updated main to compute integer cloud mask. added debug mode to optionally...

updated main to compute integer cloud mask. added debug mode to optionally include bits in output file

mvcm/main.py

@@ -128,6 +128,7 @@ def main(
     eco_file: str = _eco_file,
     out_file: str = "temp_out.nc",
     verbose: int = 0,
+    debug: bool = False,
 ) -> None:
     """MVCM main function.
 
@@ -290,8 +291,12 @@ def main(
         cmin_g2, bits["04"] = MyScene.bt_diff_86_11um("M14-M15", cmin_g2, bits["04"])
         cmin_g2, bits["05"] = MyScene.test_11_12um_diff("M15-M16", cmin_g2, bits["05"])
         cmin_g2, bits["06"] = MyScene.variability_11um_test(m15_name, cmin_g2, bits["06"])
-        cmin_g2, bits["07"] = MyScene.bt_difference_11_4um_test_ocean("M15-M12", cmin_g2, bits["07"])
-        cmin_g2, bits["08"] = MyScene.bt_difference_11_4um_test_land("M15-M16", "M15-M12", cmin_g2, bits["08"])
+        cmin_g2, bits["07"] = MyScene.bt_difference_11_4um_test_ocean(
+            "M15-M12", cmin_g2, bits["07"]
+        )
+        cmin_g2, bits["08"] = MyScene.bt_difference_11_4um_test_land(
+            "M15-M16", "M15-M12", cmin_g2, bits["08"]
+        )
         cmin_g2, bits["09"] = MyScene.oceanic_stratus_11_4um_test("M15-M12", cmin_g2, bits["09"])
 
         # Group 3
@@ -348,7 +353,9 @@ def main(
     cmin[idx], bits["r01"]["test"][idx] = Restore.spatial_variability(cmin, idx, bits["r01"])
 
     # Sun Glint
-    sunglint_bits = restoral_bits["01"] * restoral_bits["03"] * restoral_bits["05"] * restoral_bits["15"]
+    sunglint_bits = (
+        restoral_bits["01"] * restoral_bits["03"] * restoral_bits["05"] * restoral_bits["15"]
+    )
 
     idx = np.nonzero(
         (scene_flags["day"] == 1)
@@ -367,8 +374,12 @@ def main(
         "nir_2": restoral_bits["15"],
         "sst": restoral_bits["03"],
     }
-    idx = np.nonzero((scene_flags["day"] == 1) & (scene_flags["water"] == 1) & (scene_flags["ice"] == 0))
-    cmin[idx], bits["r03"]["test"][idx] = Restore.shallow_water(sh_water_bits, cmin, idx, bits["r03"])
+    idx = np.nonzero(
+        (scene_flags["day"] == 1) & (scene_flags["water"] == 1) & (scene_flags["ice"] == 0)
+    )
+    cmin[idx], bits["r03"]["test"][idx] = Restore.shallow_water(
+        sh_water_bits, cmin, idx, bits["r03"]
+    )
 
     desert_bits = restoral_bits["15"] * restoral_bits["05"]
     # make sure that the land_bits are calculated properly
@@ -486,10 +497,20 @@ def main(
     #     # cmin = MVCM.clear_sky_restoral(cmin)
     #
     # # return cmin
+    csc = cmin_final
+    cloud_mask = np.zeros(csc.shape)
+    cloud_mask[csc > 0.99] = 3
+    cloud_mask[(csc <= 0.99) & (csc > 0.95)] = 2
+    cloud_mask[(csc <= 0.95) & (csc > 0.66)] = 1
+    cloud_mask[csc <= 0.66] = 0
+
     d = {
         "latitude": {"dims": ("x", "y"), "data": viirs_data.latitude.values},
         "longitude": {"dims": ("x", "y"), "data": viirs_data.longitude.values},
         "confidence": {"dims": ("x", "y"), "data": cmin_final},
+        "cloud_mask": {"dims": ("x", "y"), "data": cloud_mask},
+    }
+    d_debug = {
         "ndvi": {"dims": ("x", "y"), "data": viirs_data.ndvi.values},
         "sunglint_bits": {"dims": ("x", "y"), "data": sunglint_bits},
         "eco": {"dims": ("x", "y"), "data": viirs_data.ecosystem.values},
@@ -530,6 +551,8 @@ def main(
         #         'data': viirs_data.M16.values},
         "GEMI": {"dims": ("x", "y"), "data": viirs_data.GEMI.values},
     }
+    if debug is True:
+        d.update(d_debug)
 
     sf = {k: {"dims": ("x", "y"), "data": scene_flags[k]} for k in scene_flags}
     out_dict = d | sf
@@ -632,6 +655,7 @@ if __name__ == "__main__":
         help="print version and exit",
     )
     parser.add_argument("-v", "--verbose", action="store_true", help="print verbose information")
+    parser.add_argument("-d", "--debug", action="store_true", help="activate debug mode")
 
     args = parser.parse_args()
 
@@ -653,6 +677,7 @@ if __name__ == "__main__":
     eco_file = args.eco or _eco_file
     out_file = args.out or "test_out.nc"
     verbose = args.verbose or False
+    debug = args.debug or False
 
     main(
         satellite=satellite,
@@ -673,4 +698,5 @@ if __name__ == "__main__":
         eco_file=eco_file,
         out_file=out_file,
         verbose=verbose,
+        debug=debug,
     )