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¶
DryMass uses the Python library qpimage for
background correction. For detailed information on the
algorithms (and the corresponding keyword arguments) used,
please see qpimage.bg_estimate
.
- amplitude data = none (
int_or_path
) – Amplitude bg correction file or indexImage indexing starts with 1. If a file, either specify the full path or the relative path to the directory containing the input data. - amplitude offset = mean (
lcstr
) – Amplitude bg correction offset methodValid values are defined inqpimage.bg_estimate.VALID_FIT_OFFSETS
. - amplitude profile = tilt (
lcstr
) – Amplitude bg correction profile methodValid values are defined inqpimage.bg_estimate.VALID_FIT_PROFILES
. - amplitude binary threshold = nan (
float_or_str
) – Binary image threshold value or methodIf not nan, defines either a threshold for background segmentation or a method inskimage.filters
. - 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 globallySet to False when manually editing roi_slices.txt. - phase data = none (
int_or_path
) – Phase bg correction file or indexImage indexing starts with 1. If a file, either specify the full path or the relative path to the directory containing the input data. - phase offset = mean (
lcstr
) – Phase bg correction offset methodValid values are defined inqpimage.bg_estimate.VALID_FIT_OFFSETS
. - phase profile = tilt (
lcstr
) – Phase bg correction profile methodValid values are defined inqpimage.bg_estimate.VALID_FIT_PROFILES
. - phase binary threshold = nan (
float_or_str
) – Binary image threshold value or methodIf not nan, defines either a threshold for background segmentation or a method inskimage.filters
. - phase border perc = 10 (
float
) – Phase bg border region to analyze [%] - phase border px = 5 (
int
) – Phase bg border region to analyze [px]
[holo] Hologram analysis¶
These parameters tune the hologram analysis step (if applicable).
The parameters shown are passed to qpimage.holo.get_field()
.
- filter name = disk (
str
) – Filter name for sideband isolation - filter size = 1/3 (
float
) – Filter size (fraction of the sideband frequency - sideband = 1 (
floattuple_or_one
) – Sideband ±1 or frequency coordinates
[meta] Image meta data¶
This section contains meta data of the experiment.
[output] Supplementary data output¶
This section defines what additional data are written to disk.
[roi] Extraction of regions of interest¶
The extraction of ROIs is done in drymass.extractroi.extract_roi()
.
- dist border px = 10 (
int
) – Minimum distance of objects to image border [px] - eccentricity max = 0.7 (
float
) – Allowed maximal eccentricity of the specimen - enabled = True (
fbool
) – Perform automated search for ROIsIf set to False, the file “roi_slices.txt” must contain ROIs. - exclude overlap px = 30.0 (
float
) – Allowed distance between two objects [px] - force = () (
tupletupleint
) – Force ROI coordinates (x1,x2,y1,y2) [px] - pad border px = 40 (
int
) – Padding of object regions [px] - size variation = 0.5 (
float01
) – Allowed variation relative to specimen size
[specimen] Specimen parameters¶
Prior information about the analyzed object(s).
- size um = 10 (
float
) – Approximate diameter of the specimen [µm]This is used as the initial value for the sphere analysis.
[sphere] Sphere-based image analysis¶
Retrieval of refractive index and radius is done with the Python module
qpsphere. The parameters either apply to
qpsphere.edgefit.contour_canny()
or to
qpsphere.imagefit.alg.match_phase()
, depending on
which analysis approach is used.
- edge coarse = 0.4 (
float
) – Coarse edge detection filter size - edge fine = 0.1 (
float
) – Fine edge detection filter size - edge clip radius min = 0.9 (
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 - image fit range position = 0.05 (
float
) – Fit interpolation range for radius - image fit range radius = 0.05 (
float
) – Fit interpolation range for radius - image fit range refractive index = 0.10 (
float
) – Fit interpolation range for refractive index - image fix phase offset = False (
fbool
) – Fix the simulation background phase to zero - image iter = 100 (
int
) – Maximum number of iterations for image fitting - image stop delta position = 1 (
float
) – Stopping criterion for position - image stop delta radius = 0.0010 (
float
) – Stopping criterion for radius - image stop delta refractive index = 0.0005 (
float
) – Stopping criterion for refractive index - image verbosity = 1 (
int
) – Verbosity level of image fitting algorithm - method = edge (
lcstr
) – Method for determining sphere parametersValid values are edge (edge-detection approach) or image (2D phase image fitting). - model = projection (
lcstr
) – Physical sphere modelValid values are defined inqpsphere.models.available
. If method=edge, then model must be set to projection. If method=image, setting model to rytov-sc has the best trade-off between accuracy and speed. - refraction increment = 0.18 (
float
) – Refraction increment [mL/g] - radial inclusion factor = 1.2 (
float
) – Radial inclusion factor for dry mass computation