from __future__ import print_function, division

import os

import torch

import numpy as np

import pandas as pd

import math

import re

import pdb

import pickle

from scipy import stats

from torch.utils.data import Dataset

import h5py

from utils.utils import generate_split, nth

def save_splits(split_datasets, column_keys, filename, boolean_style=False):

    splits = [split_datasets[i].slide_data['slide_id'] for i in range(len(split_datasets))]

    if not boolean_style:

        df = pd.concat(splits, ignore_index=True, axis=1)

        df.columns = column_keys

    else:

        df = pd.concat(splits, ignore_index = True, axis=0)

        index = df.values.tolist()

        one_hot = np.eye(len(split_datasets)).astype(bool)

        bool_array = np.repeat(one_hot, [len(dset) for dset in split_datasets], axis=0)

        df = pd.DataFrame(bool_array, index=index, columns = ['train', 'val', 'test'])

    df.to_csv(filename)

    print()

class Generic_WSI_Classification_Dataset(Dataset):

    def __init__(self,

        csv_path = 'dataset_csv/ccrcc_clean.csv',

        shuffle = False, 

        seed = 7, 

        print_info = True,

        label_dict = {},

        ignore=[],

        patient_strat=False,

        label_col = None,

        patient_voting = 'max',

        multi_site = False,

        filter_dict = {},

                patient_level = False

        ):

        """

        Args:

            csv_file (string): Path to the csv file with annotations.

            shuffle (boolean): Whether to shuffle

            seed (int): random seed for shuffling the data

            print_info (boolean): Whether to print a summary of the dataset

            label_dict (dict): Dictionary with key, value pairs for converting str labels to int

            ignore (list): List containing class labels to ignore

            patient_voting (string): Rule for deciding the patient-level label

        """

        self.custom_test_ids = None

        self.seed = seed

        self.print_info = print_info

        self.patient_strat = patient_strat

        self.train_ids, self.val_ids, self.test_ids  = (None, None, None)

        self.data_dir = None

        self.split_gen = None

        self.patient_level = patient_level

        if not label_col:

            label_col = 'label'

        self.label_col = label_col

        slide_data = pd.read_csv(csv_path)

        slide_data = self.filter_df(slide_data, filter_dict)

        if multi_site:

            label_dict = self.init_multi_site_label_dict(slide_data, label_dict)

        self.label_dict = label_dict

        self.num_classes=len(set(self.label_dict.values()))

        slide_data = self.df_prep(slide_data, self.label_dict, ignore, self.label_col, multi_site)

        ###shuffle data

        if shuffle:

            np.random.seed(seed)

            np.random.shuffle(slide_data)

        self.slide_data = slide_data

        self.patient_data_prep(patient_voting)

        self.cls_ids_prep()

        if print_info:

            self.summarize()

        if self.patient_level:

            self.patient_dict = self.build_patient_dict()

            #self.slide_data   = self.slide_data.drop_duplicates(subset=['case_id'])

        else:

            self.patient_dict = {}

    def build_patient_dict(self):

        patient_dict = {}   

        patient_cases = self.slide_data['case_id'].unique()

        slide_cases   = self.slide_data.set_index('case_id')

        for patient in patient_cases:

            slide_ids = slide_cases.loc[patient,'slide_id']

            if isinstance(slide_ids, str):

                slide_ids = np.array(slide_ids).reshape(-1)

            else:

                slide_ids = slide_ids.values

            patient_dict.update({patient:slide_ids})

        return patient_dict

    def cls_ids_prep(self):

        # store ids corresponding each class at the patient or case level

        self.patient_cls_ids = [[] for i in range(self.num_classes)]        

        for i in range(self.num_classes):

            self.patient_cls_ids[i] = np.where(self.patient_data['label'] == i)[0]

        # store ids corresponding each class at the slide level

        self.slide_cls_ids = [[] for i in range(self.num_classes)]

        for i in range(self.num_classes):

            self.slide_cls_ids[i] = np.where(self.slide_data['label'] == i)[0]

    def patient_data_prep(self, patient_voting='max'):

        patients = np.unique(np.array(self.slide_data['case_id'])) # get unique patients

        patient_labels = []

        for p in patients:

            locations = self.slide_data[self.slide_data['case_id'] == p].index.tolist()

            assert len(locations) > 0

            label = self.slide_data['label'][locations].values

            if patient_voting == 'max':

                label = label.max() # get patient label (MIL convention)

            elif patient_voting == 'maj':

                label = stats.mode(label)[0]

            else:

                raise NotImplementedError

            patient_labels.append(label)

        self.patient_data = {'case_id':patients, 'label':np.array(patient_labels)}

    @staticmethod

    def init_multi_site_label_dict(slide_data, label_dict):

        print('initiating multi-source label dictionary')

        sites = np.unique(slide_data['site'].values)

        multi_site_dict = {}

        num_classes = len(label_dict)

        for key, val in label_dict.items():

            for idx, site in enumerate(sites):

                site_key = (key, site)

                site_val = val+idx*num_classes

                multi_site_dict.update({site_key:site_val})

                print('{} : {}'.format(site_key, site_val))

        return multi_site_dict

    @staticmethod

    def filter_df(df, filter_dict={}):

        if len(filter_dict) > 0:

            filter_mask = np.full(len(df), True, bool)

            # assert 'label' not in filter_dict.keys()

            for key, val in filter_dict.items():

                mask = df[key].isin(val)

                filter_mask = np.logical_and(filter_mask, mask)

            df = df[filter_mask]

        return df

    @staticmethod

    def df_prep(data, label_dict, ignore, label_col, multi_site=False):

        if label_col != 'label':

            data['label'] = data[label_col].copy()

        mask = data['label'].isin(ignore)

        data = data[~mask]

        data.reset_index(drop=True, inplace=True)

        for i in data.index:

            key = data.loc[i, 'label']

            if multi_site:

                site = data.loc[i, 'site']

                key = (key, site)

            data.at[i, 'label'] = label_dict[key]

        return data

    def __len__(self):

        if self.patient_strat:

            return len(self.patient_data['case_id'])

        else:

            return len(self.slide_data)

    def summarize(self):

        print("label column: {}".format(self.label_col))

        print("label dictionary: {}".format(self.label_dict))

        print("number of classes: {}".format(self.num_classes))

        print("slide-level counts: ", self.slide_data['label'].value_counts(sort = False))

        for i in range(self.num_classes):

            print('Patient-LVL; Number of samples registered in class %d: %d' % (i, self.patient_cls_ids[i].shape[0]))

            print('Slide-LVL; Number of samples registered in class %d: %d' % (i, self.slide_cls_ids[i].shape[0]))

    def create_splits(self, k = 3, val_num = (25, 25), test_num = (40, 40), label_frac = 1.0, custom_test_ids = None):

        settings = {

                    'n_splits' : k, 

                    'val_num' : val_num, 

                    'test_num': test_num,

                    'label_frac': label_frac,

                    'seed': self.seed,

                    'custom_test_ids': custom_test_ids

                    }

        if self.patient_strat:

            settings.update({'cls_ids' : self.patient_cls_ids, 'samples': len(self.patient_data['case_id'])})

        else:

            settings.update({'cls_ids' : self.slide_cls_ids, 'samples': len(self.slide_data)})

        self.split_gen = generate_split(**settings)

    def sample_held_out(self, test_num = (40, 40)):

        test_ids = []

        np.random.seed(self.seed) #fix seed

        if self.patient_strat:

            cls_ids = self.patient_cls_ids

        else:

            cls_ids = self.slide_cls_ids

        for c in range(len(test_num)):

            test_ids.extend(np.random.choice(cls_ids[c], test_num[c], replace = False)) # validation ids

        # if self.patient_strat:

        #   slide_ids = [] 

        #   for idx in test_ids:

        #       case_id = self.patient_data['case_id'][idx]

        #       slide_indices = self.slide_data[self.slide_data['case_id'] == case_id].index.tolist()

        #       slide_ids.extend(slide_indices)

        #   return slide_ids

        # else:

        #   return test_ids

        return test_ids

    def set_splits(self,start_from=None):

        if start_from:

            ids = nth(self.split_gen, start_from)

        else:

            ids = next(self.split_gen)

        if self.patient_strat:

            slide_ids = [[] for i in range(len(ids))] 

            for split in range(len(ids)): 

                for idx in ids[split]:

                    case_id = self.patient_data['case_id'][idx]

                    slide_indices = self.slide_data[self.slide_data['case_id'] == case_id].index.tolist()

                    slide_ids[split].extend(slide_indices)

            self.train_ids, self.val_ids, self.test_ids = slide_ids[0], slide_ids[1], slide_ids[2]

        else:

            self.train_ids, self.val_ids, self.test_ids = ids

    def get_split_from_df(self, all_splits=None, split_key='train', split=None, return_ids_only=False):

        if split is None:

            split = all_splits[split_key]

            split = split.dropna().reset_index(drop=True)

        if len(split) > 0:

            mask = self.slide_data['slide_id'].isin(split.tolist())

            if return_ids_only:

                ids = np.where(mask)[0]

                return ids

            df_slice = self.slide_data[mask].dropna().reset_index(drop=True)

            split = Generic_Split(df_slice, data_dir=self.data_dir, num_classes=self.num_classes, patient_level=self.patient_level)

        else:

            split = None

        return split

    def get_merged_split_from_df(self, all_splits, split_keys=['train']):

        merged_split = []

        for split_key in split_keys:

            split = all_splits[split_key]

            split = split.dropna().reset_index(drop=True).tolist()

            merged_split.extend(split)

        if len(split) > 0:

            mask = self.slide_data['slide_id'].isin(merged_split)

            df_slice = self.slide_data[mask].dropna().reset_index(drop=True)

            split = Generic_Split(df_slice, data_dir=self.data_dir, num_classes=self.num_classes, patient_level = self.patient_level)

        else:

            split = None

        return split

    def return_splits(self, from_id=True, csv_path=None):

        if from_id:

            if len(self.train_ids) > 0:

                train_data = self.slide_data.loc[self.train_ids].reset_index(drop=True)

                train_split = Generic_Split(train_data, data_dir=self.data_dir, num_classes=self.num_classes, patient_level = self.patient_level)

            else:

                train_split = None

            if len(self.val_ids) > 0:

                val_data = self.slide_data.loc[self.val_ids].reset_index(drop=True)

                val_split = Generic_Split(val_data, data_dir=self.data_dir, num_classes=self.num_classes, patient_level = self.patient_level)

            else:

                val_split = None

            if len(self.test_ids) > 0:

                test_data = self.slide_data.loc[self.test_ids].reset_index(drop=True)

                test_split = Generic_Split(test_data, data_dir=self.data_dir, num_classes=self.num_classes, patient_level = self.patient_level)

            else: # NO TEST SET - USE COPY OF VALIDATION SET

                                #test_split = None

                                test_data  = self.slide_data.loc[self.val_ids].reset_index(drop=True)

                                test_split = Generic_Split(test_data, data_dir=self.data_dir, num_classes=self.num_classes, patient_level = self.patient_level)

        else:

            assert csv_path 

            all_splits = pd.read_csv(csv_path)

            train_split = self.get_split_from_df(all_splits, 'train')

            val_split = self.get_split_from_df(all_splits, 'val')

            test_split = self.get_split_from_df(all_splits, 'test')

        return train_split, val_split, test_split

    def get_list(self, ids):

        return self.slide_data['slide_id'][ids]

    def getlabel(self, ids):

        return self.slide_data['label'][ids]

    def __getitem__(self, idx):

        return None

    def test_split_gen(self, return_descriptor=False):

        if return_descriptor:

            index = [list(self.label_dict.keys())[list(self.label_dict.values()).index(i)] for i in range(self.num_classes)]

            columns = ['train', 'val', 'test']

            df = pd.DataFrame(np.full((len(index), len(columns)), 0, dtype=np.int32), index= index,

                            columns= columns)

        count = len(self.train_ids)

        print('\nnumber of training samples: {}'.format(count))

        labels = self.getlabel(self.train_ids)

        unique, counts = np.unique(labels, return_counts=True)

        missing_classes = np.setdiff1d(np.arange(self.num_classes), unique)

        unique = np.append(unique, missing_classes)

        counts = np.append(counts, np.full(len(missing_classes), 0))

        inds = unique.argsort()

        counts = counts[inds]

        for u in range(len(unique)):

            print('number of samples in cls {}: {}'.format(unique[u], counts[u]))

            if return_descriptor:

                df.loc[index[u], 'train'] = counts[u]

        count = len(self.val_ids)

        print('\nnumber of val samples: {}'.format(count))

        labels = self.getlabel(self.val_ids)

        unique, counts = np.unique(labels, return_counts=True)

        missing_classes = np.setdiff1d(np.arange(self.num_classes), unique)

        unique = np.append(unique, missing_classes)

        counts = np.append(counts, np.full(len(missing_classes), 0))

        inds = unique.argsort()

        counts = counts[inds]

        for u in range(len(unique)):

            print('number of samples in cls {}: {}'.format(unique[u], counts[u]))

            if return_descriptor:

                df.loc[index[u], 'val'] = counts[u]

        count = len(self.test_ids)

        print('\nnumber of test samples: {}'.format(count))

        labels = self.getlabel(self.test_ids)

        unique, counts = np.unique(labels, return_counts=True)

        missing_classes = np.setdiff1d(np.arange(self.num_classes), unique)

        unique = np.append(unique, missing_classes)

        counts = np.append(counts, np.full(len(missing_classes), 0))

        inds = unique.argsort()

        counts = counts[inds]

        for u in range(len(unique)):

            print('number of samples in cls {}: {}'.format(unique[u], counts[u]))

            if return_descriptor:

                df.loc[index[u], 'test'] = counts[u]

        assert len(np.intersect1d(self.train_ids, self.test_ids)) == 0

        assert len(np.intersect1d(self.train_ids, self.val_ids)) == 0

        assert len(np.intersect1d(self.val_ids, self.test_ids)) == 0

        if return_descriptor:

            return df

    def save_split(self, filename):

        train_split = self.get_list(self.train_ids)

        val_split = self.get_list(self.val_ids)

        test_split = self.get_list(self.test_ids)

        df_tr = pd.DataFrame({'train': train_split})

        df_v = pd.DataFrame({'val': val_split})

        df_t = pd.DataFrame({'test': test_split})

        df = pd.concat([df_tr, df_v, df_t], axis=1) 

        df.to_csv(filename, index = False)

class Generic_MIL_Dataset(Generic_WSI_Classification_Dataset):

    def __init__(self,

        data_dir, 

        **kwargs):

        super(Generic_MIL_Dataset, self).__init__(**kwargs)

        self.data_dir = data_dir

        self.use_h5 = False

    def load_from_h5(self, toggle):

        self.use_h5 = toggle

    def __getitem__(self, idx):

        if not self.patient_level:

            slide_id = self.slide_data['slide_id'][idx]

            label = self.slide_data['label'][idx]

            if type(self.data_dir) == dict:

                source = self.slide_data['source'][idx]

                data_dir = self.data_dir[source]

            else:

                data_dir = self.data_dir

            if not self.use_h5:

                if self.data_dir:

                    full_path = os.path.join(data_dir, 'pt_files', '{}.pt'.format(slide_id))

                    features = torch.load(full_path)

                    return features, label

                else:

                    return slide_id, label

            else:

                full_path = os.path.join(data_dir,'h5_files','{}.h5'.format(slide_id))

                with h5py.File(full_path,'r') as hdf5_file:

                    features = hdf5_file['features'][:]

                    coords = hdf5_file['coords'][:]

                features = torch.from_numpy(features)

                return features, label, coords

        else:

            case_id   = self.slide_data['case_id'][idx]

            label     = self.slide_data['label'][idx]

            slide_ids = self.patient_dict[case_id]

            if type(self.data_dir) == dict:

                source = self.slide_data['source'][idx]

                data_dir = self.data_dir[source]

            else:

                data_dir = self.data_dir

            if not self.use_h5:

                features_list = []

                for slide_id in slide_ids:

                    full_path = os.path.join(data_dir, 'pt_files', '{}.pt'.format(slide_id))

                    slide_features = torch.load(full_path)

                    features_list.append(slide_features)

                features = torch.cat( features_list, dim = 0)

                return features, label  

            else:

                features_list = []

                coords_list   = []

                for slide_id in slide_ids:

                    full_path = os.path.join(data_dir,'h5_files','{}.h5'.format(slide_id))

                    with h5py.File(full_path,'r') as hdf5_file:

                        slide_features   = hdf5_file['features'][:]

                        slide_coords     = hdf5_file['coords'][:]

                        silide_features_t = torch.from_numpy(slide_features)

                        slide_coords_t   = torch.from_numpy(slide_coords)

                        features_list.append( slide_features_t )

                        coords_list.append(   slide_coords_t   )

                features = troch.cat( features_list, dim = 0)

                coords   = torch.cat( coords_list,   dim = 0)

                return features, label, coords

class Generic_Split(Generic_MIL_Dataset):

    def __init__(self, slide_data, data_dir=None, num_classes=2, patient_level=False):

        self.use_h5 = False

        self.slide_data = slide_data

        self.data_dir = data_dir

        self.num_classes = num_classes

        self.slide_cls_ids = [[] for i in range(self.num_classes)]

        for i in range(self.num_classes):

            self.slide_cls_ids[i] = np.where(self.slide_data['label'] == i)[0]

        self.patient_level = patient_level

        if self.patient_level:

            self.patient_dict = self.build_patient_dict()

            #self.slide_data   = self.slide_data.drop_duplicates(subset=['case_id'])

        else:

            self.patient_dict = {}

    def __len__(self):

        return len(self.slide_data)

class Generic_WSI_Inference_Dataset(Dataset):

    def __init__(self,

        data_dir,

        csv_path = None,

        print_info = True,

        ):

        self.data_dir = data_dir

        self.print_info = print_info

        if csv_path is not None:

            data = pd.read_csv(csv_path)

            self.slide_data = data['slide_id'].values

        else:

            data = np.array(os.listdir(data_dir))

            self.slide_data = np.char.strip(data, chars ='.pt') 

        if print_info:

            print('total number of slides to infer: ', len(self.slide_data))

    def __len__(self):

        return len(self.slide_data)

    def __getitem__(self, idx):

        slide_file = self.slide_data[idx]+'.pt'

        full_path = os.path.join(self.data_dir, 'pt_files',slide_file)

        features = torch.load(full_path)

        return features