updated the path to the downloadable data

OceanParcels · Jul 12, 2024 · 8d8a6f8 · 8d8a6f8
1 parent dd7b5bb
commit 8d8a6f8
Show file tree

Hide file tree

Showing 15 changed files with 7 additions and 3,030 deletions.
diff --git a/analysis/Map_origin_particles_surface.ipynb b/analysis/Map_origin_particles_surface.ipynb
@@ -68,7 +68,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mask = xr.open_dataset('/storage/shared/oceanparcels/input_data/MOi/domain_ORCA0083-N006/PSY4V3R1_mask.nc')\n",
+    "mask = xr.open_dataset('../data/PSY4V3R1_mask.nc')\n",
     "indices = {'lat': range(400, 1600), 'lon': range(2000, 4300)}\n",
     "landmask = mask['tmask'][0, 0, indices['lat'], indices['lon']]\n",
     "xlon = mask['nav_lon'][indices['lat'], indices['lon']].values\n",

diff --git a/analysis/size_distribution.py b/analysis/size_distribution.py
@@ -34,7 +34,7 @@
 
 for ft in tqdm(simulations):
     # print('Computing fragmentation timescale: ', ft)
-    local_path = f'/storage/shared/oceanparcels/output_data/data_Claudio/hc13_3/hc13_{ft}.zarr'
+    local_path = f'../data/simulations/hc13_{ft}.zarr'
     sim = xr.open_zarr(local_path)
     sim = sim.where(sim.time >= np.datetime64('2007-01-01'), drop=True) # analysis stops at 2007-01-01
 

diff --git a/analysis/supplementary_material_plots.ipynb b/analysis/supplementary_material_plots.ipynb
@@ -48,7 +48,7 @@
     "\n",
     "depth_bins = np.linspace(-5500, 0, 56)  # creates a 100m bins\n",
     "\n",
-    "simulations = ['_k2', '', '_k4']\n",
+    "simulations = ['_k2', '_k3', '_k4']\n",
     "sim_names = ['k2', 'k3', 'k4']"
    ]
   },
@@ -113,7 +113,7 @@
     "\n",
     "for k, ft in enumerate(tqdm(simulations)):\n",
     "    # print('Computing fragmentation timescale: ', ft)\n",
-    "    local_path = f'/storage/shared/oceanparcels/output_data/data_Claudio/hc13_2/hc13_1000{ft}.zarr'\n",
+    "    local_path = f'../data/simulations/hc13_1000{ft}.zarr'\n",
     "    sim = xr.open_zarr(local_path)\n",
     "    nano = sim.where(sim.radius < 1e-6/2, drop=False)\n",
     "    sim_dict = {}\n",
@@ -196,7 +196,7 @@
     "\n",
     "for k, ft in enumerate(tqdm(simulations)):\n",
     "    # print('Computing fragmentation timescale: ', ft)\n",
-    "    local_path = f'/storage/shared/oceanparcels/output_data/data_Claudio/hc13_2/hc13_1000{ft}.zarr'\n",
+    "    local_path = f'../data/simulations/hc13_1000{ft}.zarr'\n",
     "    sim = xr.open_zarr(local_path)\n",
     "\n",
     "    # loading fields as np arrays to do some nasty indexing\n",

diff --git a/analysis/surface_and_near_shore_particles_stats.ipynb b/analysis/surface_and_near_shore_particles_stats.ipynb
@@ -85,7 +85,7 @@
     "\n",
     "for k, ft in enumerate(tqdm(simulations)):\n",
     "    # print('Computing fragmentation timescale: ', ft)\n",
-    "    local_path = f'/storage/shared/oceanparcels/output_data/data_Claudio/hc13_3/hc13_{ft}.zarr'\n",
+    "    local_path = f'../data/simulations/hc13_{ft}.zarr'\n",
     "    sim = xr.open_zarr(local_path)\n",
     "\n",
     "    # loading fields as np arrays to do some nasty indexing\n",

diff --git a/analysis/vertical_Kz_profiles.py b/analysis/vertical_Kz_profiles.py
diff --git a/analysis/vertical_histograms.py b/analysis/vertical_histograms.py
@@ -46,7 +46,7 @@
         sim_dict = {}
 
         # Load the data from the simulation
-        local_path = f'/storage/shared/oceanparcels/output_data/data_Claudio/hc13_3/hc13_{ft}.zarr'
+        local_path = f'../data/simulations/hc13_{ft}.zarr'
         sim = xr.open_zarr(local_path)
         sim = sim.where(sim.time >= np.datetime64('2007-01-01'), drop=True) # analysis stops at 2007-01-01
         nano = sim.where(sim.radius < 1e-6/2, drop=False)

diff --git a/article_figs/Figure3_legend_patch.png b/article_figs/Figure3_legend_patch.png
diff --git a/article_figs/stats_frag_into_NPs.csv b/article_figs/stats_frag_into_NPs.csv
diff --git a/notebooks/julia/about_fragmentation.jl b/notebooks/julia/about_fragmentation.jl
diff --git a/notebooks/julia/density_profile.npy b/notebooks/julia/density_profile.npy
diff --git a/notebooks/julia/depth_profile.npy b/notebooks/julia/depth_profile.npy
diff --git a/notebooks/julia/reverse-fragmentation-analysis.ipynb b/notebooks/julia/reverse-fragmentation-analysis.ipynb
diff --git a/simulation/submit-abyssal-backtrack_copy_1.sh b/simulation/submit-abyssal-backtrack_copy_1.sh
diff --git a/simulation/submit-abyssal-backtrack_copy_2.sh b/simulation/submit-abyssal-backtrack_copy_2.sh
diff --git a/simulation/submit-part2.sh b/simulation/submit-part2.sh