How to use the hickle.dump function in hickle

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github telegraphic / hickle / tests / test_hickle.py View on Github external
def test_list_order():
    """ https://github.com/telegraphic/hickle/issues/26 """
    d = [np.arange(n + 1) for n in range(20)]
    hickle.dump(d, 'test.h5')
    d_hkl = hickle.load('test.h5')

    try:
        for ii, xx in enumerate(d):
            assert d[ii].shape == d_hkl[ii].shape
        for ii, xx in enumerate(d):
            assert np.allclose(d[ii], d_hkl[ii])
    except AssertionError:
        print(d[ii], d_hkl[ii])
        raise
github telegraphic / hickle / tests / test_hickle_dev.py View on Github external
def test_ndarray():

    a = np.array([1,2,3])
    b = np.array([2,3,4])
    z = (a, b)

    print "Original:"
    pprint(z)
    dump(z, 'test.hkl', mode='w')

    print "\nReconstructed:"
    z = load('test.hkl')
    pprint(z)
github telegraphic / hickle / tests / test_hickle.py View on Github external
def test_embedded_array():
    """ See https://github.com/telegraphic/hickle/issues/24 """

    d_orig = [[np.array([10., 20.]), np.array([10, 20, 30])], [np.array([10, 2]), np.array([1.])]]
    hickle.dump(d_orig, 'test.h5')
    d_hkl = hickle.load('test.h5')

    for ii, xx in enumerate(d_orig):
        for jj, yy in enumerate(xx):
            assert np.allclose(d_orig[ii][jj], d_hkl[ii][jj])

    print(d_hkl)
    print(d_orig)
github telegraphic / hickle / tests / test_scipy.py View on Github external
sm0 = csr_matrix((3, 4), dtype=np.int8).toarray()

    row = np.array([0, 0, 1, 2, 2, 2])
    col = np.array([0, 2, 2, 0, 1, 2])
    data = np.array([1, 2, 3, 4, 5, 6])
    sm1 = csr_matrix((data, (row, col)), shape=(3, 3))
    sm2 = csc_matrix((data, (row, col)), shape=(3, 3))

    indptr = np.array([0, 2, 3, 6])
    indices = np.array([0, 2, 2, 0, 1, 2])
    data = np.array([1, 2, 3, 4, 5, 6]).repeat(4).reshape(6, 2, 2)
    sm3 = bsr_matrix((data,indices, indptr), shape=(6, 6))

    hickle.dump(sm1, 'test_sp.h5')
    sm1_h = hickle.load('test_sp.h5')
    hickle.dump(sm2, 'test_sp2.h5')
    sm2_h = hickle.load('test_sp2.h5')
    hickle.dump(sm3, 'test_sp3.h5')
    sm3_h = hickle.load('test_sp3.h5')

    assert isinstance(sm1_h, csr_matrix)
    assert isinstance(sm2_h, csc_matrix)
    assert isinstance(sm3_h, bsr_matrix)

    assert np.allclose(sm1_h.data, sm1.data)
    assert np.allclose(sm2_h.data, sm2.data)
    assert np.allclose(sm3_h.data, sm3.data)

    assert sm1_h. shape == sm1.shape
    assert sm2_h. shape == sm2.shape
    assert sm3_h. shape == sm3.shape
github colingogo / caffe-pretrained-feature-extraction / feature_extract.py View on Github external
lines = [line.rstrip() for line in lines]
    feats = []
    labels = []
    for line_i, line in enumerate(lines):
        img_path, label = line.split()
        img = caffe.io.load_image(img_path)
        feat = net.extract_feature(img)
        feats.append(feat)
        label = int(label)
        labels.append(label)
        if (line_i + 1) % 100 == 0:
            print "processed", line_i + 1
    feats = np.asarray(feats)
    labels = np.asarray(labels)
    hkl.dump(feats, dbprefix + "_features.hkl", mode="w")
    hkl.dump(labels, dbprefix + "_labels.hkl", mode="w")
github msracver / FCIS / lib / dataset / pascal_voc.py View on Github external
def mask_path_from_index(self, index, gt_mask):
        """
        given image index, cache high resolution mask and return full path of masks
        :param index: index of a specific image
        :return: full path of this mask
        """
        if self.image_set == 'val':
            return []
        cache_file = os.path.join(self.cache_path, 'VOCMask')
        if not os.path.exists(cache_file):
            os.makedirs(cache_file)
        # instance level segmentation
        gt_mask_file = os.path.join(cache_file, index + '.hkl')
        if not os.path.exists(gt_mask_file):
            hkl.dump(gt_mask.astype('bool'), gt_mask_file, mode='w', compression='gzip')
        # cache flip gt_masks
        gt_mask_flip_file = os.path.join(cache_file, index + '_flip.hkl')
        if not os.path.exists(gt_mask_flip_file):
            hkl.dump(gt_mask[:, :, ::-1].astype('bool'), gt_mask_flip_file, mode='w', compression='gzip')
        return gt_mask_file
github coxlab / prednet / process_kitti.py View on Github external
im_list = []
        source_list = []  # corresponds to recording that image came from
        for category, folder in splits[split]:
            im_dir = os.path.join(DATA_DIR, 'raw/', category, folder, folder[:10], folder, 'image_03/data/')
            files = list(os.walk(im_dir, topdown=False))[-1][-1]
            im_list += [im_dir + f for f in sorted(files)]
            source_list += [category + '-' + folder] * len(files)

        print( 'Creating ' + split + ' data: ' + str(len(im_list)) + ' images')
        X = np.zeros((len(im_list),) + desired_im_sz + (3,), np.uint8)
        for i, im_file in enumerate(im_list):
            im = imread(im_file)
            X[i] = process_im(im, desired_im_sz)

        hkl.dump(X, os.path.join(DATA_DIR, 'X_' + split + '.hkl'))
        hkl.dump(source_list, os.path.join(DATA_DIR, 'sources_' + split + '.hkl'))
github QuTech-Delft / qtt / qtt / measurements / storage.py View on Github external
tag = datestring

    obj = {'gatevalues': gv, 'snapshot': snapshot,
           'datestring': datestring, 'data': data}

    if verbose:
        print('save_state: writing to file %s, tag %s' % (statefile, tag))
    with h5py.File(statefile, 'a') as h5group:
            # implementation using dev branch of hickle
            if (tag in h5group):
                if overwrite:
                    del h5group[tag]
                else:
                    raise Exception(
                        'tag %s already exists in state file %s' % (tag, statefile))
            hickle.dump(obj, h5group, path=tag)
github MichaelHills / seizure-detection / common / io.py View on Github external
def save_hkl_file(filename, data):
    hkl_filename = filename + '.hkl'
    try:
        hkl.dump(data, hkl_filename, mode="w")
        return True
    except Exception:
        if os.path.isfile(filename):
            os.remove(hkl_filename)
github aviveise / 2WayNet / DataSetReaders / dataset_base.py View on Github external
path = os.path.dirname(os.path.abspath(self.dataset_path))

        train_file = os.path.join(path, 'train{0}.p'.format(suffix))
        test_file = os.path.join(path, 'test{0}.p'.format(suffix))
        validate_file = os.path.join(path, 'validate{0}.p'.format(suffix))
        params_file = os.path.join(path, 'params{0}.p'.format(suffix))
        mapping_file = os.path.join(path, 'mapping{0}.p'.format(suffix))

        numpy.save('x_{0}'.format(train_file), self.trainset[0])
        numpy.save('y_{0}'.format(train_file), self.trainset[1])

        # hickle.dump(self.trainset, file(train_file, 'w'))
        hickle.dump(self.testset, file(test_file, 'w'))
        hickle.dump(self.tuning, file(validate_file, 'w'))
        hickle.dump(self.data_set_parameters, file(params_file, 'w'))
        hickle.dump({'map': self.x_y_mapping, 'reduce': self.x_reduce}, file(mapping_file, 'w'))