_constants.py

from enum import unique

from spatialdata_io._constants._enum import ModeEnum


@unique
class CodexKeys(ModeEnum):
    """Keys for *CODEX* formatted dataset."""

    # files and directories
    FCS_FILE = ".fcs"
    FCS_FILE_CSV = ".csv"
    # metadata
    REGION_KEY = "region"
    INSTANCE_KEY = "cell_id"
    SPATIAL_KEY = "spatial"
    # images
    IMAGE_TIF = ".tif"


class CurioKeys(ModeEnum):
    """Keys for *Curio* formatted dataset."""

    # files and directories
    ANNDATA_FILE = "anndata.h5ad"
    CLUSTER_ASSIGNMENT = "cluster_assignment.txt"
    METRICS_FILE = "Metrics.csv"
    VAR_FEATURES_CLUSTERS = "variable_features_clusters.txt"
    VAR_FEATURES_MORANSI = "variable_features_spatial_moransi.txt"
    # metadata
    CATEGORY = "Category"
    REGION = "cells"
    REGION_KEY = "region"
    INSTANCE_KEY = "instance_id"
    TOP_CLUSTER_DEFINING_FEATURES = "Top_cluster_defining_features"


@unique
class CosmxKeys(ModeEnum):
    """Keys for *Nanostring Cosmx* formatted dataset."""

    # files and directories
    COUNTS_SUFFIX = "exprMat_file.csv"
    TRANSCRIPTS_SUFFIX = "tx_file.csv"
    METADATA_SUFFIX = "metadata_file.csv"
    FOV_SUFFIX = "fov_positions_file.csv"
    IMAGES_DIR = "CellComposite"
    LABELS_DIR = "CellLabels"
    # metadata
    FOV = "fov"
    REGION_KEY = "fov_labels"
    INSTANCE_KEY = "cell_ID"
    X_GLOBAL_CELL = "CenterX_global_px"
    Y_GLOBAL_CELL = "CenterY_global_px"
    X_LOCAL_CELL = "CenterX_local_px"
    Y_LOCAL_CELL = "CenterY_local_px"
    X_LOCAL_TRANSCRIPT = "x_local_px"
    Y_LOCAL_TRANSCRIPT = "y_local_px"
    TARGET_OF_TRANSCRIPT = "target"


@unique
class SeqfishKeys(ModeEnum):
    """Keys for *Spatial Genomics SeqFISH* formatted dataset."""

    # file extensions
    CSV_FILE = ".csv"
    TIFF_FILE = ".tiff"
    GEOJSON_FILE = ".geojson"
    # file identifiers
    ROI = "Roi"
    TRANSCRIPT_COORDINATES = "TranscriptList"
    DAPI = "DAPI"
    COUNTS_FILE = "CellxGene"
    SEGMENTATION = "Segmentation"
    CELL_COORDINATES = "CellCoordinates"
    BOUNDARIES = "Boundaries"
    # transcripts
    TRANSCRIPTS_X = "x"
    TRANSCRIPTS_Y = "y"
    FEATURE_KEY = "name"
    INSTANCE_KEY_POINTS = "cell"
    # cells
    AREA = "area"
    CELL_X = "center_x"
    CELL_Y = "center_y"
    # metadata
    SPATIAL_KEY = "spatial"
    REGION_KEY = "region"
    INSTANCE_KEY_TABLE = "instance_id"
    SCALEFEFACTOR_X = "PhysicalSizeX"
    SCALEFEFACTOR_Y = "PhysicalSizeY"


@unique
class XeniumKeys(ModeEnum):
    """Keys for *10X Genomics Xenium* formatted dataset."""

    # specifications
    XENIUM_SPECS = "experiment.xenium"

    # cell identifiers
    CELL_ID = "cell_id"

    # nucleus and cell boundaries
    NUCLEUS_BOUNDARIES_FILE = "nucleus_boundaries.parquet"
    CELL_BOUNDARIES_FILE = "cell_boundaries.parquet"
    BOUNDARIES_VERTEX_X = "vertex_x"
    BOUNDARIES_VERTEX_Y = "vertex_y"

    # transcripts
    TRANSCRIPTS_FILE = "transcripts.parquet"
    TRANSCRIPTS_X = "x_location"
    TRANSCRIPTS_Y = "y_location"
    TRANSCRIPTS_Z = "z_location"
    QUALITY_VALUE = "qv"
    OVERLAPS_NUCLEUS = "overlaps_nucleus"
    FEATURE_NAME = "feature_name"

    # cell features matrix
    CELL_FEATURE_MATRIX_FILE = "cell_feature_matrix.h5"
    CELL_METADATA_FILE = "cells.parquet"
    CELL_X = "x_centroid"
    CELL_Y = "y_centroid"
    CELL_AREA = "cell_area"
    CELL_NUCLEUS_AREA = "nucleus_area"

    # morphology images
    # before version 2.0.0
    MORPHOLOGY_MIP_FILE = "morphology_mip.ome.tif"
    MORPHOLOGY_FOCUS_FILE = "morphology_focus.ome.tif"
    # from version 2.0.0
    MORPHOLOGY_FOCUS_DIR = "morphology_focus"
    MORPHOLOGY_FOCUS_CHANNEL_IMAGE = "morphology_focus_{:04}.ome.tif"
    # from analysis_summary.html > Image QC of https://www.10xgenomics.com/datasets/preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard
    MORPHOLOGY_FOCUS_CHANNEL_0 = "DAPI"  # nuclear
    MORPHOLOGY_FOCUS_CHANNEL_1 = "ATP1A1/CD45/E-Cadherin"  # boundary
    MORPHOLOGY_FOCUS_CHANNEL_2 = "18S"  # interior - RNA
    MORPHOLOGY_FOCUS_CHANNEL_3 = "AlphaSMA/Vimentin"  # interior - protein

    # post-xenium images
    ALIGNED_IF_IMAGE_SUFFIX = "if_image.ome.tif"
    ALIGNED_HE_IMAGE_SUFFIX = "he_image.ome.tif"

    # image alignment suffix
    ALIGNMENT_FILE_SUFFIX_TO_REMOVE = ".ome.tif"
    ALIGNMENT_FILE_SUFFIX_TO_ADD = "alignment.csv"

    # specs keys
    ANALYSIS_SW_VERSION = "analysis_sw_version"
    # spec which contains xeniumranger version whenever xeniumranger is used to resegment the data; the new, resegmented data
    # needs to be parsed by considering the xeniumranger version
    XENIUM_RANGER = "xenium_ranger"

    # zarr file with labels file and cell summary keys
    CELLS_ZARR = "cells.zarr.zip"
    NUCLEUS_COUNT = "nucleus_count"
    Z_LEVEL = "z_level"

    EXPLORER_SELECTION_X = "X"
    EXPLORER_SELECTION_Y = "Y"
    EXPLORER_SELECTION_KEY = "Selection"


@unique
class VisiumKeys(ModeEnum):
    """Keys for *10X Genomics Visium* formatted dataset."""

    # files and directories
    FILTERED_COUNTS_FILE = "filtered_feature_bc_matrix.h5"
    RAW_COUNTS_FILE = "raw_feature_bc_matrix.h5"

    # images
    IMAGE_HIRES_FILE = "spatial/tissue_hires_image.png"
    IMAGE_LOWRES_FILE = "spatial/tissue_lowres_image.png"

    # scalefactors
    SCALEFACTORS_FILE = "scalefactors_json.json"
    SCALEFACTORS_HIRES = "tissue_hires_scalef"
    SCALEFACTORS_LOWRES = "tissue_lowres_scalef"

    # spots
    SPOTS_FILE_1 = "tissue_positions_list.csv"
    SPOTS_FILE_2 = "tissue_positions.csv"
    SPOTS_X = "pxl_col_in_fullres"
    SPOTS_Y = "pxl_row_in_fullres"


@unique
class SteinbockKeys(ModeEnum):
    """Keys for *Steinbock* formatted dataset."""

    # files and directories
    CELLS_FILE = "cells.h5ad"
    DEEPCELL_MASKS_DIR = "masks_deepcell"
    ILASTIK_MASKS_DIR = "masks_ilastik"
    IMAGES_DIR = "ome"

    # suffixes for images and labels
    IMAGE_SUFFIX = ".ome.tiff"
    LABEL_SUFFIX = ".tiff"


@unique
class StereoseqKeys(ModeEnum):
    """Keys for *Stereo-seq* formatted dataset."""

    # file extensions
    GEF_FILE = ".gef"
    TIF_FILE = ".tif"
    # directories
    MERGE = "01.merge"
    COUNT_DIRECTORY = "02.count"
    REGISTER = "03.register"
    TISSUECUT = "04.tissuecut"
    SPATIALCLUSTER = "05.spatialcluster"
    SATURATION = "06.saturation"
    CELLCUT = "041.cellcut"
    CELLCLUSTER = "051.cellcluster"
    # file identifiers
    MASK_TIF = "_mask.tif"
    REGIST_TIF = "_regist.tif"
    TISSUE_TIF = "_tissue_cut.tif"
    CELL_CLUSTER_H5AD = "cell.cluster.h5ad"
    RAW_GEF = ".raw.gef"
    CELLBIN_GEF = ".cellbin.gef"
    TISSUECUT_GEF = ".tissuecut.gef"
    TISSUE_GEM = ".tissue.gem.gz"
    # transcripts
    FEATURE_KEY = "gene"
    GENE_NAME = "geneName"
    CELL_COUNT = "cellCount"
    MAX_MID_COUNT = "maxMIDcount"
    GENE_EXP = "geneExp"
    EXPRESSION = "expression"
    EXON = "exon"
    GENE_ID = "geneID"
    GENE_EXP_EXON = "geneExpExon"
    # cells
    ID = "id"
    CELL_ID = "cellID"
    GENE_COUNT = "geneCount"
    DNBCOUNT = "dnbCount"
    CELL_AREA = "area"
    CELL_TYPE_ID = "cellTypeID"
    CLUSTER_ID = "clusterID"
    CELL_BIN = "cellBin"
    CELL_EXON = "cellExon"
    CELL_DATASET = "cell"
    GENE_EXON = "geneExon"
    CELL_BORDER = "cellBorder"
    CELL_EXP = "cellExp"
    CELL_EXP_EXON = "cellExpExon"
    PADDING_VALUE = 32767
    # metadata
    COUNT = "count"
    EXP_COUNT = "expCount"
    OFFSET = "offset"
    COORD_X = "x"
    COORD_Y = "y"
    SPATIAL_KEY = "spatial"
    REGION = "cells"
    REGION_KEY = "region"
    INSTANCE_KEY = "instance_id"
    BLOCK_INDEX = "blockIndex"
    BLOCK_SIZE = "blockSize"
    CELL_TYPE_LIST = "cellTypeList"
    # bin data and metadata
    BIN1 = "bin1"
    MIN_X = "minX"
    MIN_Y = "minY"
    MAX_X = "maxX"
    MAX_Y = "maxY"
    RESOLUTION = "resolution"


@unique
class McmicroKeys(ModeEnum):
    """Keys for *Mcmicro* formatted dataset."""

    # files and directories
    QUANTIFICATION_DIR = "quantification"
    MARKERS_FILE = "markers.csv"
    IMAGES_DIR_WSI = "registration"
    IMAGES_DIR_TMA = "dearray"
    IMAGE_SUFFIX = ".ome.tif"
    LABELS_DIR = "segmentation"
    ILLUMINATION_DIR = "illumination"
    PARAMS_FILE = "qc/params.yml"
    RAW_DIR = "raw"
    COREOGRAPH_CENTROIDS = "qc/coreograph/centroidsY-X.txt"
    COREOGRAPH_TMA_MAP = "qc/coreograph/TMA_MAP.tif"

    # metadata
    COORDS_X = "X_centroid"
    COORDS_Y = "Y_centroid"
    INSTANCE_KEY = "CellID"
    ILLUMINATION_SUFFIX_DFP = "-dfp"
    ILLUMINATION_SUFFIX_FFP = "-ffp"


@unique
class MerscopeKeys(ModeEnum):
    """Keys for *MERSCOPE* data (Vizgen plateform)"""

    # files and directories
    IMAGES_DIR = "images"
    TRANSFORMATION_FILE = "micron_to_mosaic_pixel_transform.csv"
    TRANSCRIPTS_FILE = "detected_transcripts.csv"
    BOUNDARIES_FILE = "cell_boundaries.parquet"
    COUNTS_FILE = "cell_by_gene.csv"
    CELL_METADATA_FILE = "cell_metadata.csv"

    # VPT default outputs
    CELLPOSE_BOUNDARIES = "cellpose_micron_space.parquet"
    WATERSHED_BOUNDARIES = "watershed_micron_space.parquet"
    VPT_NAME_COUNTS = "cell_by_gene"
    VPT_NAME_OBS = "cell_metadata"
    VPT_NAME_BOUNDARIES = "cell_boundaries"

    # metadata
    METADATA_CELL_KEY = "EntityID"
    COUNTS_CELL_KEY = "cell"
    CELL_X = "center_x"
    CELL_Y = "center_y"
    GLOBAL_X = "global_x"
    GLOBAL_Y = "global_y"
    GLOBAL_Z = "global_z"
    Z_INDEX = "ZIndex"
    REGION_KEY = "cells_region"
    GENE_KEY = "gene"


@unique
class DbitKeys(ModeEnum):
    """Keys for DBiT formatted dataset."""

    # files and directories
    COUNTS_FILE = ".h5ad"
    # barcodes_file
    BARCODE_POSITION = "barcode_list"
    # image
    IMAGE_LOWRES_FILE = "tissue_lowres_image.png"


@unique
class VisiumHDKeys(ModeEnum):
    """Keys for *10X Genomics Visium hd* formatted dataset."""

    # directories
    SPATIAL = "spatial"
    DEFAULT_BIN = "square_008um"
    BIN_PREFIX = "square_"
    MICROSCOPE_IMAGE = "microscope_image"
    BINNED_OUTPUTS = "binned_outputs"

    # counts and locations files
    FILTERED_COUNTS_FILE = "filtered_feature_bc_matrix.h5"
    RAW_COUNTS_FILE = "raw_feature_bc_matrix.h5"
    TISSUE_POSITIONS_FILE = "tissue_positions.parquet"

    # images
    IMAGE_HIRES_FILE = "tissue_hires_image.png"
    IMAGE_LOWRES_FILE = "tissue_lowres_image.png"
    IMAGE_CYTASSIST = "cytassist_image.tiff"

    # scalefactors
    SCALEFACTORS_FILE = "scalefactors_json.json"

    # scalefactors keys
    SCALEFACTORS_HIRES = "tissue_hires_scalef"
    SCALEFACTORS_LOWRES = "tissue_lowres_scalef"
    SCALEFACTORS_SPOT_DIAMETER_FULLRES = "spot_diameter_fullres"
    SCALEFACTORS_BIN_SIZE_UM = "bin_size_um"
    SCALEFACTORS_MICRONS_PER_PIXEL = "microns_per_pixel"

    # locations keys
    LOCATIONS_X = "pxl_col_in_fullres"
    LOCATIONS_Y = "pxl_row_in_fullres"
    BARCODE = "barcode"
    IN_TISSUE = "in_tissue"
    ARRAY_ROW = "array_row"
    ARRAY_COL = "array_col"

    # table keys
    REGION_KEY = "region"
    INSTANCE_KEY = "location_id"

    # feature slice file (it contains transformation matrices in the metadata)
    FEATURE_SLICE_FILE = "feature_slice.h5"

    # METADATA_KEYS
    METADATA_JSON = "metadata_json"
    HD_LAYOUT_JSON = "hd_layout_json"
    TRANSFORM = "transform"
    TRANSFORM_MATRICES = "transform_matrices"
    CYTASSIST_COLROW_TO_SPOT_COLROW = ("cytassist_colrow_to_spot_colrow",)
    SPOT_COLROW_TO_CYTASSIST_COLROW = ("spot_colrow_to_cytassist_colrow",)
    MICROSCOPE_COLROW_TO_SPOT_COLROW = ("microscope_colrow_to_spot_colrow",)
    SPOT_COLROW_TO_MICROSCOPE_COLROW = ("spot_colrow_to_microscope_colrow",)
    FILE_FORMAT = "file_format"


class G4XKeys(ModeEnum):
    """Keys for G4X formatted dataset."""

    # H&E
    HE_DIR = "h_and_e"
    HE_PATTERN = "*.jp2"

    # Nuclei
    NUCLEI_BOUNDARIES_KEY = "nuclei"
    CELL_BOUNDARIES_KEY = "nuclei_exp"
    SEGMENTATION_DIR = "segmentation"
    SEGMENTATION_PATTERN = "segmentation_mask.npz"
    OFFSET = "-0.5"

    # Protein
    PROTEIN_KEY = "protein"
    PROTEIN_DIR = "protein"
    PROTEIN_PATTERN = "*.jp2"

    # Transcripts
    TRANSCRIPTS_KEY = "transcripts"
    TRANSCRIPTS_DIR = "rna"
    TRANSCRIPTS_PATTERN = "*transcript_table.csv.gz"
    TRANSCRIPTS_COORD_X = "x_pixel_coordinate"
    TRANSCRIPTS_COORD_Y = "y_pixel_coordinate"
    TRANSCRIPTS_FEATURE_KEY = "gene_name"
    TRANSCRIPTS_SWAP_XY = False

    # Tables
    TABLES_DIR = "single_cell_data"
    TABLE_PATTERN = "feature_matrix.h5"
    TABLE_KEY = "table"