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Fixed crash due to collapsed lung and non-dicom inputs #50

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Fixed crash due to collapsed lung and non-dicom inputs #50

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a1bef50
fixed min_intensity and max_intensity for non-dicom image inouts
adityaapte Mar 31, 2021
750520a
handled crash on failure to detect left/right lungs.
adityaapte Mar 31, 2021
c9a2df2
handled failure when no bronchi indices are available.
adityaapte Apr 7, 2021
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10 changes: 8 additions & 2 deletions Library/Airways/PTKComputeRadiusForBranch.m
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Original file line number Diff line number Diff line change
Expand Up @@ -181,8 +181,14 @@
% tissue
min_hu = -1024;
max_hu = 0;
min_intensity = lung_image_as_double.HounsfieldToGreyscale(min_hu);
max_intensity = lung_image_as_double.HounsfieldToGreyscale(max_hu);
try
min_intensity = lung_image_as_double.HounsfieldToGreyscale(min_hu);
max_intensity = lung_image_as_double.HounsfieldToGreyscale(max_hu);
catch
imgV = lung_image_as_double.RawImage(:);
min_intensity = max(min_hu,min(imgV));
max_intensity = min(max_hu,max(imgV));
end
interp_image = max(double(min_intensity), interp_image);
interp_image = min(double(max_intensity), interp_image);
midpoint = ceil(size(interp_image, 1)/2);
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3 changes: 3 additions & 0 deletions Library/Airways/PTKReallocateAirwaysByLobe.m
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,9 @@

uncertain_bronchi = start_branches.LeftUncertain;
for bonchus = uncertain_bronchi
if ~isfield(bonchus(1).GetCentrelineTree,'GlobalIndex')
continue;
end
indices = GetVoxelsForTheseBranches(bonchus, lobes);
lobe_values = lobes.RawImage(indices);
lobe_values = setdiff(lobe_values, 0);
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6 changes: 4 additions & 2 deletions Library/Lungs/PTKSeparateAndLabelLungs.m
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Original file line number Diff line number Diff line change
Expand Up @@ -89,8 +89,10 @@
num_pixels = cellfun(@numel, CC.PixelIdxList);
total_num_pixels = sum(num_pixels);
[largest_area_numpixels, largest_areas_indices] = sort(num_pixels, 'descend');

if ~isempty(trachea_top_local)

if ~isempty(trachea_top_local) && ...
length(trachea_top_local) > 1 && ...
length(size(both_lungs.RawImage)) > 2
left_region = both_lungs.RawImage(:, 1:trachea_top_local(2), :);
right_region = both_lungs.RawImage(:, trachea_top_local(2) + 1:end, :);
left_sum = sum(left_region(:));
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