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"),