function definitions updated

Author: ankit7540

README.md

@@ -1,11 +1,11 @@
 # RamanSpec_BasicOperations
-This repository contains the procedures for the mentioned job needed in day to day analysis of spectra which can be, for example, Raman or IR spectra etc... The procedures are for analyzing raw data (x,y columns) of data loaded in Igor-Pro application. (Python codes for the same will be added later).
 
-1. `average_2D.ipf` : Procedure to average selected 2-D waves in a folder keep the averaged data in the 'averaged data' folder. More than one 2-D wave maybe selected.
+This repository contains procedures for the analysis of spectra. These can be, for example, Raman or IR spectra or others. The procedures are for analyzing raw data (x,y columns) of data loaded in IgorPro application.
 
-2. `plot_2D.ipf` : Takes a 2D wave and plots all the individual columns against the points, with some constant off set, or wavemax dependent offset. 
+Refer to the few lines before each function to understand the purpose and the scheme. Edits might be needed for the correct usage of a function depending on the dataset.
 
-3. `analysis.ipf` : A set of procedures for analysis of waves.
-  a) function = standard_dev_eachPnt_spectra : takes a set of waves, calculate the mean and std dev (1 sigma) and % error at each point of the wave.
-  
-4. `add_offset.ipf` : Two functions therein. One applies a constant offset to a traces on a plot ( offset is defined manually). Second, the offset is calculated such that two traces will never touch each other.
+Question and suggestions are welcome via the Issues tab.
+
+***
+
+## Citing this repository

folder_operations/extract_from_folders.ipf

@@ -1,10 +1,12 @@
 
-
 //*************************************************************
 //*************************************************************
 
 // Extract data from a wave (having same name) in all subfolders and place in a 2D wave
-//		Argument : name of the wave, Example, "data1"
+//  along the columns
+
+//	Argument : name of the wave,
+//	For example, "data1"
 
 
 Function extract_data_from_subfolders (name)
@@ -57,7 +59,7 @@ Function extract_data_from_subfolders (name)
 	make /o /d /n=(nRows, index) output
 
 
-	// iterate over the folders and keep the wave in the 2D destination
+	// iterate over the folders and keep the wave in the 2D wave as the destination
 	index2=0
 	do
 		objName = GetIndexedObjNameDFR(dfr, 4, index2)
@@ -87,7 +89,7 @@ Function extract_data_from_subfolders (name)
 	while(index2 < index)
 
 	setdatafolder dfr
-	print "done."
+	print "\tdone."
 End
 
 //*************************************************************

folder_operations/folder_contents.ipf

@@ -1,11 +1,10 @@
-
 #pragma rtGlobals=3		// Use modern global access method and strict wave access.
 
 
 //*************************************************************
 //*************************************************************
 
-// to print name of all waves in the current data folder
+// Print name of all waves in the current data folder
 
 Function PrintAllWaveNames()
 	String objName
@@ -23,7 +22,13 @@ End
 
 //*************************************************************
 //*************************************************************
-// to print name of all subfolders in the current data folder
+// Print name of all subfolders in the current data folder
+
+// Arguments :
+//	startingDFR , for example, root:
+//	level , for exmaple, 0 or 1
+
+// PrintDataFolderPaths( root:, 0)
 
 Function PrintDataFolderPaths(startingDFR, level)
     DFREF startingDFR

loading_data/load_all_txt.ipf

@@ -10,7 +10,7 @@
 // For each loaded file, a new folder is created in the databrowser
 // the column in the txt file is loaded as waves ( autonamed as the header)
 
-function load_all_txt_files()
+function loadTXT_files_all()
 
 	String s
 
@@ -49,6 +49,8 @@ function load_all_txt_files()
 		print folder_name
 
 		newdatafolder /o/s $folder_name
+
+		// /A=Auto, /J = delimited text, /W = header as name, /D=double precision
 		LoadWave /A /J /W /D  /P=path fileName;
 
 		setdatafolder savedDF

merge_2D.ipf

@@ -0,0 +1,81 @@
+//**************************************************************
+//**************************************************************
+
+// To merge any number of 2D waves selected in the data browser
+// Output is generated in the same folder as "mergedWave2D"
+
+// Usage : select waves in the data browser and run the command
+
+function merge_2Dwaves_to_2D()
+
+string name1
+variable  j, jmax , k
+variable rows, columns
+variable x1,x2
+variable totalCol
+variable counter
+
+
+// purpose is to count the number of waves selected
+do
+		name1 = GETBROWSERSELECTION(j)
+		wave wav1=$name1
+		if(strlen(name1)<=0)
+			break
+		endif
+		x1=dimsize(wav1,0)
+		j=j+1
+while(1)
+jmax=j	// jmax is the number of selected waves
+
+make /o /d  /n=(jmax) tempCol
+wave tempCol
+
+print tempCol
+j=0
+// purpose is to count the number of columns per wave selected
+do
+		name1 = GETBROWSERSELECTION(j)
+		wave wav1=$name1
+		if(strlen(name1)<=0)
+			break
+		endif
+		columns=dimsize(wav1,1)
+		print columns
+		tempCol [j] = columns
+
+		counter=counter+columns
+		j=j+1
+while(1)
+
+
+// print counter
+
+// Construct and assign the 2D wave
+make /o /d /n=(x1, counter) mergedWave2D=0
+wave mergedWave=mergedWave2D
+
+counter=0
+// Assign the columns of data
+for (j=0 ; j <  jmax ; j=j+1)
+
+	name1 = GETBROWSERSELECTION(j)
+	wave wav1=$name1
+	columns = tempCol [j]
+
+	for ( k=0 ; k <  columns ; k=k+1)
+
+		// print j, k,  name1, counter
+		mergedWave[][ counter ] = wav1[p][k]
+		counter=counter+1
+	endfor
+endfor
+
+totalCol = dimsize (mergedWave, 1)
+printf "\tProcess finished. 'mergedWave2D' created as output with dimensions : %g x %g.\r", x1, totalCol
+
+killwaves /Z tempCol
+end
+
+//**************************************************************
+//**************************************************************