Merge pull request #97 from hMRI-group/add-denoising-module

add denoising module to toolbox: Java-Matlab interface for LCPCA denoising

Author: Barisevrenugur

CHANGELOG.md

@@ -10,14 +10,15 @@ Most recent version numbers *should* follow the [Semantic Versioning](https://se
 - set default WM percent value in hmri_defaults.
 - spatial processing: add explicit mask creation and fix implicit mask (0 to NaN in float images)
 - update FIL seste seq parameters in get_metadata_val_classic
+- denoising module-first part: Java-Matlab interface for LCPCA denoising
 
 ### Fixed
 - replace `datestr(now)` with `datetime('now')` in line with [MATLAB recommendation](https://mathworks.com/help/matlab/matlab_prog/replace-discouraged-instances-of-serial-date-numbers-and-date-strings.html)
 - fix crash if input images have different matrix sizes, and warn
 - make B1-map creation using 3DEPI SE/STE and AFI methods fall back to defaults without sidecar files, rather than crash
 - Modify the filenames as files are copied to RFsensCalc to prevent overwriting in further processing
 - batch interface now enforces the number of B1 input images correctly for B1 mapping methods which only need two images.
-- Fix error if optimization toolbox not present during NLLS R2* calculation
+- fix error if optimization toolbox not present during NLLS R2* calculation
 
 ## [v0.6.1]
 ### Fixed

config/hmri_denoising_defaults.m

@@ -0,0 +1,19 @@
+function hmri_denoising_defaults
+
+%init the global variable which carries the params
+global hmri_def;
+
+%Enter denoising default values as: hmri_def.denoising.(denoising-protocol).(default-value)
+
+%The default values for lcpca denoising protocol
+%all optional parameters turned off
+hmri_def.denoising.lcpca_denoise.mag_input = {}; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.phase_input = {}; %%optional-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.output_path=''; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.min_dimension= 0; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.max_dimension = -1; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.unwrap = false; %%optional
+hmri_def.denoising.lcpca_denoise.rescale_phs = false; %%optional
+hmri_def.denoising.lcpca_denoise.process_2d=false; %%optional
+hmri_def.denoising.lcpca_denoise.use_rmt=false; %%optional
+end

config/local/hmri_local_denoising_defaults.m

@@ -0,0 +1,16 @@
+%init the global variable which carries the params
+global hmri_def;
+
+%Enter denoising default values as: hmri_def.denoising.(denoising-protocol).(default-value)
+
+%The default values for lcpca denoising protocol
+%all optional parameters turned off
+hmri_def.denoising.lcpca_denoise.mag_input = {}; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.phase_input = {}; %%optional-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.output_path=''; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.min_dimension= 0; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.max_dimension = -1; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.unwrap = false; %%optional
+hmri_def.denoising.lcpca_denoise.rescale_phs = false; %%optional
+hmri_def.denoising.lcpca_denoise.process_2d=false; %%optional
+hmri_def.denoising.lcpca_denoise.use_rmt=false; %%optional