tqdm

graphql/stage.graphql

@@ -3,7 +3,19 @@ fragment ExportStage on Stage {
   positions {
     name
     id
+    x
+    z
+    y
     omeros {
+      timepoints {
+        era {
+          name
+        }
+        deltaT
+      }
+      views {
+
+      }
       acquisitionDate
       representation {
         store
@@ -17,6 +29,11 @@ fragment ExportStage on Stage {
           id
           store
           name
+          metrics {
+            id
+            key
+            value
+          }
         }
       }
     }

gucker/api/schema.py

@@ -1,12 +1,12 @@
-from rath.scalars import ID
-from mikro.funcs import execute, aexecute
+from pydantic import Field, BaseModel
+from mikro.traits import Position, Representation, Omero, Stage
+from mikro.rath import MikroRath
+from typing import Tuple, Literal, Optional
 from enum import Enum
-from mikro.traits import Representation, Stage, Position, Omero
-from mikro.scalars import Store, File
-from pydantic import BaseModel, Field
+from mikro.scalars import Store, MetricValue
+from rath.scalars import ID
 from datetime import datetime
-from typing import Tuple, Literal, Optional
-from mikro.rath import MikroRath
+from mikro.funcs import aexecute, execute
 
 
 class OmeroFileType(str, Enum):
@@ -24,16 +24,50 @@ class OmeroFileType(str, Enum):
     "Unwknon File Format"
 
 
+class ExportStageFragmentPositionsOmerosTimepointsEra(BaseModel):
+    """Era(id, created_by, created_through, created_while, name, start, end, created_at)"""
+
+    typename: Optional[Literal["Era"]] = Field(alias="__typename", exclude=True)
+    name: str
+    "The name of the era"
+
+    class Config:
+        frozen = True
+
+
+class ExportStageFragmentPositionsOmerosTimepoints(BaseModel):
+    """The relative position of a sample on a microscope stage"""
+
+    typename: Optional[Literal["Timepoint"]] = Field(alias="__typename", exclude=True)
+    era: ExportStageFragmentPositionsOmerosTimepointsEra
+    delta_t: Optional[float] = Field(alias="deltaT")
+
+    class Config:
+        frozen = True
+
+
 class ExportStageFragmentPositionsOmerosRepresentationFileorigins(BaseModel):
     typename: Optional[Literal["OmeroFile"]] = Field(alias="__typename", exclude=True)
     id: ID
-    file: Optional[File]
+    file: str
     "The file"
 
     class Config:
         frozen = True
 
 
+class ExportStageFragmentPositionsOmerosRepresentationDerivedMetrics(BaseModel):
+    typename: Optional[Literal["Metric"]] = Field(alias="__typename", exclude=True)
+    id: ID
+    key: str
+    "The Key"
+    value: Optional[MetricValue]
+    "Value"
+
+    class Config:
+        frozen = True
+
+
 class ExportStageFragmentPositionsOmerosRepresentationDerived(
     Representation, BaseModel
 ):
@@ -76,6 +110,13 @@ class ExportStageFragmentPositionsOmerosRepresentationDerived(
     store: Optional[Store]
     name: Optional[str]
     "Cleartext name"
+    metrics: Optional[
+        Tuple[
+            Optional[ExportStageFragmentPositionsOmerosRepresentationDerivedMetrics],
+            ...,
+        ]
+    ]
+    "Associated metrics of this Imasge"
 
     class Config:
         frozen = True
@@ -142,6 +183,10 @@ class ExportStageFragmentPositionsOmeros(Omero, BaseModel):
     """
 
     typename: Optional[Literal["Omero"]] = Field(alias="__typename", exclude=True)
+    timepoints: Optional[
+        Tuple[Optional[ExportStageFragmentPositionsOmerosTimepoints], ...]
+    ]
+    "Associated Timepoints"
     acquisition_date: Optional[datetime] = Field(alias="acquisitionDate")
     representation: ExportStageFragmentPositionsOmerosRepresentation
 
@@ -156,6 +201,12 @@ class ExportStageFragmentPositions(Position, BaseModel):
     name: str
     "The name of the possition"
     id: ID
+    x: float
+    "pixelSize for x in microns"
+    z: float
+    "pixelSize for z in microns"
+    y: float
+    "pixelSize for y in microns"
     omeros: Optional[Tuple[Optional[ExportStageFragmentPositionsOmeros], ...]]
     "Associated images through Omero"
 
@@ -180,7 +231,7 @@ class ExportDatasetFragmentOmerofiles(BaseModel):
     "The name of the file"
     type: OmeroFileType
     "The type of the file"
-    file: Optional[File]
+    file: str
     "The file"
 
     class Config:
@@ -206,7 +257,7 @@ class Arguments(BaseModel):
         id: ID
 
     class Meta:
-        document = "fragment ExportStage on Stage {\n  name\n  positions {\n    name\n    id\n    omeros {\n      acquisitionDate\n      representation {\n        store\n        name\n        id\n        fileOrigins {\n          id\n          file\n        }\n        derived(flatten: 4) {\n          id\n          store\n          name\n        }\n      }\n    }\n  }\n}\n\nquery GetExportStage($id: ID!) {\n  stage(id: $id) {\n    ...ExportStage\n  }\n}"
+        document = "fragment ExportStage on Stage {\n  name\n  positions {\n    name\n    id\n    x\n    z\n    y\n    omeros {\n      timepoints {\n        era {\n          name\n        }\n        deltaT\n      }\n      acquisitionDate\n      representation {\n        store\n        name\n        id\n        fileOrigins {\n          id\n          file\n        }\n        derived(flatten: 4) {\n          id\n          store\n          name\n          metrics {\n            id\n            key\n            value\n          }\n        }\n      }\n    }\n  }\n}\n\nquery GetExportStage($id: ID!) {\n  stage(id: $id) {\n    ...ExportStage\n  }\n}"
 
 
 class GetExportDatasetQuery(BaseModel):

gucker/main.py

@@ -23,6 +23,7 @@
 from mikro import Stage, Image
 import tifffile
 from arkitekt.tqdm import tqdm
+import json
 
 logger = logging.getLogger(__name__)
 
@@ -235,6 +236,15 @@ def export_representation(self, representation: Image, dir: str) -> None:
             os.path.join(dir, f"ID({representation.id}) {representation.name}.tiff"),
             representation.data,
         )
+        with open(
+            os.path.join(
+                dir, f"ID({representation.id}) {representation.name} meta.json"
+            ),
+            "w",
+        ) as f:
+            f.write(
+                json.dumps(representation.dict(), indent=4, sort_keys=True, default=str)
+            )
 
     def export_stage(self, stage: Stage) -> None:
         """Export Stage
@@ -250,15 +260,23 @@ def export_stage(self, stage: Stage) -> None:
 
         stage_dir = os.path.join(self.export_dir, f"ID({stage.id}) {export_stage.name}")
         os.makedirs(stage_dir, exist_ok=True)
-        for item in export_stage.positions:
+        for item in tqdm(export_stage.positions):
             pos_dir = os.path.join(stage_dir, f"ID({item.id}) {item.name}")
             os.makedirs(pos_dir, exist_ok=True)
+            with open(os.path.join(pos_dir, "position.json"), "w") as f:
+                f.write(
+                    json.dumps(item.dict(), indent=4, sort_keys=True, default=str),
+                )
             for image in item.omeros:
                 image_dir = os.path.join(
                     pos_dir,
                     f"ID({image.representation.id}) {image.representation.name} {image.acquisition_date}",
                 )
                 os.makedirs(image_dir, exist_ok=True)
+                with open(os.path.join(image_dir, "raw.json"), "w") as f:
+                    f.write(
+                        json.dumps(image.dict(), indent=4, sort_keys=True, default=str)
+                    )
                 self.export_representation(image.representation, image_dir)
 
                 for file in image.representation.derived: