magmap.settings.config module

Configuration storage module.

This module allows customization of settings for various imaging systems, such as grouped settings for particular microscopes. Additional parameters such as command-line flag settings and databases can also be stored here for program access.

class magmap.settings.config.ABAKeys(value)

Bases: Enum

Allen Brain Atlas ontology hierarchy keys.

Values of each enumeration maps to key values in the ABA ontology specification.

ABA_ID = 'id'

ACRONYM = 'acronym'

CHILDREN = 'children'

LEVEL = 'st_level'

NAME = 'name'

PARENT_ID = 'parent_structure_id'

magmap.settings.config.APP_NAME = 'MagellanMapper'

Application name.

Type:

str

class magmap.settings.config.AtlasLabels(value)

Bases: Enum

An enumeration.

BINARY = 6

ID = 3

LEVEL = 2

ORIG_COLORS = 4

PATH_REF = 1

SYMMETRIC_COLORS = 5

TRANSLATE_CHILDREN = 8

TRANSLATE_LABELS = 7

class magmap.settings.config.AtlasMetrics(value)

Bases: Enum

General atlas metric enumerations.

CHANNEL = 'Channel'

CONDITION = 'Condition'

DSC_ATLAS_LABELS = 'DSC_atlas_labels'

DSC_ATLAS_LABELS_HEM = 'DSC_atlas_labels_hemisphere'

DSC_ATLAS_SAMPLE = 'DSC_atlas_sample'

DSC_ATLAS_SAMPLE_CUR = 'DSC_atlas_sample_curated'

DSC_LABELS_ORIG_NEW_COMBINED = 'DSC_labels_orig_new_combined'

DSC_LABELS_ORIG_NEW_INDIV = 'DSC_labels_orig_new_individual'

DSC_SAMPLE_LABELS = 'DSC_sample_labels'

LAT_UNLBL_PLANES = 'Lateral_unlabeled_planes'

LAT_UNLBL_VOL = 'Lateral_unlabeled_volume'

LEVEL = 'Level'

OFFSET = 'Offset'

PARENT = 'Parent'

REGION = 'Region'

REGION_ABBR = 'RegionAbbr'

REGION_NAME = 'RegionName'

SAMPLE = 'Sample'

SIDE = 'Side'

SIMILARITY_METRIC = 'Similarity_metric'

SIZE = 'Size'

VOL_ATLAS = 'Vol_atlas'

VOL_LABELS = 'Vol_labels'

class magmap.settings.config.ClassifierData(model=None, include=None)

Bases: object

Classifier data class for CLI arguments.

include: Union[int, Sequence[int], None] = None

Classification flags (confirmed column) to include.

model: Optional[str] = None

Path to pre-trained classifier model.

class magmap.settings.config.Cmaps(value)

Bases: Enum

Custom colormap names.

CMAP_BUBK_NAME = 'Blue_black'

CMAP_CYBK_NAME = 'Cyan_black'

CMAP_GRBK_NAME = 'Green_black'

CMAP_MGBK_NAME = 'Magenta_black'

CMAP_RDBK_NAME = 'Red_black'

CMAP_YLBK_NAME = 'Yellow_black'

magmap.settings.config.DEFAULT_SAVEFIG = 'png'

Default extension for saving figures.

Type:

str

class magmap.settings.config.DFTasks(value)

Bases: Enum

Enum: Data frame module tasks.

ADD_CSV_COLS = 6

APPEND_CSVS_COLS = 3

DIVIDE_COLS = 12

EXPS_BY_REGION = 4

EXTRACT_FROM_CSV = 5

MERGE_CSVS = 1

MERGE_CSVS_COLS = 2

MERGE_EXCELS = 8

MULTIPLY_COLS = 11

NORMALIZE = 7

REPLACE_VALS = 13

SUBTRACT_COLS = 10

SUM_COLS = 9

magmap.settings.config.DNS_REVERSE = 'io.github.sanderslab.MagellanMapper'

Reverse Domain Name System identifier.

Type:

str

class magmap.settings.config.DataClass

Type hint for data classes.

alias of TypeVar(‘DataClass’, bound=DataClassProtocol)

class magmap.settings.config.DataClassProtocol(*args, **kwargs)

Bases: Protocol

Typing protocol for data classes.

class magmap.settings.config.DocsURLs(value)

Bases: Enum

URLs to online documentation.

DOCS_URL = 'https://magellanmapper.readthedocs.io/en/latest'

Docs base URL.

DOCS_URL_SETTINGS = 'settings.html'

Settings doc URL.

DOCS_URL_VIEWER = 'viewers.html'

Viewer doc suffix.

magmap.settings.config.FORMATS_3D = ('obj', 'x3d')

Extension for 3D renderings.

Type:

tuple[str, …]

class magmap.settings.config.HemSides(value)

Bases: Enum

Hemisphere side enumerations.

BOTH = 'both'

LEFT = 'L'

RIGHT = 'R'

magmap.settings.config.ICON_PATH = PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/magellanmapper/envs/fix_rtd_py39/lib/python3.9/site-packages/images/magmap.png')

Absolution path to main application icon.

Type:

PurePath

class magmap.settings.config.ItkSnapLabels(value)

Bases: Enum

Column names to use for ITK-SNAP description labels.

Labels description file is assumed to have this column ordering.

A = 'a'

B = 'b'

G = 'g'

ID = 'id'

MESH = 'mesh'

NAME = 'name'

R = 'r'

VIS = 'vis'

class magmap.settings.config.LoadData(value)

Bases: Enum

Enumerations for specifying data to load.

BLOBS = 1

BLOB_MATCHES = 2

class magmap.settings.config.LoadIO(value)

Bases: Enum

Enumerations for I/O load packages.

BRAIN_GLOBE = 3

NP = 1

SITK = 2

TIFFFILE = 4

class magmap.settings.config.MetaKeys(value)

Bases: Enum

Metadata keys for command-line parsing.

DTYPE = 5

Data type as a string.

MAGNIFICATION = 2

Objective magnification.

RESOLUTIONS = 1

Image resolutions in XYZ.

SHAPE = 4

Image shape.

ZOOM = 3

Objective zoom.

class magmap.settings.config.MetricGroups(value)

Bases: Enum

An enumeration.

POINT_CLOUD = 2

SHAPES = 1

magmap.settings.config.PLANE = ('xy', 'xz', 'yz')

Plane orientations based on the two axes specifying the plane.

Type:

Tuple[str]

magmap.settings.config.POS_THRESH = 0.001

Threshold for positive values for float comparison.

Type:

float

magmap.settings.config.PREFS_PATH: Path = PosixPath('/home/docs/.local/share/MagellanMapper/prefs.yaml')

Preferences file path.

class magmap.settings.config.Plot2DTypes(value)

Bases: Enum

2D plot tasks.

BAR_PLOT = 1

BAR_PLOT_VOLS_STATS = 2

BAR_PLOT_VOLS_STATS_EFFECTS = 3

CAT_PLOT = 8

Generate a category plot through Seaborn.

DECORATE_PLOT = 9

Decorate plot labels.

LINE_PLOT = 6

ROC_CURVE = 4

SCATTER_PLOT = 5

SWARM_PLOT = 7

class magmap.settings.config.PlotLabels(value)

Bases: Enum

Plot label keys for command-line sub-arguments.

ALPHAS_CHL = 14

ANNOT_COL = 22

BACKGROUND = 37

Background color as a Matplotlib or RGBA string.

CONDITION = 34

DPI = 31

DROP_DUPS = 30

ERR_COL = 20

Error column(s) with values relative to the data points.

ERR_COL_ABS = 21

Error column(s) with absolute.

GROUP_COL = 17

HLINE = 24

ID_COL = 19

LAYOUT = 13

LEGEND_NAMES = 25

MARGIN = 27

MARKER = 29

NAN_COLOR = 32

# Color for NaN values as a Matplotlib or RGBA string.

PADDING = 26

ROTATION = 38

Rotation angle in degrees.

SCALE_BAR = 28

SIZE = 12

TEXT_POS = 33

TITLE = 1

VSPAN_COL = 35

Column indicating grouping for vertical span.

VSPAN_FORMAT = 36

WT_COL = 18

X_COL = 15

X_LABEL = 2

X_LIM = 6

X_SCALE = 10

X_TICK_LABELS = 8

X_UNIT = 4

Y_COL = 16

Y_LABEL = 3

Y_LIM = 7

Y_SCALE = 11

Y_TICK_LABELS = 9

Y_UNIT = 5

ZOOM_SHIFT = 23

class magmap.settings.config.PreProcessKeys(value)

Bases: Enum

Pre-processing task enumerations.

DENOISE = 2

REMAP = 3

ROTATE = 4

SATURATE = 1

class magmap.settings.config.ProcessTypes(value)

Bases: Enum

Whole image processing task enumerations.

ANIMATED = 10

Generate an animated GIF of successive planes in an image.

CLASSIFY = 5

Classify blobs.

COLOC_MATCH = 4

Detect blobs along with match-based colocalization.

DETECT = 2

Detect blobs in the whole image.

DETECT_COLOC = 3

Detect blobs along with intensity-based colocalization.

EXPORT_BLOBS = 11

Export blobs to a CSV file.

EXPORT_PLANES = 12

Export a 3/4D image to individual planes.

EXPORT_PLANES_CHANNELS = 13

EXPORT_RAW = 14

Export an array as a raw data file.

EXPORT_ROIS = 8

Export ROIs from the database to serial 2D plots.

EXPORT_TIF = 15

Export an array as TIF files for each channel.

EXTRACT = 7

Extract a single plane defined by the z-value in --offset.

IMPORT_ONLY = 1

Import image stack to NumPy format.

LOAD = 6

use --load CLI parameter instead.

Type:

Load previously processed images and blobs. DEPRECATED

PREPROCESS = 16

Pre-process the whole image.

TRANSFORM = 9

Transform an image (see magmap.atlas.transformer.transpose_img`()).

class magmap.settings.config.RegNames(value)

Bases: Enum

An enumeration.

COMBINED = 'combined.mhd'

IMG_ATLAS = 'atlasVolume.mhd'

IMG_ATLAS_EDGE = 'atlasEdge.mhd'

IMG_ATLAS_LOG = 'atlasLoG.mhd'

IMG_ATLAS_MASK = 'atlasMask.mhd'

IMG_ATLAS_PRECUR = 'atlasVolumePrecur.mhd'

IMG_BORDERS = 'borders.mhd'

IMG_EXP = 'exp.mhd'

IMG_EXP_MASK = 'expMask.mhd'

IMG_GROUPED = 'grouped.mhd'

IMG_HEAT_COLOC = 'heatColoc.mhd'

IMG_HEAT_MAP = 'heat.mhd'

IMG_LABELS = 'annotation.mhd'

IMG_LABELS_DIFF = 'annotationDiff.mhd'

IMG_LABELS_DIST = 'annotationDist.mhd'

IMG_LABELS_EDGE = 'annotationEdge.mhd'

IMG_LABELS_EDGE_LEVEL = 'annotationEdgeLevel{}.mhd'

IMG_LABELS_INTERIOR = 'annotationInterior.mhd'

IMG_LABELS_LEVEL = 'annotationLevel{}.mhd'

IMG_LABELS_MARKERS = 'annotationMarkers.mhd'

IMG_LABELS_PRECUR = 'annotationPrecur.mhd'

IMG_LABELS_SUBSEG = 'annotationSubseg.mhd'

IMG_LABELS_TRANS = 'annotationTrans.mhd'

IMG_LABELS_TRUNC = 'annotationTrunc.mhd'

IMG_LABELS_TRUNC_PRECUR = 'annotationTruncPrecur.mhd'

class magmap.settings.config.RegSuffixes(value)

Bases: Enum

Registered image suffix type keys for command-line parsing.

ANNOTATION = 2

Labels image.

ATLAS = 1

Intensity image.

BORDERS = 3

Borders image.

DENSITY = 6

Density image.

FIXED_MASK = 4

Fixed mask for image registration.

MOVING_MASK = 5

Moving mask for image registration

class magmap.settings.config.RegisterTypes(value)

Bases: Enum

An enumeration.

CLUSTER_BLOBS = 36

COEFVAR = 29

COMBINE_COLS = 27

CONVERT_ITKSNAP_LABELS = 9

EXPORT_COMMON_LABELS = 8

EXPORT_METRICS_COMPACTNESS = 18

EXPORT_REGIONS = 5

GROUP = 2

IMPORT_ATLAS = 7

LABELS_DIFF = 24

LABELS_DIFF_STATS = 25

LABELS_DIST = 39

MAKE_DENSITY_IMAGES = 15

MAKE_EDGE_IMAGES = 10

MAKE_EDGE_IMAGES_EXP = 11

MAKE_LABELS_LEVEL = 26

MAKE_SUBSEGS = 17

MEAS_IMPROVEMENT = 35

MELT_COLS = 30

MERGE_ATLAS_SEGS = 12

MERGE_ATLAS_SEGS_EXP = 16

MERGE_IMAGES = 22

MERGE_IMAGES_CHANNELS = 23

NEW_ATLAS = 6

OVERLAYS = 4

PIVOT_CONDS = 34

PLOT_CLUSTER_BLOBS = 38

PLOT_INTENS_NUC = 33

PLOT_KNNS = 37

PLOT_LATERAL_UNLABELED = 32

PLOT_REGION_DEV = 31

PLOT_SMOOTHING_METRICS = 19

REGISTER_REV = 3

SINGLE = 1

SMOOTHING_METRICS_AGGR = 21

SMOOTHING_PEAKS = 20

VOL_COMPARE = 14

VOL_STATS = 13

ZSCORES = 28

magmap.settings.config.STR_FN = {'mean': <function nanmean>, 'med': <function nanmedian>}

Dictionary mapping function names as lower-case strings to functions.

Type:

dict

magmap.settings.config.SUFFIX_BLOBS = 'blobs.npz'

Suffix for blobs archive.

Type:

str

magmap.settings.config.SUFFIX_BLOB_CLUSTERS = 'blobclusters.npy'

Suffix for blob clusters archive.

Type:

str

magmap.settings.config.SUFFIX_IMAGE5D = 'image5d.npy'

Suffix for main image.

Type:

str

magmap.settings.config.SUFFIX_META = 'meta.yml'

Suffix for metadata of main image.

Type:

str

magmap.settings.config.SUFFIX_SUBIMG = 'subimg.npy'

Suffix for ROI image.

Type:

str

class magmap.settings.config.SmoothingMetrics(value)

Bases: Enum

Smoothing metric enumerations.

Generally with reference to the smoothed stat, so original stats will have an “orig” suffix, while smoothed stats will not have any suffix.

COMPACTION = 'Compaction'

COMPACTNESS = 'Compactness'

COMPACTNESS_CV = 'Compactness_CV'

COMPACTNESS_ORIG = 'Compactness_orig'

COMPACTNESS_SD = 'Compactness_SD'

DISPLACEMENT = 'Displacement'

FILTER_SIZE = 'Filter_size'

LABEL_LOSS = 'Label_loss'

SA_VOL = 'SA_to_vol'

SA_VOL_FRAC = 'SA_to_vol_frac'

SA_VOL_ORIG = 'SA_to_vol_orig'

SM_QUALITY = 'Smoothing_quality'

VOL = 'Vol'

VOL_ORIG = 'Vol_orig'

class magmap.settings.config.SmoothingModes(value)

Bases: Enum

Enum: Label smoothing modes.

adaptive_closing = 3

adaptive_erosion = 4

adaptive_opening = 2

closing = 6

gaussian = 5

opening = 1

class magmap.settings.config.Themes(value)

Bases: Enum

GUI themes, where each theme currently contains RC parameters to apply to the Matplotlib style.

DARK = {'axes.edgecolor': '3b3b3b', 'axes.facecolor': '7a7a7a', 'axes.labelcolor': 'w', 'figure.edgecolor': '3b3b3b', 'figure.facecolor': '3b3b3b', 'grid.color': 'w', 'savefig.edgecolor': '3b3b3b', 'savefig.facecolor': '3b3b3b', 'text.color': 'w', 'xtick.color': 'w', 'ytick.color': 'w'}

DEFAULT = {'axes.titlesize': 12, 'font.family': 'sans-serif', 'font.sans-serif': ['Arial', 'Helvetica', 'Tahoma'], 'image.composite_image': False}

class magmap.settings.config.Transforms(value)

Bases: Enum

Image transformation keys for command-line parsing.

FLIP = 5

Axis to invert (z = 0, y = 1, …).

FLIP_HORIZ = 4

Flip the image horizontally if 1, no flip if 0.

FLIP_VERT = 3

Flip the image vertically if 1, no flip if 0.

INTERPOLATION = 7

Interpolate using the given order, which corresponds to skimage.transform.resize().

RESCALE = 6

Rescale the image by the given factor.

ROTATE = 1

Rotate by 90 deg the number of specified times.

ROTATE_DEG = 2

Rotate by specific degrees clockwise.

class magmap.settings.config.TruthDB(value)

Bases: Enum

Enum: Enum class for truth database settings.

MODE = 1

PATH = 2

class magmap.settings.config.TruthDBModes(value)

Bases: Enum

An enumeration.

EDIT = 4

VERIFIED = 3

VERIFY = 2

VIEW = 1

magmap.settings.config.URI_SCHEME = 'magmap'

Uniform Resource Identifier scheme.

Type:

str

class magmap.settings.config.Verbosity(value)

Bases: Enum

An enumeration.

LEVEL = 1

LOG_PATH = 2

magmap.settings.config.app_dir = PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/magellanmapper/envs/fix_rtd_py39/lib/python3.9/site-packages')

Application root directory path.

Type:

PurePath

magmap.settings.config.blobs: detector.Blobs | None = None

Blobs object.

magmap.settings.config.channel: Sequence[int] | None = None

Channel(s) of interest, where None specifies all channels.

magmap.settings.config.classifier: ClassifierData = ClassifierData(model=None, include=None)

Classifier settings.

magmap.settings.config.cmap_labels = None

Labels image colormap.

Type:

magmap.plot.colormaps.DiscreteColormap

magmap.settings.config.filenames = None

List of multiple image paths.

Type:

List[str]

magmap.settings.config.format_import_err(dist_name, name=None, task=None)

Format import error message.

Parameters:

• dist_name (str) – Distribution name of package to install.

• name (Optional[str], default: None) – More descriptive name; if None (default), dist_name is used with capitalization.

• task (Optional[str], default: None) – Description of task where this package is required; defaults to None.

Return type:

str

Returns:

Message to display for error.

magmap.settings.config.get_roi_profile(i)

Get the region of interest profile for the given channel.

Parameters:

i – Index, typically a channel number.

Returns:

The profile settings for corresponding to the given channel number, or the default profile if only one is available.

magmap.settings.config.grid_search_profile = None

Grid search profile.

Type:

settings.grid_search_prof.GridSearchProfile

magmap.settings.config.image5d_io = None

I/O source for image5d array.

Type:

LoadIO

magmap.settings.config.img5d: np_io.Image5d | None = None

Image5d object.

magmap.settings.config.labels_img: Optional = None

Numpy array of a labels image file, typically corresponding to img5d.

magmap.settings.config.labels_img_orig: ndarray | None = None

Original labels image, before any processing.

magmap.settings.config.labels_img_sitk: sitk.Image | itk.Image | None = None

Labels image as a SimpleITK Image instance.

magmap.settings.config.labels_level: int | None = None

Labels ontology level set by the CLI.

magmap.settings.config.labels_metadata: labels_meta.LabelsMeta | None = None

Loaded labels metadata.

magmap.settings.config.labels_ref: ontology.LabelsRef | None = None

Labels reference IDs corresponding to the labels image values.

magmap.settings.config.labels_scaling: Sequence[float] | None = None

Scaling factors from labels_img to img5d.

magmap.settings.config.load_labels: str | None = None

Path to the labels reference file set by the CLI.

magmap.settings.config.log_path: Path | None = None

Path to log file.

magmap.settings.config.logger = <RootLogger root (INFO)>

Root logger for the application.

Type:

logging.Logger

magmap.settings.config.magnification = 1.0

objective magnification

Type:

float

magmap.settings.config.matplotlib_style = 'default'

Matplotlib style sheet.

Type:

str

magmap.settings.config.meta_dict: Dict[MetaKeys, Any] = {MetaKeys.DTYPE: None, MetaKeys.MAGNIFICATION: None, MetaKeys.RESOLUTIONS: None, MetaKeys.SHAPE: None, MetaKeys.ZOOM: None}

Dictionary of metadata for image import.

magmap.settings.config.metadata_paths = None

Metadata file paths.

Type:

List[str]

magmap.settings.config.metadatas = None

Metadata dictionaries.

Type:

List[dict]

magmap.settings.config.plot_labels = {PlotLabels.ALPHAS_CHL: None, PlotLabels.ANNOT_COL: None, PlotLabels.BACKGROUND: None, PlotLabels.CONDITION: None, PlotLabels.DPI: 150.0, PlotLabels.DROP_DUPS: None, PlotLabels.ERR_COL: None, PlotLabels.ERR_COL_ABS: None, PlotLabels.GROUP_COL: None, PlotLabels.HLINE: None, PlotLabels.ID_COL: None, PlotLabels.LAYOUT: None, PlotLabels.LEGEND_NAMES: None, PlotLabels.MARGIN: None, PlotLabels.MARKER: None, PlotLabels.NAN_COLOR: None, PlotLabels.PADDING: None, PlotLabels.ROTATION: None, PlotLabels.SCALE_BAR: True, PlotLabels.SIZE: None, PlotLabels.TEXT_POS: None, PlotLabels.TITLE: None, PlotLabels.VSPAN_COL: None, PlotLabels.VSPAN_FORMAT: None, PlotLabels.WT_COL: None, PlotLabels.X_COL: None, PlotLabels.X_LABEL: None, PlotLabels.X_LIM: None, PlotLabels.X_SCALE: None, PlotLabels.X_TICK_LABELS: None, PlotLabels.X_UNIT: None, PlotLabels.Y_COL: None, PlotLabels.Y_LABEL: None, PlotLabels.Y_LIM: None, PlotLabels.Y_SCALE: None, PlotLabels.Y_TICK_LABELS: None, PlotLabels.Y_UNIT: None, PlotLabels.ZOOM_SHIFT: None}

Plot labels set from command-line.

Type:

dict[Any]

magmap.settings.config.prefix: str | None = None

Input/output base path.

magmap.settings.config.prefix_out: str | None = None

Output base path.

magmap.settings.config.prefixes: Sequence[str] | None = None

Input/output base paths.

magmap.settings.config.prefixes_out: Sequence[str] | None = None

Output base paths.

magmap.settings.config.prefs: prefs_prof.PrefsProfile | None = None

Preferences dictionary.

magmap.settings.config.proc_type: Dict[ProcessTypes, Any] = {ProcessTypes.ANIMATED: None, ProcessTypes.CLASSIFY: None, ProcessTypes.COLOC_MATCH: None, ProcessTypes.DETECT: None, ProcessTypes.DETECT_COLOC: None, ProcessTypes.EXPORT_BLOBS: None, ProcessTypes.EXPORT_PLANES: None, ProcessTypes.EXPORT_PLANES_CHANNELS: None, ProcessTypes.EXPORT_RAW: None, ProcessTypes.EXPORT_ROIS: None, ProcessTypes.EXPORT_TIF: None, ProcessTypes.EXTRACT: None, ProcessTypes.IMPORT_ONLY: None, ProcessTypes.LOAD: None, ProcessTypes.PREPROCESS: None, ProcessTypes.TRANSFORM: None}

Processing tasks.

magmap.settings.config.rc_params = [Themes.DEFAULT]

List of theme enums.

Type:

List[Enum]

magmap.settings.config.reg_suffixes: Dict[RegSuffixes, str | Sequence[str] | None] = {RegSuffixes.ANNOTATION: None, RegSuffixes.ATLAS: None, RegSuffixes.BORDERS: None, RegSuffixes.DENSITY: None, RegSuffixes.FIXED_MASK: None, RegSuffixes.MOVING_MASK: None}

Dictionary of registered suffix names for each suffix type.

magmap.settings.config.rgb: bool = False

CLI flag to open images in RGB(A) mode if True; defaults to False.

magmap.settings.config.savefig = 'png'

# File extension (without period) for saving figures.

Type:

str

magmap.settings.config.series = None

Selected image series index for multi-stack files; None for no series.

Type:

int

magmap.settings.config.series_list = None

List of image series/tiles.

Type:

list[int]

magmap.settings.config.show = False

Show images after a task is performed, if applicable

Type:

bool

magmap.settings.config.suffix: str | None = None

Modifier to existing base path, typically inserted just before the extension.

magmap.settings.config.truth_db_mode = None

truth database mode enum

Type:

TruthDBModes

magmap.settings.config.unit_factor = 1000.0

measurement unit factor to convert to next larger prefix (eg um to mm)

Type:

float

magmap.settings.config.user_app_dirs = <appdirs.AppDirs object>

Accessor to application-related user directories.

Type:

str

magmap.settings.config.verbose = False

True for verbose debugging output.

Type:

bool

magmap.settings.config.verbosity = {Verbosity.LEVEL: None, Verbosity.LOG_PATH: None}

Command-line arguments for verbosity.

Type:

dict

magmap.settings.config.zoom = 1.0

objective zoom

Type:

float