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Merge pull request #323 from GSTT-CSC/322-li-threhsold-too-low
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Increase starting threshold to 0.5 quantile
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@laurencejackson
laurencejackson authored Feb 27, 2023
2 parents 6a25640 + 5566bc4 commit ffe6e04
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion hazenlib/tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ def find_contours(self):
# convert the resized image to grayscale, blur it slightly, and threshold it
self.blurred = cv.GaussianBlur(self.arr.copy(), (5, 5), 0) # magic numbers

optimal_threshold = filters.threshold_li(self.blurred, initial_guess=np.quantile(self.blurred, 0.25))
optimal_threshold = filters.threshold_li(self.blurred, initial_guess=np.quantile(self.blurred, 0.50))
self.thresh = np.where(self.blurred > optimal_threshold, 255, 0).astype(np.uint8)

# have to convert type for find contours
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2 comments on commit ffe6e04

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Coverage

Coverage Report
FileStmtsMissCoverMissing
hazenlib
   HazenTask.py26485%18, 32–34
   __init__.py1473874%138, 142, 152, 157, 194, 201–206, 217, 220–227, 247–249, 267–269, 288–290, 299, 304, 310, 361, 384–386, 394–395, 399
   exceptions.py21481%17–21
   relaxometry.py3179072%238–256, 631, 690–692, 746, 794–816, 834–849, 1174–1177, 1186–1189, 1201–1214, 1217–1222, 1233–1263
   shapes.py20955%13, 16, 24–29, 32
   snr_map.py111595%408, 413–415, 444
   tools.py84890%43–50, 92, 101, 117
hazenlib/tasks
   acr_ghosting.py1164264%33–53, 91–93, 123–125, 161–194
   acr_uniformity.py893264%34–54, 121–138
   ghosting.py1505166%18–32, 47, 109–110, 114, 124–125, 151–153, 170–172, 218–256
   relaxometry.py7271%10–11
   slice_position.py1182281%31, 40–41, 103–104, 130, 210, 217–234
   slice_width.py3595286%34–37, 107, 166–186, 451, 456–457, 463, 468, 530–531, 780–821
   snr.py1636660%62–67, 161–179, 194–203, 221–231, 258–268, 273–283, 314–327, 332–340, 369–382
   snr_map.py770%1–11
   spatial_resolution.py2474482%36–39, 62, 147, 206, 332–368
   uniformity.py781976%42–45, 91–92, 99, 133–147
TOTAL207649576% 

Tests Skipped Failures Errors Time
180 0 💤 0 ❌ 0 🔥 2m 5s ⏱️

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Coverage

Coverage Report
FileStmtsMissCoverMissing
hazenlib
   HazenTask.py25484%18, 32–34
   __init__.py1473874%138, 142, 152, 157, 194, 201–206, 217, 220–227, 247–249, 267–269, 288–290, 299, 304, 310, 361, 384–386, 394–395, 399
   exceptions.py21481%17–21
   relaxometry.py3179072%238–256, 631, 690–692, 746, 794–816, 834–849, 1174–1177, 1186–1189, 1201–1214, 1217–1222, 1233–1263
   shapes.py20955%13, 16, 24–29, 32
   snr_map.py111595%408, 413–415, 444
   tools.py84890%43–50, 92, 101, 117
hazenlib/tasks
   acr_ghosting.py1164264%33–53, 91–93, 123–125, 161–194
   acr_uniformity.py893264%34–54, 121–138
   ghosting.py1505166%18–32, 47, 109–110, 114, 124–125, 151–153, 170–172, 218–256
   relaxometry.py7271%10–11
   slice_position.py1182281%31, 40–41, 103–104, 130, 210, 217–234
   slice_width.py3565285%34–37, 107, 166–186, 451, 456–457, 463, 468, 530–531, 780–821
   snr.py1636660%62–67, 161–179, 194–203, 221–231, 258–268, 273–283, 314–327, 332–340, 369–382
   snr_map.py770%1–11
   spatial_resolution.py2464482%36–39, 62, 147, 206, 332–368
   uniformity.py781976%42–45, 91–92, 99, 133–147
TOTAL207149576% 

Tests Skipped Failures Errors Time
180 0 💤 0 ❌ 0 🔥 2m 24s ⏱️

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