initial template for testing read_data

ancillary.pyx

@@ -21,7 +21,7 @@ cimport numpy as np
 np.import_array()
 
 ctypedef np.float_t DTYPE_t
-DTYPE = np.float
+DTYPE = np.float32
 
 @cython.boundscheck(False)
 @cython.wraparound(False)
@@ -87,21 +87,21 @@ def py_get_GEOS(np.ndarray[float, ndim=1] lat, np.ndarray[float, ndim=1] lon, in
             geos_data[v] = np.ascontiguousarray(geos_data[v])
 
     cdef float[::1] tpw_mv = geos_data['tpw']
-    cdef float[::1] snowfr_mv = geos_data['snowfr']
-    cdef float[::1] icefr_mv = geos_data['icefr']
-    cdef float[::1] ocnfr_mv = geos_data['ocnfr']
-    cdef float[::1] landicefr_mv = geos_data['landicefr']
-    cdef float[::1] sfct_mv = geos_data['sfct']
+    cdef float[::1] snowfr_mv = geos_data['snow_fraction']
+    cdef float[::1] icefr_mv = geos_data['ice_fraction']
+    cdef float[::1] ocnfr_mv = geos_data['ocean_fraction']
+    cdef float[::1] landicefr_mv = geos_data['land_ice_fraction']
+    cdef float[::1] sfct_mv = geos_data['surface_temperature']
 
     get_GEOS(&lat[0], &lon[0], res, startTime, anc_dir, geos1, geos2, geos_lnd, geos_ocn, geos_cnst,
              &tpw_mv[0], &snowfr_mv[0], &icefr_mv[0], &ocnfr_mv[0], &landicefr_mv[0], &sfct_mv[0])
 
     geos_dict = {'tpw': geos_data['tpw'],
-                 'snowfr': geos_data['snowfr'],
-                 'icefr': geos_data['icefr'],
-                 'ocnfr': geos_data['ocnfr'],
-                 'landicefr': geos_data['landicefr'],
-                 'sfct': geos_data['sfct']
+                 'snow_fraction': geos_data['snow_fraction'],
+                 'ice_fraction': geos_data['ice_fraction'],
+                 'ocean_fraction': geos_data['ocean_fraction'],
+                 'land_ice_fraction': geos_data['land_ice_fraction'],
+                 'surface_temperature': geos_data['surface_temperature']
                  }
 
     return geos_dict

pyproject.toml

@@ -18,3 +18,7 @@ classifiers = ['Programming Language :: Python :: 3',
 [project.urls]
 'Homepage' = 'https://gitlab.ssec.wisc.edu/pveglio/mvcm'
 
+[tool.pytest.ini_options]
+addopts = [
+    '--import-mode=importlib',
+]

read_data.py

@@ -13,7 +13,7 @@ from attrs import define, field, validators, Factory
 _DTR = np.pi/180.
 _RTD = 180./np.pi
 _bad_data = -999.0
-_datapath = '/ships19/hercules/pveglio/mvcm_viirs_hires'
+_datapath = '/ships19/hercules/pveglio/mvcm_test_data'
 
 logging.basicConfig(level=logging.INFO, format='%(name)s - %(levelname)s - %(message)s')
 # logging.basicConfig(level=logging.INFO, filename='logfile.log', 'filemode='w',
@@ -60,7 +60,7 @@ class CollectInputs(object):
                           validator=[validators.instance_of(str), ])
     eco_file: str = field(default='goge1_2_img.v1',
                           validator=[validators.instance_of(str), ])
-    ndvi_file: str = field(default='NDVI.FM.c004.v2.0.WS.00-04-177.hdf',
+    ndvi_file: str = field(default='NDVI.FM.c004.v2.0.WS.00-04.177.hdf',
                            validator=[validators.instance_of(str), ])
     geos_file_1: str = field(default='GEOS.fpit.asm.inst3_2d_asm_Nx.GEOS5124.20220622_1200.V01.nc4',
                              validator=[validators.instance_of(str), ])
@@ -402,15 +402,15 @@ class ReadAncillary(CollectInputs):
         geos_data: Dict
             dictionary containing all quantities required by MVCM (see geos_variables here below)
         """
-        if not os.path.isfile(os.path.join(self.ancillary, self.geos_file_1)):
+        if not os.path.isfile(os.path.join(self.ancillary_dir, self.geos_file_1)):
             logging.error('GEOS-5 file 1 not found')
-        if not os.path.isfile(os.path.join(self.ancillary, self.geos_file_2)):
+        if not os.path.isfile(os.path.join(self.ancillary_dir, self.geos_file_2)):
             logging.error('GEOS-5 file 2 not found')
-        if not os.path.isfile(os.path.join(self.ancillary, self.geos_land_file)):
+        if not os.path.isfile(os.path.join(self.ancillary_dir, self.geos_land)):
             logging.error('GEOS-5 land file not found')
-        if not os.path.isfile(os.path.join(self.ancillary, self.geos_ocean_file)):
+        if not os.path.isfile(os.path.join(self.ancillary_dir, self.geos_ocean)):
             logging.error('GEOS-5 ocean file not found')
-        if not os.path.isfile(os.path.join(self.ancillary, self.geos_constants_file)):
+        if not os.path.isfile(os.path.join(self.ancillary_dir, self.geos_constants)):
             logging.error('GEOS-5 constants file not found')
 
         geos_variables = ['tpw', 'snow_fraction', 'ice_fraction', 'ocean_fraction',

tests/test_read_data.py

@@ -12,14 +12,14 @@ def fixturepath():
     return os.path.join(os.path.dirname(__file__), 'fixtures')
 
 
-# @pytest.fixture()
-# def l1b_file(fixturepath):
-#     return os.path.join(fixturepath, '')
+@pytest.fixture
+def l1b_file():
+    return 'VNP02MOD.A2022173.1312.001.2022174011547.uwssec.nc'
 
 
-# @pytest.fixture()
-# def geo_file(fixturepath):
-#     return os.path.join(fixturepath, '')
+@pytest.fixture
+def geo_file():
+    return 'VNP03MOD.A2022173.1312.001.2022174012746.uwssec.nc'
 
 
 # @pytest.fixture
@@ -67,6 +67,18 @@ def ref_file(fixturepath):
     return os.path.join(fixturepath, 'ref_ancillary.nc')
 
 
+# this is only temporary. At some point I'll write a better test
+def test_l1b(fixturepath, l1b_file, geo_file):
+    viirs = rd.ReadData(satellite='snpp',
+                        sensor='viirs',
+                        file_name_l1b=l1b_file,
+                        file_name_geo=geo_file)
+    geo = viirs.read_viirs_geo()
+    l1b = viirs.read_l1b(geo.solar_zenith.values)
+
+    assert 'M11' in l1b.data_vars
+
+
 def test_sst(fixturepath, sst_file, ref_file):
     viirs = rd.ReadData(satellite='snpp',
                         sensor='viirs')