import json
from pathlib import Path
import tempfile

import marshmallow
import argschema


from ophys_etl.transforms.postprocess_rois import (
    PostProcessROIsInputSchema, PostProcessROIs)
from ophys_etl.transforms.suite2p_wrapper import (Suite2PWrapper,
                                                  Suite2PWrapperSchema)


class PostProcessInputSchema(PostProcessROIsInputSchema):

    # Override the default "suite2p_stat_field" required parameter of the
    # PostProcessROIsInputSchema.
    # When run in pipeline, the suite2p_stat_path won't be known until
    # after segmentation has run.
    suite2p_stat_path = argschema.fields.Str(
        required=False,
        validate=lambda x: Path(x).exists(),
        description=("Path to s2p output stat file containing ROIs generated "
                     "during source extraction"))


class SegmentPostProcessSchema(argschema.ArgSchema):
    suite2p_args = argschema.fields.Nested(Suite2PWrapperSchema,
                                           required=True)
    postprocess_args = argschema.fields.Nested(PostProcessInputSchema,
                                               required=True)

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.tmpdir = None

    @marshmallow.pre_load
    def setup_default_suite2p_args(self, data: dict, **kwargs) -> dict:

        # suite2p_args
        if "output_dir" not in data["suite2p_args"]:
            self.tmpdir = tempfile.TemporaryDirectory()
            data["suite2p_args"]["output_dir"] = self.tmpdir.name

        if "output_json" not in data["suite2p_args"]:
            Suite2p_output = (Path(data["suite2p_args"]["output_dir"])
                              / "Suite2P_output.json")
            data["suite2p_args"]["output_json"] = str(Suite2p_output)

        data["suite2p_args"]["log_level"] = data["log_level"]

        # postprocess_args
        if "motion_corrected_video" not in data["postprocess_args"]:
            data["postprocess_args"]["motion_corrected_video"] = (
                data["suite2p_args"]["h5py"])

        if "output_json" not in data["postprocess_args"]:
            data["postprocess_args"]["output_json"] = data["output_json"]

        data["postprocess_args"]["log_level"] = data["log_level"]

        return data


class SegmentAndPostProcess(argschema.ArgSchemaParser):
    default_schema = SegmentPostProcessSchema

    def run(self):

        # segment with Suite2P, almost all default args
        suite2p_args = self.args['suite2p_args']
        segment = Suite2PWrapper(input_data=suite2p_args, args=[])
        segment.run()

        # postprocess and output LIMS format
        with open(suite2p_args["output_json"], "r") as f:
            stat_path = json.load(f)['output_files']['stat.npy'][0]

        postprocess_args = self.args['postprocess_args']
        if "suite2p_stat_path" not in postprocess_args:
            postprocess_args["suite2p_stat_path"] = stat_path

        postprocess = PostProcessROIs(input_data=postprocess_args, args=[])
        postprocess.run()

        # Clean up temporary directories and/or files created during
        # Schema invocation
        if self.schema.tmpdir is not None:
            self.schema.tmpdir.cleanup()


if __name__ == "__main__":  # pragma: nocover
    sbmod = SegmentAndPostProcess()
    sbmod.run()

2fe337532ea726184da98a1aee62846ac68314ab
<mask token>


class SegmentPostProcessSchema(argschema.ArgSchema):
    <mask token>
    <mask token>

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.tmpdir = None

    @marshmallow.pre_load
    def setup_default_suite2p_args(self, data: dict, **kwargs) ->dict:
        if 'output_dir' not in data['suite2p_args']:
            self.tmpdir = tempfile.TemporaryDirectory()
            data['suite2p_args']['output_dir'] = self.tmpdir.name
        if 'output_json' not in data['suite2p_args']:
            Suite2p_output = Path(data['suite2p_args']['output_dir']
                ) / 'Suite2P_output.json'
            data['suite2p_args']['output_json'] = str(Suite2p_output)
        data['suite2p_args']['log_level'] = data['log_level']
        if 'motion_corrected_video' not in data['postprocess_args']:
            data['postprocess_args']['motion_corrected_video'] = data[
                'suite2p_args']['h5py']
        if 'output_json' not in data['postprocess_args']:
            data['postprocess_args']['output_json'] = data['output_json']
        data['postprocess_args']['log_level'] = data['log_level']
        return data


class SegmentAndPostProcess(argschema.ArgSchemaParser):
    default_schema = SegmentPostProcessSchema

    def run(self):
        suite2p_args = self.args['suite2p_args']
        segment = Suite2PWrapper(input_data=suite2p_args, args=[])
        segment.run()
        with open(suite2p_args['output_json'], 'r') as f:
            stat_path = json.load(f)['output_files']['stat.npy'][0]
        postprocess_args = self.args['postprocess_args']
        if 'suite2p_stat_path' not in postprocess_args:
            postprocess_args['suite2p_stat_path'] = stat_path
        postprocess = PostProcessROIs(input_data=postprocess_args, args=[])
        postprocess.run()
        if self.schema.tmpdir is not None:
            self.schema.tmpdir.cleanup()


<mask token>

<mask token>


class PostProcessInputSchema(PostProcessROIsInputSchema):
    <mask token>


class SegmentPostProcessSchema(argschema.ArgSchema):
    suite2p_args = argschema.fields.Nested(Suite2PWrapperSchema, required=True)
    postprocess_args = argschema.fields.Nested(PostProcessInputSchema,
        required=True)

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.tmpdir = None

    @marshmallow.pre_load
    def setup_default_suite2p_args(self, data: dict, **kwargs) ->dict:
        if 'output_dir' not in data['suite2p_args']:
            self.tmpdir = tempfile.TemporaryDirectory()
            data['suite2p_args']['output_dir'] = self.tmpdir.name
        if 'output_json' not in data['suite2p_args']:
            Suite2p_output = Path(data['suite2p_args']['output_dir']
                ) / 'Suite2P_output.json'
            data['suite2p_args']['output_json'] = str(Suite2p_output)
        data['suite2p_args']['log_level'] = data['log_level']
        if 'motion_corrected_video' not in data['postprocess_args']:
            data['postprocess_args']['motion_corrected_video'] = data[
                'suite2p_args']['h5py']
        if 'output_json' not in data['postprocess_args']:
            data['postprocess_args']['output_json'] = data['output_json']
        data['postprocess_args']['log_level'] = data['log_level']
        return data


class SegmentAndPostProcess(argschema.ArgSchemaParser):
    default_schema = SegmentPostProcessSchema

    def run(self):
        suite2p_args = self.args['suite2p_args']
        segment = Suite2PWrapper(input_data=suite2p_args, args=[])
        segment.run()
        with open(suite2p_args['output_json'], 'r') as f:
            stat_path = json.load(f)['output_files']['stat.npy'][0]
        postprocess_args = self.args['postprocess_args']
        if 'suite2p_stat_path' not in postprocess_args:
            postprocess_args['suite2p_stat_path'] = stat_path
        postprocess = PostProcessROIs(input_data=postprocess_args, args=[])
        postprocess.run()
        if self.schema.tmpdir is not None:
            self.schema.tmpdir.cleanup()


<mask token>

<mask token>


class PostProcessInputSchema(PostProcessROIsInputSchema):
    suite2p_stat_path = argschema.fields.Str(required=False, validate=lambda
        x: Path(x).exists(), description=
        'Path to s2p output stat file containing ROIs generated during source extraction'
        )


class SegmentPostProcessSchema(argschema.ArgSchema):
    suite2p_args = argschema.fields.Nested(Suite2PWrapperSchema, required=True)
    postprocess_args = argschema.fields.Nested(PostProcessInputSchema,
        required=True)

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.tmpdir = None

    @marshmallow.pre_load
    def setup_default_suite2p_args(self, data: dict, **kwargs) ->dict:
        if 'output_dir' not in data['suite2p_args']:
            self.tmpdir = tempfile.TemporaryDirectory()
            data['suite2p_args']['output_dir'] = self.tmpdir.name
        if 'output_json' not in data['suite2p_args']:
            Suite2p_output = Path(data['suite2p_args']['output_dir']
                ) / 'Suite2P_output.json'
            data['suite2p_args']['output_json'] = str(Suite2p_output)
        data['suite2p_args']['log_level'] = data['log_level']
        if 'motion_corrected_video' not in data['postprocess_args']:
            data['postprocess_args']['motion_corrected_video'] = data[
                'suite2p_args']['h5py']
        if 'output_json' not in data['postprocess_args']:
            data['postprocess_args']['output_json'] = data['output_json']
        data['postprocess_args']['log_level'] = data['log_level']
        return data


class SegmentAndPostProcess(argschema.ArgSchemaParser):
    default_schema = SegmentPostProcessSchema

    def run(self):
        suite2p_args = self.args['suite2p_args']
        segment = Suite2PWrapper(input_data=suite2p_args, args=[])
        segment.run()
        with open(suite2p_args['output_json'], 'r') as f:
            stat_path = json.load(f)['output_files']['stat.npy'][0]
        postprocess_args = self.args['postprocess_args']
        if 'suite2p_stat_path' not in postprocess_args:
            postprocess_args['suite2p_stat_path'] = stat_path
        postprocess = PostProcessROIs(input_data=postprocess_args, args=[])
        postprocess.run()
        if self.schema.tmpdir is not None:
            self.schema.tmpdir.cleanup()


if __name__ == '__main__':
    sbmod = SegmentAndPostProcess()
    sbmod.run()

import json
from pathlib import Path
import tempfile
import marshmallow
import argschema
from ophys_etl.transforms.postprocess_rois import PostProcessROIsInputSchema, PostProcessROIs
from ophys_etl.transforms.suite2p_wrapper import Suite2PWrapper, Suite2PWrapperSchema


class PostProcessInputSchema(PostProcessROIsInputSchema):
    suite2p_stat_path = argschema.fields.Str(required=False, validate=lambda
        x: Path(x).exists(), description=
        'Path to s2p output stat file containing ROIs generated during source extraction'
        )


class SegmentPostProcessSchema(argschema.ArgSchema):
    suite2p_args = argschema.fields.Nested(Suite2PWrapperSchema, required=True)
    postprocess_args = argschema.fields.Nested(PostProcessInputSchema,
        required=True)

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.tmpdir = None

    @marshmallow.pre_load
    def setup_default_suite2p_args(self, data: dict, **kwargs) ->dict:
        if 'output_dir' not in data['suite2p_args']:
            self.tmpdir = tempfile.TemporaryDirectory()
            data['suite2p_args']['output_dir'] = self.tmpdir.name
        if 'output_json' not in data['suite2p_args']:
            Suite2p_output = Path(data['suite2p_args']['output_dir']
                ) / 'Suite2P_output.json'
            data['suite2p_args']['output_json'] = str(Suite2p_output)
        data['suite2p_args']['log_level'] = data['log_level']
        if 'motion_corrected_video' not in data['postprocess_args']:
            data['postprocess_args']['motion_corrected_video'] = data[
                'suite2p_args']['h5py']
        if 'output_json' not in data['postprocess_args']:
            data['postprocess_args']['output_json'] = data['output_json']
        data['postprocess_args']['log_level'] = data['log_level']
        return data


class SegmentAndPostProcess(argschema.ArgSchemaParser):
    default_schema = SegmentPostProcessSchema

    def run(self):
        suite2p_args = self.args['suite2p_args']
        segment = Suite2PWrapper(input_data=suite2p_args, args=[])
        segment.run()
        with open(suite2p_args['output_json'], 'r') as f:
            stat_path = json.load(f)['output_files']['stat.npy'][0]
        postprocess_args = self.args['postprocess_args']
        if 'suite2p_stat_path' not in postprocess_args:
            postprocess_args['suite2p_stat_path'] = stat_path
        postprocess = PostProcessROIs(input_data=postprocess_args, args=[])
        postprocess.run()
        if self.schema.tmpdir is not None:
            self.schema.tmpdir.cleanup()


if __name__ == '__main__':
    sbmod = SegmentAndPostProcess()
    sbmod.run()

import json
from pathlib import Path
import tempfile

import marshmallow
import argschema


from ophys_etl.transforms.postprocess_rois import (
    PostProcessROIsInputSchema, PostProcessROIs)
from ophys_etl.transforms.suite2p_wrapper import (Suite2PWrapper,
                                                  Suite2PWrapperSchema)


class PostProcessInputSchema(PostProcessROIsInputSchema):

    # Override the default "suite2p_stat_field" required parameter of the
    # PostProcessROIsInputSchema.
    # When run in pipeline, the suite2p_stat_path won't be known until
    # after segmentation has run.
    suite2p_stat_path = argschema.fields.Str(
        required=False,
        validate=lambda x: Path(x).exists(),
        description=("Path to s2p output stat file containing ROIs generated "
                     "during source extraction"))


class SegmentPostProcessSchema(argschema.ArgSchema):
    suite2p_args = argschema.fields.Nested(Suite2PWrapperSchema,
                                           required=True)
    postprocess_args = argschema.fields.Nested(PostProcessInputSchema,
                                               required=True)

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.tmpdir = None

    @marshmallow.pre_load
    def setup_default_suite2p_args(self, data: dict, **kwargs) -> dict:

        # suite2p_args
        if "output_dir" not in data["suite2p_args"]:
            self.tmpdir = tempfile.TemporaryDirectory()
            data["suite2p_args"]["output_dir"] = self.tmpdir.name

        if "output_json" not in data["suite2p_args"]:
            Suite2p_output = (Path(data["suite2p_args"]["output_dir"])
                              / "Suite2P_output.json")
            data["suite2p_args"]["output_json"] = str(Suite2p_output)

        data["suite2p_args"]["log_level"] = data["log_level"]

        # postprocess_args
        if "motion_corrected_video" not in data["postprocess_args"]:
            data["postprocess_args"]["motion_corrected_video"] = (
                data["suite2p_args"]["h5py"])

        if "output_json" not in data["postprocess_args"]:
            data["postprocess_args"]["output_json"] = data["output_json"]

        data["postprocess_args"]["log_level"] = data["log_level"]

        return data


class SegmentAndPostProcess(argschema.ArgSchemaParser):
    default_schema = SegmentPostProcessSchema

    def run(self):

        # segment with Suite2P, almost all default args
        suite2p_args = self.args['suite2p_args']
        segment = Suite2PWrapper(input_data=suite2p_args, args=[])
        segment.run()

        # postprocess and output LIMS format
        with open(suite2p_args["output_json"], "r") as f:
            stat_path = json.load(f)['output_files']['stat.npy'][0]

        postprocess_args = self.args['postprocess_args']
        if "suite2p_stat_path" not in postprocess_args:
            postprocess_args["suite2p_stat_path"] = stat_path

        postprocess = PostProcessROIs(input_data=postprocess_args, args=[])
        postprocess.run()

        # Clean up temporary directories and/or files created during
        # Schema invocation
        if self.schema.tmpdir is not None:
            self.schema.tmpdir.cleanup()


if __name__ == "__main__":  # pragma: nocover
    sbmod = SegmentAndPostProcess()
    sbmod.run()
