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Commit 2b4f48c4 authored by Christoph Knote's avatar Christoph Knote
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Cleanup tests, add test for 2110, format all documents with black

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Makefile deleted 100644 → 0
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− 3
View file @ 3fd50c35
.Phony: coverage
coverage:
coverage run --source=tests -m unittest discover
src/icartt/__init__.py
+ 2
− 2
View file @ 2b4f48c4
......@@ -11,12 +11,12 @@ def get_version():
return pkg_resources.get_distribution("icartt").version
__version__ = get_version()
del get_version
# EXPORTED TYPES
from .dataset import Dataset, StandardNormalComments, Variable, Formats, VariableType
__all__ = ("Dataset", "StandardNormalComments", "Variable", "Formats", "VariableType")
\ No newline at end of file
__all__ = ("Dataset", "StandardNormalComments", "Variable", "Formats", "VariableType")
src/icartt/dataset.py
+ 55
− 28
View file @ 2b4f48c4
from ctypes import ArgumentError
import datetime
import sys
import pathlib
......@@ -22,11 +21,14 @@ class Formats(IntEnum):
class VariableType(IntEnum):
"""ICARTT Variable Types"""
IndependentVariable = 1
IndependentBoundedVariable = 2
AuxiliaryVariable = 3
DependentVariable = 4
class DataStore1001:
def __init__(self, ivar, dvars):
self.ivarname = ivar.shortname
......@@ -64,7 +66,7 @@ class DataStore1001:
self.add(newData)
def add(self, newData):
"""bulk add data, providing a (structured) numpy array.
"""(bulk) add data, providing a (structured) numpy array.
Array has to have shape [ (ivar, dvar, dvar, ...), ... ],
missing values have to be set to np.nan.
......@@ -72,13 +74,13 @@ class DataStore1001:
:param newData: data to be added
:type newData: numpy.ndarray
"""
if not type(newData) is np.ndarray: # TODO: isinstance(arr, np.ndarray)?
raise ArgumentError("Input data needs to be numpy ndarray.")
if not isinstance(newData, np.ndarray):
raise TypeError("Input data needs to be numpy ndarray.")
if newData.dtype.names is None:
try:
newData.dtype = [(name, newData.dtype) for name in self.varnames]
except:
ArgumentError(
ValueError(
"Could not assign names to data structure, are you providing an array containing all variables?"
)
......@@ -96,10 +98,15 @@ class DataStore1001:
def write(
self, f=sys.stdout, fmt=DEFAULT_NUM_FORMAT, delimiter=DEFAULT_FIELD_DELIM
):
# TODO the fact that we need to clean before writing suggests we need to be more careful what to "add" in the first place!
d = self.denanify(self.data)
# single line data is 0D, savetxt cannot work with 0D. Make 1D.
# single line data is 0D if passed as tuple, savetxt cannot work with 0D. Make 1D.
if d.ndim == 0:
d = np.array( [ d ] )
d = np.array([d])
# need to squeeze extra dimension added for one liners added as np.array
if len(d.shape) == 2:
d = np.squeeze(d, axis=1)
np.savetxt(f, d, fmt=fmt, delimiter=delimiter)
......@@ -141,16 +148,18 @@ class DataStore2110(collections.UserDict):
# we are at the end of the file if this happens
break
ndeprows = int( auxds[self.nauxvarname] )
ndeprows = int(auxds[self.nauxvarname])
try:
depds.addFromTxt(f, splitChar, max_rows=ndeprows)
except:
break
# it is indeed possible to have zero dependent data lines
if ndeprows > 0:
try:
depds.addFromTxt(f, splitChar, max_rows=ndeprows)
except:
raise IOError("Could not read dependent data lines.")
ivarValue = float(auxds[self.ivar.shortname])
self.data[ivarValue] = { "AUX": auxds, "DEP": depds }
self.data[ivarValue] = {"AUX": auxds, "DEP": depds}
def add(self, newAuxData, newDepData):
auxds = DataStore1001(self.ivar, self.auxvars)
......@@ -161,7 +170,7 @@ class DataStore2110(collections.UserDict):
ivarValue = float(auxds[self.ivar.shortname])
self.data[ivarValue] = { "AUX": auxds, "DEP": depds }
self.data[ivarValue] = {"AUX": auxds, "DEP": depds}
def write(
self, f=sys.stdout, fmt=DEFAULT_NUM_FORMAT, delimiter=DEFAULT_FIELD_DELIM
......@@ -192,10 +201,10 @@ class StandardNormalComments(collections.UserList):
# shortnames line is always there:
n = 1
# freeform comment might or might not be there:
n += sum(len(s.split('\n')) for s in self.freeform)
n += sum(len(s.split("\n")) for s in self.freeform)
# tagged comments have at least one line:
for k in self.keywords.values():
n += sum(len(s.split('\n')) for s in k.data) or 1
n += sum(len(s.split("\n")) for s in k.data) or 1
return n
@property
......@@ -219,18 +228,24 @@ class StandardNormalComments(collections.UserList):
keywordLine = False
for l in raw:
possibleKeyword = l.split(":")[0].strip()
if possibleKeyword in self.keywords or re.match("R[a-zA-Z0-9]{1,2}[ ]*", possibleKeyword):
if possibleKeyword in self.keywords or re.match(
"R[a-zA-Z0-9]{1,2}[ ]*", possibleKeyword
):
currentKeyword = possibleKeyword
keywordLine = True
if not currentKeyword in self.keywords: # for the revisions only...
self.keywords[currentKeyword] = KeywordComment(currentKeyword, False)
self.keywords[currentKeyword] = KeywordComment(
currentKeyword, False
)
else:
keywordLine = False
if currentKeyword is None:
self.freeform.append(l)
elif keywordLine:
self.keywords[currentKeyword].append(l.replace(l.split(":")[0] + ":", "").strip())
self.keywords[currentKeyword].append(
l.replace(l.split(":")[0] + ":", "").strip()
)
else:
self.keywords[currentKeyword].append(l.strip())
......@@ -405,15 +420,28 @@ class Dataset:
:return: numpy array of time steps
:rtype: numpy.ndarray
"""
if self.data.data is None or self.independentVariable is None:
if self.defineMode:
return np.datetime64("NaT")
if self.data.data is None or self.data.data == {}:
return np.datetime64("NaT")
ref_dt = np.datetime64(datetime.datetime(*self.dateOfCollection), "ns")
time_values = []
if self.format == Formats.FFI1001:
time_values = self.data[self.independentVariable.shortname]
elif self.format == Formats.FFI2110:
# for 2110, data keys are independent variable values by definition in out implementation
time_values = np.array(list(self.data.keys()))
else:
raise NotImplementedError(
"times method not implemented for this ICARTT format!"
)
# ivar unit is seconds as per standard; need to convert to ns to use timedelta64[ns] type.
return ref_dt + (
self.data[self.independentVariable.shortname] * 10**9
).astype("timedelta64[ns]")
return ref_dt + (time_values * 10**9).astype("timedelta64[ns]")
@property
def variables(self):
......@@ -423,6 +451,7 @@ class Dataset:
:rtype: dict of Variable(s)
"""
variables = {}
if self.independentVariable is not None:
variables[self.independentVariable.shortname] = self.independentVariable
if self.independentBoundedVariable is not None:
......@@ -849,12 +878,10 @@ class Dataset:
def __repr__(self):
# TODO: this could be more meaningful
return "ICARTT Dataset object repr"
return "icartt.Dataset()"
def __str__(self):
# TODO: this could be more meaningful
return "ICARTT Dataset string representation"
return f"ICARTT Dataset {self.makeFileName()}"
def __init__(self, f=None, loadData=True, splitChar=",", format=Formats.FFI1001):
"""Constructor method"""
......@@ -910,4 +937,4 @@ class Dataset:
self.readHeader(splitChar)
if loadData:
self.endDefineMode()
self.readData(splitChar)
\ No newline at end of file
self.readData(splitChar)
tests/_utils.py
+ 1
− 0
View file @ 2b4f48c4
......@@ -2,6 +2,7 @@
import numpy as np
def compareFiles(fn, strIn, strOut, skiplines=0, nlines=-1): # pragma: no cover
"""compare two icartt files line by line"""
strOut.seek(0)
......
tests/read_and_write.py
+ 3
− 3
View file @ 2b4f48c4
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument('input_file', type=str)
parser.add_argument('output_file', type=str)
parser.add_argument("input_file", type=str)
parser.add_argument("output_file", type=str)
args = parser.parse_args()
......@@ -11,5 +11,5 @@ import icartt
ict = icartt.Dataset(args.input_file)
ict.splitChar = ", "
with open(args.output_file, 'w') as f:
with open(args.output_file, "w") as f:
ict.write(f)
tests/test_1001.py
+ 5
− 5
View file @ 2b4f48c4
......@@ -5,17 +5,16 @@ import datetime
import numpy as np
import icartt
try:
from _utils import compareFiles # we're executing from the directory of this script
from _utils import compareFiles # we're executing from the directory of this script
except ImportError:
from ._utils import compareFiles # we're executing from another directory
from ._utils import compareFiles # we're executing from another directory
# working directory, example files
wd = pathlib.Path(__file__).parent
class Simple1001TestCase(unittest.TestCase):
def setUp(self):
self.fn = wd / "example_data" / "expect_ok" / "NOx_RHBrown_20040830_R0.ict"
......@@ -164,6 +163,7 @@ class Simple1001TestCase(unittest.TestCase):
["Use of these data requires PRIOR OK from the PI"],
)
self.assertEqual(ict.normalComments.keywords["OTHER_COMMENTS"].data, ["N/A"])
# TODO test revision information
def testReadData(self):
ict = icartt.Dataset(self.fn, loadData=True)
......@@ -325,4 +325,4 @@ class Create1001TestCase(unittest.TestCase):
if __name__ == "__main__": # pragma: no cover
unittest.main()
\ No newline at end of file
unittest.main()
tests/test_2110.py 0 → 100644
+ 470
− 0
View file @ 2b4f48c4
import unittest
import pathlib
import io
import datetime
import numpy as np
import icartt
try:
from _utils import compareFiles # we're executing from the directory of this script
except ImportError:
from ._utils import compareFiles # we're executing from another directory
# working directory, example files
wd = pathlib.Path(__file__).parent
class Simple2110TestCase(unittest.TestCase):
def setUp(self):
self.fn = wd / "example_data" / "expect_warn" / "PAVE-AR_DC8_20050203_R0.ict"
self.nHeader = 55
def tearDown(self):
pass
def testOpen(self):
ict = icartt.Dataset(self.fn, loadData=False)
self.assertEqual(type(ict), icartt.Dataset)
def testFormat(self):
ict = icartt.Dataset(self.fn, loadData=False)
self.assertEqual(ict.format, icartt.Formats.FFI2110)
def testN(self):
ict = icartt.Dataset(self.fn, loadData=False)
self.assertEqual(ict.nHeader, self.nHeader)
self.assertEqual(len(ict.auxiliaryVariables), 11)
self.assertEqual(len(ict.dependentVariables), 7)
self.assertEqual(len(ict.normalComments), 18)
self.assertEqual(len(ict.specialComments), 1)
def testIvar(self):
ict = icartt.Dataset(self.fn, loadData=False)
self.assertEqual(ict.independentVariable.shortname, "UTC")
self.assertEqual(ict.independentVariable.units, "seconds")
self.assertEqual(ict.independentVariable.standardname, "Time_Start")
self.assertEqual(
ict.independentVariable.longname, "number of seconds from 00:00 UTC"
)
self.assertEqual(ict.independentVariable.scale, 1.0)
self.assertEqual(ict.independentVariable.miss, -99999.0)
def testAuxvar(self):
ict = icartt.Dataset(self.fn, loadData=False)
self.assertEqual(
[AUXVAR.shortname for AUXVAR in ict.auxiliaryVariables.values()],
[
"NumAlts",
"Year",
"Month",
"Day",
"AvgTime",
"Lat",
"Lon",
"PAlt",
"GPSAlt",
"SAT",
"SZA",
],
)
self.assertEqual(
[AUXVAR.units for AUXVAR in ict.auxiliaryVariables.values()],
[
"#",
"yyyy",
"mm",
"dd",
"minutes",
"degrees",
"degrees",
"meters",
"meters",
"K",
"degrees",
],
)
self.assertEqual(
[AUXVAR.standardname for AUXVAR in ict.auxiliaryVariables.values()],
[
"Number_of_altitudes",
"Year_UTC",
"Month_UTC",
"Day_UTC",
"Averaging_time",
"Latitude",
"Longitude",
"pressure_altitude",
"GPS_altitude",
"Static_air_temperature",
"Sun_Zenith_Angle",
],
)
self.assertEqual(
[AUXVAR.longname for AUXVAR in ict.auxiliaryVariables.values()],
[
"Number_of_altitudes_reported",
"Year_UTC",
"Month_UTC",
"Day_UTC",
"Averaging_time_of_presented_data xxx.x_minutes",
None,
None,
None,
None,
None,
None,
],
)
self.assertEqual(
[AUXVAR.scale for AUXVAR in ict.auxiliaryVariables.values()],
["1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1"],
)
self.assertEqual(
[AUXVAR.miss for AUXVAR in ict.auxiliaryVariables.values()],
[
"-9999",
"-9999",
"-9999",
"-9999",
"-9999",
"-9999",
"-9999",
"-9999",
"-9999",
"-9999",
"-9999",
],
)
def testDvar(self):
ict = icartt.Dataset(self.fn, loadData=False)
self.assertEqual(
[DVAR.shortname for DVAR in ict.dependentVariables.values()],
[
"TempK[]",
"Log10_NumDensity[]",
"TempK_Err[]",
"AerKlet[]",
"Log10_O3NumDensity[]",
"O3_MR[]",
"Log10_O3NumDensity_Err[]",
],
)
self.assertEqual(
[DVAR.units for DVAR in ict.dependentVariables.values()],
[
"K",
"part/cc",
"K",
"Klet",
"part/cc",
"ppb",
"part/cc",
],
)
self.assertEqual(
[DVAR.standardname for DVAR in ict.dependentVariables.values()],
[
"Temperature",
"Log10_NumDensity",
"Temperature_Error",
"Aerosol",
"Log10_O3NumDensity",
"Ozone_mixing_ratio",
"Log10_O3NumDensity_Error",
],
)
self.assertEqual(
[DVAR.longname for DVAR in ict.dependentVariables.values()],
[
"Temperature_array",
"Log10_NumDensity_array",
"Temperature_error_array",
"Aerosol_array",
"Log10_Ozone_NumDensity_array",
"Ozone_mixing_ratio_array",
"Log10_NumDensity_error_array",
],
)
self.assertEqual(
[DVAR.scale for DVAR in ict.dependentVariables.values()],
[
"0.1",
"0.0001",
"0.1",
"0.01",
"0.0001",
"0.1",
"0.0001",
],
)
self.assertEqual(
[DVAR.miss for DVAR in ict.dependentVariables.values()],
[
"-999999",
"-999999",
"-999999",
"-999999",
"-999999",
"-999999",
"-999999",
],
)
def testNCOM(self):
ict = icartt.Dataset(self.fn, loadData=False)
self.assertEqual(
ict.normalComments.keywords["PI_CONTACT_INFO"].data,
["Enter PI Address here"],
)
self.assertEqual(
ict.normalComments.keywords["PLATFORM"].data,
["NASA DC8"],
)
self.assertEqual(
ict.normalComments.keywords["LOCATION"].data,
["Lat, Lon, and Alt included in the data records"],
)
self.assertEqual(ict.normalComments.keywords["ASSOCIATED_DATA"].data, ["N/A"])
self.assertEqual(
ict.normalComments.keywords["INSTRUMENT_INFO"].data,
["N/A"],
)
self.assertEqual(
ict.normalComments.keywords["DATA_INFO"].data,
["N/A"],
)
self.assertEqual(
ict.normalComments.keywords["UNCERTAINTY"].data,
["Contact PI"],
)
self.assertEqual(ict.normalComments.keywords["ULOD_FLAG"].data, ["-7777"])
self.assertEqual(ict.normalComments.keywords["ULOD_VALUE"].data, ["N/A"])
self.assertEqual(ict.normalComments.keywords["LLOD_FLAG"].data, ["-8888"])
self.assertEqual(
ict.normalComments.keywords["LLOD_VALUE"].data,
["N/A"],
)
self.assertEqual(
ict.normalComments.keywords["DM_CONTACT_INFO"].data,
["Enter Data Manager Info here"],
)
self.assertEqual(
ict.normalComments.keywords["PROJECT_INFO"].data,
["PAVE MISSION: Jan-Feb 2005"],
)
self.assertEqual(
ict.normalComments.keywords["STIPULATIONS_ON_USE"].data,
["Use of these data should be done in consultation with the PI"],
)
self.assertEqual(ict.normalComments.keywords["OTHER_COMMENTS"].data, ["N/A"])
# TODO test revision information
def testReadData(self):
ict = icartt.Dataset(self.fn, loadData=True)
self.assertEqual(type(ict), icartt.Dataset)
def testWriteHeader(self):
ict = icartt.Dataset(self.fn, loadData=False)
strIn = open(self.fn)
strOut = io.StringIO()
ict.writeHeader(f=strOut)
self.assertTrue(compareFiles(self.fn, strIn, strOut, nlines=self.nHeader))
def testWriteData(self):
ict = icartt.Dataset(self.fn, loadData=True)
strIn = open(self.fn)
strOut = io.StringIO()
ict.write(f=strOut)
self.assertTrue(compareFiles(self.fn, strIn, strOut, skiplines=self.nHeader))
def testWrite(self):
ict = icartt.Dataset(self.fn, loadData=True)
strIn = open(self.fn)
strOut = io.StringIO()
ict.write(f=strOut)
self.assertTrue(compareFiles(self.fn, strIn, strOut))
class Create2110TestCase(unittest.TestCase):
def testCreateDs(self):
now = datetime.datetime.today()
ict = icartt.Dataset(format=icartt.Formats.FFI2110)
ict.PIName = "Knote, Christoph"
ict.PIAffiliation = "Faculty of Medicine, University Augsburg, Germany"
ict.dataSourceDescription = "Example data"
ict.missionName = "MBEES"
ict.dateOfCollection = now.timetuple()[:3]
ict.dateOfRevision = now.timetuple()[:3]
ict.dataIntervalCode = [0]
ict.independentVariable = icartt.Variable(
"Time_Start",
"seconds_from_0_hours_on_valid_date",
"Time_Start",
"Time_Start",
vartype=icartt.VariableType.IndependentVariable,
scale=1.0,
miss=-9999999,
)
ict.independentBoundedVariable = icartt.Variable(
"Altitude",
"altitude_above_ground_in_meters",
"Altitude",
"Altitude",
vartype=icartt.VariableType.IndependentBoundedVariable,
scale=1.0,
miss=-9999999,
)
# ICARTT convention: first aux variable contains number of dependent elements
ict.auxiliaryVariables["nAltitudes"] = icartt.Variable(
"nAltitudes",
"number_of_dependent_variable_items",
"variable",
"nAltitudes",
scale=1.0,
miss=-9999999,
)
ict.auxiliaryVariables["Time_Stop"] = icartt.Variable(
"Time_Stop",
"seconds_from_0_hours_on_valid_date",
"Time_Stop",
"Time_Stop",
scale=1.0,
miss=-9999999,
)
ict.auxiliaryVariables["Longitude"] = icartt.Variable(
"Longitude",
"longitude_in_degrees",
"Longitude",
"Longitude",
scale=1.0,
miss=-9999999,
)
ict.auxiliaryVariables["Latitude"] = icartt.Variable(
"Latitude",
"latitude_in_degrees",
"Latitude",
"Latitude",
scale=1.0,
miss=-9999999,
)
ict.dependentVariables["Payload1"] = icartt.Variable(
"Payload1", "some_units", "Payload1", "Payload1", scale=1.0, miss=-9999999
)
ict.dependentVariables["Payload2"] = icartt.Variable(
"Payload2", "some_units", "Payload2", "Payload2", scale=1.0, miss=-9999999
)
ict.specialComments.append("Some comments on this dataset:")
ict.specialComments.append("They are just examples!")
ict.specialComments.append("Adapt as needed.")
# we can just use len of the list to check number of comments
self.assertEqual(len(ict.specialComments), 3)
# let's define some normal comments... 21 lines
ncom = {
"PI_CONTACT_INFO": "PI1 pi-email@mail.com\nPI2 more-email@what.com",
"PLATFORM": "a platform",
"LOCATION": "somewhere",
"ASSOCIATED_DATA": "met sensor data",
"INSTRUMENT_INFO": "super cool instrument",
"DATA_INFO": f"icartt Python package version: {icartt.__version__}",
"UNCERTAINTY": "not much",
"ULOD_FLAG": "-7777",
"ULOD_VALUE": "N/A",
"LLOD_FLAG": "-8888",
"LLOD_VALUE": "N/A",
"DM_CONTACT_INFO": "datamanager@mail.edu",
"PROJECT_INFO": "the campaign",
"STIPULATIONS_ON_USE": "no",
"OTHER_COMMENTS": "a lot more info\non multiple lines",
"REVISION": (
"R1\n"
"R1: revised time synchronization.\n"
"R0: initial, preliminary version."
),
}
for k, v in ncom.items():
ict.normalComments.keywords[k].append(v)
# we can check if nlines method of normalComments class works
self.assertEqual(ict.normalComments.nlines, 21)
ict.normalComments.freeform.append("free comment line 1")
ict.normalComments.freeform.append("free comment line 2")
self.assertEqual(ict.normalComments.nlines, 23)
ict.endDefineMode()
# and times must be NaT
self.assertTrue(np.isnat(ict.times))
# note, the second variable ('4') is the number of dependent lines to follow
# ivar, ndepvar, auxvar1, auxvar2, auxvar3
auxData = np.array([(12.3, 4, 12.5, 48.21, 10.3)])
# ibvar, dvar1, dvar2
depData = np.array(
[(0, 123, 8.4e4), (100, 122, 9.1e4), (250, 115, 9.3e4), (500, 106, 9.8e4)]
)
ict.data.add(auxData, depData)
# ... and so forth
auxData = np.array([(12.4, 2, 12.8, 48.41, 12.1)])
# ibvar, dvar1, dvar2
depData = np.array([(0, 153, 7.3e4), (270, 172, 8.9e4)])
ict.data.add(auxData, depData)
# import pdb; pdb.set_trace()
# elements of the time array must be equal to our input
t0 = np.datetime64(datetime.datetime(*now.timetuple()[:3]), "ns")
for have, want in zip(ict.times, (12.3, 12.4)):
self.assertEqual(int(have - t0), int(want * 10**9))
strOut = io.StringIO()
ict.write(f=strOut)
return True
if __name__ == "__main__": # pragma: no cover
unittest.main()
tests/test_bulkIO.py
+ 32
− 47
View file @ 2b4f48c4
......@@ -5,58 +5,43 @@ import io
# import pytest
import icartt
try:
from _utils import compareFiles # we're executing from the directory of this script
from _utils import compareFiles # we're executing from the directory of this script
except ImportError:
from ._utils import compareFiles # we're executing from another directory
from ._utils import compareFiles # we're executing from another directory
# working directory, example files
wd = pathlib.Path(__file__).parent / "example_data"
# file : (ffi, nlscom, nlncom, nHeaderLines, exception) <- want
fileinfo = {
# should warn; has multiple keywords per line in normalComments
'AROTAL-RAY_DC8_20040715_R1.ict': (2110, 1, 19, 68, None),
'AR_DC8_20050203_R0.ict': (2110, 0, 18, 54, None), # warns
'BB-FLUX_CU-SOF_20180808_R2.ict': (1001, 0, 18, 38, None), # ok
'DC8-20160517.ict': (1001, 0, 18, 36, None), # ok
'discoveraq-CO2_p3b_20140721_R0.ict': (1001, 1, 18, 37, None), # ok
# ok
'DISCOVERAQ-NOXYO3_P3B_20140720_R0.ict': (1001, 0, 27, 47, None),
'Dongdaemun_NIER_20160520_RA.ict': (1001, 0, 18, 36, None), # warns
'HOX_DC8_20040712_R0.ict': (1001, 0, 18, 36, None), # ok
# warns
'korusaq-flexpart-dc8_trajectory_20160529_R2.ict': (2110, 27, 20, 101, None),
# ok
'korusaq-mrg01-HANSEO-KING-AIR_merge_20160507_RA.ict': (1001, 0, 18, 45, None),
# error: 2310 not implemented
'LIDARO3_WP3_20040830_R0.ict': (2310, 0, 18, 46, NotImplementedError),
'NOx_RHBrown_20040830_R0.ict': (1001, 0, 18, 41, None), # ok
# error: invalid number of variables / columns
'output.ict': (1001, 8, 17, 41, Exception),
'PAVE-AR_DC8_20050203_R0.ict': (2110, 1, 18, 55, None), # warns
# ok
'SEAC4RS-PTRMS-acetaldehyde_DC8_20130806_R1.ict': (1001, 0, 26, 44, None),
'bt_Munich_2020061000_72.ict.txt': (1001, 29, 18, 91, None), # warns
# warns (variable names)
'korusaq-mrg10-dc8_merge_20160510_R4.ict': (1001, 0, 29, 397, None),
}
# should warn; has multiple keywords per line in normalComments
"AROTAL-RAY_DC8_20040715_R1.ict": (2110, 1, 19, 68, None),
"AR_DC8_20050203_R0.ict": (2110, 0, 18, 54, None), # warns
"BB-FLUX_CU-SOF_20180808_R2.ict": (1001, 0, 18, 38, None), # ok
"DC8-20160517.ict": (1001, 0, 18, 36, None), # ok
"discoveraq-CO2_p3b_20140721_R0.ict": (1001, 1, 18, 37, None), # ok
# ok
"DISCOVERAQ-NOXYO3_P3B_20140720_R0.ict": (1001, 0, 27, 47, None),
"Dongdaemun_NIER_20160520_RA.ict": (1001, 0, 18, 36, None), # warns
"HOX_DC8_20040712_R0.ict": (1001, 0, 18, 36, None), # ok
# warns
"korusaq-flexpart-dc8_trajectory_20160529_R2.ict": (2110, 27, 20, 101, None),
# ok
"korusaq-mrg01-HANSEO-KING-AIR_merge_20160507_RA.ict": (1001, 0, 18, 45, None),
# error: 2310 not implemented
"LIDARO3_WP3_20040830_R0.ict": (2310, 0, 18, 46, NotImplementedError),
"NOx_RHBrown_20040830_R0.ict": (1001, 0, 18, 41, None), # ok
# error: invalid number of variables / columns
"output.ict": (1001, 8, 17, 41, Exception),
"PAVE-AR_DC8_20050203_R0.ict": (2110, 1, 18, 55, None), # warns
# ok
"SEAC4RS-PTRMS-acetaldehyde_DC8_20130806_R1.ict": (1001, 0, 26, 44, None),
"bt_Munich_2020061000_72.ict.txt": (1001, 29, 18, 91, None), # warns
# warns (variable names)
"korusaq-mrg10-dc8_merge_20160510_R4.ict": (1001, 0, 29, 397, None),
}
# TODO: dataset -> close file pointer after read ?!
......@@ -65,9 +50,9 @@ fileinfo = {
class BulkIOTestCase(unittest.TestCase):
def setUp(self):
self.files_ok = list((wd / "expect_ok").glob("*.ict"))
self.files_warn = list(
(wd / "expect_warn").glob("*.ict")
) + list((wd / "example_data" / "expect_warn").glob("*.txt"))
self.files_warn = list((wd / "expect_warn").glob("*.ict")) + list(
(wd / "example_data" / "expect_warn").glob("*.txt")
)
self.files_fail = list((wd / "expect_fail").glob("*.ict"))
def tearDown(self):
......
tests/usage_examples/create_ffi2110.py
+ 2
− 0
View file @ 2b4f48c4
......@@ -96,6 +96,8 @@ depData = np.array(
[(0, 123, 8.4e4), (100, 122, 9.1e4), (250, 115, 9.3e4), (500, 106, 9.8e4)]
)
ict.data.add(auxData, depData)
# ... and so forth
auxData = np.array([(12.4, 2, 12.8, 48.41, 12.1)])
......
tests/usage_examples/read_ffi1001.py
+ 6
− 6
View file @ 2b4f48c4
......@@ -3,7 +3,7 @@ import pathlib
# load a new dataset from an existing file
wd = pathlib.Path(__file__).parent
ict = icartt.Dataset( wd / ".." / "example_data" / 'expect_ok' / 'DC8-20160517.ict')
ict = icartt.Dataset(wd / ".." / "example_data" / "expect_ok" / "DC8-20160517.ict")
# read some metadata
ict.PIName
......@@ -14,17 +14,17 @@ ict.dataID
ict.locationID
# list variable names
[ x for x in ict.variables ]
[x for x in ict.variables]
# some info on a variable
ict.variables['Alt_ft'].units
ict.variables['Alt_ft'].miss
ict.variables["Alt_ft"].units
ict.variables["Alt_ft"].miss
# get data for variable 'UTC':
ict.data['UTC']
ict.data["UTC"]
# get all data (NumPy array):
ict.data[:]
# get the altitude in feet for those data where UTC < 86400.0:
ict.data[ ict.data['UTC'] < 86400.0 ]['Alt_ft']
\ No newline at end of file
ict.data[ict.data["UTC"] < 86400.0]["Alt_ft"]
tests/usage_examples/read_ffi2110.py
+ 9
− 7
View file @ 2b4f48c4
......@@ -3,10 +3,12 @@ import pathlib
# load a new dataset from an existing file
wd = pathlib.Path(__file__).parent
ict = icartt.Dataset( wd / ".." / "example_data" / 'expect_warn' / 'AR_DC8_20050203_R0.ict')
ict = icartt.Dataset(
wd / ".." / "example_data" / "expect_warn" / "AR_DC8_20050203_R0.ict"
)
# list variable names
[ x for x in ict.variables ]
[x for x in ict.variables]
# independent, independent bounded, dependent, auxiliary variables?
print(f"Independent variable: {ict.independentVariable.shortname}")
......@@ -19,19 +21,19 @@ print(f"Units of variable Latitude are {ict.variables['Latitude'].units}")
print(f"... and its missing value is {ict.variables['Latitude'].miss}")
# get steps for which data is available:
tsteps = [ x for x in ict.data ]
tsteps = [x for x in ict.data]
# let's look at the first time step data
print("First time step data:")
print(ict.data[ tsteps[0] ])
print(ict.data[tsteps[0]])
# auxiliary data at this time step:
print("First time step auxiliary data:")
print(ict.data[ tsteps[0] ]['AUX'][:])
print(ict.data[tsteps[0]]["AUX"][:])
# dependent data at this time step:
tstepdata = ict.data[ tsteps[0] ]['DEP'][:]
tstepdata = ict.data[tsteps[0]]["DEP"][:]
# get the ozone mixing ratio for those data where Altitude < 10000.0:
print(f"Ozone mixing ratio for altitudes < 10000 at time step {tsteps[0]}")
print(tstepdata[ tstepdata['Altitude[]'] < 10000.0 ]['O3_MR[]'])
print(tstepdata[tstepdata["Altitude[]"] < 10000.0]["O3_MR[]"])
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