Changeset 969 for sans/Dev

Timestamp:

Nov 13, 2015 4:03:38 PM (7 years ago)

Author:

srkline

Message:

more additions to the R/W functions to access VSANS data files

Location:

sans/Dev/trunk/NCNR_User_Procedures/Reduction

Files:

• SANS/EventModeProcessing.ipf (modified) (2 diffs)
• VSANS/VC_HDF5_VSANS_Utils.ipf (modified) (1 diff)
• VSANS/V_HDF5_RW_Utils.ipf (modified) (4 diffs)
• VSANS/V_HDF5_Read.ipf (modified) (7 diffs)
• VSANS/V_HDF5_Write.ipf (modified) (2 diffs)
• VSANS/V_NexusFromIgor.ipf (modified) (1 diff)

sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/EventModeProcessing.ipf

@@ -2065 +2065 @@
 //      IndexForHistogram(data1,data2,myhist)
 //      Wave index=SavedIndex
-//      JointHistogram(data1,data2,myHist,index)
+//      EV_JointHistogram(data1,data2,myHist,index)
 //      NewImage myHist
 //      
@@ -2073 +2073 @@
 
 
-Function JointHistogram(w0,w1,hist,index)
+Function EV_JointHistogram(w0,w1,hist,index)
         wave w0,w1,hist,index
  

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/VC_HDF5_VSANS_Utils.ipf

@@ -2 +2 @@
 
 //
-// This file has lots of utility procedures to be able to read/write
-// test HDF5 files for SANS and VSANS in Nexus format
-//
-// It doesn't have the NICE logs, but has everything that I 
-// can think of here.
-//
+// This file has utility procedures to be able to read/write
+// test HDF5 (from Igor) for SANS and VSANS in Nexus format
+//
+// It is predominantly to be able to WRITE a full Nexus file from Igor
+// -- this is only necessary to be able to write out "fake" VSANS files from VCALC
+//    since I need a "template" of the Nexus folder structure to start from and fill in
+//
+// It doesn't reproduce the NICE logs, but will leave a spece for them if
+// it is read in and is part of the xref.
+//
+// It may be easier to hard-wire my own folder definition (NewDataFolder)
+// that is MY Nexus file to write out and use that as the base case
+// rather than rely on Pete's code, which is terribly slow for writing.
+// Attributes are the issue, but it may be unimportant if they are missing.
+//
+
+
 
 //

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_HDF5_RW_Utils.ipf

@@ -1 +1 @@
 #pragma rtGlobals=3             // Use modern global access method and strict wave access.
 
-
-
-//
-// Start to build up and test the r/w accessors for VSANS
-// (SANS has a template, VSANS does not, so just start from scratch here, since the 
-// file structure will be different)
-//
-//
+//
+// The base functions for R/W from HDF5 files.
+// All of the specific "get" and "write" functions call these base functions which are responsible
+// for all of the open/close mechanics.
+//
+// These VSANS file-specific functions are in:
+// V_HDF5_Read.ipf
+//               and
+// V_HDF5_Write.ipf
+//
+
 
 
 // thought this would be useful, but the file name (folder) is stuck in the middle...
-Strconstant ksPathPrefix = "root:(folder):entry:entry1:"
+//Strconstant ksPathPrefix = "root:(folder):entry:entry1:"
 
 
@@ -152 +155 @@
 End
 
+// Returns a wave reference, not just a single value
+// ---then you pick what you need from the wave
+// 
+// - fname passed in is the full path to the file on disk
+// - path is the path to the value in the HDF tree
+//
+// check to see if the value exists (It will be a wave)
+// -- if it does, return the value from the local folder
+// -- if not, read the file in, then return the value
+//
+Function/WAVE V_getTextWaveFromHDF5(fname,path)
+        String fname,path
+
+        String folderStr=""
+        Variable valExists=0
+        
+        folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname))
+        
+        if(Exists("root:"+folderStr+":"+path))
+                valExists=1
+        endif
+        
+        if(!valExists)
+                //then read in the file
+                V_LoadHDF5_NoAtt(fname)
+        endif
+
+// this should exist now - if not, I need to see the error
+        Wave/T wOut = $("root:"+folderStr+":"+path)
+        
+        return wOut
+        
+End
+
+
 //
 //   TODO
@@ -159 +197 @@
 //
 // truncate to integer before returning??
+//
+//  TODO
+// write a "getIntegerWave" function??
 //
 //////  integer values
@@ -390 +431 @@
         return err
 end
+
+//////////////////////////////
+//////////////////////////////
+//////////////////////////////
+
+Function V_KillNamedDataFolder(fname)
+        String fname
+        
+        Variable err=0
+        
+        String folderStr = V_GetFileNameFromPathNoSemi(fname)
+        folderStr = V_RemoveDotExtension(folderStr)
+        
+        KillDataFolder/Z $("root:"+folderStr)
+        err = V_flag
+        
+        return(err)
+end
+
+//given a filename of a SANS data filename of the form
+// name.anything
+//returns the name as a string without the ".fbdfasga" extension
+//
+// returns the input string if a"." can't be found (maybe it wasn't there"
+Function/S V_RemoveDotExtension(item)
+        String item
+        String invalid = item   //
+        Variable num=-1
+        
+        //find the "dot"
+        String runStr=""
+        Variable pos = strsearch(item,".",0)
+        if(pos == -1)
+                //"dot" not found
+                return (invalid)
+        else
+                //found, get all of the characters preceeding it
+                runStr = item[0,pos-1]
+                return (runStr)
+        Endif
+End
+
+//returns a string containing filename (WITHOUT the ;vers)
+//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
+//with the folders separated by colons
+//
+// called by MaskUtils.ipf, ProtocolAsPanel.ipf, WriteQIS.ipf
+//
+Function/S V_GetFileNameFromPathNoSemi(fullPath)
+        String fullPath
+        
+        Variable offset1,offset2
+        String filename=""
+        //String PartialPath
+        offset1 = 0
+        do
+                offset2 = StrSearch(fullPath, ":", offset1)
+                if (offset2 == -1)                              // no more colons ?
+                        fileName = FullPath[offset1,strlen(FullPath) ]
+                        //PartialPath = FullPath[0, offset1-1]
+                        break
+                endif
+                offset1 = offset2+1
+        while (1)
+        
+        //remove version number from name, if it's there - format should be: filename;N
+        filename =  StringFromList(0,filename,";")              //returns null if error
+        
+        Return filename
+End

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_HDF5_Read.ipf

@@ -1080 +1080 @@
 // so the FHWM will be different in each direction. May need to return
 // "dummy" value for "B" detector if pixels there are square
-Function V_getDet_PixelFWHM(fname,detStr)
-        String fname,detStr
-
-        String path = "entry:instrument:detector_"+detStr+":PixelFWHM"
+Function V_getDet_PixelFWHM_X(fname,detStr)
+        String fname,detStr
+
+        String path = "entry:instrument:detector_"+detStr+":PixelFWHM_X"
 
 // TODO -- different behavior for "B"
@@ -1093 +1093 @@
 End
 
+// TODO -- write and X and Y version of this. Pixels are not square
+// so the FHWM will be different in each direction. May need to return
+// "dummy" value for "B" detector if pixels there are square
+Function V_getDet_PixelFWHM_Y(fname,detStr)
+        String fname,detStr
+
+        String path = "entry:instrument:detector_"+detStr+":PixelFWHM_Y"
+
+// TODO -- different behavior for "B"
+        if(cmpstr(detStr,"B") == 0)
+                return(V_getRealValueFromHDF5(fname,path))
+        else
+                return(V_getRealValueFromHDF5(fname,path))
+        endif
+End
+
 Function V_getDet_PixelNumX(fname,detStr)
         String fname,detStr
@@ -1468 +1484 @@
 
         String path = "entry:instrument:sample_aperture:shape:size"
+        WAVE w = V_getRealWaveFromHDF5(fname,path)
+
+        outW = w
+        return(0)
+End             
+
+///////  sample_aperture_2 (data folder)
+
+Function/S V_getSampleAp2_Description(fname)
+        String fname
+
+        String path = "entry:instrument:sample_aperture_2:description"
+        Variable num=60
+        return(V_getStringFromHDF5(fname,path,num))
+End
+
+Function V_getSampleAp2_distance(fname)
+        String fname
+
+        String path = "entry:instrument:sample_aperture_2:distance"
+        return(V_getRealValueFromHDF5(fname,path))
+End
+//      shape (data folder)
+
+Function/S V_getSampleAp2_shape(fname)
+        String fname
+
+        String path = "entry:instrument:sample_aperture_2:shape:shape"
+        Variable num=60
+        return(V_getStringFromHDF5(fname,path,num))
+End
+
+// TODO -- this needs to return a WAVE, since the shape may be circle, or rectangle
+// and will need to return more than a single dimension
+// TODO -- be careful of the UNITS
+Function V_getSampleAp2_size(fname,outW)
+        String fname
+        Wave outW
+
+        String path = "entry:instrument:sample_aperture_2:shape:size"
         WAVE w = V_getRealWaveFromHDF5(fname,path)
 
@@ -1613 +1669 @@
 
 
-Function V_getSample_rotationAngle(fname)
-        String fname
-        
-        String path = "entry:sample:rotation_angle"     
-        return(V_getRealValueFromHDF5(fname,path))
-end
-
-
 //Sample Rotation Angle
 Function V_getSampleRotationAngle(fname)
@@ -1666 +1714 @@
 
 
-
-
-
-// sample label
-//
-// TODO
-// limit to 60 characters?? do I need to do this with HDF5?
-//
-// do I need to pad to 60 characters?
-//
-Function V_WriteSamLabelToHeader(fname,str)
-        String fname,str
-        
-//      if(strlen(str) > 60)
-//              str = str[0,59]
-//      endif   
-        
-        Make/O/T/N=1 tmpTW
-        String groupName = "/sample"    //      /entry is automatically prepended -- so just explicitly state the group
-        String varName = "description"
-        tmpTW[0] = str //
-
-        variable err
-        err = V_WriteTextWaveToHDF(fname, groupName, varName, tmpTW)
-        if(err)
-                Print "HDF write err = ",err
-        endif
-        
-        // now be sure to kill the data folder to force a re-read of the data next time this file is read in
-        err = V_KillNamedDataFolder(fname)
-        if(err)
-                Print "DataFolder kill err = ",err
-        endif
-                
-        return(err)
-End
-
-// sample transmission
-Function V_WriteTransmissionToHeader(fname,trans)
-        String fname
-        Variable trans
-        
-        Make/O/D/N=1 wTmpWrite
-        String groupName = "/sample"    //      skip "entry" - /entry/sample becomes groupName /entry/entry/sample
-        String varName = "transmission"
-//      Make/O/R/N=1 wTmpWrite
-//      String groupName = "/data"      //      skip "entry" - /entry/sample becomes groupName /entry/entry/sample
-//      String varName = "Transmission"
-        wTmpWrite[0] = trans //
-
-        variable err
-        err = V_WriteWaveToHDF(fname, groupName, varName, wTmpWrite)
-        if(err)
-                Print "HDF write err = ",err
-        endif
-        // now be sure to kill the data folder to force a re-read of the data next time this file is read in
-        err = V_KillNamedDataFolder(fname)
-        if(err)
-                Print "DataFolder kill err = ",err
-        endif
-        return(err)
-End
 
 
@@ -1905 +1891 @@
 End
 
+Function/S V_getTransmissionFileName(fname)
+        String fname
+
+        String path = "entry:reduction:transmission_file_name"  
+        Variable num=60
+        return(V_getStringFromHDF5(fname,path,num))
+End
+
+Function/S V_getEmptyBeamFileName(fname)
+        String fname
+
+        String path = "entry:reduction:empty_beam_file_name"    
+        Variable num=60
+        return(V_getStringFromHDF5(fname,path,num))
+End
+
 
 //whole detector trasmission
@@ -2000 +2002 @@
 
 
-//////////////////////////////
-//////////////////////////////
-//////////////////////////////
-
-Function V_KillNamedDataFolder(fname)
-        String fname
-        
-        Variable err=0
-        
-        String folderStr = V_GetFileNameFromPathNoSemi(fname)
-        folderStr = V_RemoveDotExtension(folderStr)
-        
-        KillDataFolder/Z $("root:"+folderStr)
-        err = V_flag
-        
-        return(err)
-end
-
-//given a filename of a SANS data filename of the form
-// name.anything
-//returns the name as a string without the ".fbdfasga" extension
-//
-// returns the input string if a"." can't be found (maybe it wasn't there"
-Function/S V_RemoveDotExtension(item)
-        String item
-        String invalid = item   //
-        Variable num=-1
-        
-        //find the "dot"
-        String runStr=""
-        Variable pos = strsearch(item,".",0)
-        if(pos == -1)
-                //"dot" not found
-                return (invalid)
-        else
-                //found, get all of the characters preceeding it
-                runStr = item[0,pos-1]
-                return (runStr)
-        Endif
-End
-
-//returns a string containing filename (WITHOUT the ;vers)
-//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
-//with the folders separated by colons
-//
-// called by MaskUtils.ipf, ProtocolAsPanel.ipf, WriteQIS.ipf
-//
-Function/S V_GetFileNameFromPathNoSemi(fullPath)
-        String fullPath
-        
-        Variable offset1,offset2
-        String filename=""
-        //String PartialPath
-        offset1 = 0
-        do
-                offset2 = StrSearch(fullPath, ":", offset1)
-                if (offset2 == -1)                              // no more colons ?
-                        fileName = FullPath[offset1,strlen(FullPath) ]
-                        //PartialPath = FullPath[0, offset1-1]
-                        break
-                endif
-                offset1 = offset2+1
-        while (1)
-        
-        //remove version number from name, if it's there - format should be: filename;N
-        filename =  StringFromList(0,filename,";")              //returns null if error
-        
-        Return filename
-End

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_HDF5_Write.ipf

@@ -3012 +3012 @@
 // so the FHWM will be different in each direction. May need to return
 // "dummy" value for "B" detector if pixels there are square
-Function V_writeDet_PixelFWHM(fname,detStr)
+Function V_writeDet_PixelFWHM_X(fname,detStr,val)
         String fname,detStr
-
-        String path = "entry:instrument:detector_"+detStr+":PixelFWHM"
-
-// TODO -- different behavior for "B"
-        if(cmpstr(detStr,"B") == 0)
-//              return(V_writeRealValueFromHDF5(fname,path))
-                return(-99999)
-        else
-//              return(V_writeRealValueFromHDF5(fname,path))
-                return(-99999)
-        endif
-End
+        Variable val
+
+//      String path = "entry:instrument:detector_"+detStr+":PixelFWHM_X"
+        
+        Make/O/D/N=1 wTmpWrite
+//      Make/O/R/N=1 wTmpWrite
+        String groupName = "/entry/instrument/detector_"+detStr 
+        String varName = "PixelFWHM_X"
+        wTmpWrite[0] = val
+
+        variable err
+        err = V_WriteWaveToHDF(fname, groupName, varName, wTmpWrite)
+        if(err)
+                Print "HDF write err = ",err
+        endif
+        // now be sure to kill the data folder to force a re-read of the data next time this file is read in
+        err = V_KillNamedDataFolder(fname)
+        if(err)
+                Print "DataFolder kill err = ",err
+        endif
+        return(err)
+End
+
+
+// TODO -- write and X and Y version of this. Pixels are not square
+// so the FHWM will be different in each direction. May need to return
+// "dummy" value for "B" detector if pixels there are square
+Function V_writeDet_PixelFWHM_Y(fname,detStr,val)
+        String fname,detStr
+        Variable val
+
+//      String path = "entry:instrument:detector_"+detStr+":PixelFWHM_Y"
+        
+        Make/O/D/N=1 wTmpWrite
+//      Make/O/R/N=1 wTmpWrite
+        String groupName = "/entry/instrument/detector_"+detStr 
+        String varName = "PixelFWHM_Y"
+        wTmpWrite[0] = val
+
+        variable err
+        err = V_WriteWaveToHDF(fname, groupName, varName, wTmpWrite)
+        if(err)
+                Print "HDF write err = ",err
+        endif
+        // now be sure to kill the data folder to force a re-read of the data next time this file is read in
+        err = V_KillNamedDataFolder(fname)
+        if(err)
+                Print "DataFolder kill err = ",err
+        endif
+        return(err)
+End
+
 
 Function V_writeDet_PixelNumX(fname,detStr,val)
@@ -5070 +5110 @@
 End
 
+Function V_writeTransmissionFileName(fname,str)
+        String fname,str
+
+//      String path = "entry:reduction:transmission_file_name"  
+
+        Make/O/T/N=1 tmpTW
+        String groupName = "/entry/reduction"
+        String varName = "transmission_file_name"
+        tmpTW[0] = str //
+
+        variable err
+        err = V_WriteTextWaveToHDF(fname, groupName, varName, tmpTW)
+        if(err)
+                Print "HDF write err = ",err
+        endif
+        
+        // now be sure to kill the data folder to force a re-read of the data next time this file is read in
+        err = V_KillNamedDataFolder(fname)
+        if(err)
+                Print "DataFolder kill err = ",err
+        endif
+                
+        return(err)
+End
+
+Function V_writeEmptyBeamFileName(fname,str)
+        String fname,str
+
+//      String path = "entry:reduction:empty_beam_file_name"    
+
+        Make/O/T/N=1 tmpTW
+        String groupName = "/entry/reduction"
+        String varName = "empty_beam_file_name"
+        tmpTW[0] = str //
+
+        variable err
+        err = V_WriteTextWaveToHDF(fname, groupName, varName, tmpTW)
+        if(err)
+                Print "HDF write err = ",err
+        endif
+        
+        // now be sure to kill the data folder to force a re-read of the data next time this file is read in
+        err = V_KillNamedDataFolder(fname)
+        if(err)
+                Print "DataFolder kill err = ",err
+        endif
+                
+        return(err)
+End
+
 
 //whole detector transmission

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_NexusFromIgor.ipf

@@ -5 +5 @@
 //////////////////////////////
 // 
-// THIS IS DEPRICATED -- LOAD A NEXUS FILE INSTEAD AS A TEMPLATE
+// This is not really used anymore - but may still be used in the future. I need somenthing like this
+// to be able to write a full Nexus file from Igor, but I still don't know the best way to 
+// do the setup to match the "real" NICE-generated file structure. Modifying the DataFolderTree.ipf
+// to generate the NewDataFolder and Make statements may be a reliable way to reproduce the correct
+// structure from NICE, with the exception that NOT EVERY field is written out from NICE, depending
+// on the experiment setup!!!
 //
 // AUG 2015
+// NOV 2015
 //
 //////////////////////////////