bug fixes for adaptive patch denoising. Algorithm and shrinkage were mistakenly hard coded previously.

Author: Benjamin Aron

designer2/designer.py

@@ -85,7 +85,8 @@ def usage(cmdline): #pylint: disable=unused-variable
     mp_options.add_argument('-extent', metavar=('<size>'), help='MPPCA Denoising extent. Default is 5,5,5')
     mp_options.add_argument('-phase', metavar=('<image>'), help='Diffusion phases - for performing denoising on complex data. This option should not be used alongside "-rician" since denoising complex data reduces the noise floor.', default=None)
     mp_options.add_argument('-adaptive_patch', action='store_true', help='Run MPPCA with adaptive patching')
-    
+    mp_options.add_argument('-adaptive_patch_length', metavar=('<len>'), help='Size of the adaptive patch for MPPCA denoising. Default is 80% of the kernel size')
+
     rpe_options = cmdline.add_argument_group('Options for eddy and to specify the acquisition phase-encoding design')
     rpe_options.add_argument('-eddy', action='store_true', help='run fsl eddy (note that if you choose this command you must also choose a phase encoding option')
     rpe_options.add_argument('-eddy_groups',metavar=('<index1,index2,...'),help='specify how input series should be grouped when running eddy, for use with variable TE or b-shape data. (Comma separated list of integers beginning with 1, i.e. 1,1,1,2,2,2 for 6 series where the first 3 series and second 3 series have different echo times).', default=None)

docs/docs/designer/usage.md

@@ -90,6 +90,10 @@ Olesen, J. L., Ianus, A., Østergaard, L., Shemesh, N., & Jespersen, S. N. (2023
 - Note when this argument is used, the patch size will be chosen based on the extent, where the total number of voxels in the adaptive patch is 80% of the total voxels in a patch.
 - Without the `-adaptive_patch` option, the patches are chosen as blocks with a step size of floor(extent/2), this increases speed at the expense of accuracy in noise estimation.
 
+### `-adaptive_patch_length`
+- Manually Specify the size of the adaptive patch.
+- choose a range from 1 to prod(extent). Default is 80% of the kernel size.
+
 ### `-phase <phase_image1,phase_image2,...>`
 - Include a volume (or volumes) of phase images corresponding to the input(s) to Designer. For example, if two series are input to Designer with a total of 100 directions, there should be two phase series with 100 total volumes.
 - Used in conjunction with `-denoise` option.

lib/designer_func_wrappers.py

@@ -56,8 +56,14 @@ def run_mppca(args_extent, args_phase, args_shrinkage, args_algorithm):
     start_time = time.time()
 
     if app.ARGS.adaptive_patch:
+        
+        if app.ARGS.adaptive_patch_length:
+            adapt_length = int(app.ARGS.adaptive_patch_length)
+        else:
+            adapt_length = None
+
         Signal, Sigma, Nparameters = mp.denoise(
-            dwi, phase=args_phase, patchtype='nonlocal', shrinkage=args_shrinkage, algorithm=args_algorithm
+            dwi, phase=args_phase, kernel=extent, patchtype='nonlocal', patchsize=adapt_length, shrinkage=args_shrinkage, algorithm=args_algorithm
             )
     else:    
         Signal, Sigma, Nparameters = mp.denoise(

lib/mpdenoise_adaptive.py

@@ -355,12 +355,6 @@ def process(self):
         # # parallel
         signal, sigma, npars = zip(*Parallel(n_jobs=num_cores, prefer='processes')\
            (delayed(self.denoise)(coords[:,i]) for i in inputs))
-        
-    #   #  serial
-        # k = self.kernel // 2
-        # #for t in inputs:
-        # crds = np.array([48+k[0], 38+k[1], 25+k[2]])
-        # a, b, c = self.denoise(crds)
 
         # reconstruct original data matrix
         Sigma = np.zeros((sx, sy, sz))
@@ -406,23 +400,22 @@ def denoise(img, kernel=None, patchtype=None, patchsize=None, shrinkage=None, al
         # ants.image_write(out, 'phase_dn.nii')
         out = ants.from_numpy(phi_dn, origin=nii.origin, spacing=nii.spacing, direction=nii.direction)
         ants.image_write(out, 'phase_dn.nii')
-        # import pdb; pdb.set_trace()
 
         print('magnitude denoising - adaptive patching')
         img_np = np.real(img*np.exp(-1j*phi_dn))
-        mp = MP(img_np, kernel, patchtype='adaptive', patchsize=None, shrinkage='frob', algorithm='jespersen', crop=0)
+        mp = MP(img_np, kernel, patchtype='adaptive', patchsize=patchsize, shrinkage=shrinkage, algorithm=algorithm, crop=0)
         Signal, Sigma, Npars = mp.process()
 
     else:
         zeroinds = np.where(img==0)
         img[zeroinds] = np.finfo(img.dtype).eps
 
-        mp = MP(img.copy(), kernel, patchtype='adaptive', patchsize=None, shrinkage='frob', algorithm='cordero-grande', crop=0)
+        mp = MP(img.copy(), kernel, patchtype='adaptive', patchsize=patchsize, shrinkage=shrinkage, algorithm=algorithm, crop=0)
         Signal, Sigma, Npars = mp.process()
         Signal[zeroinds] = 0
 
     return abs(Signal), Sigma, Npars
 
-# if __name__ == "__main__":
-#     denoise()
+if __name__ == "__main__":
+    denoise()
 

rpg_cpp/fftw-3.3.10/FFTW3Config.cmake

@@ -0,0 +1,17 @@
+# defined since 2.8.3
+if (CMAKE_VERSION VERSION_LESS 2.8.3)
+  get_filename_component (CMAKE_CURRENT_LIST_DIR ${CMAKE_CURRENT_LIST_FILE} PATH)
+endif ()
+
+# Allows loading FFTW3 settings from another project
+set (FFTW3_CONFIG_FILE "${CMAKE_CURRENT_LIST_FILE}")
+
+set (FFTW3_LIBRARIES fftw3)
+set (FFTW3_LIBRARY_DIRS /Users/benaron/Desktop/DESIGNER-v2/rpg_cpp/fftw-3.3.10/build/lib)
+set (FFTW3_INCLUDE_DIRS /Users/benaron/Desktop/DESIGNER-v2/rpg_cpp/fftw-3.3.10/build/include)
+
+include ("${CMAKE_CURRENT_LIST_DIR}/FFTW3LibraryDepends.cmake")
+
+if (CMAKE_VERSION VERSION_LESS 2.8.3)
+  set (CMAKE_CURRENT_LIST_DIR)
+endif ()

rpg_cpp/fftw-3.3.10/FFTW3ConfigVersion.cmake

@@ -0,0 +1,12 @@
+
+set (PACKAGE_VERSION "3.3.10")
+
+# Check whether the requested PACKAGE_FIND_VERSION is compatible
+if ("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}")
+  set (PACKAGE_VERSION_COMPATIBLE FALSE)
+else ()
+  set (PACKAGE_VERSION_COMPATIBLE TRUE)
+  if ("${PACKAGE_VERSION}" VERSION_EQUAL "${PACKAGE_FIND_VERSION}")
+    set (PACKAGE_VERSION_EXACT TRUE)
+  endif ()
+endif ()