diff --git a/README.md b/README.md
index 2d808bc..2acf694 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,12 @@ collected by the NEON AOP. This code was created as part of an effort to generat
 
 A full description of the effort can be found at:
 
-> K. Dana Chadwick, Philip Brodrick, Kathleen Grant, Tristan Goulden, Amanda Henderson, Nicola Falco, Haruko Wainwright, Kenneth H. Williams, Markus Bill, Ian Breckheimer, Eoin L. Brodie, Heidi Steltzer, C. F. Rick Williams, Benjamin Blonder, Jiancong Chen, Baptiste Dafflon, Joan Damerow, Matt Hancher, Aizah Khurram, Jack Lamb, Corey Lawrence, Maeve McCormick. John Musinsky, Samuel Pierce, Alexander Polussa, Maceo Hastings Porro, Andea Scott, Hans Wu Singh, Patrick O. Sorensen, Charuleka Varadharajan, Bizuayehu Whitney, Katharine Maher. Integrating airborne remote sensing and field campaigns for ecology and Earth system science. <i>In Review</i>, 2020.
+> K. Dana Chadwick, Philip Brodrick, Kathleen Grant, Tristan Goulden, Amanda Henderson, Nicola Falco, Haruko Wainwright, Kenneth H. Williams, Markus Bill, Ian Breckheimer, Eoin L. Brodie, Heidi Steltzer, C. F. Rick Williams, Benjamin Blonder, Jiancong Chen, Baptiste Dafflon, Joan Damerow, Matt Hancher, Aizah Khurram, Jack Lamb, Corey Lawrence, Maeve McCormick. John Musinsky, Samuel Pierce, Alexander Polussa, Maceo Hastings Porro, Andea Scott, Hans Wu Singh, Patrick O. Sorensen, Charuleka Varadharajan, Bizuayehu Whitney, Katharine Maher. Integrating airborne remote sensing and field campaigns for ecology and Earth system science. Methods in Ecology and Evolution, 2020.
 
 and use of this code should cite that manuscript.
 
 ### Visualization code in GEE for all products in this project can be found here: 
-https://code.earthengine.google.com/5c96bbc96ffd50e3c8b1433b34a0bb86
+https://code.earthengine.google.com/?scriptPath=users%2Fpgbrodrick%2Feast_river%3Aneon_aop_collection_visuals
 <br>
 
 
diff --git a/apply_cover_model.py b/apply_cover_model.py
index cc4dd96..c0c41a7 100644
--- a/apply_cover_model.py
+++ b/apply_cover_model.py
@@ -2,82 +2,108 @@
 import gdal
 import os
 import argparse
-import keras
+from tensorflow import keras
 from tqdm import tqdm
-from sklearn.externals import joblib
-
+#from sklearn.externals import joblib
+import joblib
+#check order of bn & standarization
 
 import warnings
 warnings.filterwarnings('ignore')
 
-parser = argparse.ArgumentParser(description='Apply chem equation to BIL')
-parser.add_argument('refl_dat_f')
-parser.add_argument('output_name')
-parser.add_argument('-model_f', default='trained_models/conifer_nn_set_29.h5')
-parser.add_argument('-scaler', default='trained_models/nn_conifer_scaler')
-parser.add_argument('-bn', default=True, type=bool)
-args = parser.parse_args()
-
-if (os.path.isfile(args.output_name)):
-    print('output file: {} found.  terminating'.format(args.output_name))
-    quit()
-
-# make sure these match the settings file corresponding to the coefficient file
-
-# open up chemical equation data
-model = keras.models.load_model(args.model_f)
-
-# open up raster sets
-dataset = gdal.Open(args.refl_dat_f, gdal.GA_ReadOnly)
-data_trans = dataset.GetGeoTransform()
-
-max_y = dataset.RasterYSize
-max_x = dataset.RasterXSize
-
-
-# create blank output file
-driver = gdal.GetDriverByName('GTiff')
-driver.Register()
-
-
-outDataset = driver.Create(args.output_name,
-                           max_x,
-                           max_y,
-                           1,
-                           gdal.GDT_Float32,
-                           options=['COMPRESS=DEFLATE', 'TILED=YES'])
-
-outDataset.SetProjection(dataset.GetProjection())
-outDataset.SetGeoTransform(dataset.GetGeoTransform())
-
-full_bad_bands = np.zeros(426).astype(bool)
-full_bad_bands[:8] = True
-full_bad_bands[192:205] = True
-full_bad_bands[284:327] = True
-full_bad_bands[417:] = True
-
-bad_bands = np.zeros(142).astype(bool)
-bad_bands[:2] = True
-bad_bands[64:68] = True
-bad_bands[95:109] = True
-bad_bands[139:] = True
-output_predictions = np.zeros((max_y, max_x))
-
-
-if args.scaler is not None:
-    scaler = joblib.load(args.scaler)
-
-# loop through lines [y]
-for l in tqdm(range(0, max_y), ncols=80):
-    dat = np.squeeze(dataset.ReadAsArray(0, l, max_x, 1)).astype(np.float32)
-    dat = dat[np.logical_not(full_bad_bands), ...]
-    dat = np.transpose(dat)
-    if (np.nansum(dat) > 0):
-        if (args.bn):
-            dat = dat / np.sqrt(np.nanmean(np.power(dat, 2), axis=1))[:, np.newaxis]
-
-        dat = scaler.transform(dat)
-        output_predictions[l, :] = model.predict(dat)[:, 0]
-
-outDataset.GetRasterBand(1).WriteArray(output_predictions, 0, 0)
-del outDataset
+def main():
+    parser = argparse.ArgumentParser(description='Apply chem equation to BIL')
+    parser.add_argument('refl_dat_f')
+    parser.add_argument('output_name')
+    parser.add_argument('-model_f', default='trained_models/cover_model_nl_2_dr_0.4_nn_550_it_49.h5')
+    parser.add_argument('-scaler', default=None)
+    parser.add_argument('-bn', default=1, type=int, choices=[0, 1])
+    parser.add_argument('-argmax', default=1, type=int, choices=[0, 1])
+    args = parser.parse_args()
+    
+    args.bn = args.bn == 1
+    args.argmax = args.argmax == 1
+
+    if os.path.isfile(args.output_name):
+        print('output file: {} found.  terminating'.format(args.output_name))
+        quit()
+
+    apply_model(args.model_f, args.refl_dat_f, args.output_name, args.bn, args.scaler, args.argmax)
+
+
+def apply_model(model_file: str, refl_dat_f: str, output_name: str, bn: bool = True, scaler: str = None, argmax: bool = True):
+    # open up chemical equation data
+    model = keras.models.load_model(model_file)
+    
+    # open up raster sets
+    dataset = gdal.Open(refl_dat_f, gdal.GA_ReadOnly)
+    data_trans = dataset.GetGeoTransform()
+    
+    max_y = dataset.RasterYSize
+    max_x = dataset.RasterXSize
+    
+    
+    # create blank output file
+    driver = gdal.GetDriverByName('GTiff')
+    driver.Register()
+    
+    
+    full_bad_bands = np.zeros(426).astype(bool)
+    full_bad_bands[:8] = True
+    full_bad_bands[192:205] = True
+    full_bad_bands[284:327] = True
+    full_bad_bands[417:] = True
+    
+    bad_bands = np.zeros(142).astype(bool)
+    bad_bands[:2] = True
+    bad_bands[64:68] = True
+    bad_bands[95:109] = True
+    bad_bands[139:] = True
+    
+    
+    if scaler is not None:
+        scaler = joblib.load(scaler)
+    
+    n_bands = 1
+    if argmax is False:
+        dat_bands = np.squeeze(dataset.ReadAsArray(0, 0, 5, 1)).astype(np.float32)
+        dat_bands = dat_bands[np.logical_not(full_bad_bands), ...]
+        dat_bands = np.transpose(dat_bands)
+        pred_shape = model.predict(dat_bands)
+        n_bands = len(pred_shape[-1])
+    
+    output_predictions = np.zeros((max_y, max_x, n_bands))
+    outDataset = driver.Create(output_name,
+                               max_x,
+                               max_y,
+                               n_bands,
+                               gdal.GDT_Float32,
+                               options=['COMPRESS=DEFLATE', 'TILED=YES'])
+    
+    outDataset.SetProjection(dataset.GetProjection())
+    outDataset.SetGeoTransform(dataset.GetGeoTransform())
+    
+    # loop through lines [y]
+    #for l in tqdm(range(0, max_y), ncols=80):
+    for l in tqdm(range(0, 200), ncols=80):
+        dat = np.squeeze(dataset.ReadAsArray(0, l, max_x, 1)).astype(np.float32)
+        dat = dat[np.logical_not(full_bad_bands), ...]
+        dat = np.transpose(dat)
+        if np.nansum(dat) > 0:
+            if bn:
+                dat = dat / np.sqrt(np.nanmean(np.power(dat, 2), axis=1))[:, np.newaxis]
+    
+            if scaler is not None:
+                dat = scaler.transform(dat)
+    
+            if argmax is True:
+                output_predictions[l, :, 0] = np.argmax(model.predict(dat), axis=-1)
+            else:
+                output_predictions[l, ...] = model.predict(dat)
+    
+    for _band in range(n_bands):
+        outDataset.GetRasterBand(_band + 1).WriteArray(output_predictions[...,_band], 0, 0)
+    del outDataset
+
+if __name__ == "__main__":
+    main()
diff --git a/cover_class_spec_plotting.py b/cover_class_spec_plotting.py
new file mode 100644
index 0000000..0900611
--- /dev/null
+++ b/cover_class_spec_plotting.py
@@ -0,0 +1,101 @@
+
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+import os
+import warnings
+warnings.filterwarnings('ignore')
+
+
+plt.rcParams.update({'font.size': 20})
+plt.rcParams['font.family'] = "serif"
+plt.rcParams['font.serif'] = "Times New Roman"
+plt.rcParams['axes.grid'] = True
+plt.rcParams['axes.axisbelow'] = True
+plt.rcParams['axes.labelpad'] = 6
+
+
+def main():
+    file_path = '~/Google Drive File Stream/My Drive/CB_share/NEON/cover_classification/extraction_output/cover_extraction_20201021.csv'
+    wavelengths_file = 'raster_data/neon_wavelengths.txt'
+    spectra, cover_types, wv = spec_cleaning(file_path, wavelengths_file, 'refl_B_')
+    plot_avg_spectra(spectra, cover_types, wv)
+
+
+def find_nearest(array_like, v):
+    index = np.argmin(np.abs(np.array(array_like) - v))
+    return index
+
+def spec_cleaning(file_path, wavelengths_file, band_preface):
+    extract = pd.read_csv(file_path)
+    headerSpec = list(extract)  # Reflectance bands start at 18 (17 in zero base)
+
+    # defining wavelengths
+    wv = np.genfromtxt(wavelengths_file)
+    bad_bands = []
+    good_band_ranges = []
+
+    bad_band_ranges = [[0, 425], [1345, 1410], [1805, 2020], [2470, 2700]]
+    for _bbr in range(len(bad_band_ranges)):
+        bad_band_ranges[_bbr] = [find_nearest(wv, x) for x in bad_band_ranges[_bbr]]
+        if (_bbr > 0):
+            good_band_ranges.append([bad_band_ranges[_bbr-1][1], bad_band_ranges[_bbr][0]])
+
+        for n in range(bad_band_ranges[_bbr][0], bad_band_ranges[_bbr][1]):
+            bad_bands.append(n)
+    bad_bands.append(len(wv)-1)
+
+    good_bands = np.array([x for x in range(0, 426) if x not in bad_bands])
+
+    # first column of reflectance data
+    rfdat = list(extract).index(band_preface + '1')
+
+    all_band_indices = (np.array(good_bands)+rfdat).tolist()
+    all_band_indices.extend((np.array(bad_bands)+rfdat).tolist())
+    all_band_indices = np.sort(all_band_indices)
+
+    spectra = np.array(extract[np.array(headerSpec)[all_band_indices]])
+    spectra[:, bad_bands] = np.nan
+
+    cover_types = extract['covertype']
+
+    return spectra, cover_types, wv
+
+
+def plot_avg_spectra(spectra, cover_types, wv, brightness_normalize=False):
+
+    c_types = cover_types.unique()
+
+    color_sets = ['navy', 'tan', 'forestgreen', 'royalblue', 'gray', 'darkorange', 'black', 'brown', 'purple']
+
+    # Plot the difference between needles and noneedles in reflectance data
+    figure_export_settings = {'dpi': 200, 'bbox_inches': 'tight'}
+
+    fig = plt.figure(figsize=(8, 5), constrained_layout=True)
+    for _c, cover in enumerate(c_types):
+        c_spectra = spectra[cover_types == cover]
+        print(color_sets[_c])
+        if brightness_normalize:
+            scale_factor = 1.
+        else:
+            scale_factor = 100.
+        plt.plot(wv, np.nanmean(c_spectra, axis=0) / scale_factor, c=color_sets[_c], linewidth=2)
+        plt.fill_between(wv, np.nanmean(c_spectra, axis=0) / scale_factor - np.nanstd(c_spectra, axis=0) / scale_factor,
+                         np.nanmean(
+                             c_spectra, axis=0) / scale_factor + np.nanstd(c_spectra, axis=0) / scale_factor, alpha=.15,
+                         facecolor=color_sets[_c])
+
+    plt.legend(c_types, prop={'size':10})
+    plt.ylabel('Reflectance (%)')
+    if brightness_normalize:
+        plt.ylabel('Brightness Norm. Reflectance')
+    else:
+        plt.ylabel('Reflectance (%)')
+    plt.xlabel('Wavelength (nm)')
+
+    plt.savefig(os.path.join('figs', 'class_spectra.png'), **figure_export_settings)
+    del fig
+
+
+if __name__ == "__main__":
+    main()
diff --git a/cover_model.py b/cover_model.py
index 93230a8..bc35a45 100644
--- a/cover_model.py
+++ b/cover_model.py
@@ -2,40 +2,109 @@
 
 import numpy as np
 import pandas as pd
-import keras
+from tensorflow import keras
 import matplotlib as mpl
 import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+import os
 
 from tqdm import tqdm
-from sklearn.externals import joblib
+import joblib
+#from sklearn.externals import joblib
 from sklearn import preprocessing
 from sklearn.metrics import confusion_matrix
-from keras.layers import BatchNormalization, Conv2D, Dense, Flatten, MaxPooling2D, Concatenate, SeparableConv2D, Dropout
+from tensorflow.keras.layers import BatchNormalization, Conv2D, Dense, Flatten, MaxPooling2D, Concatenate, SeparableConv2D, Dropout
+from itertools import product
+import gdal
+from apply_cover_model import apply_model
 
+import warnings
+warnings.filterwarnings('ignore')
 
-
-#mpl.use('Agg')
+mpl.use('Agg')
 
 
 def main():
+    file_path = '~/Google Drive File Stream/My Drive/CB_share/NEON/cover_classification/extraction_output_20201106/cover_extraction.csv'
+    #file_path = 'data/cover_extraction_20201021.csv'
+    layers_range = [2]
+    node_range = [250]
+    dropout_range = [0.4]
+    epochs_per_save = 20
+    iterations = 1
+    run_name = 'data_splits_9'  # with scaling, weighting, and shade masking
+    run_name = 'data_splits_10'  # with scaling, weighting and no shade masking
+    run_name = 'data_splits_11'  # with scaling, weighting and inverted shade masking
+    run_name = 'data_splits_12'  # with scaling, weighting and shade masking, without bn
+    run_name = 'data_splits_13'  # with scaling, weighting, shade masking, no batch normalization, with bn
+    run_name = 'data_splits_14'  # with scaling, weighting, no shade masking, no batch normalization, with bn, change sigmoid to linear
+    run_name = 'data_splits_8'
+    run_name = 'data_splits_9'
+    data_munge_dir = 'munged/' + run_name + '.npz'
+    output_filename = 'output/' + run_name + '.npz'
+
+
+    scaling=True
+    brightness_norm=True
+
+    # only reimport and munge data if this has not already been done, otherwise import data to save compute time
+    if os.path.isfile(data_munge_dir):
+        npzf = np.load(data_munge_dir, allow_pickle=True)
+        refl = npzf['refl']
+        Y = npzf['Y']
+        test = npzf['test']
+        train = npzf['train']
+        weights = npzf['weights']
+        covertype = npzf['covertype']
+        y_labels = npzf['y_labels'].tolist()
+    else:
+        refl, Y, test, train, weights, covertype, y_labels = manage_datasets(file_path, run_name, shade_mask=False,
+                                                                             category=None, scaling=scaling,
+                                                                             brightness_norm=brightness_norm)
+
+        np.savez(data_munge_dir, refl=refl, Y=Y, test=test, train=train, weights=weights, covertype=covertype, y_labels=y_labels)
+
+    # Run
+    preds, dim_names = nn_scenario_test(output_filename, refl, Y, weights, test, train, y_labels, covertype, run_name,
+                                        n_epochs=epochs_per_save, its=iterations, layers_range=layers_range,
+                                        node_range=node_range, dropout_range=dropout_range, classes=Y.shape[1],
+                                        output_activation='sigmoid')
+
+    ##plotting_model_fits(Y, test, covertype, layers_range, node_range, dropout_range, y_labels)
+    # for cover in y_labels:
+    #    plotting_model_fits_singleclass(output_filename, test, covertype, layers_range, node_range, dropout_range,
+    #                                    matchcover=cover, classlabels=y_labels)
+
+    plot_confusion_matrix(output_filename, train, np.argmax(Y,axis=1), layers_range, node_range, dropout_range, y_labels)
+
+    scaling_file=None
+    if scaling:
+        scaling_file='output/trained_models/nn_cover_scaler_' + run_name + '.pkl'
+        if os.path.isfile(scaling_file) is False:
+            raise AttributeError(f'cant find scaling file: {scaling_file}')
+
+    model_file = f'output/trained_models/cover_model{run_name}_nl_{layers_range[0]}_dr_{dropout_range[0]}_nn_{node_range[0]}_it_{iterations-1}.h5'
+    if os.path.isfile(model_file) is False:
+        raise AttributeError(f'cant find model file: {model_file}')
+
+    apply_model(model_file,'data_subset/refl_subset','data_subset/test_out.tif',bn=brightness_norm, scaler=scaling_file, argmax=True)
+
+
+
+
+
+
+def manage_datasets(import_data, run_name, category='aspen', weighting=False, scaling=False, wtrl_include=False,
+                    tch_include=False, shade_mask=True, brightness_norm=True):
 
-    layers_range=[2, 4]
-    node_range = [5, 10]
-    dropout_range = [0, 4]
-    refl, Y, test, train, weights = manage_datasets('~/Google Drive File Stream/My Drive/CB_share/NEON/cover_classification/extraction_output/cover_extraction.csv')
-    #preds, dim_names = nn_scenario_test(refl, Y, weights, test, train, n_epochs=2, its=10, layers_range=layers_range,
-    #                                    node_range=node_range, dropout_range=dropout_range)
-    plotting_model_fits(Y, layers_range, node_range, dropout_range)
-
-
-def manage_datasets(import_data, category='aspen', weighting=False):
     # Import extraction csv
     data_set = pd.read_csv(import_data)
 
     # extract x y coordinates for each pixel
     xy = np.array(data_set[['X_UTM', 'Y_UTM']])
-    #shade = np.array(data_set['ered_B_1']).flatten()
-    #tch = np.array(data_set['_tch_B_1']).flatten()
+    shade = np.array(data_set['hade_B_1']).flatten()
+    tch = np.array(data_set['h_me_B_1']).flatten()
+    wtrl = np.array(data_set['wtrl_B_1']).flatten()
 
     # extract reflectance data from csv
     refl = np.array(data_set)[:, -427:-1].astype(np.float32)
@@ -44,10 +113,6 @@ def manage_datasets(import_data, category='aspen', weighting=False):
     covertype = np.array(data_set[['covertype']]).flatten()
     print(np.unique(covertype))
 
-    # Identifying aspen in boolian vector format
-    aspen = np.zeros(len(xy)).astype(bool)
-    aspen[covertype == category] = True
-
     # Managing bad bands
     bad_bands_refl = np.zeros(426).astype(bool)
     bad_bands_refl[:8] = True
@@ -57,22 +122,44 @@ def manage_datasets(import_data, category='aspen', weighting=False):
     refl[:, bad_bands_refl] = np.nan
     refl = refl[:, np.all(np.isnan(refl) == False, axis=0)]
 
+    # indexing good pixels for inclusion
     good_data = np.ones(len(xy)).astype(bool)
-    #good_data[shade == 0] = False
+    if shade_mask:
+        good_data[shade == 0] = False
     good_data = good_data.flatten()
+    # if there are any nans in the entire row, remove that pixel
+    good_data[np.any(np.isnan(refl), axis=1)] = False
+    good_data[np.all(refl == 0, axis=1)] = False
 
+    # Keep only data from good pixels
     refl = refl[good_data, ...]
-    aspen = aspen[good_data, ...]
+    covertype = covertype[good_data, ...]
     xy = xy[good_data, :]
+    tch = tch[good_data]
+    wtrl = wtrl[good_data]
+    tch = tch.reshape((-1,1))
+    wtrl = wtrl.reshape((-1,1))
+
+    if category is not None:
+        Y = np.zeros((len(covertype),2)).astype(bool)
+        Y[:,1] = covertype == category
+        Y[:,0] = covertype != category
+        y_labels = ['not ' + category, category]
+    else:
+        # If None, one-hot-encode
+        unique_categories = np.unique(covertype)
+        Y = np.zeros((len(covertype), len(unique_categories))).astype(bool)
+        for _cat, cat in enumerate(unique_categories):
+            Y[:,_cat] = covertype == cat
+        y_labels = list(unique_categories)
 
-    Y = (aspen == True).reshape(-1, 1)
 
     np.random.seed(13)
     perm = np.random.permutation(Y.shape[0])
     train = np.zeros(perm.shape).astype(bool)
 
-    n_xstep = 100
-    n_ystep = 100
+    n_xstep = 1000
+    n_ystep = 1000
     x_space = np.linspace(np.min(xy[:, 0]), np.max(xy[:, 0]), n_xstep)
     y_space = np.linspace(np.min(xy[:, 1]), np.max(xy[:, 1]), n_ystep)
     grids = np.zeros((len(y_space), len(x_space))).flatten()
@@ -90,54 +177,59 @@ def manage_datasets(import_data, category='aspen', weighting=False):
     print('Fraction Training Data: {}'.format((np.sum(train) / float(len(train)))))
     print('Fraction Testing Data: {}'.format((np.sum(test) / float(len(train)))))
 
-    #initialize weights vector and set to one for use in case where weighting == False
-    weights = np.zeros(Y.shape[0])
-    weights[:] = 1
-
-    # If weighting is needed or desired, adapt code here
-    if weighting == True:
-        weights = np.zeros(Y.shape[0])
-        needles_w = float(len(Y[train]))/float(np.sum(Y == 1))**0.8
-        noneedles_w = float(len(Y[train]))/float(np.sum(Y == 0))**0.8
-        print('needles_weight: {}'.format(needles_w/(needles_w+noneedles_w)))
-        print('noneedles_weight: {}'.format(noneedles_w/(needles_w+noneedles_w)))
-        weights[Y.flatten() == 1] = needles_w / (needles_w+noneedles_w) * 100
-        weights[Y.flatten() == 0] = noneedles_w / (needles_w+noneedles_w) * 100
+    for cover in np.unique(covertype):
+        fraction = 100*np.sum(covertype[train] == cover) / len(covertype[train])
+        print(f'% Training data is {cover}: {fraction}')
+    for cover in np.unique(covertype):
+        fraction = 100*np.sum(covertype[test] == cover) / len(covertype[test])
+        print(f'% Testing data is {cover}: {fraction}')
+
+    # initialize weights vector and set to one for use in case where weighting == False
+    weights = np.ones(Y.shape[0])
+    if weighting:
+        standardized_count = len(covertype[train]) / float(len(y_labels))
+        for _cover, cover in enumerate(y_labels):
+            w = standardized_count / np.sum(covertype[train] == cover)
+            weights[cover == covertype] = w
+            print(f'cover: {cover}, weight: {w}')
 
     # brightness normalize
-    brightness = np.sqrt(np.mean(np.power(refl, 2), axis=-1))
-    refl = refl / brightness[:, np.newaxis]
+    if brightness_norm:
+        brightness = np.sqrt(np.mean(np.power(refl, 2), axis=-1))
+        refl = refl / brightness[:, np.newaxis]
+    if wtrl_include:
+        refl = np.append(refl, wtrl, axis=-1)
+    if tch_include:
+        refl = np.append(refl, tch, axis=-1)
 
     # Scale brightness normalized reflectance data and save scaling information
-    scaler = preprocessing.StandardScaler()
-    scaler.fit(refl[train, :])
-    refl = scaler.transform(refl)
-    joblib.dump(scaler, 'output/trained_models/nn_aspen_scaler')
+    if scaling:
+        scaler = preprocessing.StandardScaler()
+        scaler.fit(refl[train, :])
+        refl = scaler.transform(refl)
+        joblib.dump(scaler, 'output/trained_models/nn_cover_scaler_' + run_name + '.pkl')
 
     # Return outputs of function
-    return refl, Y, test, train, weights
-
-
-
-    # Create NN model structure, and compile.  Ultimate structure desided after pretty
-    # extensive (heuristically guided) testing
+    return refl, Y, test, train, weights, covertype, y_labels
 
 
+# Create NN model structure, and compile.  Ultimate structure desided after pretty
+# extensive (heuristically guided) testing
 def nn_model(refl, num_layers, num_nodes, classes, dropout, loss_function, output_activation):
     inlayer = keras.layers.Input(shape=(refl.shape[1],))
     output_layer = inlayer
 
-  # defining internal layer structure
+    # defining internal layer structure
     for n in range(num_layers):
         output_layer = Dense(units=num_nodes)(output_layer)
 
         # Activation: makes it non-linear, remove line for nested linear models. many options here.
         output_layer = keras.layers.LeakyReLU(alpha=0.3)(output_layer)
 
-        #Regularization term: Removes nodes that are underutilized - more likely to need adjustment than leaky
+        # Regularization term: Removes nodes that are underutilized - more likely to need adjustment than leaky
         output_layer = Dropout(dropout)(output_layer)
 
-        #Normalization: amplifys signal by normalizing finite differences to look larger. consider turning this off
+        # Normalization: amplifys signal by normalizing finite differences to look larger. consider turning this off
         output_layer = BatchNormalization()(output_layer)
 
     # Activation for output layer defined here: sigmoid forces the results to look more binary. Could also be linear.
@@ -146,18 +238,19 @@ def nn_model(refl, num_layers, num_nodes, classes, dropout, loss_function, outpu
     # Initializing the model structure
     model = keras.models.Model(inputs=[inlayer], outputs=[output_layer])
 
-  # Optimization function and loss functions defined here - leave as is for now
-    model.compile(loss=loss_function, optimizer='adam') # change loss function to categorical_crossentropy
+    # Optimization function and loss functions defined here - leave as is for now
+    optimizer=keras.optimizers.Adam(learning_rate=0.001)
+    model.compile(loss=loss_function, optimizer=optimizer) # change loss function to categorical_crossentropy
 
     return model
 
 
-def nn_scenario_test(refl, Y, weights, test, train, layers_range=[4], node_range=[400], classes=2, dropout_range=[0.4],
-                     loss_function='binary_crossentropy', output_activation='sigmoid', n_epochs=5, its=20):
-    # reformat Y data for crossentropy loss function
-    cY = np.hstack([Y, 1-Y])
+def nn_scenario_test(output_filename, refl, Y, weights, test, train, y_labels, covertype, run_name,
+                     layers_range=[4], node_range=[400], classes=2, dropout_range=[0.4],
+                     loss_function='categorical_crossentropy', output_activation='sigmoid', n_epochs=5, its=20):
 
     predictions = np.zeros((len(layers_range), len(dropout_range), len(node_range), len(range(its)), len(Y))).astype(np.float32)
+    predictions[...] = np.nan
     dim_names = ['layers', 'dropout', 'node', 'iteration']
 
     # Run through and train model in 5 epoch steps - basically instituting a manual stopping criteria
@@ -173,28 +266,297 @@ def nn_scenario_test(refl, Y, weights, test, train, layers_range=[4], node_range
                     print('layers {}, nodes {}, dropout {}, iteration {}'.format(nl, nn, dr, _i))
                     # weights - this is to even out the importance of small classes -
                     # needs to be updated for categorical rather than binary
-                    model.fit(refl[train, ...], cY[train, ...], epochs=n_epochs, sample_weight=weights[train],
-                              validation_data=(refl[test, ...], cY[test, ...], weights[test]),
+                    model.fit(refl[train, ...], Y[train, ...], epochs=n_epochs, sample_weight=weights[train],
+                              validation_data=(refl[test, ...], Y[test, ...], weights[test]),
                               batch_size=1000)  # can be adjusted if getting memory errors
 
                     pred = model.predict(refl)
-                    pred = 1 - np.argmax(pred, axis=1)
+                    pred = np.argmax(pred, axis=1)
                     predictions[_nl, _dr, _nn, _i, :] = pred
 
-                    out_name = 'output/test_output.npz'
-                    np.savez(out_name, predictions=predictions, dim_names=dim_names)
+                    np.savez(output_filename, predictions=predictions, dim_names=dim_names)
+                    model.save(f'output/trained_models/cover_model{run_name}_nl_{nl}_dr_{dr}_nn_{nn}_it_{_i}.h5')
+
+                for cover in y_labels:
+                    plotting_model_fits_singleclass(output_filename, test, covertype, layers_range, node_range, dropout_range,
+                                                    matchcover=cover, classlabels=y_labels)
 
     return predictions, dim_names
 
 
-def plotting_model_fits(layers_range, node_range, dropout_range):
-    npzf = np.load('output/test_output.npz')
+def plotting_model_fits(output_filename, to_plot, covertype, layers_range, node_range, dropout_range, y_labels):
+    npzf = np.load(output_filename)
     predictions = npzf['predictions']
     dim_names = npzf['dim_names']
-    print(dim_names)
 
-    these_are_my_predictions = predictions[:, :, node_range.index(10), :]
-    print(these_are_my_predictions.shape)
+    # Predictions has dimensions: layers, dropout, nodes, iterations, predictions
+
+    # To limit the predictions to only those that we want to plot (probably the test set) based on the 'to_plot' variable,
+    # we can take a slice in the samples dimension, as:
+    predictions = predictions[..., to_plot]  # this is the same as predictions[:,:,:,:,to_plot]
+
+    # Do the same thing for the Y (truth) and for the covertype
+    covertype = covertype[to_plot]
+
+    # Now let's calculate the true positives, false_positives, etc.
+    # This is how you'd do it for Y
+    #true_positives  = np.sum(np.logical_and(predictions == Y, Y == 1), axis=-1)
+    #false_positives = np.sum(np.logical_and(predictions != Y, predictions == 1), axis=-1)
+    #true_negatives  = np.sum(np.logical_and(predictions == Y, Y == 0), axis=-1)
+    #false_negatives = np.sum(np.logical_and(predictions != Y, predictions == 0), axis=-1)
+
+    # But to be interesting, let's do it for the covertype
+    #un_covertype = np.unique(covertype)
+    for _c, cover in enumerate(y_labels):
+        # defining the index where covertype is one of the unique covers
+        cover_Y = covertype == cover
+
+        # all these are being done over the entire 5-D array and result in 4-D arrays for each
+
+        # defining where cover is equal to this class and where this class is predicted as aspen.
+        true_positives = np.nansum(np.logical_and(predictions == cover_Y, cover_Y == _c), axis=-1)
+
+        # prediction is aspen, actual is not this cover type - only useful for aspen
+        false_positives = np.nansum(np.logical_and(predictions != cover_Y, predictions == 1), axis=-1)
+
+        # prediction is not aspen, cover is this cover type
+        true_negatives = np.nansum(np.logical_and(predictions == cover_Y, cover_Y == 0), axis=-1)
+
+        # prediction is not aspen, actual is not this cover type - only meaningful for aspen now
+        false_negatives = np.nansum(np.logical_and(predictions != cover_Y, predictions == 0), axis=-1)
+        # Dimensions of the above sums are: layers, dropout, nodes, iterations
+
+        # And some bulk numbers about the particular cover type
+        num_cover = np.nansum(cover_Y)
+        num_not_cover = np.nansum(np.logical_not(cover_Y))
+
+        # Now lets make some aggregate plots
+        axis_names = ['Layers','Dropout','Nodes']
+        axis_legends = [layers_range, node_range, dropout_range]
+        gs = gridspec.GridSpec(ncols=len(axis_names), nrows=2, wspace=0.1, hspace=0.4)
+        fig = plt.figure(figsize=(4*len(axis_names)*1.1, 4))
+
+        for _ax, axname in enumerate(axis_names):
+
+
+            sumaxis = [0,1,2]
+            sumaxis.pop(_ax)
+            # Do layers TPR (axis 0)
+            ax = fig.add_subplot(gs[0,_ax])
+            # averaged across two of the axes - tuple is required instead of list for denoting multiple axes to sum over
+            mean_slice = np.nanmean(true_positives / num_cover, axis=tuple(sumaxis))
+            # transpose to allow different treatments to be in second axis and iterations in first for plotting
+            # this is because we want the iterations on the x axis
+            plt.plot(np.transpose(mean_slice))
+            plt.xlabel('Iteration')
+            plt.ylabel('True Positive Rate')
+            plt.title(axname)
+            plt.legend(axis_legends[_ax])
+
+            # Do layers FPP (False positives / # true elements)
+            ax = fig.add_subplot(gs[1,_ax])
+            plt.plot(np.transpose(np.nanmean(false_positives / num_cover, axis=tuple(sumaxis))))
+            plt.xlabel('Iteration')
+            plt.ylabel('False Positive Rate Prime')
+            plt.title(axname)
+            plt.legend(axis_legends[_ax])
+
+        baseout = os.path.splitext(os.path.basename(output_filename))[0]
+        plt.savefig(f'figs/{baseout}_{cover}.png', dpi=200, bbox_inches='tight')
+
+
+def plotting_model_fits_singleclass(output_filename, to_plot, covertype, layers_range, node_range, dropout_range, matchcover, classlabels):
+    npzf = np.load(output_filename)
+    predictions = npzf['predictions']
+    dim_names = npzf['dim_names']
+
+    # Predictions has dimensions: layers, dropout, nodes, iterations, predictions
+
+    # To limit the predictions to only those that we want to plot (probably the test set) based on the 'to_plot' variable,
+    # we can take a slice in the samples dimension, as:
+    predictions = predictions[..., to_plot]  # this is the same as predictions[:,:,:,:,to_plot]
+
+    # Do the same thing for the Y (truth) and for the covertype
+    covertype = covertype[to_plot]
+
+    # But to be interesting, let's do it for the covertype
+
+    # Now lets make some aggregate plots
+    axis_names = ['Layers', 'Dropout', 'Nodes']
+    axis_legends = [layers_range, dropout_range, node_range]
+    fig = plt.figure(figsize=(4 * len(axis_names)*1.2, 4 * (len(classlabels)+1)))
+    gs = gridspec.GridSpec(ncols=len(axis_names), nrows=len(classlabels)+1, wspace=0.1, hspace=0.4)
+    # defining where cover is equal to this class and where this class is predicted as aspen.
+    true_positives = np.nansum(np.logical_and(predictions == classlabels.index(matchcover), covertype == matchcover), axis=-1)
+
+    # falsely predicted 0 when this class was matchcover
+    false_negatives = np.nansum(np.logical_and(predictions != classlabels.index(matchcover), covertype == matchcover), axis=-1)
+
+
+    for _cover, cover in enumerate(classlabels):
+
+        # prediction is of class matchcover, actual is of multiple classes.
+        false_positives = np.nansum(np.logical_and(covertype == cover, predictions == classlabels.index(matchcover)), axis=-1)
+
+        # And some bulk numbers about the particular cover type
+        num_cover = np.nansum(covertype == matchcover)
+        num_not_cover = np.nansum(covertype != matchcover)
+
+        for _ax, axname in enumerate(axis_names):
+            sumaxis = [0,1,2]
+            sumaxis.pop(_ax)
+
+            if cover == matchcover:
+                # Do TPR
+                ax = fig.add_subplot(gs[0, _ax])
+                # averaged across two of the axes - tuple is required instead of list for denoting multiple axes to sum over
+                mean_slice = np.nanmean(true_positives / num_cover, axis=tuple(sumaxis))
+                # transpose to allow different treatments to be in second axis and iterations in first for plotting
+                # this is because we want the iterations on the x axis
+                plt.plot(np.transpose(mean_slice))
+                plt.xlabel('Iteration')
+                if _ax == 0:
+                    plt.ylabel('True Positive Rate')
+                plt.title(axname)
+                plt.legend(axis_legends[_ax])
+                plt.ylim([-0.05, 1.05])
+
+                # Do false negatives
+                ax = fig.add_subplot(gs[1, _ax])
+                # averaged across two of the axes - tuple is required instead of list for denoting multiple axes to sum over
+                mean_slice = np.nanmean(false_negatives / num_cover, axis=tuple(sumaxis))
+
+                # transpose to allow different treatments to be in second axis and iterations in first for plotting
+                # this is because we want the iterations on the x axis
+                plt.plot(np.transpose(mean_slice))
+                plt.xlabel('Iteration')
+                if _ax == 0:
+                    plt.ylabel('False negative rate')
+                plt.title(axname)
+                plt.legend(axis_legends[_ax])
+                plt.ylim([-0.05, 1.05])
+
+            else:
+                # Do per-class false positives
+                offset = 0
+                if classlabels.index(matchcover) < _cover:
+                    offset = -1
+                ax = fig.add_subplot(gs[2 + _cover + offset,_ax])
+                plt.plot(np.transpose(np.nanmean(false_positives / num_cover, axis=tuple(sumaxis))))
+                plt.xlabel('Iteration')
+                if _ax == 0:
+                    plt.ylabel(f'Predicted {cover} but actually {matchcover}\n relative to true {matchcover}')
+                plt.title(axname)
+                plt.legend(axis_legends[_ax])
+                plt.ylim([-0.05, 1.05])
+
+    baseout = os.path.splitext(os.path.basename(output_filename))[0]
+    plotname = f'figs/multiclass/{baseout}_{matchcover}_class_breakout.png'
+    print(f'Saving {plotname}')
+    plt.savefig(plotname, dpi=200, bbox_inches='tight')
+    plt.clf()
+    del fig
+
+
+def add_cm_plot(cm, ax, display_labels=None, cmap='viridis', include_values=True, values_format=None, xticks_rotation='vertical'):
+    # Borrowed in large part from https://github.com/scikit-learn/scikit-learn/blob/0fb307bf3/sklearn/metrics/_plot/confusion_matrix.py#L135
+    n_classes = cm.shape[0]
+    im_ = ax.imshow(cm, interpolation='nearest', cmap=cmap)
+    text_ = None
+    cmap_min, cmap_max = im_.cmap(0), im_.cmap(256)
+
+    if include_values:
+        text_ = np.empty_like(cm, dtype=object)
+
+        # print text with appropriate color depending on background
+        thresh = (cm.max() + cm.min()) / 2.0
+
+        for i, j in product(range(n_classes), range(n_classes)):
+            color = cmap_max if cm[i, j] < thresh else cmap_min
+
+            if values_format is None:
+                text_cm = format(cm[i, j], '.2g')
+                if cm.dtype.kind != 'f':
+                    text_d = format(cm[i, j], 'd')
+                    if len(text_d) < len(text_cm):
+                        text_cm = text_d
+            else:
+                text_cm = format(cm[i, j], values_format)
+
+            text_[i, j] = ax.text(
+                j, i, text_cm,
+                ha="center", va="center",
+                color=color)
+
+    if display_labels is None:
+        display_labels = np.arange(n_classes)
+    else:
+        display_labels = display_labels
+
+    plt.colorbar(im_, ax=ax)
+    ax.set(xticks=np.arange(n_classes),
+           yticks=np.arange(n_classes),
+           xticklabels=display_labels,
+           yticklabels=display_labels,
+           ylabel="True label",
+           xlabel="Predicted label")
+
+    ax.set_ylim((n_classes - 0.5, -0.5))
+    plt.setp(ax.get_xticklabels(), rotation=xticks_rotation)
+
+
+def plot_confusion_matrix(output_filename, train, covertype, layers_range, node_range, dropout_range, classlabels):
+    npzf = np.load(output_filename)
+    predictions = npzf['predictions']
+    dim_names = npzf['dim_names']
+
+
+    for _nl, nl in enumerate(layers_range):
+
+        for _dr, dr in enumerate(dropout_range):
+
+            for _nn, nn in enumerate(node_range):
+                fig = plt.figure(figsize=(13,4))
+                gs = gridspec.GridSpec(ncols=2, nrows=1, wspace=0.1, hspace=0.6)
+                baseout = os.path.splitext(os.path.basename(output_filename))[0]
+
+                ax = fig.add_subplot(gs[0,0])
+
+                pred = predictions[_nl, _dr, _nn, -1, :]
+                cm = confusion_matrix(covertype[train], pred[train])
+
+                add_cm_plot(cm, ax, classlabels)
+                plt.title('Train') 
+                np.savetxt(f'figs/cm/{baseout}_nl_{nl}_dr_{dr}_nn_{nn}_class_breakout_train.csv',cm,delimiter=',')
+
+
+
+                ax = fig.add_subplot(gs[0,1])
+
+                cm = confusion_matrix(covertype[np.logical_not(train)], pred[np.logical_not(train)])
+
+                add_cm_plot(cm, ax, classlabels)
+                plt.title('Test') 
+
+                np.savetxt(f'figs/cm/{baseout}_nl_{nl}_dr_{dr}_nn_{nn}_class_breakout_test.csv',cm,delimiter=',')
+
+                plotname = f'figs/cm/{baseout}_nl_{nl}_dr_{dr}_nn_{nn}_class_breakout.png'
+                print(f'Saving {plotname}')
+                plt.savefig(plotname, dpi=200, bbox_inches='tight')
+                
+                
+                plt.clf()
+                del fig
+
+
+
+
+
+
+#    true_positives = predictions[...,to_plot] - Y[np.newaxis,np.newaxis, np.newaxis, to_plot]
+
+
+#    print(these_are_my_predictions.shape)
 
 
 
diff --git a/vector_data/aspen/CRBU2018_AOP_aspen_additional.geojson b/vector_data/aspen/CRBU2018_AOP_aspen_additional.geojson
index 9e143f6..6c3b44e 100644
--- a/vector_data/aspen/CRBU2018_AOP_aspen_additional.geojson
+++ b/vector_data/aspen/CRBU2018_AOP_aspen_additional.geojson
@@ -3,34 +3,152 @@
 "name": "CRBU2018_AOP_aspen_additional",
 "crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:EPSG::32613" } },
 "features": [
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diff --git a/vector_data/conifer/CRBU2018_AOP_conifer_additional.geojson b/vector_data/conifer/CRBU2018_AOP_conifer_additional.geojson
index 7d35e3f..6fa7f80 100644
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index 2a0fbfe..322b1b0 100644
--- a/vector_data/meadow/CRBU2018_AOP_mesic_meadow.geojson
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diff --git a/vector_data/meadow/CRBU2018_AOP_wet_meadow.geojson b/vector_data/meadow/CRBU2018_AOP_wet_meadow.geojson
index d6bfc7c..1302d91 100644
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diff --git a/vector_data/shrubs/CRBU2018_AOP_misc_shrub.geojson b/vector_data/shrubs/CRBU2018_AOP_misc_shrub.geojson
index 7d28650..55cfd9d 100644
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index d6469a2..0e5220e 100644
--- a/vector_data/shrubs/CRBU2018_AOP_sage.geojson
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diff --git a/vector_data/water/CRBU2018_AOP_water.geojson b/vector_data/water/CRBU2018_AOP_water.geojson
index b98fc39..c35d8e6 100644
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diff --git a/vector_data/shrubs/CRBU2018_AOP_willow.geojson b/vector_data/willows/CRBU2018_AOP_willow.geojson
similarity index 69%
rename from vector_data/shrubs/CRBU2018_AOP_willow.geojson
rename to vector_data/willows/CRBU2018_AOP_willow.geojson
index 08e17b1..272d3a2 100644
--- a/vector_data/shrubs/CRBU2018_AOP_willow.geojson
+++ b/vector_data/willows/CRBU2018_AOP_willow.geojson
@@ -3,18 +3,76 @@
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