Merge branch 'TissUUmaps:master' into master

Author: cavenel

CHANGELOG.md

@@ -17,6 +17,7 @@
 - Move to PySide6 instead of PyQt6
 - Add installers for MacOS X (.dmg) and Linux (.deb)
 - Update to OpenSeadragon 4.1.0
+- Add dzi support (opening as images directly)
 - Lots of minor fixes
 
 ## 3.1.1.6

container/requirements.txt

@@ -1,4 +1,4 @@
-scipy<1.9.0
+scipy>=1.10.1
 Flask>=2.0.0
 openslide-python>=1.1.2
 packaging>=21.0

setup.cfg

@@ -29,7 +29,7 @@ install_requires =
     pyvips>=2.1.14
     pyyaml>=6.0
     h5py>=3.6.0
-    scipy>=1.7.2
+    scipy>=1.10.1
     packaging>=21.0
     tissuumaps-schema~=1.2.0
 

standalone/requirements.txt

@@ -8,5 +8,5 @@ PySide6-Addons==6.4.3
 matplotlib>=3.2.2
 pyyaml>=5.0
 h5py>=3.6.0
-scipy>=1.7.2
+scipy>=1.10.1
 tissuumaps-schema~=1.2.0

tissuumaps/VERSION

@@ -1 +1 @@
-3.2
+3.2.0.1

tissuumaps/read_h5ad.py

@@ -293,13 +293,19 @@ def h5ad_to_tmap(basedir, path, library_id=None):
     obsListNumerical = []
     palette = {}
 
+    obsIndex = str(adata.get("/obs").attrs["_index"])
     for obs in obsList:
         if adata.get(f"/obs/{obs}/categories") is not None:
             obsListCategorical.append(obs)
             p = getPalette(adata, obs)
             palette[obs] = p
-        else:
+        elif adata.get(f"/obs/{obs}").dtype.kind in "iuf":
             obsListNumerical.append(obs)
+        elif obs == obsIndex:
+            continue
+        else:
+            obsListCategorical.append(obs)
+            palette[obs] = {}
 
     new_tmap_project["markerFiles"].append(
         {

tissuumaps/static/js/utils/glUtils.js

@@ -535,6 +535,7 @@ glUtils._regionsVS = `
     #define MAX_NUM_IMAGES 192
 
     uniform mat2 u_viewportTransform;
+    uniform vec2 u_canvasSize;
     uniform int u_transformIndex;
     uniform vec4 u_imageBounds;
     uniform int u_numScanlines;
@@ -551,6 +552,7 @@ glUtils._regionsVS = `
     out vec2 v_texCoord;
     out vec2 v_localPos;
     out float v_scanline;
+    flat out float v_pixelWidth;
 
     void main()
     {
@@ -568,6 +570,13 @@ glUtils._regionsVS = `
         ndcPos.y = -ndcPos.y;
         ndcPos = u_viewportTransform * ndcPos;
 
+        // Calculate pixel width in local coordinates. Need to do it here in the
+        // vertex shader, because using pixel derivatives in the fragment shader
+        // can cause broken stroke lines for large coordinates.
+        vec2 ndcPos2 = ndcPos + 0.7 / u_canvasSize;
+        mat2 viewportToLocal = inverse(u_viewportTransform * mat2(imageToViewport));
+        v_pixelWidth = length(viewportToLocal * (ndcPos2 - ndcPos));
+
         gl_Position = vec4(ndcPos, 0.0, 1.0);
     }
 `;
@@ -599,6 +608,7 @@ glUtils._regionsFS = `
     in vec2 v_texCoord;
     in vec2 v_localPos;
     in float v_scanline;
+    flat in float v_pixelWidth;
 
     layout(location = 0) out vec4 out_color;
 
@@ -625,7 +635,9 @@ glUtils._regionsFS = `
         vec2 p = v_localPos;  // Current sample position
         int scanline = int(v_scanline);
 
-        float pixelWidth = length(dFdx(p.xy));
+        // float pixelWidth = length(dFdx(p.xy));  // Can cause precision problems!
+        float pixelWidth = v_pixelWidth;  // Safer
+
         float strokeWidthPixels = u_regionStrokeWidth *
             (u_regionFillRule == FILL_RULE_NEVER ? STROKE_WIDTH : STROKE_WIDTH_FILLED);
         // For proper anti-aliasing, clamp stroke width to at least 1 pixel, and
@@ -2129,6 +2141,7 @@ glUtils._drawRegionsColorPass = function(gl, viewportTransform) {
 
         // Set per-scene uniforms
         gl.uniformMatrix2fv(gl.getUniformLocation(program, "u_viewportTransform"), false, viewportTransform);
+        gl.uniform2fv(gl.getUniformLocation(program, "u_canvasSize"), [gl.canvas.width, gl.canvas.height]);
         gl.uniform1i(gl.getUniformLocation(program, "u_transformIndex"), collectionIndex);
         gl.uniform4fv(gl.getUniformLocation(program, "u_imageBounds"), imageBounds);
         gl.uniform1i(gl.getUniformLocation(program, "u_numScanlines"), numScanlines);

tissuumaps/templates/tissuumaps.html

@@ -492,6 +492,7 @@ <h6 class="my-2">List of plugins:</h6>
 
     if (window!=window.top) {
       /* I'm in a frame! */
+      OpenSeadragon.MouseTracker.passiveWheelEvents = false;
       document.getElementById("main-navbar").classList.add("collapse");
       document
         .getElementById("floating-navbar-toggler")