setup.cfg

 [metadata]
 name = napari-3dtimereg
-version = 0.0.10
+version = 0.0.11
 description = Registration of 3D movies applied to all channels
 long_description = file: README.md
 long_description_content_type = text/markdown

src/napari_3dtimereg/movieRegistration.py

@@ -177,7 +177,7 @@ def rigid_map( iterations, rig_resolution, rig_final_spacing, use_points=True ):
     parameter_map_rigid['MaximumStepLength'] = ['2.0']
     parameter_map_rigid["NumberOfResolutions"] = [rig_resolution]
     parameter_map_rigid['NumberOfSpatialSamples'] = ['10000']
-    parameter_map_rigid['MaximumNumberOfSamplingAttempts'] = ['10']
+    parameter_map_rigid['MaximumNumberOfSamplingAttempts'] = ['8']
     parameter_map_rigid['RequiredRatioOfValidSamples'] = ['0.05']
     parameter_map_rigid['CheckNumberOfSamples'] = ['false']
     parameter_map_rigid['FinalGridSpacingInPhysicalUnits'] = [str(rig_final_spacing)]
@@ -200,12 +200,12 @@ def bspline_map( spline_resolution, iterations, final_order, spline_final_spacin
     parameter_map["NumberOfResolutions"] = [spline_resolution]
     parameter_map["WriteIterationInfo"] = ["false"]
     parameter_map['MaximumStepLength'] = ['2.0']
-    parameter_map['NumberOfSpatialSamples'] = ['10000']
+    parameter_map['NumberOfSpatialSamples'] = ['8000']
     parameter_map['MaximumNumberOfSamplingAttempts'] = ['10']
     parameter_map['RequiredRatioOfValidSamples'] = ['0.05']
     parameter_map['MaximumNumberOfIterations'] = [iterations]
     parameter_map['FinalBSplineInterpolationOrder'] = [final_order]
-    parameter_map['BSplineInterpolationOrder'] = ['3']
+    parameter_map['BSplineInterpolationOrder'] = ['2']
     parameter_map['HowToCombineTransform'] = ['Compose']
     nres = int(spline_resolution)
     spaces = []
@@ -276,6 +276,111 @@ def time_registration( do_rigid, do_bspline, iterations, rigid_resolution, rigid
             # transform the current slice and append it to the reconstructed stack
             apply_registration(t, curr_transform_object)
 
+def middle_time_registration( do_rigid, do_bspline, iterations, rigid_resolution, rigid_final_spacing, use_reference_points, spline_resolution, spline_final_spacing, final_order, show_log=True ):
+    """ Go for frame by frame registration, reference frame middle one """
+        
+    ## Build registration parameter maps from GUI parameters
+    registration_parameter_object = itk.ParameterObject.New()
+    nmap = 0
+    if do_rigid:
+        pmap_rigid = rigid_map( iterations=str(iterations), rig_resolution=str(rigid_resolution), rig_final_spacing=int(rigid_final_spacing), use_points=use_reference_points )
+        registration_parameter_object.AddParameterMap(pmap_rigid)
+        nmap = nmap + 1
+    if do_bspline:
+        pmap_spline = bspline_map( spline_resolution=str(spline_resolution), iterations=str(iterations), final_order=str(final_order), spline_final_spacing=int(spline_final_spacing) )
+        registration_parameter_object.AddParameterMap(pmap_spline)
+        nmap = nmap + 1
+            
+    ## reference frame
+    reft = int( resimg.shape[0]/2 )
+
+    ## apply "alignement" to first frame
+    apply_registration(reft, None)
+
+    # initialise a parameter object to which the transforms will be appended that result from the pairwise slice registrations
+    curr_transform_object = itk.ParameterObject.New()
+
+    # the first fixed image will be the reference slice
+    fixed_image_itk = img_to_itk(resimg[reft])
+
+    ## Register all frames to following one and add it
+    t = reft - 1
+    while t >= 0:
+        print("Calculate registration for time point "+str(t))
+
+        # the moving image is the current slice
+        moving_image_itk = img_to_itk(resimg[t])
+
+        # perform the pairwise registration between two slices
+        elastix_object = itk.ElastixRegistrationMethod.New(fixed_image_itk, moving_image_itk)
+        elastix_object.SetParameterObject(registration_parameter_object)
+            
+        if use_reference_points:
+            get_ref_points(t+1, t)
+            elastix_object.SetFixedPointSetFileName(os.path.join(aligndir, imagename+"_refpts_fixed.txt"))
+            elastix_object.SetMovingPointSetFileName(os.path.join(aligndir, imagename+"_refpts_moving.txt"))
+            
+        elastix_object.SetLogToConsole( show_log==True )
+
+        # Update filter object (required)
+        elastix_object.UpdateLargestPossibleRegion()
+
+        # Results of Registration
+        results_transform_parameters = elastix_object.GetTransformParameterObject()
+
+        # set the current moving image as the fixed image for the registration in the next iteration
+        fixed_image_itk = moving_image_itk
+
+        # append the obtained transform to the transform parameter object
+        for i in range(nmap):
+            curr_transform_object.AddParameterMap(results_transform_parameters.GetParameterMap(i))
+
+        # transform the current slice and append it to the reconstructed stack
+        apply_registration(t, curr_transform_object)
+
+        ## next time
+        t = t - 1
+   
+    ## Next phase go from refframe to the end
+    t = reft + 1
+    fixed_image_itk = img_to_itk( resimg[reft] )
+    curr_transform_object = itk.ParameterObject.New()
+    while t < resimg.shape[0]:
+        print("Calculate registration for time point "+str(t))
+
+        # the moving image is the current slice
+        moving_image_itk = img_to_itk(resimg[t])
+
+        # perform the pairwise registration between two slices
+        elastix_object = itk.ElastixRegistrationMethod.New(fixed_image_itk, moving_image_itk)
+        elastix_object.SetParameterObject(registration_parameter_object)
+            
+        if use_reference_points:
+            get_ref_points(t-1, t)
+            elastix_object.SetFixedPointSetFileName(os.path.join(aligndir, imagename+"_refpts_fixed.txt"))
+            elastix_object.SetMovingPointSetFileName(os.path.join(aligndir, imagename+"_refpts_moving.txt"))
+            
+        elastix_object.SetLogToConsole( show_log==True )
+
+        # Update filter object (required)
+        elastix_object.UpdateLargestPossibleRegion()
+
+        # Results of Registration
+        results_transform_parameters = elastix_object.GetTransformParameterObject()
+
+        # set the current moving image as the fixed image for the registration in the next iteration
+        fixed_image_itk = moving_image_itk
+
+        # append the obtained transform to the transform parameter object
+        for i in range(nmap):
+            curr_transform_object.AddParameterMap(results_transform_parameters.GetParameterMap(i))
+
+        # transform the current slice and append it to the reconstructed stack
+        apply_registration(t, curr_transform_object)
+
+        ## next time
+        t = t + 1
+
 def iterative_registration():
     """ use Elastix to perform registration with possible deformation, iteratively in time """     
     
@@ -294,6 +399,7 @@ def iterative_registration():
             refpoints_file = pathlib.Path(os.path.join(imagedir, imagename+"_reference_points.csv")),
             do_rigid = True,
             do_bspline = True,
+            middle_reference_frame = True,
             show_advanced_parameters = False,
             rigid_resolution=4,
             spline_resolution=4,
@@ -310,7 +416,10 @@ def iterative_registration():
         if use_reference_points:
             read_points( refpoints_file )
             #move_points = True 
-        time_registration( do_rigid=do_rigid, do_bspline=do_bspline, iterations=iterations, rigid_resolution=rigid_resolution, rigid_final_spacing=rigid_final_spacing, use_reference_points=use_reference_points, spline_resolution=spline_resolution, spline_final_spacing=spline_final_spacing, final_order=final_order, show_log=show_log )
+        if not middle_reference_frame:
+            time_registration( do_rigid=do_rigid, do_bspline=do_bspline, iterations=iterations, rigid_resolution=rigid_resolution, rigid_final_spacing=rigid_final_spacing, use_reference_points=use_reference_points, spline_resolution=spline_resolution, spline_final_spacing=spline_final_spacing, final_order=final_order, show_log=show_log )
+        else:
+            middle_time_registration( do_rigid=do_rigid, do_bspline=do_bspline, iterations=iterations, rigid_resolution=rigid_resolution, rigid_final_spacing=rigid_final_spacing, use_reference_points=use_reference_points, spline_resolution=spline_resolution, spline_final_spacing=spline_final_spacing, final_order=final_order, show_log=show_log )
         finish_image()
     
     def show_advanced(booly):