Aye

Makefile

+.Phony: coverage
+coverage:
+	coverage run --source=tests -m unittest discover && coverage report && coverage html

icartt/__init__.py

-from .dataset import Dataset, SimpleNormalComments, StandardNormalComments
\ No newline at end of file
+from .dataset import Dataset, StandardNormalComments
\ No newline at end of file

setup.py

@@ -8,6 +8,7 @@ def read(filename):
 setup(name='icartt',
       description='ICARTT format reader and writer',
       long_description=read('README.rst') + '\n\n' + read('INSTALL.rst') + '\n\n' + read('CHANGES.rst'),
+      long_description_content_type='text/markdown',
       version='1.0.1',
       url='https://boxmodeling.meteo.physik.uni-muenchen.de',
       author='Christoph Knote',
@@ -30,4 +31,6 @@ setup(name='icartt',
         ],
       keywords='',
       packages=['icartt'],
+      test_suite = 'tests',
+      tests_require = [],
       zip_safe=False)

tests/examples/AROTAL-RAY_DC8_20040715_R1.ict

+68, 2110, V02_2016
+MAHONEY, MJ
+M/S 169-237; Jet Propulsion Laboratory; Pasadena, CA 91109-8099
+MTP - Microwave Temperature Profiler
+SEAC4RS
+1, 1
+2013, 08, 01, 2013, 08, 18
+0, 0
+Palt[], meters, Pressure_Altitude, Pressure_Altitude_array
+Start_UTC, seconds, Time_Start, elapsed time from 0000 UTC
+4
+1.0, 1.0, 1.0, 1E+21
+-99999, -99999, -99999, -99999
+Temperature[], K, Temperature, Temperature_array
+Temperture_SE[], K, Temperature_Standard_Error, Temperature_Standard_Error_array 
+Geometric_altitude[], meters, Geometric_Altitude, Geometric_Altitude_array 
+Molecular_air_density[], number_per_cubic_meter, Molecular_air_density, Molecular_air_density_array
+17
+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
+-9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999
+NZ, none, number_of_altitudes_in_data_record 
+Stop_UTC, seconds, Time_Stop, end of scan
+Mid_UTC, seconds, Time_Mid, horizon location of scan
+Zp, km, Pressure_altitude
+Pitch, deg, Aircraft_Pitch
+Roll, deg, Aircraft_Roll
+OAT, K, Outside_air_temperature
+Zt1, km, Tropopause_1_pressure_altitude
+Zt2, km, Tropopause_2_pressure_altitude
+PTt1, K, Potential_Temperature_tropopause_1
+PTt2, K, Potential_Temperature_tropopause_2
+Latitude, deg, Aircraft_Latitude
+Longitude, deg, Aircraft_Longitude
+LRac, K/km, Lapse_Rate_at_Flight_Level
+MRI, none, Retrieval_quality_metric
+Tcp, K, Cold_point_temperature
+Zcp, km, Cold_point_pressure_altitude
+1
+*** Preliminary Data Preliminary Data Preliminary Data Preliminary Data Preliminary Data *** 
+19
+Here's a brief free-form tutorial on how to decipher the MTP data:
+Data groups consist of the following group of lines per 15-second observing cycle. 
+First line is: UTstart, number of retrieval levels, UTend, UTmid, Pressure Altitude, Pitch, Roll, Outside air temp (K), tropopause altitude #1 (km), tropopause altitude #2 (km) [if present], potential temperatures of tropopause #1 and #2, latitude, longitude, & lapse rate near flight level.
+Remaining set of lines for each cycle consist of 5 columns: col#1 is pressure altitude (meters), col#2 is temperature from MTP (Kelvin), col#3 is temperature error estimate (K), col#4 is geometric altitude (meters), based on GPS altitude (meters), and col#5 is molecular air density [1E+21/m3].
+PI_CONTACT_INFO: M/S 246-102; Jet Propulsion Laboratory; Pasadena, CA 91109- 8099; Michael.J.Mahoney@jpl.nasa.gov
+PLATFORM: NASA Global Hawk 872
+LOCATION: see http://espoarchive.nasa.gov/archive/info ASSOCIATED_DATA: See http://espoarchive.nasa.gov/archive/browse/attrex INSTRUMENT_INFO: See http://mtp.jpl.nasa.gov/
+DATA_INFO: See text above
+UNCERTAINTY: Contact PI
+ULOD_FLAG: -7777
+ULOD_VALUE: N/A
+LLOD_FLAG: -8888
+LLOD_VALUE: N/A
+DM_CONTACT_INFO: M/S 169-237; Jet Propulsion Laboratory; Pasadena, CA 91109-8099; Michael.J.Mahoney@jpl.nasa.gov
+PROJECT_INFO: SEAC4RS mission 01 August - 30 September 2013; DAOF and Ellington Field, Houston, Texas
+STIPULATIONS_ON_USE: Use of these data should be done in consultation with the PI OTHER_COMMENTS:
+REVISION: R0
+R0: Preliminary Data
+Start_UTC, NZ, Stop_UTC, Mid_UTC, Zp, Pitch, Roll, OAT, Zt1, Zt2, PTt1, PTt2, Latitude, Longitude, LRac, MRI, Tcp, Zcp, Palt[], Temperature[], Temperture_SE[], Geometric_altitude[], Molecular_air_density[]
+77381, 0, 77394, 77386, 6.358, 15.8, -0.2, 261.9, -9999, -9999, -9999, -9999, 34.779, -118.165, -9999, 0.25, 200.66, 15.36
+77394, 0, 77407, 77399, 6.618, 11.9, -0.6, 259.7, -9999, -9999, -9999, -9999, 34.792, -118.171, -9999, 0.17, 202.05, 15.62
+77407, 13, 77420, 77412, 6.790, 6.1, 0.2, 258.2, 15.2, 99.9, 373.2, 999.9, 34.805, -118.177, -6.7, 0.21, 201.61, 15.79
+13690, 208.0, 1.4, 14295, 5150
+10790, 229.1, 1.0, 11364, 7387 
+9290, 241.3, 0.8, 9775, 8827
+8390, 248.4, 0.7, 8816, 9799 
+7790, 252.3, 0.5, 8176, 10526 
+7290, 255.6, 0.4, 7643, 11160 
+6940, 257.9, 0.2, 7270, 11623 
+6640, 259.7, 0.3, 6950, 12035 
+6290, 262.3, 0.5, 6577, 12512 
+5790, 265.6, 0.8, 6045, 13239 
+5211, 269.0, 1.0, 5429, 14142 
+4343, 274.6, 1.0, 4506, 15559 
+1834, 288.6, 9.1, 1839, 20460
+77621, 14, 77634, 77626, 10.279, 6.1, -0.1, 230.2, 15.0, 99.9, 386.7, 999.9, 35.058, -118.258, -5.1, 0.32, 210.34, 15.48
+17179, 211.0, 1.3, 17650, 2929
+14279, 213.0, 1.4, 14814, 4582 
+12779, 218.4, 1.1, 13314, 5662 
+11879, 221.8, 0.8, 12397, 6425 
+11279, 225.0, 0.5, 11776, 6963 
+10779, 228.1, 0.3, 11252, 7433 
+10429, 229.9, 0.2, 10885, 7789 
+10129, 231.3, 0.2, 10571, 8109 
+9779, 233.2, 0.3, 10206, 8485
+9279, 236.2, 0.4, 9686, 9034 
+8679, 240.0, 0.6, 9062, 9720 
+7779, 246.8, 0.8, 8125, 10777 
+6279, 259.0, 0.9, 6554, 12691 
+3779, 279.4, 1.2, 3910, 16472

tests/examples/AR_DC8_20050203_R0.ict

+54, 2110
+PI LastName, First Name
+Code 916, Goddard Space Flight Center, Greenbelt, MD 20771
+AROTAL
+PAVE Mission
+1, 1
+2005, 02, 03, 2006, 01, 18
+1
+Altitude[], meters, Altitude_array
+UTC, XX.XXXX_hours_from_0_hours_on_flight_date
+7
+0.1, 0.0001, 0.1, 0.01, 0.0001, 0.1, 0.0001
+-9999, -999999, -999999, -999999, -999999, -99999, -999999
+TempK[], K, Temperature_array
+Log10_NumDensity[], part/cc, Log10_NumDensity_array
+TempK_Err[], K, Temperature_error_array
+AerKlet[], Klet, Aerosol_array
+Log10_O3NumDensity[], part/cc, Log10_Ozone_NumDensity_array
+O3_MR[], ppb, Ozone_mixing_ratio_array
+Log10_O3NumDensity_Err[], part/cc, Log10_NumDensity_error_array
+11
+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
+-9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999
+NumAlts, none, Number_of_altitudes_reported
+Year, UT
+Month, UT
+Day, UT
+AvgTime, xxx.x_minutes, Averaging_time_of_presented_data
+Latitude, degrees
+Longitude, degrees
+PAlt, meters, pressure_altitude
+GPSAlt, meters, GPS_altitude
+SAT, K, Static_air_temperature
+SZA, degrees
+0
+18
+PI_CONTACT_INFO: Enter PI Address here
+PLATFORM: NASA DC8
+LOCATION: Lat, Lon, and Alt included in the data records
+ASSOCIATED_DATA: N/A
+INSTRUMENT_INFO:N/A
+DATA_INFO:N/A
+UNCERTAINTY: Contact PI
+ULOD_FLAG: -7777
+ULOD_VALUE: N/A
+LLOD_FLAG: -8888
+LLOD_VALUE: N/A
+DM_CONTACT_INFO: Enter Data Manager Info here
+PROJECT_INFO: PAVE MISSION: Jan-Feb 2005
+STIPULATIONS_ON_USE: Use of these data should be done in consultation with the PI
+OTHER_COMMENTS: N/A
+REVISION: R0;
+R0: Version 2005-0: AROTAL T & O3 Rayleigh Retrievals. Further revisions may be needed to fine-tune aerosol characterization.
+UTC, NumAlts, Year, Month, Day, AvgTime, Latitude, Longitude, PAlt, GpsAlt, SAT, SZA, Altitude[], TempK[], Log10_NumDensity[], TempK_Err[], AerKlet[], Log10_O3NumDensity[], O3_MR[], Log10_O3NumDensity_Err[]
+54000, 9, 2005, 2, 3, 0, 42.308, -70.582, 6910, 6979, 242.5, 65.5
+   9154, -9999, -999999, -9999, -9999, 113178, 212, -999999
+   9304, -9999, -999999, -9999, -9999, 123353, 2250, -999999
+   9454, -9999, -999999, -9999, -9999, 123008, 2116, -999999
+   9604, -9999, -999999, -9999, -9999, 120933, 1337, -999999
+   9754, -9999, -999999, -9999, -9999, 119675, 1019, -999999
+   9904, -9999, -999999, -9999, -9999, 122655, 2061, -999999
+   10054, -9999, -999999, -9999, -9999, 124384, 3126, -999999
+   10204, -9999, -999999, -9999, -9999, 124632, 3371, -999999
+   10354, -9999, -999999, -9999, -9999, 121341, 1609, -999999
+54001, 8, 2005, 02, 03, 0, 42.278, -70.613, 6978, 7043, 241.7, 65.5
+   10118, 9999, -999999, -9999, -9999, 124458, 3205, -999999
+   10268, -9999, -999999, -9999, -9999, 123160, 2421, -999999
+   10418, -9999, -999999, -9999, -9999, 121221, 1582, -999999
+   10568, -9999, -999999, -9999, -9999, 120950, 1523, -999999
+   10718, -9999, -999999, -9999, -9999, 117339, 680, -999999
+   10868, -9999, -999999, -9999, -9999, 122751, 2423, -999999
+   11018, -9999, -999999, -9999, -9999, 124230, 3491, -999999
+   11168, -9999, -999999, -9999, -9999, 124039, 3424, -999999

tests/examples/HOX_DC8_20040712_R0.ict

+36, 1001
+Brune, William
+Penn State University
+ATHOS - OH and HO2 concentrations using cryo water mix ratio data for quenching corrections
+ICARTT_INTEX
+1, 1
+2004, 07, 12, 2005, 01, 12
+0
+Start_UTC, seconds
+4
+1, 1, 1, 1
+-9999, -9999, -9999, -9999
+Stop_UTC, seconds
+Mid_UTC, seconds
+OH_pptv, pptv
+HO2_pptv, pptv
+0
+18
+PI_CONTACT_INFO: Address: 503 Walker Building, University Park, PA 16802; email: brune@essc.psu.edu;
+PLATFORM: NASA DFRC DC8 - sampling underneath aircraft forward cargo bay location
+LOCATION: Aircraft location data in nav_dc8_20040712_R0.ict file
+ASSOCIATED_DATA: see ftp://ftp-air.larc.nasa.gov/pub-air/INTEXNA/
+INSTRUMENT_INFO: OH/HO2 LIF
+DATA_INFO: Units are pptv.
+UNCERTAINTY: The absolute accuracy is conservatively estimated to be +/- 32% at two sigma confidence
+ULOD_FLAG: -7777
+ULOD_VALUE: N/A
+LLOD_FLAG: -8888
+LLOD_VALUE: N/A
+DM_CONTACT_INFO: Bob Lesher; Penn State University; blesher@psu.edu
+PROJECT_INFO: INTEX Mission 26 June-14 August 2004; California, Illinois, and New Hampshire
+STIPULATIONS_ON_USE: Use of these data requires prior approval from William Brune
+OTHER_COMMENTS: N/A
+REVISION: R0
+R0: Final Data
+Start_UTC, Stop_UTC, Mid_UTC, OH_pptv, HO2_pptv
+55526, 55545, 55535, 0.171, 9.791
+55546, 55565, 55555, 0.180, 9.218
+55566, 55585, 55575, 0.186, 9.767
+55586, 55605, 55595, 0.176, 9.996
+55606, 55625, 55615, 0.192, 9.513
+55626, 55645, 55635, 0.185, 9.798
+55646, 55665, 55655, 0.160, 9.834

tests/examples/LIDARO3_WP3_20040830_R0.ict

+46, 2310
+Williams, Eric
+NOAA/Earth System Research Laboratory
+Ozone number density profile from WP3 aircraft LIDAR
+ICARTT_ITCT
+1, 1
+2004, 08, 30, 2009, 09, 04
+1
+Geo_Alt, meters, Geometric_altitude_of_observation
+UT_TIME, seconds, Elapsed_time_from_0_hours_on_day_given_by_date
+1 ;{Number of PRIMARY variables}
+1.0e9
+-9999
+O3_NumDensity[], molecules/cc, Ozone_NumDensity_Array
+9 ;{Number of AUXILIARY variable}
+1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
+-9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999
+Num_Altitudes, none, number_of_altitudes_at_current_time_mark
+Geo_Alt_Begin, meters, geometric_altitude_at_which_data_begin
+Alt_Increment, meters, altitude_increment_between_observations
+Geo_Alt_Aircraft, meters, geometric_altitude_of_aircraft
+UT_hour, hours
+UT_min, minutes
+UT_sec, seconds
+Lon_aircraft, degrees_E
+Lat_aircraft, degrees_N
+0
+18
+PI_CONTACT_INFO: 325 Broadway, Boulder, CO 80305; 303-497-3226; eric.j.williams@noaa.gov
+PLATFORM: NOAA WP3
+LOCATION: Lat, Lon, and Alt data included in the data records
+ASSOCIATED_DATA: N/A
+INSTRUMENT_INFO: Differential absorption LIDAR. See Williams et al., BigScience, 42, p. 50-51, 2001
+DATA_INFO: The units are number density (#/cc). The vertical averaging interval is 975 m at 1-7 km above the aircraft and 2025 m > 7 km above the aircraft. Horizontal averaging interval: 60 km.
+UNCERTAINTY: Contact PI
+ULOD_FLAG: -7777
+ULOD_VALUE: N/A
+LLOD_FLAG: -8888
+LLOD_VALUE: N/A
+DM_CONTACT_INFO: Contact PI
+PROJECT_INFO: ICARTT study; 1 July-15 August 2004
+STIPULATIONS_ON_USE: Use of these data requires PRIOR OK from the PI
+OTHER_COMMENTS: N/A
+REVISION: R0
+R0: No comments for this revision.
+UT_TIME, Num_Altitudes, Geo_Alt_Begin, Alt_Increment, Geo_Alt_Aircraft, UT_hour, UT_min, UT_sec, Lon_aircraft, Lat_aircraft, O3_NumDensity[]
+30335, 26, 12819, 75, 10389, 8, 25, 35, -133.24, -9.45
+   1340, 1519, 1660, 1779, 1868, 1939, 1973, 1992, 1989, 1955, 1934, 1897, 1817, 1721, 1619, 1514, 1434, 1343, 1258, 1203, 1140, 1088, 1037, 956, 892, 878
+30336, 22, 12819, 75, 10383, 8, 26, 0, -133.22, -9.93
+   1351, 1523, 1658, 1774, 1860,1930, 1962, 1974, 1966, 1932, 1909, 1877, 1803, 1706, 1600, 1493, 1407, 1310, -9999, -9999, 1094, 1045

tests/examples/NOx_RHBrown_20040830_R0.ict

+41, 1001
+Williams, Eric
+Earth System Research Laboratory/NOAA
+Nitric oxide and nitrogen dioxide mixing ratios from R/V Ronald H. Brown
+ICARTT_NEAQS
+1, 1
+2004, 08, 30, 2004, 12, 25
+0
+Start_UTC, seconds, number_of_seconds_from_0000_UTC
+9
+1, 1, 1, 1, 1, 1, 1, 1, 1
+-9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999, -9999
+Stop_UTC, seconds
+Mid_UTC, seconds
+DLat, deg_N
+DLon, deg_E
+Elev, meters
+NO_ppbv, ppbv
+NO_1sig, ppbv
+NO2_ppbv, ppbv
+NO2_1sig, ppbv
+0
+18
+PI_CONTACT_INFO: 325 Broadway, Boulder, CO 80305; 303-497-3226; email:eric.j.williams@noaa.gov
+PLATFORM: NOAA research vessel Ronald H. Brown
+LOCATION: Latitude, longitude and elevation data are included in the data records
+ASSOCIATED_DATA: N/A
+INSTRUMENT_INFO: NO: chemiluminescence; NO2: narrow-band photolysis/chemiluminescence
+DATA_INFO: All data with the exception of the location data are in ppbv. All oneminute averages contain at least 35 seconds of data, otherwise missing.
+UNCERTAINTY: included in the data records as variables with a _1sig suffix
+ULOD_FLAG: -7777
+ULOD_VALUE: N/A
+LLOD_FLAG: -8888
+LLOD_VALUE: N/A, N/A, N/A, N/A, N/A, 0.005, N/A, 0.025, N/A
+DM_CONTACT_INFO: N/A
+PROJECT_INFO: ICARTT study; 1 July-15 August 2004; Gulf of Maine and North Atlantic Ocean
+STIPULATIONS_ON_USE: Use of these data requires PRIOR OK from the PI
+OTHER_COMMENTS: N/A
+REVISION: R0
+R0: No comments for this revision.
+Start_UTC, Stop_UTC, Mid_UTC, DLat, DLon, Elev, NO_ppbv, NO_1sig, NO2_ppv, NO2_1sig
+43200, 43259, 43229, 41.00000, -71.00000, 15, 0.555, 0.033, 2.220, 0.291
+43260, 43319, 43289, 41.01234, -71.01234, 15, 10.333, 0.522, 31.000, 0.375

tests/test_dataset.py

+import unittest
+import os
+import io
+import sys
+import icartt
+
+def compare_files(str_in, str_out, diff=0):
+    str_out.seek(0)
+    str_in.seek(0)
+    input  = str_in.readlines()
+    output = str_out.readlines()
+    str_in.close()
+    str_out.close()
+    
+    if not len(input) == len(output):
+        raise Exception("Input ({:d}) and output ({:d}) do not have the same number of lines!".format(len(input), len(output)))
+    
+    for i in range(len(input)):
+        inline  = input[i].strip().replace(" ", "")
+        outline = output[i].strip().replace(" ", "")
+        if not inline == outline:
+            print("Line {:d} differs:".format(i))
+            print("  input: {:s}".format(inline))
+            print(" output: {:s}".format(outline))
+    
+    return True
+
+class DatasetTestCase(unittest.TestCase):
+    def test_simple_1001_NOx(self):
+        fn = 'tests/examples/NOx_RHBrown_20040830_R0.ict'
+        
+        print(fn)
+        
+        str_in  = open(fn)
+        str_out = io.StringIO()
+        
+        ict = icartt.Dataset(fn, loadData=False)
+        
+        ict.read_data()
+        ict.write(str_out)
+        
+        assert compare_files(str_in, str_out)
+
+    def test_simple_1001_HOx(self):        
+        fn = 'tests/examples/HOX_DC8_20040712_R0.ict'
+
+        print(fn)
+        
+        str_in  = open(fn)
+        str_out = io.StringIO()
+        
+        ict = icartt.Dataset(fn, loadData=False)
+        
+        ict.read_data()
+        ict.write(str_out)
+        
+        assert compare_files(str_in, str_out)
+
+    def test_simple_2110_AR(self):
+        fn = 'tests/examples/AR_DC8_20050203_R0.ict'
+        
+        print(fn)
+        
+        str_in  = open(fn)
+        str_out = io.StringIO()
+        
+        ict = icartt.Dataset(fn, loadData=False)
+        
+        ict.read_data()
+        ict.write(str_out)
+        
+        assert compare_files(str_in, str_out)
+
+    def test_simple_2110_AROTAL(self):
+        fn = 'tests/examples/AROTAL-RAY_DC8_20040715_R1.ict'
+        
+        print(fn)
+        
+        str_in  = open(fn)
+        str_out = io.StringIO()
+        
+        ict = icartt.Dataset(fn, loadData=False)
+        
+        ict.read_data()
+        ict.write(str_out)
+        
+        assert compare_files(str_in, str_out)
+
+def suite():
+    suite = unittest.TestSuite()
+    suite.addTest( DatasetTestCase('test_simple_1001_NOx') )
+    suite.addTest( DatasetTestCase('test_simple_1001_HOx') )
+    suite.addTest( DatasetTestCase('test_simple_2110_AR') )    
+    suite.addTest( DatasetTestCase('test_simple_2110_AROTAL') )    
+    return suite
+
+if __name__ == '__main__':
+    runner = unittest.TextTestRunner()
+    runner.run(suite())