Error while trying to calculate connectivity #4
Description
Hi Nicholas,
Sorry to be bothering you with these issues, which most of the time are due to my lack of experience with Icthyop and in Python.
This time, I am trying to use the compute_connectivity function from ichthyop.connectivity
I read my .nc output file using ichhtyop.read.extract_dataset and then I tried to use compute_connectivity like so:
import ichthyop.read as ichread
import ichthyop.connectivity as ichconnectivity
data = ichread.extract_dataset("mercator3d_ichthyop-run202508041513.nc")
connect = ichconnectivity.compute_connectivity(data)
When I run the last line I get this big error, which as much as I understand means that there is not release_zone variable
KeyError Traceback (most recent call last)
~/miniforge3/envs/ichthyop/lib/python3.13/site-packages/xarray/core/dataset.py in ?(self, name)
1153 variable = self._variables[name]
1154 except KeyError:
-> 1155 _, name, variable = _get_virtual_variable(self._variables, name, self.sizes)
1156
KeyError: 'release_zone'
During handling of the above exception, another exception occurred:
KeyError Traceback (most recent call last)
File ~/miniforge3/envs/ichthyop/lib/python3.13/site-packages/xarray/core/dataset.py:1252, in Dataset.__getitem__(self, key)
1251 try:
-> 1252 return self._construct_dataarray(key)
1253 except KeyError as e:
File ~/miniforge3/envs/ichthyop/lib/python3.13/site-packages/xarray/core/dataset.py:1155, in Dataset._construct_dataarray(self, name)
1154 except KeyError:
-> 1155 _, name, variable = _get_virtual_variable(self._variables, name, self.sizes)
1157 needed_dims = set(variable.dims)
File ~/miniforge3/envs/ichthyop/lib/python3.13/site-packages/xarray/core/dataset_utils.py:79, in _get_virtual_variable(variables, key, dim_sizes)
78 if len(split_key) != 2:
---> 79 raise KeyError(key)
81 ref_name, var_name = split_key
KeyError: 'release_zone'
The above exception was the direct cause of the following exception:
KeyError Traceback (most recent call last)
<ipython-input-6-6f91ac6cb2a0> in ?()
----> 1 connect = ichconnectivity.compute_connectivity(data)
~/miniforge3/envs/ichthyop/lib/python3.13/site-packages/ichthyop/connectivity.py in ?(data, retention)
33
34 ntime = data.dims['time']
35 ndrifter = data.dims['drifter']
36
---> 37 release_zones = process_release_zones(data)
38 release_names = [zone.name for zone in release_zones]
39 nrel_zones = len(release_zones)
40 zone = data['release_zone'].values
~/miniforge3/envs/ichthyop/lib/python3.13/site-packages/ichthyop/connectivity.py in ?(data)
11 def process_release_zones(data):
12
---> 13 release_zones = data['release_zone']
14 attrs = [v for v in release_zones.attrs if v.startswith('release_zone_')]
15
16 zone_names = []
~/miniforge3/envs/ichthyop/lib/python3.13/site-packages/xarray/core/dataset.py in ?(self, key)
1261
1262 # If someone attempts `ds['foo' , 'bar']` instead of `ds[['foo', 'bar']]`
1263 if isinstance(key, tuple):
1264 message += f"\nHint: use a list to select multiple variables, for example `ds[{list(key)}]`"
-> 1265 raise KeyError(message) from e
1266
1267 if utils.iterable_of_hashable(key):
1268 return self._copy_listed(key)
KeyError: "No variable named 'release_zone'. Did you mean one of ('recruited_zone',)?"
And actually, if I use ncdump -h on my output file, there is no variable named release_zone.
Below is the description of my output file:
netcdf mercator3d_ichthyop-run202508041513 {
dimensions:
time = UNLIMITED ; // (7261 currently)
drifter = 33000 ;
type_zone = 3 ;
recruitment_zone = 2 ;
edge = 1224 ;
latlon = 2 ;
zone0 = 1 ;
geozone0 = 5 ;
zone1 = 745 ;
geozone1 = 5 ;
zone2 = 23 ;
geozone2 = 5 ;
variables:
double time(time) ;
time:calendar = "gregorian" ;
time:units = "seconds since 1900-01-01 00:00" ;
float lon(time, drifter) ;
lon:long_name = "particle longitude" ;
lon:unit = "degree east" ;
float lat(time, drifter) ;
lat:long_name = "particle latitude" ;
lat:unit = "degree north" ;
int mortality(time, drifter) ;
mortality:long_name = "particle cause of mortality" ;
mortality:unit = "death cause" ;
mortality:alive = 0 ;
mortality:dead_cold = 1 ;
mortality:out_of_domain = 2 ;
mortality:old = 3 ;
mortality:beached = 4 ;
mortality:starvation = 5 ;
mortality:dead_hot = 6 ;
mortality:dead_fresh = 7 ;
mortality:dead_saline = 8 ;
float depth(time, drifter) ;
depth:long_name = "particle depth" ;
depth:unit = "meter" ;
int zone(time, drifter, type_zone) ;
zone:long_name = "In which zones is the particle ?" ;
zone:unit = "the index of the zone" ;
zone:type_zone_0 = "release" ;
zone:release_zone_0 = "Emed release 1" ;
zone:type_zone_1 = "recruitment" ;
zone:recruitment_zone_0 = "Emed recruitment 1" ;
zone:recruitment_zone_1 = "Emed recruitment 2" ;
zone:type_zone_2 = "target" ;
zone:target_zone = "none for this run" ;
zone:not_released_yet = -99 ;
zone:out_of_zone = -1 ;
int recruited_zone(time, drifter, recruitment_zone) ;
recruited_zone:long_name = "Is particle recruited in zone ?" ;
recruited_zone:unit = "0:false 1:true" ;
recruited_zone:recruitment_zone_0 = "Emed recruitment 1" ;
recruited_zone:recruitment_zone_1 = "Emed recruitment 2" ;
float region_edge(edge, latlon) ;
region_edge:long_name = "geoposition of region edge" ;
region_edge:unit = "lat degree north lon degree east" ;
int drifter(drifter) ;
drifter:long_name = "drifter index" ;
drifter:unit = "" ;
float coord_zone0(zone0, latlon) ;
coord_zone0:long_name = "Emed release 1" ;
coord_zone0:unit = "x and y coordinates of the center of the cells in the zone" ;
coord_zone0:type = "release" ;
coord_zone0:color = "[r=255,g=0,b=255]" ;
float coord_geo_zone0(geozone0, latlon) ;
float coord_zone1(zone1, latlon) ;
coord_zone1:long_name = "Emed recruitment 1" ;
coord_zone1:unit = "x and y coordinates of the center of the cells in the zone" ;
coord_zone1:type = "recruitment" ;
coord_zone1:color = "[r=102,g=255,b=102]" ;
float coord_geo_zone1(geozone1, latlon) ;
float coord_zone2(zone2, latlon) ;
coord_zone2:long_name = "Emed recruitment 2" ;
coord_zone2:unit = "x and y coordinates of the center of the cells in the zone" ;
coord_zone2:type = "recruitment" ;
coord_zone2:color = "[r=255,g=153,b=0]" ;
float coord_geo_zone2(geozone2, latlon) ;
// global attributes:
:transport_dimension = "3d" ;
:release.schedule.is_enabled = "true" ;
:release.schedule.events = "\"year 2013 month 06 day 01 at 12:00\" \"year 2013 month 06 day 03 at 12:00\" \"year 2013 month 06 day 06 at 12:00\" \"year 2013 month 06 day 09 at 12:00\" \"year 2013 month 06 day 12 at 12:00\" \"year 2013 month 06 day 15 at 12:00\" \"year 2013 month 06 day 18 at 12:00\" \"year 2013 month 06 day 21 at 12:00\" \"year 2013 month 06 day 24 at 12:00\" \"year 2013 month 06 day 27 at 12:00\" \"year 2013 month 06 day 30 at 12:00\" \"year 2013 month 07 day 03 at 12:00\" \"year 2013 month 07 day 06 at 12:00\" \"year 2013 month 07 day 09 at 12:00\" \"year 2013 month 07 day 12 at 12:00\" \"year 2013 month 07 day 15 at 12:00\" \"year 2013 month 07 day 18 at 12:00\" \"year 2013 month 07 day 21 at 12:00\" \"year 2013 month 07 day 24 at 12:00\" \"year 2013 month 07 day 27 at 12:00\" \"year 2013 month 07 day 30 at 12:00\" \"year 2013 month 08 day 02 at 12:00\" \"year 2013 month 08 day 15 at 12:00\" \"year 2013 month 08 day 30 at 12:00\" \"year 2013 month 09 day 01 at 12:00\" \"year 2013 month 09 day 15 at 12:00\" \"year 2013 month 09 day 30 at 12:00\" \"year 2013 month 10 day 01 at 12:00\" \"year 2013 month 10 day 15 at 12:00\" \"year 2013 month 10 day 31 at 12:00\" \"year 2013 month 11 day 01 at 12:00\" \"year 2013 month 11 day 15 at 12:00\" \"year 2013 month 11 day 30 at 12:00\"" ;
:app.time.initial_time = "year 2013 month 01 day 01 at 12:00" ;
:app.time.transport_duration = "0030 day(s) 00 hour(s) 00 minute(s)" ;
:app.time.time_step = "360" ;
:app.output.netcdf_output_format = "netcdf3" ;
:app.output.file_prefix = "mercator3d" ;
:app.output.output_path = "/home/yotam/Documents/oceanographic_processes_biological_implications/output/" ;
:app.output.record_frequency = "12" ;
:app.particle_length.initial_length = "0.89" ;
:app.particle_length.hatch_length = "2.09" ;
:app.particle_length.yolk2feeding_length = "2.6" ;
:app.transport.coastline_behavior = "Standstill" ;
:action.recruitment.stain.enabled = "false" ;
:action.lethal_temp.enabled = "false" ;
:action.recruitment.zone.enabled = "true" ;
:action.recruitment.zone.criterion = "Age criterion" ;
:action.recruitment.zone.limit_age = "12.0" ;
:action.recruitment.zone.limit_length = "6.0" ;
:action.recruitment.zone.duration_min = "2.0" ;
:action.recruitment.zone.stop_moving = "true" ;
:action.recruitment.zone.zone_file = "/home/yotam/Downloads/cfg/east_med_zones.xml" ;
:action.advection.enabled = "true" ;
:action.advection.scheme = "Runge Kutta 4" ;
:action.swimming.enabled = "false" ;
:action.growth.enabled = "false" ;
:action.hdisp.enabled = "true" ;
:action.hdisp.epsilon = "1E-9" ;
:action.wind.enabled = "false" ;
:release.txtfile.enabled = "false" ;
:release.ncfile.enabled = "false" ;
:release.zone.enabled = "false" ;
:release.patches.enabled = "true" ;
:release.patches.number_patches = "10" ;
:release.patches.number_agregated = "100" ;
:release.patches.radius_patch = "2000.0" ;
:release.patches.thickness_patch = "2.0" ;
:release.patches.zone_file = "/home/yotam/Downloads/cfg/east_med_zones.xml" ;
:release.stain.enabled = "false" ;
:dataset.mercator3d.enabled = "true" ;
:dataset.mercator3d.input_path = "/home/yotam/Documents/oceanographic_processes_biological_implications/bashscripts/bashscripts_all/copernicusdata/" ;
:dataset.mercator3d.hgr_pattern = "MED-MFC_006_004_coordinates_cropped.nc" ;
:dataset.mercator3d.zgr_pattern = "MED-MFC_006_004_coordinates_cropped.nc" ;
:dataset.mercator3d.byte_mask_pattern = "MED-MFC_006_004_mask_bathy_cropped.nc" ;
:dataset.mercator3d.gridu_pattern = "*stks_data_*.nc" ;
:dataset.mercator3d.gridv_pattern = "*stks_data_*.nc" ;
:dataset.mercator3d.gridt_pattern = "*stks_data_*.nc" ;
:dataset.mercator3d.field_dim_x = "longitude" ;
:dataset.mercator3d.field_dim_y = "latitude" ;
:dataset.mercator3d.field_dim_z = "depth" ;
:dataset.mercator3d.field_dim_time = "time" ;
:dataset.mercator3d.field_var_lon = "longitude" ;
:dataset.mercator3d.field_var_lat = "latitude" ;
:dataset.mercator3d.field_var_mask = "mask" ;
:dataset.mercator3d.field_var_u = "uo" ;
:dataset.mercator3d.field_var_v = "vo" ;
:dataset.mercator3d.field_var_time = "time" ;
:dataset.mercator3d.field_var_e3t = "e3t" ;
:dataset.mercator3d.field_var_e2t = "e2t" ;
:dataset.mercator3d.field_var_e1t = "e1t" ;
:xml_file = "/home/yotam/Downloads/cfg/cfg-mercator3d-phd_1.xml" ;
:nb_zones = 3 ;
}
Any help would be appreciated, and again I apologize for all these questions
Thank you