Generate notebooks and solutions

jorisvandenbossche · jorisvandenbossche · commit 6494251ba822 · 2021-05-26T08:01:49.000+02:00
diff --git a/notebooks/14-xarray-intro.ipynb b/notebooks/14-xarray-intro.ipynb
diff --git a/notebooks/15-xarray-datasets.ipynb b/notebooks/15-xarray-datasets.ipynb
diff --git a/notebooks/_solutions2/14-xarray-intro1.py b/notebooks/_solutions2/14-xarray-intro1.py
@@ -0,0 +1 @@
+tc_data = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_True_color.tiff")
diff --git a/notebooks/_solutions2/14-xarray-intro10.py b/notebooks/_solutions2/14-xarray-intro10.py
@@ -0,0 +1,4 @@
+# Create the histogram plots
+fig, (ax0, ax1) = plt.subplots(1, 2, sharey=True)
+b4_data.plot.hist(bins=30, log=True, ax=ax0)
+b4_data_f.plot.hist(bins=30, log=True, ax=ax1);
diff --git a/notebooks/_solutions2/14-xarray-intro11.py b/notebooks/_solutions2/14-xarray-intro11.py
@@ -0,0 +1,3 @@
+# Calculate the min and max for each channel
+h_min = herstappe_data.min(dim=["x", "y"])
+h_max = herstappe_data.max(dim=["x", "y"])
diff --git a/notebooks/_solutions2/14-xarray-intro12.py b/notebooks/_solutions2/14-xarray-intro12.py
@@ -0,0 +1,2 @@
+# Rescale the data
+herstappe_rescaled = ((herstappe_data - h_min)/(h_max - h_min))
diff --git a/notebooks/_solutions2/14-xarray-intro13.py b/notebooks/_solutions2/14-xarray-intro13.py
@@ -0,0 +1,2 @@
+# Make a plot
+herstappe_rescaled.plot.imshow(figsize=(9, 5))
diff --git a/notebooks/_solutions2/14-xarray-intro14.py b/notebooks/_solutions2/14-xarray-intro14.py
@@ -0,0 +1,2 @@
+gent = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_True_color.tiff")
+gent
diff --git a/notebooks/_solutions2/14-xarray-intro15.py b/notebooks/_solutions2/14-xarray-intro15.py
@@ -0,0 +1 @@
+gent.plot.imshow()
diff --git a/notebooks/_solutions2/14-xarray-intro16.py b/notebooks/_solutions2/14-xarray-intro16.py
@@ -0,0 +1,3 @@
+# Convert to float and make 65535 equal to Nan
+gent_f = gent.astype(float)
+gent_f = gent_f.where(gent != 65535)
diff --git a/notebooks/_solutions2/14-xarray-intro17.py b/notebooks/_solutions2/14-xarray-intro17.py
@@ -0,0 +1,2 @@
+# Divide by the maximum of the int16 range to get [0-1] data
+gent_f = gent_f / 2**16
diff --git a/notebooks/_solutions2/14-xarray-intro18.py b/notebooks/_solutions2/14-xarray-intro18.py
@@ -0,0 +1,2 @@
+# Make a RGB plot
+gent_f.plot.imshow(figsize=(9, 5))
diff --git a/notebooks/_solutions2/14-xarray-intro19.py b/notebooks/_solutions2/14-xarray-intro19.py
@@ -0,0 +1,2 @@
+# Make a Grey scale plot
+gent_f.sum(dim="band").plot.imshow(cmap="Greys", figsize=(9, 5))
diff --git a/notebooks/_solutions2/14-xarray-intro2.py b/notebooks/_solutions2/14-xarray-intro2.py
@@ -0,0 +1,2 @@
+# Get the green channel
+tc_g = tc_data.sel(band=2)
diff --git a/notebooks/_solutions2/14-xarray-intro20.py b/notebooks/_solutions2/14-xarray-intro20.py
@@ -0,0 +1,2 @@
+# Squeeze to 2D float array 
+b4_data = b4_data.sel(band=1).astype(float)
diff --git a/notebooks/_solutions2/14-xarray-intro21.py b/notebooks/_solutions2/14-xarray-intro21.py
@@ -0,0 +1,2 @@
+# Rescale the data
+b4_data = (b4_data - b4_data.min())/(b4_data.max() - b4_data.min())
diff --git a/notebooks/_solutions2/14-xarray-intro22.py b/notebooks/_solutions2/14-xarray-intro22.py
@@ -0,0 +1,2 @@
+# Classify the array into 3 bins
+b4_data_classified = xr.apply_ufunc(np.digitize, b4_data, [0.05, 0.1])
diff --git a/notebooks/_solutions2/14-xarray-intro23.py b/notebooks/_solutions2/14-xarray-intro23.py
@@ -0,0 +1,4 @@
+# Create an image plot
+fig, ax = plt.subplots(figsize=(12, 5))
+img = b4_data_classified.plot.imshow(ax=ax, add_colorbar=False, interpolation="antialiased")
+fig.colorbar(img, values=[0, 1, 2], ticks=[0, 1, 2])
diff --git a/notebooks/_solutions2/14-xarray-intro24.py b/notebooks/_solutions2/14-xarray-intro24.py
@@ -0,0 +1,2 @@
+b4_data = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_B04.tiff").sel(band=1)
+b8_data = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_B08.tiff").sel(band=1)
diff --git a/notebooks/_solutions2/14-xarray-intro25.py b/notebooks/_solutions2/14-xarray-intro25.py
@@ -0,0 +1,3 @@
+# Rescale the data to 0-1
+b4_data = (b4_data - b4_data.min())/(b4_data.max() - b4_data.min())
+b8_data = (b8_data - b8_data.min())/(b8_data.max() - b8_data.min())
diff --git a/notebooks/_solutions2/14-xarray-intro26.py b/notebooks/_solutions2/14-xarray-intro26.py
@@ -0,0 +1,2 @@
+# Calculate the ndvi
+ndvi = (b8_data - b4_data)/(b8_data + b4_data)
diff --git a/notebooks/_solutions2/14-xarray-intro27.py b/notebooks/_solutions2/14-xarray-intro27.py
@@ -0,0 +1,6 @@
+# A Sequential colormap `YlGn` with a normalization on the color limits
+import matplotlib.colors as mcolors
+div_norm = mcolors.Normalize(0.1, 0.8)
+fig, ax = plt.subplots(figsize=(14, 5))
+ll = ndvi.plot.imshow(ax=ax, cmap="YlGn", norm=div_norm)
+ax.set_aspect("equal")
diff --git a/notebooks/_solutions2/14-xarray-intro28.py b/notebooks/_solutions2/14-xarray-intro28.py
@@ -0,0 +1,6 @@
+# A Diverging colormap `RdYlGn` with a normalization on the color limits in two directions of the central point:
+div_norm = mcolors.TwoSlopeNorm(vmin=-0.1, vcenter=0.4, vmax=0.8)
+fig, ax = plt.subplots(figsize=(14, 5))
+ll = ax.imshow(ndvi.values, cmap="RdYlGn", norm=div_norm)
+fig.colorbar(ll);
+ax.set_axis_off();
diff --git a/notebooks/_solutions2/14-xarray-intro3.py b/notebooks/_solutions2/14-xarray-intro3.py
@@ -0,0 +1,2 @@
+# Convert all values above 15000
+tc_g.where(tc_g < 15000, 65535)
diff --git a/notebooks/_solutions2/14-xarray-intro4.py b/notebooks/_solutions2/14-xarray-intro4.py
@@ -0,0 +1 @@
+tc_data = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_True_color.tiff")
diff --git a/notebooks/_solutions2/14-xarray-intro5.py b/notebooks/_solutions2/14-xarray-intro5.py
@@ -0,0 +1,2 @@
+# subsample the data
+tc_data[:, ::5, ::5].shape
diff --git a/notebooks/_solutions2/14-xarray-intro6.py b/notebooks/_solutions2/14-xarray-intro6.py
@@ -0,0 +1 @@
+b4_data = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_B04.tiff")
diff --git a/notebooks/_solutions2/14-xarray-intro7.py b/notebooks/_solutions2/14-xarray-intro7.py
@@ -0,0 +1,2 @@
+# Count the number of cells with value 65535
+np.sum(b4_data == 65535)
diff --git a/notebooks/_solutions2/14-xarray-intro8.py b/notebooks/_solutions2/14-xarray-intro8.py
@@ -0,0 +1,3 @@
+# Convert to float and make 65535 equal to Nan
+b4_data_f = b4_data.astype(float)
+b4_data_f = b4_data_f.where(b4_data != 65535)
diff --git a/notebooks/_solutions2/14-xarray-intro9.py b/notebooks/_solutions2/14-xarray-intro9.py
@@ -0,0 +1,2 @@
+# Count the number of cells with value 0
+np.sum(np.isnan(b4_data_f))
diff --git a/notebooks/_solutions2/15-xarray-datasets1.py b/notebooks/_solutions2/15-xarray-datasets1.py
@@ -0,0 +1 @@
+argo["temperature_kelvin"] = argo["temperature"] + 273.15
diff --git a/notebooks/_solutions2/15-xarray-datasets10.py b/notebooks/_solutions2/15-xarray-datasets10.py
@@ -0,0 +1 @@
+argo.sel(level=[1, 5, 25, 50]).plot.scatter(x="lat", y="temperature", col="level")
diff --git a/notebooks/_solutions2/15-xarray-datasets11.py b/notebooks/_solutions2/15-xarray-datasets11.py
@@ -0,0 +1,5 @@
+argo.temperature.plot.pcolormesh(yincrease=False, 
+                                 cbar_kwargs={'label': 'Temperature (°C)'},
+                                 cmap='Reds',
+                                 levels=[5, 15]
+                                );
diff --git a/notebooks/_solutions2/15-xarray-datasets12.py b/notebooks/_solutions2/15-xarray-datasets12.py
@@ -0,0 +1 @@
+subset_mean = argo.sel(date=slice('2012-10-01', '2012-12-01')).mean(dim="date")
diff --git a/notebooks/_solutions2/15-xarray-datasets13.py b/notebooks/_solutions2/15-xarray-datasets13.py
@@ -0,0 +1,4 @@
+fig, (ax0, ax1) = plt.subplots(1, 2)
+subset_mean["salinity"].plot.line(y="level", yincrease=False, ax=ax0)
+subset_mean["temperature"].plot.line(y="level", yincrease=False, ax=ax1)
+plt.tight_layout()
diff --git a/notebooks/_solutions2/15-xarray-datasets2.py b/notebooks/_solutions2/15-xarray-datasets2.py
@@ -0,0 +1 @@
+argo.plot.scatter(x="pressure", y="level")
diff --git a/notebooks/_solutions2/15-xarray-datasets3.py b/notebooks/_solutions2/15-xarray-datasets3.py
@@ -0,0 +1 @@
+argo["buoyancy"] = 9.8 * (2e-4 * argo["temperature"] - 7e-4 * argo["pressure"])
diff --git a/notebooks/_solutions2/15-xarray-datasets4.py b/notebooks/_solutions2/15-xarray-datasets4.py
@@ -0,0 +1 @@
+argo["buoyancy"].plot(yincrease=False)  # xarray decides the plot type when no specific method is used
diff --git a/notebooks/_solutions2/15-xarray-datasets5.py b/notebooks/_solutions2/15-xarray-datasets5.py
@@ -0,0 +1,2 @@
+# More explicit version defining the x and y axis
+argo["buoyancy"].plot.pcolormesh(x="date", y="level", yincrease=False)  # pcolormesh instead of imshow
diff --git a/notebooks/_solutions2/15-xarray-datasets6.py b/notebooks/_solutions2/15-xarray-datasets6.py
@@ -0,0 +1 @@
+argo["salinity"].sel(level=10).plot.line()
diff --git a/notebooks/_solutions2/15-xarray-datasets7.py b/notebooks/_solutions2/15-xarray-datasets7.py
@@ -0,0 +1 @@
+argo["temperature"].sel(level=[10, 20, 30]).plot.line(hue="level");
diff --git a/notebooks/_solutions2/15-xarray-datasets8.py b/notebooks/_solutions2/15-xarray-datasets8.py
@@ -0,0 +1 @@
+argo["temperature"].sel(level=[10, 20, 30]).plot.line(col="level");
diff --git a/notebooks/_solutions2/15-xarray-datasets9.py b/notebooks/_solutions2/15-xarray-datasets9.py
@@ -0,0 +1 @@
+argo.plot.scatter(x="temperature", y="level", hue="lat", s=2)

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+tc_data = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_True_color.tiff")`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+# Calculate the min and max for each channel`
	`2`	`+h_min = herstappe_data.min(dim=["x", "y"])`
	`3`	`+h_max = herstappe_data.max(dim=["x", "y"])`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+# Rescale the data`
	`2`	`+herstappe_rescaled = ((herstappe_data - h_min)/(h_max - h_min))`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+# Make a plot`
	`2`	`+herstappe_rescaled.plot.imshow(figsize=(9, 5))`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+gent = xr.open_rasterio("./data/gent/raster/2020-09-17_Sentinel_2_L1C_True_color.tiff")`
	`2`	`+gent`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+# Convert to float and make 65535 equal to Nan`
	`2`	`+gent_f = gent.astype(float)`
	`3`	`+gent_f = gent_f.where(gent != 65535)`