Merge pull request #73 from kschan0214/dev1.2.2.6

Dev1.2.2.6

README.md

@@ -41,7 +41,11 @@ If you have a more general question regarding the usage of SEPIA and/or other QS
 
 For full update log, please visit https://sepia-documentation.readthedocs.io/en/latest/getting_started/Release-note.html.
 
-### 1.2.2.5 (current master)
+### 1.2.2.6 (current master)
+* Support read Input/Output information from sepia_config.m 
+* Phase DICOM values are rescaled using the max/min values in the data instead of rescale slope/intercept of the NIFTI
+
+### 1.2.2.5 (commit 8630efe)
 * Fix the mismatch between SEPIA defined B0 direction and LPCNN when it is not along the z-direction
 * Fix the shared library issue when using ROMEO with latest versions of Matlab on Linux (see [here](https://github.com/korbinian90/ROMEO))
 * Allow user to define atlases' directory paths

SpecifyToolboxesDirectory.m

@@ -15,12 +15,12 @@
 % Date modified: 25 Feb 2022 (v1.2)
 %
 %% Specify the directories of the toolbox here
-MEDI_HOME       = '/path/to/MEDI/Toolboxes/';
+MEDI_HOME       = '/path/to/MEDI/Toolbox/';
 STISuite_HOME   = '/path/to/STI/Suite/';
-FANSI_HOME      = '/path/to/FANSI/Toolboxes/';
-SEGUE_HOME      = '/path/to/SEGUE/Toolboxes/';
-MRITOOLS_HOME   = '/path/to/ROMEO/Toolboxes/';
-MRISC_HOME      = '/path/to/MRISusceptibilityCalculationmethods/Toolboxes/';
+FANSI_HOME      = '/path/to/FANSI/Toolbox/';
+SEGUE_HOME      = '/path/to/SEGUE/Toolbox/';
+MRITOOLS_HOME   = '/path/to/MRITOOLS/mritools_ubuntu-20.04_3.6.6/';
+MRISC_HOME      = '/path/to/MRISusceptibilityCalculationmethods/Toolbox/';
 ANTS_HOME       = '/path/to/ANTs/bin/';
 
 %% if you have any missing toolboxes, then specify it as empty array

gui_func/callback/config/set_config_Callback.m

@@ -24,7 +24,13 @@ function set_config_Callback(config_filename,h)
 isModifyUnwrap  = false;
 isModifyBFR     = false;
 isModifyQSM     = false;
+isModifyIO      = false;
 
+str_pattern	= 'input';
+idx         = regexp(config_txt,str_pattern,'once');
+if ~isempty(idx)
+    isModifyIO = true;
+end
 str_pattern	= '.general.';
 idx         = regexp(config_txt,str_pattern,'once');
 if ~isempty(idx)
@@ -47,6 +53,116 @@ function set_config_Callback(config_filename,h)
 end 
 
 %% Panel: I/O
+if isModifyIO
+input_action_handle  = h.dataIO.edit.input;
+input1_action_handle = h.dataIO.edit.inputData1;
+input2_action_handle = h.dataIO.edit.inputData2;
+input3_action_handle = h.dataIO.edit.inputData3;
+header_action_handle = h.dataIO.edit.inputHeader;
+mask_action_handle   = h.dataIO.edit.maskdir;
+output_action_handle = h.dataIO.edit.output;
+
+isAllInputEmpty = (isempty(input_action_handle.String) .* isempty(input1_action_handle.String) .* ...
+                  isempty(input2_action_handle.String).* isempty(input3_action_handle.String) .* ...
+                  isempty(header_action_handle.String))>0;
+
+isModifyOutput = true;
+
+% check which input method was used in the config file
+ind = regexp(config_txt, regexptranslate('wildcard','input(*).name'), 'once');
+if ~isempty(ind)
+    isFileIO = true;
+else
+    isFileIO = false;
+end
+
+% Directory input method
+action_handle = input_action_handle;
+if isAllInputEmpty && ~isFileIO     % only modify the field if all IO fields are empty
+    str_pattern     = 'input';
+    str_end_idx     = regexp(config_txt,str_pattern,'end');
+    indicator_idx   = regexp(config_txt,'''');
+    str = config_txt(indicator_idx(find(indicator_idx > str_end_idx(1), 1 ))+1:indicator_idx(find(indicator_idx > str_end_idx(1), 1 )+1)-1);
+
+    if prod(~isnan(str)) && isfolder(str)
+        set(action_handle,'String',str);
+    else
+        isModifyOutput = false;
+    end
+end
+
+% File input method
+% input 1
+action_handle = input1_action_handle;
+if and(isempty(input_action_handle.String),isempty(get(action_handle,'String')))
+    str_pattern     = 'input\(1).name';
+    str = get_string_as_string(config_txt, str_pattern);
+    if prod(~isnan(str)) && isfile(str)
+        set(action_handle,'String',str);
+    else
+        isModifyOutput = false;
+    end
+end
+
+% input 2
+action_handle = input2_action_handle;
+if and(isempty(input_action_handle.String),isempty(get(action_handle,'String')))
+    str_pattern     = 'input\(2).name';
+    str = get_string_as_string(config_txt, str_pattern);
+    if prod(~isnan(str)) && isfile(str)
+        set(action_handle,'String',str);
+    else
+        isModifyOutput = false;
+    end
+end
+
+% input 3
+action_handle = input3_action_handle;
+if and(isempty(input_action_handle.String),isempty(get(action_handle,'String')))
+    str_pattern     = 'input\(3).name';
+    str = get_string_as_string(config_txt, str_pattern);
+    if prod(~isnan(str)) && isfile(str)
+        set(action_handle,'String',str);
+    else
+        isModifyOutput = false;
+    end
+end
+
+% header input
+action_handle = header_action_handle;
+if and(isempty(input_action_handle.String),isempty(get(action_handle,'String')))
+    str_pattern     = 'input\(4).name';
+    str = get_string_as_string(config_txt, str_pattern);
+    if prod(~isnan(str)) && isfile(str)
+        set(action_handle,'String',str);
+    else
+        isModifyOutput = false;
+    end
+end
+
+% mask 
+action_handle = mask_action_handle;
+if isempty(get(action_handle,'String'))
+    str_pattern     = 'mask_filename = ';
+    str = get_string_as_string(config_txt, str_pattern);
+    if prod(~isnan(str))
+        set(action_handle,'String',str);
+    end
+end
+
+% output 
+action_handle = output_action_handle;
+if isempty(get(action_handle,'String'))
+    str_pattern     = 'output_basename = ';
+    str = get_string_as_string(config_txt, str_pattern);
+    if prod(~isnan(str)) && isModifyOutput
+        set(action_handle,'String',str);
+    end
+end
+
+
+end
+
 if isModifyGeneral
 
 % invert phase data

sepia_universal_variables.m

@@ -14,7 +14,7 @@
 % DO NOT change the order of the entities, add a new one at the end instead
 %
 %% Version
-SEPIA_version = 'v1.2.2.5';
+SEPIA_version = 'v1.2.2.6';
 
 %% PATH
 SEPIA_HOME = fileparts(mfilename('fullpath'));

utils/DICOM2Phase.m

@@ -18,37 +18,14 @@
 % Date created: 11 April 2018
 % Date modified: 12 June 2018
 % Date modified: 4 August 2022 (v1.0.1)
-%
+% Date modified: 3 December 2023 (v1.2.6.6)
 %
 function phase = DICOM2Phase(niiPhase)
-% % change datatype to double
-% dicomPhase = double(niiPhase.img);
-% get scale slope
-scaleSlope=niiPhase.hdr.dime.scl_slope;
-% get scale inetercept
-scaleIntercept=niiPhase.hdr.dime.scl_inter;
-
-% rescale phase
-phase_rescale = single(niiPhase.img) * scaleSlope + scaleIntercept;
-% find maximum and minimum in the data after rescaling
-max_rescale = max(phase_rescale(:));
-min_rescale = min(phase_rescale(:));
-
-% rescale phase data between -pi and pi usng the max and min in the data
-% the limitation of this method is that if the max and min values might not
-% corresponding to pi and -pi
-phase = (phase_rescale - min_rescale) / (max_rescale - min_rescale) *2*pi - pi;
 
-% % compute the new maximum value
-% newMax = niiPhase.hdr.dime.glmax*scaleSlope + scaleIntercept;
-% % compute the new minimum value
-% newMin = niiPhase.hdr.dime.glmin*scaleSlope + scaleIntercept;
-% % +1 for 0
-% fullRange = newMax-newMin + 1;
-% 
-% % scale to true value of nifti file
-% dicomPhaseRescale = (dicomPhase*scaleSlope) + scaleIntercept ;
-% % scale the full range to [-pi,pi)
-% phase = (dicomPhaseRescale-newMin) / fullRange * 2*pi - pi;
+% suggested by Simon
+phase       = single(niiPhase.img); clear niiPhase;
+max_phase   = max(phase(:));
+min_phase   = min(phase(:));
+phase       = (phase - min_phase) / (max_phase - min_phase) *2*pi - pi;
 
 end

utils/get_filename_in_directory.m

@@ -32,8 +32,8 @@
 numFiles    = 0;    
 
 % check all files in the list
-for klist = 1:length(fileList)
-    if ContainName(fileList(klist).name,pattern)
+for klist = 1:length(fileList)                      % ignore hidden file
+    if ContainName(fileList(klist).name,pattern) && ~strcmp(fileList(klist).name(1),'.')
         numFiles = numFiles + 1;
         file(numFiles).name = fullfile(fileList(klist).folder,fileList(klist).name);
     end