#!/usr/bin/env python
# Copyright 2018 Division of Medical Image Computing, German Cancer Research Center (DKFZ).
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# ==============================================================================

'''
Example Data Loader for the LIDC data set. This dataloader expects preprocessed data in .npy or .npz files per patient and
a pandas dataframe in the same directory containing the meta-info e.g. file paths, labels, foregound slice-ids.
'''


import numpy as np
import os
from collections import OrderedDict
import pandas as pd
import pickle
import time
import subprocess
import SimpleITK as sitk

# batch generator tools from https://github.com/MIC-DKFZ/batchgenerators
from batchgenerators.dataloading.data_loader import SlimDataLoaderBase
from batchgenerators.transforms.spatial_transforms import MirrorTransform as Mirror
from batchgenerators.transforms.abstract_transforms import Compose
from batchgenerators.dataloading.multi_threaded_augmenter import MultiThreadedAugmenter
from batchgenerators.dataloading import SingleThreadedAugmenter
from batchgenerators.transforms.spatial_transforms import SpatialTransform
from batchgenerators.transforms.crop_and_pad_transforms import CenterCropTransform
from batchgenerators.transforms.utility_transforms import ConvertSegToBoundingBoxCoordinates

import utils.dataloader_utils as dutils
import utils.exp_utils as utils

def convert(seconds): 
    return time.strftime("%H:%M:%S:%f", time.gmtime(seconds)) 

def get_train_generators(cf, logger):
    """
    wrapper function for creating the training batch generator pipeline. returns the train/val generators.
    selects patients according to cv folds (generated by first run/fold of experiment):
    splits the data into n-folds, where 1 split is used for val, 1 split for testing and the rest for training. (inner loop test set)
    If cf.hold_out_test_set is True, adds the test split to the training data.
    """
    all_data = load_dataset(cf, logger)
    #whole_data = load_dataset(cf,logger,pp_data_path=cf.pp_whole_data_path, pp_name=cf.pp_whole_name)
    all_pids_list = np.unique([v['pid'] for (k, v) in all_data.items()])

    splits_file = os.path.join(cf.exp_dir, 'folds_ids.pickle')
    if not os.path.exists(splits_file) and not cf.created_fold_id_pickle:
        fg = dutils.fold_generator(seed=cf.seed, n_splits=cf.n_cv_splits, len_data=len(all_pids_list)).get_fold_names()
        with open(splits_file, 'wb') as handle:
            pickle.dump(fg, handle)
        cf.created_fold_id_pickle = True
    else:
        with open(splits_file, 'rb') as handle:
            fg = pickle.load(handle)

    train_ix, val_ix, test_ix, _ = fg[cf.fold]

    train_pids = [all_pids_list[ix] for ix in train_ix]
    val_pids = [all_pids_list[ix] for ix in val_ix]

    if cf.hold_out_test_set:
        train_pids += [all_pids_list[ix] for ix in test_ix]

    train_data = {k: v for (k, v) in all_data.items() if any(p == v['pid'] for p in train_pids)}
    val_data = {k: v for (k, v) in all_data.items() if any(p == v['pid'] for p in val_pids)}

    logger.info("data set loaded with: {} train / {} val / {} test patients".format(len(train_ix), len(val_ix), len(test_ix)))
    batch_gen = {}
    batch_gen['train'] = create_data_gen_pipeline(train_data, cf=cf, is_training=True)
    batch_gen['val_sampling'] = create_data_gen_pipeline(val_data, cf=cf, is_training=False)
    if cf.val_mode == 'val_patient':
        batch_gen['val_patient'] = PatientBatchIterator(val_data, cf=cf)
        batch_gen['n_val'] = len(val_ix) if cf.max_val_patients is None else min(len(val_ix), cf.max_val_patients)
    else:
        batch_gen['n_val'] = cf.num_val_batches

    return batch_gen


def get_test_generator(cf, logger):
    """
    wrapper function for creating the test batch generator pipeline.
    selects patients according to cv folds (generated by first run/fold of experiment)
    If cf.hold_out_test_set is True, gets the data from an external folder instead.
    """
    if cf.hold_out_test_set:
        pp_name = cf.pp_name
        #test_ix = None
        test_ix = np.arange((len(os.listdir(cf.pp_test_data_path))/3)-2,dtype=np.int16)
    else:
        pp_name = None
        with open(os.path.join(cf.exp_dir, 'folds_ids.pickle'), 'rb') as handle:
            fold_list = pickle.load(handle)
        _, _, test_ix, _ = fold_list[cf.fold]
        # warnings.warn('WARNING: using validation set for testing!!!')

    test_data = load_dataset(cf, logger, test_ix, pp_data_path=cf.pp_data_path, pp_name=pp_name)
    logger.info("data set loaded with: {} test patients".format(len(test_ix)))
    batch_gen = {}
    batch_gen['test'] = PatientBatchIterator(test_data, cf=cf)
    batch_gen['n_test'] = len(test_ix) if cf.max_test_patients=="all" else \
        min(cf.max_test_patients, len(test_ix))
    return batch_gen



def load_dataset(cf, logger, subset_ixs=None, pp_data_path=None, pp_name=None):
    """
    loads the dataset. if deployed in cloud also copies and unpacks the data to the working directory.
    :param subset_ixs: subset indices to be loaded from the dataset. used e.g. for testing to only load the test folds.
    :return: data: dictionary with one entry per patient (in this case per patient-breast, since they are treated as
    individual images for training) each entry is a dictionary containing respective meta-info as well as paths to the preprocessed
    numpy arrays to be loaded during batch-generation
    """
    if pp_data_path is None:
        pp_data_path = cf.pp_data_path
    if pp_name is None:
        pp_name = cf.pp_name
    if cf.server_env:
        copy_data = True
        target_dir = os.path.join(cf.data_dest, pp_name)
        if not os.path.exists(target_dir):
            cf.data_source_dir = pp_data_path
            os.makedirs(target_dir)
            subprocess.call('rsync -av {} {}'.format(
                os.path.join(cf.data_source_dir, cf.input_df_name), os.path.join(target_dir, cf.input_df_name)), shell=True)
            logger.info('created target dir and info df at {}'.format(os.path.join(target_dir, cf.input_df_name)))

        elif subset_ixs is None:
            copy_data = False

        pp_data_path = target_dir


    p_df = pd.read_pickle(os.path.join(pp_data_path, cf.input_df_name))

    if cf.select_prototype_subset is not None:
        prototype_pids = p_df.pid.tolist()[:cf.select_prototype_subset]
        p_df = p_df[p_df.pid.isin(prototype_pids)]
        logger.warning('WARNING: using prototyping data subset!!!')

    if subset_ixs is not None:
        subset_pids = [np.unique(p_df.pid.tolist())[ix] for ix in subset_ixs]
        p_df = p_df[p_df.pid.isin(subset_pids)]
        logger.info('subset: selected {} instances from df'.format(len(p_df)))

    if cf.server_env:
        if copy_data:
            copy_and_unpack_data(logger, p_df.pid.tolist(), cf.fold_dir, cf.data_source_dir, target_dir)

    class_targets = p_df['class_target'].tolist()
    pids = p_df.pid.tolist()
    imgs = [os.path.join(pp_data_path, '{}_img.npy'.format(pid)) for pid in pids]
    segs = [os.path.join(pp_data_path,'{}_rois.npy'.format(pid)) for pid in pids]

    data = OrderedDict()
    for ix, pid in enumerate(pids):
        # for the experiment conducted here, malignancy scores are binarized: (benign: 1-2, malignant: 3-5)
        targets = [1 if ii >= 3 else 0 for ii in class_targets[ix]]
        #targets = [ii for ii in class_targets[ix]]
        data[pid] = {'data': imgs[ix], 'seg': segs[ix], 'pid': pid, 'class_target': targets}
        data[pid]['fg_slices'] = p_df['fg_slices'].tolist()[ix]
    print ("Finished load_dataset...")   
    return data



def create_data_gen_pipeline(patient_data, cf, is_training=True):
    """
    create mutli-threaded train/val/test batch generation and augmentation pipeline.
    :param patient_data: dictionary containing one dictionary per patient in the train/test subset.
    :param is_training: (optional) whether to perform data augmentation (training) or not (validation/testing)
    :return: multithreaded_generator
    """

    # create instance of batch generator as first element in pipeline.
    print ("Start BatchGenerator create_data_gen_pipeline...",)
    start = time.time()
    data_gen = BatchGenerator(patient_data, batch_size=cf.batch_size, cf=cf)
    print ("Finished BatchGenerator create_data_gen_pipeline...",time.time()-start)
    # add transformations to pipeline.
    my_transforms = []
    if is_training:
        mirror_transform = Mirror(axes=np.arange(cf.dim))
        my_transforms.append(mirror_transform)
        print ("Dimension",cf.dim)
        spatial_transform = SpatialTransform(patch_size=cf.patch_size[:cf.dim],
                                             patch_center_dist_from_border=cf.da_kwargs['rand_crop_dist'],
                                             do_elastic_deform=cf.da_kwargs['do_elastic_deform'],
                                             alpha=cf.da_kwargs['alpha'], sigma=cf.da_kwargs['sigma'],
                                             do_rotation=cf.da_kwargs['do_rotation'], angle_x=cf.da_kwargs['angle_x'],
                                             angle_y=cf.da_kwargs['angle_y'], angle_z=cf.da_kwargs['angle_z'],
                                             p_rot_per_sample=0.05, p_scale_per_sample=0.05,
                                             do_scale=cf.da_kwargs['do_scale'], scale=cf.da_kwargs['scale'],
                                             random_crop=cf.da_kwargs['random_crop'], order_data=0,order_seg=0)

        my_transforms.append(spatial_transform)
    else:
        my_transforms.append(CenterCropTransform(crop_size=cf.patch_size[:cf.dim]))

    my_transforms.append(ConvertSegToBoundingBoxCoordinates(cf.dim, get_rois_from_seg_flag=False, class_specific_seg_flag=cf.class_specific_seg_flag))
    all_transforms = Compose(my_transforms)
    #print ("Define MultiThreadedAugmenter...")

    multithreaded_generator = SingleThreadedAugmenter(data_gen, all_transforms)
    #multithreaded_generator = MultiThreadedAugmenter(data_gen, all_transforms, num_processes=cf.n_workers, seeds=range(cf.n_workers))
    return multithreaded_generator


class BatchGenerator(SlimDataLoaderBase):
    """
    creates the training/validation batch generator. Samples n_batch_size patients (draws a slice from each patient if 2D)
    from the data set while maintaining foreground-class balance. Returned patches are cropped/padded to pre_crop_size.
    Actual patch_size is obtained after data augmentation.
    :param data: data dictionary as provided by 'load_dataset'.
    :param batch_size: number of patients to sample for the batch
    :return dictionary containing the batch data (b, c, y, x(, z)) / seg (b, 1, y, x(, z)) / pids / class_target
    """
    def __init__(self, data, batch_size, cf):
        super(BatchGenerator, self).__init__(data, batch_size)

        self.cf = cf
        self.crop_margin = np.array(self.cf.patch_size)/8. #min distance of ROI center to edge of cropped_patch.
        self.p_fg = 0.5

    def generate_train_batch(self):

        batch_data, batch_segs, batch_pids, batch_targets, batch_patient_labels = [], [], [], [], []
        class_targets_list =  [v['class_target'] for (k, v) in self._data.items()]

        if self.cf.head_classes > 2:
            # samples patients towards equilibrium of foreground classes on a roi-level (after randomly sampling the ratio "batch_sample_slack).
            batch_ixs = dutils.get_class_balanced_patients(
                class_targets_list, self.batch_size, self.cf.head_classes - 1, slack_factor=self.cf.batch_sample_slack)
        else:
            batch_ixs = np.random.choice(len(class_targets_list), self.batch_size)

        patients = list(self._data.items())
        for b in batch_ixs:
            patient = patients[b][1]
            print ("Adding patient ",patients[b][0]," to a batch")
            # data shape: from (z,y,x,c) or (y,x,c) to (c, y, x, z) depending on input data shape.
            data = np.load(patient['data'],mmap_mode='r')
            if len(data.shape)==4:
                data = np.transpose(data, axes=(3, 1, 2, 0)) ##[np.newaxis]
            else:
                data = np.transpose(data, axes=(1, 2, 0))[np.newaxis]
            seg = np.transpose(np.load(patient['seg'], mmap_mode='r'), axes=(1, 2, 0))
            batch_pids.append(patient['pid'])
            batch_targets.append(patient['class_target'])
            #print ("Print data shape before sampling: ",data.shape)            
            if self.cf.dim == 2:
                # draw random slice from patient while oversampling slices containing foreground objects with p_fg.
                if len(patient['fg_slices']) > 0:
                    fg_prob = self.p_fg / len(patient['fg_slices'])
                    bg_prob = (1 - self.p_fg) / (data.shape[3] - len(patient['fg_slices']))
                    slices_prob = [fg_prob if ix in patient['fg_slices'] else bg_prob for ix in range(data.shape[3])]
                    slice_id = np.random.choice(data.shape[3], p=slices_prob)
                else:
                    slice_id = np.random.choice(data.shape[3])

                # if set to not None, add neighbouring slices to each selected slice in channel dimension.
                if self.cf.n_3D_context is not None:
                    padded_data = dutils.pad_nd_image(data[0], [(data.shape[-1] + (self.cf.n_3D_context*2))], mode='constant')
                    padded_slice_id = slice_id + self.cf.n_3D_context
                    data = (np.concatenate([padded_data[..., ii][np.newaxis] for ii in range(
                        padded_slice_id - self.cf.n_3D_context, padded_slice_id + self.cf.n_3D_context + 1)], axis=0))
                else:
                    data = data[..., slice_id]
                seg = seg[..., slice_id]
            

            # pad data if smaller than pre_crop_size.
            if np.any([data.shape[dim + 1] < ps for dim, ps in enumerate(self.cf.pre_crop_size)]):
                new_shape = [np.max([data.shape[dim + 1], ps]) for dim, ps in enumerate(self.cf.pre_crop_size)]
                data = dutils.pad_nd_image(data, new_shape, mode='constant')
                seg = dutils.pad_nd_image(seg, new_shape, mode='constant')

            # crop patches of size pre_crop_size, while sampling patches containing foreground with p_fg.
            crop_dims = [dim for dim, ps in enumerate(self.cf.pre_crop_size) if data.shape[dim + 1] > ps]
            if len(crop_dims) > 0:
                fg_prob_sample = np.random.rand(1)
                # with p_fg: sample random pixel from random ROI and shift center by random value.
                if fg_prob_sample < self.p_fg and np.sum(seg) > 0:
                    seg_ixs = np.argwhere(seg == np.random.choice(np.unique(seg)[1:], 1))
                    roi_anchor_pixel = seg_ixs[np.random.choice(seg_ixs.shape[0], 1)][0]
                    assert seg[tuple(roi_anchor_pixel)] > 0
                    # sample the patch center coords. constrained by edges of images - pre_crop_size /2. And by
                    # distance to the desired ROI < patch_size /2.
                    # (here final patch size to account for center_crop after data augmentation).
                    sample_seg_center = {}
                    for ii in crop_dims:
                        low = np.max((self.cf.pre_crop_size[ii]//2, roi_anchor_pixel[ii] - (self.cf.patch_size[ii]//2 - self.crop_margin[ii])))
                        high = np.min((data.shape[ii + 1] - self.cf.pre_crop_size[ii]//2,
                                       roi_anchor_pixel[ii] + (self.cf.patch_size[ii]//2 - self.crop_margin[ii])))
                        # happens if lesion on the edge of the image. dont care about roi anymore,
                        # just make sure pre-crop is inside image.
                        if low >= high:
                            low = data.shape[ii + 1] // 2 - (data.shape[ii + 1] // 2 - self.cf.pre_crop_size[ii] // 2)
                            high = data.shape[ii + 1] // 2 + (data.shape[ii + 1] // 2 - self.cf.pre_crop_size[ii] // 2)
                        sample_seg_center[ii] = np.random.randint(low=low, high=high)

                else:
                    # not guaranteed to be empty. probability of emptiness depends on the data.
                    sample_seg_center = {ii: np.random.randint(low=self.cf.pre_crop_size[ii]//2,
                                                           high=data.shape[ii + 1] - self.cf.pre_crop_size[ii]//2) for ii in crop_dims}

                for ii in crop_dims:
                    min_crop = int(sample_seg_center[ii] - self.cf.pre_crop_size[ii] // 2)
                    max_crop = int(sample_seg_center[ii] + self.cf.pre_crop_size[ii] // 2)
                    data = np.take(data, indices=range(min_crop, max_crop), axis=ii + 1)
                    seg = np.take(seg, indices=range(min_crop, max_crop), axis=ii)
            #print ("Post BatchGenerator data shape: ",data.shape)
            # if "g1" in patients[b][0]:
            #     print ("############Writing images for ",patients[b][0])
            #     write_nii_gz(data,seg,patients[b][0])
            batch_data.append(data)
            batch_segs.append(seg[np.newaxis])

        data = np.array(batch_data)
        seg = np.array(batch_segs).astype(np.uint8)
        class_target = np.array(batch_targets)
        print ("Pre batchgenerator input :", data.shape,seg.shape,batch_pids,class_target.shape,class_target)
        
        return {'data': data, 'seg': seg, 'pid': batch_pids, 'class_target': class_target}



class PatientBatchIterator(SlimDataLoaderBase):
    """
    creates a test generator that iterates over entire given dataset returning 1 patient per batch.
    Can be used for monitoring if cf.val_mode = 'patient_val' for a monitoring closer to actualy evaluation (done in 3D),
    if willing to accept speed-loss during training.
    :return: out_batch: dictionary containing one patient with batch_size = n_3D_patches in 3D or
    batch_size = n_2D_patches in 2D .
    """
    def __init__(self, data, cf): #threads in augmenter
        super(PatientBatchIterator, self).__init__(data, 0)
        self.cf = cf
        self.patient_ix = 0
        self.dataset_pids = [v['pid'] for (k, v) in data.items()]
        self.patch_size = cf.patch_size
        if len(self.patch_size) == 2:
            self.patch_size = self.patch_size + [1]


    def generate_train_batch(self):


        pid = self.dataset_pids[self.patient_ix]
        patient = self._data[pid]

        data = np.load(patient['data'],mmap_mode='r')
        if len(data.shape)==4:
             data = np.transpose(data, axes=(3, 1, 2, 0))  ##[np.newaxis] (c, y, x, z)
        else:
             data = np.transpose(data, axes=(1, 2, 0))[np.newaxis] # (c, y, x, z)
        seg = np.transpose(np.load(patient['seg'], mmap_mode='r'), axes=(1, 2, 0))
        batch_class_targets = np.array([patient['class_target']])
        
        print ("Sanity Check ####",data.shape)

        # pad data if smaller than patch_size seen during training.
        if np.any([data.shape[dim + 1] < ps for dim, ps in enumerate(self.patch_size)]):
            new_shape = [data.shape[0]] + [np.max([data.shape[dim + 1], self.patch_size[dim]]) for dim, ps in enumerate(self.patch_size)]
            data = dutils.pad_nd_image(data, new_shape) # use 'return_slicer' to crop image back to original shape.
            seg = dutils.pad_nd_image(seg, new_shape)

        # get 3D targets for evaluation, even if network operates in 2D. 2D predictions will be merged to 3D in predictor.
        if self.cf.dim == 3 or self.cf.merge_2D_to_3D_preds:
            out_data = data[np.newaxis]
            out_seg = seg[np.newaxis, np.newaxis]
            out_targets = batch_class_targets

            batch_3D = {'data': out_data, 'seg': out_seg, 'class_target': out_targets, 'pid': pid}
            converter = ConvertSegToBoundingBoxCoordinates(dim=3, get_rois_from_seg_flag=False, class_specific_seg_flag=self.cf.class_specific_seg_flag)
            batch_3D = converter(**batch_3D)
            batch_3D.update({'patient_bb_target': batch_3D['bb_target'],
                                  'patient_roi_labels': batch_3D['class_target'],
                                  'original_img_shape': out_data.shape})

        if self.cf.dim == 2:
            out_data = np.transpose(data, axes=(3, 0, 1, 2))  # (z, c, y, x )
            out_seg = np.transpose(seg, axes=(2, 0, 1))[:, np.newaxis]
            out_targets = np.array(np.repeat(batch_class_targets, out_data.shape[0], axis=0))

            # if set to not None, add neighbouring slices to each selected slice in channel dimension.
            if self.cf.n_3D_context is not None:
                slice_range = range(self.cf.n_3D_context, out_data.shape[0] + self.cf.n_3D_context)
                out_data = np.pad(out_data, ((self.cf.n_3D_context, self.cf.n_3D_context), (0, 0), (0, 0), (0, 0)), 'constant', constant_values=0)
                out_data = np.array(
                    [np.concatenate([out_data[ii] for ii in range(
                        slice_id - self.cf.n_3D_context, slice_id + self.cf.n_3D_context + 1)], axis=0) for slice_id in
                     slice_range])

            batch_2D = {'data': out_data, 'seg': out_seg, 'class_target': out_targets, 'pid': pid}
            converter = ConvertSegToBoundingBoxCoordinates(dim=2, get_rois_from_seg_flag=False, class_specific_seg_flag=self.cf.class_specific_seg_flag)
            batch_2D = converter(**batch_2D)

            if self.cf.merge_2D_to_3D_preds:
                batch_2D.update({'patient_bb_target': batch_3D['patient_bb_target'],
                                      'patient_roi_labels': batch_3D['patient_roi_labels'],
                                      'original_img_shape': out_data.shape})
            else:
                batch_2D.update({'patient_bb_target': batch_2D['bb_target'],
                                 'patient_roi_labels': batch_2D['class_target'],
                                 'original_img_shape': out_data.shape})

        out_batch = batch_3D if self.cf.dim == 3 else batch_2D
        patient_batch = out_batch

        # crop patient-volume to patches of patch_size used during training. stack patches up in batch dimension.
        # in this case, 2D is treated as a special case of 3D with patch_size[z] = 1.
        if np.any([data.shape[dim + 1] > self.patch_size[dim] for dim in range(3)]):
            patch_crop_coords_list = dutils.get_patch_crop_coords(data[0], self.patch_size)
            new_img_batch, new_seg_batch, new_class_targets_batch = [], [], []

            for cix, c in enumerate(patch_crop_coords_list):

                seg_patch = seg[c[0]:c[1], c[2]: c[3], c[4]:c[5]]
                new_seg_batch.append(seg_patch)

                # if set to not None, add neighbouring slices to each selected slice in channel dimension.
                # correct patch_crop coordinates by added slices of 3D context.
                if self.cf.dim == 2 and self.cf.n_3D_context is not None:
                    tmp_c_5 = c[5] + (self.cf.n_3D_context * 2)
                    if cix == 0:
                        data = np.pad(data, ((0, 0), (0, 0), (0, 0), (self.cf.n_3D_context, self.cf.n_3D_context)), 'constant', constant_values=0)
                else:
                    tmp_c_5 = c[5]

                new_img_batch.append(data[:, c[0]:c[1], c[2]:c[3], c[4]:tmp_c_5])

            data = np.array(new_img_batch) # (n_patches, c, x, y, z)
            seg = np.array(new_seg_batch)[:, np.newaxis]  # (n_patches, 1, x, y, z)
            batch_class_targets = np.repeat(batch_class_targets, len(patch_crop_coords_list), axis=0)

            if self.cf.dim == 2:
                if self.cf.n_3D_context is not None:
                    data = np.transpose(data[:, 0], axes=(0, 3, 1, 2))
                else:
                    # all patches have z dimension 1 (slices). discard dimension
                    data = data[..., 0]
                seg = seg[..., 0]

            print ("Patient Batch Generator Post Data Shape",data.shape)
            patch_batch = {'data': data, 'seg': seg, 'class_target': batch_class_targets, 'pid': pid}
            patch_batch['patch_crop_coords'] = np.array(patch_crop_coords_list)
            patch_batch['patient_bb_target'] = patient_batch['patient_bb_target']
            patch_batch['patient_roi_labels'] = patient_batch['patient_roi_labels']
            patch_batch['original_img_shape'] = patient_batch['original_img_shape']

            converter = ConvertSegToBoundingBoxCoordinates(self.cf.dim, get_rois_from_seg_flag=False, class_specific_seg_flag=self.cf.class_specific_seg_flag)
            patch_batch = converter(**patch_batch)
            out_batch = patch_batch

        self.patient_ix += 1
        if self.patient_ix == len(self.dataset_pids):
            self.patient_ix = 0

        return out_batch



def copy_and_unpack_data(logger, pids, fold_dir, source_dir, target_dir):

    start_time = time.time()
    with open(os.path.join(fold_dir, 'file_list.txt'), 'w') as handle:
        for pid in pids:
            handle.write('{}_img.npz\n'.format(pid))
            handle.write('{}_rois.npz\n'.format(pid))

    subprocess.call('rsync -av --files-from {} {} {}'.format(os.path.join(fold_dir, 'file_list.txt'),
        source_dir, target_dir), shell=True)
    n_threads = 8
    dutils.unpack_dataset(target_dir, threads=n_threads)
    copied_files = os.listdir(target_dir)
    t = utils.get_formatted_duration(time.time() - start_time)
    logger.info("\ncopying and unpacking data set finished using {} threads.\n{} files in target dir: {}. Took {}\n"
        .format(n_threads, len(copied_files), target_dir, t))
    
def write_nii_gz(data,seg,ii):
    arr = np.copy(data)
    art = arr[1]
    nc = arr[0]
    ven=arr[2]
    three_phases = {'art':art,'noncon':nc,'ven':ven}
    for phase,jj in three_phases.items():
        np.swapaxes(jj,0,2)
        sitk.WriteImage(sitk.GetImageFromArray(jj),os.path.join('/home/aisinai/data/testing', '{}_img.nii.gz'.format(ii+"_"+phase)))
    sarr = np.copy(seg)
    np.swapaxes(seg,0,2)
    sitk.WriteImage(sitk.Cast(sitk.GetImageFromArray(sarr),5),os.path.join('/home/aisinai/data/testing', '{}_seg.nii.gz'.format(ii)))

if __name__=="__main__":

    total_stime = time.time()

    cf_file = utils.import_module("cf", "configs.py")
    cf = cf_file.configs()

    cf.created_fold_id_pickle = False
    cf.exp_dir = "dev/"
    cf.plot_dir = cf.exp_dir + "plots"
    os.makedirs(cf.exp_dir, exist_ok=True)
    cf.fold = 0
    logger = utils.get_logger(cf.exp_dir)

    batch_gen = get_train_generators(cf, logger)
    train_batch = next(batch_gen["train"])

    print (train_batch.shape+" entire batch shape")

    test_gen = get_test_generator(cf, logger)
    test_batch = next(test_gen["test"])

    mins, secs = divmod((time.time() - total_stime), 60)
    h, mins = divmod(mins, 60)
    t = "{:d}h:{:02d}m:{:02d}s".format(int(h), int(mins), int(secs))
    print("{} total runtime: {}".format(os.path.split(__file__)[1], t))