CoastSat_WRL/functions/utils.py

# -*- coding: utf-8 -*-
"""
Created on Thu Mar  1 11:30:31 2018

@author: z5030440

Contains all the utilities, convenience functions and small functions that do simple things
"""

import matplotlib.pyplot as plt
from datetime import datetime, timedelta
import numpy as np
import scipy.io as sio
import pdb


def ecdf(x):
    """convenience function for computing the empirical CDF"""
    vals, counts = np.unique(x, return_counts=True)
    ecdf = np.cumsum(counts).astype(np.float64)
    ecdf /= ecdf[-1]
    return vals, ecdf

def intensity_histogram(image):
    """plots histogram and cumulative distribution of the pixel intensities in an image"""
    imSize = image.shape
    if len(imSize) == 2:
        im = image[:,:].reshape(imSize[0] * imSize[1])
        im = im[~np.isnan(im)] 
        fig, (ax1, ax2) = plt.subplots(2,1, sharex=True, figsize = (8,6))
        ax1.hist(im, bins=300)
        ax1.set_title('Probability density function')
        ax2.hist(im, bins=300, cumulative=True, histtype='step')
        ax2.set_title('Cumulative distribution')
        plt.show()
    
    else:       
        for i in range(imSize[2]):
            im = image[:,:,i].reshape(imSize[0] * imSize[1])
            im = im[~np.isnan(im)] 
            fig, (ax1, ax2) = plt.subplots(2,1, sharex=True, figsize = (8,6))
            ax1.hist(im, bins=300)
            ax1.set_title('Probability density function')
            ax2.hist(im, bins=300, cumulative=True, histtype='step')
            ax2.set_title('Cumulative distribution')
            plt.show()
            
def compare_images(im1, im2):
    """plots 2 images next to each other, sharing the axis"""
    plt.figure()
    ax1 = plt.subplot(121)
    plt.imshow(im1, cmap='gray')
    ax2 = plt.subplot(122, sharex=ax1, sharey=ax1)
    plt.imshow(im2, cmap='gray')
    plt.show()  
    
def find_indices(lst, condition):
    "imitation of MATLAB find function"
    return [i for i, elem in enumerate(lst) if condition(elem)]

def reject_outliers(data, m=2):
    "rejects outliers in a numpy array"
    return data[abs(data - np.mean(data)) < m * np.std(data)]

def duplicates_dict(lst):
    "return duplicates and indices"
    # nested function
    def duplicates(lst, item):
            return [i for i, x in enumerate(lst) if x == item]
        
    return dict((x, duplicates(lst, x)) for x in set(lst) if lst.count(x) > 1)

def datenum2datetime(datenum):
    "convert datenum to datetime"
    #takes in datenum and outputs python datetime
    time = [datetime.fromordinal(int(dn)) + timedelta(days=float(dn)%1) - timedelta(days = 366) for dn in datenum]
    return time

def loadmat(filename):
    '''
    this function should be called instead of direct spio.loadmat
    as it cures the problem of not properly recovering python dictionaries
    from mat files. It calls the function check keys to cure all entries
    which are still mat-objects
    '''
    data = sio.loadmat(filename, struct_as_record=False, squeeze_me=True)
    return _check_keys(data)

def _check_keys(dict):
    '''
    checks if entries in dictionary are mat-objects. If yes
    todict is called to change them to nested dictionaries
    '''
    for key in dict:
        if isinstance(dict[key], sio.matlab.mio5_params.mat_struct):
            dict[key] = _todict(dict[key])
    return dict        

def _todict(matobj):
    '''
    A recursive function which constructs from matobjects nested dictionaries
    '''
    dict = {}
    for strg in matobj._fieldnames:
        elem = matobj.__dict__[strg]
        if isinstance(elem, sio.matlab.mio5_params.mat_struct):
            dict[strg] = _todict(elem)
        else:
            dict[strg] = elem
    return dict