def plot_predicted_probabilities(predictions, groundtruth, n_classes, uncertainty):
""" plot predictions with ground truth
arguments
---------
predictions: numpy nd.array
probability maps of classes of patches
shape = (n_patches, patch_size_padded, patch_size_padded, n_classes)
groundtruth: numpy nd.array
one-hot lables of patches
shape = (n_patches, patch_size_padded, patch_size_padded, n_classes)
nclasses: int
number of prediction classes
uncertainty: float between 0 and 1
if uncertainty is higher than this number, class 'unsure' is assigned
output
------
figure with predictionsmaps plotted in first n rows and ground truth in last row.
The columns represent differnet patches.
"""
#colors_extra = ['linen', 'lightgreen', 'limegreen', 'darkgreen', 'yellow', 'black']
colors_extra = np.array([(194/256,230/256,153/256),(120/256,198/256,121/256),
(49/256,163/256,84/256),(0/256,76/256,38/256),(229/256,224/256,204/256),(0,0,0)])
cmap_extra = ListedColormap(colors_extra)
n_patches = len(predictions)
rows = 7
# prepare
fig, ax = plt.subplots(rows,n_patches)
for i in range(n_patches):
im = predictions[i]
gt = groundtruth[i]
# prepare prediction plot
plt_im = np.zeros_like(im, dtype=np.uint8)
plt_im = np.argmax(im, axis=2)
plt_im[np.max(im, axis=2)<(1-uncertainty)] = 5
# plot probability maps
for j in range(n_classes):
ax[j,i].imshow(im[:,:,j], vmin=0, vmax=1)
# prepare gt plot
plt_gt = np.zeros_like(gt, dtype=np.uint8)
plt_gt = np.argmax(gt, axis=2)
# plot prediction
im = ax[5,i].imshow(plt_im, cmap=cmap_extra, vmin=0, vmax=5)
# plot gt
grtr = ax[6,i].imshow(plt_gt, cmap=cmap, vmin=0, vmax=4)
ep.draw_legend(im,titles=["tara0", "tara20", "tara50", "forest","non-cultivable","not sure"],classes=[0, 1, 2, 3,4,5])
def NDVI(bands, year):
"""Normalized Difference Vegetation Index (NDVI)"""
#ndvi = es.normalized_diff(band4, band3) # (band4-band3)/(band4+band3)
ndvi = es.normalized_diff(bands[3], bands[2]) # (band4-band3)/(band4+band3)
titles = ['Normalized Difference Vegetation Index (NDVI) Year: %s' %year]
# Turn off bytescale scaling due to float values for NDVI
ep.plot_bands(ndvi, cmap="RdYlGn", cols=1, title=titles, vmin=-1, vmax=1)
# Create classes and apply to NDVI results
ndvi_class_bins = [-np.inf, 0, 0.25, 0.5, 0.75, np.inf]
ndvi_landsat_class = np.digitize(ndvi, ndvi_class_bins)
# Define color map and class names
ndvi_colors = ListedColormap(['gray', 'y', 'yellowgreen', 'g', 'darkgreen'])
ndvi_names = ['0.00 No Vegetation','0.25 Bare Area','0.50 Low Vegetation','0.75 Moderate Vegetation','1.00 High Vegetation']
# Get list of classes
classes = np.unique(ndvi_landsat_class).tolist()
fig, ax = plt.subplots(figsize=(8, 8))
im = ax.imshow(ndvi_landsat_class, cmap=ndvi_colors)
ep.draw_legend(im_ax=im, classes=classes, titles=ndvi_names)
ax.set_title('Normalized Difference Vegetation Index (NDVI) Classes. \nYear: %s' %yr,fontsize=14)
ax.set_axis_off(); plt.tight_layout()
plt.show()
def test_non_ax_obj():
"""Draw_legend fun should raise AttributeError if provided with a
non mpl axis object"""
with pytest.raises(
AttributeError,
match="The legend function requires a matplotlib axis object",
):
ep.draw_legend(im_ax=list())
def plot_predicted_patches(predictions, groundtruth, patch=None):
""" plot predicted patches with ground truth
arguments
---------
predictions: numpy nd.array
probability maps of classes of patches
shape = (n_patches, patch_size_padded, patch_size_padded, n_classes)
groundtruth: numpy nd.array
one-hot lables of patches
shape = (n_patches, patch_size_padded, patch_size_padded, n_classes)
patch: numpy.ndarray
image of patch
shape = (n_patches, patch_size_padded, patch_size_padded, n_classes)
output
------
figure with n predictions plotted in first row and ground truth in second row.
if patch is specified the third row contains RGB image
"""
n_patches = len(predictions)
cols = 2
if np.any(patch != None):
cols = 3
# prepare
fig, ax = plt.subplots(n_patches,cols, figsize=(15,15))
for i in range(n_patches):
im = predictions[i]
gt = groundtruth[i]
# prepare prediction plot
plt_im = np.zeros_like(im, dtype=np.uint8)
plt_im = np.argmax(im, axis=2)
# prepare gt plot
plt_gt = np.zeros_like(gt, dtype=np.uint8)
plt_gt = np.argmax(gt, axis=2)
# plot training image
ax[i,0].imshow(plt_im, cmap=cmap, vmin=0, vmax=4)
# plot gt
grtr = ax[i,1].imshow(plt_gt, cmap=cmap, vmin=0, vmax=4)
# plot RGB
if np.any(patch != None):
plt_im = patch[i][:, :, [0,1,2]].astype(np.float64)
ax[i,2].imshow(plt_im)
ep.draw_legend(grtr,titles=["tara0", "tara20", "tara50", "woods","no coltivable"],classes=[0, 1, 2, 3,4])
def test_listedcmap_ncol_equals_nclasses(vals_missing_plot_list_cmap):
"""If a 5 color listed cmap is provided and 6 classes are specified, return value error"""
n_classes = 5
im_ax, arr = vals_missing_plot_list_cmap
with pytest.raises(
ValueError,
match="There are more classes than colors in your cmap"):
ep.draw_legend(im_ax, classes=np.arange(0, n_classes + 1))
plt.close()
def test_subplots(binned_array):
"""Test to ensure that a plot with subplots still has a legend."""
bins, arr_class = binned_array
f, (ax1, ax2) = plt.subplots(2, 1)
im_ax = ax1.imshow(arr_class)
ep.draw_legend(im_ax)
im_ax2 = ax2.imshow(arr_class)
ep.draw_legend(im_ax2)
plt.close(f)
def plot_random_patches(patches_path, n_patches, classes, class_names):
""" plot random patches with ground truth
arguments
---------
patches_path: string
path to folder containing the patches
n_patches: int
number of random patches to plot
classes: list
list of predicted classes
class_names: list
output
------
figure with n_patches plotted in first row and ground truth in second row.
"""
images_path = patches_path + 'images/'
labels_path = patches_path + 'labels/'
rows = 2
cols = n_patches
# get path images list
im_list = list_files(images_path, '.npy')
gt_list = list_files(labels_path, '.npy')
# prepare
index = np.array([0,1,2])
fig, ax = plt.subplots(rows,cols)
for i in range(n_patches):
idx=np.random.randint(len(im_list))
im = np.load(images_path + im_list[idx])
gt = np.load(labels_path + gt_list[idx])
# prepare RGB plot
plt_im = im[:, :, index].astype(np.float64)
# prepare gt plot
plt_gt = np.zeros_like(gt, dtype=np.uint8)
plt_gt = np.argmax(gt, axis=2)
# plot training image
image = ax[0,i].imshow(plt_im)
# plot gt
grtr = ax[1,i].imshow(plt_gt, cmap=cmap, vmin=0, vmax=4) #colors not right
ep.draw_legend(grtr,titles=class_names,classes=classes)
def plot_categorical_w_window(self, output_file, labels, cmap, xy, width, height, box=True):
"""Creates a figure of a categorical raster with a zoomed window
:param output_file: path, file path of the figure
:param labels: list of strings, labels (i.e., titles)for the categories
:param cmap: string, colormap to plot the raster
:param xy: tuple (x,y), origin of the zoomed window, the upper left corner
:param width: integer, width (number of cells) of the zoomed window
:param height: integer, height (number of cells) of the zoomed window
:returns: saves the figure of the raster
"""
raster_np = read_raster(self.path)
print('Classes identified in the raster: ', np.unique(raster_np))
# cmap = matplotlib.colors.ListedColormap(list_colors)
fig, ax = plt.subplots(1, 2)
ax[0].imshow(raster_np, cmap=cmap)
rectangle = patches.Rectangle(xy, width, height, fill=False)
ax[0].add_patch(rectangle)
plt.setp(ax, xticks=[], yticks=[])
# Plot Patch
box_np = raster_np[xy[1]: xy[1] + height, xy[0]: xy[0] + width]
im = ax[1].imshow(box_np, cmap=cmap)
cbar = ep.draw_legend(im, titles=labels)
# cbar.ax[].tick_params(labelsize=20)
if not box:
ax.axis('off')
fig.savefig(output_file, dpi=700, bbox_inches='tight')
def test_listed_cmap(arr_plot_list_cmap):
"""Test that the the legend generates properly when provided with a ListedColormap"""
im_ax, arr = arr_plot_list_cmap
leg = ep.draw_legend(im_ax)
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == len(np.unique(arr))
plt.close()
def test_num_titles_classes(binned_array_3bins):
"""Test to ensure the the number of "handles" or classes provided for each
legend items matches the number of classes being used to build the legend.
This case should return a ValueError if these items are different"""
bins, im_arr_bin = binned_array_3bins
im_arr_bin[im_arr_bin == 2] = 3
fig, ax = plt.subplots(figsize=(5, 5))
im_ax = ax.imshow(im_arr_bin, cmap="Blues")
with pytest.raises(ValueError):
ep.draw_legend(im_ax=im_ax,
classes=[1, 2],
titles=["small", "medium", "large"])
with pytest.raises(ValueError):
ep.draw_legend(im_ax=im_ax,
classes=[1, 2, 3],
titles=["small", "large"])
def plot_patches(patch, gt, n_patches):
""" plot patches with ground truth
arguments
---------
patch: numpy.ndarray
image of patch
shape = (n_patches, patch_size_padded, patch_size_padded, n_classes)
gt: numpy.ndarray
one-hot lables of patches
shape = (n_patches, patch_size_padded, patch_size_padded, n_classes)
n_patches: int
number of random patches to plot
output
------
figure with n_patches plotted in first row and ground truth in second row.
"""
rows = 2
cols = n_patches
# prepare
index = np.array([0,1,2])
fig, ax = plt.subplots(rows,cols)
for i in range(n_patches):
# prepare RGB plot
plt_im = patch[i][:, :, index].astype(np.float64)
# prepare gt plot
plt_gt = np.zeros_like(gt[i], dtype=np.uint8)
plt_gt = np.argmax(gt[i], axis=2)
# plot training image
image = ax[0,i].imshow(plt_im)
# plot gt
grtr = ax[1,i].imshow(plt_gt, cmap=cmap, vmin=0, vmax=4)
ep.draw_legend(grtr,titles=["tara0", "tara20", "tara50", "forest","non-cultivable"],classes=[0, 1, 2, 3,4])
def test_noncont_listed_cmap(vals_missing_plot_list_cmap):
"""An arr with 3 vals (missing the 1, and 5) which requires normalization
produces creates a legend with 3 handles."""
im_ax, arr = vals_missing_plot_list_cmap
leg = ep.draw_legend(im_ax)
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == len(np.unique(arr))
plt.close()
def test_classes_provided_as_array(arr_plot_list_cmap):
"""Test that draw_legend works when classes are provided as an arr (not a list)."""
im_ax, arr = arr_plot_list_cmap
n_classes = 5
leg = ep.draw_legend(im_ax, classes=np.arange(n_classes))
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == n_classes
plt.close()
def test_neg_vals():
"""Test that the legend plots when positive and negative values are provided"""
arr = np.array([[-1, 0, 1], [1, 0, -1]])
f, ax = plt.subplots()
im_ax = ax.imshow(arr)
leg_neg = ep.draw_legend(im_ax)
legend_cols = [i.get_facecolor() for i in leg_neg.get_patches()]
assert len(legend_cols) == len(np.unique(arr))
plt.close(f)
def test_neg_vals(binned_array):
"""Test that the things plot when positive and negative vales
are provided"""
bins, arr_class = binned_array
f, ax = plt.subplots()
im_ax = ax.imshow(arr_class)
leg_neg = ep.draw_legend(im_ax)
legend_cols = [i.get_facecolor() for i in leg_neg.get_patches()]
assert len(legend_cols) == len(bins) - 1
plt.close(f)
def plot_categorical_raster(self, output_file, labels, cmap, box=True):
"""Creates a figure of a categorical raster
:param output_file: path, file path of the figure
:param labels: list of strings, labels (i.e., titles)for the categories
:param cmap: string, colormap to plot the raster
:param box: boolean, if False it sets off the frame of the picture
:returns: saves the figure of the raster
"""
raster_np = read_raster(self.path)
print('Classes identified in the raster: ', np.unique(raster_np))
# cmap = matplotlib.colors.ListedColormap(list_colors)
fig, ax = plt.subplots()
im = ax.imshow(raster_np, cmap=cmap)
ep.draw_legend(im, titles=labels)
ax.set_axis_off()
# plt.show()
if not box:
ax.axis('off')
fig.savefig(output_file, dpi=200, bbox_inches='tight')
def test_num_titles_classes(arr_plot_blues):
"""Test that the number of classes equals the number of legend titles"""
im_ax, _ = arr_plot_blues
with pytest.raises(
ValueError,
match="The number of classes should equal the number of titles",
):
ep.draw_legend(im_ax=im_ax,
classes=[1, 2],
titles=["small", "medium", "large"])
with pytest.raises(
ValueError,
match="The number of classes should equal the number of titles",
):
ep.draw_legend(im_ax=im_ax,
classes=[1, 2, 3],
titles=["small", "large"])
plt.close()
def test_cont_cmap_3_classes(vals_missing_plot_cont_cmap):
"""Test legend for a listed cmap where
the user wants all classes to be drawn in the legend. IE the classified
image has classes 2,3,4 and the user wants classes 1-5 to appear """
im_ax, arr = vals_missing_plot_cont_cmap
class_list = list(range(5))
leg = ep.draw_legend(im_ax, classes=class_list)
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == len(class_list)
plt.close()
def test_stock_legend_titles(arr_plot_blues):
"""Test that the correct number of default titles plot"""
im_ax, im_arr_bin = arr_plot_blues
# Default legend title values
def_titles = ["Category {}".format(i) for i in np.unique(im_arr_bin)]
the_legend = ep.draw_legend(im_ax=im_ax)
# Legend handle titles should equal unique values in ax array
assert len(the_legend.get_texts()) == len(np.unique(
im_ax.get_array().data))
assert def_titles == [text.get_text() for text in the_legend.get_texts()]
plt.close()
def test_colors(arr_plot_blues):
"""Test that the correct colors appear in the patches of the legend"""
im_ax, _ = arr_plot_blues
the_legend = ep.draw_legend(im_ax=im_ax)
legend_cols = [i.get_facecolor() for i in the_legend.get_patches()]
# Get the array and cmap from axis object
cmap_name = im_ax.axes.get_images()[0].get_cmap().name
unique_vals = np.unique(im_ax.get_array().data)
image_colors = ep.make_col_list(unique_vals, cmap=cmap_name)
assert image_colors == legend_cols
plt.close()
def test_custom_legend_titles(arr_plot_blues):
"""Test that the correct number of custom legend titles plot"""
im_ax, _ = arr_plot_blues
custom_titles = ["one", "two", "three"]
the_legend = ep.draw_legend(im_ax=im_ax, titles=custom_titles)
assert len(the_legend.get_texts()) == len(np.unique(
im_ax.get_array().data))
assert custom_titles == [
text.get_text() for text in the_legend.get_texts()
]
plt.close()
def test_custom_legend_titles(binned_array_3bins):
"""Test that the correct number of and text for custom legend titles
plot when titles parameter = None"""
bins, im_arr_bin = binned_array_3bins
f, ax = plt.subplots()
imp2 = ax.imshow(im_arr_bin, cmap="Blues")
custom_titles = ["one", "two", "three"]
the_legend = ep.draw_legend(im_ax=imp2, titles=custom_titles)
assert len(the_legend.get_texts()) == len(np.unique(imp2.get_array().data))
assert custom_titles == [
text.get_text() for text in the_legend.get_texts()
]
plt.close(f)
def test_noncont_listed_cmap_3_classes(binned_array, listed_cmap):
"""Test legend for a non continuous listed cmap where
the user wants all classes to be drawn in the legend. IE the classified
image has classes 2,3,4 and the user wants classes 1-5 to appear """
cmap, norm = listed_cmap
bins, arr_class = binned_array
f, ax = plt.subplots(figsize=(5, 5))
im = ax.imshow(arr_class, cmap=cmap, norm=norm)
leg = ep.draw_legend(im, classes=[1, 2, 3, 4, 5])
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == len([1, 2, 3, 4, 5])
plt.close(f)
def test_listed_cmap(binned_array):
"""Test that the the legend generates properly when provided with a Listed
colormap"""
bins, arr_class = binned_array
# TODO make the list of colors a fixture for reuse
cmap_list = ListedColormap(
["white", "tan", "purple", "springgreen", "darkgreen"])
f, ax = plt.subplots()
im_plt = ax.imshow(arr_class, cmap=cmap_list)
leg = ep.draw_legend(im_plt)
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == len(bins) - 1
plt.close(f)
def test_masked_vals():
"""Test to ensure that a masked array plots properly"""
im_arr = np.random.uniform(-2, 1, (15, 15))
bins = [-0.8, -0.2, 0.2, 0.8, np.Inf]
im_arr_bin = np.digitize(im_arr, bins)
arr_bin_ma = np.ma.masked_equal(im_arr_bin, 0)
unmasked_vals = [
val for val in np.unique(arr_bin_ma) if val is not np.ma.core.masked
]
f, ax = plt.subplots()
im_ax = ax.imshow(arr_bin_ma)
leg = ep.draw_legend(im_ax)
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == len(unmasked_vals)
plt.close(f)
def test_colors(binned_array_3bins):
"""Test that the correct colors appear in the patches of the legend"""
bins, im_arr_bin = binned_array_3bins
f, ax = plt.subplots()
im = ax.imshow(im_arr_bin, cmap="Blues")
the_legend = ep.draw_legend(im_ax=im)
# NOTE: Do I know for sure things are rendering in the right order?
legend_cols = [i.get_facecolor() for i in the_legend.get_patches()]
# Get the array and cmap from axis object
cmap_name = im.axes.get_images()[0].get_cmap().name
unique_vals = np.unique(im.get_array().data)
image_colors = ep.make_col_list(unique_vals, cmap=cmap_name)
assert image_colors == legend_cols
def test_stock_legend_titles(binned_array_3bins):
"""Test that the correct number of generic titles plot when titles
parameter = None"""
bins, im_arr_bin = binned_array_3bins
f, ax = plt.subplots()
imp2 = ax.imshow(im_arr_bin, cmap="Blues")
# Default legend title values should be
def_titles = ["Category {}".format(i) for i in np.unique(im_arr_bin)]
the_legend = ep.draw_legend(im_ax=imp2)
# Legend handle titles should equal unique values in ax array
assert len(the_legend.get_texts()) == len(np.unique(imp2.get_array().data))
assert def_titles == [text.get_text() for text in the_legend.get_texts()]
plt.close(f)
def test_noncont_listed_cmap(binned_array, listed_cmap):
"""Test that an arr with 3 classes (missing the 1, and 5) which
would need to be normalized, only creates a legend with x handles
by default"""
cmap, norm = listed_cmap
bins, arr_class = binned_array
arr_class[arr_class == 1] = 2
arr_class[arr_class == 5] = 4
f, ax = plt.subplots(figsize=(5, 5))
im = ax.imshow(arr_class, cmap=cmap, norm=norm)
leg = ep.draw_legend(im)
legend_cols = [i.get_facecolor() for i in leg.get_patches()]
assert len(legend_cols) == len(np.unique(arr_class))
plt.close(f)
nbr_cmap = ListedColormap(nbr_colors)
# Define class names
ndvi_cat_names = [
"No Vegetation",
"Bare Area",
"Low Vegetation",
"Moderate Vegetation",
"High Vegetation",
]
# Get list of classes
classes = np.unique(ndvi_landsat_class)
classes = classes.tolist()
# The mask returns a value of none in the classes. remove that
classes = classes[0:5]
# Plot your data
fig, ax = plt.subplots(figsize=(12, 12))
im = ax.imshow(ndvi_landsat_class, cmap=nbr_cmap)
ep.draw_legend(im_ax=im, classes=classes, titles=ndvi_cat_names)
ax.set_title(
"Landsat 8 - Normalized Difference Vegetation Index (NDVI) Classes",
fontsize=14,
)
ax.set_axis_off()
# Auto adjust subplot to fit figure size
plt.tight_layout()
# Create a colormap with 11 colors
cmap = plt.cm.get_cmap('tab20b', 11)
# Get a list of unique values in the qa layer
vals = np.unique(landsat_qa).tolist()
bins = [0] + vals
# Normalize the colormap
bounds = [((a + b) / 2) for a, b in zip(bins[:-1], bins[1::1])] + \
[(bins[-1] - bins[-2]) + bins[-1]]
norm = colors.BoundaryNorm(bounds, cmap.N)
# Plot the data
fig, ax = plt.subplots(figsize=(12, 8))
im = ax.imshow(landsat_qa, cmap=cmap, norm=norm)
ep.draw_legend(im, classes=vals, cmap=cmap, titles=vals)
ax.set_title("Landsat Collection Quality Assessment Layer")
ax.set_axis_off()
plt.show()
# -
# In the image above, you can see the cloud and the shadow that is obstructing our landsat image.
# Unfortunately for you, this cloud covers a part of your analysis area in the Cold Springs
# Fire location. There are a few ways to handle this issue. We will look at one:
# simply masking out or removing the cloud for your analysis, first.
#
# To remove all pixels that are cloud and cloud shadow covered we need to first
# determine what each value in our qa raster represents. The table below is from the USGS landsat website.
# It describes what all of the values in the pixel_qa layer represent.
#