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Update formatting and syntax errors
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@kushalbakshi
kushalbakshi committed Aug 25, 2023
1 parent 65a293f commit c92e816
Showing 1 changed file with 104 additions and 55 deletions.
159 changes: 104 additions & 55 deletions element_calcium_imaging/export/nwb/nwb.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
import pathlib

import datajoint as dj
import numpy as np

from datajoint import DataJointError
from element_interface.utils import find_full_path
from neuroconv import ConverterPipe
from pynwb import NWBHDF5IO, NWBFile
from pynwb.image import ImageSeries
from pynwb.ophys import (
Expand All @@ -16,17 +17,18 @@
RoiResponseSeries,
TwoPhotonSeries,
)
from neuroconv import ConverterPipe

from ... import imaging, scan
from ...scan import get_imaging_root_data_dir, get_image_files
from ...scan import get_image_files, get_imaging_root_data_dir


def create_raw_data_nwbfile(session_key, output_directory, nwb_path):

acquisition_software = (scan.Scan & session_key).fetch1("acq_software")
if acquisition_software == "NIS":
raise NotImplementedError("Packaging raw data from Nikon NIS acquisition software (.nd2 file format) is not currently supported.")
raise NotImplementedError(
"Packaging raw data from Nikon NIS acquisition software (.nd2 file format) is not currently supported."
)

session_paramset_key = (imaging.ProcessingTask & session_key).fetch1("paramset_idx")
processing_method = (
Expand All @@ -51,8 +53,8 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):

elif acquisition_software == "ScanImage" and processing_method == "CaImAn":
from neuroconv.datainterfaces import (
ScanImageImagingInterface,
CaimanSegmentationInterface,
ScanImageImagingInterface,
)

caiman_hdf5 = list(processing_folder_location.rglob("caiman_analysis.hdf5"))
Expand All @@ -64,8 +66,8 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):

elif acquisition_software == "ScanImage" and processing_method == "extract":
from neuroconv.datainterfaces import (
ScanImageImagingInterface,
ExtractSegmentationInterface,
ScanImageImagingInterface,
)

processing_file_location = pathlib.Path(output_directory).as_posix()
Expand Down Expand Up @@ -94,8 +96,8 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):

elif acquisition_software == "Scanbox" and processing_method == "CaImAn":
from neuroconv.datainterfaces import (
SbxImagingInterface,
CaimanSegmentationInterface,
SbxImagingInterface,
)

caiman_hdf5 = list(processing_folder_location.rglob("caiman_analysis.hdf5"))
Expand All @@ -104,11 +106,11 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):
)
caiman_interface = CaimanSegmentationInterface(file_path=caiman_hdf5[0])
converter = ConverterPipe(data_interfaces=[scan_interface, caiman_interface])

elif acquisition_software == "Scanbox" and processing_method == "extract":
from neuroconv.datainterfaces import (
SbxImagingInterface,
ExtractSegmentationInterface,
SbxImagingInterface,
)

processing_file_location = pathlib.Path(output_directory).as_posix()
Expand All @@ -120,19 +122,25 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):
file_path=processing_file_location
)
converter = ConverterPipe(data_interfaces=[scan_interface, extract_interface])

elif acquisition_software == "PrairieView" and processing_method == "suite2p":
n_planes = (scan.ScanInfo & session_key).fetch1("ndepths")
if n_planes > 1:
from neuroconv.datainterfaces import BrukerTiffMultiPlaneConverter as BrukerTiffConverter
from neuroconv.datainterfaces import (
BrukerTiffMultiPlaneConverter as BrukerTiffConverter,
)
else:
from neuroconv.datainterfaces import BrukerTiffSinglePlaneConverter as BrukerTiffConverter
from neuroconv.datainterfaces import (
BrukerTiffSinglePlaneConverter as BrukerTiffConverter,
)
from neuroconv.datainterfaces import Suite2pSegmentationInterface

processing_folder_location = pathlib.Path(output_directory).as_posix()
raw_data_files_location = get_image_files(session_key, "*.tif")
bruker_interface = BrukerTiffConverter(
file_path=raw_data_files_location[0], fallback_sampling_frequency=30, **bruker_kwargs
file_path=raw_data_files_location[0],
fallback_sampling_frequency=30,
**bruker_kwargs,
)
s2p_interface = Suite2pSegmentationInterface(
folder_path=processing_folder_location
Expand All @@ -142,15 +150,21 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):
elif acquisition_software == "PrairieView" and processing_method == "caiman":
n_planes = (scan.ScanInfo & session_key).fetch1("ndepths")
if n_planes > 1:
from neuroconv.datainterfaces import BrukerTiffMultiPlaneConverter as BrukerTiffConverter
from neuroconv.datainterfaces import (
BrukerTiffMultiPlaneConverter as BrukerTiffConverter,
)
else:
from neuroconv.datainterfaces import BrukerTiffSinglePlaneConverter as BrukerTiffConverter
from neuroconv.datainterfaces import (
BrukerTiffSinglePlaneConverter as BrukerTiffConverter,
)
from neuroconv.datainterfaces import CaimanSegmentationInterface

processing_folder_location = pathlib.Path(output_directory).as_posix()
raw_data_files_location = get_image_files(session_key, "*.tif")
bruker_interface = BrukerTiffConverter(
file_path=raw_data_files_location[0], fallback_sampling_frequency=30, **bruker_kwargs
file_path=raw_data_files_location[0],
fallback_sampling_frequency=30,
**bruker_kwargs,
)
caiman_hdf5 = list(processing_folder_location.rglob("caiman_analysis.hdf5"))
caiman_interface = CaimanSegmentationInterface(file_path=caiman_hdf5[0])
Expand All @@ -159,15 +173,21 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):
elif acquisition_software == "PrairieView" and processing_method == "extract":
n_planes = (scan.ScanInfo & session_key).fetch1("ndepths")
if n_planes > 1:
from neuroconv.datainterfaces import BrukerTiffMultiPlaneConverter as BrukerTiffConverter
from neuroconv.datainterfaces import (
BrukerTiffMultiPlaneConverter as BrukerTiffConverter,
)
else:
from neuroconv.datainterfaces import BrukerTiffSinglePlaneConverter as BrukerTiffConverter
from neuroconv.datainterfaces import (
BrukerTiffSinglePlaneConverter as BrukerTiffConverter,
)
from neuroconv.datainterfaces import ExtractSegmentationInterface

processing_file_location = pathlib.Path(output_directory).as_posix()
raw_data_files_location = get_image_files(session_key, "*.tif")
bruker_interface = BrukerTiffConverter(
file_path=raw_data_files_location[0], fallback_sampling_frequency=30, **bruker_kwargs
file_path=raw_data_files_location[0],
fallback_sampling_frequency=30,
**bruker_kwargs,
)
extract_interface = ExtractSegmentationInterface(
file_path=processing_file_location
Expand All @@ -176,7 +196,10 @@ def create_raw_data_nwbfile(session_key, output_directory, nwb_path):

metadata = converter.get_metadata()
metadata["NWBFile"].update(session_description="DataJoint Session")
converter.run_conversion(nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'), metadata=metadata)
converter.run_conversion(
nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'), metadata=metadata
)


def create_processed_data_nwbfile(session_key, output_directory, nwb_path):
session_paramset_key = (imaging.ProcessingTask & session_key).fetch1("paramset_idx")
Expand All @@ -186,21 +209,27 @@ def create_processed_data_nwbfile(session_key, output_directory, nwb_path):

if processing_method == "suite2p":
from neuroconv.datainterfaces import Suite2pSegmentationInterface

s2p_interface = Suite2pSegmentationInterface(
folder_path=processing_folder_location
)
metadata = interface.get_metadata()
s2p_interface.run_conversion(nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'), metadata=metadata)

s2p_interface.run_conversion(
nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'),
metadata=metadata,
)

elif processing_method == "caiman":
from neuroconv.datainterfaces import CaimanSegmentationInterface

processing_folder_location = pathlib.Path(output_directory).as_posix()
caiman_hdf5 = list(processing_folder_location.rglob("caiman_analysis.hdf5"))
caiman_interface = CaimanSegmentationInterface(file_path=caiman_hdf5[0])
metadata = caiman_interface.get_metadata()
caiman_interface.run_conversion(nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'), metadata=metadata)
caiman_interface.run_conversion(
nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'),
metadata=metadata,
)

elif processing_method == "extract":
from neuroconv.datainterfaces import ExtractSegmentationInterface
Expand All @@ -210,7 +239,10 @@ def create_processed_data_nwbfile(session_key, output_directory, nwb_path):
file_path=processing_file_location
)
metadata = extract_interface.get_metadata()
extract_interface.run_conversion(nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'), metadata=metadata)
extract_interface.run_conversion(
nwbfile_path=(nwb_path / f'{session_key["subject"]}_nwbfile'),
metadata=metadata,
)


def add_scan_to_nwb(session_key, nwbfile):
Expand Down Expand Up @@ -341,16 +373,16 @@ def add_segmentation_data_to_nwb(session_key, nwbfile, imaging_plane):
name=f"Deconvolved_{channel}",
data=np.stack(
(
imaging.Activity.Trace
& session_key
& f"fluo_channel='{channel}'"
imaging.Activity.Trace & session_key & f"fluo_channel='{channel}'"
).fetch("activity_trace")
).T,
rois=rt_region,
unit="a.u.",
rate=(scan.ScanInfo & session_key).fetch1("fps"),
)
fl = Fluorescence(roi_response_series=[roi_resp_series, neuorpil_series, deconvolved_series])
fl = Fluorescence(
roi_response_series=[roi_resp_series, neuorpil_series, deconvolved_series]
)
ophys_module.add(fl)


Expand All @@ -363,10 +395,12 @@ def imaging_session_to_nwb(
project_key=None,
protocol_key=None,
nwbfile_kwargs=None,
):
):

if processed_data_source not in ["database", "filesystem"]:
raise ValueError("Invalid processed data source. Expected one of 'database', 'filesystem'")
raise ValueError(
"Invalid processed data source. Expected one of 'database', 'filesystem'"
)

session_to_nwb = getattr(imaging._linking_module, "session_to_nwb", False)

Expand All @@ -382,9 +416,13 @@ def imaging_session_to_nwb(
save_path = find_full_path(get_imaging_root_data_dir(), output_relative_dir)

if include_raw_data:
processed_data_source="filesystem"
create_raw_data_nwbfile(session_key, output_directory=output_dir, nwb_path=save_path)
with NWBHDF5IO((save_path / f'{session_key["subject"]}_nwbfile'), mode="r+") as io:
processed_data_source = "filesystem"
create_raw_data_nwbfile(
session_key, output_directory=output_dir, nwb_path=save_path
)
with NWBHDF5IO(
(save_path / f'{session_key["subject"]}_nwbfile'), mode="r+"
) as io:
nwb_file = io.read()
if session_to_nwb:
nwb_file = session_to_nwb(
Expand All @@ -398,6 +436,7 @@ def imaging_session_to_nwb(
else:
if "Subject" in nwbfile_kwargs:
from pynwb.file import Subject

nwb_file.subject = Subject(**nwbfile_kwargs["Subject"])
else:
nwb_file = NWBFile(**nwbfile_kwargs)
Expand All @@ -417,27 +456,37 @@ def imaging_session_to_nwb(

imaging_plane = add_scan_to_nwb(session_key, nwbfile=nwb_file)
add_image_series_to_nwb(session_key, imaging_plane=imaging_plane)
add_segmentation_data_to_nwb(session_key, nwbfile=nwb_file, imaging_plane=imaging_plane)
add_segmentation_data_to_nwb(
session_key, nwbfile=nwb_file, imaging_plane=imaging_plane
)

return nwb_file

elif processed_data_source == "filesystem":
create_processed_data_nwbfile(session_key, output_directory=output_dir, nwb_path=save_path)
with NWBHDF5IO((save_path / f'{session_key["subject"]}_nwbfile'), mode="r+") as io:
nwb_file = io.read()
if session_to_nwb:
nwb_file = session_to_nwb(
session_key,
lab_key=lab_key,
project_key=project_key,
protocol_key=protocol_key,
additional_nwbfile_kwargs=nwbfile_kwargs,
)
with NWBHDF5IO(
(save_path / f'{session_key["subject"]}_nwbfile'), mode="w"
) as io:
io.write(nwb_file)
else:
if "Subject" in nwbfile_kwargs:
from pynwb.file import Subject
nwb_file.subject = Subject(**nwbfile_kwargs["Subject"])

elif processed_data_source == "filesystem":
create_processed_data_nwbfile(
session_key, output_directory=output_dir, nwb_path=save_path
)
with NWBHDF5IO(
(save_path / f'{session_key["subject"]}_nwbfile'), mode="r+"
) as io:
nwb_file = io.read()
if session_to_nwb:
nwb_file = session_to_nwb(
session_key,
lab_key=lab_key,
project_key=project_key,
protocol_key=protocol_key,
additional_nwbfile_kwargs=nwbfile_kwargs,
)
io.write(nwb_file)
else:
nwb_file = NWBFile(**nwbfile_kwargs)
io.write(nwb_file)
if "Subject" in nwbfile_kwargs:
from pynwb.file import Subject

nwb_file.subject = Subject(**nwbfile_kwargs["Subject"])
else:
nwb_file = NWBFile(**nwbfile_kwargs)
io.write(nwb_file)

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