Made roi_corners for FoI multivalued so we can add one roi per image

MontpellierRessourcesImagerie · Nov 14, 2024 · ef89828 · ef89828
1 parent cca0cef
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Showing 12 changed files with 2,298 additions and 2,289 deletions.
diff --git a/project/excel/microscopemetrics_schema.xlsx b/project/excel/microscopemetrics_schema.xlsx
diff --git a/project/graphql/microscopemetrics_schema.graphql b/project/graphql/microscopemetrics_schema.graphql
@@ -192,7 +192,7 @@ type FieldIlluminationOutput
     keyMeasurements: FieldIlluminationKeyMeasurements
     intensityProfiles: [Table]
     roiProfiles: [Roi]
-    roiCorners: Roi
+    roiCorners: [Roi]
     roiCentersOfMass: [Roi]
     roiCentersGeometric: [Roi]
     roiCentersFitted: [Roi]

diff --git a/project/jsonld/microscopemetrics_schema.context.jsonld b/project/jsonld/microscopemetrics_schema.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-10-18T16:23:49",
+      "generation_date": "2024-11-14T12:43:10",
       "source": "microscopemetrics_schema.yaml"
    },
    "@context": {

diff --git a/project/jsonld/microscopemetrics_schema.jsonld b/project/jsonld/microscopemetrics_schema.jsonld
@@ -3973,6 +3973,7 @@
         "FieldIlluminationOutput"
       ],
       "range": "Roi",
+      "multivalued": true,
       "inlined": true,
       "@type": "SlotDefinition"
     },
@@ -6157,6 +6158,7 @@
           "name": "roi_corners",
           "description": "Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images.",
           "range": "Roi",
+          "multivalued": true,
           "@type": "SlotDefinition"
         },
         {
@@ -6657,7 +6659,7 @@
   "source_file": "microscopemetrics_schema.yaml",
   "source_file_date": "2024-10-16T16:49:39",
   "source_file_size": 848,
-  "generation_date": "2024-10-18T16:23:49",
+  "generation_date": "2024-11-14T12:43:10",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/microscopemetrics_schema.context.jsonld",

diff --git a/project/jsonschema/microscopemetrics_schema.schema.json b/project/jsonschema/microscopemetrics_schema.schema.json
@@ -915,8 +915,11 @@
                     "type": "array"
                 },
                 "roi_corners": {
-                    "$ref": "#/$defs/Roi",
-                    "description": "Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images."
+                    "description": "Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images.",
+                    "items": {
+                        "$ref": "#/$defs/Roi"
+                    },
+                    "type": "array"
                 },
                 "roi_profiles": {
                     "description": "line ROIs used to compute the intensity profiles",

diff --git a/project/owl/microscopemetrics_schema.owl.ttl b/project/owl/microscopemetrics_schema.owl.ttl
diff --git a/project/protobuf/microscopemetrics_schema.proto b/project/protobuf/microscopemetrics_schema.proto
@@ -175,7 +175,7 @@ message FieldIlluminationOutput
   fieldIlluminationKeyMeasurements keyMeasurements = 0
  repeated  table intensityProfiles = 0
  repeated  roi roiProfiles = 0
-  roi roiCorners = 0
+ repeated  roi roiCorners = 0
  repeated  roi roiCentersOfMass = 0
  repeated  roi roiCentersGeometric = 0
  repeated  roi roiCentersFitted = 0

diff --git a/project/shacl/microscopemetrics_schema.shacl.ttl b/project/shacl/microscopemetrics_schema.shacl.ttl
diff --git a/project/shex/microscopemetrics_schema.shex b/project/shex/microscopemetrics_schema.shex
@@ -390,7 +390,7 @@ CLOSED {
           <https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema/roi_profiles>
           @<https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema/Roi> * ;
           <https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema/roi_corners>
-          @<https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema/Roi> ? ;
+          @<https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema/Roi> * ;
           <https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema/roi_centers_of_mass>
           @<https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema/Roi> * ;
 

diff --git a/project/sqlschema/microscopemetrics_schema.sql b/project/sqlschema/microscopemetrics_schema.sql
@@ -355,7 +355,6 @@
 --     * Slot: validated Description: Has the dataset been validated by a human
 --     * Slot: validation_datetime Description: The datetime of the validation
 --     * Slot: key_measurements_id Description: Key-Value pairs containing the Key measurements for the field illumination analysis
---     * Slot: roi_corners_id Description: Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images.
 --     * Slot: comment_id Description: A human readable comment about the dataset
 -- # Class: "FieldIlluminationKeyMeasurements" Description: ""
 --     * Slot: id Description: 
@@ -454,6 +453,9 @@
 -- # Class: "FieldIlluminationOutput_roi_profiles" Description: ""
 --     * Slot: FieldIlluminationOutput_id Description: Autocreated FK slot
 --     * Slot: roi_profiles_id Description: line ROIs used to compute the intensity profiles
+-- # Class: "FieldIlluminationOutput_roi_corners" Description: ""
+--     * Slot: FieldIlluminationOutput_id Description: Autocreated FK slot
+--     * Slot: roi_corners_id Description: Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images.
 -- # Class: "FieldIlluminationOutput_roi_centers_of_mass" Description: ""
 --     * Slot: FieldIlluminationOutput_id Description: Autocreated FK slot
 --     * Slot: roi_centers_of_mass_id Description: Point ROIs marking the center of mass of the area of maximum illumination. When the image is very flat, the 99 percentile is used instead. One point per channel.
@@ -1194,11 +1196,9 @@ CREATE TABLE "FieldIlluminationOutput" (
 	validated BOOLEAN NOT NULL, 
 	validation_datetime DATETIME, 
 	key_measurements_id INTEGER, 
-	roi_corners_id INTEGER, 
 	comment_id INTEGER, 
 	PRIMARY KEY (id), 
 	FOREIGN KEY(key_measurements_id) REFERENCES "FieldIlluminationKeyMeasurements" (id), 
-	FOREIGN KEY(roi_corners_id) REFERENCES "Roi" (id), 
 	FOREIGN KEY(comment_id) REFERENCES "Comment" (id)
 );
 CREATE TABLE "FieldIlluminationKeyMeasurements" (
@@ -1551,6 +1551,13 @@ CREATE TABLE "FieldIlluminationOutput_roi_profiles" (
 	FOREIGN KEY("FieldIlluminationOutput_id") REFERENCES "FieldIlluminationOutput" (id), 
 	FOREIGN KEY(roi_profiles_id) REFERENCES "Roi" (id)
 );
+CREATE TABLE "FieldIlluminationOutput_roi_corners" (
+	"FieldIlluminationOutput_id" INTEGER, 
+	roi_corners_id INTEGER, 
+	PRIMARY KEY ("FieldIlluminationOutput_id", roi_corners_id), 
+	FOREIGN KEY("FieldIlluminationOutput_id") REFERENCES "FieldIlluminationOutput" (id), 
+	FOREIGN KEY(roi_corners_id) REFERENCES "Roi" (id)
+);
 CREATE TABLE "FieldIlluminationOutput_roi_centers_of_mass" (
 	"FieldIlluminationOutput_id" INTEGER, 
 	roi_centers_of_mass_id INTEGER, 

diff --git a/src/microscopemetrics_schema/datamodel/microscopemetrics_schema.py b/src/microscopemetrics_schema/datamodel/microscopemetrics_schema.py
@@ -1,5 +1,5 @@
 # Auto generated from microscopemetrics_schema.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-10-18T16:23:51
+# Generation date: 2024-11-14T12:43:12
 # Schema: microscopemetrics-schema
 #
 # id: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
@@ -1370,7 +1370,7 @@ class FieldIlluminationOutput(MetricsOutput):
     key_measurements: Optional[Union[dict, "FieldIlluminationKeyMeasurements"]] = None
     intensity_profiles: Optional[Union[Union[dict, Table], List[Union[dict, Table]]]] = empty_list()
     roi_profiles: Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]] = empty_list()
-    roi_corners: Optional[Union[dict, Roi]] = None
+    roi_corners: Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]] = empty_list()
     roi_centers_of_mass: Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]] = empty_list()
     roi_centers_geometric: Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]] = empty_list()
     roi_centers_fitted: Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]] = empty_list()
@@ -1389,8 +1389,9 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             self.roi_profiles = [self.roi_profiles] if self.roi_profiles is not None else []
         self.roi_profiles = [v if isinstance(v, Roi) else Roi(**as_dict(v)) for v in self.roi_profiles]
 
-        if self.roi_corners is not None and not isinstance(self.roi_corners, Roi):
-            self.roi_corners = Roi(**as_dict(self.roi_corners))
+        if not isinstance(self.roi_corners, list):
+            self.roi_corners = [self.roi_corners] if self.roi_corners is not None else []
+        self.roi_corners = [v if isinstance(v, Roi) else Roi(**as_dict(v)) for v in self.roi_corners]
 
         if not isinstance(self.roi_centers_of_mass, list):
             self.roi_centers_of_mass = [self.roi_centers_of_mass] if self.roi_centers_of_mass is not None else []
@@ -3102,7 +3103,7 @@ class slots:
                    model_uri=MICROSCOPEMETRICS_SCHEMA.fieldIlluminationOutput__roi_profiles, domain=None, range=Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]])
 
 slots.fieldIlluminationOutput__roi_corners = Slot(uri=MICROSCOPEMETRICS_SCHEMA['analyses/field_illumination_schema/roi_corners'], name="fieldIlluminationOutput__roi_corners", curie=MICROSCOPEMETRICS_SCHEMA.curie('analyses/field_illumination_schema/roi_corners'),
-                   model_uri=MICROSCOPEMETRICS_SCHEMA.fieldIlluminationOutput__roi_corners, domain=None, range=Optional[Union[dict, Roi]])
+                   model_uri=MICROSCOPEMETRICS_SCHEMA.fieldIlluminationOutput__roi_corners, domain=None, range=Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]])
 
 slots.fieldIlluminationOutput__roi_centers_of_mass = Slot(uri=MICROSCOPEMETRICS_SCHEMA['analyses/field_illumination_schema/roi_centers_of_mass'], name="fieldIlluminationOutput__roi_centers_of_mass", curie=MICROSCOPEMETRICS_SCHEMA.curie('analyses/field_illumination_schema/roi_centers_of_mass'),
                    model_uri=MICROSCOPEMETRICS_SCHEMA.fieldIlluminationOutput__roi_centers_of_mass, domain=None, range=Optional[Union[Union[dict, Roi], List[Union[dict, Roi]]]])

diff --git a/src/microscopemetrics_schema/schema/analyses/field_illumination_schema.yaml b/src/microscopemetrics_schema/schema/analyses/field_illumination_schema.yaml
@@ -67,7 +67,7 @@ classes:
         range: Roi
         description: >-
           Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images.
-        multivalued: false
+        multivalued: true
       roi_centers_of_mass:
         range: Roi
         description: >-