Merge pull request #702 from rijobro/process_undeprecate

remove NiftyResample::process deprecation, improve documentation

CHANGES.md

@@ -5,7 +5,7 @@
 * A passthrough for both the maximum and minimum relative change during OSMAPOSL reconstruction has been added.
 * We have now corrected the geometrical information of `.h5` images (coming from ISMRMRD and Gadgetron). This means we can now convert them to other SIRF image types (e.g., `NiftiImageData` and `STIRImageData`). This is necessary for any kind of synergistic reconstruction. Further, to the best of our knowledge, this is the first ISMRMRD to NIfTI converter out there!
 * The adjoint transformation has now been implemented for `NiftyResample` through the wrapping of NiftyMoMo.
-* `Resample::process()` has been marked as deprecated. Instead, the following methods have been added to C++, python and matlab NiftyResample:
+* The following methods have been added to C++, python and matlab NiftyResample:
 	* `out = forward(in)`
 	* `forward(out, in)`
 	* `out = adjoint(in)`

doc/UserGuide.md

@@ -595,12 +595,22 @@ Below examples are given for rigid/affine and non-rigid registrations, as well a
 ##### Resampling (NiftyResample)
 ###### Methods
 
-	set_reference_image						Set the reference image
-	set_floating_image						Set the floating
-	process									Start the registration process
-	get_output								Get the registered image
-	add_transformation						Add transformation (any type)
-	set_interpolation_type					Set interpolation type
+	set_reference_image		Set the reference image
+	set_floating_image		Set the floating
+	process					Start the resampling process. 
+								This is the equivalent of 
+								forward(floating_image).
+	get_output				Get the registered image
+	add_transformation		Add transformation (any type)
+	clear_transformations	Remove all transformations
+	set_interpolation_type	Set interpolation type
+	forward(im, out=None)	Resample image in forward direction.
+								Image should have same properties as
+								floating image used in set_up.
+	backward(im, out=None)	Resample image in backward/adjoint direction. 
+								Image should have same properties as
+								reference image used in set_up.
+	adjoint(im, out=None)	Alias of backward.
 
 ###### Example
 	res = NiftyResample()
@@ -609,8 +619,11 @@ Below examples are given for rigid/affine and non-rigid registrations, as well a
 	res.set_interpolation_type(1)
 	res.add_transformation(trans1)
 	res.add_transformation(trans2)
-	res.process()
-	output = res.get_output()
+	out = res.forward(flo)
+	# No allocation, faster
+	res.forward(flo, out=out)
+	# Backwards/adjoint
+	out2 = res.adjoint(ref)
 
 ### Other classes <a name="Other_classes"></a>
 

src/Registration/cReg/include/sirf/Reg/NiftyResample.h

@@ -108,8 +108,8 @@ class NiftyResample : public Resample<dataType>
     /// Destructor
     virtual ~NiftyResample() {}
 
-    /// Process
-    DEPRECATED virtual void process();
+    /// Process. Equivalent of calling forward(floating_image). Use get_output to get resampled image.
+    virtual void process();
 
     /// Do the forward transformation
     virtual std::shared_ptr<ImageData> forward(const std::shared_ptr<const ImageData> input_sptr);

src/Registration/cReg/include/sirf/Reg/Resample.h

@@ -104,8 +104,8 @@ class Resample
     /// Set padding value
     void set_padding_value(const float padding_value) { _padding_value = padding_value; }
 
-    /// Process - will call forward
-    DEPRECATED virtual void process() = 0;
+    /// Process. Equivalent of calling forward(floating_image). Use get_output to get resampled image.
+    virtual void process() = 0;
 
     /// Get output
     const std::shared_ptr<const ImageData> get_output_sptr() const { return _output_image_sptr; }

src/Registration/mReg/+sirf/+Reg/NiftyResample.m

@@ -97,7 +97,7 @@ function set_padding_value(self, val)
             sirf.Reg.setParameter(self.handle_, self.name, 'padding', val, 'f')
         end
         function process(self)
-            %Process.
+            %Process. Equivalent of calling forward(floating_image). Use get_output to get resampled image.
             h = calllib('mreg', 'mReg_NiftyResample_process', self.handle_);
             sirf.Utilities.check_status([self.name ':process'], h);
             sirf.Utilities.delete(h)

src/Registration/pReg/Reg.py.in

@@ -21,7 +21,6 @@ Object-Oriented wrap for the cReg-to-Python interface pyreg.py
 
 import abc
 import sys
-import deprecation
 
 from pUtilities import *
 from sirf import SIRF
@@ -954,10 +953,8 @@ class NiftyResample(object):
         """Set padding value."""
         parms.set_float_par(self.handle, self.name, 'padding', val)
 
-    @deprecation.deprecated(deprecated_in="2.1.0",
-                            details="Use forward(image) instead")
     def process(self):
-        """Process."""
+        """Process. Equivalent of calling forward(floating_image). Use get_output to get resampled image."""
         try_calling(pyreg.cReg_NiftyResample_process(self.handle))
 
     def get_output(self):