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Feat 33 schema version #40

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merged 8 commits into from
Apr 8, 2024
Merged

Feat 33 schema version #40

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4b692cd
feat: updating schema
jtyoung84 Apr 4, 2024
806aed8
feat: updates bergamo session
jtyoung84 Apr 5, 2024
5d263a9
feat: updates bergamo session test json
jtyoung84 Apr 5, 2024
a3f5fa4
feat: updates bergamo tests
jtyoung84 Apr 5, 2024
88ec972
feat: updates ephys session
jtyoung84 Apr 5, 2024
d4ced3c
feat: updates fip session
jtyoung84 Apr 5, 2024
32de7f8
feat: updates mesoscope session
jtyoung84 Apr 5, 2024
f735151
feat: runs linters
jtyoung84 Apr 5, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ readme = "README.md"
dynamic = ["version"]

dependencies = [
"aind-data-schema==0.26.5",
"aind-data-schema==0.33.3",
"scanimage-tiff-reader==1.4.1.4",
"tifffile==2024.2.12",
"pydantic-settings>=2.0",
Expand Down
163 changes: 85 additions & 78 deletions src/aind_metadata_mapper/bergamo/session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,13 @@
LaserConfig,
Modality,
Session,
StimulusEpoch,
StimulusModality,
Stream,
)
from aind_data_schema.models.stimulus import (
PhotoStimulation,
PhotoStimulationGroup,
StimulusEpoch,
)
from aind_data_schema.models.units import PowerUnit, SizeUnit
from pydantic import Field
Expand Down Expand Up @@ -401,8 +402,6 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
]

data_stream = Stream(
mouse_platform_name=self.job_settings.mouse_platform_name,
active_mouse_platform=self.job_settings.active_mouse_platform,
stream_start_time=self.job_settings.stream_start_time,
stream_end_time=self.job_settings.stream_end_time,
stream_modalities=[Modality.POPHYS],
Expand Down Expand Up @@ -451,6 +450,8 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
),
],
)
stimulus_name = "PhotoStimulation"
photostim_interval = self.job_settings.photo_stim_inter_trial_interval
return Session(
experimenter_full_name=self.job_settings.experimenter_full_name,
session_start_time=self.job_settings.session_start_time,
Expand All @@ -462,93 +463,99 @@ def _transform(self, extracted_source: RawImageInfo) -> Session:
data_streams=[data_stream],
stimulus_epochs=[
StimulusEpoch(
stimulus=PhotoStimulation(
stimulus_name="PhotoStimulation",
number_groups=(
self.job_settings.num_of_photo_stim_groups
),
groups=[
PhotoStimulationGroup(
group_index=(
self.job_settings.photo_stim_groups[0][
"group_index"
]
),
number_of_neurons=int(
np.array(
stimulus_name=stimulus_name,
stimulus_modalities=[
StimulusModality.OPTOGENETICS,
],
stimulus_parameters=[
PhotoStimulation(
stimulus_name="PhotoStimulation",
number_groups=(
self.job_settings.num_of_photo_stim_groups
),
groups=[
PhotoStimulationGroup(
group_index=(
self.job_settings.photo_stim_groups[0][
"group_index"
]
),
number_of_neurons=int(
np.array(
photostim_groups[0]["rois"][1][
"scanfields"
]["slmPattern"]
).shape[0]
),
stimulation_laser_power=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["slmPattern"]
).shape[0]
),
stimulation_laser_power=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["powers"]
),
number_trials=(
self.job_settings.photo_stim_groups[0][
"number_trials"
]
),
number_spirals=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["repetitions"]
),
spiral_duration=photostim_groups[0]["rois"][1][
"scanfields"
]["duration"],
inter_spiral_interval=photostim_groups[0][
"rois"
][2]["scanfields"]["duration"],
),
PhotoStimulationGroup(
group_index=(
self.job_settings.photo_stim_groups[1][
"group_index"
]
),
number_of_neurons=int(
np.array(
]["powers"]
),
number_trials=(
self.job_settings.photo_stim_groups[0][
"number_trials"
]
),
number_spirals=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["slmPattern"]
).shape[0]
),
stimulation_laser_power=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["powers"]
),
number_trials=(
self.job_settings.photo_stim_groups[1][
"number_trials"
]
]["repetitions"]
),
spiral_duration=photostim_groups[0][
"rois"
][1]["scanfields"]["duration"],
inter_spiral_interval=photostim_groups[0][
"rois"
][2]["scanfields"]["duration"],
),
number_spirals=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["repetitions"]
PhotoStimulationGroup(
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@jtyoung84 This looks like a duplicate

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I think they're close, but there is a slight difference with the group index

group_index=(
self.job_settings.photo_stim_groups[1][
"group_index"
]
),
number_of_neurons=int(
np.array(
photostim_groups[0]["rois"][1][
"scanfields"
]["slmPattern"]
).shape[0]
),
stimulation_laser_power=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["powers"]
),
number_trials=(
self.job_settings.photo_stim_groups[1][
"number_trials"
]
),
number_spirals=int(
photostim_groups[0]["rois"][1][
"scanfields"
]["repetitions"]
),
spiral_duration=photostim_groups[0][
"rois"
][1]["scanfields"]["duration"],
inter_spiral_interval=photostim_groups[0][
"rois"
][2]["scanfields"]["duration"],
),
spiral_duration=photostim_groups[0]["rois"][1][
"scanfields"
]["duration"],
inter_spiral_interval=photostim_groups[0][
"rois"
][2]["scanfields"]["duration"],
),
],
inter_trial_interval=(
self.job_settings.photo_stim_inter_trial_interval
),
),
],
inter_trial_interval=(photostim_interval),
)
],
stimulus_start_time=(
self.job_settings.stimulus_start_time
),
stimulus_end_time=self.job_settings.stimulus_end_time,
)
],
mouse_platform_name=self.job_settings.mouse_platform_name,
active_mouse_platform=self.job_settings.active_mouse_platform,
)

def run_job(self) -> JobResponse:
Expand Down
13 changes: 7 additions & 6 deletions src/aind_metadata_mapper/ephys/session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,12 +106,6 @@ def _transform(self, extracted_source: ParsedInformation) -> Session:
session_stream["stream_end_time"] = datetime.strptime(
stage[-1][0], "%Y/%m/%d %H:%M:%S.%f"
)
session_stream["mouse_platform_name"] = data_stream[
"mouse_platform_name"
]
session_stream["active_mouse_platform"] = data_stream[
"active_mouse_platform"
]
session_stream["stream_modalities"] = [Modality.ECEPHYS]
session_stream["stick_microscopes"] = stick_microscopes
session_stream["camera_names"] = camera_names
Expand All @@ -134,6 +128,13 @@ def _transform(self, extracted_source: ParsedInformation) -> Session:

ephys_session["data_streams"].append(session_stream)

ephys_session["mouse_platform_name"] = data_stream[
"mouse_platform_name"
]
ephys_session["active_mouse_platform"] = data_stream[
"active_mouse_platform"
]

end_times = [
datetime.strptime(x[-1][0], "%Y/%m/%d %H:%M:%S.%f")
for x in stage_logs
Expand Down
34 changes: 22 additions & 12 deletions src/aind_metadata_mapper/fib/session.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,14 +11,12 @@
FiberConnectionConfig,
LightEmittingDiodeConfig,
Session,
StimulusEpoch,
StimulusModality,
Stream,
)
from aind_data_schema.models.modalities import Modality
from aind_data_schema.models.stimulus import (
OptoStimulation,
PulseShape,
StimulusEpoch,
)
from aind_data_schema.models.stimulus import OptoStimulation, PulseShape
from pydantic import Field
from pydantic_settings import BaseSettings

Expand Down Expand Up @@ -148,10 +146,18 @@ def _transform(self, extracted_source: ParsedMetadata) -> Session:
opto_stim = OptoStimulation(
stimulus_name=stimulus_name,
pulse_shape=PulseShape.SQUARE,
pulse_frequency=frequency,
number_pulse_trains=trial_num,
pulse_width=pulse_width,
pulse_train_duration=opto_duration,
pulse_frequency=[
frequency,
],
number_pulse_trains=[
trial_num,
],
pulse_width=[
pulse_width,
],
pulse_train_duration=[
opto_duration,
],
pulse_train_interval=opto_interval,
baseline_duration=opto_base,
fixed_pulse_train_interval=True, # TODO: Check this is right
Expand All @@ -165,7 +171,11 @@ def _transform(self, extracted_source: ParsedMetadata) -> Session:
seconds=experiment_duration
)
stimulus_epochs = StimulusEpoch(
stimulus=opto_stim,
stimulus_name=stimulus_name,
stimulus_modalities=[StimulusModality.OPTOGENETICS],
stimulus_parameters=[
opto_stim,
],
stimulus_start_time=session_start_time,
stimulus_end_time=end_datetime,
)
Expand Down Expand Up @@ -193,8 +203,6 @@ def _transform(self, extracted_source: ParsedMetadata) -> Session:
stream_end_time=end_datetime,
light_sources=light_source,
stream_modalities=[Modality.FIB],
mouse_platform_name=mouse_platform_name,
active_mouse_platform=active_mouse_platform,
detectors=detectors,
fiber_connections=fiber_connections,
)
Expand All @@ -211,6 +219,8 @@ def _transform(self, extracted_source: ParsedMetadata) -> Session:
session_type=session_type,
notes=notes,
data_streams=data_stream,
mouse_platform_name=mouse_platform_name,
active_mouse_platform=active_mouse_platform,
)

return ophys_session
Expand Down
14 changes: 5 additions & 9 deletions src/aind_metadata_mapper/mesoscope/session.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
"""Mesoscope ETL"""

import argparse
import json
import sys
Expand Down Expand Up @@ -99,7 +100,8 @@ def _extract(self) -> dict:
behavior_source = self.job_settings.behavior_source
session_metadata = {}
if behavior_source.is_dir():
for ftype in behavior_source.glob("*json"):
# deterministic order
for ftype in sorted(list(behavior_source.glob("*json"))):
if (
"Behavior" in ftype.stem
or "Eye" in ftype.stem
Expand Down Expand Up @@ -167,8 +169,6 @@ def _transform(self, extracted_source: dict) -> Session:
stream_start_time=self.job_settings.session_start_time,
stream_end_time=self.job_settings.session_end_time,
ophys_fovs=fovs,
mouse_platform_name=self.job_settings.mouse_platform_name,
active_mouse_platform=True,
stream_modalities=[Modality.POPHYS],
)
)
Expand All @@ -188,10 +188,6 @@ def _transform(self, extracted_source: dict) -> Session:
camera_names=[camera_name],
stream_start_time=start_time,
stream_end_time=end_time,
mouse_platform_name=(
self.job_settings.mouse_platform_name
),
active_mouse_platform=True,
stream_modalities=[Modality.BEHAVIOR_VIDEOS],
)
)
Expand All @@ -216,8 +212,6 @@ def _transform(self, extracted_source: dict) -> Session:
camera_names=["Vasculature"],
stream_start_time=vasculature_dt,
stream_end_time=vasculature_dt,
mouse_platform_name=self.job_settings.mouse_platform_name,
active_mouse_platform=True,
stream_modalities=[
Modality.CONFOCAL
], # TODO: ask Saskia about this
Expand All @@ -232,6 +226,8 @@ def _transform(self, extracted_source: dict) -> Session:
session_end_time=self.job_settings.session_end_time,
rig_id=extracted_source["platform"]["rig_id"],
data_streams=data_streams,
mouse_platform_name=self.job_settings.mouse_platform_name,
active_mouse_platform=True,
)

def run_job(self) -> None:
Expand Down
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