<commit_before>from __future__ import absolute_import
import tempfile
import copy

from ndio.ramon.RAMONBase import *
from ndio.ramon.RAMONGeneric import *
from ndio.ramon.RAMONNeuron import *
from ndio.ramon.RAMONOrganelle import *
from ndio.ramon.RAMONSegment import *
from ndio.ramon.RAMONSynapse import *
from ndio.ramon.RAMONVolume import *

from .errors import *

"""

The enumerables in this file are to afford compatibility with CAJAL, which uses
integers as types. To convert from integer to string (for instance, if you want
to specify the ANNOTATION_TYPE in a RAMON hdf5 file), use:

    >>> AnnotationType.get_str(1)
    "GENERIC"

To convert from an integer to an actual RAMON type (say, if you want to create
a new RAMON object dynamically), use:

    >>> AnnotationType.get_class(1)
    ndio.ramon.RAMONGeneric.RAMONGeneric

So you can create a new RAMON object of dynamic type like this:

    >>> anno_type = 5
    >>> r = AnnotationType.get_class(anno_type)()
    >>> type(r)
    ndio.ramon.RAMONNeuron.RAMONNeuron

NOTE! If you already have an HDF5 file that contains a RAMON object, it is far
easier to use the prebuilt `hdf5_to_ramon()` function (below).

    >>> import h5py
    >>> f = h5py.File('myfile.hdf5', 'r')
    >>> r = hdf5_to_ramon(f)

"""

# str: int
_types = {
    "generic": 1,
    "synapse": 2,
    "seed": 3,
    "segment": 4,
    "neuron": 5,
    "organelle": 6,
    "attributedregion": 7,
    "volume": 8
}

# int: str
_reverse_types = {v: k for k, v in list(_types.items())}

# int: class type
_ramon_types = {
    _types["generic"]: RAMONGeneric,
    _types["synapse"]: RAMONSynapse,
    _types["seed"]:  None,
    _types["segment"]: RAMONSegment,
    _types["neuron"]: RAMONNeuron,
    _types["organelle"]: RAMONOrganelle,
    # _types["ATTRIBUTEDREGION"]: None,
    _types["volume"]: RAMONVolume
}

# class type: int
_reverse_ramon_types = {v: k for k, v in list(_ramon_types.items())}


class AnnotationType:
    GENERIC = _types["generic"]
    SYNAPSE = _types["synapse"]
    SEED = _types["seed"]
    SEGMENT = _types["segment"]
    NEURON = _types["neuron"]
    ORGANELLE = _types["organelle"]
    ATTRIBUTEDREGION = _types["attributedregion"]
    VOLUME = _types["volume"]

    @staticmethod
    def get_str(typ):
        return _reverse_types[typ]

    @staticmethod
    def get_class(typ):
        return _ramon_types[typ]

    @staticmethod
    def get_int(typ):
        return _reverse_ramon_types[typ]

    @staticmethod
    def RAMON(typ):
        """
        Takes str or int, returns class type
        """
        if type(typ) is int:
            return _ramon_types[typ]
        elif type(typ) in [str, unicode]:
            return _ramon_types[_types[typ]]


def to_json(ramons):
    """
    Converts RAMON objects into a JSON string which can be directly written out
    to a .json file. You can pass either a single RAMON or a list. If you pass
    a single RAMON, it will still be exported with the ID as the key. In other
    words:

        type(from_json(to_json(ramon))) → list

    ...even if `type(ramon)` is a RAMON, not a list.

    Arguments:
        ramons (RAMON or list): The RAMON object(s) to convert to JSON.

    Returns:
        str: The JSON representation of the RAMON objects, in the schema:

            {
                <id>: {
                    type: . . . ,
                    metadata: {
                        . . .
                    }
                },
            }

    Raises:
        ValueError: If an invalid RAMON is passed.
    """
    raise NotImplementedError

def from_json(json, cutout=None):
    """
    Converts JSON to a python list of RAMON objects. if `cutout` is provided,
    the `cutout` attribute of the RAMON object is populated. Otherwise, it's
    left empty. `json` should be an ID-level dictionary, like so:

        {
            16: {
                type: "segment",
                metadata: {
                    . . .
                }
            },
        }

    NOTE: If more than one item is in the dictionary, then a Python list of
    RAMON objects is returned instead of a single RAMON.
    """<commit_msg>finish ramon#to_json<commit_after>from __future__ import absolute_import
import tempfile
import json
import copy

from ndio.ramon.RAMONBase import *
from ndio.ramon.RAMONGeneric import *
from ndio.ramon.RAMONNeuron import *
from ndio.ramon.RAMONOrganelle import *
from ndio.ramon.RAMONSegment import *
from ndio.ramon.RAMONSynapse import *
from ndio.ramon.RAMONVolume import *

from .errors import *

"""

The enumerables in this file are to afford compatibility with CAJAL, which uses
integers as types. To convert from integer to string (for instance, if you want
to specify the ANNOTATION_TYPE in a RAMON hdf5 file), use:

    >>> AnnotationType.get_str(1)
    "GENERIC"

To convert from an integer to an actual RAMON type (say, if you want to create
a new RAMON object dynamically), use:

    >>> AnnotationType.get_class(1)
    ndio.ramon.RAMONGeneric.RAMONGeneric

So you can create a new RAMON object of dynamic type like this:

    >>> anno_type = 5
    >>> r = AnnotationType.get_class(anno_type)()
    >>> type(r)
    ndio.ramon.RAMONNeuron.RAMONNeuron

NOTE! If you already have an HDF5 file that contains a RAMON object, it is far
easier to use the prebuilt `hdf5_to_ramon()` function (below).

    >>> import h5py
    >>> f = h5py.File('myfile.hdf5', 'r')
    >>> r = hdf5_to_ramon(f)

"""

# str: int
_types = {
    "generic": 1,
    "synapse": 2,
    "seed": 3,
    "segment": 4,
    "neuron": 5,
    "organelle": 6,
    "attributedregion": 7,
    "volume": 8
}

# int: str
_reverse_types = {v: k for k, v in list(_types.items())}

# int: class type
_ramon_types = {
    _types["generic"]: RAMONGeneric,
    _types["synapse"]: RAMONSynapse,
    _types["seed"]:  None,
    _types["segment"]: RAMONSegment,
    _types["neuron"]: RAMONNeuron,
    _types["organelle"]: RAMONOrganelle,
    # _types["ATTRIBUTEDREGION"]: None,
    _types["volume"]: RAMONVolume
}

# class type: int
_reverse_ramon_types = {v: k for k, v in list(_ramon_types.items())}


class AnnotationType:
    GENERIC = _types["generic"]
    SYNAPSE = _types["synapse"]
    SEED = _types["seed"]
    SEGMENT = _types["segment"]
    NEURON = _types["neuron"]
    ORGANELLE = _types["organelle"]
    ATTRIBUTEDREGION = _types["attributedregion"]
    VOLUME = _types["volume"]

    @staticmethod
    def get_str(typ):
        return _reverse_types[typ]

    @staticmethod
    def get_class(typ):
        return _ramon_types[typ]

    @staticmethod
    def get_int(typ):
        return _reverse_ramon_types[typ]

    @staticmethod
    def RAMON(typ):
        """
        Takes str or int, returns class type
        """
        if type(typ) is int:
            return _ramon_types[typ]
        elif type(typ) in [str, unicode]:
            return _ramon_types[_types[typ]]


def to_json(ramons):
    """
    Converts RAMON objects into a JSON string which can be directly written out
    to a .json file. You can pass either a single RAMON or a list. If you pass
    a single RAMON, it will still be exported with the ID as the key. In other
    words:

        type(from_json(to_json(ramon))) # ALWAYS returns a list

    ...even if `type(ramon)` is a RAMON, not a list.

    Arguments:
        ramons (RAMON or list): The RAMON object(s) to convert to JSON.

    Returns:
        str: The JSON representation of the RAMON objects, in the schema:

            {
                <id>: {
                    type: . . . ,
                    metadata: {
                        . . .
                    }
                },
            }

    Raises:
        ValueError: If an invalid RAMON is passed.
    """
    if type(ramons) is not list:
        ramons = [ramons]

    out_ramons = {}
    for r in ramons:
        out_ramons[r.id] = vars(r)

    return json.dumps(out_ramons)


def from_json(json, cutout=None):
    """
    Converts JSON to a python list of RAMON objects. if `cutout` is provided,
    the `cutout` attribute of the RAMON object is populated. Otherwise, it's
    left empty. `json` should be an ID-level dictionary, like so:

        {
            16: {
                type: "segment",
                metadata: {
                    . . .
                }
            },
        }

    NOTE: If more than one item is in the dictionary, then a Python list of
    RAMON objects is returned instead of a single RAMON.
    """
{'fraction_non_alphanumeric': 0.10186717088158828, 'fraction_numerical': 0.004727014890096904, 'mean_word_length': 2.4599345870809484, 'pattern_counts': {'":': 16, '<': 5, '<?xml version=': 0, '>': 53, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7183718', 'n_tokens_mistral': 2835, 'n_tokens_neox': 2690, 'n_words': 867}