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feat: puts hard-coded vals into settings class
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@jtyoung84
jtyoung84 committed Oct 28, 2023
1 parent dcca38d commit 207d387
Showing 1 changed file with 79 additions and 26 deletions.
105 changes: 79 additions & 26 deletions src/aind_metadata_mapper/bergamo/session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
from datetime import datetime, time
from os import PathLike
from pathlib import Path
from typing import List, Tuple, Union
from typing import Dict, List, Tuple, Union

import numpy as np
from aind_data_schema.session import (
Expand All @@ -26,14 +26,15 @@
PhotoStimulationGroup,
StimulusEpoch,
)
from aind_data_schema.utils.units import PowerUnit, SizeUnit
from pydantic import BaseSettings, Extra
from ScanImageTiffReader import ScanImageTiffReader

from aind_metadata_mapper.core import BaseEtl


@dataclass(frozen=True)
class UserSettings:
"""Data that need to be input by user or pulled from config file"""
class UserSettings(BaseSettings):
"""Data that needs to be input by user. Can be pulled from env files"""

experimenter_full_name: List[str]
subject_id: str
Expand All @@ -45,10 +46,40 @@ class UserSettings:
stimulus_start_time: time
stimulus_end_time: time

# Dat that might change but can have default values
# Data that might change but can have default values
session_type: str = "BCI"
iacuc_protocol: str = "2115"
rig_id: str = "Bergamo photostim."
camera_names: Tuple[str] = ("Side Camera",)
laser_a_name: str = "Laser A"
laser_a_wavelength: int = 920
laser_a_wavelength_unit: SizeUnit = SizeUnit.NM
detector_a_name: str = "PMT A"
detector_a_exposure_time: float = 0.1
detector_a_trigger_type: str = "Internal"
fov_0_index: int = 0
fov_0_imaging_depth: int = 150
fov_0_targeted_structure: str = "M1"
fov_0_coordinate_ml: float = 1.5
fov_0_coordinate_ap: float = 1.5
fov_0_reference: str = "Bregma"
fov_0_magnification: str = "16x"
photo_stim_inter_trial_interval: int = 10
photo_stim_groups: List[Dict[str, int]] = [
{"group_index": 0, "number_trials": 5},
{"group_index": 0, "number_trials": 5},
]

@property
def num_of_photo_stim_groups(self):
"""Compute number of photo stimulation groups from list of groups"""
return len(self.photo_stim_groups)

class Config:
"""Config to set env var prefix to BERGAMO"""

extra = Extra.forbid
env_prefix = "BERGAMO_"


@dataclass(frozen=True)
Expand Down Expand Up @@ -364,37 +395,39 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
camera_names=list(self.user_settings.camera_names),
light_sources=[
Laser(
name="Laser A",
wavelength=920,
wavelength_unit="nanometer",
name=self.user_settings.laser_a_name,
wavelength=self.user_settings.laser_a_wavelength,
wavelength_unit=self.user_settings.laser_a_wavelength_unit,
excitation_power=int(
siHeader.metadata["hBeams"]["powers"][1:-1].split()[0]
),
excitation_power_unit="percent",
excitation_power_unit=PowerUnit.PERCENT,
),
],
detectors=[
Detector(
name="PMT A",
exposure_time=0.1,
trigger_type="Internal",
name=self.user_settings.detector_a_name,
exposure_time=self.user_settings.detector_a_exposure_time,
trigger_type=self.user_settings.detector_a_trigger_type,
),
],
ophys_fovs=[
FieldOfView(
index=0,
imaging_depth=150,
targeted_structure="M1",
fov_coordinate_ml=1.5,
fov_coordinate_ap=1.5,
fov_reference="Bregma",
index=self.user_settings.fov_0_index,
imaging_depth=self.user_settings.fov_0_imaging_depth,
targeted_structure=(
self.user_settings.fov_0_targeted_structure
),
fov_coordinate_ml=self.user_settings.fov_0_coordinate_ml,
fov_coordinate_ap=self.user_settings.fov_0_coordinate_ap,
fov_reference=self.user_settings.fov_0_reference,
fov_width=int(
siHeader.metadata["hRoiManager"]["pixelsPerLine"]
),
fov_height=int(
siHeader.metadata["hRoiManager"]["linesPerFrame"]
),
magnification="16x",
magnification=self.user_settings.fov_0_magnification,
fov_scale_factor=float(
siHeader.metadata["hRoiManager"]["scanZoomFactor"]
),
Expand All @@ -409,18 +442,24 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
session_start_time=self.user_settings.session_start_time,
session_end_time=self.user_settings.session_end_time,
subject_id=self.user_settings.subject_id,
session_type="BCI",
session_type=self.user_settings.session_type,
iacuc_protocol=self.user_settings.iacuc_protocol,
rig_id=self.user_settings.rig_id,
data_streams=[data_stream],
stimulus_epochs=[
StimulusEpoch(
stimulus=PhotoStimulation(
stimulus_name="PhotoStimulation",
number_groups=2,
number_groups=(
self.user_settings.num_of_photo_stim_groups
),
groups=[
PhotoStimulationGroup(
group_index=0,
group_index=(
self.user_settings.photo_stim_groups[0][
"group_index"
]
),
number_of_neurons=int(
np.array(
photostim_groups[0]["rois"][1][
Expand All @@ -433,7 +472,11 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
"scanfields"
]["powers"]
),
number_trials=5,
number_trials=(
self.user_settings.photo_stim_groups[0][
"number_trials"
]
),
number_spirals=int(
photostim_groups[0]["rois"][1][
"scanfields"
Expand All @@ -447,7 +490,11 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
][2]["scanfields"]["duration"],
),
PhotoStimulationGroup(
group_index=0,
group_index=(
self.user_settings.photo_stim_groups[1][
"group_index"
]
),
number_of_neurons=int(
np.array(
photostim_groups[0]["rois"][1][
Expand All @@ -460,7 +507,11 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
"scanfields"
]["powers"]
),
number_trials=5,
number_trials=(
self.user_settings.photo_stim_groups[1][
"number_trials"
]
),
number_spirals=int(
photostim_groups[0]["rois"][1][
"scanfields"
Expand All @@ -474,7 +525,9 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
][2]["scanfields"]["duration"],
),
],
inter_trial_interval=10,
inter_trial_interval=(
self.user_settings.photo_stim_inter_trial_interval
),
),
stimulus_start_time=(
self.user_settings.stimulus_start_time
Expand Down

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