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Help

Usage

icemet-server [options] config.yaml

Options

  • -h Print this help message and exit.
  • -V Print version info and exit.
  • -t Test config file and exit.
  • -p Particles only.
  • -s Stats only. Particles will be fetched from the database.
  • -Q Quit after processing all available files.
  • -d Enable debug messages.

Config

Config template: icemet-server.yaml

Files

  • path_watch <str> Path to watch. ICEMET Server looks for readable files from this directory and its subdirectories recursively.
  • path_results <str> Path where ICEMET Server saves the processed results.
  • save_results <str> Which results will be saved.
    • o Original images.
    • p Preprocessed images.
    • m Minimum images.
    • r Reconstructed particles.
    • t Thresholded particles
    • v Preview images.
  • save_empty <bool> Save empty files.
  • save_skipped <bool> Save skipped files.
  • type_results(|_lossy) <str> File type for regular and lossy (preview) images.

SQL server

  • sql_host <str> SQL server host.
  • sql_port <int> SQL server port.
  • sql_user <str> SQL server username.
  • sql_passwd <str> SQL server password.
  • sql_database <str> SQL server database.
  • sql_table_particles <str> Particles table name.
  • sql_table_stats <str> Stats table name.
  • sql_table_meta <str> Meta table name. If empty, the meta information will not be written.

Preprocessing

  • img_(x|y|w|h) <int> Image cropping rectangle.
  • img_rotation <int> Image rotation in degrees.
  • empty_th_original <int> Original images with max-min value smaller than this will be marked as empty.
  • empty_th_preproc <int> Preprocessed images with max-min value smaller than this will be marked as empty.
  • empty_th_recon <int> After preprocessing, a minimum image is created with 10x sparser step than holo_dz. If the max-min value of the minimum image is smaller than the value, the image will be marked as empty.
  • noisy_th_recon <int> After preprocessing, a minimum image is created with 10x sparser step than holo_dz. The minimum image is binarized and contours will be extracted. If the number of contours is higher than the value, the image will be marked as skipped.
  • bgsub_stack_len <int> Background subtraction stack length. 0 for no background subtraction.
  • filt_lowpass <int> Super-gaussian lowpass filter frequency. 0 for no filter.

Reconstruction

  • holo_(z0|z1) <float> Hologram reconstruction range start and stop in meters.

  • holo_(dz0|dz1) <float> Hologram reconstruction step start and stop in meters.

  • holo_pixel_size <float> Camera single pixel size in meters.

  • holo_lambda <float> Laser wavelength in meters.

  • holo_distance <float> Distance between the camera and laser in meters for uncollimated beams. 0 for collimated beams.

  • recon_step <int> The number of frames in each reconstruction batch. Can be used to limit the memory usage.

  • focus_step <int> The number of frames between frames that will be used in the focusing. Can be used to speed up the focusing.

  • focus_method(|_small) <int> Autofocus scoring function for regular and small segments.

  • 0 Minimum value.

  • 1 Maximum value.

  • 2 Dynamic range.

  • 3 StdDev of StdDev filter.

  • 4 Tamura of gradient.

  • segment_th_method <int> Segment thresholding method. th = f · bg

  • 0 Minimum of amplitude.

  • 1 Minimum of phase.

  • segment_th_bg <int> Segment thresholding background value bg. -1 uses preprocessed image median.

  • segment_th_factor <float> Segment threshold factor f.

  • segment_size_(min|max) <int> Size range of the segments (width or height) in pixels.

  • segment_size_small <int> Segments smaller than this will be focused using a minimum based method.

  • segment_pad <int> Padding around the segments in pixels.

  • img_ignore_(x|y) <int> Image border area in pixels that will be ignored.

Analysis

  • segment_scale <float> The size (width or height) the smaller segments will be upscaled to in pixels.
  • particle_th_factor <float> Particle threshold factor f: bg = Median(preproc) min = Min(segm) th = bg - f · (bg - min)
  • diam_corr <bool> Enable particle diamater correction.
  • diam_corr_(d0|d1) <float> Diameter correction start and end sizes.
  • diam_corr_(f0|f1) <float> Diameter correction start and end factors. The factor changes linearly between d0 and d1.

Statistics

  • stats_time <int> Time between stats points in seconds.
  • stats_frames <int> Fixed number of frames used for stats calculation. Required only in the stats only mode.
  • stats_temp <float> Constant air temperature in deg C.
  • stats_wind <float> Constant wind speed in m/s.
  • particle_z_(min|max) <float> Particle min/max z-position for stats calculation.
  • particle_diam_(min|max) <float> Particle min/max size for stats calculation.
  • particle_circ_(min|max) <float> Particle min/max Heywood circularity factor for stats calculation: circ = perim / (2 · Sqrt(π · area))
  • particle_dynrange_(min|max) <int> Particle min/max dynamic range for stats calculation.

OpenCL

  • ocl_device <str> OpenCL device.