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Merge pull request #30 from uw-loci/22-consistent-test-struct
Consistent test data structure for processImage, newCurv
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‎.github/workflows/ci.yml‎

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Original file line numberDiff line numberDiff line change
@@ -1,14 +1,11 @@
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name: ci
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on:
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# Allow manual runs from the Actions tab
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workflow_dispatch:
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# Run on pushes to any branch (including feature branches)
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push:
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branches: [ "**" ]
9-
# And on PRs targeting main
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branches: ["**"]
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pull_request:
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branches: [ main ]
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branches: [main]
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jobs:
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test:
@@ -19,19 +16,28 @@ jobs:
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steps:
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- uses: actions/checkout@v4
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# Install system dependencies (like in your Docker container)
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- name: Install system dependencies
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run: sudo apt-get update && sudo apt-get install -y libgl1 libglib2.0-0 python3-venv
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# Set up Python
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- uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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# Create virtual environment
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- name: Create virtual environment
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run: |
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python -m pip install --upgrade pip
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# Install without curvelops to avoid FFTW/CurveLab build on CI
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python -m pip install --break-system-packages -e .
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python -m pip install --break-system-packages pytest ruff
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python -m venv venv
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source venv/bin/activate
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python -m pip install --upgrade pip setuptools wheel
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python -m pip install -e .
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python -m pip install pytest ruff
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# Run tests in the venv
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- name: Run tests
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env:
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QT_QPA_PLATFORM: "offscreen"
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run: |
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pytest -q
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source venv/bin/activate
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pytest -rs

‎.gitignore‎

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@@ -14,6 +14,7 @@ local.properties
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.classpath
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.settings/
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.loadpath
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*.idea
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# External tool builders
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.externalToolBuilders/
@@ -59,6 +60,7 @@ local.properties
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*.tli
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*.tlh
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*.tmp
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*.xlsx
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*.vspscc
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.builds
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*.dotCover
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*.tif
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pycurvelets/opt/*.*
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# test tmp folder
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tests/test_images/CA_Out/
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# referenced MATLAB files
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*.m

‎pyproject.toml‎

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Original file line numberDiff line numberDiff line change
@@ -9,16 +9,17 @@ description = "Python translation of CurveAlign; curvelet-based quantification a
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authors = [{ name = "Eliceiri Lab" }]
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requires-python = ">=3.11"
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dependencies = [
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"pandas",
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"numpy",
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"matplotlib",
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"scipy",
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"opencv-python",
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"scikit-image",
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"openpyxl",
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"matplotlib>=3.10.1",
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"napari",
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"numpy>=2.2.6",
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"opencv-python-headless>=4.10.0.84",
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"openpyxl>=3.1.5",
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"pandas>=2.2.3",
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"pyqt6",
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"qtpy",
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"scikit-image>=0.25.0",
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"scikit-learn>=1.7.1",
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"scipy>=1.15.2",
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]
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[dependency-groups]

‎src/curvealign_matlab/getTifBoundary.m‎

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function [resMat,resMatNames,numImPts] = getTifBoundary(coords,img,object,imgName,distThresh,fibKey,endLength,fibProcMeth,distMini)
2+
3+
% getTifBoundary.m - This function takes the coordinates from the boundary file, associates them with curvelets, and produces relative angle measures.
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%
5+
% Inputs:
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% coords - the locations of the endpoints of each line segment making up the boundary
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% img - the image being measured
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% object - a struct containing the center and angle of each measured curvelet, generated by the newCurv function
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% distThresh - number of pixels from boundary we should evaluate curvelets
10+
% boundaryImg - tif file with boundary outlines, must be a mask file
11+
% fibKey - list indicating the beginning of each new fiber in the object struct, allows for fiber level processing
12+
% distMini - minimum distrance to the boundary, to get rid of the fiber on or very close to the boundary
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%
14+
% Output:
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% measAngs - all relative angle measurements, not filtered by distance
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% measDist - all distances between the curvelets and the boundary points, not filtered
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% inCurvsFlag - curvelets that are considered
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% outCurvsFlag - curvelets that are not considered
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% measBndry = points on the boundary that are associated with each curvelet
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% inDist = distance between boundary and curvelet for each curvelet considered
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% numImPts = number of points in the image that are less than distThresh from boundary
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% insCt = number of curvelets inside an epithelial region
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%
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%
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% By Jeremy Bredfeldt, LOCI, Morgridge Institute for Research, 2013
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%Note: a "curv" could be a curvelet or a fiber segment, depending on if CT or FIRE is used
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imHeight = size(img,1);
30+
imWidth = size(img,2);
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sz = [imHeight,imWidth];
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% figure(600);
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% imshow(img);
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% figure(500);
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% hold on;
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% for k = 1:length(coords)
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% boundary = coords{k};
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% plot(boundary(:,2), boundary(:,1), 'y', 'LineWidth', 2);
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% end
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%collect all fiber points
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allCenterPoints = vertcat(object.center);
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%collect all boundary points
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% coords = vertcat(coords{2:end,1});
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coords = vertcat(coords{1:end,1});
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%collect all region points
50+
linIdx = sub2ind(sz, allCenterPoints(:,1), allCenterPoints(:,2));
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[idx_dist,dist] = knnsearch(coords,allCenterPoints); %closest point to a boundary
53+
reg_dist = img(linIdx);
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%YL: test the boundary association
57+
% figure(1002);clf;set(gcf,'pos',[200 300 imWidth imHeight ]);
58+
% plot(coords(:,2),coords(:,1),'k.'); axis ij
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% axis([1 imWidth 1 imHeight ]);hold on
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61+
%[idx_reg,reg_dist] = knnsearch([reg_col,reg_row],allCenterPoints); %closest point to a filled in region
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%Make a list of points in the image (points scattered throughout the image)
64+
C = floor(imWidth/20); %use at least 20 per row in the image, this is done to speed this process up
65+
[I, J] = ind2sub(size(img),1:C:imHeight*imWidth);
66+
allImPoints = [I; J]';
67+
%Get list of image points that are a certain distance from the boundary
68+
[~,dist_im] = knnsearch(coords(1:3:end,:),allImPoints); %returns nearest dist to each point in image
69+
%threshold distance
70+
if isempty(distMini) % keep all the fibers within the distance threshold
71+
inIm = dist_im <= distThresh;
72+
else % get rid of fibers on or very close to the boundary
73+
inIm = (dist_im <= distThresh & dist_im > distMini);
74+
end
75+
%count number of points
76+
inPts = allImPoints(inIm);
77+
numImPts = length(inPts)*C;
78+
% numImPts = 0;
79+
80+
81+
%process all curvs, at this point
82+
curvsLen = length(object);
83+
nbDist = nan(1,curvsLen); %nearest boundary distance
84+
nrDist = nan(1,curvsLen); %nearest region distance
85+
nbAng = nan(1,curvsLen); %nearest boundary relative angle
86+
epDist = nan(1,curvsLen); %distance to extension point intersection
87+
epAng = nan(1,curvsLen); %relative angle of extension point intersection
88+
measBndry = nan(curvsLen,2);
89+
inCurvsFlag = ~logical(1:curvsLen);
90+
outCurvsFlag = ~logical(1:curvsLen);
91+
% %ROI properties
92+
% bwROI.coords = coords;
93+
% bwROI.imageWidth = imWidth;
94+
% bwROI.imageHeight = imHeight;
95+
if isempty(distMini)
96+
for i = 1:curvsLen
97+
%-- inside region?
98+
nrDist(i) = reg_dist(i)==255|reg_dist(i)== 1; %YL: mask can be 1-0(matlab lab) or 255-0(ImageJ)
99+
%-- distance to nearest epithelial boundary
100+
nbDist(i) = dist(i);
101+
%-- relative angle at nearest boundary point
102+
if dist(i) <= distThresh
103+
[nbAng(i), bPt] = GetRelAng([coords(:,2),coords(:,1)],idx_dist(i),object(i).angle,imHeight,imWidth,i); % add i as an input argument for debug
104+
% %%
105+
% bwROI.index2object = idx_dist(i);
106+
% fiberobject.center = object(i).center;
107+
% fiberobject.angle = object(i).angle;
108+
% angleOption = 0; % caclulate all angles
109+
% [relativeAngles, ROImeasurements] = getRelativeangles(bwROI,fiberobject,angleOption);
110+
% fprintf(' original relative angle is %3.2f \n re-calculated relative angle is %3.2f \n ',nbAng(i),relativeAngles.angle2boundaryEdge);
111+
% fprintf(' relative angle to ROI orientation is %3.2f \n',relativeAngles.angle2boundaryCenter);
112+
% fprintf('relative angle to ROI-fiber centers line is %3.2f \n',relativeAngles.angle2centersLine);
113+
%%
114+
else
115+
nbAng(i) = nan; % if out of the region
116+
bPt = nan(1,2); % if out of the region
117+
end
118+
%-- extension point features
119+
[lineCurv orthoCurv] = getPointsOnLine(object(i),imWidth,imHeight,distThresh);
120+
[intLine, iLa, iLb] = intersect([lineCurv(:,2) lineCurv(:,1)],coords,'rows');
121+
if (~isempty(intLine))
122+
%get the closest distance from the curvelet center to the
123+
%intersection (get rid of the farther one(s))
124+
[idxLineDist, lineDist] = knnsearch(intLine,object(i).center);
125+
boundaryPtIdx = iLb(idxLineDist);
126+
%%tentatively turn the extension feature off
127+
% %-- extension point distance
128+
% epDist(i) = lineDist;
129+
% %-- extension point angle
130+
% [epAng(i) bPt1] = GetRelAng([coords(:,2),coords(:,1)],boundaryPtIdx,object(i).angle,imHeight,imWidth,i);
131+
else
132+
epDist(i) = nan;% no intersection exists
133+
epAng(i) = nan; % no angle exists
134+
bPt1 = nan(1,2); % if no intersection set boundary to be [NaN NaN]
135+
end
136+
measBndry(i,:) = bPt; % nearest boundary
137+
end %of for loop
138+
else % get rid of fibers on or within the minimum distance to the boundary
139+
for i = 1:curvsLen
140+
%-- inside region?
141+
nrDist(i) = reg_dist(i)==255|reg_dist(i)== 1; %YL: mask can be 1-0(matlab lab) or 255-0(ImageJ)
142+
%-- distance to nearest epithelial boundary
143+
nbDist(i) = dist(i);
144+
%-- relative angle at nearest boundary point
145+
if (dist(i) <= distThresh & dist(i) > distMini)
146+
[nbAng(i), bPt] = GetRelAng([coords(:,2),coords(:,1)],idx_dist(i),object(i).angle,imHeight,imWidth,i); % add i as an input argument for debug
147+
else
148+
nbAng(i) = nan; % if out of the region
149+
bPt = nan(1,2); % if out of the region
150+
end
151+
%-- extension point features
152+
[lineCurv orthoCurv] = getPointsOnLine(object(i),imWidth,imHeight,distThresh);
153+
[intLine, iLa, iLb] = intersect([lineCurv(:,2) lineCurv(:,1)],coords,'rows');
154+
if (~isempty(intLine))
155+
%get the closest distance from the curvelet center to the
156+
%intersection (get rid of the farther one(s))
157+
[idxLineDist, lineDist] = knnsearch(intLine,object(i).center);
158+
boundaryPtIdx = iLb(idxLineDist);
159+
%%tentatively turn the extension feature off
160+
% %-- extension point distance
161+
% epDist(i) = lineDist;
162+
% %-- extension point angle
163+
% [epAng(i) bPt1] = GetRelAng([coords(:,2),coords(:,1)],boundaryPtIdx,object(i).angle,imHeight,imWidth,i);
164+
else
165+
epDist(i) = nan;% no intersection exists
166+
epAng(i) = nan; % no angle exists
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bPt1 = nan(1,2); % if no intersection set boundary to be [NaN NaN]
168+
end
169+
measBndry(i,:) = bPt; % nearest boundary
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end %of for loopend
171+
end
172+
173+
174+
175+
resMat = [nbDist', ... %nearest dist to a boundary
176+
nrDist', ... %flag, 0 for outside boundary, 1 for inside boundary
177+
nbAng', ... %nearest relative boundary angle
178+
epDist', ... %extension point distance
179+
epAng', ... %extension point relative boundary angle
180+
measBndry]; %list of boundary points associated with fibers
181+
resMatNames = {
182+
'nearestBoundDist', ...
183+
'nearestRegionDist', ...
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'nearestBoundAng', ...
185+
'extensionPointDist', ...
186+
'extensionPointAng', ...
187+
'bndryPtRow', ...
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'bndryPtCol'};
189+
190+
end %of main function
191+
192+
function [relAng, boundaryPt] = GetRelAng(coords,idx,fibAng,imHeight,imWidth,fnum)
193+
boundaryAngle = FindOutlineSlope([coords(:,2),coords(:,1)],idx);
194+
boundaryPt = coords(idx,:);
195+
if (boundaryPt(1) == 1 || boundaryPt(2) == 1 || boundaryPt(1) == imHeight || boundaryPt(2) == imWidth)
196+
%don't count fiber if boundary point is along edge of image
197+
tempAng = 0;
198+
else
199+
%--compute relative angle here--
200+
%There is a 90 degree phase shift in fibAng and boundaryAngle due to image orientation issues in Matlab.
201+
% -therefore no need to invert (ie. 1-X) circ_r here.
202+
tempAng = circ_r([fibAng*2*pi/180; boundaryAngle*2*pi/180]);
203+
tempAng = 180*asin(tempAng)/pi;
204+
% %YL debug the NaN angle
205+
% if isnan(tempAng)
206+
% figure(1002),plot(coords(idx,1),coords(idx,2),'ro','MarkerSize',10)
207+
% text(coords(idx,1),coords(idx,2),sprintf('%d',fnum));
208+
% disp(sprintf('fiber %d relative angle is Nan, fibAng = %f, boundaryAngle = %f, idx_dist = %d',fnum,fibAng,boundaryAngle,idx))
209+
% % pause(3)
210+
% end
211+
end
212+
relAng = tempAng;
213+
end
214+
215+
function [lineCurv orthoCurv] = getPointsOnLine(object,imWidth,imHeight,boxSz)
216+
center = object.center;
217+
angle = object.angle;
218+
slope = -tand(angle);
219+
%orthoSlope = -tand(angle + 90); %changed from tand(obj.ang) to -tand(obj.ang + 90) 10/12 JB
220+
intercept = center(1) - (slope)*center(2);
221+
%orthoIntercept = center(1) - (orthoSlope)*center(2);
222+
223+
%[p1 p2] = getBoxInt(slope, intercept, imWidth, imHeight, center, boxSz);
224+
if isinf(slope)
225+
dist_y = 0;
226+
dist_x = boxSz;
227+
else
228+
dist_y = boxSz/sqrt(1+slope*slope);
229+
dist_x = dist_y*slope;
230+
end
231+
p1 = [center(2) - dist_y, center(1) - dist_x];
232+
p2 = [center(2) + dist_y, center(1) + dist_x];
233+
[lineCurv ~] = GetSegPixels(p1,p2);
234+
235+
%Not using the orthogonal slope for anything now
236+
%[p1 p2] = getIntImgEdge(orthoSlope, orthoIntercept, imWidth, imHeight, center);
237+
%[orthoCurv, ~] = GetSegPixels(p1,p2);
238+
orthoCurv = [];
239+
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end
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‎src/pycurvelets/__init__.py‎

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@@ -1,10 +1,11 @@
1-
# Optional import: allow the package to be imported without native curvelet deps.
21
try:
32
from .new_curv import new_curv # type: ignore
3+
44
HAS_CURVELETS = True
55
except Exception:
66
HAS_CURVELETS = False
77

8-
__all__ = ["new_curv", "HAS_CURVELETS"]
9-
10-
8+
__all__ = [
9+
"HAS_CURVELETS",
10+
"new_curv",
11+
]

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