Add plots

README.md

@@ -143,6 +143,10 @@ vfrecovery describe WMO CYC
 vfrecovery describe WMO CYC1 CYC2 CYC3
 ```
 
+```bash
+vfrecovery describe velocity WMO CYC
+```
+
 ## Other commands
 
 ```bash

environment.yml

@@ -7,7 +7,7 @@ dependencies:
   - parcels>=3.0.0
   - dask
   - distributed
-  - dask-kubernetes
+#  - dask-kubernetes
   - bottleneck
   - gcsfs
   - zarr
@@ -57,4 +57,4 @@ dependencies:
     - geojson
     - dominate
     - copernicusmarine>=1.0<=2.0
-    - git+https://github.com/euroargodev/VirtualFleet.git@master
+#    - git+https://github.com/euroargodev/VirtualFleet.git@master  # better with `pip install --editable`

vfrecovery/command_line_interface/group_describe.py

@@ -4,26 +4,32 @@
 import argopy.plot as argoplot
 from argopy.errors import DataNotFound
 from argopy import ArgoIndex
+import os
+from pathlib import Path
+import glob
 
+from vfrecovery.utils.misc import list_float_simulation_folders
 
-from vfrecovery.core.describe import describe_function
 
 root_logger = logging.getLogger("vfrecovery_root_logger")
 blank_logger = logging.getLogger("vfrecovery_blank_logger")
 
 
-
 @click.group()
 def cli_group_describe() -> None:
     pass
 
+
 @cli_group_describe.command(
     "describe",
-    short_help="Describe VirtualFleet-Recovery simulation results",
+    short_help="Describe VirtualFleet-Recovery data and simulation results",
     help="""
-    Returns data about an existing VirtualFleet-Recovery prediction
+
+    TARGET select what is to be described. A string in: 'all', 'obs', 'velocity'.
+    
+    WMO is the float World Meteorological Organisation number
     
-    Data could be a JSON file, specific metrics or images
+    CYC is the cycle number location to restrict description to
     """,
     epilog="""
     Examples:
@@ -34,7 +40,7 @@ def cli_group_describe() -> None:
     \b
     vfrecovery describe 6903091 112
     """,  # noqa
- )
+)
 @click.option(
     "--log-level",
     type=click.Choice(["DEBUG", "INFO", "WARN", "ERROR", "CRITICAL", "QUIET"]),
@@ -45,9 +51,11 @@ def cli_group_describe() -> None:
             "(based on standard logging library)."
     ),
 )
+@click.argument('TARGET', nargs=1, type=str)
 @click.argument('WMO', nargs=1, type=int)
 @click.argument("CYC", nargs=-1, type=int)
 def describe(
+        target,
         wmo,
         cyc,
         log_level,
@@ -61,19 +69,45 @@ def describe(
         root_logger.debug("DEBUG mode activated")
 
     # Validate arguments:
+    if target.lower() not in ["all", "obs", "velocity"]:
+        raise ValueError("The first argument TARGET must be one in ['all', 'obs', 'velocity']")
+
     assert is_wmo(wmo)
     wmo = check_wmo(wmo)[0]
     cyc = list(cyc)
     if len(cyc) > 0:
         assert is_cyc(cyc)
         cyc = check_cyc(cyc)
 
-    #
     # json_dump = describe_function(wmo,
     #                               cyc=cyc,
     #                              log_level=log_level)
     # blank_logger.info(json_dump)
 
+    if target == 'obs':
+        describe_obs(wmo, cyc)
+
+    elif target == 'velocity':
+        describe_velocity(wmo, cyc)
+
+
+def describe_velocity(wmo, cyc):
+
+    # List folders to examine:
+    plist = list_float_simulation_folders(wmo, cyc)
+
+    # List all available velocity files:
+    for c in plist.keys():
+        p = plist[c]
+        click.secho("Velocity file(s) for WMO=%s / CYC=%s:" % (wmo, c), fg='green')
+        vlist = sorted(p.glob("velocity_*.nc"))
+        if len(vlist) > 0:
+            [click.secho("\t- %s" % v) for v in vlist]
+        else:
+            click.secho("\tNo velocity file", fg='red')
+
+
+def describe_obs(wmo, cyc):
     url = argoplot.dashboard(wmo, url_only=True)
     # txt = "You can check this float dashboard while we search for float profiles in the index: %s" % url
     click.secho("\nYou can check this float dashboard while we search for float profile(s) in the index:")

vfrecovery/command_line_interface/group_plot.py

@@ -0,0 +1,81 @@
+import click
+import logging
+from argopy.utils import is_wmo, is_cyc, check_cyc, check_wmo
+import argopy.plot as argoplot
+from argopy.errors import DataNotFound
+from argopy import ArgoIndex
+import os
+from pathlib import Path
+import glob
+
+from vfrecovery.core.plot import plot_velocity
+
+root_logger = logging.getLogger("vfrecovery_root_logger")
+blank_logger = logging.getLogger("vfrecovery_blank_logger")
+
+
+@click.group()
+def cli_group_plot() -> None:
+    pass
+
+
+@cli_group_plot.command(
+    "plot",
+    short_help="Plot VirtualFleet-Recovery data or simulation results",
+    help="""
+
+    TARGET select what is to be plotted. A string in: 'velocity'.
+
+    WMO is the float World Meteorological Organisation number
+
+    CYC is the cycle number location to restrict plots to
+    """,
+    epilog="""
+    Examples:
+
+    \b
+    vfrecovery plot velocity 6903091 80
+    """,  # noqa
+)
+@click.option(
+    "--log-level",
+    type=click.Choice(["DEBUG", "INFO", "WARN", "ERROR", "CRITICAL", "QUIET"]),
+    default="INFO",
+    show_default=True,
+    help=(
+            "Set the details printed to console by the command "
+            "(based on standard logging library)."
+    ),
+)
+@click.argument('TARGET', nargs=1, type=str)
+@click.argument('WMO', nargs=1, type=int)
+@click.argument("CYC", nargs=-1, type=int)
+def plot(
+        target,
+        wmo,
+        cyc,
+        log_level,
+) -> None:
+    if log_level == "QUIET":
+        root_logger.disabled = True
+        log_level = "CRITICAL"
+    root_logger.setLevel(level=getattr(logging, log_level.upper()))
+
+    if root_logger.isEnabledFor(logging.DEBUG):
+        root_logger.debug("DEBUG mode activated")
+
+    # Validate arguments:
+    if target.lower() not in ["all", "obs", "velocity"]:
+        raise ValueError("The first argument TARGET must be one in ['all', 'obs', 'velocity']")
+
+    assert is_wmo(wmo)
+    wmo = check_wmo(wmo)[0]
+    cyc = list(cyc)
+    if len(cyc) > 0:
+        assert is_cyc(cyc)
+        cyc = check_cyc(cyc)
+
+    if target == 'velocity':
+        plot_velocity(wmo, cyc,
+                      log_level=log_level,
+                      )

vfrecovery/command_line_interface/virtualfleet_recovery.py

@@ -2,12 +2,14 @@
 
 from vfrecovery.command_line_interface.group_describe import cli_group_describe
 from vfrecovery.command_line_interface.group_predict import cli_group_predict
+from vfrecovery.command_line_interface.group_plot import cli_group_plot
 
 @click.command(
     cls=click.CommandCollection,
     sources=[
         cli_group_describe,
         cli_group_predict,
+        cli_group_plot,
     ],
     context_settings=dict(help_option_names=["-h", "--help"]),
 )

vfrecovery/core/__init__.py

@@ -1,4 +1,4 @@
 # from deployment_plan import setup_deployment_plan
 from .trajfile_handler import Trajectories
-from .run_handler import Simulation
+from .run_handler import RunAnalyser
 # from predict import predict_function

vfrecovery/core/describe.py

@@ -11,15 +11,7 @@
 root_logger = logging.getLogger("vfrecovery_root_logger")
 
 
-def describe_function(
-        wmo: int,
-        cyc: Union[int, None],
-        log_level: str,
-) -> str:
-    if log_level == "QUIET":
-        root_logger.disabled = True
-        log_level = "CRITICAL"
-    root_logger.setLevel(level=getattr(logging, log_level.upper()))
+def describe_obs(wmo, cyc):
 
     # Validate arguments:
     assert is_wmo(wmo)
@@ -28,7 +20,6 @@ def describe_function(
         assert is_cyc(cyc)
         cyc = check_cyc(cyc)[0]
 
-
     #
     url = argoplot.dashboard(wmo, url_only=True)
     txt = "You can check this float dashboard while we search for float profiles in the index: %s" % url
@@ -48,8 +39,23 @@ def describe_function(
     df = df.sort_values(by='date')
     root_logger.info("\n%s" % df.to_string(max_colwidth=15))
 
-    output = {'wmo': wmo, 'cyc': cyc}
-    json_dump = json.dumps(
-        output, sort_keys=False, indent=2
-    )
-    return json_dump
+    # output = {'wmo': wmo, 'cyc': cyc}
+    # json_dump = json.dumps(
+    #     output, sort_keys=False, indent=2
+    # )
+    # return json_dump
+
+
+def describe_function(
+        wmo: int,
+        cyc: Union[int, None],
+        target: str,
+        log_level: str,
+) -> str:
+    if log_level == "QUIET":
+        root_logger.disabled = True
+        log_level = "CRITICAL"
+    root_logger.setLevel(level=getattr(logging, log_level.upper()))
+
+    if target == 'obs':
+        describe_obs(wmo, cyc)

vfrecovery/core/plot.py

@@ -0,0 +1,66 @@
+import logging
+import xarray as xr
+from virtualargofleet import Velocity
+
+from vfrecovery.utils.misc import list_float_simulation_folders
+import vfrecovery.plots.velocity as pltvel
+
+
+root_logger = logging.getLogger("vfrecovery_root_logger")
+plot_logger = logging.getLogger("vfrecovery_plot")
+
+
+class log_this:
+
+    def __init__(self, txt, log_level):
+        """Log text to simulation and possibly root logger(s)"""
+        getattr(root_logger, log_level.lower())(txt)
+        getattr(plot_logger, log_level.lower())(txt)
+
+    @staticmethod
+    def info(txt) -> 'log_this':
+        return log_this(txt, 'INFO')
+
+    @staticmethod
+    def debug(txt) -> 'log_this':
+        return log_this(txt, 'DEBUG')
+
+    @staticmethod
+    def warning(txt) -> 'log_this':
+        return log_this(txt, 'WARNING')
+
+    @staticmethod
+    def error(txt) -> 'log_this':
+        return log_this(txt, 'ERROR')
+
+
+def plot_velocity(
+        wmo: int,
+        cyc: int,
+        log_level: str,
+):
+    if log_level == "QUIET":
+        root_logger.disabled = True
+        log_level = "CRITICAL"
+    root_logger.setLevel(level=getattr(logging, log_level.upper()))
+
+    # List folders to examine:
+    plist = list_float_simulation_folders(wmo, cyc)
+
+    #
+    for c in plist.keys():
+        p = plist[c]
+        log_this.info("Velocity figure(s) for WMO=%s / CYC=%s:" % (wmo, c))
+        ilist = sorted(p.glob("velocity_*.png"))
+        if len(ilist) > 0:
+            [log_this.info("\t- %s" % i) for i in ilist]
+        else:
+            log_this.info("No velocity figures ! Generating new ones from velocity files")
+
+            # Load velocity field
+            vlist = sorted(p.glob("velocity_*.nc"))
+            for v in vlist:
+                log_this.info("Loading '%s'" % v)
+                # ds_vel = xr.open_dataset(v)
+                # VEL = Velocity(model='GLORYS12V1' if 'GLORYS' in str(v) else 'ARMOR3D', src=ds_vel)
+                # pltvel.plot(VEL, wmo, cyc, save_figure=False, workdir=p)