python save for 3 or 4 images to prevent header issue

bioimagesuiteweb · Aug 4, 2023 · fff544c · fff544c
1 parent 7041a6f
commit fff544c
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Showing 4 changed files with 20 additions and 13 deletions.
diff --git a/biswebpython/core/bis_objects.py b/biswebpython/core/bis_objects.py
@@ -374,9 +374,11 @@ def save(self,fname):
         try:
             out_image = nib.Nifti1Image(self.data_array, self.affine);
             # Preserve temporal spacing
-            out_image.header['pixdim'][4]=self.spacing[3]
-            out_image.header['pixdim'][5]=self.spacing[4]
-
+            try:
+                out_image.header['pixdim'][4]=self.spacing[3]
+                out_image.header['pixdim'][5]=self.spacing[4]
+            except:
+                print('')
 
             nib.save(out_image, fname)
             self.filename=fname;

diff --git a/biswebpython/core/bis_wasmutils.py b/biswebpython/core/bis_wasmutils.py
@@ -55,7 +55,7 @@ def load_library(name=''):
         print('____ Recomputing name:',name);
 
 
-    print('___ Loading library from',name);
+#    print('___ Loading library from',name);
     m=ctypes.CDLL(name);
     if (m.uses_gpl()):
         print("____ Library Loaded from",name,"result=",m.test_wasm(),' (should be 1700)');

diff --git a/cpp/bisExportedFunctions.cpp b/cpp/bisExportedFunctions.cpp
@@ -425,9 +425,9 @@ unsigned char* extractImageFrameWASM(unsigned char* input,
   int target_type=bisDataTypes::getTypeCodeFromName(params->getValue("datatype"),header[1]);
 
   switch (target_type)
-      {
-	bisvtkTemplateMacro( return extractImageFrameTemplate(input,params.get(),debug, static_cast<BIS_TT*>(0)));
-      }
+    {
+      bisvtkTemplateMacro( return extractImageFrameTemplate(input,params.get(),debug, static_cast<BIS_TT*>(0)));
+    }
   return 0;
 
 
@@ -885,7 +885,6 @@ unsigned char* butterworthFilterWASM(unsigned char* input_ptr,const char* jsonst
 // Butterworth Filter Image
 // ------------------------
 
-
 unsigned char* butterworthFilterImageWASM(unsigned char* input_ptr,const char* jsonstring,int debug)
 {
 

diff --git a/cpp/bisfMRIAlgorithms.cpp b/cpp/bisfMRIAlgorithms.cpp
@@ -413,7 +413,7 @@ namespace bisfMRIAlgorithms {
                              std::string passType,float frequency,float sampleRate,int removeMean,int debug) {
 
 
-    std::cout << "Begin FILTER IMage TR=" << sampleRate << ", removeMean=" << removeMean << std::endl;
+    std::cout << "Begin FILTER Image TR=" << sampleRate << ", removeMean=" << removeMean << std::endl;
 
     int dim[5]; input_image->getDimensions(dim);
     Eigen::MatrixXf temp;
@@ -427,7 +427,7 @@ namespace bisfMRIAlgorithms {
 
     int ok=1;
 
-    //std::cout << "Dim=" << dim[0] << "," << dim[1] << "," << dim[2] << ", frames=" << dim[3] << " nv=" << numvoxels << std::endl;
+    std::cout << "Dim=" << dim[0] << "," << dim[1] << "," << dim[2] << ", frames=" << dim[3] << " nv=" << numvoxels << std::endl;
 
     for (int i=0;i<numvoxels;i++)
       {
@@ -462,9 +462,15 @@ namespace bisfMRIAlgorithms {
         //std::cout << "Output" << std::endl;
 
         for (int f=0;f<dim[3];f++) {
-          outdata[numvoxels*f+i]=output(f,0);
-          /*if (i==0)
-            std::cout <<  outdata[numvoxels*f+i] << std::endl;*/
+          float v=output(f,0);
+          if (std::isnan(v))
+            {
+              std::cerr << "Nan " << i << "," << f << std::endl;
+              v=0.0;
+            }
+          outdata[numvoxels*f+i]=v;
+          /*          if (i==0)
+                      std::cout <<  outdata[numvoxels*f+i] << std::endl;*/
         }
       }
     return ok;