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Feat 36 bump version pins #87

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Feat 36 bump version pins #87

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d0627db
Update pyproject.toml
Sun-flow Jul 12, 2024
4af5499
changes to examples
Sun-flow Jul 12, 2024
26d3e1b
example changes
Sun-flow Jul 12, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
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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==0.36.0",
"aind-data-schema==0.38.0",
"aind-data-schema-models==0.1.7",
"pydantic-settings>=2.0",
"pandas",
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5 changes: 3 additions & 2 deletions src/aind_metadata_mapper/bergamo/session.py
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@@ -1,4 +1,5 @@
"""Module to map bergamo metadata into a session model."""

import argparse
import bisect
import json
Expand Down Expand Up @@ -1154,15 +1155,15 @@ def run_job(self) -> JobResponse: # noqa: C901
stimulus_parameters=[photostim],
# opticalBCI class to be added in future
stimulus_device_names=self.job_settings.stimulus_device_names,
light_source_config=LaserConfig(
light_source_config=[LaserConfig(
# from rig json
name=self.job_settings.photostim_laser_name,
wavelength=self.job_settings.photostim_laser_wavelength,
# user set value
excitation_power=np.nanmean(group_powers),
# from tiff header,
excitation_power_unit=PowerUnit.PERCENT,
),
)],
output_parameters={
"tiff_files": tiff_list,
"tiff_stem": tiff_stem,
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12 changes: 6 additions & 6 deletions src/aind_metadata_mapper/open_ephys/utils/behavior_utils.py
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Expand Up @@ -730,9 +730,9 @@ def fix_omitted_end_frame(stim_pres_table: pd.DataFrame) -> pd.DataFrame:
stim_pres_table[stim_pres_table["omitted"]]["start_frame"]
+ median_stim_frame_duration
)
stim_pres_table.loc[
stim_pres_table["omitted"], "end_frame"
] = omitted_end_frames
stim_pres_table.loc[stim_pres_table["omitted"], "end_frame"] = (
omitted_end_frames
)

stim_dtypes = stim_pres_table.dtypes.to_dict()
stim_dtypes["start_frame"] = int
Expand Down Expand Up @@ -796,9 +796,9 @@ def compute_is_sham_change(
if np.array_equal(
active_images, stim_image_names[passive_block_mask].values
):
stim_df.loc[
passive_block_mask, "is_sham_change"
] = stim_df[active_block_mask]["is_sham_change"].values
stim_df.loc[passive_block_mask, "is_sham_change"] = (
stim_df[active_block_mask]["is_sham_change"].values
)

return stim_df.sort_index()

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1 change: 1 addition & 0 deletions src/aind_metadata_mapper/open_ephys/utils/constants.py
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@@ -1,4 +1,5 @@
""" Constants for the naming utils of metadata mapper """

import re

INT_NULL = -99
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2 changes: 1 addition & 1 deletion tests/resources/bergamo/expected_session.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.2.6",
"schema_version": "0.3.1",
"protocol_id": [],
"experimenter_full_name": [
"John Apple"
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2 changes: 1 addition & 1 deletion tests/resources/bruker/expected_session.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.2.6",
"schema_version": "0.3.1",
"protocol_id": [
""
],
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7 changes: 2 additions & 5 deletions tests/resources/dynamic_routing/base-missing-probe_rig.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.3.8",
"schema_version": "0.5.1",
"rig_id": "327_NP2_240401",
"modification_date": "2024-04-01",
"mouse_platform": {
Expand Down Expand Up @@ -233,7 +233,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -375,7 +374,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -514,7 +512,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -1007,7 +1004,7 @@
"data_interface": "Other",
"cooling": "Air",
"computer_name": null,
"max_frame_rate": null,

"frame_rate_unit": "hertz",
"immersion": null,
"chroma": null,
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7 changes: 2 additions & 5 deletions tests/resources/dynamic_routing/base_rig.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.3.8",
"schema_version": "0.5.1",
"rig_id": "327_NP2_240401",
"modification_date": "2024-04-01",
"mouse_platform": {
Expand Down Expand Up @@ -233,7 +233,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -375,7 +374,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -514,7 +512,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -1050,7 +1047,7 @@
"data_interface": "Other",
"cooling": "Air",
"computer_name": null,
"max_frame_rate": null,

"frame_rate_unit": "hertz",
"immersion": null,
"chroma": null,
Expand Down
11 changes: 4 additions & 7 deletions tests/resources/dynamic_routing/mvr_rig.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.3.8",
"schema_version": "0.5.1",
"rig_id": "327_NP2_240401",
"modification_date": "2024-04-01",
"mouse_platform": {
Expand Down Expand Up @@ -233,8 +233,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -380,7 +379,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -524,8 +522,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -1065,7 +1062,7 @@
"data_interface": "Other",
"cooling": "Air",
"computer_name": null,
"max_frame_rate": null,

"frame_rate_unit": "hertz",
"immersion": null,
"chroma": null,
Expand Down
7 changes: 2 additions & 5 deletions tests/resources/dynamic_routing/sync_rig.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.3.8",
"schema_version": "0.5.1",
"rig_id": "327_NP2_240401",
"modification_date": "2024-04-01",
"mouse_platform": {
Expand Down Expand Up @@ -233,7 +233,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -375,7 +374,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -514,7 +512,6 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
Expand Down Expand Up @@ -1050,7 +1047,7 @@
"data_interface": "Other",
"cooling": "Air",
"computer_name": null,
"max_frame_rate": null,

"frame_rate_unit": "hertz",
"immersion": null,
"chroma": null,
Expand Down
2 changes: 1 addition & 1 deletion tests/resources/fip/000000_ophys_session.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.2.6",
"schema_version": "0.3.1",
"protocol_id": [],
"experimenter_full_name": [
"Don Key"
Expand Down
2 changes: 1 addition & 1 deletion tests/resources/gather_metadata_job/metadata_files/instrument.json
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Expand Up @@ -80,7 +80,7 @@
"data_interface": "Coax",
"cooling": "Air",
"computer_name": null,
"max_frame_rate": null,

"frame_rate_unit": "hertz",
"immersion": null,
"chroma": null,
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3 changes: 2 additions & 1 deletion tests/resources/mesoscope/expected_session.json
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@@ -1,13 +1,14 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.2.6",
"schema_version": "0.3.1",
"protocol_id": [],
"experimenter_full_name": [
"John Doe"
],
"session_start_time": "2024-02-22T15:30:00Z",
"session_end_time": "2024-02-22T17:30:00Z",
"session_type": "Mesoscope",
"headframe_registration": None,
"iacuc_protocol": "12345",
"rig_id": "MESO.1",
"calibrations": [],
Expand Down
2 changes: 1 addition & 1 deletion tests/resources/open_ephys/ephys_session.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py",
"schema_version": "0.2.6",
"schema_version": "0.3.1",
"protocol_id": [],
"experimenter_full_name": [
"Al Dente"
Expand Down
13 changes: 5 additions & 8 deletions tests/resources/open_ephys/open-ephys-inferred_rig.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.3.8",
"schema_version": "0.5.1",
"rig_id": "327_NP2_240401",
"modification_date": "2024-04-01",
"mouse_platform": {
Expand Down Expand Up @@ -233,8 +233,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -375,8 +374,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -514,8 +512,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -1050,7 +1047,7 @@
"data_interface": "Other",
"cooling": "Air",
"computer_name": null,
"max_frame_rate": null,

"frame_rate_unit": "hertz",
"immersion": null,
"chroma": null,
Expand Down
13 changes: 5 additions & 8 deletions tests/resources/open_ephys/open-ephys_rig.json
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@@ -1,6 +1,6 @@
{
"describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/rig.py",
"schema_version": "0.3.8",
"schema_version": "0.5.1",
"rig_id": "327_NP2_240401",
"modification_date": "2024-04-01",
"mouse_platform": {
Expand Down Expand Up @@ -233,8 +233,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -375,8 +374,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -514,8 +512,7 @@
"data_interface": "Ethernet",
"cooling": "None",
"computer_name": "127.0.0.1",
"max_frame_rate": "102",
"frame_rate_unit": "hertz",
"frame_rate_unit": "hertz",
"immersion": null,
"chroma": "Monochrome",
"sensor_width": 7400,
Expand Down Expand Up @@ -1050,7 +1047,7 @@
"data_interface": "Other",
"cooling": "Air",
"computer_name": null,
"max_frame_rate": null,

"frame_rate_unit": "hertz",
"immersion": null,
"chroma": null,
Expand Down
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