👌 DeepBedMap DEM v1.1.0 release candidate 1

A release candidate for DeepBedMap_DEM v1.1.0, based on 31aaa5b with model weights from https://www.comet.ml/weiji14/deepbedmap/77126218f3504a06adbc7dfe3851bb28. Updated figures in both deepbedmap.ipynb and paper_figures.ipynb to reflect the changed Digital Elevation Model. Renamed deepbedmap3_big_int16.tif into a more sensible deepbedmap_dem.tif. Note that the Pine Island Glacier test region's raster inputs have been uploaded to Quilt to speed up inference. Repositioned a "T" for terrace label over the Gamburtsev Subglacial Mountains, and modified the maxstddev of the Figure 5 2D plots of roughness to be 200 for both DeepBedMap and BedMachine Antarctica.

deepbedmap.py

@@ -112,12 +112,12 @@ def get_image_with_bounds(filepaths: list, indexers: dict = None) -> xr.DataArra
 
 
 # %%
-# test_filepaths = ["highres/2007tx", "highres/2010tr", "highres/istarxx"]
-test_filepaths = ["highres/20xx_Antarctica_DC8_THW"]
+test_filepaths = ["highres/2007tx", "highres/2010tr", "highres/istarxx"]
+# test_filepaths = ["highres/20xx_Antarctica_DC8_THW"]
 groundtruth = get_image_with_bounds(
     filepaths=[f"{t}.nc" for t in test_filepaths],
     # indexers={"y": slice(1, -2), "x": slice(1, -2)},  # for 2007tx
-    # indexers={"x": slice(1, -2)},  # for 2007tx, 2010tr and istarxx
+    indexers={"x": slice(1, -2)},  # for 2007tx, 2010tr and istarxx
 )
 window_bound = rasterio.coords.BoundingBox(*groundtruth.bounds)
 print(window_bound)
@@ -146,6 +146,9 @@ def get_deepbedmap_model_inputs(
         rasterio.coords.BoundingBox(
             left=-1_594_000.0, bottom=-166_500.0, right=-1_575_000.0, top=-95_500.0
         ),
+        rasterio.coords.BoundingBox(
+            left=-1_631_500.0, bottom=-259_000.0, right=-1_536_500.0, top=-95_000.0
+        ),
         rasterio.coords.BoundingBox(
             left=-1_524_500.0, bottom=-650_000.0, right=-1_274_500.0, top=-300_000.0
         ),
@@ -376,7 +379,7 @@ def plot_3d_view(
 
 # %%
 def load_trained_model(
-    experiment_key: str = "83748fcb506849d78c275d33f8dd3893",  # or simply use "latest"
+    experiment_key: str = "77126218f3504a06adbc7dfe3851bb28",  # or simply use "latest"
     model_weights_path: str = "model/weights/srgan_generator_model_weights.npz",
 ):
     """
@@ -746,7 +749,7 @@ class Shape:
 _ = data_prep.save_array_to_grid(
     window_bound=window_bound_big,
     array=Y_hat.astype(dtype=np.int16),
-    outfilepath="model/deepbedmap3_big_int16",
+    outfilepath="model/deepbedmap_dem",
     dtype=np.int16,
     tiled=True,
     compression=rasterio.enums.Compression.lzw.value,  # Lempel-Ziv-Welch, lossless
@@ -760,7 +763,7 @@ class Shape:
 fig = gmt.Figure()
 gmt.makecpt(cmap="oleron", series=[-4500, 4500])
 fig.grdimage(
-    grid="model/deepbedmap3_big_int16.tif",
+    grid="model/deepbedmap_dem.tif",
     region=[-2700000, 2800000, -2200000, 2300000],
     projection="x1:60000000",
     frame="f",  # add minor tick labels only

paper/figures/fig1_deepbedmap_architecture.tex

@@ -11,7 +11,7 @@
 \def\UnpoolColor{rgb:blue,2;green,1;black,0.3}
 \def\FcColor{rgb:blue,5;red,2.5;white,5}
 \def\FcReluColor{rgb:blue,5;red,5;white,4}
-\def\SoftmaxColor{rgb:magenta,5;black,7}   
+\def\SoftmaxColor{rgb:magenta,5;black,7}
 
 \newcommand{\copymidarrow}{\tikz \draw[-Stealth,line width=0.8mm,draw={rgb:blue,4;red,1;green,1;black,3}] (-0.3,0) -- ++(0.3,0);}
 

paper_figures.py

@@ -123,7 +123,7 @@
 fig = gmt.Figure()
 gmt.makecpt(cmap="oleron", series=[-2000, 4500])
 fig.grdimage(
-    grid="model/deepbedmap3_big_int16.tif",
+    grid="model/deepbedmap_dem.tif",
     region=[-2700000, 2800000, -2200000, 2300000],
     projection="x1:30000000",
     cmap=True,
@@ -444,7 +444,7 @@ def sizes(cl=(64, 9), scale=(30, 2.5), offset="(1.0,0,0)"):
     ),
 ]
 
-# %% {"jupyter": {"outputs_hidden": true}}
+# %%
 arch = [
     to_head("paper/figures/PlotNeuralNet"),
     to_cor(),
@@ -521,7 +521,7 @@ def sizes(cl=(64, 9), scale=(30, 2.5), offset="(1.0,0,0)"):
 # Plot DeepBedMap Digital Elevation Model (DEM)
 gmt.makecpt(cmap="oleron", series=[-2000, 4500])
 fig.grdimage(
-    grid="model/deepbedmap3_big_int16.tif",
+    grid="model/deepbedmap_dem.tif",
     # grid="@BEDMAP_elevation.nc",
     region=[-2700000, 2800000, -2200000, 2300000],
     projection="x1:30000000",
@@ -530,7 +530,7 @@ def sizes(cl=(64, 9), scale=(30, 2.5), offset="(1.0,0,0)"):
 )
 # Plot Antactic grounding line
 fig.coast(
-    region="model/deepbedmap3_big_int16.tif",
+    region="model/deepbedmap_dem.tif",
     projection="s0/-90/-71/1:30000000",
     area_thresh="+ag",
     resolution="i",
@@ -686,7 +686,7 @@ def closeup_fig(
     # Plot DeepBedMap Digital Elevation Model (DEM)
     gmt.makecpt(cmap="oleron", series=[-2000, 4500])
     fig.grdimage(
-        grid="model/deepbedmap3_big_int16.tif",
+        grid="model/deepbedmap_dem.tif",
         # grid="@BEDMAP_elevation.nc",
         region=region,
         projection="x1:1500000",
@@ -816,7 +816,7 @@ def closeup_fig(
     name="Gamburtsev Subglacial Mountains",
     midx=800_000,
     midy=200_000,
-    annot_xyt=[(710000, 240000, "T")],
+    annot_xyt=[(750000, 280000, "T")],
     fig=fig,
 )
 deepbedmap.subplot(directive="end")
@@ -880,9 +880,9 @@ def prepare_grid(file: str, region: list):
 
 
 # %%
-#!gmt grdcut model/deepbedmap3_big_int16.tif -Gmodel/deepbedmap3_thwaites.nc -R-1550000/-1250000/-550000/-300000
-# deepbedmap3grid = prepare_grid(file="model/deepbedmap3_thwaites.nc", region=region)
-deepbedmap3grid = prepare_grid(file="model/deepbedmap3_big_int16.tif", region=region)
+#!gmt grdcut model/deepbedmap_dem.tif -Gmodel/deepbedmap_thwaites.nc -R-1550000/-1250000/-550000/-300000
+# deepbedmap3grid = prepare_grid(file="model/deepbedmap_thwaites.nc", region=region)
+deepbedmap3grid = prepare_grid(file="model/deepbedmap_dem.tif", region=region)
 groundtruthgrid = prepare_grid(file="highres/20xx_Antarctica_DC8.nc", region=region)
 bedmap2grid = prepare_grid(file="lowres/bedmap2_bed.tif", region=region)
 cubicbedmap2 = skimage.transform.rescale(
@@ -993,7 +993,7 @@ def prepare_grid(file: str, region: list):
     elevpoints[name]["roughness"] = roughness
 
 # %% [raw]
-# # deepbedmap3_error = elevpoints["model/deepbedmap3_thwaites.nc"].z - oibpoints.z
+# # deepbedmap3_error = elevpoints["model/deepbedmap_thwaites.nc"].z - oibpoints.z
 # # cubicbedmap_error = elevpoints["lowres/bedmap2_bed.tif"].z - oibpoints.z
 # deepbedmap3_error = (
 #     elevpoints["DeepBedMap"].roughness - elevpoints["Groundtruth"].roughness
@@ -1048,10 +1048,8 @@ def prepare_grid(file: str, region: list):
 for letter, (name, grid) in zip(["b", "c", "d"], roughDict.items()):
     if name == "BEDMAP2":
         maxstddev = 100  # lower scale as few pixels with high standard dev
-    elif name == "BedMachine":
-        maxstddev = 200
     else:
-        maxstddev = 400
+        maxstddev = 200
     deepbedmap.subplot(directive="set")
     # fig = gmt.Figure()
     fig.basemap(
@@ -1170,10 +1168,10 @@ def prepare_grid(file: str, region: list):
 # https://doi.org/10.1130/G46772.1
 
 # %%
-#!gmt grdcut model/deepbedmap3_big_int16.tif -Gdeepbedmap3_thwaites_int16.tif -R-1435000/-1275000/-475000/-432500
+#!gmt grdcut model/deepbedmap_dem.tif -Gdeepbedmap_thwaites.tif -R-1435000/-1275000/-475000/-432500
 gridDict = {
     "Groundtruth": "highres/20xx_Antarctica_TO.nc",
-    "DeepBedMap": "model/deepbedmap3_thwaites.nc",
+    "DeepBedMap": "model/deepbedmap_thwaites.tif",
     # "BedMachine": "model/BedMachineAntarctica_2019-11-05_v01.nc",
     "BEDMAP2": "lowres/bedmap2_bed.tif",
 }