Merge branch 'rf/linevector-scaling' into 'master'

Scale line vector colours in addition to lengths

See merge request fsl/fsleyes/fsleyes!285

CHANGELOG.rst

@@ -9,9 +9,12 @@ This document contains the ``fsleyes`` release history in reverse
 chronological order.
 
 
+1.2.0 (Monday 13th September 2021)
+----------------------------------
+
 
-1.2.0 (Under development)
--------------------------
+Added
+^^^^^
 
 
 * The **Display space** setting can now be set to *Scaled voxel coordinates*
@@ -20,6 +23,24 @@ chronological order.
   ``(0, 0, 0)`` (!286).
 
 
+Changed
+^^^^^^^
+
+
+* The *scale vectors to unit length* option for line vector overlays now
+  scales the vector colouring, in addition to lengths (!285).
+
+
+Fixed
+^^^^^
+
+
+* Fixed an issue on macOS / Big Sur whereby an image specified on the
+  command-line could be loaded twice (!285).
+* Fixed some rendering issues for images stored as type ``NIFTI_TYPE_RGB24``
+  (!285).
+
+
 1.1.0 (Friday 6th August 2021)
 ------------------------------
 

fsleyes/assets/gl/gl14/glvector_frag.prog

@@ -88,9 +88,9 @@ PARAM zColour      = {{ param_zColour         }};
 PARAM colourXform  = {{ param_colourXform     }};
 
 
-# Bail if the textureq coordinate
+# Bail if the texture coordinate
 # is out of the image space.
-# We use voxValue out of convenience
+# We use voxValue as a temporary
 {{
 arb_call('textest.prog',
          texCoord='{{ varying_vecTexCoord }}',
@@ -105,6 +105,26 @@ TEX voxValue,  {{ varying_vecTexCoord  }}, {{ texture_vectorTexture   }}, 3D;
 TEX modValue,  {{ varying_modTexCoord  }}, {{ texture_modulateTexture }}, 3D;
 TEX clipValue, {{ varying_clipTexCoord }}, {{ texture_clipTexture     }}, 3D;
 
+# Kill the fragment if this vector
+# has length 0 or contains NaNs
+# We use clipResult as a temporary
+# kill if length is 0
+DP3 clipResult.x, voxValue, voxValue;
+MUL clipResult.x, clipResult.x, -1;
+SGE clipResult.x, clipResult.x, 0;
+MUL clipResult.x, clipResult.x, -1;
+KIL clipResult.x;
+# kill if vector contains NaNs.
+# There is no nan test, or equality
+# test, so we test whether
+# (value >= value) || (value < value)
+DP3 clipResult.x, voxValue, voxValue;
+SGE clipResult.y, clipResult.x, clipResult.x;
+SLT clipResult.z, clipResult.x, clipResult.x;
+ADD clipResult.x, clipResult.y, clipResult.z;
+SUB clipResult.x, clipResult.x, 0.5;
+KIL clipResult.x;
+
 # Clobber the clipping/modulation
 # values we just looked up if their
 # texture coords were out of bounds.
@@ -164,11 +184,17 @@ MAD voxValue, voxValue, voxValXform.x, voxValXform.y;
 ABS voxValue, voxValue;
 
 # Cumulatively combine the rgb
-# channels of those three colours
-MOV fragColour, 0;
-MAD fragColour, voxValue.x, xColour, fragColour;
-MAD fragColour, voxValue.y, yColour, fragColour;
-MAD fragColour, voxValue.z, zColour, fragColour;
+# channels of those three colours.
+# Opacity is not modulated by
+# vector values.
+MOV fragColour,   0;
+MAD fragColour,   voxValue.x, xColour, fragColour;
+MAD fragColour,   voxValue.y, yColour, fragColour;
+MAD fragColour,   voxValue.z, zColour, fragColour;
+MOV fragColour.w, xColour.w;
+ADD fragColour.w, fragColour.w, yColour.w;
+ADD fragColour.w, fragColour.w, zColour.w;
+MUL fragColour.w, fragColour.w, 0.333333;
 
 # Apply the bri/con scale and offset
 MAD fragColour.rgb, fragColour, colourXform.x, colourXform.y;

fsleyes/assets/gl/gl21/gllinevector_vert.glsl

@@ -12,7 +12,7 @@
 uniform sampler3D vectorTexture;
 
 /*
- * Transformations between voxel and 
+ * Transformations between voxel and
  * display coordinate systems.
  */
 uniform mat4 displayToVoxMat;
@@ -44,7 +44,7 @@ uniform vec3 imageShape;
 uniform vec3 imageDims;
 
 /*
- * If true, the vectors are 
+ * If true, the vectors are
  * inverted about the x axis.
  */
 uniform bool xFlip;
@@ -56,12 +56,6 @@ uniform bool xFlip;
  */
 uniform bool directed;
 
-/*
- * If true, each vector is scaled to have a length 
- * of 1*lengthScale in the image coordinate system.
- */
-uniform bool unitLength;
-
 /*
  * Scale vector lengths by this amount.
  */
@@ -88,11 +82,9 @@ varying vec4 fragColourFactor;
 
 void main(void) {
 
-  
-  vec3  texCoord;
-  vec3  vector;
-  vec3  voxCoord;
-  float vectorLen;
+  vec3 texCoord;
+  vec3 vector;
+  vec3 voxCoord;
 
   /*
    * Normalise the voxel coordinates to [0.0, 1.0],
@@ -114,41 +106,26 @@ void main(void) {
    * texture range of [0,1] to the original
    * data range
    */
-  vector   *= voxValXform[0].x;
-  vector   += voxValXform[3].x;
-  vectorLen = length(vector);
+  vector *= voxValXform[0].x;
+  vector += voxValXform[3].x;
 
   /* Invert about the x axis if necessary */
-  if (xFlip)
+  if (xFlip) {
     vector.x = -vector.x;
+  }
 
-  /* 
-   * Kill the vector if its length is 0. 
-   * We have to be tolerant of errors, 
+  /*
+   * Kill the vector if its length is 0.
+   * We have to be tolerant of errors,
    * because of the transformation to/
-   * from the texture data range. This 
+   * from the texture data range. This
    * may end up being too tolerant.
    */
-  if (vectorLen < 0.0001) {
+  if (length(vector) < 0.0001) {
     fragColourFactor = vec4(0, 0, 0, 0);
     return;
   }
 
-
-  if (unitLength) {
-
-    /*
-     * Scale the vector so it has length 0.5. 
-     */
-    vector /= 2 * vectorLen;
-
-    /*
-     * Scale the vector by the minimum voxel length,
-     * so it is a unit vector within real world space 
-     */
-    vector /= imageDims / min(imageDims.x, min(imageDims.y, imageDims.z));
-  }
-
   vector *= lengthScale;
 
   /*

fsleyes/assets/gl/gl21/glvector_frag.glsl

@@ -142,6 +142,12 @@ void main(void) {
     voxValue = texture3D(vectorTexture, fragVecTexCoord).xyz;
   }
 
+  /* Do not draw vectors with length 0 or with NaNs */
+  float len = length(voxValue.xyz);
+  if (len == 0 || len != len) {
+    discard;
+  }
+
   /* Look up the modulation and clipping values */
   float modValue;
   float clipValue;
@@ -199,10 +205,17 @@ void main(void) {
   voxValue += voxValXform[3].x;
   voxValue  = abs(voxValue);
 
-  /* Combine the xyz component colours. */
+  /* Combine the xyz component colours,
+   * modulating them by the vector values.
+   * Opacity is not modulated by vector
+   * value.
+   */
   vec4 voxColour = voxValue.x * xColour +
                    voxValue.y * yColour +
                    voxValue.z * zColour;
+  voxColour.a    = (xColour.a +
+                    yColour.a +
+                    zColour.a) / 3;
 
   /*
    * Apply the colour scale/offset -

fsleyes/gl/gl21/gllinevector_funcs.py

@@ -65,7 +65,6 @@ def init(self):
     # changes.
     self.opts.addListener('orientFlip',  name, update, weak=False)
     self.opts.addListener('directed',    name, update, weak=False)
-    self.opts.addListener('unitLength',  name, update, weak=False)
     self.opts.addListener('lengthScale', name, update, weak=False)
     self.opts.addListener('transform',
                           name,
@@ -79,7 +78,6 @@ def destroy(self):
 
     self.opts.removeListener('orientFlip',  self.name)
     self.opts.removeListener('directed',    self.name)
-    self.opts.removeListener('unitLength',  self.name)
     self.opts.removeListener('lengthScale', self.name)
     self.opts.removeListener('transform',   self.name)
 
@@ -114,20 +112,32 @@ def updateShaderState(self):
         vvxMat = self.imageTexture.voxValXform
 
     directed    = opts.directed
-    unitLength  = opts.unitLength
     lengthScale = opts.lengthScale / 100.0
     imageDims   = image.pixdim[:3]
     d2vMat      = opts.getTransform('display', 'voxel')
     v2dMat      = opts.getTransform('voxel',   'display')
     xFlip       = opts.orientFlip
 
+    # If the unitLength option is on, the vector
+    # data will have already been scaled to have
+    # length 1 (see GLLineVector.__init__). But
+    # we draw vectors in two parts, from the voxel
+    # centre. So we have to half the vector lengths.
+    if opts.unitLength:
+        lengthScale /= 2
+        # We also scale the vector data by the
+        # minimum voxel length, so that each
+        # vector has unit length relative to
+        # the voxel dimensions.
+        fac          = (image.pixdim[:3] / min(image.pixdim[:3]))
+        lengthScale /= fac
+
     changed |= shader.set('vectorTexture',   4)
     changed |= shader.set('displayToVoxMat', d2vMat)
     changed |= shader.set('voxToDisplayMat', v2dMat)
     changed |= shader.set('voxValXform',     vvxMat)
     changed |= shader.set('imageDims',       imageDims)
     changed |= shader.set('directed',        directed)
-    changed |= shader.set('unitLength',      unitLength)
     changed |= shader.set('lengthScale',     lengthScale)
     changed |= shader.set('xFlip',           xFlip)
 

fsleyes/gl/gllinevector.py

@@ -7,10 +7,8 @@
 """This module provides the :class:`GLLineVector` class, for displaying 3D
 vector :class:`.Image` overlays in line mode.
 
-
 The :class:`.GLLineVertices` class is also defined in this module, and is used
-in certain rendering situations - specifically, when running in OpenGL
-1.4. See the :mod:`.gl14.gllinevector_funcs` and
+when running in OpenGL 1.4. See the :mod:`.gl14.gllinevector_funcs` and
 :mod:`.gl21.gllinevector_funcs` modules for more details.
 """
 
@@ -70,17 +68,55 @@ class GLLineVector(glvector.GLVector):
         if isinstance(image, dtifit.DTIFitTensor): vecImage = image.V1()
         else:                                      vecImage = image
 
+        def prefilter(data):
+            # Scale to unit length if required.
+            if not self.opts.unitLength:
+                return data
+
+            data = np.copy(data)
+
+            with np.errstate(invalid='ignore'):
+
+                # Vector images stored as RGB24 data
+                # type are assumed to map from [0, 255]
+                # to [-1, 1], so cannot be normalised
+                if vecImage.nvals > 1:
+                    return data
+
+                # calculate lengths
+                x    = data[0, ...]
+                y    = data[1, ...]
+                z    = data[2, ...]
+                lens = np.sqrt(x ** 2 + y ** 2 + z ** 2)
+
+                # scale lengths to 1
+                data[0, ...] = x / lens
+                data[1, ...] = y / lens
+                data[2, ...] = z / lens
+
+            return data
+
+        def prefilterRange(dmin, dmax):
+            if self.opts.unitLength:
+                return 0, 1
+            else:
+                return dmin, dmax
+
         glvector.GLVector.__init__(self,
                                    image,
                                    overlayList,
                                    displayCtx,
                                    canvas,
                                    threedee,
+                                   prefilter=prefilter,
+                                   prefilterRange=prefilterRange,
                                    vectorImage=vecImage,
                                    init=lambda: fslgl.gllinevector_funcs.init(
                                        self))
 
-        self.opts.addListener('lineWidth', self.name, self.notify)
+        self.opts.addListener('lineWidth',  self.name, self.notify)
+        self.opts.addListener('unitLength', self.name,
+                              self.__unitLengthChanged)
 
 
     def destroy(self):
@@ -89,7 +125,8 @@ class GLLineVector(glvector.GLVector):
         instance, calls the OpenGL version-specific ``destroy``
         function, and calls the :meth:`.GLVector.destroy` method.
         """
-        self.opts.removeListener('lineWidth', self.name)
+        self.opts.removeListener('lineWidth',  self.name)
+        self.opts.removeListener('unitLength', self.name)
         fslgl.gllinevector_funcs.destroy(self)
         glvector.GLVector.destroy(self)
 
@@ -159,11 +196,26 @@ class GLLineVector(glvector.GLVector):
         fslgl.gllinevector_funcs.postDraw(self, xform, bbox)
 
 
-class GLLineVertices(object):
-    """The ``GLLineVertices`` class is used in some cases when rendering a
-    :class:`GLLineVector`. It contains logic to generate vertices for every
-    vector in the vector :class:`.Image` that is being displayed by a
-    ``GLLineVector`` instance.
+    def __unitLengthChanged(self, *a):
+        """Called when the :attr:`.LineVectorOptsunitLength` property
+        changes. Refreshes the vector image texture data.
+        """
+        self.imageTexture.refresh()
+        self.updateShaderState()
+
+
+class GLLineVertices:
+    """The ``GLLineVertices`` class is used when rendering a
+    :class:`GLLineVector` with OpenGL 1.4. It contains logic to generate
+    vertices for every vector in the vector :class:`.Image` that is being
+    displayed by a ``GLLineVector`` instance.
+
+
+    This class is used by the OpenGL 1.4 implementation - when using OpenGL
+    2.1, the logic encoded in this class is implemented in the line vector
+    vertex shader. This is because OpenGL 1.4 vertex programs (using the
+    ARB_vertex_program extension) are unable to perform texture lookups,
+    so cannot retrieve the vector data.
 
 
     After a ``GLLineVertices`` instance has been created, the :meth:`refresh`
@@ -259,7 +311,6 @@ class GLLineVertices(object):
 
         # The image may either
         # have shape (X, Y, Z, 3)
-
         if image.nvals == 1:
             vertices = np.array(data, dtype=np.float32)
         # Or (we assume) a RGB

fsleyes/gl/glrgbvector.py

@@ -82,6 +82,13 @@ class GLRGBVector(glvector.GLVector):
         else:                                      vecImage = image
 
         def prefilter(data):
+
+            # Vector images stored as RGB24 data
+            # type are assumed to map from [0, 255]
+            # to [-1, 1], so cannot be normalised
+            if vecImage.nvals > 1:
+                return data
+
             # make absolute, and scale to unit
             # length if required. We must make
             # the data absolute, otherwise we

fsleyes/gl/glrgbvolume.py

@@ -13,6 +13,7 @@ import numpy                as np
 import OpenGL.GL            as gl
 
 import fsl.utils.idle       as idle
+import fsl.transform.affine as affine
 
 import fsleyes.gl           as fslgl
 import fsleyes.gl.routines  as glroutines
@@ -190,6 +191,23 @@ class GLRGBVolume(glimageobject.GLImageObject):
         self.updateShaderState()
 
 
+    def generateVertices2D(self, zpos, axes, bbox=None):
+        """Overrides :meth:`.GLImageObject.generateVertices2D`.
+
+        Appliies the :meth:`.ImageTextureBase.texCoordXform` to the texture
+        coordinates - this is performed to support 2D images/textures.
+        """
+
+        vertices, voxCoords, texCoords = \
+            glimageobject.GLImageObject.generateVertices2D(
+                self, zpos, axes, bbox)
+
+        texCoords = affine.transform(
+            texCoords, self.imageTexture.texCoordXform(self.overlay.shape))
+
+        return vertices, voxCoords, texCoords
+
+
     def channelColours(self):
         """Returns a ``numpy`` array of shape ``(3, 4)``, containing the
         colours to use for each of the three channels.

fsleyes/gl/textures/texture2d.py

@@ -303,9 +303,6 @@ class Texture2D(texture.Texture):
         if origShape is None:
             return None
 
-        if self.nvals > 1:
-            origShape = origShape[1:]
-
         # Here we apply a rotation to the
         # coordinates to force the two major
         # voxel axes to map to the first two

fsleyes/main.py

@@ -189,6 +189,14 @@ class FSLeyesApp(wx.App):
         # queue the files to open them later
         # in SetOverlayListAndDisplayContext
         if self.__overlayList is None:
+
+            # On certain systems (observed on Big Sur), when
+            # files are passed as command-line arguments, they
+            # are passed to MacOpenFiles. We don't want that,
+            # because cli arguments are parsed separately. So
+            # we remove dupes here.
+
+            filenames = [f for f in filenames if f not in sys.argv]
             self.__filesToOpen.extend(filenames)
             return
 

fsleyes/tests/__init__.py

@@ -793,8 +793,6 @@ def zero_centre(infile):
     return outfile
 
 
-
-
 def complex():
 
     data =      np.linspace(0, 1, 1000).reshape((10, 10, 10)) + \
@@ -829,6 +827,16 @@ def invert(infile):
     return outfile
 
 
+def mul(infile, factor):
+    basename = fslimage.removeExt(op.basename(infile))
+    outfile  = '{}_mul_{}.nii.gz'.format(basename, factor)
+    img      = fslimage.Image(infile)
+    data     = img[:]
+    img[:]   = data * factor
+    img.save(outfile)
+    return outfile
+
+
 def mockMouseEvent(profile, canvas, evType, canvasLoc):
     """Mock a mouse event on a SliceCanvas
     """

fsleyes/tests/overlays/test_overlay_linevector.py

@@ -5,9 +5,13 @@
 # Author: Paul McCarthy <pauldmccarthy@gmail.com>
 #
 
+import os.path as op
+
 import pytest
 
-from fsleyes.tests import run_cli_tests, roi, asrgb
+import fsl.data.image as fslimage
+
+from fsleyes.tests import run_cli_tests, roi, asrgb, mul
 
 
 pytestmark = pytest.mark.overlayclitest
@@ -35,13 +39,20 @@ dti/dti_FA.nii.gz {{asrgb('dti/dti_V1.nii.gz')}} -ot linevector
 
 # test anisotropic voxels
 dti/anisotropic/dti_FA dti/anisotropic/dti_V1 -ot linevector
-"""
 
+# unit length / colour scaling
+dti/dti_FA.nii.gz        dti/dti_V1.nii.gz          -ot linevector -nu
+dti/dti_FA.nii.gz {{mul('dti/dti_V1.nii.gz', 0.5)}} -ot linevector
+dti/dti_FA.nii.gz {{mul('dti/dti_V1.nii.gz', 0.5)}} -ot linevector -nu
+dti/dti_FA.nii.gz {{mul('dti/dti_V1.nii.gz', 2.0)}} -ot linevector
+dti/dti_FA.nii.gz {{mul('dti/dti_V1.nii.gz', 2.0)}} -ot linevector -nu
+"""
 
 def test_overlay_linevector():
     extras = {
         'roi'   : roi,
         'asrgb' : asrgb,
+        'mul'   : mul,
     }
     run_cli_tests('test_overlay_linevector',
                   cli_tests,

fsleyes/tests/overlays/test_overlay_nifti2d.py

@@ -62,6 +62,9 @@ cli_tests = """
 {{asrgb(roi('dti/dti_V1', (0, 8, 0, 8, 4, 5)))}}
 {{asrgb(roi('dti/dti_V1', (0, 8, 4, 5, 0, 8)))}}
 {{asrgb(roi('dti/dti_V1', (4, 5, 0, 8, 0, 8)))}}
+{{asrgb(roi('dti/dti_V1', (0, 8, 0, 8, 4, 5)))}} -ot rgb
+{{asrgb(roi('dti/dti_V1', (0, 8, 4, 5, 0, 8)))}} -ot rgb
+{{asrgb(roi('dti/dti_V1', (4, 5, 0, 8, 0, 8)))}} -ot rgb
 {{asrgb(roi('dti/dti_V1', (0, 8, 0, 8, 4, 5)))}} -ot rgbvector
 {{asrgb(roi('dti/dti_V1', (0, 8, 4, 5, 0, 8)))}} -ot rgbvector
 {{asrgb(roi('dti/dti_V1', (4, 5, 0, 8, 0, 8)))}} -ot rgbvector

fsleyes/tests/overlays/test_overlay_rgbvector.py

@@ -9,7 +9,7 @@ from unittest import mock
 
 import pytest
 
-from fsleyes.tests import run_cli_tests, asrgb
+from fsleyes.tests import run_cli_tests, asrgb, mul
 
 import fsleyes.gl.textures.data as texdata
 
@@ -32,11 +32,18 @@ dti/dti_V1 -ot rgbvector -in linear -b 25 -c 25
 dti/dti_V1 -ot rgbvector -in spline -b 25 -c 25
 
 {{asrgb('dti/dti_V1')}} -ot rgbvector
+
+# unit length scaling
+{{mul('dti/dti_V1', 0.5)}} -ot rgbvector -u
+{{mul('dti/dti_V1', 0.5)}} -ot rgbvector
+{{mul('dti/dti_V1', 2.0)}} -ot rgbvector -u
+{{mul('dti/dti_V1', 2.0)}} -ot rgbvector
 """
 
 def test_overlay_rgbvector():
     extras = {
         'asrgb' : asrgb,
+        'mul'   : mul,
     }
     run_cli_tests('test_overlay_rgbvector', cli_tests, extras=extras)