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 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 [%]Set to 0 to disable. - amplitude border px = 5 (
int
) – Amplitude bg border region to analyze [px]Set to 0 to disable. - 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 mask sphere = nan (
float
) – Circular mask for amplitude bg correctionIf not nan, a mask is used for background correction. A value of “1.0” results in a mask with the radius as determined with the edge-detection approach from phase [sic]. Set this to “1.1” to exclude peripheral phase values. If the amplitude border values or binary thresholds are set, the intersection of the resulting masks is used for background correction. For procedural details seeqpsphere.cnvnc.bg_phase_mask_for_qpi()
. - 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
. - enabled = True (
fbool
) – Enable bg correction globallySet to False to disable background correction. - 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 [%]Set to 0 to disable. - phase border px = 5 (
int
) – Phase bg border region to analyze [px]Set to 0 to disable. - 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 mask sphere = nan (
float
) – Circular mask for phase bg correctionIf not nan, a mask is used for background correction. A value of “1.0” results in a mask with the radius as determined with the edge-detection approach from phase. Set this to “1.1” to exclude peripheral phase values. If the phase border values or binary thresholds are set, the intersection of the resulting masks is used for background correction. For procedural details seeqpsphere.cnvnc.bg_phase_mask_for_qpi()
. - 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
.
[holo] Hologram analysis¶
These parameters tune the analysis of off-axis hologram data (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 = None (
tupletupleint
) – Force ROI coordinates (x1,x2,y1,y2) [px] - ignore data = None (
strlist
) – Exclude images and ROIs from the analysisTo exclude individual ROIs found in a previous run, simply type the ROI index, i.e. ‘exclude = 1.0, 2.2’. You may additionally exclude a full sensor image (e.g. image 3) with ‘exclude = 1.0, 2.2, 3’. - 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 = True (
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