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Ensure Units Immutability #730

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merged 4 commits into from
Apr 5, 2024
+70 −41
Merged

Ensure Units Immutability #730

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e1fb886
Block units editing and render summary
garrettmflynn Apr 4, 2024
5d77fd4
Fix ordering
garrettmflynn Apr 4, 2024
c24532d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 4, 2024
9d93629
Merge branch 'main' into block-units-editing-and-render-summary
CodyCBakerPhD Apr 5, 2024
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51 changes: 32 additions & 19 deletions pyflask/manageNeuroconv/manage_neuroconv.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@
}
}

EXTRA_SORTING_INTERFACE_PROPERTIES = ["unit_name", *EXTRA_INTERFACE_PROPERTIES.keys()]
EXTRA_SORTING_INTERFACE_PROPERTIES = ["unit_id", *EXTRA_INTERFACE_PROPERTIES.keys()]

SORTING_INTERFACE_PROPERTIES_TO_RECAST = {
"quality": {
Expand All @@ -52,14 +52,20 @@
}

SORTING_INTERFACE_PROPERTY_OVERRIDES = {
"unit_name": {"description": "The unique name for the unit", "data_type": "str"},
"unit_id": {"description": "The unique ID for this unit", "data_type": "str"},
"brain_area": {
"description": "The brain area where the unit is located.",
**EXTRA_INTERFACE_PROPERTIES["brain_area"],
},
**SORTING_INTERFACE_PROPERTIES_TO_RECAST,
}

# NOTE: No need to show this if it isn't editable
del SORTING_INTERFACE_PROPERTY_OVERRIDES["brain_area"]
brain_area_idx = EXTRA_SORTING_INTERFACE_PROPERTIES.index("brain_area")
EXTRA_SORTING_INTERFACE_PROPERTIES.pop(brain_area_idx)


EXCLUDED_SORTING_INTERFACE_PROPERTIES = ["location", "spike_times", "electrodes"] # Not validated

# NOTE: These are the only accepted dtypes...
Expand Down Expand Up @@ -721,19 +727,22 @@ def update_conversion_progress(**kwargs):
has_units = "Units" in ecephys_metadata

if has_units:
shared_units_columns = ecephys_metadata["UnitColumns"]
for interface_name, interface_unit_results in ecephys_metadata["Units"].items():
interface = converter.data_interface_objects[interface_name]

update_sorting_properties_from_table_as_json(
interface,
unit_table_json=interface_unit_results,
unit_column_info=shared_units_columns,
)

ecephys_metadata["UnitProperties"] = [
{"name": entry["name"], "description": entry["description"]} for entry in shared_units_columns
]
## NOTE: Currently do not allow editing units properties
# shared_units_columns = ecephys_metadata["UnitColumns"]
# for interface_name, interface_unit_results in ecephys_metadata["Units"].items():
# interface = converter.data_interface_objects[interface_name]

# update_sorting_properties_from_table_as_json(
# interface,
# unit_table_json=interface_unit_results,
# unit_column_info=shared_units_columns,
# )

# ecephys_metadata["UnitProperties"] = [
# {"name": entry["name"], "description": entry["description"]} for entry in shared_units_columns
# ]

del ecephys_metadata["Units"]
del ecephys_metadata["UnitColumns"]

Expand Down Expand Up @@ -1232,9 +1241,12 @@ def get_unit_table_json(interface) -> List[Dict[str, Any]]:

for property_name in properties:

# Separate this so that unit_id and unit_name exist (LOOK FURTHER)
if property_name == "unit_name":
sorting_property_value = str(unit_id) # Insert unit_id as name (str)
if property_name == "unit_id":
sorting_property_value = str(unit_id) # Insert unit_id to view

# elif property_name == "unit_name":
# sorting_property_value = str(unit_id) # By default, unit_name is unit_id (str)

elif property_name in SORTING_INTERFACE_PROPERTY_OVERRIDES:
try:
sorting_property_value = SORTING_INTERFACE_PROPERTY_OVERRIDES[property_name][
Expand Down Expand Up @@ -1417,11 +1429,11 @@ def update_sorting_properties_from_table_as_json(
for entry_index, entry in enumerate(unit_table_json):
unit_properties = dict(entry) # copy

unit_id = unit_properties.pop("unit_name", None) # NOTE: Is called unit_name in the actual units table
unit_id = unit_properties.pop("unit_id", None) # NOTE: Is called unit_name in the actual units table

for property_name, property_value in unit_properties.items():

if property_name == "unit_name":
if property_name == "unit_id":
continue # Already controlling unit_id with the above variable

dtype = unit_column_data_types[property_name]
Expand All @@ -1433,4 +1445,5 @@ def update_sorting_properties_from_table_as_json(
key=property_name,
values=np.array([property_value], dtype=dtype),
ids=[int(unit_id)],
# ids=[unit_id]
)
13 changes: 9 additions & 4 deletions schemas/base-metadata.schema.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -144,8 +144,8 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
ecephys.properties.Device.title = 'Devices'
ecephys.properties.ElectrodeGroup.title = 'Electrode Groups'

if (ecephys.properties.ElectrodeColumns) ecephys.properties.ElectrodeColumns.order = COLUMN_SCHEMA_ORDER
if (ecephys.properties.UnitProperties) ecephys.properties.UnitProperties.order = COLUMN_SCHEMA_ORDER
if (ecephys.properties.ElectrodeColumns) ecephys.properties.ElectrodeColumns.items.order = COLUMN_SCHEMA_ORDER
if (ecephys.properties.UnitColumns) ecephys.properties.UnitColumns.items.order = COLUMN_SCHEMA_ORDER


updateEcephysTable("Electrodes", copy, {
Expand All @@ -156,10 +156,15 @@ export const preprocessMetadataSchema = (schema: any = baseMetadataSchema, globa
order: ["channel_name", "group_name", "shank_electrode_number", ...UV_PROPERTIES]
})

// ecephys.properties["Units"].title = "Unit Summaries"
ecephys.properties["Units"].title = "Summarized Units"

updateEcephysTable("Units", copy, {
order: ["unit_name", "clu_id", "group_id"]
properties: {
clu_id: {
title: 'Cluster ID',
}
},
order: ["unit_id", "unit_name", "clu_id", "group_id"]
})

}
Expand Down
11 changes: 8 additions & 3 deletions src/renderer/src/stories/BasicTable.js
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,7 @@ export class BasicTable extends LitElement {
onLoaded,
onUpdate,
editable = true,
truncated = false,
} = {}) {
super();
this.name = name ?? "data_table";
Expand All @@ -147,7 +148,8 @@ export class BasicTable extends LitElement {
if (onStatusChange) this.onStatusChange = onStatusChange;
if (onLoaded) this.onLoaded = onLoaded;

this.editable = editable;
this.truncated = truncated;
this.editable = editable && !truncated;
}

#schema = {};
Expand Down Expand Up @@ -419,8 +421,6 @@ export class BasicTable extends LitElement {
}); // Only include data from schema
});

console.log(header, data, structuredData, this.data, this.#itemProps);

if (this.onUpdate) this.onUpdate([], data); // Update the whole table
}

Expand All @@ -431,6 +431,8 @@ export class BasicTable extends LitElement {
this.schema = this.schema; // Always update the schema
const entries = this.#itemProps;

if (this.truncated) this.data = this.data.slice(0, 5); // Limit to 5 rows when truncated

// Add existing additional properties to the entries variable if necessary
if (this.#itemSchema.additionalProperties) {
Object.values(this.data).reduce((acc, v) => {
Expand Down Expand Up @@ -535,6 +537,9 @@ export class BasicTable extends LitElement {
>
</div>`
: ""}
${this.truncated
? html`<p style="margin: 0; width: 100%; text-align: center; font-size: 150%;">...</p>`
: ""}
${description
? html`<p style="margin: 0; margin-top: 10px">
<small style="color: gray;">${description}</small>
Expand Down
36 changes: 21 additions & 15 deletions src/renderer/src/stories/pages/guided-mode/data/GuidedMetadata.js
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ const parentTableRenderConfig = {
return true;
},
Units: (metadata) => {
metadata.editable = false;
metadata.truncated = true;
metadata.schema.description = "Update unit information directly on your source data.";
return true;
},
Expand Down Expand Up @@ -60,21 +60,27 @@ const tableRenderConfig = {
});
},
UnitColumns: function (metadata) {
const aggregateRequirements = getAggregateRequirements.call(this, ["Ecephys", "Units"]);
metadata.editable = false;
console.log("Column metadata", metadata);
metadata.schema.description = "Update unit information directly on your source data.";

return new SimpleTable({
...metadata,
contextOptions: {
row: {
add: false,
remove: false,
},
},
editable: {
name: (value) => !aggregateRequirements.has(value),
data_type: (_, row) => !aggregateRequirements.has(row.name),
},
});
return true;

// const aggregateRequirements = getAggregateRequirements.call(this, ["Ecephys", "Units"]);
//
// return new SimpleTable({
// ...metadata,
// contextOptions: {
// row: {
// add: false,
// remove: false,
// },
// },
// editable: {
// name: (value) => !aggregateRequirements.has(value),
// data_type: (_, row) => !aggregateRequirements.has(row.name),
// },
// });
},
};

Expand Down
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