ENH:

1. Finish merging JMR patch for writting DICOM from scratch
2. Fix -hopefully- bug with MONOCHROME and space vs null character
3. Use const ref when possible
4. Add a new function InitializeDefaultHeader, which create a template DICOM header (CT image for now)
5. A few more comments
6. CreateUniqueUID can now be called without parameter

diff --git a/src/gdcmFile.cxx b/src/gdcmFile.cxx
index b5de832e9f59741c52597ffb7aced3ab12230b10..2cf2c255f869988c03edd0c15d826682f333149b 100644 (file)
--- a/src/gdcmFile.cxx
+++ b/src/gdcmFile.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmFile.cxx,v $
   Language:  C++
-  Date:      $Date: 2004/11/16 02:54:35 $
-  Version:   $Revision: 1.155 $
+  Date:      $Date: 2004/11/16 05:03:35 $
+  Version:   $Revision: 1.156 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -18,6 +18,7 @@
 
 #include "gdcmFile.h"
 #include "gdcmDebug.h"
+#include "gdcmUtil.h"
 #include <fstream>
 
 namespace gdcm 
@@ -346,7 +347,7 @@ uint8_t* File::GetImageData()
       if ( HeaderInternal->HasLUT() )
       {
          // The LUT interpretation failed
-         std::string photometricInterpretation = "MONOCHROME1 ";
+         std::string photometricInterpretation = Util::DicomString("MONOCHROME1");
          HeaderInternal->SetEntryByNumber( photometricInterpretation,
                                            0x0028, 0x0004 );
          PixelRead = 0; // no PixelRaw

diff --git a/src/gdcmHeader.cxx b/src/gdcmHeader.cxx
index bf44c55c4a62c94b0a0d325b642481731431fc38..a950ddbba17ad88c957fba21e363d7cdc27e02f1 100644 (file)
--- a/src/gdcmHeader.cxx
+++ b/src/gdcmHeader.cxx
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmHeader.cxx,v $
   Language:  C++
-  Date:      $Date: 2004/11/10 18:27:23 $
-  Version:   $Revision: 1.200 $
+  Date:      $Date: 2004/11/16 05:03:35 $
+  Version:   $Revision: 1.201 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -79,11 +79,12 @@ Header::Header( std::string const & filename ):
 }
 
 /**
- * \brief Constructor  
+ * \brief Constructor used when we want to generate dicom files from scratch
  */
 Header::Header()
            :Document()
 {
+   InitializeDefaultHeader();
 }
 
 /**
@@ -93,7 +94,6 @@ Header::~Header ()
 {
 }
 
-
 /**
  * \brief Performs some consistency checking on various 'File related' 
  *       (as opposed to 'DicomDir related') entries 
@@ -463,8 +463,8 @@ int Header::GetNumberOfScalarComponents()
    // beware of trailing space at end of string      
    // DICOM tags are never of odd length
    if ( strPhotometricInterpretation == GDCM_UNFOUND   || 
-        strPhotometricInterpretation == "MONOCHROME1 " || 
-        strPhotometricInterpretation == "MONOCHROME2 " )
+        Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
+        Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
    {
       return 1;
    }
@@ -822,7 +822,7 @@ int Header::GetBitsAllocated()
  */
 int Header::GetSamplesPerPixel()
 {
-   std::string strSize = GetEntryByNumber(0x0028,0x0002);
+   const std::string& strSize = GetEntryByNumber(0x0028,0x0002);
    if ( strSize == GDCM_UNFOUND )
    {
       dbg.Verbose(0, "Header::GetBitsStored: this is supposed to "
@@ -840,9 +840,9 @@ int Header::GetSamplesPerPixel()
  */
 bool Header::IsMonochrome()
 {
-   std::string PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
-   if (   PhotometricInterp == "MONOCHROME1 "
-       || PhotometricInterp == "MONOCHROME2 " )
+   const std::string& PhotometricInterp = GetEntryByNumber( 0x0028, 0x0004 );
+   if (  Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+      || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
    {
       return true;
    }
@@ -1302,6 +1302,92 @@ void Header::GetImageOrientationPatient( float iop[6] )
    }
 }
 
+/**
+ * \brief Initialize a default DICOM header that should contain all the
+ *        field require by other reader. DICOM standart does not 
+ *        explicitely defines thoses fields, heuristic has been choosen.
+ *        This is not perfect as we are writting a CT image...
+ */
+void Header::InitializeDefaultHeader()
+{
+   typedef struct
+   {
+      const char *value;
+      uint16_t group;
+      uint16_t elem;
+   } DICOM_DEFAULT_VALUE;
+
+   const char *date = Util::GetCurrentDate().c_str();
+   const char *time = Util::GetCurrentTime().c_str();
+   const char *uid  = Util::CreateUniqueUID().c_str();
+
+   static DICOM_DEFAULT_VALUE defaultvalue[] = {
+    "76", 0x0002, 0x0000,  // MetaElementGroup Length // FIXME: how to recompute ?
+    "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002,  // MediaStorageSOPInstanceUID (CT Image Storage)
+    uid,      0x0002, 0x0012,  // META Implementation Class UID
+    "ISO_IR 100", 0x0008, 0x0005,  // Specific Character Set
+    "DERIVED\\SECONDARY\\OTHER\\GDCM", 0x0008, 0x0008,  // Image Type    
+    "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016,  // SOP Class UID
+    "",       0x0008, 0x0050,  // Accession Number
+    "GDCM",   0x0008, 0x0070,  // Manufacturer
+    "GDCM",   0x0008, 0x0080,  // Institution Name
+    "http://www-creatis.insa-lyon.fr/Public/Gdcm/", 0x0008, 0x0081,  // Institution Address
+    "",       0x0008, 0x0090,  // Refering Physician Name
+    "",       0x0008, 0x1030,  // Study Description
+    "",       0x0008, 0x1050,  // Performing Physician's Name
+    "",       0x0008, 0x1060,  // Name of Physician(s) Reading Study
+    "",       0x0010, 0x0040,  // Patient's Sex
+    uid,      0x0020, 0x000d,  // StudyInstanceUID
+    uid,      0x0020, 0x000e,  // SeriesInstanceUID
+    "",       0x0020, 0x0011,   // AcquisitionNumber
+    "1\\0\\0\\0\\1\\0", 0x0020, 0x0037,  // Image Orientation Patient
+    "1",      0x0028, 0x0002,  // Samples per pixel 1 or 3
+    "MONOCHROME2", 0x0028, 0x0004,  // photochromatic interpretation
+
+// Date and time
+
+    date,       0x0008, 0x0012,  // Instance Creation Date
+    time,       0x0008, 0x0013,  // Instance Creation Time
+    date,       0x0008, 0x0020,  // Study Date
+    date,       0x0008, 0x0022,  // Acquisition Date
+    date,       0x0008, 0x0023,  // Content Date
+    time,       0x0008, 0x0030,  // Study Time
+    "CT",       0x0008, 0x0060,  // Modality    
+    "GDCM",     0x0010, 0x0010,  // Patient's Name
+    "GDCMID",   0x0010, 0x0020,  // Patient ID
+    "1",        0x0020, 0x0010,  // StudyID
+    "1",        0x0020, 0x0011,  // SeriesNumber
+    "1.0",      0x0018, 0x0050,  // slice Thickness
+    "1.0",      0x0018, 0x0088,  // space between slices
+    "1.0\\1.0", 0x0028, 0x0030,  // pixelSpacing
+    "64",       0x0028, 0x0010,  // nbRows
+    "64",       0x0028, 0x0011,  // nbCols
+    "16",       0x0028, 0x0100,  // BitsAllocated 8 or 16
+    "12",       0x0028, 0x0101,  // BitsStored    8 or 12
+    "11",       0x0028, 0x0102,  // HighBit       7 or 11
+    "0",        0x0028, 0x0103,  // Pixel Representation 0(unsigned) or 1(signed)
+    "1000.0",   0x0028, 0x1051,  // Window Width
+    "500.0",    0x0028, 0x1050,  // Window Center
+     0, 0, 0
+   };
+
+   // default value
+   // Special case this is the image (not a string)
+   GrPixel = 0x7fe0;
+   NumPixel = 0x0010;
+   ReplaceOrCreateByNumber(0, 0, GrPixel, NumPixel);
+
+   // All remaining strings:
+   unsigned int i = 0;
+   DICOM_DEFAULT_VALUE current = defaultvalue[i];
+   while( current.value )
+   {
+      std::string value = Util::DicomString( current.value ); //pad the string properly
+      ReplaceOrCreateByNumber(value, current.group, current.elem);
+      current = defaultvalue[++i];
+   }
+}
+
 //-----------------------------------------------------------------------------
 // Private
 

diff --git a/src/gdcmHeader.h b/src/gdcmHeader.h
index 13a5d39817ccc3cdc4d03975c684b3d3c93b2d22..d7d7d87065aa364aa0ff40e74ab9a78c8cd84425 100644 (file)
--- a/src/gdcmHeader.h
+++ b/src/gdcmHeader.h
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmHeader.h,v $
   Language:  C++
-  Date:      $Date: 2004/10/28 03:10:58 $
-  Version:   $Revision: 1.92 $
+  Date:      $Date: 2004/11/16 05:03:35 $
+  Version:   $Revision: 1.93 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -160,6 +160,7 @@ public:
    bool   HasLUT();
    int    GetLUTNbits();
 
+   /// Return the Transfer Syntax as a string
    std::string GetTransfertSyntaxName();
 
    /// Accessor to \ref Header::GrPixel
@@ -172,9 +173,16 @@ public:
    void SetImageDataSize(size_t expectedSize);
 
    void Write(std::ofstream* fp, FileType filetype);
+
+   /// Initialize DICOM header when none
+   void InitializeDefaultHeader();
  
 protected:
+   /// Replace patient's specific information by 'anonymous'
    bool AnonymizeHeader();
+
+   /// Helper function needed to organize DICOM files based on 
+   /// their x,y,z position
    void GetImageOrientationPatient( float iop[6] );
 
 private:

diff --git a/src/gdcmUtil.h b/src/gdcmUtil.h
index bf8970157e28d472376924b80cf2adf3d5515d03..6893f4d231cc7a121eade443f7d7c83538ee925e 100644 (file)
--- a/src/gdcmUtil.h
+++ b/src/gdcmUtil.h
@@ -3,8 +3,8 @@
   Program:   gdcm
   Module:    $RCSfile: gdcmUtil.h,v $
   Language:  C++
-  Date:      $Date: 2004/11/16 02:54:35 $
-  Version:   $Revision: 1.44 $
+  Date:      $Date: 2004/11/16 05:03:35 $
+  Version:   $Revision: 1.45 $
                                                                                 
   Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
   l'Image). All rights reserved. See Doc/License.txt or
@@ -54,7 +54,7 @@ public:
    static std::string DicomString(const char* s, size_t l);
    static std::string DicomString(const char* s);
    static bool        DicomStringEqual(const std::string& s1, const char *s2);
-   static std::string CreateUniqueUID(const std::string& root);
+   static std::string CreateUniqueUID(const std::string& root = "");
 
 private:
    static std::string GetIPAddress(); //Do not expose this method