Configuration file

The DryMass configuration file drymass.cfg is located in the root of the output folder (“_dm” appended to the data path). The configuration file is divided into sections.

[bg] Background correction

# indexing starts at 1
"amplitude data":
    ("none", int_or_str, "Amplitude bg correction file or index"),
# see qpimage library: e.g. fit, gauss, mean, mode
"amplitude offset":
    ("mean", lcstr, "Amplitude bg correction offset method"),
# see qpimage library: e.g. tilt, offset
"amplitude profile":
    ("tilt", lcstr, "Amplitude bg correction profile method"),
# see skimage.filters.threshold_*
"amplitude binary threshold":
    (np.nan, float_or_str, "Binary image threshold value or method"),
"amplitude border perc":
    (10, float, "Amplitude bg border region to analyze [%]"),
"amplitude border px":
    (5, int, "Amplitude bg border region to analyze [px]"),
"enabled":
    (True, fbool, "Enable bg correction globally"),
# indexing starts at 1
"phase data":
    ("none", int_or_str, "Phase bg correction file or index"),
# see qpimage library: e.g. fit, gauss, mean, mode
"phase offset":
    ("mean", lcstr, "Phase bg correction offset method"),
# see qpimage library: e.g. tilt, offset
"phase profile":
    ("tilt", lcstr, "Phase bg correction profile method"),
# see skimage.filters.threshold_*
"phase binary threshold":
    (np.nan, float_or_str, "Binary image threshold value or method"),
"phase border perc":
    (10, float, "Phase bg border region to analyze [%]"),
"phase border px":
    (5, int, "Phase bg border region to analyze [px]"),

[meta] Image meta data

"medium index":
    (np.nan, float, "Refractive index of the surrounding medium"),
"pixel size um":
    (np.nan, float, "Detector pixel size [µm]"),
"wavelength nm":
    (np.nan, float, "Imaging wavelength [nm]"),

[roi] Extraction of regions of interest

"dist border":
    (10, int, "Minimum distance of objects to image border [px]"),
"eccentricity max":
    (.7, float, "Allowed maximal eccentricity of the specimen"),
# If set to false, the file "roi_slices.txt" must contain ROIs
"enabled":
    (True, fbool, "Perform automated search for ROIs"),
"exclude overlap":
    (30., float, "Allowed distance between two objects [px]"),
"force":
    ((), tupletupleint, "Force ROI coordinates (x1,x2,y1,y2) [px]"),
"pad border":
    (40, int, "Padding of object regions [px]"),
"size variation":
    (.5, float, "Allowed variation relative to specimen size"),

[output] Supplementary data output

"roi images":
    (True, fbool, "Rendered phase images with ROI location"),
"sphere images":
    (True, fbool, "Phase/Intensity images for sphere analysis"),
"sensor tif data":
    (True, fbool, "Phase/Amplitude sensor tif data"),

[specimen] Specimen parameters

# this is used as the initial value for the sphere analysis
"size um":
    (10, float, "Approximate diameter of the specimen [µm]"),

[sphere] Sphere-based image analysis

# see qpsphere.edgefit.contour_canny
"edge coarse":
    (.4, float, "Coarse edge detection filter size"),
"edge fine":
    (.1, float, "Fine edge detection filter size"),
"edge clip radius min":
    (.9, float, "Interior edge point filtering radius"),
"edge clip radius max":
    (1.1, float, "Exterior edge point filtering radius"),
"edge iter":
    (20, int, "Maximum number iterations for coarse edge detection"),
# see qpsphere.imagefit.alg.match_phase
"image fit range position":  # crel
    (.05, float, "Fit interpolation range for radius"),
"image fit range radius":  # rrel
    (.05, float, "Fit interpolation range for radius"),
"image fit range refractive index":  # nrel
    (.10, float, "Fit interpolation range for refractive index"),
"image fix phase offset":  # fix_pha_offset
    (False, fbool, "Fix the simulation background phase to zero"),
"image iter":  # max_iter
    (100, int, "Maximum number of iterations for image fitting"),
"image stop delta position":  # stop_dc
    (1, float, "Stopping criterion for position"),
"image stop delta radius":  # stop_dr
    (.0010, float, "Stopping criterion for radius"),
"image stop delta refractive index":  # stop_dn
    (.0005, float, "Stopping criterion for refractive index"),
"image verbosity":  # verbose
    (1, int, "Verbosity level of image fitting algorithm"),
# see qpsphere.analyze
"method":
    ("edge", lcstr, "Method for determining sphere parameters"),
# see qpsphere.models
"model":
    ("projection", lcstr, "Physical sphere model"),
"refraction increment":
    (.18, float, "Refraction increment [mL/g]"),
"radial inclusion factor":
    (1.2, float, "Radial inclusion factor for dry mass computation"),