Switch to YAML config files; add model pickles

See issues #26, #29, #30

examples/classifiers/RandomForest.yaml

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+# Default configuration file for Random Forest algorithm
+#
+# See sklearn implementation API here:
+# http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html
+
+# Specify algorithm and hyperparameters
+algorithm: RandomForest
+    # Number of trees in forest
+    n_estimators: 500
+    # Criterion for qualify of split ['gini', 'entropy']
+    criterion: "gini"
+    # number of features tried at each node
+    max_features: "auto"
+    # maximum depth of tree
+    max_depth:
+    # minimum number of samples required to split an internal node
+    min_samples_split: 2
+    # minimum number of samples in newly created leaves
+    min_samples_leaf: 1
+    # maximum leaf nodes -- if not None max_depth is ignored
+    max_leaf_nodes:
+    # Use bootstrap sample
+    bootstrap: True
+    # use out-of-bag sample for generalization error
+    oob_score: True
+    # number of jobs in parallel for fit and predict
+    n_jobs: 1
+
+# Algorithm fit parameters
+fit:
+    # Sample weights for training data
+    sample_weight:

examples/p022r049_example.yaml

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+# Example configuration file for YATSM
+# As of v0.5.0, config files are to be written in YAML
+#
+# Quotes around strings are optional, but encouraged, except where the leading
+# character would produce a parsing error (e.g., when writing the
+# date_format, "%Y%j")
+
+version: "0.5.0"
+
+dataset:
+    # Text file containing dates and images
+    input_file: "/home/ceholden/Documents/yatsm/examples/p022r049_input.csv"
+    # Input date format
+    date_format: "%Y%j"
+    # Output location
+    output: "/home/ceholden/Documents/landsat_stack/p022r049/images/YATSM"
+    # Output file prefix (e.g., [prefix]_[line].npz)
+    output_prefix: "yatsm_r"
+    # Total number of bands
+    n_bands: 8
+    # Mask band (e.g., Fmask)
+    mask_band: 8
+    # List of integer values to mask within the mask band
+    mask_values: [2, 3, 4, 255]
+    # Valid range of non-mask band data
+    # specify 1 range for all bands, or specify ranges for each band
+    valid_range: [0, 10000]
+    # Indices for multi-temporal cloud masking (indexed on 1)
+    green_band: 2
+    swir1_band: 5
+    # Use BIP image reader? If not, use GDAL to read in
+    use_bip_reader: true
+    # Directory location for caching dataset lines
+    cache_line_dir: "/home/ceholden/Documents/landsat_stack/p022r049/images/.yatsm_cache"
+
+# Parameters common to all timeseries analysis models within YATSM package
+YATSM:
+    algorithm: "CCDCesque"
+    prediction: "LassoCV"
+    design_matrix: "1 + x + harm(x, 1)"
+    reverse: False
+    robust: False
+    commission_alpha:
+
+# Parameters for CCDCesque algorithm -- referenced by "algorithm" key in YATSM
+CCDCesque:
+    consecutive: 5
+    threshold: 3.0
+    min_obs: 16
+    min_rmse: 150
+    test_indices: 2, 4, 5
+    retrain_time: 365.25
+    screening: RLM
+    screening_crit: 400.0
+    slope_test: False
+    remove_noise: True
+    dynamic_rmse: False
+
+# Regression estimator
+LassoCV:
+    pickle: "/home/ceholden/Documents/yatsm/examples/regression/LassoCV_n100_alpha_0-50.pkl"
+
+# Section for phenology fitting
+phenology:
+    calc_pheno: False
+    # Specification for dataset indices required for EVI based phenology monitoring
+    red_index: 2
+    nir_index: 3
+    blue_index: 0
+    # Scale factor for reflectance bands
+    scale: 0.0001
+    # You can also specify index of EVI if contained in dataset to override calculation
+    evi_index:
+    evi_scale:
+    # Number of years to group together when normalizing EVI to upper and lower percentiles
+    year_interval: 3
+    # Upper and lower percentiles of EVI used for max/min scaling
+    q_min: 10
+    q_max: 90
+
+# Section for segmentation
+segment:
+    # Segmentation image
+    segmentation:
+    # Resegmentation threshold (0 turns off resegmentation)
+    resegment_crit: 0
+    # Resegmentation size thresholds
+    resegment_minpix: 5
+    resegment_maxpix: 50
+
+# Section for training and classification
+classification:
+    # Training data file
+    training_image: "/home/ceholden/Documents/yatsm/examples/training_data.gtif"
+    # Training data masked values
+    roi_mask_values: [0, 255]
+    # Date range
+    training_start: "1999-01-01"
+    training_end: "2001-01-01"
+    training_date_format: "%Y-%m-%d"
+    # Cache X feature input and y labels for training data image into file?
+    cache_training: