LifeTracer/config.json at main · amirgroup-codes/LifeTracer · GitHub

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{
    "mz_list_path": "data/all_mz_values.csv",
    "labels_path": "data/labels.csv",
    "m_z_column_name": "M/Z",
    "area_column_name": "Area",
    "first_time_column_name": "1st Time (s)",
    "second_time_column_name": "2nd Time (s)",
    "csv_file_name_column": "csv_file_name",
    "label_column_name": "label",

    "output_dir_heatmap": "/usr/scratch/lifetracer/heatmaps/",
    "extract_heatmaps": {
        "raw_csv_path": "/usr/scratch/NASA/raw/",
        "m_z_threshold": 0.5,
        "parallel_processing": true
    },

    "find_peaks": {
        "peaks_dir_path": "/usr/scratch/lifetracer/peaks/",
        "parallel_processing": true,
        "lambda1": 0.75,
        "lambda2": 5.0,
        "peak_max_neighbor_distance": 20,
        "area_min_threshold": 15000,
        "strict_noise_filtering": true,
        "column_noise_removal":{
            "noise_column_removal": true,
            "max_distance_removal_noisy_columns": 50,
            "noisy_columns": [7700,8700],
            "non_zero_ratio_column_threshold": 0.1
        },
        "noisy_regions_removal": true,
        "noisy_regions": [
            {
                "first_time_start": -1,
                "second_time_start": 0,
                "first_time_end": -1,
                "second_time_end": 1,
                "non_zero_ratio_region_threshold": 0.001
            }
        ],
        "convolution_filtering": true,
        "convolution_filter": {
            "lambda3": 10,
            "rt1_window_size": 2000,
            "rt2_window_size": 0.1,
            "rt1_stride": 0.1,
            "rt2_stride": 2000,
            "non_zero_ratio_mean_subtracted":  0.99999,
            "non_zero_ratio_lambda3_filter": 0.05
        },
        "delta_rt1" : 10,
        "delta_rt2" : 0.12
    },

    "retention_alignment":{

    },

    "parameter_selection":{

    },

    "train_model":{

    },

    "evaluation": {

    },

    "predict" :{

    },

    "plot":{
        "plot_dir" : "/usr/scratch/danial_stuff/Chromalyzer/plots/"
    }
}