def get_incorrect_pixels(inputpath, referencepath, vitimeseriespath, startdoy, interval, nodata=None): #Open images inputimage = openImage(inputpath) referenceimage = openImage(referencepath) timeseries = openImage(vitimeseriespath) #Get band 1 of input and reference images and read as arrays inband = inputimage[5].GetRasterBand(1) inarray = inband.ReadAsArray(0, 0, inputimage[0], inputimage[1]) inband = "" refband = referenceimage[5].GetRasterBand(1) refarray = refband.ReadAsArray(0, 0, referenceimage[0], referenceimage[1]) refband = "" #Close in and ref images #Find unique values in the input image uniquevals = set(numpy.unique(inarray).tolist()) uniquevals.remove(nodata) print uniquevals #Iterate through pixels in images, comparing arrays for each value in input image, making note of tested values and excluding them from comparison with 0 value in input image #Return pixel coordinates and the identified and true identities of the pixels from the input and reference images coordinatelist = {} for value in uniquevals: coordinatelist[value] = [] numincorrect = 0 for col in range(0, inputimage[0]): for row in range(0, inputimage[1]): if (inarray[row, col] != 0) and (inarray[row, col] != refarray[row, col]) and (inarray[row, col] != nodata): if refarray[row, col] in uniquevals: coordinatelist[refarray[row, col]].append([col, row, inarray[row, col], refarray[row, col]]) numincorrect += 1 else: coordinatelist[0].append([col, row, inarray[row, col], refarray[row, col]]) numincorrect += 1 elif (inarray[row,col] == 0) and (refarray[row, col] in uniquevals): coordinatelist[refarray[row, col]].append([col, row, inarray[row, col], refarray[row, col]]) numincorrect += 1 #For each returned pixel, extract and plot the curve from vitimeseries and export plot as image; be sure to label plot correctly bandcnt = timeseries[5].RasterCount arrays = {} for i in range(1, bandcnt + 1): band = timeseries[5].GetRasterBand(i) data = band.ReadAsArray(0, 0, timeseries[0], timeseries[1]) arrays[i] = data print("Found {0} incorrect pixels to process...".format(numincorrect))
def plot_points(multidateraster, pointfile, startdoy, doyinterval): """ """ import os from utils import unique_name from plotting import PixelPlot from core import pixel as pixelObject from vectorFunctions import get_px_coords_from_shapefile from imageFunctions import openImage outpath = unique_name(os.path.dirname(multidateraster), "plots", ext=".pdf", usetime=True) coords = get_px_coords_from_shapefile(multidateraster, pointfile) plot = PixelPlot(os.path.dirname(outpath), os.path.basename(outpath)) raster = openImage(multidateraster) for coord in coords: pixel = pixelObject(coord[0], coord[1]) pixel.get_pixel_values(raster, startdoy, doyinterval) plot.add_pixel(pixel, closefigure=True) plot.close_plot() raster = None
def get_px_coords_from_shapefile(raster, shapefile): """ Takes geographic coordinates from a shapefile and finds the corresponding pixel coordinates on a raster. rst = "/Users/phoetrymaster/Documents/School/Geography/Thesis/Data/MODIS_KANSAS_2007-2012/reprojected/clips/KansasEVI_2012_clip1.tif" #rst = "/Users/phoetrymaster/Documents/School/Geography/Thesis/Data/polygonclip_20130929223024_325071991/resampled/newclips/2012clip1.tif" shp = "/Users/phoetrymaster/Documents/School/Geography/Thesis/Data/MODIS_KANSAS_2007-2012/SampleAreas/samplepoints2012_clip1_new.shp" print get_px_coords_from_shapefile(rst, shp) """ #TODO docstrings from imageFunctions import openImage # open, close image file and get properties raster = openImage(raster) imageproperties = gdalProperties(raster) rasterwkt = raster.GetProjectionRef() oSRSop = osr.SpatialReference() oSRSop.ImportFromWkt(rasterwkt) raster = None shppoints = load_points(shapefile, oSRSop) # get pixel coords from point coords pxcoords = get_px_coords_from_geographic_coords(imageproperties, shppoints) return pxcoords
def fit_refs_to_image(imagetoprocess, outputdirectory, signaturecollection, startDOY, doyinterval, bestguess, threshold=None, ndvalue=-3000, fitmethod=None, subset=None, meantype=None, workers=4, timebounds=None, xbounds=None, ybounds=None): """ imagepath = "/Users/phoetrymaster/Documents/School/Geography/Thesis/Data/ARC_Testing/ClipTesting/ENVI_1/test_clip_envi_3.dat" outdir = "/Users/phoetrymaster/Documents/School/Geography/Thesis/Data/OutImages/" newfoldername = "Testing" drivercode1 = 'ENVI' #ndvalue = -3000 startDOY = 1 interval = 16 threshold = 500 bestguess = 0 fitmthd = 'SLSQP' mean = geometric # Acceptable values are geometric (geometric mean) and arithmetic (arithmetic mean). It is an optional argument for the classifier. refs = { 'soy': {1: 174.5, 97: 1252.25, 65: 1139.5, 209: 7659.0, 273: 4606.75, 337: 1371.75, 17: 1055.5, 33: 1098.0, 49: 1355.25, 129: 1784.75, 257: 6418.0, 321: 1644.5, 305: 1472.75, 193: 5119.75, 289: 1878.75, 177: 3439.5, 241: 7565.75, 81: 1205.5, 225: 7729.75, 145: 1736.25, 161: 1708.25, 353: 1358.25, 113: 1340.0}, 'corn': {1: 392.25, 97: 1433.25, 65: 1258.5, 209: 6530.0, 273: 1982.5, 337: 1658.5, 17: 1179.25, 33: 1196.75, 49: 1441.25, 129: 1885.25, 257: 2490.25, 321: 1665.75, 305: 1439.0, 193: 6728.25, 289: 1634.5, 177: 6356.75, 241: 4827.25, 81: 1355.75, 225: 5547.5, 145: 2196.5, 161: 3143.25, 353: 1704.75, 113: 1716.5}, 'wheat': {1: 719.75, 97: 6594.75, 65: 1935.25, 209: 2013.5, 273: 1493.5, 337: 1498.25, 17: 1816.5, 33: 1815.0, 49: 1985.25, 129: 6758.0, 257: 1685.75, 321: 1582.5, 305: 1163.25, 193: 2186.25, 289: 1264.5, 177: 2222.5, 241: 2301.0, 81: 4070.5, 225: 1858.0, 145: 6228.5, 161: 3296.5, 353: 1372.5, 113: 7035.25} } sys.exit(fit_refs_to_image(imagepath, outdir, newfoldername, refs, startDOY, interval, threshold, bestguess, fitmthd, meantype=mean)) """ #TODO docstrings start = dt.now() print(start) try: print("\nProcessing {0}...".format(imagetoprocess)) print("Outputting files to {0}\n".format(outputdirectory)) #Open multi-date image to analyze image = openImage(imagetoprocess) imageproperties = gdalProperties(image) print("Input image dimensions are {0} columns by {1} rows and contains {2} bands.".format(imageproperties.cols, imageproperties.rows, imageproperties.bands)) array = read_image_into_array(image) # Read all bands into a 3d array representing the image stack (x, y, time orientation) image = "" if timebounds: timebounds = (bestguess + timebounds[0], bestguess + timebounds[1]) else: timebounds = (bestguess - 10, bestguess + 10) if not xbounds: xbounds = (0.6, 1.4) if not ybounds: ybounds = (0.6, 1.4) bounds = (xbounds, ybounds, timebounds) print(bounds) if subset: subset = get_px_coords_from_shapefile(imagetoprocess, subset) processes = [] for signum, signature in enumerate(signaturecollection.signatures, start=1): p = multiprocessing.Process(target=process_reference, args=(outputdirectory, signature, array, imageproperties, startDOY, doyinterval, bestguess, ndvalue), kwargs={"subset": subset, "fitmthd": fitmethod, "meantype": meantype, "thresh": threshold, "bounds": bounds}) #TODO: Problem with joining/starting processes--original thread closes before others are completed -- believe this is now fixed. p.start() processes.append(p) if len(processes) == workers: for p in processes: p.join() processes.remove(p) for p in processes: p.join() except Exception as e: import traceback exc_type, exc_value, exc_traceback = sys.exc_info() print(e) traceback.print_exception(exc_type, exc_value, exc_traceback, limit=2, file=sys.stdout) finally: print(dt.now() - start)
def classify_and_assess_accuracy(outputdir, cropimgpath, searchstringsvals, filevalist, nodata, thresholdsandlength, classifiedimagename=None, numberofprocesses=4): """ """ #TODO Docstring #from multiprocessing import Pool #pool = Pool(numberofprocesses) if classifiedimagename is None: today = dt.now() classifiedimagename = today.strftime("%Y-%m-%d_%H%M_") + os.path.splitext(os.path.basename(cropimgpath))[0] classificationimage = os.path.join(outputdir, classifiedimagename + ".tif") accuracyimage = os.path.join(outputdir, classifiedimagename + "_accuracy.tif") accuracyreport = os.path.join(outputdir, classifiedimagename + ".txt") #np.set_printoptions(threshold=np.nan) # For debug: Makes numpy print whole contents of an array. #Crop image is constant for all iterations cropimg = openImage(cropimgpath) cropimgproperties = gdalProperties(cropimg) croparray = read_image_into_array(cropimg) cropimg = None arraylist = [(read_image_into_array(openImage(f[0])), f[1]) for f in filevalist] # fit images with crop vals writestring = "The fit rasters and truth values used for this classification process are:\n" for f in filevalist: writestring = writestring + "\t{0}\t{1}\n".format(f[0], f[1]) writestring = writestring + "\n" bestacc = 0 bestthresh = None thresholdlist, lengthofthresholdlist = thresholdsandlength try: if lengthofthresholdlist == 1: writestring = writestring + "\n\n**Only using a single threshold value--not iterating.**\n\n" bestthresh = thresholdlist[0] else: #TODO: Refactor to allow use of multiprocessing.Pool.map -- need to reason about the output/logging for thresh in thresholdlist: start = dt.now() accuracy, classification, outstring = classify_with_threshold(croparray, arraylist, searchstringsvals, thresh, nodata, cropimgproperties.nodata) writestring = writestring + outstring if accuracy > bestacc: bestacc = accuracy bestthresh = thresh elapsed = dt.now() - start toprint = [thresh, "{}:{}".format(elapsed.seconds, str(elapsed.microseconds).zfill(6)), accuracy, bestacc, bestthresh] width = (6 * len(arraylist)) sys.stdout.write("Thresh: {: <{width}} Time: {} Acc: {: <14} Best: {: <14} at {}\r".format(*toprint, width=width)) sys.stdout.flush() except Exception as e: import traceback exc_type, exc_value, exc_traceback = sys.exc_info() print e traceback.print_exception(exc_type, exc_value, exc_traceback, limit=2, file=sys.stdout) finally: accuracy, classificationarray, outstring = classify_with_threshold(croparray, arraylist, searchstringsvals, bestthresh, nodata, cropimgproperties.nodata) writestring = writestring + outstring accuracyarray = find_correct_incorrect_array(croparray, classificationarray, ndvalue=nodata, truthndvalue=cropimgproperties.nodata) with open(accuracyreport, 'w') as text: text.write("Classification using fit images from {0}\n\n".format(os.path.dirname(filevalist[0][0]))) text.write("{0}\nBest:\n{1} {2}".format(writestring, bestthresh, accuracy)) print("\n{0}, {1}".format(bestthresh, accuracy)) driver = gdal.GetDriverByName("ENVI") driver.Register() write_output_image(cropimgproperties, classificationimage, classificationarray, nodata) write_output_image(cropimgproperties, accuracyimage, accuracyarray, nodata) print("outputted") return 0