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Chapter 3 Plotting and Visualizing Your Data

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Chapter 3 Plotting and Visualizing Your Data

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Ha
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Patrick Gray (patrick.c.gray at duke) - https://github.com/patrickcgray Chapter 3: Plotting and visualizing your data with matplotlib Introduction matplotlib is avery powerful plotting library for making amazing visualizations for publications, personal use, or even web and desktop applications. matplotlib can create almost any two dimensional visualization you can think of, including histograms, scatter plots, bivariate plots, and image displays. For some inspiration, check out the natplotlit example gallery which includes the source code required to generate each example. matplotlib API - state-machine versus object-oriented One part of matplotlib that may be initially confusing is that matplotlib contains two main methods of making plots - the object-oriented method, and the state-machine method. A very good overview of the difference between the two usages is provided by Jake Vanderplas, Specifically, # Pyplot state-machine © Object-oriented f you need a primer on matplotlib beyond what is here | suggest: Python Like you Mean tor the matplotlib users guide, in general, | think you should use the object-oriented API. While more complicated, is a much more powerful way of creating plots and should be used when developing more complicatec visualizations. | always recommend the OO API. Image display We will begin by reading our example image into a NumPy memory array as shown in Chapter 2 import rasterio import numpy as np # open our raster dataset dataset = rasterio.open(' . . /data/L£70220491999322EDCO1_stack.gtif") image = dataset. read() Let's check out some of this datasets characteristics # How many bands does this image have? ‘nun_bands = dataset.count print("Number of bands in image: (n}\n'format(nsnum_bands)) # How many rows and columns? rows, cols = dataset.shape print('Inage size is: (r} rows x (c} colunns\n’ format (r=rows, ¢=cols)) # what driver was used to open the raster? driver = dataset.driver print('Raster driver: {4)\n" «format (d=driver)) # What is the raster's projection? proj = dataset.crs print(‘*Inage projection:') print(proj) Number of bands in image: 8 Image size is: 25@ rows x 25@ columns Raster driver: GTift Image projection: =PSG:32615 Note that if you have the full dataset read in with you can do: red_band = image[2, :, :] # this pulls out the 3rd band print(red_band. shape) (250, 258) This pulls out the band at index 2 which is the 3rd band because python indexing starts at 0 Which is equal to simply doing red_band_read = dataset.read(3) # this pulls out the 3rd band print (red_band_read. shape) if mp.array_equal(red_band_read, red_band): + ore they equal? print(‘They are the sane.) (250, 250) They are the same. f you have a large dataset the second dataset read(3) may be preferable because you save on memory Basic plotting First thing to do is to import matplot Lit into our namespace. | will be using a special feature of the [Python utility which allows me to “inline" matplotlib figures by entering the %natplotlib inline command. 5]: Amport matplotlib.pyplot as plt Xmatplotlib inline With natplotlib imported, we can summon up a figure and make our first plot: # Array of @ - 9 x = np.arange(1@) # 10 random numbers, between @ and 10 y = np.randon.randint (2, 10, size=10) # plot them as Lines plt.plot(x, y) 5]: [ specify "Ls" (“Linestyle") as a null string # plot them as just points plt.plot(x, y, ‘ro', >), [ematplotlib.lines.Line2d at @x7f35a225d100> 8 . . 6 . . 4 . 2 . ° 0 2 a 6 3 As | mentioned earlier, we'll be using Matplotib’s object oriented API, instead of its function-based API. Let's briefly draw a distinction between these two APIs: # prepare 50 x-coordinates and 58 y-coordinates x = np.Linspace(-np.pi, np.pi, 50) 8 y = np.sin(x) # Plot using motplotlib's functional apr: # a single function call produces a plot; conventent but Less flexible plt.plot(x, y) [ 100 075 050 025 0.00 025 -0850 -075 100 # Plot using matplotlib's object-oriented API: # we generate o figure and axis object: “fig’ and “ax” fig, ax = plt-subplots() # we then use these objects to draw-on and manipulate our plot ax.plot(x, y) [ 100 075 050 025 0.00 025 -0850 -075 100 3 2 4 o© @ 2 3 Although the code that invokes the functional API is simpler, its far less powerful and flexible than the object-oriented API, which produces figure (fig) and axes (ax) objects that we can leverage to customize our plot. You will ikely see tutorials utilize the functional API in their examples, so itis useful to understand the distinction here, Shortly, you will learn how to leverage Matplotlib’s object- oriented API in powerful ways Plotting 2D arrays One typical thing that we might want to do would be to plot one band against another. In order to do this, we will need to transform, or flatten , our 2 dimensional arrays of each band's values into 1 dimensional arrays red image[3, :, :] image[4, :, :] print(*Array shape before: {shp} (size is {sz})'.format(shp=red.shape, szered.size)) red_flat = np.ndarray.flatten(red) nir_flat = np.ndarray.flatten(nir) print(‘Array shape after: {shp} (size is {sz})'.format(shp=red_flat.shape, sz=red_flat. Array shape before: (250, 250) (size is 62500) Array shape after: (62500,) (size is 62500) We have retained the number of entries in each of these raster bands, but we have flattened them from 2 dimensions into 1. Now we can plot them. Since we just want points, we can use scatter for a scatterplot. Since there are no lines in a scatterplot, it has a slightly different syntax. Fig, ax = plt.subplots() # Make the plot ax.scatter(red_flat, nir_flat, color: # Add some oxis Labels ax.set_xlabel( ‘Red Reflectance" ) ax.set_ylabel(‘NIR label’) # Add a title ax.set_title(‘Tasseled Cap, eh?') Text(0.5, 1.0, ‘Tasseled Cap, eh?') Tasseled Cap, eh? #08 200 3000 NR tabet y 1000 300 1500 2000 2500 3000 3500 4000 4500 5000 Red Reflectance f we wanted the two axes to have the same limits, we can calculate the limits and apply them fig, ax = plt.subplots() # Make the plot ax.scatter(red_flat, nir_flat, color="r', marker='0") # Calculate min and max plot_min = min(red.min(), nir.min()) plot_max = max(ned.max(), nir.max()) ax.set_xLim((plot_min, plot_max)) ax.set_ylim((plot_min, plot_max)) # Add some oxis Labels ax.set_xlabel( ‘Red Reflectance" ) ax.set_ylabel(‘NIR label’) # Add a title ax.set_title(‘Tasseled Cap, eh?') Text(0.5, 1.0, ‘Tasseled Cap, eh?") Tasseled Cap, eh? s000 4000 2200 . 2000 1000 1000 ~~=«2000~=~=«ODS*«OSC«C Red Reflectance What if we want to view average intensities of each band? # numbers 1-8 x = np.arange(1,9) # Lets get the average value of each band y = npemean(inage, axis=(1,2)) Fig, ax = plt.subplots() # plot them as Lines ax.plot(x, y) # Add some axis Labels ax.set_xlabel( ‘Band #') ax,set_ylabel( ‘Reflectance Value") w Add a title ax,set_title("Band Intensities") Text(@.5, 1.0, "Band Intensities") In Band Intensities Reflectance Value Ba 8 ss 8 500 1 2 3 4 § 6 9 68 Band = ‘tis common to have this high reflectance in the NIR band (band 4 here) Plotting 2D arrays - images With so much data available to look at, it can be hard to understand what is going on with the mess of points shown above. Luckily our datasets aren't just a mess of points - they have a spatia structure. To show the spatial structure of our images, we could make an image plot of one of our bands using imshow to display an image on the axes: # use the matpLotltb.pyplot function “imshow" for an image -- nir at first fig, ax = plt.subplots() ax.imshow(image[3, :, :]) 0 50 «100150200 Well, it looks like there is something going on - maybe a river in the center and some bright vegetation to the bottom left of the image. What's lacking is any knowledge of what the colors mean Luckily, matplotlib can provide us a colorbar, # use "imshow" for an image -- nir at first fig, ax = plt-subplots() ing = ax.imshow(image[3, :, :]) fig.colorbar(img, ax=ax) # we have to pass the current plot as an argument thus have to 0150-200 ff we want a greyscale image, we can manually specify a colormap: Well also begin showing some more advanced plotting capabilities in matplotlb such as putting ‘multiple plots in a single output. Here we'll compare the NIR to Red in greyscale. fig, (ax, ax2) = plt-subplots(1,2, figsize=(10,3)) # 2 axes on a 1x2 grid # note that we could also use indexing for our axes: # fig, ox = plt.subplots(1, 2) # axl = ax[@] # find max reflectance to put them on the same colorbar scale max_ref = np.anax([np.anax(image[3:,:]), np-amax(image[2:,:])]) # nin in first subplot nir = ax1.imshow(image[3, :, axd.set_title("NIR Sand! nir.set_clim(vmin=@, vmax=max_ref) J, crap=plt.cm.Greys) fig.colorbar(nir, ax=ax1) # Now red band in the second subplot ed = ax2.imshow(inage[2, :, :], chap=plt.cm.Greys) ax2.set_title("Red Band") ed.set_clim(vmin=@, vmax=max_ref) Fig.colorbar(red, ax=ax2) NIR Band Red Band o 5000 0 5000 % 000 0 / 000 100 3000 100 . , 3000 150 200 80 2000 20 1000 20 1000 ° ° os 100 150. 200 o 2 io so ao Plotting 3D arrays - multispectral images Greyscale images are nice, but the most information we can receive comes from looking at the interplay among different bands. To accomplish this, we can map different spectral bands to the Red, Green, and Blue channels on our monitors Before we can do this, the natplotlib imshow help tells us that we need to normalize our bands into a 0 - 1 range. To do so, we will perform a simple linear scale fitting 0 reflectance to 0 and 80% reflectance to 1, clipping anything larger or smaller. Remember If we are going from a Int16 datatype (e.g., reflectance scaled by 10,000x) to a decimal between @ and 1, we will need to use a Float! from rasterio.plot import reshape_as_raster, reshape_as_image # Extract reference to SWIRL, NIR, and Red bands index = np.array([4, 3, 2)) colors = image[index, :, :].astype(np.floatss) max_val = 5000 mmin_val # Enforce maximum and minimum values colors{colors{:, :, :] > max_val] = max_val colors{colors(:, :, :] < min_val] = min_val for b in range(colors.shape(@]): colors(b, :, :] = colors[b, :, :] *1/ (max_val = min_val) # rasters are in the format (bands, rows, cols] whereas images are typically [rows, col # and so our array needs to be reshaped print(colors.shape) colors_reshaped = reshape_as_image(colors) print(colors_reshaped. shape) (3, 250, 250) (250, 250, 3) We've got a correctly shaped and normalized image now. Let's calculate NDVI on this dataset to compare it to the color image. In [18. np.seterr(divide='ignore’, invalid=' ignore’) bandNIR banded ndvi = (bandNIR.astype( float) -bandRed. astype( float) )/(bandNIR.astype(float)+bandRed.ast Now let's plot it all 1) 18)" 44g, axs = plt.subplots(1, 2, Flgsize=(10, 5)) # Show the color image axs[@].imshow(colors_reshaped) axs[@].set_title(‘Color Image’) # Show Nor axs[1].imshow(ndvi, cmap="Rdy1Gn") axs[1].set_title('NOVI') outfie): Text(@.5, 1.8, "NDVI') Color image 100 350 200 so 00200 Pretty informative now! There is a slighly easier way to do this rasterio has its own show function that is built to handle rasters. We saw this in chapter 1 briefly. in [201 4 this functions build on matplotlib and make them custom for rasterio from rasterio.plot import show In [21 Fig, ax = plt. subplots (Figsize=(6,6)) # display just band 4 (WIR) show((dataset.read(4)), axeax) ° 0 300 150 700 And if we want to show a color image we can use raste adjust_band function from rasterio.plot import adjust_band rgb = image[0:3] # read in red, green, blue rgb_norm = adjust_band(rgb) # normalize bands to range between 1.0 to 0.0 rgb_reshaped = reshape_as_image(rgb_norm) # reshape to [rows, cols, bands] Fig, axs = plt.subplots(1, 2, figsize=(10, 5)) # the rasterio show function takes in [bands, rows, cols] so we don't need to reshape show(rgb_norm, axzaxs[@]) axs(0].set_title("RG8 from rasterio show") # plot with normal matpLotlib functions axs[ 1] -imshow(rgb_reshaped) axs[1]-set_title("RG8 in matplotlib inshow") Text(@.5, 1.0, ‘RGB in matplotlib imshow' ) RGB in matplotlib imshow RGB from rasterio show 50 50 100 100 150 150 200 200 30 S000 displaying all three bands side by side (22,7) red channel" ) green channel" ) subplots(1,3, figsiz ds’, title ‘Greens’, title: cmap="Blues', title='blue channel’) fig, (axr, axg, axb) = plt. show( (dataset, 1), axsaxr, show((dataset, 2), ax=axg, show((dataset, 3), ax=axb, ‘center’: "blue channel"}> If we want to see a histogram of the data we use the show_| function from rasterio.plot inport show hist Fig, ax = plt.subplots(#igsize=(19,5)) show_hist(dataset, ax-ax) Histogram mE _. at Ox7135a05c5e40> 3 100 20000 10000 | ° al 0 2000 3000) ow Let's look at an overlapping histogram, maybe that'll be more informative: fig, ax = plt.subplots(Figsize=(10,5)) show_hist(dataset, ax=ax, bins=50, lw=0.0, histtype='stepfilled’, title World Histogram overlaid tacked=False, alpha=0.3, "World Histogram overlai 3000 “. at Ox7F35a0619d60> 0 1000 2000 3000 2000 ow Let's look at another raster world = rasterio.open("../data/world.rgb.tif") print(world. shape) fig, ax = plt.subplots(Figsize=(10,5)) show((world), axeax, cnap='viridis") (256, 512) 3000 In Check out more documentation for the rasteric plotting functions here: https://rasterio.readthedocs.io/en/latest/api/rasterio.plot html#rasterio.plot show Wrapup We've seen how natplotlib canbe combined with aumpy and rasterio to easily visualize and explore our remote sensing data. In the next chapter (link to webpage or Notebook) we wil cover how to open and read vector data

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