colormap(parula);
-    p = pcolor(ATL09.(profile).delta_time - min(ATL09.(profile).delta_time), cab_elevs, flipud(ATL09.(profile).cab_prof));
+
+    if subtract_min
+        x_prof=ATL09.(profile).(x_var) - min(ATL09.(profile).(x_var));
+    else
+        x_prof=ATL09.(profile).(x_var);
+    end
+
+    p = pcolor(x_prof, cab_elevs, flipud(ATL09.(profile).cab_prof));
+
     shading flat
     set(p,'DisplayName', 'CAB')
     cdat = get(p, 'cdata');
@@ -67,14 +84,16 @@ function plot_ATL09_cab(ATL09, inName, figVis, saveFigures, outDir)
 
     %% Plot labels
 
-    xlabel('Delta Segment Time (seconds)')
+    xlabel(xlabel_str)
+
     ylabel('Elevation (meters)')
     title({'Calibrated attenuated backscatter profile',...
         [profile ' - ' inName]}, ...
         'interpreter', 'none')
     axis tight
     legend('-DynamicLegend','Location','Best')
-    dragzoom()
+
+    %dragzoom()
 
     %% Save figure(s)
     % Uncomment savefig line if MATLAB figure desired. It will take longer

matlab/generic_ATL09_Quickview/readATL09.m

@@ -18,7 +18,7 @@
 
 profile = {'profile_1','profile_2','profile_3'};
 
-vars = {'apparent_surf_reflec','bsnow_con','cab_prof','cloud_flag_asr','cloud_flag_atm','delta_time','latitude','layer_attr','layer_con','longitude','msw_flag','segment_id','solar_elevation'};
+vars = {'apparent_surf_reflec','bsnow_con','cab_prof','cloud_flag_asr','cloud_flag_atm','delta_time','latitude','layer_attr','layer_con','longitude','msw_flag','prof_dist_x','segment_id','solar_elevation'};
 vars_orbit = {'cycle_number','delta_time','orbit_number','rgt'};
 vars_anc =  {'data_end_utc';'data_start_utc';'end_cycle';'end_geoseg';'end_orbit';'end_region';'end_rgt';'granule_end_utc';'granule_start_utc';'start_cycle';'start_geoseg';'start_orbit';'start_region';'start_rgt'};
 

python/photon_height.py

@@ -108,14 +108,14 @@ def photon_heights(infile, track, outroot, confidence, plot=False,
     if verbose:
         print(len(distance), "photons with confidence >=", confidence)
         print(len(height), "photons with confidence >=", confidence)
-
-    outfile = outroot + ".txt"
-    try:
-        write_data(outfile, distance, height, overwrite=overwrite,
-                   verbose=verbose)
-    except (IOError, RuntimeError) as err:
-        print("{0}: error: {1}".format(__file__, err), file=sys.stderr)
-        return 1
+    if outroot is not None:
+        outfile = outroot + ".txt"
+        try:
+            write_data(outfile, distance, height, overwrite=overwrite,
+                       verbose=verbose)
+        except (IOError, RuntimeError) as err:
+            print("{0}: error: {1}".format(__file__, err), file=sys.stderr)
+            return 1
 
     if plot:
         """
@@ -342,10 +342,10 @@ def cl_args(description):
     """Parse command line arguments."""
     parser = argparse.ArgumentParser(description=description)
     parser.add_argument("infile", type=str,
-                        help="nput ATL03 file")
+                        help="input ATL03 file")
     parser.add_argument("track", type=str,
                         help="ground track: gt1l,gt1r,gt2l,gt2r,gt3l,gt3r,")
-    parser.add_argument("outroot", type=str,
+    parser.add_argument("-o", type=str, default=None,
                         help="output file root name")
     parser.add_argument("-c", type=int, default=2,
                         help="minimum signal confidence to plot (0-4)"
@@ -367,7 +367,7 @@ def main(argv=None):
 
     infile = args.infile
     track = args.track
-    outroot = args.outroot
+    outroot = args.o
     confidence_min = args.c
     overwrite = args.f
     plot = args.p

python/run_ATL09_query.py

@@ -0,0 +1,90 @@
+#! /usr/bin/env python3
+
+import argparse
+import subprocess
+import sys
+import re
+import os
+import shutil
+
+description="Download ATL09 data from NSIDC." +\
+    "  To use this, you must generate a token, using the setup_token script, which will be saved in a file called NSIDC_token.txt"+\
+    "The script will search for NSIDC_token.txt in the current directory (first) and in the directory where the script is located (second)."
+
+
+parser=argparse.ArgumentParser(description=description)
+parser.add_argument('-f', dest='full_file', default=False, action='store_true')
+parser.add_argument('-o', dest='output_directory', type=str)
+parser.add_argument('-d', dest='dry_run', default=False, action='store_true')
+parser.add_argument('-t', dest='time_str', required=True, default=None, help="Time range for query.  Format is YYYY-MM-DDTHH:MM:SS,YYYY-MM-DDTHH:MM:SS")
+args=parser.parse_args()
+
+# look for a NSIDC_identity.txt file in the current directory
+try:
+    fh=open('NSIDC_token.txt','r')
+except(FileNotFoundError):
+    # also look in the script's directory
+    fh=open(sys.path[0]+'/NSIDC_token.txt','r')
+
+token=None
+token_re=re.compile('<id>(.*)</id>')
+for line in fh:
+    m=token_re.search(line)
+    if m is not None:
+        token=m.group(1)
+if token is None:
+    raise RuntimeError('missing token string')
+
+token_str='&token=%s' % token
+
+if 'out_dir' in args:
+    os.chdir(args.output_directory)
+
+if args.full_file:
+    subset_str="&agent=NO"
+else:
+    subset_str=""
+
+time_str="&time=%s" % args.time_str
+
+# build the query to submit via curl
+cmd_base='curl -O -J --dump-header response-header.txt "https://n5eil02u.ecs.nsidc.org/egi/request?short_name=ATL09&version=200&page_size=1000' 
+cmd=cmd_base+'%s%s%s"' % (token_str, subset_str, time_str)
+
+print(cmd)
+
+if args.dry_run:
+    # if this is a dry run, exit after reporting the string
+    exit()
+
+# run the curl string
+p=subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+text=p.stdout.read()
+retcode=p.wait()
+
+# check the response header to get the filename with the output
+zip_re=re.compile('filename="(.*.zip)"')
+with open('response-header.txt') as ff:
+    for line in ff:
+        m=zip_re.search(line)
+        if m is not None:
+            zip_file=m.group(1)
+zip_str=subprocess.check_output(['unzip',zip_file])
+#print(zip_str)
+
+# pull the indivicual h5 files into the current directory
+cleanup_list=list()
+for h5_file in re.compile('(\S+\.h5)').findall(zip_str.decode('utf-8')):
+    shutil.move(h5_file,'.')
+    thedir=os.path.dirname(h5_file)
+    if thedir not in cleanup_list:
+        cleanup_list.append( thedir)
+
+# delete the directories that contained the hdf5 files
+for entry in cleanup_list:
+    os.rmdir(entry)
+os.remove(zip_file)
+
+
+
+

python/setup_token

@@ -0,0 +1,12 @@
+#! /usr/bin/env bash
+
+if [ $# -eq 0]; then
+   echo "USAGE: setup_token username password ip_address"
+fi
+
+username=$1
+password=$2
+ip_address=$3
+
+curl -X POST --header "Content-Type: application/xml" -d "<token><username>$username</username><password>$password</password><client_id>NSIDC_client_id</client_id><user_ip_address>$ip_address</user_ip_address></token>" https://api.echo.nasa.gov/echo-rest/tokens > NSIDC_token
+

python/test.txt

@@ -1,5 +1 @@
-<<<<<<< HEAD
-Another test
-=======
 TEST
->>>>>>> d3ba45b... testing fork workflow