PConsC2.py 文件源码

def extract_patches(self, all_seqdata, with_targets=True, inplace=False):
        print("\tConverting dataset to Numpy array...")
        L0_X, L0_Y = list(), list()
        for seqdata in all_seqdata:
            if not inplace:
                seqdata = copy.deepcopy(seqdata)
            L = len(seqdata)
            tril_indices = np.tril_indices(L, -1) # Lower triangle without diagonal
            cpreds = seqdata.cpreds
            for cpred in cpreds:
                assert(len(cpred.shape) == 2)
                if cpred is not None:
                    cpred_shape = cpred.shape
            # Create contact maps from file data
            print(len(cpreds))
            for i in range(len(cpreds)):
                if cpreds[i] is None:
                    cpreds[i] = np.full(cpred_shape, Params.DISTANCE_NAN, dtype=Params.FLOAT_DTYPE)
                else:
                    cpreds[i][np.isnan(cpreds[i])] = Params.DISTANCE_NAN
                cpreds[i] = np.asarray(cpreds[i][tril_indices], dtype=Params.FLOAT_DTYPE)
            cpreds = np.asarray(cpreds, dtype=Params.FLOAT_DTYPE).T
            L0_X.append(cpreds)
            if with_targets:
                contacts = distances_to_contacts(seqdata.distances)
                contacts = contacts[tril_indices]
                L0_Y.append(contacts)

        L0_X = np.concatenate(L0_X, axis=0)
        if with_targets:
            L0_Y = np.concatenate(L0_Y, axis=0)
        return (L0_X, L0_Y) if with_targets else L0_X