Ngff branch

[mzouink]

By running :

from funlib.persistence import open_ome_ds
from pathlib import Path
ome_data = open_ome_ds(Path("/nrs/cellmap/data/jrc_mus-pancreas-5/jrc_mus-pancreas-5.zarr/recon-1/em/fibsem-uint8"),"s0")

I get :

AttributeError                            Traceback (most recent call last)
File /groups/cellmap/cellmap/zouinkhim/cellmap_vit/tmp.py:5
      2 from pathlib import Path
      4 p = Path("/nrs/cellmap/data/jrc_mus-pancreas-5/jrc_mus-pancreas-5.zarr/recon-1/em/fibsem-uint8")
----> 5 d = open_ome_ds(p,"s0")

File ~/miniconda3/envs/cflow_v2/lib/python3.11/site-packages/funlib/persistence/arrays/ome_datasets.py:59, in open_ome_ds(store, name, mode, **kwargs)
     56 units = [axis.unit for axis in axes if axis.unit is not None]
     57 types = [axis.type for axis in axes if axis.type is not None]
---> 59 scale = get_effective_scale(ome_zarr, name)
     60 offset = get_effective_translation(ome_zarr, name)
     62 dataset = ome_zarr[name]

File ~/miniconda3/envs/cflow_v2/lib/python3.11/site-packages/funlib/persistence/arrays/ome_tmp.py:57, in get_effective_scale(node, image)
     38 def get_effective_scale(
     39     node,
     40     image: str | Literal["*"],
     41 ) -> list[float]:
     42     """Get the effective coordinate scale metadata
     43     for one image array or the whole FOV.
     44 
   (...)
     55         for the image or FOV for each axis.
     56     """
...
     26     )
     27     if image != "*" and image in node:
     28         for i, dataset_meta in enumerate(node.metadata.multiscales[0].datasets):

AttributeError: 'Position' object has no attribute 'metadata'

.zattrs:

{
    "axes": [
        "x",
        "y",
        "z"
    ],
    "multiscales": [
        {
            "axes": [
                {
                    "name": "z",
                    "type": "space",
                    "unit": "nanometer"
                },
                {
                    "name": "y",
                    "type": "space",
                    "unit": "nanometer"
                },
                {
                    "name": "x",
                    "type": "space",
                    "unit": "nanometer"
                }
            ],
            "coordinateTransformations": [
                {
                    "scale": [
                        1.0,
                        1.0,
                        1.0
                    ],
                    "type": "scale"
                }
            ],
            "datasets": [
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                8.0,
                                8.0,
                                8.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                0.0,
                                0.0,
                                0.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s0"
                },
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                16.0,
                                16.0,
                                16.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                4.0,
                                4.0,
                                4.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s1"
                },
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                32.0,
                                32.0,
                                32.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                12.0,
                                12.0,
                                12.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s2"
                },
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                64.0,
                                64.0,
                                64.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                28.0,
                                28.0,
                                28.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s3"
                },
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                128.0,
                                128.0,
                                128.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                60.0,
                                60.0,
                                60.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s4"
                },
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                256.0,
                                256.0,
                                256.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                124.0,
                                124.0,
                                124.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s5"
                },
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                512.0,
                                512.0,
                                512.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                252.0,
                                252.0,
                                252.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s6"
                },
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                1024.0,
                                1024.0,
                                1024.0
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                508.0,
                                508.0,
                                508.0
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "s7"
                }
            ],
            "name": "/recon-1/em/fibsem-uint8",
            "version": "0.4"
        }
    ],
    "ordering": "F",
    "pixelResolution": {
        "dimensions": [
            8.0,
            8.0,
            8.0
        ],
        "unit": "nm"
    },
    "renderExport": {
        "runParameters": {
            "blockSizeString": "128,128,64",
            "downsampleFactorsString": "2,2,2",
            "exportMask": false,
            "layerBounds": {},
            "layerRange": {},
            "n5Dataset": "/render/jrc_mus_pancreas_5/v3_acquire_align_destreak_ic3d_64x64_zd_1___20240906_081518",
            "n5Path": "/nrs/cellmap/data/jrc_mus-pancreas-5/jrc_mus-pancreas-5.n5",
            "renderWeb": {
                "baseDataUrl": "http://10.40.3.113:8080/render-ws/v1",
                "owner": "cellmap",
                "project": "jrc_mus_pancreas_5"
            },
            "stack": "v3_acquire_align_destreak_ic3d_64x64_zd_1",
            "stackResolutionUnit": "nm",
            "tileHeight": 4096,
            "tileWidth": 4096
        },
        "runTimestamp": "Sep 6, 2024, 8:16:09 AM",
        "stackMetadata": {
            "currentVersion": {
                "createTimestamp": "Aug 31, 2024, 10:30:33 AM",
                "stackResolutionX": 8.0,
                "stackResolutionY": 8.0,
                "stackResolutionZ": 8.0,
                "versionNotes": "derived from stack with owner 'cellmap', project 'jrc_mus_pancreas_5', and name 'v3_acquire_align_destreak'"
            },
            "currentVersionNumber": 0,
            "lastModifiedTimestamp": "Sep 1, 2024, 2:50:21 PM",
            "stackId": {
                "owner": "cellmap",
                "project": "jrc_mus_pancreas_5",
                "stack": "v3_acquire_align_destreak_ic3d_64x64_zd_1"
            },
            "state": "COMPLETE",
            "stats": {
                "channelNames": [],
                "maxTileHeight": 8281,
                "maxTileWidth": 8610,
                "minTileHeight": 8264,
                "minTileWidth": 8597,
                "nonIntegralSectionCount": 0,
                "sectionCount": 151,
                "stackBounds": {
                    "maxX": 16723.0,
                    "maxY": 8132.0,
                    "maxZ": 7250.0,
                    "minX": -17044.0,
                    "minY": -8219.0,
                    "minZ": 7100.0
                },
                "tileCount": 1208,
                "transformCount": 1
            }
        }
    },
    "scales": [
        [
            1,
            1,
            1
        ],
        [
            2,
            2,
            2
        ],
        [
            4,
            4,
            4
        ],
        [
            8,
            8,
            8
        ],
        [
            16,
            16,
            16
        ],
        [
            32,
            32,
            32
        ],
        [
            64,
            64,
            64
        ],
        [
            128,
            128,
            128
        ]
    ],
    "translate": [
        -17044,
        -8219,
        7100
    ],
    "units": [
        "nm",
        "nm",
        "nm"
    ]
}

@pattonw

[pattonw]

I don't think it's valid ome zarr metadata unless there's a "omero" attribute with a list of channel names.
At least that is what iohub seems to expect and the ngff spec says it should be there. The language makes it a little unclear if it's mandatory or not

[mzouink]

@yuriyzubov can you check this ?

[yuriyzubov]

@pattonw is right, the lack of "omero" attribute caused the error.
Adding

{
    "id": 1,                            
    "name": "mus-pancreas-5",              
    "version": "0.4",                     
    "channels": [                        
       {
          "active": true,
          "coefficient": 1,
          "color": "FFFFFF",
          "inverted": false,
          "label": "mus-pancreas-5",
          "window": {
                "end": 255,
                "max": 255,
                "min": 0,
                "start": 0
          }
       }
    ],
    "rdefs": {
       "defaultT": 0,                    
       "defaultZ": 0,                 
       "model": "greyscale"                  
    }
},

fixed the validation issue.