Updated README. Added saving of input arguments to text file.

README.md

@@ -45,22 +45,22 @@ The output projections are HDF5 (.h5) files (864x864 px float64) with datasets f
 
 Create processed projections as in sample data folder `Figure_5/Figure_5ad/processed` from the raw data in `Figure_5/raw` using each of the 361 sample and reference projections, and all 10 phase steps.
 ```
-extract_images_tomoseries('/path_to_sample_data/Figure_5/raw/','pork%04d',[1:361],'ref%04d',[1:361],[1:1:10],'/path_to_sample_data/Figure_5/Figure_5ad/processed_2','im','clamp2pi',[0,0,0,0,0,1,1,0,0]);
+extract_images_tomoseries('/path_to_sample_data/Figure_5/raw/','pork%04d','[1:361]','ref%04d','[1:361]','[1:1:10]','/path_to_sample_data/Figure_5/Figure_5ad/processed_2','im','clamp2pi','[0,0,0,0,0,1,1,0,0]');
 ```
 
-# Input parameters
+# Input parameters (as strings)
 - **datapath**  
     Absolute path to folder containing the raw image data
 - **prefix_template**  
     Template for the prefix of a single piezo stepping scan (e.g. 'sample%04d' will give sample0001, sample0002, etc.; make sure this matches the actual names of the raw images
 - **tomoind**  
-    List of image numbers for the tomo series; specify a range or single projection (e.g. [1:361] or [165]); other than full ranges or a single image might not work currently!
+    List of image numbers for the tomo series; specify a range or single projection (e.g. '[1:361]' or '[165]'); other than full ranges or a single image might not work currently!
 - **ref_prefix_template**  
     Template for the prefix of the reference scans (e.g. 'ref%04d')
 - **ref_tomoind**  
     List of image numbers for reference images (see 'tomoind'); partial ranges can be used with restrictions (e.g. must be at even intervals)
 - **step_template**  
-    E.g. [1:1:10] for 10 consecutive phase-step images; can be used to choose only part of phase-steps
+    E.g. '[1:1:10]' for 10 consecutive phase-step images; can be used to choose only part of phase-steps
 - **outpath**  
     Folder where output data will be saved
 - **outprefix**  
@@ -97,7 +97,10 @@ extract_images_tomoseries('/path_to_sample_data/Figure_5/raw/','pork%04d',[1:361
  E.g., for templates 'im%04d' and 'ref%04d': 'im0001_01.smv' and 'ref0001_01.smv', where the 1st number is the tomo angle, and the 2nd the phase-step. While the prefix can be specified here, the part after that is fixed in the code.
  
  # Sample data
- (TODO: Add link to sample data including params.txt and scan.csv)
+ Raw .smv files, processed projections and reconstructed data is available at:
+ ```
+ https://doi.org/10.23729/60132ae3-1ce3-41eb-935f-d0721ad464aa
+ ```
  
  # TODO
  - Improve image import and creation time

extract_images_tomoseries.m

@@ -32,7 +32,6 @@
 %
 % NAMING OF RAW IMAGE FILES
 % e.g. 'im0001_01.smv' and 'ref0001_01.smv'; 1st number is tomo angle, 2nd phase step
-%
 
 function extract_images_tomoseries(datapath,prefix_template,tomoind,ref_prefix_template,ref_tomoind,step_template,outpath,outprefix,unwrapopt,options)
 
@@ -40,6 +39,16 @@ function extract_images_tomoseries(datapath,prefix_template,tomoind,ref_prefix_t
     %%% PREPARATIONS %%%
     %%%%%%%%%%%%%%%%%%%%
     
+    % Write given arguments to file (for later reference)
+    fn = fullfile(outpath,'arguments.txt');
+    save_input_args(fn,datapath,prefix_template,tomoind,ref_prefix_template,ref_tomoind,step_template,outpath,outprefix,unwrapopt,options);
+    
+    % Evaluate given expressions
+    tomoind = eval(tomoind);
+    ref_tomoind = eval(ref_tomoind);
+    step_template = eval(step_template);
+    options = eval(options);
+    
     % Parameter file name
     paramsfname = 'params.txt';
     

get_image_params.m

@@ -41,7 +41,7 @@ function params = get_image_params(paramsfilename)
     params.y_start = 1; %Start location (y, in initial image)
     params.y_end = 864; %End location (y, in initial image)
     yw = params.y_end-params.y_start;
-    params.xpoints_bg = unique([10:10:200 xw-200:10:xw-10 xw-10]);
+    params.xpoints_bg = unique([10:10:150 xw-150:10:xw-10 xw-10]);
     params.ypoints_bg = unique([10:10:yw-10 yw-10]);
     params.rotate = 180; %Specify in degrees how the images should be rotated
     

save_input_args.m

+function save_input_args(fname,varargin)
+
+    writecell(varargin',fname);
+    
+end
+
+    
\ No newline at end of file