Merge pull request #6 from eurec4a/platform_generalization

moved HALO specifics navigation data to function

scripts/navdata.py

@@ -0,0 +1,40 @@
+# the individual loaders should import dependencies within the function
+# that way it is possible to run the code for one platform if dependencies
+# for another platform are not met
+
+_catalog_cache = {}
+
+def get_navdata_HALO(flight):
+    """
+    :param flight: flight id
+    """
+    import xarray as xr
+    from intake import open_catalog
+    if "HALO" not in _catalog_cache:
+        _catalog_cache["HALO"] = open_catalog("https://raw.githubusercontent.com/d70-t/eurec4a-intake/HALO_QL/catalog.yml")
+
+    catalog = _catalog_cache["HALO"]
+    bahamas = catalog.halo.bahamas.ql.by_flight_id[flight].to_dask()
+    ds = bahamas.rename({"tid": "time"})
+    return xr.Dataset({
+        "time": ds.TIME,
+        "lat": ds.IRS_LAT,
+        "lon": ds.IRS_LON,
+        "alt": ds.IRS_ALT,
+        "roll": ds.IRS_PHI,
+        "pitch": ds.IRS_THE,
+        "heading": ds.IRS_HDG,
+    })
+
+NAVDATA_GETTERS = {
+    "HALO": get_navdata_HALO,
+}
+
+def get_navdata(platform, flight):
+    """
+    :param platform: platform id
+    :param flight: flight id
+    """
+    return NAVDATA_GETTERS[platform](flight)
+
+__all__ = ["get_navdata"]

scripts/report.py

@@ -8,6 +8,8 @@
 from io import BytesIO
 from base64 import b64encode
 
+from navdata import get_navdata
+
 border_time = np.timedelta64(3, "m")
 
 color_before = "C2"
@@ -33,11 +35,11 @@ def fig2data_url(fig):
     url = "data:{};base64,{}".format("image/png", b64.decode("ascii"))
     return url
 
-def start_end_lims(bahamas):
-    lat_min = min(*bahamas.lat.data[[0,-1]])
-    lat_max = max(*bahamas.lat.data[[0,-1]])
-    lon_min = min(*bahamas.lon.data[[0,-1]])
-    lon_max = max(*bahamas.lon.data[[0,-1]])
+def start_end_lims(navdata):
+    lat_min = min(*navdata.lat.data[[0,-1]])
+    lat_max = max(*navdata.lat.data[[0,-1]])
+    lon_min = min(*navdata.lon.data[[0,-1]])
+    lon_max = max(*navdata.lon.data[[0,-1]])
     delta = ((lat_max - lat_min) ** 2 + (lon_max - lon_min) ** 2)**.5
     lat_center = (lat_min + lat_max) / 2
     lon_center = (lon_min + lon_max) / 2
@@ -68,7 +70,7 @@ def default_segment_plot(seg, sonde_tracks_by_flag, seg_before, seg_after):
     overview_ax.set_xlabel("longitude [deg]")
     overview_ax.set_ylabel("latitude [deg]")
 
-    for ax, var, unit in [(alt_ax, "altitude", "m"),
+    for ax, var, unit in [(alt_ax, "alt", "m"),
                           (roll_ax, "roll", "deg"),
                           (pitch_ax, "pitch", "deg"),
                           (yaw_ax, "heading", "deg")]:
@@ -173,11 +175,11 @@ def plot(seg, sonde_tracks_by_flag, seg_before, seg_after):
     "circle": [circle_detail_plot, zoom_on("roll", "deg")],
     "circling": [zoom_on("roll", "deg", tofs=np.timedelta64(3, "m")),
                  zoom_on("pitch", "deg", tofs=np.timedelta64(3, "m")),
-                 zoom_on("altitude", "m", tofs=np.timedelta64(3, "m"))],
+                 zoom_on("alt", "m", tofs=np.timedelta64(3, "m"))],
     "straight_leg": [straight_leg_detail_plot, zoom_on("roll", "deg")],
     "radar_calibration_wiggle": [zoom_on("roll", "deg")],
     "radar_calibration_tilted": [zoom_on("roll", "deg")],
-    "lidar_leg": [timeline_of("altitude", "m"), zoom_on("altitude", "m")],
+    "lidar_leg": [timeline_of("alt", "m"), zoom_on("alt", "m")],
     "baccardi_calibration": [straight_leg_detail_plot, zoom_on("roll", "deg")],
 }
 
@@ -198,7 +200,7 @@ def __init__(self, flight):
         self.used_segment_ids = set()
         self.flight_id = flight.get("flight_id", "")
 
-    def check_segment(self, seg, bahamas, sondes_by_flag):
+    def check_segment(self, seg, navdata, sondes_by_flag):
         if "segment_id" in seg:
             segment_id = seg["segment_id"]
             if not segment_id.startswith(self.flight_id):
@@ -283,14 +285,10 @@ def _main():
     parser = argparse.ArgumentParser()
     parser.add_argument("infile")
     parser.add_argument("outfile")
-    parser.add_argument("-d", "--data_path", default="../data")
     parser.add_argument("-s", "--sonde_info", help="sonde info yaml file", default=os.path.join(basedir, "sondes.yaml"))
     args = parser.parse_args()
 
     flightdata = yaml.load(open(args.infile), Loader=yaml.SafeLoader)
-    bahamas_path = os.path.join(args.data_path,
-                                "bahamas_{:%Y%m%d}_v0.4.nc".format(flightdata["date"]))
-    bahamas = xr.open_dataset(bahamas_path)
 
     global_warnings = []
     if "flight_id" in flightdata:
@@ -302,20 +300,21 @@ def _main():
     if "platform" in flightdata:
         platform = flightdata["platform"]
     else:
-        platform = "HALO"
-        global_warnings.append("platform is missing, assuming 'HALO'")
+        global_warnings.append("platform is missing")
 
     if args.sonde_info is not None:
         sonde_info = yaml.load(open(args.sonde_info), Loader=yaml.SafeLoader)
     else:
         sonde_info = []
         global_warnings.append("no sonde_info is specified, using data from unified dataset")
 
+    navdata = get_navdata(platform, flight_id).load()
+
     sonde_info = [s for s in sonde_info if s["platform"] == platform]
     sondes_by_id = {s["sonde_id"]: s for s in sonde_info}
 
     fig, ax = plt.subplots()
-    ax.plot(bahamas.lon, bahamas.lat)
+    ax.plot(navdata.lon, navdata.lat)
     im = fig2data_url(fig)
     plt.close("all")
     flightdata["plot_data"] = im
@@ -325,9 +324,9 @@ def _main():
     for seg in flightdata["segments"]:
         t_start = np.datetime64(seg["start"])
         t_end = np.datetime64(seg["end"])
-        seg_bahamas = bahamas.sel(time=slice(t_start, t_end))
-        seg_before = bahamas.sel(time=slice(t_start - border_time, t_start))
-        seg_after = bahamas.sel(time=slice(t_end, t_end + border_time))
+        seg_navdata = navdata.sel(time=slice(t_start, t_end))
+        seg_before = navdata.sel(time=slice(t_start - border_time, t_start))
+        seg_after = navdata.sel(time=slice(t_end, t_end + border_time))
 
         sondes_in_segment = [s
                              for s in sonde_info
@@ -343,18 +342,18 @@ def _main():
         sonde_times = [s["launch_time"] for s in sondes_in_segment]
 
         sonde_tracks_by_flag = {
-            f: bahamas.sel(time=[s["launch_time"] for s in sondes], method="nearest")
+            f: navdata.sel(time=[s["launch_time"] for s in sondes], method="nearest")
             #for f, sondes in sondes_by_flag.items()
             for f, sondes in manual_sondes_by_flag.items()
         }
 
         plot_data = []
-        warnings = list(checker.check_segment(seg, seg_bahamas, sondes_by_flag))
+        warnings = list(checker.check_segment(seg, seg_navdata, sondes_by_flag))
 
         for plot in plots_for_kinds(seg.get("kinds", [])):
             try:
                 plot_data.append(fig2data_url(
-                    plot(seg_bahamas, sonde_tracks_by_flag, seg_before, seg_after)))
+                    plot(seg_navdata, sonde_tracks_by_flag, seg_before, seg_after)))
                 plt.close("all")
             except Exception as e:
                 warnings.append("plot could not be created: {}".format(e))
@@ -363,7 +362,7 @@ def _main():
         if len(sonde_times) > 0:
             seg["time_to_first_sonde"] = (np.datetime64(sonde_times[0]) - t_start) / np.timedelta64(1, "s")
         if kinds_is_circle(seg.get("kinds", [])):
-            seg["heading_difference"] = (seg_bahamas.heading.data[-1] - seg_bahamas.heading.data[0]) % 360
+            seg["heading_difference"] = (seg_navdata.heading.data[-1] - seg_navdata.heading.data[0]) % 360
 
         seg["warnings"] = warnings