Catheter Utils

Catheter Utils#

This project contains utils related to our catheter tracking projects.

cathcoords#

Contains things for manipulating “cathcoords” files and data. These are localized catheter coordinates combined with metadata like trigger time and snr.

geometry#

Contains things for reasoning about the catheter’s geometry. Things like distances between distal, proximal, and tip locations, as well as helpers for extrapolating the tip.

localization#

Contains things for producing estimates of a coil location from projection data. This includes single projection localization all the way up to full catheter location fit using constrains and snr-like error weighting.

metrics#

Contains evaluation and display of tracking sequence error metrics. Metric methods include Bias and Chebyshev.

projections#

Contains code for reading raw projection data, as well as basic calculations like snr.

Tests#

Make sure that your current terminal/CMD directory is the catheter_utils folder

Can run all tests with the command python -m unittest discover tests.

test_localization#

The localization test ensures that the current localization algorithms match the original/target localization algorithms output for the same dataset.

Note: Currently tests the PNG (peak-normed gaussian) and JPNG (joint peak-normed gaussian) algorithm, to ensure it outputs the same coordinates as when originally run based on data acquired and reconstructed during Jay Soni’s experiments in April 2020

Based on testing from multiple systems/numpy versions, the test precision is 2 decimal places. Decimal place should not exceed precision of test data.

Example Code: np.testing.assert_almost_equal(output, target, decimal=2) # check for 2 decimal place precision/accuracy between current output and target

Adding New Test Data#

  1. Copy test data and target algorithm folder to catheter_utils/tests/testdata

  2. Add a copy of ‘localization_settings_template.yaml’ file (from catheter_utils/tests/testdata) to each added test data folder and edit file parameters accordingly

  3. Test settings for the test data and localization algorithms to be modified in the localization_settings_template.yaml file

See /testdata/FH_512_dithered_original-2020-07-09T12_16_32.222 for FH example format,

See /testdata/SRI_April-2020-07-09T12_20_56.765 for SRI example format

Example: Directory Structure

  • /testdata/SRI_April-2020-07-09T12_20_56.765

    • .projections files

    • localization_settings.yaml

    • /target

      • png

      • other algorithm folders etc..

localization_settings.yaml template SRI example:

settings:
  #path to tracking sequence test data folder
  testdata_path: "./tests/testdata/SRI_April-2020-07-09T12_20_56.765"
  #path to algorithm target folder
  target_path: "./tests/testdata/SRI_April-2020-07-09T12_20_56.765/target"
  #catheter coils
  distal_index : 7
  proximal_index : 6
  #catheter geometry (0 if 2018 specs, 1 if 2019+ specs)
  geometry_index: 1
  #dither (0 if tracking sequence test data not dithered)
  dither_index : 0
  #algorithm parameters - width: window size, sigma: std, for png=> tolerance: min difference between current and previous value, for jpng=> tolerance: MSE threshold (mm)
  width: 3.5
  sigma: 0.75
  png_tol: 1e-6
  jpng_tol: 1e-2
  png_max_iter: 32
  jpng_max_iter: 256

Note: Not all algorithm parameters are used in some localization algorithms. Width used by centroid_around_peak, png, jpng. Sigma used by png and jpng. Png and jpng have individual tolerances/max iterations parameters.

Test Localization Results#

  • Summary of latest test saved in /tests/testdata/test_localization_summary.csv

  • Last test failure saved in /tests/testdata/test_localization_fail.log

Developer Notes:#

test_localization.py

  • To add more localization algorithms to test function “def localize_test”, refer to loc_fns structure found in cathy

  • To add new test to the test case “algorithm_localizer(TestCase)”, add new def function with name ‘test_’

Example

class algorithm_localizer(TestCase) …

def setUp(self): …

def test_localize(self): …

def test_XXXXXXXX(self): …

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