Merge branch 'devel' of github.com:bioimagesuiteweb/bisweb into devel

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;

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)');

biswebpython/modules/dualImageRegression.py

@@ -44,11 +44,11 @@ def createDescription(self):
                 },
                 {
                     "type": "image",
-                    "name": "Input Image",
+                    "name": "Regressor Image",
                     "description": "The input image (uv) to preprocess",
                     "varname": "regressor",
                     "shortname" : "r",
-                    "required": False
+                    "required": True
                 }
             ],
             "outputs": [
@@ -130,10 +130,15 @@ def directInvokeAlgorithm(self,vals):
         if (doregress):
             print('.... computing dual image regression')
             outdata=self.dualRegress(idata,rdata,debug);
+        else:   
+            print('.... not computing dual image regression')
+            outdata=idata;
 
         if (df):
             print('.... computing df/f')
             outdata=np.transpose((np.transpose(outdata)+mean)/mean)
+        else:
+            print('.... not computing df/f')
 
         outdata=np.reshape(outdata,sz);
         self.outputs['output'] = bis_objects.bisImage().create(outdata,input.spacing,input.affine);

biswebpython/modules/initializeCalciumStudy.py

@@ -120,13 +120,26 @@ def loadChannels(self,infilename,movies,usedframes,mat,spacing,triggers):
             imgl=page.convert(mode='F')
             v=np.array(imgl)
             channel=triggers[c][1]-1
-            if (channel>0):
+            flag=0
+#            if (usedframes[0]>5900 or ( usedframes[0]>15 and usedframes[0]<20)):
+#                print('Channel=',triggers[c][1],'c=',c,' channel=',channel,' usedrames=',usedframes);
+#                flag=1
+
+            if (channel>=0):
                 movies[channel][:,:,0,usedframes[channel]] = np.array(imgl,dtype=np.uint16)
-                if (c%125==0 or c<4 or c>(expected_num_frames-4)):
-                    s='...\t added frame {:5d}/{:5d} to channel {:d} as new frame {:5d} based on trigger {:s}'.format(c+1,expected_num_frames,channel+1,usedframes[channel]+1,str(triggers[c]))
+            else:
+                print('....\t\t Skipping ',triggers[c][1] ,' < 0 c=',c)
+
+            if (c%125==0 or c<4 or c>(expected_num_frames-4) or flag>0):
+                q='added';
+                if (channel<0):
+                    q='not '+q;
+
+                s='...\t '+q+' frame {:5d}/{:5d} to channel {:d} as new frame {:5d} based on trigger {:s}'.format(c+1,expected_num_frames,channel+1,usedframes[channel]+1,str(triggers[c]))
                 print(s)
             c=c+1;
-            usedframes[channel]=usedframes[channel]+1
+            if (channel>=0):
+                usedframes[channel]=usedframes[channel]+1
             if (c>100 and DUMMY_MODE):
                 break
 
@@ -216,7 +229,10 @@ def convertRuns(self,data,indir,outdir):
                 lt=len(triggers)
                 for k in range(0,lt):
                     v=triggers[k][1]-1;
-                    numframes[v]=numframes[v]+1;
+                    if (v>=0 and v<numchannels):
+                        numframes[v]=numframes[v]+1;
+                    else:
+                        print('........ ignoring part',part,' frame=',k,' as v=',v+1)
                 print('...\t processing', nm, 'cumulative numframes per channel=',numframes)
 
 

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)
 {
 

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;

js/coreweb/bisweb_connectivityvis.js

@@ -867,6 +867,7 @@ var createlines = function() {
                   attribcomponent : attribcomponent,
                   filter: filter,
                   radius : globalParams.internal.parameters.radius,
+                  maxdegree : globalParams.internal.parameters.maxdegree,
                   matrixthreshold : matrixthreshold};
 
     if (globalParams.internal.hadlinesonce)
@@ -886,6 +887,7 @@ var drawlines=function(state) {
                                                            state.degreethreshold, // metric threshold
                                                            state.filter); // sum
 
+
     if (ok===0) {
         bootbox.alert('Failed to create flag matrix for connectivity data!');
         return 0;

js/coreweb/bisweb_connectivityvis3d.js

@@ -805,11 +805,11 @@ var drawlines3d=function(state,doNotUpdateFlagMatrix) {
     if (!doNotUpdateFlagMatrix) {
         console.log('.... Updating Flag Matrix\n');
         let ok=globalParams.internal.conndata.createFlagMatrix(globalParams.internal.parcellation,
-                                                  state.mode, // mode
-                                                  state.singlevalue, // singlevalue
-                                                  state.attribcomponent, // attribcomponent
-                                                  state.degreethreshold, // metric threshold
-                                                  state.filter); // sum
+                                                               state.mode, // mode
+                                                               state.singlevalue, // singlevalue
+                                                               state.attribcomponent, // attribcomponent
+                                                               state.degreethreshold, // metric threshold
+                                                               state.filter); // sum
 
         if (ok===0) {
             bootbox.alert('Failed to create flag matrix for 3D connectivity data!');
@@ -820,7 +820,7 @@ var drawlines3d=function(state,doNotUpdateFlagMatrix) {
 
 
     // Now add lines
-    let pos=[],neg=[],total=0;
+    let pos=[],eg=[],total=0;
     if (state.linestodraw == globalParams.internal.gui_Lines[0] ||
         state.linestodraw == globalParams.internal.gui_Lines[2] ) {
         pos=globalParams.internal.conndata.createLinePairs(0,state.matrixthreshold);
@@ -844,8 +844,9 @@ var drawlines3d=function(state,doNotUpdateFlagMatrix) {
     //        console.log('Drawing 3D',state.poscolor,state.negcolor);
 
     const ATLASHEADER=atlasutils.getCurrentAtlasHeader();
+    console.log('State=',JSON.stringify(state));
     let lparr = globalParams.internal.conndata.draw3DLines(globalParams.internal.parcellation,
-                                                           pos,neg,2.0,1.0,
+                                                           pos,neg,2.0,1.0,state.maxdegree,
                                                            ATLASHEADER);
     for (let i=0;i<=1;i++) {
         let lp=lparr[i];