metaspace.types

This module contains type annotations for data structures so that IDEs such as PyCharm can assist when accessing structures such as metaspace.sm_annotation_utils.SMDataset.metadata

class metaspace.types.DSConfig(**kwargs)

SMDataset.config should be accessed as a Python dict, e.g.

>>> instrument = dataset.config['isotope_generation']['instrument']

analysis_version: int

database_ids: List[int]

fdr: metaspace.types.DSConfigFDR

image_generation: metaspace.types.DSConfigImageGeneration

isotope_generation: metaspace.types.DSConfigIsotopeGeneration

class metaspace.types.DSConfigFDR(**kwargs)

decoy_sample_size: int

class metaspace.types.DSConfigImageGeneration(**kwargs)

min_px: int

n_levels: int

ppm: int

class metaspace.types.DSConfigIsotopeGeneration(**kwargs)

adducts: List[str]

charge: int

chem_mods: List[str]

instrument: str

isocalc_sigma: float

n_peaks: int

neutral_losses: List[str]

class metaspace.types.DatabaseDetails(**kwargs)

DEPRECATED - this has been replaced by metaspace.sm_annotation_utils.MolecularDB

archived: bool

id: int

isPublic: bool

name: str

version: str

class metaspace.types.DatasetDiagnostic(**kwargs)

Represents the results of one category of diagnostics/metadata for the dataset. The type field indicates the content:

• type==TIC - data contains information about the Total Ion Current across the dataset - images contains an image with the TIC for each spectrum

• type==IMZML_METADATA - data contains a summary of metadata from the ImzML file header - images contains a boolean image of which pixels had spectra in the input data.

  Useful for non-square acquisition areas.

data: Any

database: Optional[MolecularDB]

id: str

images: List[metaspace.types.DiagnosticImage]

jobId: Optional[int]

type: str

class metaspace.types.DatasetDownload(**kwargs)

contributors: List[metaspace.types.DatasetDownloadContributor]

files: List[metaspace.types.DatasetDownloadFile]

license: metaspace.types.DatasetDownloadLicense

class metaspace.types.DatasetDownloadContributor(**kwargs)

institution: Optional[str]

name: Optional[str]

class metaspace.types.DatasetDownloadFile(**kwargs)

filename: str

link: str

class metaspace.types.DatasetDownloadLicense(**kwargs)

code: str

link: Optional[str]

name: str

class metaspace.types.DatasetGroup(**kwargs)

id: str

name: str

shortName: str

class metaspace.types.DatasetProject(**kwargs)

id: str

name: str

publicationStatus: str

class metaspace.types.DatasetUser(**kwargs)

id: str

name: str

class metaspace.types.DiagnosticImage(**kwargs)

Represents one image associated with a category of diagnostics/metadata.

The key field indicates the content.

The image field is only present when sm_annotation_utils.SMDataset.diagnostics

is called with include_images=True

format: typing_extensions.Literal[‘PNG’, ‘NPY’]

image: Optional[numpy.ndarray]

index: Optional[int]

key: Optional[str]

url: str

class metaspace.types.Metadata(**kwargs)

SMDataset.metadata should be accessed as a Python dict, e.g.

>>> organism = dataset.metadata['Sample_Information']['Organism']

Data_Type: str

MS_Analysis: metaspace.types.MetadataMSAnalysis

Sample_Information: metaspace.types.MetadataSampleInformation

Sample_Preparation: metaspace.types.MetadataSamplePreparation

class metaspace.types.MetadataMSAnalysis(**kwargs)

Analyzer: str

Detector_Resolving_Power: metaspace.types.MetadataResolvingPower

Ionisation_Source: str

Pixel_Size: metaspace.types.MetadataPixelSize

Polarity: typing_extensions.Literal[‘Positive’, ‘Negative’]

class metaspace.types.MetadataPixelSize(**kwargs)

Xaxis: float

Yaxis: float

class metaspace.types.MetadataResolvingPower(**kwargs)

Resolving_Power: float

mz: float

class metaspace.types.MetadataSampleInformation(**kwargs)

Condition: str

Organism: str

Organism_Part: str

Sample_Growth_Conditions: Optional[str]

class metaspace.types.MetadataSamplePreparation(**kwargs)

MALDI_Matrix: str

MALDI_Matrix_Application: str

Sample_Stabilisation: str

Solvent: Optional[str]

Tissue_Modification: str